hyperspy →
1.6.1-1 →
armhf → 2022-09-19 12:01:56
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-01
+==============================================================================+
| hyperspy 1.6.1-1 (armhf) Mon, 19 Sep 2022 09:59:09 +0000 |
+==============================================================================+
Package: hyperspy
Version: 1.6.1-1
Source Version: 1.6.1-1
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bookworm-staging-armhf-sbuild-b6b3bf49-c4d6-45cf-98ea-258945b88ca0' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.3 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.1 MB]
Fetched 27.4 MB in 31s (885 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/bookworm-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'hyperspy' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/science-team/hyperspy.git
Please use:
git clone https://salsa.debian.org/science-team/hyperspy.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 39.7 MB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main hyperspy 1.6.1-1 (dsc) [2212 B]
Get:2 http://172.17.4.1/private bookworm-staging/main hyperspy 1.6.1-1 (tar) [39.7 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main hyperspy 1.6.1-1 (diff) [3032 B]
Fetched 39.7 MB in 3s (12.9 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/hyperspy-cYAcFi/hyperspy-1.6.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/hyperspy-cYAcFi' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-hOrLvN/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-hOrLvN/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-hOrLvN/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-hOrLvN/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-hOrLvN/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-hOrLvN/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-hOrLvN/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-hOrLvN/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-hOrLvN/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (1847 B/s)
Reading package lists...
W: copy:/<<BUILDDIR>>/resolver-hOrLvN/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-hOrLvN/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 2 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-hOrLvN/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (22.5 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12798 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 12), dh-python, python3-all, python3-dev, python3-dask, python3-dateutil, python3-dill, python3-h5py, python3-imageio, python3-ipython, python3-matplotlib, python3-mock, python3-natsort, python3-nose, python3-numba, python3-numexpr, python3-numpy, python3-pint, python3-ptable, python3-pytest, python3-pytest-instafail, python3-pytest-mpl, python3-pytest-rerunfailures, python3-pytest-runner, python3-pytest-xdist, python3-yaml, python3-requests, python3-scipy, python3-setuptools, python3-skimage, python3-sklearn, python3-sparse, python3-statsmodels, python3-sympy, python3-tqdm, python3-traits, python3-traitsui
Filtered Build-Depends: debhelper (>= 12), dh-python, python3-all, python3-dev, python3-dask, python3-dateutil, python3-dill, python3-h5py, python3-imageio, python3-ipython, python3-matplotlib, python3-mock, python3-natsort, python3-nose, python3-numba, python3-numexpr, python3-numpy, python3-pint, python3-ptable, python3-pytest, python3-pytest-instafail, python3-pytest-mpl, python3-pytest-rerunfailures, python3-pytest-runner, python3-pytest-xdist, python3-yaml, python3-requests, python3-scipy, python3-setuptools, python3-skimage, python3-sklearn, python3-sparse, python3-statsmodels, python3-sympy, python3-tqdm, python3-traits, python3-traitsui
dpkg-deb: building package 'sbuild-build-depends-hyperspy-dummy' in '/<<BUILDDIR>>/resolver-hOrLvN/apt_archive/sbuild-build-depends-hyperspy-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-hyperspy-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-hOrLvN/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-hOrLvN/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-hOrLvN/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-hOrLvN/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-hOrLvN/apt_archive ./ Sources [677 B]
Get:5 copy:/<<BUILDDIR>>/resolver-hOrLvN/apt_archive ./ Packages [762 B]
Fetched 2772 B in 1s (2464 B/s)
Reading package lists...
W: copy:/<<BUILDDIR>>/resolver-hOrLvN/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-hOrLvN/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...
Install hyperspy build dependencies (apt-based resolver)
--------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev blt bsdextrautils ca-certificates
debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file
fontconfig fontconfig-config fonts-dejavu-core fonts-lyx gettext
gettext-base groff-base intltool-debian iso-codes libaec0
libarchive-zip-perl libavahi-client3 libavahi-common-data libavahi-common3
libblas3 libbrotli1 libbsd0 libcups2 libcurl4 libdbus-1-3 libdebhelper-perl
libdeflate0 libdouble-conversion3 libdrm-common libdrm2 libdw1 libedit2
libegl-mesa0 libegl1 libelf1 libevdev2 libexpat1 libexpat1-dev
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0
libgbm1 libgfortran5 libglapi-mesa libgles2 libglib2.0-0 libglvnd0
libgraphite2-3 libgstreamer-plugins-base1.0-0 libgstreamer1.0-0
libgudev-1.0-0 libharfbuzz0b libhdf5-103-1 libhdf5-hl-100 libhyphen0 libice6
libicu71 libimagequant0 libinput-bin libinput10 libjbig0 libjpeg62-turbo
libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore liblapack3
liblbfgsb0 liblcms2-2 liblerc4 libllvm11 liblzf1 libmagic-mgc libmagic1
libmd0 libmd4c0 libmpdec3 libmtdev1 libncurses6 libnghttp2-14 libopenjp2-7
liborc-0.4-0 libpcre2-16-0 libpfm4 libpipeline1 libpng16-16 libprocps8
libpsl5 libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev
libpython3.10-minimal libpython3.10-stdlib libqhull-r8.0 libqt5core5a
libqt5dbus5 libqt5designer5 libqt5gui5 libqt5help5 libqt5network5
libqt5opengl5 libqt5positioning5 libqt5printsupport5 libqt5qml5
libqt5qmlmodels5 libqt5quick5 libqt5sensors5 libqt5sql5 libqt5svg5
libqt5test5 libqt5webchannel5 libqt5webkit5 libqt5widgets5 libqt5xml5
libraqm0 librtmp1 libsm6 libssh2-1 libsub-override-perl libsz2 libtbb12
libtbbmalloc2 libtcl8.6 libtiff5 libtk8.6 libtool libuchardet0 libunwind8
libwacom-common libwacom9 libwayland-client0 libwayland-server0 libwebp7
libwebpdemux2 libwebpmux3 libwoff1 libx11-6 libx11-data libx11-xcb1 libxau6
libxcb-dri2-0 libxcb-dri3-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1
libxcb-present0 libxcb-randr0 libxcb-render-util0 libxcb-render0
libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-util1 libxcb-xfixes0
libxcb-xinerama0 libxcb-xinput0 libxcb-xkb1 libxcb1 libxdmcp6 libxext6
libxft2 libxkbcommon-x11-0 libxkbcommon0 libxml2 libxrender1 libxshmfence1
libxslt1.1 libxss1 libyaml-0-2 libz3-4 llvm-11 llvm-11-linker-tools
llvm-11-runtime m4 mailcap man-db media-types mime-support openssl
po-debconf procps python-matplotlib-data python3 python3-all python3-appdirs
python3-attr python3-backcall python3-brotli python3-certifi python3-chardet
python3-charset-normalizer python3-cloudpickle python3-cycler python3-dask
python3-dateutil python3-decorator python3-dev python3-dill
python3-distutils python3-execnet python3-fonttools python3-fs
python3-fsspec python3-h5py python3-h5py-serial python3-idna python3-imageio
python3-iniconfig python3-ipython python3-jedi python3-joblib
python3-kiwisolver python3-lib2to3 python3-llvmlite python3-locket
python3-lxml python3-lz4 python3-matplotlib python3-matplotlib-inline
python3-minimal python3-mock python3-more-itertools python3-mpmath
python3-natsort python3-networkx python3-nose python3-numba python3-numexpr
python3-numpy python3-packaging python3-pandas python3-pandas-lib
python3-parso python3-partd python3-patsy python3-pbr python3-pexpect
python3-pickleshare python3-pil python3-pil.imagetk python3-pint
python3-pkg-resources python3-pluggy python3-prompt-toolkit python3-ptable
python3-ptyprocess python3-py python3-pyface python3-pygments
python3-pyparsing python3-pyqt5 python3-pyqt5.qtopengl python3-pyqt5.qtsvg
python3-pyqt5.qtwebkit python3-pyqt5.sip python3-pytest
python3-pytest-forked python3-pytest-instafail python3-pytest-mpl
python3-pytest-rerunfailures python3-pytest-runner python3-pytest-xdist
python3-pywt python3-requests python3-scipy python3-setuptools python3-six
python3-skimage python3-skimage-lib python3-sklearn python3-sklearn-lib
python3-sparse python3-statsmodels python3-statsmodels-lib python3-sympy
python3-threadpoolctl python3-tifffile python3-tk python3-tomli
python3-toolz python3-tqdm python3-traitlets python3-traits python3-traitsui
python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3
python3-wcwidth python3-yaml python3.10 python3.10-dev python3.10-minimal
shared-mime-info tk8.6-blt2.5 ucf unicode-data x11-common xkb-data
zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc blt-demo dh-make flit
python3-build python3-installer gettext-doc libasprintf-dev libgettextpo-dev
groff isoquery cups-common libvisual-0.4-plugins gstreamer1.0-tools
libjs-jquery-ui-docs liblcms2-utils libthai0 qt5-image-formats-plugins
qtwayland5 qt5-qmltooling-plugins tcl8.6 tk8.6 libtool-doc gfortran
| fortran95-compiler gcj-jdk libwacom-bin llvm-11-doc m4-doc apparmor less
www-browser libmail-box-perl python3-doc python3-venv python-attr-doc
python-cycler-doc ipython python-dask-doc python3-bcolz python3-blosc
python3-boto python3-distributed python3-graphviz python3-jinja2
python3-psutil python3-sqlalchemy python3-tables python3-objgraph
execnet-doc python-fsspec-doc python-h5py-doc python-imageio-doc
python3-astropy python3-gdal ffmpeg python-ipython-doc llvmlite-doc
python-lxml-doc cm-super-minimal dvipng fonts-staypuft ghostscript
gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python-matplotlib-doc
python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-sip
python3-tornado texlive-extra-utils texlive-latex-extra python-mock-doc
python-mpmath-doc python3-gmpy2 python-natsort-doc python-networkx-doc
python-nose-doc gfortran python-numpy-doc python-pandas-doc python-patsy-doc
python-pexpect-doc python-pil-doc subversion python-pygments-doc
ttf-bitstream-vera python-pyparsing-doc python-pytest-instafail-doc
python-pywt-doc python3-cryptography python3-openssl python3-socks
python-requests-doc python-scipy-doc python-setuptools-doc
python-skimage-doc python3-dap python-sklearn-doc python-statsmodels-doc
texlive-fonts-extra python-sympy-doc tix python3-tk-dbg python-toolz-doc
python3.10-venv python3.10-doc binfmt-support
Recommended packages:
curl | wget | lynx dbus libarchive-cpio-perl libglib2.0-data xdg-user-dirs
gstreamer1.0-plugins-base javascript-common libgpm2 publicsuffix
qttranslations5-l10n qt5-gtk-platformtheme geoclue-2.0 libgl1 libglx-mesa0
libqt5sql5-sqlite | libqt5sql5-mysql | libqt5sql5-odbc | libqt5sql5-psql
| libqt5sql5-tds | libqt5sql5-ibase libltdl-dev llvm-11-dev binfmt-support
libmail-sendmail-perl psmisc git python3-distributed python3-dropbox
python3-fusepy python3-libarchive-c python3-paramiko python3-pygit2
python3-simplejson python3-psutil python3-bs4 python3-html5lib python3-gdal
python3-pydot python3-pygraphviz numba-doc python3-pip python3-bottleneck
python3-odf python3-openpyxl python3-xlwt python3-tables python3-jinja2
python3-blosc python3-zmq python3-olefile python3-colorama python3-cvxopt
isympy-common
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev blt bsdextrautils ca-certificates
debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file
fontconfig fontconfig-config fonts-dejavu-core fonts-lyx gettext
gettext-base groff-base intltool-debian iso-codes libaec0
libarchive-zip-perl libavahi-client3 libavahi-common-data libavahi-common3
libblas3 libbrotli1 libbsd0 libcups2 libcurl4 libdbus-1-3 libdebhelper-perl
libdeflate0 libdouble-conversion3 libdrm-common libdrm2 libdw1 libedit2
libegl-mesa0 libegl1 libelf1 libevdev2 libexpat1 libexpat1-dev
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0
libgbm1 libgfortran5 libglapi-mesa libgles2 libglib2.0-0 libglvnd0
libgraphite2-3 libgstreamer-plugins-base1.0-0 libgstreamer1.0-0
libgudev-1.0-0 libharfbuzz0b libhdf5-103-1 libhdf5-hl-100 libhyphen0 libice6
libicu71 libimagequant0 libinput-bin libinput10 libjbig0 libjpeg62-turbo
libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore liblapack3
liblbfgsb0 liblcms2-2 liblerc4 libllvm11 liblzf1 libmagic-mgc libmagic1
libmd0 libmd4c0 libmpdec3 libmtdev1 libncurses6 libnghttp2-14 libopenjp2-7
liborc-0.4-0 libpcre2-16-0 libpfm4 libpipeline1 libpng16-16 libprocps8
libpsl5 libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev
libpython3.10-minimal libpython3.10-stdlib libqhull-r8.0 libqt5core5a
libqt5dbus5 libqt5designer5 libqt5gui5 libqt5help5 libqt5network5
libqt5opengl5 libqt5positioning5 libqt5printsupport5 libqt5qml5
libqt5qmlmodels5 libqt5quick5 libqt5sensors5 libqt5sql5 libqt5svg5
libqt5test5 libqt5webchannel5 libqt5webkit5 libqt5widgets5 libqt5xml5
libraqm0 librtmp1 libsm6 libssh2-1 libsub-override-perl libsz2 libtbb12
libtbbmalloc2 libtcl8.6 libtiff5 libtk8.6 libtool libuchardet0 libunwind8
libwacom-common libwacom9 libwayland-client0 libwayland-server0 libwebp7
libwebpdemux2 libwebpmux3 libwoff1 libx11-6 libx11-data libx11-xcb1 libxau6
libxcb-dri2-0 libxcb-dri3-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1
libxcb-present0 libxcb-randr0 libxcb-render-util0 libxcb-render0
libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-util1 libxcb-xfixes0
libxcb-xinerama0 libxcb-xinput0 libxcb-xkb1 libxcb1 libxdmcp6 libxext6
libxft2 libxkbcommon-x11-0 libxkbcommon0 libxml2 libxrender1 libxshmfence1
libxslt1.1 libxss1 libyaml-0-2 libz3-4 llvm-11 llvm-11-linker-tools
llvm-11-runtime m4 mailcap man-db media-types mime-support openssl
po-debconf procps python-matplotlib-data python3 python3-all python3-appdirs
python3-attr python3-backcall python3-brotli python3-certifi python3-chardet
python3-charset-normalizer python3-cloudpickle python3-cycler python3-dask
python3-dateutil python3-decorator python3-dev python3-dill
python3-distutils python3-execnet python3-fonttools python3-fs
python3-fsspec python3-h5py python3-h5py-serial python3-idna python3-imageio
python3-iniconfig python3-ipython python3-jedi python3-joblib
python3-kiwisolver python3-lib2to3 python3-llvmlite python3-locket
python3-lxml python3-lz4 python3-matplotlib python3-matplotlib-inline
python3-minimal python3-mock python3-more-itertools python3-mpmath
python3-natsort python3-networkx python3-nose python3-numba python3-numexpr
python3-numpy python3-packaging python3-pandas python3-pandas-lib
python3-parso python3-partd python3-patsy python3-pbr python3-pexpect
python3-pickleshare python3-pil python3-pil.imagetk python3-pint
python3-pkg-resources python3-pluggy python3-prompt-toolkit python3-ptable
python3-ptyprocess python3-py python3-pyface python3-pygments
python3-pyparsing python3-pyqt5 python3-pyqt5.qtopengl python3-pyqt5.qtsvg
python3-pyqt5.qtwebkit python3-pyqt5.sip python3-pytest
python3-pytest-forked python3-pytest-instafail python3-pytest-mpl
python3-pytest-rerunfailures python3-pytest-runner python3-pytest-xdist
python3-pywt python3-requests python3-scipy python3-setuptools python3-six
python3-skimage python3-skimage-lib python3-sklearn python3-sklearn-lib
python3-sparse python3-statsmodels python3-statsmodels-lib python3-sympy
python3-threadpoolctl python3-tifffile python3-tk python3-tomli
python3-toolz python3-tqdm python3-traitlets python3-traits python3-traitsui
python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3
python3-wcwidth python3-yaml python3.10 python3.10-dev python3.10-minimal
sbuild-build-depends-hyperspy-dummy shared-mime-info tk8.6-blt2.5 ucf
unicode-data x11-common xkb-data zlib1g-dev
0 upgraded, 311 newly installed, 0 to remove and 2 not upgraded.
Need to get 221 MB of archives.
After this operation, 878 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-hOrLvN/apt_archive ./ sbuild-build-depends-hyperspy-dummy 0.invalid.0 [1044 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.73.3-3+rpi1 [1263 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf libicu71 armhf 71.1-3 [8855 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1 [591 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf shared-mime-info armhf 2.2-1 [726 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf libdouble-conversion3 armhf 3.2.1-1 [38.8 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf libpcre2-16-0 armhf 10.40-1+b2 [208 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libqt5core5a armhf 5.15.4+dfsg-5+rpi1 [1524 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.8-1 [84.1 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b2 [260 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf libpng16-16 armhf 1.6.37-5 [272 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf libfreetype6 armhf 2.12.1+dfsg-3 [352 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf ucf all 3.0043 [74.0 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf fonts-dejavu-core all 2.37-2 [1069 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf fontconfig-config all 2.13.1-4.4 [281 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf libfontconfig1 armhf 2.13.1-4.4 [331 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf fontconfig armhf 2.13.1-4.4 [416 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf libdrm-common all 2.4.112-3+rpi1 [15.7 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf libdrm2 armhf 2.4.112-3+rpi1 [41.2 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf libglvnd0 armhf 1.5.0-1 [51.5 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf libwayland-server0 armhf 1.21.0-1 [29.3 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf libgbm1 armhf 22.2.0~rc3-1+rpi1 [74.8 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf libglapi-mesa armhf 22.2.0~rc3-1+rpi1 [84.5 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf libwayland-client0 armhf 1.21.0-1 [23.3 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf libmd0 armhf 1.0.4-2 [28.6 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.6-1 [109 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf libxcb1 armhf 1.15-1 [139 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf libx11-data all 2:1.8.1-2 [308 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf libx11-6 armhf 2:1.8.1-2 [704 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf libx11-xcb1 armhf 2:1.8.1-2 [203 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf libxcb-dri2-0 armhf 1.15-1 [107 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf libxcb-dri3-0 armhf 1.15-1 [107 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf libxcb-present0 armhf 1.15-1 [105 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libxcb-sync1 armhf 1.15-1 [108 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf libxcb-xfixes0 armhf 1.15-1 [109 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf libxshmfence1 armhf 1.3-1 [8636 B]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf libegl-mesa0 armhf 22.2.0~rc3-1+rpi1 [129 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf libegl1 armhf 1.5.0-1 [29.6 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf libgles2 armhf 1.5.0-1 [18.6 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf libgraphite2-3 armhf 1.3.14-1 [70.3 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf libharfbuzz0b armhf 2.7.4-1+b1 [1420 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf x11-common all 1:7.7+23 [252 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf libice6 armhf 2:1.0.10-1 [51.7 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf libevdev2 armhf 1.13.0+dfsg-1+rpi1 [27.9 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf libmtdev1 armhf 1.1.6-1 [22.0 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf libgudev-1.0-0 armhf 237-2 [13.2 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf libwacom-common all 2.4.0-3 [58.0 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf libwacom9 armhf 2.4.0-3 [19.6 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf libinput-bin armhf 1.21.0-1 [24.5 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf libinput10 armhf 1.21.0-1 [108 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf libjpeg62-turbo armhf 1:2.1.2-1 [144 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf libmd4c0 armhf 0.4.8-1 [39.4 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf libdbus-1-3 armhf 1.14.0-2 [210 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf libqt5dbus5 armhf 5.15.4+dfsg-5+rpi1 [208 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf libqt5network5 armhf 5.15.4+dfsg-5+rpi1 [595 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf libsm6 armhf 2:1.2.3-1 [32.9 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf libxcb-icccm4 armhf 0.4.1-1.1 [26.3 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf libxcb-shm0 armhf 1.15-1 [106 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf libxcb-util1 armhf 0.4.0-1 [22.1 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf libxcb-image0 armhf 0.4.0-2 [21.9 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf libxcb-keysyms1 armhf 0.4.0-1+b2 [15.9 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf libxcb-randr0 armhf 1.15-1 [116 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf libxcb-render0 armhf 1.15-1 [114 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf libxcb-render-util0 armhf 0.3.9-1+b1 [17.3 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf libxcb-shape0 armhf 1.15-1 [106 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf libxcb-xinerama0 armhf 1.15-1 [105 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf libxcb-xinput0 armhf 1.15-1 [127 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf libxcb-xkb1 armhf 1.15-1 [126 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf xkb-data all 2.35.1-1 [764 kB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf libxkbcommon0 armhf 1.4.1-1 [96.2 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf libxkbcommon-x11-0 armhf 1.4.1-1 [15.9 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf libxrender1 armhf 1:0.9.10-1.1 [30.0 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf libqt5gui5 armhf 5.15.4+dfsg-5+rpi1 [2570 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf libqt5widgets5 armhf 5.15.4+dfsg-5+rpi1 [2068 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf libqt5svg5 armhf 5.15.4-2 [117 kB]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-2+rpi2 [177 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf libdw1 armhf 0.187-2+rpi2 [216 kB]
Get:80 http://172.17.4.1/private bookworm-staging/main armhf libunwind8 armhf 1.3.2-2 [47.3 kB]
Get:81 http://172.17.4.1/private bookworm-staging/main armhf libgstreamer1.0-0 armhf 1.20.3-1 [2195 kB]
Get:82 http://172.17.4.1/private bookworm-staging/main armhf liborc-0.4-0 armhf 1:0.4.32-2 [151 kB]
Get:83 http://172.17.4.1/private bookworm-staging/main armhf iso-codes all 4.11.0-1 [2834 kB]
Get:84 http://172.17.4.1/private bookworm-staging/main armhf libgstreamer-plugins-base1.0-0 armhf 1.20.3-2 [2174 kB]
Get:85 http://172.17.4.1/private bookworm-staging/main armhf libhyphen0 armhf 2.8.8-7 [30.0 kB]
Get:86 http://172.17.4.1/private bookworm-staging/main armhf libqt5positioning5 armhf 5.15.4+dfsg-2 [175 kB]
Get:87 http://172.17.4.1/private bookworm-staging/main armhf libavahi-common-data armhf 0.8-6+b1 [124 kB]
Get:88 http://172.17.4.1/private bookworm-staging/main armhf libavahi-common3 armhf 0.8-6+b1 [55.8 kB]
Get:89 http://172.17.4.1/private bookworm-staging/main armhf libavahi-client3 armhf 0.8-6+b1 [58.5 kB]
Get:90 http://172.17.4.1/private bookworm-staging/main armhf libcups2 armhf 2.4.2-1+b1 [311 kB]
Get:91 http://172.17.4.1/private bookworm-staging/main armhf libqt5printsupport5 armhf 5.15.4+dfsg-5+rpi1 [207 kB]
Get:92 http://172.17.4.1/private bookworm-staging/main armhf libqt5qml5 armhf 5.15.4+dfsg-4+rpi1 [1108 kB]
Get:93 http://172.17.4.1/private bookworm-staging/main armhf libqt5qmlmodels5 armhf 5.15.4+dfsg-4+rpi1 [170 kB]
Get:94 http://172.17.4.1/private bookworm-staging/main armhf libqt5quick5 armhf 5.15.4+dfsg-4+rpi1 [1329 kB]
Get:95 http://172.17.4.1/private bookworm-staging/main armhf libqt5sensors5 armhf 5.15.4-2 [95.2 kB]
Get:96 http://172.17.4.1/private bookworm-staging/main armhf libqt5webchannel5 armhf 5.15.4-2 [50.5 kB]
Get:97 http://172.17.4.1/private bookworm-staging/main armhf libwebp7 armhf 1.2.2-2 [237 kB]
Get:98 http://172.17.4.1/private bookworm-staging/main armhf libwoff1 armhf 1.0.2-2 [35.9 kB]
Get:99 http://172.17.4.1/private bookworm-staging/main armhf libxslt1.1 armhf 1.1.35-1 [221 kB]
Get:100 http://172.17.4.1/private bookworm-staging/main armhf libqt5webkit5 armhf 5.212.0~alpha4-21+rpi1 [8333 kB]
Get:101 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-minimal armhf 3.10.7-1 [813 kB]
Get:102 http://172.17.4.1/private bookworm-staging/main armhf python3.10-minimal armhf 3.10.7-1 [1518 kB]
Get:103 http://172.17.4.1/private bookworm-staging/main armhf python3-minimal armhf 3.10.6-1 [38.7 kB]
Get:104 http://172.17.4.1/private bookworm-staging/main armhf media-types all 8.0.0 [33.4 kB]
Get:105 http://172.17.4.1/private bookworm-staging/main armhf mailcap all 3.70+nmu1 [32.0 kB]
Get:106 http://172.17.4.1/private bookworm-staging/main armhf mime-support all 3.66 [10.9 kB]
Get:107 http://172.17.4.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:108 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-stdlib armhf 3.10.7-1 [1598 kB]
Get:109 http://172.17.4.1/private bookworm-staging/main armhf python3.10 armhf 3.10.7-1 [547 kB]
Get:110 http://172.17.4.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.10.6-1 [21.7 kB]
Get:111 http://172.17.4.1/private bookworm-staging/main armhf python3 armhf 3.10.6-1 [38.2 kB]
Get:112 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:113 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-8 [793 kB]
Get:114 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38.1-1 [137 kB]
Get:115 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.6-2 [34.2 kB]
Get:116 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.10.2-3 [1364 kB]
Get:117 http://172.17.4.1/private bookworm-staging/main armhf libncurses6 armhf 6.3+20220423-2 [79.6 kB]
Get:118 http://172.17.4.1/private bookworm-staging/main armhf libprocps8 armhf 2:3.3.17-7 [60.7 kB]
Get:119 http://172.17.4.1/private bookworm-staging/main armhf procps armhf 2:3.3.17-7 [475 kB]
Get:120 http://172.17.4.1/private bookworm-staging/main armhf openssl armhf 3.0.5-2 [1372 kB]
Get:121 http://172.17.4.1/private bookworm-staging/main armhf ca-certificates all 20211016 [156 kB]
Get:122 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:123 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:124 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:125 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-9 [171 kB]
Get:126 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.19-1 [260 kB]
Get:127 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:128 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:129 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:130 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-9 [510 kB]
Get:131 http://172.17.4.1/private bookworm-staging/main armhf libtcl8.6 armhf 8.6.12+dfsg-1 [906 kB]
Get:132 http://172.17.4.1/private bookworm-staging/main armhf libxft2 armhf 2.3.4-1 [50.2 kB]
Get:133 http://172.17.4.1/private bookworm-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:134 http://172.17.4.1/private bookworm-staging/main armhf libxss1 armhf 1:1.2.3-1 [17.3 kB]
Get:135 http://172.17.4.1/private bookworm-staging/main armhf libtk8.6 armhf 8.6.12-1 [680 kB]
Get:136 http://172.17.4.1/private bookworm-staging/main armhf tk8.6-blt2.5 armhf 2.5.3+dfsg-4.1 [477 kB]
Get:137 http://172.17.4.1/private bookworm-staging/main armhf blt armhf 2.5.3+dfsg-4.1 [14.9 kB]
Get:138 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.9.1 [196 kB]
Get:139 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-4 [526 kB]
Get:140 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:141 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:142 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-3 [10.4 kB]
Get:143 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:144 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:145 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:146 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-9 [1220 kB]
Get:147 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:148 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:149 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.9.1 [1071 kB]
Get:150 http://172.17.4.1/private bookworm-staging/main armhf python3-lib2to3 all 3.10.7-1 [79.9 kB]
Get:151 http://172.17.4.1/private bookworm-staging/main armhf python3-distutils all 3.10.7-1 [141 kB]
Get:152 http://172.17.4.1/private bookworm-staging/main armhf dh-python all 5.20220819+rpi1 [114 kB]
Get:153 http://172.17.4.1/private bookworm-staging/main armhf fonts-lyx all 2.3.6.1-1 [206 kB]
Get:154 http://172.17.4.1/private bookworm-staging/main armhf libaec0 armhf 1.0.6-1 [19.3 kB]
Get:155 http://172.17.4.1/private bookworm-staging/main armhf libblas3 armhf 3.10.1-2 [109 kB]
Get:156 http://172.17.4.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.49.0-1 [69.8 kB]
Get:157 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:158 http://172.17.4.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:159 http://172.17.4.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-3+b1 [161 kB]
Get:160 http://172.17.4.1/private bookworm-staging/main armhf libcurl4 armhf 7.85.0-1 [325 kB]
Get:161 http://172.17.4.1/private bookworm-staging/main armhf libdeflate0 armhf 1.12-1 [60.5 kB]
Get:162 http://172.17.4.1/private bookworm-staging/main armhf libedit2 armhf 3.1-20210910-1 [81.2 kB]
Get:163 http://172.17.4.1/private bookworm-staging/main armhf libexpat1-dev armhf 2.4.8-1 [137 kB]
Get:164 http://172.17.4.1/private bookworm-staging/main armhf libfribidi0 armhf 1.0.8-2.1 [63.7 kB]
Get:165 http://172.17.4.1/private bookworm-staging/main armhf libgfortran5 armhf 12.2.0-1+rpi1 [238 kB]
Get:166 http://172.17.4.1/private bookworm-staging/main armhf libsz2 armhf 1.0.6-1 [7452 B]
Get:167 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-103-1 armhf 1.10.7+repack-4+rpi1+b1 [1240 kB]
Get:168 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-hl-100 armhf 1.10.7+repack-4+rpi1+b1 [82.4 kB]
Get:169 http://172.17.4.1/private bookworm-staging/main armhf libimagequant0 armhf 2.17.0-1 [28.0 kB]
Get:170 http://172.17.4.1/private bookworm-staging/main armhf libjbig0 armhf 2.1-3.1+b2 [27.6 kB]
Get:171 http://172.17.4.1/private bookworm-staging/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:172 http://172.17.4.1/private bookworm-staging/main armhf libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get:173 http://172.17.4.1/private bookworm-staging/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-1 [119 kB]
Get:174 http://172.17.4.1/private bookworm-staging/main armhf libjs-sphinxdoc all 4.5.0-4 [142 kB]
Get:175 http://172.17.4.1/private bookworm-staging/main armhf liblapack3 armhf 3.10.1-2 [1587 kB]
Get:176 http://172.17.4.1/private bookworm-staging/main armhf liblbfgsb0 armhf 3.0+dfsg.3-11 [24.3 kB]
Get:177 http://172.17.4.1/private bookworm-staging/main armhf liblcms2-2 armhf 2.13.1-1 [125 kB]
Get:178 http://172.17.4.1/private bookworm-staging/main armhf liblerc4 armhf 4.0.0+ds-1 [121 kB]
Get:179 http://172.17.4.1/private bookworm-staging/main armhf libz3-4 armhf 4.8.12-1 [5758 kB]
Get:180 http://172.17.4.1/private bookworm-staging/main armhf libllvm11 armhf 1:11.1.0-6+rpi1+b2 [15.7 MB]
Get:181 http://172.17.4.1/private bookworm-staging/main armhf liblzf1 armhf 3.6-3 [9268 B]
Get:182 http://172.17.4.1/private bookworm-staging/main armhf libopenjp2-7 armhf 2.5.0-1 [165 kB]
Get:183 http://172.17.4.1/private bookworm-staging/main armhf libpfm4 armhf 4.11.1+git74-g5140ce5-1 [48.8 kB]
Get:184 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10 armhf 3.10.7-1 [1457 kB]
Get:185 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-4.1 [183 kB]
Get:186 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-dev armhf 3.10.7-1 [2917 kB]
Get:187 http://172.17.4.1/private bookworm-staging/main armhf libpython3-dev armhf 3.10.6-1 [22.0 kB]
Get:188 http://172.17.4.1/private bookworm-staging/main armhf libqhull-r8.0 armhf 2020.2-5 [221 kB]
Get:189 http://172.17.4.1/private bookworm-staging/main armhf libqt5xml5 armhf 5.15.4+dfsg-5+rpi1 [132 kB]
Get:190 http://172.17.4.1/private bookworm-staging/main armhf libqt5designer5 armhf 5.15.4-2 [2620 kB]
Get:191 http://172.17.4.1/private bookworm-staging/main armhf libqt5sql5 armhf 5.15.4+dfsg-5+rpi1 [132 kB]
Get:192 http://172.17.4.1/private bookworm-staging/main armhf libqt5help5 armhf 5.15.4-2 [132 kB]
Get:193 http://172.17.4.1/private bookworm-staging/main armhf libqt5opengl5 armhf 5.15.4+dfsg-5+rpi1 [150 kB]
Get:194 http://172.17.4.1/private bookworm-staging/main armhf libqt5test5 armhf 5.15.4+dfsg-5+rpi1 [154 kB]
Get:195 http://172.17.4.1/private bookworm-staging/main armhf libraqm0 armhf 0.7.0-4 [9388 B]
Get:196 http://172.17.4.1/private bookworm-staging/main armhf libtbbmalloc2 armhf 2021.5.0-12+rpi1 [43.8 kB]
Get:197 http://172.17.4.1/private bookworm-staging/main armhf libtbb12 armhf 2021.5.0-12+rpi1 [69.9 kB]
Get:198 http://172.17.4.1/private bookworm-staging/main armhf libtiff5 armhf 4.4.0-4 [290 kB]
Get:199 http://172.17.4.1/private bookworm-staging/main armhf libwebpdemux2 armhf 1.2.2-2 [97.1 kB]
Get:200 http://172.17.4.1/private bookworm-staging/main armhf libwebpmux3 armhf 1.2.2-2 [105 kB]
Get:201 http://172.17.4.1/private bookworm-staging/main armhf libyaml-0-2 armhf 0.2.5-1 [44.6 kB]
Get:202 http://172.17.4.1/private bookworm-staging/main armhf llvm-11-runtime armhf 1:11.1.0-6+rpi1+b2 [188 kB]
Get:203 http://172.17.4.1/private bookworm-staging/main armhf llvm-11-linker-tools armhf 1:11.1.0-6+rpi1+b2 [940 kB]
Get:204 http://172.17.4.1/private bookworm-staging/main armhf llvm-11 armhf 1:11.1.0-6+rpi1+b2 [6994 kB]
Get:205 http://172.17.4.1/private bookworm-staging/main armhf python-matplotlib-data all 3.5.2-2 [2741 kB]
Get:206 http://172.17.4.1/private bookworm-staging/main armhf python3-all armhf 3.10.6-1 [1060 B]
Get:207 http://172.17.4.1/private bookworm-staging/main armhf python3-appdirs all 1.4.4-3 [13.0 kB]
Get:208 http://172.17.4.1/private bookworm-staging/main armhf python3-attr all 22.1.0-1 [64.1 kB]
Get:209 http://172.17.4.1/private bookworm-staging/main armhf python3-backcall all 0.2.0-3 [12.1 kB]
Get:210 http://172.17.4.1/private bookworm-staging/main armhf python3-brotli armhf 1.0.9-2+b2 [278 kB]
Get:211 http://172.17.4.1/private bookworm-staging/main armhf python3-certifi all 2022.6.15-2 [154 kB]
Get:212 http://172.17.4.1/private bookworm-staging/main armhf python3-pkg-resources all 59.6.0-1.2 [196 kB]
Get:213 http://172.17.4.1/private bookworm-staging/main armhf python3-chardet all 4.0.0-2 [99.1 kB]
Get:214 http://172.17.4.1/private bookworm-staging/main armhf python3-charset-normalizer all 2.0.6-2 [30.6 kB]
Get:215 http://172.17.4.1/private bookworm-staging/main armhf python3-cloudpickle all 2.0.0-1 [24.0 kB]
Get:216 http://172.17.4.1/private bookworm-staging/main armhf python3-cycler all 0.11.0-1 [8020 B]
Get:217 http://172.17.4.1/private bookworm-staging/main armhf python3-fsspec all 2022.8.2-1 [100.0 kB]
Get:218 http://172.17.4.1/private bookworm-staging/main armhf python3-toolz all 0.11.2-1 [43.8 kB]
Get:219 http://172.17.4.1/private bookworm-staging/main armhf python3-pyparsing all 3.0.7-2 [140 kB]
Get:220 http://172.17.4.1/private bookworm-staging/main armhf python3-packaging all 21.3-1.1 [34.2 kB]
Get:221 http://172.17.4.1/private bookworm-staging/main armhf python3-locket all 0.2.1-2 [5436 B]
Get:222 http://172.17.4.1/private bookworm-staging/main armhf python3-partd all 1.2.0-2 [15.7 kB]
Get:223 http://172.17.4.1/private bookworm-staging/main armhf python3-yaml armhf 5.4.1-1+b1 [151 kB]
Get:224 http://172.17.4.1/private bookworm-staging/main armhf python3-dask all 2022.02.0+dfsg-2 [795 kB]
Get:225 http://172.17.4.1/private bookworm-staging/main armhf python3-six all 1.16.0-4 [17.5 kB]
Get:226 http://172.17.4.1/private bookworm-staging/main armhf python3-dateutil all 2.8.1-6 [79.2 kB]
Get:227 http://172.17.4.1/private bookworm-staging/main armhf python3-decorator all 5.1.1-2 [16.5 kB]
Get:228 http://172.17.4.1/private bookworm-staging/main armhf python3.10-dev armhf 3.10.7-1 [515 kB]
Get:229 http://172.17.4.1/private bookworm-staging/main armhf python3-dev armhf 3.10.6-1 [25.4 kB]
Get:230 http://172.17.4.1/private bookworm-staging/main armhf python3-dill all 0.3.4-2 [61.1 kB]
Get:231 http://172.17.4.1/private bookworm-staging/main armhf python3-execnet all 1.9.0-1 [41.5 kB]
Get:232 http://172.17.4.1/private bookworm-staging/main armhf python3-numpy armhf 1:1.21.5-1+b2 [3423 kB]
Get:233 http://172.17.4.1/private bookworm-staging/main armhf python3-scipy armhf 1.8.1-7 [12.9 MB]
Get:234 http://172.17.4.1/private bookworm-staging/main armhf python3-ufolib2 all 0.13.1+dfsg1-1 [32.0 kB]
Get:235 http://172.17.4.1/private bookworm-staging/main armhf python3-mpmath all 1.2.1-2 [418 kB]
Get:236 http://172.17.4.1/private bookworm-staging/main armhf python3-sympy all 1.10.1-3 [4317 kB]
Get:237 http://172.17.4.1/private bookworm-staging/main armhf python3-tz all 2022.2.1-1 [34.8 kB]
Get:238 http://172.17.4.1/private bookworm-staging/main armhf python3-fs all 2.4.16-1 [96.6 kB]
Get:239 http://172.17.4.1/private bookworm-staging/main armhf python3-lxml armhf 4.9.1-1 [959 kB]
Get:240 http://172.17.4.1/private bookworm-staging/main armhf python3-lz4 armhf 4.0.0+dfsg-1 [24.0 kB]
Get:241 http://172.17.4.1/private bookworm-staging/main armhf python3-unicodedata2 armhf 14.0.0+ds-8 [296 kB]
Get:242 http://172.17.4.1/private bookworm-staging/main armhf unicode-data all 14.0.0-1.1 [7868 kB]
Get:243 http://172.17.4.1/private bookworm-staging/main armhf python3-fonttools armhf 4.34.4-1 [814 kB]
Get:244 http://172.17.4.1/private bookworm-staging/main armhf python3-h5py-serial armhf 3.7.0-2 [712 kB]
Get:245 http://172.17.4.1/private bookworm-staging/main armhf python3-h5py all 3.7.0-2 [13.3 kB]
Get:246 http://172.17.4.1/private bookworm-staging/main armhf python3-idna all 3.3-1 [39.4 kB]
Get:247 http://172.17.4.1/private bookworm-staging/main armhf python3-tk armhf 3.10.7-1 [104 kB]
Get:248 http://172.17.4.1/private bookworm-staging/main armhf python3-pil.imagetk armhf 9.2.0-1 [78.5 kB]
Get:249 http://172.17.4.1/private bookworm-staging/main armhf python3-pil armhf 9.2.0-1 [430 kB]
Get:250 http://172.17.4.1/private bookworm-staging/main armhf python3-imageio all 2.4.1-5 [3137 kB]
Get:251 http://172.17.4.1/private bookworm-staging/main armhf python3-iniconfig all 1.1.1-2 [6396 B]
Get:252 http://172.17.4.1/private bookworm-staging/main armhf python3-parso all 0.8.1-1 [65.9 kB]
Get:253 http://172.17.4.1/private bookworm-staging/main armhf python3-jedi all 0.18.0-1 [620 kB]
Get:254 http://172.17.4.1/private bookworm-staging/main armhf python3-traitlets all 5.3.0-1 [91.6 kB]
Get:255 http://172.17.4.1/private bookworm-staging/main armhf python3-matplotlib-inline all 0.1.6-1 [8540 B]
Get:256 http://172.17.4.1/private bookworm-staging/main armhf python3-ptyprocess all 0.7.0-3 [14.9 kB]
Get:257 http://172.17.4.1/private bookworm-staging/main armhf python3-pexpect all 4.8.0-3 [55.0 kB]
Get:258 http://172.17.4.1/private bookworm-staging/main armhf python3-pickleshare all 0.7.5-5 [7600 B]
Get:259 http://172.17.4.1/private bookworm-staging/main armhf python3-wcwidth all 0.2.5+dfsg1-1 [21.7 kB]
Get:260 http://172.17.4.1/private bookworm-staging/main armhf python3-prompt-toolkit all 3.0.31-1 [274 kB]
Get:261 http://172.17.4.1/private bookworm-staging/main armhf python3-pygments all 2.12.0+dfsg-2 [765 kB]
Get:262 http://172.17.4.1/private bookworm-staging/main armhf python3-ipython all 7.31.1-1 [527 kB]
Get:263 http://172.17.4.1/private bookworm-staging/main armhf python3-joblib all 1.1.0-2 [218 kB]
Get:264 http://172.17.4.1/private bookworm-staging/main armhf python3-kiwisolver armhf 1.3.2-1+b1 [52.1 kB]
Get:265 http://172.17.4.1/private bookworm-staging/main armhf python3-llvmlite armhf 0.38.1-3 [124 kB]
Get:266 http://172.17.4.1/private bookworm-staging/main armhf python3-matplotlib armhf 3.5.2-2 [6495 kB]
Get:267 http://172.17.4.1/private bookworm-staging/main armhf python3-setuptools all 59.6.0-1.2 [401 kB]
Get:268 http://172.17.4.1/private bookworm-staging/main armhf python3-pbr all 5.8.1-2 [62.0 kB]
Get:269 http://172.17.4.1/private bookworm-staging/main armhf python3-mock all 4.0.3-3 [66.6 kB]
Get:270 http://172.17.4.1/private bookworm-staging/main armhf python3-more-itertools all 8.10.0-2 [53.0 kB]
Get:271 http://172.17.4.1/private bookworm-staging/main armhf python3-natsort all 8.0.2-2 [39.0 kB]
Get:272 http://172.17.4.1/private bookworm-staging/main armhf python3-networkx all 2.6.3-1 [943 kB]
Get:273 http://172.17.4.1/private bookworm-staging/main armhf python3-nose all 1.3.7-8 [133 kB]
Get:274 http://172.17.4.1/private bookworm-staging/main armhf python3-numba armhf 0.55.1-1 [1612 kB]
Get:275 http://172.17.4.1/private bookworm-staging/main armhf python3-numexpr armhf 2.8.3-1 [92.6 kB]
Get:276 http://172.17.4.1/private bookworm-staging/main armhf python3-pandas-lib armhf 1.3.5+dfsg-5 [5080 kB]
Get:277 http://172.17.4.1/private bookworm-staging/main armhf python3-pandas all 1.3.5+dfsg-5 [2654 kB]
Get:278 http://172.17.4.1/private bookworm-staging/main armhf python3-patsy all 0.5.2-2 [173 kB]
Get:279 http://172.17.4.1/private bookworm-staging/main armhf python3-pint all 0.18-1 [171 kB]
Get:280 http://172.17.4.1/private bookworm-staging/main armhf python3-pluggy all 1.0.0+repack-1 [19.7 kB]
Get:281 http://172.17.4.1/private bookworm-staging/main armhf python3-ptable all 0.9.2-4 [31.3 kB]
Get:282 http://172.17.4.1/private bookworm-staging/main armhf python3-py all 1.10.0-1 [94.2 kB]
Get:283 http://172.17.4.1/private bookworm-staging/main armhf python3-traits armhf 6.3.2-1 [4805 kB]
Get:284 http://172.17.4.1/private bookworm-staging/main armhf python3-pyqt5.sip armhf 12.11.0-1 [52.6 kB]
Get:285 http://172.17.4.1/private bookworm-staging/main armhf python3-pyqt5 armhf 5.15.7+dfsg-1 [1951 kB]
Get:286 http://172.17.4.1/private bookworm-staging/main armhf python3-pyqt5.qtopengl armhf 5.15.7+dfsg-1 [140 kB]
Get:287 http://172.17.4.1/private bookworm-staging/main armhf python3-pyqt5.qtsvg armhf 5.15.7+dfsg-1 [123 kB]
Get:288 http://172.17.4.1/private bookworm-staging/main armhf python3-pyqt5.qtwebkit armhf 5.15.7+dfsg-1 [180 kB]
Get:289 http://172.17.4.1/private bookworm-staging/main armhf python3-pyface all 7.4.0-1 [658 kB]
Get:290 http://172.17.4.1/private bookworm-staging/main armhf python3-tomli all 2.0.1-1 [18.1 kB]
Get:291 http://172.17.4.1/private bookworm-staging/main armhf python3-pytest all 7.1.2-2 [223 kB]
Ign:291 http://172.17.4.1/private bookworm-staging/main armhf python3-pytest all 7.1.2-2
Get:292 http://172.17.4.1/private bookworm-staging/main armhf python3-pytest-forked all 1.4.0-1 [7704 B]
Get:293 http://172.17.4.1/private bookworm-staging/main armhf python3-pytest-instafail all 0.4.2-2 [9544 B]
Get:294 http://172.17.4.1/private bookworm-staging/main armhf python3-pytest-mpl all 0.11-2 [21.7 kB]
Get:295 http://172.17.4.1/private bookworm-staging/main armhf python3-pytest-rerunfailures all 10.2-1 [14.2 kB]
Get:296 http://172.17.4.1/private bookworm-staging/main armhf python3-pytest-runner all 2.11.1-2 [8640 B]
Get:297 http://172.17.4.1/private bookworm-staging/main armhf python3-pytest-xdist all 2.5.0-5 [49.9 kB]
Get:298 http://172.17.4.1/private bookworm-staging/main armhf python3-pywt armhf 1.1.1-2 [1009 kB]
Get:299 http://172.17.4.1/private bookworm-staging/main armhf python3-urllib3 all 1.26.9-1 [116 kB]
Get:300 http://172.17.4.1/private bookworm-staging/main armhf python3-requests all 2.27.1+dfsg-1 [71.9 kB]
Get:301 http://172.17.4.1/private bookworm-staging/main armhf python3-skimage-lib armhf 0.19.3-2 [1656 kB]
Get:302 http://172.17.4.1/private bookworm-staging/main armhf python3-tifffile all 20220812-2 [171 kB]
Get:303 http://172.17.4.1/private bookworm-staging/main armhf python3-skimage all 0.19.3-2 [20.7 MB]
Get:304 http://172.17.4.1/private bookworm-staging/main armhf python3-threadpoolctl all 3.1.0-1 [21.2 kB]
Get:305 http://172.17.4.1/private bookworm-staging/main armhf python3-sklearn-lib armhf 1.1.2+dfsg-6 [1813 kB]
Get:306 http://172.17.4.1/private bookworm-staging/main armhf python3-sklearn all 1.1.2+dfsg-6 [2047 kB]
Get:307 http://172.17.4.1/private bookworm-staging/main armhf python3-sparse all 0.13.0-1 [63.2 kB]
Get:308 http://172.17.4.1/private bookworm-staging/main armhf python3-statsmodels-lib armhf 0.13.2+dfsg-4+rpi1 [1107 kB]
Get:309 http://172.17.4.1/private bookworm-staging/main armhf python3-statsmodels all 0.13.2+dfsg-4+rpi1 [4520 kB]
Get:310 http://172.17.4.1/private bookworm-staging/main armhf python3-tqdm all 4.64.0-2 [96.0 kB]
Get:311 http://172.17.4.1/private bookworm-staging/main armhf python3-traitsui all 7.2.1-2 [5653 kB]
Get:291 http://172.17.4.1/private bookworm-staging/main armhf python3-pytest all 7.1.2-2 [223 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 221 MB in 19s (11.5 MB/s)
Selecting previously unselected package libglib2.0-0:armhf.
(Reading database ... 12798 files and directories currently installed.)
Preparing to unpack .../000-libglib2.0-0_2.73.3-3+rpi1_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.73.3-3+rpi1) ...
Selecting previously unselected package libicu71:armhf.
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Unpacking libicu71:armhf (71.1-3) ...
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Unpacking libxml2:armhf (2.9.14+dfsg-1) ...
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Unpacking shared-mime-info (2.2-1) ...
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Unpacking libdouble-conversion3:armhf (3.2.1-1) ...
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Unpacking libpcre2-16-0:armhf (10.40-1+b2) ...
Selecting previously unselected package libqt5core5a:armhf.
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Unpacking libqt5core5a:armhf (5.15.4+dfsg-5+rpi1) ...
Selecting previously unselected package libexpat1:armhf.
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Unpacking libexpat1:armhf (2.4.8-1) ...
Selecting previously unselected package libbrotli1:armhf.
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Unpacking libbrotli1:armhf (1.0.9-2+b2) ...
Selecting previously unselected package libpng16-16:armhf.
Preparing to unpack .../009-libpng16-16_1.6.37-5_armhf.deb ...
Unpacking libpng16-16:armhf (1.6.37-5) ...
Selecting previously unselected package libfreetype6:armhf.
Preparing to unpack .../010-libfreetype6_2.12.1+dfsg-3_armhf.deb ...
Unpacking libfreetype6:armhf (2.12.1+dfsg-3) ...
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Moving old data out of the way
Unpacking ucf (3.0043) ...
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Unpacking fonts-dejavu-core (2.37-2) ...
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Preparing to unpack .../013-fontconfig-config_2.13.1-4.4_all.deb ...
Unpacking fontconfig-config (2.13.1-4.4) ...
Selecting previously unselected package libfontconfig1:armhf.
Preparing to unpack .../014-libfontconfig1_2.13.1-4.4_armhf.deb ...
Unpacking libfontconfig1:armhf (2.13.1-4.4) ...
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Unpacking fontconfig (2.13.1-4.4) ...
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Unpacking libdrm-common (2.4.112-3+rpi1) ...
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Selecting previously unselected package libglvnd0:armhf.
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Unpacking libglvnd0:armhf (1.5.0-1) ...
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Selecting previously unselected package libwayland-client0:armhf.
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Unpacking libwayland-client0:armhf (1.21.0-1) ...
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Unpacking libmd0:armhf (1.0.4-2) ...
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Unpacking libbsd0:armhf (0.11.6-1) ...
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invoke-rc.d: could not determine current runlevel
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Updating certificates in /etc/ssl/certs...
127 added, 0 removed; done.
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Setcap worked! gst-ptp-helper is not suid!
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/usr/lib/python3/dist-packages/prettytable/prettytable.py:421: SyntaxWarning: "is" with a literal. Did you mean "=="?
elif val is None or (isinstance(val, dict) and len(val) is 0):
/usr/lib/python3/dist-packages/prettytable/prettytable.py:441: SyntaxWarning: "is" with a literal. Did you mean "=="?
elif val is None or (isinstance(val, dict) and len(val) is 0):
/usr/lib/python3/dist-packages/prettytable/prettytable.py:459: SyntaxWarning: "is" with a literal. Did you mean "=="?
if val is None or (isinstance(val, dict) and len(val) is 0):
/usr/lib/python3/dist-packages/prettytable/prettytable.py:476: SyntaxWarning: "is" with a literal. Did you mean "=="?
if val is None or (isinstance(val, dict) and len(val) is 0):
/usr/lib/python3/dist-packages/prettytable/prettytable.py:674: SyntaxWarning: "is" with a literal. Did you mean "=="?
if val is None or (isinstance(val, dict) and len(val) is 0):
/usr/lib/python3/dist-packages/prettytable/prettytable.py:691: SyntaxWarning: "is" with a literal. Did you mean "=="?
if val is None or (isinstance(val, dict) and len(val) is 0):
Setting up libpython3.10-dev:armhf (3.10.7-1) ...
Setting up libqt5webchannel5:armhf (5.15.4-2) ...
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Setting up libhdf5-103-1:armhf (1.10.7+repack-4+rpi1+b1) ...
Setting up python3-lxml:armhf (4.9.1-1) ...
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Setting up python3-dateutil (2.8.1-6) ...
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Setting up python3-pygments (2.12.0+dfsg-2) ...
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/usr/lib/python3/dist-packages/imageio/plugins/_tifffile.py:2813: SyntaxWarning: "is" with a literal. Did you mean "=="?
if key is 0:
Setting up python3-scipy (1.8.1-7) ...
Setting up python3-skimage-lib:armhf (0.19.3-2) ...
Setting up python3-jedi (0.18.0-1) ...
Setting up python3-pytest (7.1.2-2) ...
Setting up python3-pytest-instafail (0.4.2-2) ...
Setting up python3-pandas-lib:armhf (1.3.5+dfsg-5) ...
Setting up python3-sklearn-lib:armhf (1.1.2+dfsg-6) ...
Setting up python3-dask (2022.02.0+dfsg-2) ...
Setting up python3-h5py-serial (3.7.0-2) ...
Setting up python3-tifffile (20220812-2) ...
Setting up python3-numba (0.55.1-1) ...
update-alternatives: using /usr/share/python3-numba/numba to provide /usr/bin/numba (numba) in auto mode
Setting up python3-pytest-forked (1.4.0-1) ...
Setting up python3-patsy (0.5.2-2) ...
Setting up python3-pint (0.18-1) ...
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Setting up python3-ipython (7.31.1-1) ...
Setting up python3-h5py (3.7.0-2) ...
Setting up python3-sklearn (1.1.2+dfsg-6) ...
Setting up python3-numexpr (2.8.3-1) ...
Setting up python3-statsmodels (0.13.2+dfsg-4+rpi1) ...
Setting up python3-pytest-rerunfailures (10.2-1) ...
Setting up python3-pytest-xdist (2.5.0-5) ...
Setting up python3-sparse (0.13.0-1) ...
Setting up python3-fonttools (4.34.4-1) ...
Setting up python3-ufolib2 (0.13.1+dfsg1-1) ...
Processing triggers for sgml-base (1.30) ...
Setting up libfontconfig1:armhf (2.13.1-4.4) ...
Setting up fontconfig (2.13.1-4.4) ...
Regenerating fonts cache... done.
Setting up libxft2:armhf (2.3.4-1) ...
Setting up libtk8.6:armhf (8.6.12-1) ...
Processing triggers for libc-bin (2.34-7+rpi1) ...
Setting up libqt5gui5:armhf (5.15.4+dfsg-5+rpi1) ...
Setting up libgstreamer-plugins-base1.0-0:armhf (1.20.3-2) ...
Setting up libqt5widgets5:armhf (5.15.4+dfsg-5+rpi1) ...
Setting up libqt5help5:armhf (5.15.4-2) ...
Setting up libqt5printsupport5:armhf (5.15.4+dfsg-5+rpi1) ...
Setting up libqt5opengl5:armhf (5.15.4+dfsg-5+rpi1) ...
Setting up libqt5quick5:armhf (5.15.4+dfsg-4+rpi1) ...
Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1) ...
Setting up libqt5designer5:armhf (5.15.4-2) ...
Setting up blt (2.5.3+dfsg-4.1) ...
Setting up libqt5svg5:armhf (5.15.4-2) ...
Setting up python3-tk:armhf (3.10.7-1) ...
Setting up libqt5webkit5:armhf (5.212.0~alpha4-21+rpi1) ...
Setting up python3-pil.imagetk:armhf (9.2.0-1) ...
Setting up python3-pyqt5 (5.15.7+dfsg-1) ...
Setting up python3-pyqt5.qtsvg (5.15.7+dfsg-1) ...
Setting up python3-matplotlib (3.5.2-2) ...
Setting up python3-pyqt5.qtopengl (5.15.7+dfsg-1) ...
Setting up python3-pytest-mpl (0.11-2) ...
Setting up python3-pyqt5.qtwebkit (5.15.7+dfsg-1) ...
Setting up python3-skimage (0.19.3-2) ...
Setting up python3-pyface (7.4.0-1) ...
Setting up python3-traitsui (7.2.1-2) ...
Setting up sbuild-build-depends-hyperspy-dummy (0.invalid.0) ...
Processing triggers for ca-certificates (20211016) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Processing triggers for libc-bin (2.34-7+rpi1) ...
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.38.90.20220713-2+rpi1 dpkg-dev_1.21.9+rpi1 g++-12_12.2.0-1+rpi1 gcc-12_12.2.0-1+rpi1 libc6-dev_2.34-7+rpi1 libstdc++-12-dev_12.2.0-1+rpi1 libstdc++6_12.2.0-1+rpi1 linux-libc-dev_5.19.6-1+rpi1
Package versions: adduser_3.129 apt_2.5.2 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-9 autotools-dev_20220109.1 base-files_12.2+rpi1 base-passwd_3.6.0 bash_5.2~rc2-2 binutils_2.38.90.20220713-2+rpi1 binutils-arm-linux-gnueabihf_2.38.90.20220713-2+rpi1 binutils-common_2.38.90.20220713-2+rpi1 blt_2.5.3+dfsg-4.1 bsdextrautils_2.38.1-1 bsdutils_1:2.38.1-1 build-essential_12.9 bzip2_1.0.8-5+b2 ca-certificates_20211016 coreutils_8.32-4.1 cpp_4:12.1.0-3+rpi1 cpp-12_12.2.0-1+rpi1 dash_0.5.11+git20210903+057cd650a4ed-9 debconf_1.5.79 debhelper_13.9.1 debianutils_5.7-0.3 dh-autoreconf_20 dh-python_5.20220819+rpi1 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-1 dirmngr_2.2.39-1 dpkg_1.21.9+rpi1 dpkg-dev_1.21.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.5-2 fakeroot_1.29-1 file_1:5.41-4 findutils_4.9.0-3 fontconfig_2.13.1-4.4 fontconfig-config_2.13.1-4.4 fonts-dejavu-core_2.37-2 fonts-lyx_2.3.6.1-1 g++_4:12.1.0-3+rpi1 g++-12_12.2.0-1+rpi1 gcc_4:12.1.0-3+rpi1 gcc-12_12.2.0-1+rpi1 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libqt5dbus5_5.15.4+dfsg-5+rpi1 libqt5designer5_5.15.4-2 libqt5gui5_5.15.4+dfsg-5+rpi1 libqt5help5_5.15.4-2 libqt5network5_5.15.4+dfsg-5+rpi1 libqt5opengl5_5.15.4+dfsg-5+rpi1 libqt5positioning5_5.15.4+dfsg-2 libqt5printsupport5_5.15.4+dfsg-5+rpi1 libqt5qml5_5.15.4+dfsg-4+rpi1 libqt5qmlmodels5_5.15.4+dfsg-4+rpi1 libqt5quick5_5.15.4+dfsg-4+rpi1 libqt5sensors5_5.15.4-2 libqt5sql5_5.15.4+dfsg-5+rpi1 libqt5svg5_5.15.4-2 libqt5test5_5.15.4+dfsg-5+rpi1 libqt5webchannel5_5.15.4-2 libqt5webkit5_5.212.0~alpha4-21+rpi1 libqt5widgets5_5.15.4+dfsg-5+rpi1 libqt5xml5_5.15.4+dfsg-5+rpi1 libraqm0_0.7.0-4 libreadline8_8.2~rc2-2 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg-8 libsasl2-modules-db_2.1.28+dfsg-8 libseccomp2_2.5.4-1+rpi1 libselinux1_3.4-1 libsemanage-common_3.4-1 libsemanage2_3.4-1 libsepol1_3.1-1 libsepol2_3.4-2 libsm6_2:1.2.3-1 libsmartcols1_2.38.1-1 libsqlite3-0_3.39.3-1 libss2_1.46.5-2 libssh2-1_1.10.0-3+b1 libssl1.1_1.1.1o-1 libssl3_3.0.5-2 libstdc++-12-dev_12.2.0-1+rpi1 libstdc++6_12.2.0-1+rpi1 libsub-override-perl_0.09-3 libsystemd0_251.3-1+rpi1 libsz2_1.0.6-1 libtasn1-6_4.18.0-4 libtbb12_2021.5.0-12+rpi1 libtbbmalloc2_2021.5.0-12+rpi1 libtcl8.6_8.6.12+dfsg-1 libtiff5_4.4.0-4 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtk8.6_8.6.12-1 libtool_2.4.7-4 libubsan1_12.2.0-1+rpi1 libuchardet0_0.0.7-1 libudev1_251.3-1+rpi1 libunistring2_1.0-1 libunwind8_1.3.2-2 libuuid1_2.38.1-1 libwacom-common_2.4.0-3 libwacom9_2.4.0-3 libwayland-client0_1.21.0-1 libwayland-server0_1.21.0-1 libwebp7_1.2.2-2 libwebpdemux2_1.2.2-2 libwebpmux3_1.2.2-2 libwoff1_1.0.2-2 libx11-6_2:1.8.1-2 libx11-data_2:1.8.1-2 libx11-xcb1_2:1.8.1-2 libxau6_1:1.0.9-1 libxcb-dri2-0_1.15-1 libxcb-dri3-0_1.15-1 libxcb-icccm4_0.4.1-1.1 libxcb-image0_0.4.0-2 libxcb-keysyms1_0.4.0-1+b2 libxcb-present0_1.15-1 libxcb-randr0_1.15-1 libxcb-render-util0_0.3.9-1+b1 libxcb-render0_1.15-1 libxcb-shape0_1.15-1 libxcb-shm0_1.15-1 libxcb-sync1_1.15-1 libxcb-util1_0.4.0-1 libxcb-xfixes0_1.15-1 libxcb-xinerama0_1.15-1 libxcb-xinput0_1.15-1 libxcb-xkb1_1.15-1 libxcb1_1.15-1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.4-1 libxft2_2.3.4-1 libxkbcommon-x11-0_1.4.1-1 libxkbcommon0_1.4.1-1 libxml2_2.9.14+dfsg-1 libxrender1_1:0.9.10-1.1 libxshmfence1_1.3-1 libxslt1.1_1.1.35-1 libxss1_1:1.2.3-1 libxxhash0_0.8.1-1 libyaml-0-2_0.2.5-1 libz3-4_4.8.12-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.19.6-1+rpi1 llvm-11_1:11.1.0-6+rpi1+b2 llvm-11-linker-tools_1:11.1.0-6+rpi1+b2 llvm-11-runtime_1:11.1.0-6+rpi1+b2 login_1:4.11.1+dfsg1-2 logsave_1.46.5-2 lsb-base_11.2+rpi1 m4_1.4.19-1 mailcap_3.70+nmu1 make_4.3-4.1 man-db_2.10.2-3 mawk_1.3.4.20200120-3.1 media-types_8.0.0 mime-support_3.66 mount_2.38.1-1 nano_6.4-1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 netbase_6.3 openssl_3.0.5-2 passwd_1:4.11.1+dfsg1-2 patch_2.7.6-7 perl_5.34.0-5 perl-base_5.34.0-5 perl-modules-5.34_5.34.0-5 pinentry-curses_1.2.0-2 po-debconf_1.0.21+nmu1 procps_2:3.3.17-7 python-matplotlib-data_3.5.2-2 python3_3.10.6-1 python3-all_3.10.6-1 python3-appdirs_1.4.4-3 python3-attr_22.1.0-1 python3-backcall_0.2.0-3 python3-brotli_1.0.9-2+b2 python3-certifi_2022.6.15-2 python3-chardet_4.0.0-2 python3-charset-normalizer_2.0.6-2 python3-cloudpickle_2.0.0-1 python3-cycler_0.11.0-1 python3-dask_2022.02.0+dfsg-2 python3-dateutil_2.8.1-6 python3-decorator_5.1.1-2 python3-dev_3.10.6-1 python3-dill_0.3.4-2 python3-distutils_3.10.7-1 python3-execnet_1.9.0-1 python3-fonttools_4.34.4-1 python3-fs_2.4.16-1 python3-fsspec_2022.8.2-1 python3-h5py_3.7.0-2 python3-h5py-serial_3.7.0-2 python3-idna_3.3-1 python3-imageio_2.4.1-5 python3-iniconfig_1.1.1-2 python3-ipython_7.31.1-1 python3-jedi_0.18.0-1 python3-joblib_1.1.0-2 python3-kiwisolver_1.3.2-1+b1 python3-lib2to3_3.10.7-1 python3-llvmlite_0.38.1-3 python3-locket_0.2.1-2 python3-lxml_4.9.1-1 python3-lz4_4.0.0+dfsg-1 python3-matplotlib_3.5.2-2 python3-matplotlib-inline_0.1.6-1 python3-minimal_3.10.6-1 python3-mock_4.0.3-3 python3-more-itertools_8.10.0-2 python3-mpmath_1.2.1-2 python3-natsort_8.0.2-2 python3-networkx_2.6.3-1 python3-nose_1.3.7-8 python3-numba_0.55.1-1 python3-numexpr_2.8.3-1 python3-numpy_1:1.21.5-1+b2 python3-packaging_21.3-1.1 python3-pandas_1.3.5+dfsg-5 python3-pandas-lib_1.3.5+dfsg-5 python3-parso_0.8.1-1 python3-partd_1.2.0-2 python3-patsy_0.5.2-2 python3-pbr_5.8.1-2 python3-pexpect_4.8.0-3 python3-pickleshare_0.7.5-5 python3-pil_9.2.0-1 python3-pil.imagetk_9.2.0-1 python3-pint_0.18-1 python3-pkg-resources_59.6.0-1.2 python3-pluggy_1.0.0+repack-1 python3-prompt-toolkit_3.0.31-1 python3-ptable_0.9.2-4 python3-ptyprocess_0.7.0-3 python3-py_1.10.0-1 python3-pyface_7.4.0-1 python3-pygments_2.12.0+dfsg-2 python3-pyparsing_3.0.7-2 python3-pyqt5_5.15.7+dfsg-1 python3-pyqt5.qtopengl_5.15.7+dfsg-1 python3-pyqt5.qtsvg_5.15.7+dfsg-1 python3-pyqt5.qtwebkit_5.15.7+dfsg-1 python3-pyqt5.sip_12.11.0-1 python3-pytest_7.1.2-2 python3-pytest-forked_1.4.0-1 python3-pytest-instafail_0.4.2-2 python3-pytest-mpl_0.11-2 python3-pytest-rerunfailures_10.2-1 python3-pytest-runner_2.11.1-2 python3-pytest-xdist_2.5.0-5 python3-pywt_1.1.1-2 python3-requests_2.27.1+dfsg-1 python3-scipy_1.8.1-7 python3-setuptools_59.6.0-1.2 python3-six_1.16.0-4 python3-skimage_0.19.3-2 python3-skimage-lib_0.19.3-2 python3-sklearn_1.1.2+dfsg-6 python3-sklearn-lib_1.1.2+dfsg-6 python3-sparse_0.13.0-1 python3-statsmodels_0.13.2+dfsg-4+rpi1 python3-statsmodels-lib_0.13.2+dfsg-4+rpi1 python3-sympy_1.10.1-3 python3-threadpoolctl_3.1.0-1 python3-tifffile_20220812-2 python3-tk_3.10.7-1 python3-tomli_2.0.1-1 python3-toolz_0.11.2-1 python3-tqdm_4.64.0-2 python3-traitlets_5.3.0-1 python3-traits_6.3.2-1 python3-traitsui_7.2.1-2 python3-tz_2022.2.1-1 python3-ufolib2_0.13.1+dfsg1-1 python3-unicodedata2_14.0.0+ds-8 python3-urllib3_1.26.9-1 python3-wcwidth_0.2.5+dfsg1-1 python3-yaml_5.4.1-1+b1 python3.10_3.10.7-1 python3.10-dev_3.10.7-1 python3.10-minimal_3.10.7-1 raspbian-archive-keyring_20120528.2 readline-common_8.2~rc2-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-hyperspy-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sgml-base_1.30 shared-mime-info_2.2-1 sysvinit-utils_3.04-1 tar_1.34+dfsg-1 tk8.6-blt2.5_2.5.3+dfsg-4.1 tzdata_2022c-1 ucf_3.0043 unicode-data_14.0.0-1.1 util-linux_2.38.1-1 util-linux-extra_2.38.1-1 x11-common_1:7.7+23 xkb-data_2.35.1-1 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-4.1 zlib1g-dev_1:1.2.11.dfsg-4.1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.r4UYOyHJ/trustedkeys.kbx': General error
gpgv: Signature made Wed Jan 20 14:38:22 2021 UTC
gpgv: using RSA key 02A4A46D5B6B5CFE3124C87710BE8983F3D59D64
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./hyperspy_1.6.1-1.dsc
dpkg-source: info: extracting hyperspy in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking hyperspy_1.6.1.orig.tar.xz
dpkg-source: info: unpacking hyperspy_1.6.1-1.debian.tar.xz
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-b6b3bf49-c4d6-45cf-98ea-258945b88ca0
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package hyperspy
dpkg-buildpackage: info: source version 1.6.1-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
dpkg-source: info: using options from hyperspy-1.6.1/debian/source/options: --extend-diff-ignore=^hyperspy/misc/etc/test_compilers.o$ --extend-diff-ignore=^hyperspy/io_plugins/unbcf_fast.c$
fakeroot debian/rules clean
dh clean --with python3 --buildsystem=pybuild
dh_auto_clean -O--buildsystem=pybuild
I: pybuild base:240: python3.10 setup.py clean
/<<PKGBUILDDIR>>/setup.py:22: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
from distutils.errors import CompileError, DistutilsPlatformError
/<<PKGBUILDDIR>>/setup.py:24: DeprecationWarning: The distutils.sysconfig module is deprecated, use sysconfig instead
import distutils.sysconfig
/<<PKGBUILDDIR>>/setup.py:145: UserWarning: WARNING: cython required to generate fast c code is not found on this system.
Only slow pure python alternative functions will be available.
To use fast implementation of some functions writen in cython either:
a) install cython and re-run the installation,
b) try alternative source distribution containing cythonized C versions of fast code,
c) use binary distribution (i.e. wheels, egg).
warnings.warn("""WARNING: cython required to generate fast c code is not found on this system.
running clean
removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build' (and everything under it)
'build/bdist.linux-armhf' does not exist -- can't clean it
'build/scripts-3.10' does not exist -- can't clean it
dh_autoreconf_clean -O--buildsystem=pybuild
dh_clean -O--buildsystem=pybuild
debian/rules build-arch
dh build-arch --with python3 --buildsystem=pybuild
dh_update_autotools_config -a -O--buildsystem=pybuild
dh_autoreconf -a -O--buildsystem=pybuild
dh_auto_configure -a -O--buildsystem=pybuild
I: pybuild base:240: python3.10 setup.py config
/<<PKGBUILDDIR>>/setup.py:22: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
from distutils.errors import CompileError, DistutilsPlatformError
/<<PKGBUILDDIR>>/setup.py:24: DeprecationWarning: The distutils.sysconfig module is deprecated, use sysconfig instead
import distutils.sysconfig
/<<PKGBUILDDIR>>/setup.py:145: UserWarning: WARNING: cython required to generate fast c code is not found on this system.
Only slow pure python alternative functions will be available.
To use fast implementation of some functions writen in cython either:
a) install cython and re-run the installation,
b) try alternative source distribution containing cythonized C versions of fast code,
c) use binary distribution (i.e. wheels, egg).
warnings.warn("""WARNING: cython required to generate fast c code is not found on this system.
running config
dh_auto_build -a -O--buildsystem=pybuild
I: pybuild base:240: /usr/bin/python3 setup.py build
/<<PKGBUILDDIR>>/setup.py:22: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
from distutils.errors import CompileError, DistutilsPlatformError
/<<PKGBUILDDIR>>/setup.py:24: DeprecationWarning: The distutils.sysconfig module is deprecated, use sysconfig instead
import distutils.sysconfig
/<<PKGBUILDDIR>>/setup.py:145: UserWarning: WARNING: cython required to generate fast c code is not found on this system.
Only slow pure python alternative functions will be available.
To use fast implementation of some functions writen in cython either:
a) install cython and re-run the installation,
b) try alternative source distribution containing cythonized C versions of fast code,
c) use binary distribution (i.e. wheels, egg).
warnings.warn("""WARNING: cython required to generate fast c code is not found on this system.
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy
copying hyperspy/Release.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy
copying hyperspy/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy
copying hyperspy/_lazy_signals.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy
copying hyperspy/api.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy
copying hyperspy/api_nogui.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy
copying hyperspy/axes.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy
copying hyperspy/component.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy
copying hyperspy/components1d.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy
copying hyperspy/components2d.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy
copying hyperspy/conftest.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy
copying hyperspy/decorators.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy
copying hyperspy/defaults_parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy
copying hyperspy/events.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy
copying hyperspy/exceptions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy
copying hyperspy/extensions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy
copying hyperspy/interactive.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy
copying hyperspy/io.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy
copying hyperspy/logger.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy
copying hyperspy/model.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy
copying hyperspy/roi.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy
copying hyperspy/samfire.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy
copying hyperspy/signal.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy
copying hyperspy/signal_tools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy
copying hyperspy/signals.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy
copying hyperspy/ui_registry.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/datasets
copying hyperspy/datasets/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/datasets
copying hyperspy/datasets/artificial_data.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/datasets
copying hyperspy/datasets/example_signals.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/datasets
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_components
copying hyperspy/_components/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_components
copying hyperspy/_components/arctan.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_components
copying hyperspy/_components/bleasdale.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_components
copying hyperspy/_components/doniach.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_components
copying hyperspy/_components/eels_arctan.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_components
copying hyperspy/_components/eels_cl_edge.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_components
copying hyperspy/_components/eels_double_power_law.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_components
copying hyperspy/_components/eels_vignetting.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_components
copying hyperspy/_components/error_function.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_components
copying hyperspy/_components/exponential.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_components
copying hyperspy/_components/expression.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_components
copying hyperspy/_components/gaussian.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_components
copying hyperspy/_components/gaussian2d.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_components
copying hyperspy/_components/gaussianhf.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_components
copying hyperspy/_components/heaviside.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_components
copying hyperspy/_components/logistic.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_components
copying hyperspy/_components/lorentzian.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_components
copying hyperspy/_components/offset.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_components
copying hyperspy/_components/pes_core_line_shape.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_components
copying hyperspy/_components/pes_see.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_components
copying hyperspy/_components/pes_voigt.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_components
copying hyperspy/_components/polynomial.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_components
copying hyperspy/_components/polynomial_deprecated.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_components
copying hyperspy/_components/power_law.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_components
copying hyperspy/_components/rc.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_components
copying hyperspy/_components/scalable_fixed_pattern.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_components
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copying hyperspy/tests/io/dm3_3D_data/test-14.dm3 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/dm3_3D_data
copying hyperspy/tests/io/dm3_3D_data/test-2.dm3 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/dm3_3D_data
copying hyperspy/tests/io/dm3_3D_data/test-23.dm3 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/dm3_3D_data
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copying hyperspy/tests/io/dm3_3D_data/test-5.dm3 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/dm3_3D_data
copying hyperspy/tests/io/dm3_3D_data/test-6.dm3 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/dm3_3D_data
copying hyperspy/tests/io/dm3_3D_data/test-7.dm3 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/dm3_3D_data
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copying hyperspy/tests/io/dm4_3D_data/test-3.dm4 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/dm4_3D_data
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copying hyperspy/tests/io/dm3_locale/Fei HAADF-FR_location.dm3 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/dm3_locale
copying hyperspy/tests/io/dm3_locale/Fei HAADF-MX_location.dm3 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/dm3_locale
copying hyperspy/tests/io/dm3_locale/Fei HAADF-UK_location.dm3 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/dm3_locale
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copying hyperspy/tests/io/FEI_old/X - Au NP EELS_2.ser -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/FEI_old
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copying hyperspy/tests/io/msa_files/example1_wrong_date.msa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/msa_files
copying hyperspy/tests/io/msa_files/example2.msa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/msa_files
copying hyperspy/tests/io/msa_files/minimum_metadata.msa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/msa_files
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copying hyperspy/tests/io/hdf5_files/example1_v1.1.hdf5 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/hdf5_files
copying hyperspy/tests/io/hdf5_files/example1_v1.2.hdf5 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/hdf5_files
copying hyperspy/tests/io/hdf5_files/none_metadata.hdf5 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/hdf5_files
copying hyperspy/tests/io/hdf5_files/test_marker_bad_marker_type.hdf5 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/hdf5_files
copying hyperspy/tests/io/hdf5_files/test_marker_point_y2_data_deleted.hdf5 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/hdf5_files
copying hyperspy/tests/io/hdf5_files/test_rgba16.hdf5 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/hdf5_files
copying hyperspy/tests/io/hdf5_files/with_lists_etc.hdf5 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/hdf5_files
copying hyperspy/tests/io/hdf5_files/example2_v2.2.hspy -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/hdf5_files
copying hyperspy/tests/io/hdf5_files/hspy_ext_missing.hspy -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/hdf5_files
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copying hyperspy/tests/io/unf_files/example_image_int16.unf -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/unf_files
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copying hyperspy/tests/io/unf_files/example_with_title.unf -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/unf_files
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copying hyperspy/tests/io/bruker_data/bcf-edx-ebsd.bcf -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/bruker_data
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copying hyperspy/tests/io/sur_data/test_profile.pro -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/sur_data
copying hyperspy/tests/io/sur_data/test_spectra.pro -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/sur_data
copying hyperspy/tests/io/sur_data/test_spectrum.pro -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/sur_data
copying hyperspy/tests/io/sur_data/test_spectrum_compressed.pro -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/sur_data
copying hyperspy/tests/io/sur_data/test_RGB.sur -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/sur_data
copying hyperspy/tests/io/sur_data/test_spectral_map.sur -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/sur_data
copying hyperspy/tests/io/sur_data/test_spectral_map_compressed.sur -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/sur_data
copying hyperspy/tests/io/sur_data/test_surface.sur -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/sur_data
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/data
copying hyperspy/tests/signal/data/test_find_peaks1D_ohaver.hdf5 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/data
copying hyperspy/tests/signal/data/EELS_LL_linescan_simulated_thickness_variation.hspy -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/data
copying hyperspy/tests/signal/data/EELS_ZLP_linescan_simulated_thickness_variation.hspy -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/data
copying hyperspy/hyperspy_extension.yaml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy
dh_auto_test -a -O--buildsystem=pybuild
I: pybuild base:240: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build; python3.10 -m pytest
============================= test session starts ==============================
platform linux -- Python 3.10.7, pytest-7.1.2, pluggy-1.0.0+repack
Matplotlib: 3.5.2
Freetype: 2.12.1
rootdir: /<<PKGBUILDDIR>>, configfile: setup.cfg
plugins: forked-1.4.0, instafail-0.4.2, mpl-0.11, rerunfailures-10.2, xdist-2.5.0
gw0 I / gw1 I / gw2 I / gw3 I
gw0 [3798] / gw1 [3798] / gw2 [3798] / gw3 [3798]
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==================================== ERRORS ====================================
_________ ERROR at setup of TestIOOverwriting.test_io_overwriting_True _________
[gw0] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_io.TestIOOverwriting object at 0x9f4b06a0>
method = <bound method TestIOOverwriting.test_io_overwriting_True of <hyperspy.tests.io.test_io.TestIOOverwriting object at 0x9f4b06a0>>
def setup_method(self, method):
self.s = Signal1D(np.arange(10))
self.new_s = Signal1D(np.ones(5))
# make sure we start from a clean state
self._clean_file()
> self.s.save(FULLFILENAME)
hyperspy/tests/io/test_io.py:42:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>, data = array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
key = 'data', signal_axes = (0,), chunks = (10,), kwds = {'compression': 'gzip'}
maxshape = (None,), got_data = True
these_kwds = {'chunks': (10,), 'compression': 'gzip', 'dtype': dtype('int32'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
________ ERROR at setup of TestIOOverwriting.test_io_overwriting_False _________
[gw0] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_io.TestIOOverwriting object at 0x9f4b0ca0>
method = <bound method TestIOOverwriting.test_io_overwriting_False of <hyperspy.tests.io.test_io.TestIOOverwriting object at 0x9f4b0ca0>>
def setup_method(self, method):
self.s = Signal1D(np.arange(10))
self.new_s = Signal1D(np.ones(5))
# make sure we start from a clean state
self._clean_file()
> self.s.save(FULLFILENAME)
hyperspy/tests/io/test_io.py:42:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>, data = array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
key = 'data', signal_axes = (0,), chunks = (10,), kwds = {'compression': 'gzip'}
maxshape = (None,), got_data = True
these_kwds = {'chunks': (10,), 'compression': 'gzip', 'dtype': dtype('int32'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
_ ERROR at setup of TestIOOverwriting.test_io_overwriting_no_existing_file[None] _
[gw0] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_io.TestIOOverwriting object at 0x9f4b06b8>
method = <bound method TestIOOverwriting.test_io_overwriting_no_existing_file of <hyperspy.tests.io.test_io.TestIOOverwriting object at 0x9f4b06b8>>
def setup_method(self, method):
self.s = Signal1D(np.arange(10))
self.new_s = Signal1D(np.ones(5))
# make sure we start from a clean state
self._clean_file()
> self.s.save(FULLFILENAME)
hyperspy/tests/io/test_io.py:42:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>, data = array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
key = 'data', signal_axes = (0,), chunks = (10,), kwds = {'compression': 'gzip'}
maxshape = (None,), got_data = True
these_kwds = {'chunks': (10,), 'compression': 'gzip', 'dtype': dtype('int32'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
_ ERROR at setup of TestIOOverwriting.test_io_overwriting_no_existing_file[True] _
[gw0] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_io.TestIOOverwriting object at 0x9f4b0730>
method = <bound method TestIOOverwriting.test_io_overwriting_no_existing_file of <hyperspy.tests.io.test_io.TestIOOverwriting object at 0x9f4b0730>>
def setup_method(self, method):
self.s = Signal1D(np.arange(10))
self.new_s = Signal1D(np.ones(5))
# make sure we start from a clean state
self._clean_file()
> self.s.save(FULLFILENAME)
hyperspy/tests/io/test_io.py:42:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>, data = array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
key = 'data', signal_axes = (0,), chunks = (10,), kwds = {'compression': 'gzip'}
maxshape = (None,), got_data = True
these_kwds = {'chunks': (10,), 'compression': 'gzip', 'dtype': dtype('int32'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
_ ERROR at setup of TestIOOverwriting.test_io_overwriting_no_existing_file[False] _
[gw0] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_io.TestIOOverwriting object at 0x9f4b0b50>
method = <bound method TestIOOverwriting.test_io_overwriting_no_existing_file of <hyperspy.tests.io.test_io.TestIOOverwriting object at 0x9f4b0b50>>
def setup_method(self, method):
self.s = Signal1D(np.arange(10))
self.new_s = Signal1D(np.ones(5))
# make sure we start from a clean state
self._clean_file()
> self.s.save(FULLFILENAME)
hyperspy/tests/io/test_io.py:42:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>, data = array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
key = 'data', signal_axes = (0,), chunks = (10,), kwds = {'compression': 'gzip'}
maxshape = (None,), got_data = True
these_kwds = {'chunks': (10,), 'compression': 'gzip', 'dtype': dtype('int32'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
_ ERROR at setup of TestIOOverwriting.test_io_overwriting_None_existing_file_y _
[gw0] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_io.TestIOOverwriting object at 0x9f4b0370>
method = <bound method TestIOOverwriting.test_io_overwriting_None_existing_file_y of <hyperspy.tests.io.test_io.TestIOOverwriting object at 0x9f4b0370>>
def setup_method(self, method):
self.s = Signal1D(np.arange(10))
self.new_s = Signal1D(np.ones(5))
# make sure we start from a clean state
self._clean_file()
> self.s.save(FULLFILENAME)
hyperspy/tests/io/test_io.py:42:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>, data = array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
key = 'data', signal_axes = (0,), chunks = (10,), kwds = {'compression': 'gzip'}
maxshape = (None,), got_data = True
these_kwds = {'chunks': (10,), 'compression': 'gzip', 'dtype': dtype('int32'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
__________ ERROR at setup of TestLoadingOOMReadOnly.test_oom_loading ___________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_hdf5.TestLoadingOOMReadOnly object at 0x9f6065f8>
method = <bound method TestLoadingOOMReadOnly.test_oom_loading of <hyperspy.tests.io.test_hdf5.TestLoadingOOMReadOnly object at 0x9f6065f8>>
def setup_method(self, method):
s = BaseSignal(np.empty((5, 5, 5)))
> s.save('tmp.hdf5', overwrite=True)
hyperspy/tests/io/test_hdf5.py:353:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>
data = array([[[7.74860419e-304, 7.74860419e-304, 7.74860419e-304,
7.74860419e-304, 7.74860419e-304],
[7.748...860419e-304],
[7.74860419e-304, 7.74860419e-304, 7.74860419e-304,
7.74860419e-304, 7.74860419e-304]]])
key = 'data', signal_axes = (2, 1, 0), chunks = (5, 5, 5)
kwds = {'compression': 'gzip'}, maxshape = (None, None, None), got_data = True
these_kwds = {'chunks': (5, 5, 5), 'compression': 'gzip', 'dtype': dtype('float64'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
_ ERROR at setup of TestIOOverwriting.test_io_overwriting_None_existing_file_n _
[gw0] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_io.TestIOOverwriting object at 0x9f549988>
method = <bound method TestIOOverwriting.test_io_overwriting_None_existing_file_n of <hyperspy.tests.io.test_io.TestIOOverwriting object at 0x9f549988>>
def setup_method(self, method):
self.s = Signal1D(np.arange(10))
self.new_s = Signal1D(np.ones(5))
# make sure we start from a clean state
self._clean_file()
> self.s.save(FULLFILENAME)
hyperspy/tests/io/test_io.py:42:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>, data = array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
key = 'data', signal_axes = (0,), chunks = (10,), kwds = {'compression': 'gzip'}
maxshape = (None,), got_data = True
these_kwds = {'chunks': (10,), 'compression': 'gzip', 'dtype': dtype('int32'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
___________ ERROR at setup of TestPassingArgs.test_compression_opts ____________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_hdf5.TestPassingArgs object at 0x9f5bf1f0>
method = <bound method TestPassingArgs.test_compression_opts of <hyperspy.tests.io.test_hdf5.TestPassingArgs object at 0x9f5bf1f0>>
def setup_method(self, method):
self.filename = 'testfile.hdf5'
> BaseSignal([1, 2, 3]).save(self.filename, compression_opts=8)
hyperspy/tests/io/test_hdf5.py:386:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>, data = array([1, 2, 3]), key = 'data'
signal_axes = (0,), chunks = (3,)
kwds = {'compression': 'gzip', 'compression_opts': 8}, maxshape = (None,)
got_data = True
these_kwds = {'chunks': (3,), 'compression': 'gzip', 'compression_opts': 8, 'dtype': dtype('int32'), ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
________ ERROR at setup of TestProtochipsGasCellCSV.test_read_metadata _________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_protochips.TestProtochipsGasCellCSV object at 0x9f3adbc8>
method = <bound method TestProtochipsGasCellCSV.test_read_metadata of <hyperspy.tests.io.test_protochips.TestProtochipsGasCellCSV object at 0x9f3adbc8>>
def setup_method(self, method):
filename = os.path.join(dirpath, 'protochips_gas_cell.csv')
> self.s_list = hs.load(filename)
hyperspy/tests/io/test_protochips.py:95:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/io.py:405: in load
objects = [load_single_file(filename, lazy=lazy, **kwds) for filename in filenames]
hyperspy/io.py:405: in <listcomp>
objects = [load_single_file(filename, lazy=lazy, **kwds) for filename in filenames]
hyperspy/io.py:456: in load_single_file
return load_with_reader(filename=filename, reader=reader, **kwds)
hyperspy/io.py:475: in load_with_reader
file_data_list = reader.file_reader(filename, **kwds)
hyperspy/io_plugins/protochips.py:54: in file_reader
csv_file = ProtochipsCSV(filename)
hyperspy/io_plugins/protochips.py:73: in __init__
self._read_data()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <hyperspy.io_plugins.protochips.ProtochipsCSV object at 0x94427d78>
def _read_data(self):
names = [name.replace(' ', '_') for name in self.column_name]
# Necessary for numpy >= 1.14
kwargs = {'encoding': 'latin1'} if np.__version__ >= LooseVersion("1.14") else {
}
data = np.genfromtxt(self.filename, delimiter=',', dtype=None,
names=names,
skip_header=self.header_last_line_number,
unpack=True, **kwargs)
self._data_dictionary = dict()
for i, name, name_dtype in zip(range(len(names)), self.column_name,
names):
if name == 'Notes':
self.notes = data[name_dtype].astype(str)
elif name == 'Time':
> self.time_axis = data[name_dtype]
E TypeError: list indices must be integers or slices, not str
hyperspy/io_plugins/protochips.py:155: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
ERROR hyperspy.io:io.py:459 If this file format is supported, please report this error to the HyperSpy developers.
____ ERROR at setup of TestProtochipsGasCellCSV.test_read_original_metadata ____
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_protochips.TestProtochipsGasCellCSV object at 0x9f3ad700>
method = <bound method TestProtochipsGasCellCSV.test_read_original_metadata of <hyperspy.tests.io.test_protochips.TestProtochipsGasCellCSV object at 0x9f3ad700>>
def setup_method(self, method):
filename = os.path.join(dirpath, 'protochips_gas_cell.csv')
> self.s_list = hs.load(filename)
hyperspy/tests/io/test_protochips.py:95:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/io.py:405: in load
objects = [load_single_file(filename, lazy=lazy, **kwds) for filename in filenames]
hyperspy/io.py:405: in <listcomp>
objects = [load_single_file(filename, lazy=lazy, **kwds) for filename in filenames]
hyperspy/io.py:456: in load_single_file
return load_with_reader(filename=filename, reader=reader, **kwds)
hyperspy/io.py:475: in load_with_reader
file_data_list = reader.file_reader(filename, **kwds)
hyperspy/io_plugins/protochips.py:54: in file_reader
csv_file = ProtochipsCSV(filename)
hyperspy/io_plugins/protochips.py:73: in __init__
self._read_data()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <hyperspy.io_plugins.protochips.ProtochipsCSV object at 0x94e177c0>
def _read_data(self):
names = [name.replace(' ', '_') for name in self.column_name]
# Necessary for numpy >= 1.14
kwargs = {'encoding': 'latin1'} if np.__version__ >= LooseVersion("1.14") else {
}
data = np.genfromtxt(self.filename, delimiter=',', dtype=None,
names=names,
skip_header=self.header_last_line_number,
unpack=True, **kwargs)
self._data_dictionary = dict()
for i, name, name_dtype in zip(range(len(names)), self.column_name,
names):
if name == 'Notes':
self.notes = data[name_dtype].astype(str)
elif name == 'Time':
> self.time_axis = data[name_dtype]
E TypeError: list indices must be integers or slices, not str
hyperspy/io_plugins/protochips.py:155: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
ERROR hyperspy.io:io.py:459 If this file format is supported, please report this error to the HyperSpy developers.
_____ ERROR at setup of TestProtochipsGasCellCSVNoUser.test_read_metadata ______
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_protochips.TestProtochipsGasCellCSVNoUser object at 0x9f3ad808>
method = <bound method TestProtochipsGasCellCSVNoUser.test_read_metadata of <hyperspy.tests.io.test_protochips.TestProtochipsGasCellCSVNoUser object at 0x9f3ad808>>
def setup_method(self, method):
filename = os.path.join(dirpath, 'protochips_gas_cell_no_user.csv')
> self.s_list = hs.load(filename)
hyperspy/tests/io/test_protochips.py:126:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/io.py:405: in load
objects = [load_single_file(filename, lazy=lazy, **kwds) for filename in filenames]
hyperspy/io.py:405: in <listcomp>
objects = [load_single_file(filename, lazy=lazy, **kwds) for filename in filenames]
hyperspy/io.py:456: in load_single_file
return load_with_reader(filename=filename, reader=reader, **kwds)
hyperspy/io.py:475: in load_with_reader
file_data_list = reader.file_reader(filename, **kwds)
hyperspy/io_plugins/protochips.py:54: in file_reader
csv_file = ProtochipsCSV(filename)
hyperspy/io_plugins/protochips.py:73: in __init__
self._read_data()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <hyperspy.io_plugins.protochips.ProtochipsCSV object at 0x94b8c688>
def _read_data(self):
names = [name.replace(' ', '_') for name in self.column_name]
# Necessary for numpy >= 1.14
kwargs = {'encoding': 'latin1'} if np.__version__ >= LooseVersion("1.14") else {
}
data = np.genfromtxt(self.filename, delimiter=',', dtype=None,
names=names,
skip_header=self.header_last_line_number,
unpack=True, **kwargs)
self._data_dictionary = dict()
for i, name, name_dtype in zip(range(len(names)), self.column_name,
names):
if name == 'Notes':
self.notes = data[name_dtype].astype(str)
elif name == 'Time':
> self.time_axis = data[name_dtype]
E TypeError: list indices must be integers or slices, not str
hyperspy/io_plugins/protochips.py:155: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
ERROR hyperspy.io:io.py:459 If this file format is supported, please report this error to the HyperSpy developers.
_ ERROR at setup of TestProtochipsGasCellCSVNoUser.test_read_original_metadata _
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_protochips.TestProtochipsGasCellCSVNoUser object at 0x9f3ad448>
method = <bound method TestProtochipsGasCellCSVNoUser.test_read_original_metadata of <hyperspy.tests.io.test_protochips.TestProtochipsGasCellCSVNoUser object at 0x9f3ad448>>
def setup_method(self, method):
filename = os.path.join(dirpath, 'protochips_gas_cell_no_user.csv')
> self.s_list = hs.load(filename)
hyperspy/tests/io/test_protochips.py:126:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/io.py:405: in load
objects = [load_single_file(filename, lazy=lazy, **kwds) for filename in filenames]
hyperspy/io.py:405: in <listcomp>
objects = [load_single_file(filename, lazy=lazy, **kwds) for filename in filenames]
hyperspy/io.py:456: in load_single_file
return load_with_reader(filename=filename, reader=reader, **kwds)
hyperspy/io.py:475: in load_with_reader
file_data_list = reader.file_reader(filename, **kwds)
hyperspy/io_plugins/protochips.py:54: in file_reader
csv_file = ProtochipsCSV(filename)
hyperspy/io_plugins/protochips.py:73: in __init__
self._read_data()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <hyperspy.io_plugins.protochips.ProtochipsCSV object at 0x95ee9460>
def _read_data(self):
names = [name.replace(' ', '_') for name in self.column_name]
# Necessary for numpy >= 1.14
kwargs = {'encoding': 'latin1'} if np.__version__ >= LooseVersion("1.14") else {
}
data = np.genfromtxt(self.filename, delimiter=',', dtype=None,
names=names,
skip_header=self.header_last_line_number,
unpack=True, **kwargs)
self._data_dictionary = dict()
for i, name, name_dtype in zip(range(len(names)), self.column_name,
names):
if name == 'Notes':
self.notes = data[name_dtype].astype(str)
elif name == 'Time':
> self.time_axis = data[name_dtype]
E TypeError: list indices must be integers or slices, not str
hyperspy/io_plugins/protochips.py:155: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
ERROR hyperspy.io:io.py:459 If this file format is supported, please report this error to the HyperSpy developers.
____ ERROR at setup of TestProtochipsGasCellCSVReader.test_read_column_name ____
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_protochips.TestProtochipsGasCellCSVReader object at 0x9f3ad358>
method = <bound method TestProtochipsGasCellCSVReader.test_read_column_name of <hyperspy.tests.io.test_protochips.TestProtochipsGasCellCSVReader object at 0x9f3ad358>>
def setup_method(self, method):
self.filename = os.path.join(dirpath, 'protochips_gas_cell.csv')
> self.pgc = ProtochipsCSV(self.filename)
hyperspy/tests/io/test_protochips.py:156:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/io_plugins/protochips.py:73: in __init__
self._read_data()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <hyperspy.io_plugins.protochips.ProtochipsCSV object at 0x96924070>
def _read_data(self):
names = [name.replace(' ', '_') for name in self.column_name]
# Necessary for numpy >= 1.14
kwargs = {'encoding': 'latin1'} if np.__version__ >= LooseVersion("1.14") else {
}
data = np.genfromtxt(self.filename, delimiter=',', dtype=None,
names=names,
skip_header=self.header_last_line_number,
unpack=True, **kwargs)
self._data_dictionary = dict()
for i, name, name_dtype in zip(range(len(names)), self.column_name,
names):
if name == 'Notes':
self.notes = data[name_dtype].astype(str)
elif name == 'Time':
> self.time_axis = data[name_dtype]
E TypeError: list indices must be integers or slices, not str
hyperspy/io_plugins/protochips.py:155: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
__ ERROR at setup of TestProtochipsGasCellCSVReader.test_read_start_datetime ___
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_protochips.TestProtochipsGasCellCSVReader object at 0x9f3ad0b8>
method = <bound method TestProtochipsGasCellCSVReader.test_read_start_datetime of <hyperspy.tests.io.test_protochips.TestProtochipsGasCellCSVReader object at 0x9f3ad0b8>>
def setup_method(self, method):
self.filename = os.path.join(dirpath, 'protochips_gas_cell.csv')
> self.pgc = ProtochipsCSV(self.filename)
hyperspy/tests/io/test_protochips.py:156:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/io_plugins/protochips.py:73: in __init__
self._read_data()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <hyperspy.io_plugins.protochips.ProtochipsCSV object at 0x94352a48>
def _read_data(self):
names = [name.replace(' ', '_') for name in self.column_name]
# Necessary for numpy >= 1.14
kwargs = {'encoding': 'latin1'} if np.__version__ >= LooseVersion("1.14") else {
}
data = np.genfromtxt(self.filename, delimiter=',', dtype=None,
names=names,
skip_header=self.header_last_line_number,
unpack=True, **kwargs)
self._data_dictionary = dict()
for i, name, name_dtype in zip(range(len(names)), self.column_name,
names):
if name == 'Notes':
self.notes = data[name_dtype].astype(str)
elif name == 'Time':
> self.time_axis = data[name_dtype]
E TypeError: list indices must be integers or slices, not str
hyperspy/io_plugins/protochips.py:155: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
_______ ERROR at setup of TestProtochipsGasCellCSVReader.test_read_data ________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_protochips.TestProtochipsGasCellCSVReader object at 0x9f3ad220>
method = <bound method TestProtochipsGasCellCSVReader.test_read_data of <hyperspy.tests.io.test_protochips.TestProtochipsGasCellCSVReader object at 0x9f3ad220>>
def setup_method(self, method):
self.filename = os.path.join(dirpath, 'protochips_gas_cell.csv')
> self.pgc = ProtochipsCSV(self.filename)
hyperspy/tests/io/test_protochips.py:156:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/io_plugins/protochips.py:73: in __init__
self._read_data()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <hyperspy.io_plugins.protochips.ProtochipsCSV object at 0x94c2ec58>
def _read_data(self):
names = [name.replace(' ', '_') for name in self.column_name]
# Necessary for numpy >= 1.14
kwargs = {'encoding': 'latin1'} if np.__version__ >= LooseVersion("1.14") else {
}
data = np.genfromtxt(self.filename, delimiter=',', dtype=None,
names=names,
skip_header=self.header_last_line_number,
unpack=True, **kwargs)
self._data_dictionary = dict()
for i, name, name_dtype in zip(range(len(names)), self.column_name,
names):
if name == 'Notes':
self.notes = data[name_dtype].astype(str)
elif name == 'Time':
> self.time_axis = data[name_dtype]
E TypeError: list indices must be integers or slices, not str
hyperspy/io_plugins/protochips.py:155: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
__ ERROR at setup of TestProtochipsGasCellCSVReader.test_read_metadata_header __
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_protochips.TestProtochipsGasCellCSVReader object at 0x9f3ade68>
method = <bound method TestProtochipsGasCellCSVReader.test_read_metadata_header of <hyperspy.tests.io.test_protochips.TestProtochipsGasCellCSVReader object at 0x9f3ade68>>
def setup_method(self, method):
self.filename = os.path.join(dirpath, 'protochips_gas_cell.csv')
> self.pgc = ProtochipsCSV(self.filename)
hyperspy/tests/io/test_protochips.py:156:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/io_plugins/protochips.py:73: in __init__
self._read_data()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <hyperspy.io_plugins.protochips.ProtochipsCSV object at 0x94f8bb50>
def _read_data(self):
names = [name.replace(' ', '_') for name in self.column_name]
# Necessary for numpy >= 1.14
kwargs = {'encoding': 'latin1'} if np.__version__ >= LooseVersion("1.14") else {
}
data = np.genfromtxt(self.filename, delimiter=',', dtype=None,
names=names,
skip_header=self.header_last_line_number,
unpack=True, **kwargs)
self._data_dictionary = dict()
for i, name, name_dtype in zip(range(len(names)), self.column_name,
names):
if name == 'Notes':
self.notes = data[name_dtype].astype(str)
elif name == 'Time':
> self.time_axis = data[name_dtype]
E TypeError: list indices must be integers or slices, not str
hyperspy/io_plugins/protochips.py:155: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
__ ERROR at setup of TestProtochipsElectricalCSVReader.test_read_column_name ___
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_protochips.TestProtochipsElectricalCSVReader object at 0x9f3ad130>
method = <bound method TestProtochipsElectricalCSVReader.test_read_column_name of <hyperspy.tests.io.test_protochips.TestProtochipsElectricalCSVReader object at 0x9f3ad130>>
def setup_method(self, method):
self.filename = os.path.join(dirpath, 'protochips_electrical.csv')
> self.pa = ProtochipsCSV(self.filename)
hyperspy/tests/io/test_protochips.py:222:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/io_plugins/protochips.py:73: in __init__
self._read_data()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <hyperspy.io_plugins.protochips.ProtochipsCSV object at 0x9668ba78>
def _read_data(self):
names = [name.replace(' ', '_') for name in self.column_name]
# Necessary for numpy >= 1.14
kwargs = {'encoding': 'latin1'} if np.__version__ >= LooseVersion("1.14") else {
}
data = np.genfromtxt(self.filename, delimiter=',', dtype=None,
names=names,
skip_header=self.header_last_line_number,
unpack=True, **kwargs)
self._data_dictionary = dict()
for i, name, name_dtype in zip(range(len(names)), self.column_name,
names):
if name == 'Notes':
self.notes = data[name_dtype].astype(str)
elif name == 'Time':
> self.time_axis = data[name_dtype]
E TypeError: list indices must be integers or slices, not str
hyperspy/io_plugins/protochips.py:155: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
_ ERROR at setup of TestProtochipsElectricalCSVReader.test_read_start_datetime _
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_protochips.TestProtochipsElectricalCSVReader object at 0x9f3ad388>
method = <bound method TestProtochipsElectricalCSVReader.test_read_start_datetime of <hyperspy.tests.io.test_protochips.TestProtochipsElectricalCSVReader object at 0x9f3ad388>>
def setup_method(self, method):
self.filename = os.path.join(dirpath, 'protochips_electrical.csv')
> self.pa = ProtochipsCSV(self.filename)
hyperspy/tests/io/test_protochips.py:222:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/io_plugins/protochips.py:73: in __init__
self._read_data()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <hyperspy.io_plugins.protochips.ProtochipsCSV object at 0x9668b130>
def _read_data(self):
names = [name.replace(' ', '_') for name in self.column_name]
# Necessary for numpy >= 1.14
kwargs = {'encoding': 'latin1'} if np.__version__ >= LooseVersion("1.14") else {
}
data = np.genfromtxt(self.filename, delimiter=',', dtype=None,
names=names,
skip_header=self.header_last_line_number,
unpack=True, **kwargs)
self._data_dictionary = dict()
for i, name, name_dtype in zip(range(len(names)), self.column_name,
names):
if name == 'Notes':
self.notes = data[name_dtype].astype(str)
elif name == 'Time':
> self.time_axis = data[name_dtype]
E TypeError: list indices must be integers or slices, not str
hyperspy/io_plugins/protochips.py:155: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
______ ERROR at setup of TestProtochipsElectricalCSVReader.test_read_data ______
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_protochips.TestProtochipsElectricalCSVReader object at 0x9f45bb20>
method = <bound method TestProtochipsElectricalCSVReader.test_read_data of <hyperspy.tests.io.test_protochips.TestProtochipsElectricalCSVReader object at 0x9f45bb20>>
def setup_method(self, method):
self.filename = os.path.join(dirpath, 'protochips_electrical.csv')
> self.pa = ProtochipsCSV(self.filename)
hyperspy/tests/io/test_protochips.py:222:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/io_plugins/protochips.py:73: in __init__
self._read_data()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <hyperspy.io_plugins.protochips.ProtochipsCSV object at 0x94c1c8f8>
def _read_data(self):
names = [name.replace(' ', '_') for name in self.column_name]
# Necessary for numpy >= 1.14
kwargs = {'encoding': 'latin1'} if np.__version__ >= LooseVersion("1.14") else {
}
data = np.genfromtxt(self.filename, delimiter=',', dtype=None,
names=names,
skip_header=self.header_last_line_number,
unpack=True, **kwargs)
self._data_dictionary = dict()
for i, name, name_dtype in zip(range(len(names)), self.column_name,
names):
if name == 'Notes':
self.notes = data[name_dtype].astype(str)
elif name == 'Time':
> self.time_axis = data[name_dtype]
E TypeError: list indices must be integers or slices, not str
hyperspy/io_plugins/protochips.py:155: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
___ ERROR at setup of TestProtochipsThermallCSVReader.test_read_column_name ____
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_protochips.TestProtochipsThermallCSVReader object at 0x9f3ae478>
method = <bound method TestProtochipsThermallCSVReader.test_read_column_name of <hyperspy.tests.io.test_protochips.TestProtochipsThermallCSVReader object at 0x9f3ae478>>
def setup_method(self, method):
self.filename = os.path.join(dirpath, 'protochips_thermal.csv')
> self.pt = ProtochipsCSV(self.filename)
hyperspy/tests/io/test_protochips.py:267:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/io_plugins/protochips.py:73: in __init__
self._read_data()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <hyperspy.io_plugins.protochips.ProtochipsCSV object at 0x94cbb3e8>
def _read_data(self):
names = [name.replace(' ', '_') for name in self.column_name]
# Necessary for numpy >= 1.14
kwargs = {'encoding': 'latin1'} if np.__version__ >= LooseVersion("1.14") else {
}
data = np.genfromtxt(self.filename, delimiter=',', dtype=None,
names=names,
skip_header=self.header_last_line_number,
unpack=True, **kwargs)
self._data_dictionary = dict()
for i, name, name_dtype in zip(range(len(names)), self.column_name,
names):
if name == 'Notes':
self.notes = data[name_dtype].astype(str)
elif name == 'Time':
> self.time_axis = data[name_dtype]
E TypeError: list indices must be integers or slices, not str
hyperspy/io_plugins/protochips.py:155: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
__ ERROR at setup of TestProtochipsThermallCSVReader.test_read_start_datetime __
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_protochips.TestProtochipsThermallCSVReader object at 0x9f3ae358>
method = <bound method TestProtochipsThermallCSVReader.test_read_start_datetime of <hyperspy.tests.io.test_protochips.TestProtochipsThermallCSVReader object at 0x9f3ae358>>
def setup_method(self, method):
self.filename = os.path.join(dirpath, 'protochips_thermal.csv')
> self.pt = ProtochipsCSV(self.filename)
hyperspy/tests/io/test_protochips.py:267:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/io_plugins/protochips.py:73: in __init__
self._read_data()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <hyperspy.io_plugins.protochips.ProtochipsCSV object at 0x94cfb730>
def _read_data(self):
names = [name.replace(' ', '_') for name in self.column_name]
# Necessary for numpy >= 1.14
kwargs = {'encoding': 'latin1'} if np.__version__ >= LooseVersion("1.14") else {
}
data = np.genfromtxt(self.filename, delimiter=',', dtype=None,
names=names,
skip_header=self.header_last_line_number,
unpack=True, **kwargs)
self._data_dictionary = dict()
for i, name, name_dtype in zip(range(len(names)), self.column_name,
names):
if name == 'Notes':
self.notes = data[name_dtype].astype(str)
elif name == 'Time':
> self.time_axis = data[name_dtype]
E TypeError: list indices must be integers or slices, not str
hyperspy/io_plugins/protochips.py:155: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
_______ ERROR at setup of TestProtochipsThermallCSVReader.test_read_data _______
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_protochips.TestProtochipsThermallCSVReader object at 0x9f3ae748>
method = <bound method TestProtochipsThermallCSVReader.test_read_data of <hyperspy.tests.io.test_protochips.TestProtochipsThermallCSVReader object at 0x9f3ae748>>
def setup_method(self, method):
self.filename = os.path.join(dirpath, 'protochips_thermal.csv')
> self.pt = ProtochipsCSV(self.filename)
hyperspy/tests/io/test_protochips.py:267:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/io_plugins/protochips.py:73: in __init__
self._read_data()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <hyperspy.io_plugins.protochips.ProtochipsCSV object at 0x969d35b0>
def _read_data(self):
names = [name.replace(' ', '_') for name in self.column_name]
# Necessary for numpy >= 1.14
kwargs = {'encoding': 'latin1'} if np.__version__ >= LooseVersion("1.14") else {
}
data = np.genfromtxt(self.filename, delimiter=',', dtype=None,
names=names,
skip_header=self.header_last_line_number,
unpack=True, **kwargs)
self._data_dictionary = dict()
for i, name, name_dtype in zip(range(len(names)), self.column_name,
names):
if name == 'Notes':
self.notes = data[name_dtype].astype(str)
elif name == 'Time':
> self.time_axis = data[name_dtype]
E TypeError: list indices must be integers or slices, not str
hyperspy/io_plugins/protochips.py:155: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
_ ERROR at setup of TestProtochipsElectrothermalCSVReader.test_read_column_name _
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_protochips.TestProtochipsElectrothermalCSVReader object at 0x9f3ae850>
method = <bound method TestProtochipsElectrothermalCSVReader.test_read_column_name of <hyperspy.tests.io.test_protochips.TestProtochipsElectrothermalCSVReader object at 0x9f3ae850>>
def setup_method(self, method):
self.filename = os.path.join(dirpath, 'protochips_electrothermal.csv')
> self.pet = ProtochipsCSV(self.filename)
hyperspy/tests/io/test_protochips.py:317:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/io_plugins/protochips.py:73: in __init__
self._read_data()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <hyperspy.io_plugins.protochips.ProtochipsCSV object at 0x94c0ef88>
def _read_data(self):
names = [name.replace(' ', '_') for name in self.column_name]
# Necessary for numpy >= 1.14
kwargs = {'encoding': 'latin1'} if np.__version__ >= LooseVersion("1.14") else {
}
data = np.genfromtxt(self.filename, delimiter=',', dtype=None,
names=names,
skip_header=self.header_last_line_number,
unpack=True, **kwargs)
self._data_dictionary = dict()
for i, name, name_dtype in zip(range(len(names)), self.column_name,
names):
if name == 'Notes':
self.notes = data[name_dtype].astype(str)
elif name == 'Time':
> self.time_axis = data[name_dtype]
E TypeError: list indices must be integers or slices, not str
hyperspy/io_plugins/protochips.py:155: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
_ ERROR at setup of TestProtochipsElectrothermalCSVReader.test_read_start_datetime _
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_protochips.TestProtochipsElectrothermalCSVReader object at 0x9f3ae820>
method = <bound method TestProtochipsElectrothermalCSVReader.test_read_start_datetime of <hyperspy.tests.io.test_protochips.TestProtochipsElectrothermalCSVReader object at 0x9f3ae820>>
def setup_method(self, method):
self.filename = os.path.join(dirpath, 'protochips_electrothermal.csv')
> self.pet = ProtochipsCSV(self.filename)
hyperspy/tests/io/test_protochips.py:317:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/io_plugins/protochips.py:73: in __init__
self._read_data()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <hyperspy.io_plugins.protochips.ProtochipsCSV object at 0x94e38808>
def _read_data(self):
names = [name.replace(' ', '_') for name in self.column_name]
# Necessary for numpy >= 1.14
kwargs = {'encoding': 'latin1'} if np.__version__ >= LooseVersion("1.14") else {
}
data = np.genfromtxt(self.filename, delimiter=',', dtype=None,
names=names,
skip_header=self.header_last_line_number,
unpack=True, **kwargs)
self._data_dictionary = dict()
for i, name, name_dtype in zip(range(len(names)), self.column_name,
names):
if name == 'Notes':
self.notes = data[name_dtype].astype(str)
elif name == 'Time':
> self.time_axis = data[name_dtype]
E TypeError: list indices must be integers or slices, not str
hyperspy/io_plugins/protochips.py:155: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
____ ERROR at setup of TestProtochipsElectrothermalCSVReader.test_read_data ____
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_protochips.TestProtochipsElectrothermalCSVReader object at 0x9f3ae8f8>
method = <bound method TestProtochipsElectrothermalCSVReader.test_read_data of <hyperspy.tests.io.test_protochips.TestProtochipsElectrothermalCSVReader object at 0x9f3ae8f8>>
def setup_method(self, method):
self.filename = os.path.join(dirpath, 'protochips_electrothermal.csv')
> self.pet = ProtochipsCSV(self.filename)
hyperspy/tests/io/test_protochips.py:317:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/io_plugins/protochips.py:73: in __init__
self._read_data()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <hyperspy.io_plugins.protochips.ProtochipsCSV object at 0x969249d0>
def _read_data(self):
names = [name.replace(' ', '_') for name in self.column_name]
# Necessary for numpy >= 1.14
kwargs = {'encoding': 'latin1'} if np.__version__ >= LooseVersion("1.14") else {
}
data = np.genfromtxt(self.filename, delimiter=',', dtype=None,
names=names,
skip_header=self.header_last_line_number,
unpack=True, **kwargs)
self._data_dictionary = dict()
for i, name, name_dtype in zip(range(len(names)), self.column_name,
names):
if name == 'Notes':
self.notes = data[name_dtype].astype(str)
elif name == 'Time':
> self.time_axis = data[name_dtype]
E TypeError: list indices must be integers or slices, not str
hyperspy/io_plugins/protochips.py:155: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
_ ERROR at setup of TestRemoveBackground1DSkewNormal.test_background_remove_skewnormal _
[gw3] linux -- Python 3.10.7 /usr/bin/python3.10
ValueError: Error from parse_expr with transformed code: "(Integer (1 )+erf (shape *Symbol ('t' )/sqrt (Integer (2 ))))/Integer (2 )"
The above exception was the direct cause of the following exception:
self = <hyperspy.tests.signal.test_remove_background.TestRemoveBackground1DSkewNormal object at 0x9c051d60>
method = <bound method TestRemoveBackground1DSkewNormal.test_background_remove_skewnormal of <hyperspy.tests.signal.test_remove_background.TestRemoveBackground1DSkewNormal object at 0x9c051d60>>
def setup_method(self, method):
> skewnormal = components1d.SkewNormal()
hyperspy/tests/signal/test_remove_background.py:163:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_components/skew_normal.py:154: in __init__
super(SkewNormal, self).__init__(
hyperspy/_components/expression.py:158: in __init__
self.compile_function(module=module, position=position)
hyperspy/_components/expression.py:209: in compile_function
expr = _parse_substitutions(self._str_expression)
hyperspy/_components/expression.py:61: in _parse_substitutions
expr = expr.subs(t[0], sympy.sympify(t[1]))
/usr/lib/python3/dist-packages/sympy/core/sympify.py:495: in sympify
expr = parse_expr(a, local_dict=locals, transformations=transformations, evaluate=evaluate)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1105: in parse_expr
raise e from ValueError(f"Error from parse_expr with transformed code: {code!r}")
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1096: in parse_expr
rv = eval_expr(code, local_dict, global_dict)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:915: in eval_expr
expr = eval(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E TypeError: unsupported operand type(s) for *: 'function' and 'Symbol'
<string>:1: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
_ ERROR at setup of TestRemoveBackground1DSkewNormal.test_background_remove_skewnormal_full_fit _
[gw3] linux -- Python 3.10.7 /usr/bin/python3.10
ValueError: Error from parse_expr with transformed code: "(Integer (1 )+erf (shape *Symbol ('t' )/sqrt (Integer (2 ))))/Integer (2 )"
The above exception was the direct cause of the following exception:
self = <hyperspy.tests.signal.test_remove_background.TestRemoveBackground1DSkewNormal object at 0x9c051e68>
method = <bound method TestRemoveBackground1DSkewNormal.test_background_remove_skewnormal_full_fit of <hyperspy.tests.signal.test_remove_background.TestRemoveBackground1DSkewNormal object at 0x9c051e68>>
def setup_method(self, method):
> skewnormal = components1d.SkewNormal()
hyperspy/tests/signal/test_remove_background.py:163:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_components/skew_normal.py:154: in __init__
super(SkewNormal, self).__init__(
hyperspy/_components/expression.py:158: in __init__
self.compile_function(module=module, position=position)
hyperspy/_components/expression.py:209: in compile_function
expr = _parse_substitutions(self._str_expression)
hyperspy/_components/expression.py:61: in _parse_substitutions
expr = expr.subs(t[0], sympy.sympify(t[1]))
/usr/lib/python3/dist-packages/sympy/core/sympify.py:495: in sympify
expr = parse_expr(a, local_dict=locals, transformations=transformations, evaluate=evaluate)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1105: in parse_expr
raise e from ValueError(f"Error from parse_expr with transformed code: {code!r}")
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1096: in parse_expr
rv = eval_expr(code, local_dict, global_dict)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:915: in eval_expr
expr = eval(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E TypeError: unsupported operand type(s) for *: 'function' and 'Symbol'
<string>:1: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
_ ERROR at setup of TestRemoveBackground1DSkewNormal.test_lazy_background_remove_skewnormal _
[gw3] linux -- Python 3.10.7 /usr/bin/python3.10
ValueError: Error from parse_expr with transformed code: "(Integer (1 )+erf (shape *Symbol ('t' )/sqrt (Integer (2 ))))/Integer (2 )"
The above exception was the direct cause of the following exception:
self = <hyperspy.tests.signal.test_remove_background.TestRemoveBackground1DSkewNormal object at 0x9c051d00>
method = <bound method TestRemoveBackground1DSkewNormal.test_background_remove_skewnormal of <hyperspy.tests.signal.test_remove_background.TestRemoveBackground1DSkewNormal object at 0x9c051d00>>
def setup_method(self, method):
> skewnormal = components1d.SkewNormal()
hyperspy/tests/signal/test_remove_background.py:163:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_components/skew_normal.py:154: in __init__
super(SkewNormal, self).__init__(
hyperspy/_components/expression.py:158: in __init__
self.compile_function(module=module, position=position)
hyperspy/_components/expression.py:209: in compile_function
expr = _parse_substitutions(self._str_expression)
hyperspy/_components/expression.py:61: in _parse_substitutions
expr = expr.subs(t[0], sympy.sympify(t[1]))
/usr/lib/python3/dist-packages/sympy/core/sympify.py:495: in sympify
expr = parse_expr(a, local_dict=locals, transformations=transformations, evaluate=evaluate)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1105: in parse_expr
raise e from ValueError(f"Error from parse_expr with transformed code: {code!r}")
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1096: in parse_expr
rv = eval_expr(code, local_dict, global_dict)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:915: in eval_expr
expr = eval(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E TypeError: unsupported operand type(s) for *: 'function' and 'Symbol'
<string>:1: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
_ ERROR at setup of TestRemoveBackground1DSkewNormal.test_lazy_background_remove_skewnormal_full_fit _
[gw3] linux -- Python 3.10.7 /usr/bin/python3.10
ValueError: Error from parse_expr with transformed code: "(Integer (1 )+erf (shape *Symbol ('t' )/sqrt (Integer (2 ))))/Integer (2 )"
The above exception was the direct cause of the following exception:
self = <hyperspy.tests.signal.test_remove_background.TestRemoveBackground1DSkewNormal object at 0x9be88088>
method = <bound method TestRemoveBackground1DSkewNormal.test_background_remove_skewnormal_full_fit of <hyperspy.tests.signal.test_remove_background.TestRemoveBackground1DSkewNormal object at 0x9be88088>>
def setup_method(self, method):
> skewnormal = components1d.SkewNormal()
hyperspy/tests/signal/test_remove_background.py:163:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_components/skew_normal.py:154: in __init__
super(SkewNormal, self).__init__(
hyperspy/_components/expression.py:158: in __init__
self.compile_function(module=module, position=position)
hyperspy/_components/expression.py:209: in compile_function
expr = _parse_substitutions(self._str_expression)
hyperspy/_components/expression.py:61: in _parse_substitutions
expr = expr.subs(t[0], sympy.sympify(t[1]))
/usr/lib/python3/dist-packages/sympy/core/sympify.py:495: in sympify
expr = parse_expr(a, local_dict=locals, transformations=transformations, evaluate=evaluate)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1105: in parse_expr
raise e from ValueError(f"Error from parse_expr with transformed code: {code!r}")
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1096: in parse_expr
rv = eval_expr(code, local_dict, global_dict)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:915: in eval_expr
expr = eval(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E TypeError: unsupported operand type(s) for *: 'function' and 'Symbol'
<string>:1: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
=================================== FAILURES ===================================
____________________ test_creation_components1d[SkewNormal] ____________________
[gw1] linux -- Python 3.10.7 /usr/bin/python3.10
ValueError: Error from parse_expr with transformed code: "(Integer (1 )+erf (shape *Symbol ('t' )/sqrt (Integer (2 ))))/Integer (2 )"
The above exception was the direct cause of the following exception:
component_name = 'SkewNormal'
@pytest.mark.filterwarnings("ignore:invalid value encountered in true_divide:RuntimeWarning")
@pytest.mark.filterwarnings("ignore:divide by zero encountered in true_divide:RuntimeWarning")
@pytest.mark.filterwarnings("ignore:invalid value encountered in cos:RuntimeWarning")
@pytest.mark.filterwarnings("ignore:The API of the")
@pytest.mark.parametrize('component_name', get_components1d_name_list())
def test_creation_components1d(component_name):
s = hs.signals.Signal1D(np.zeros(1024))
s.axes_manager[0].offset = 100
s.axes_manager[0].scale = 0.01
kwargs = {}
if component_name == 'ScalableFixedPattern':
kwargs['signal1D'] = s
elif component_name == 'Expression':
kwargs.update({'expression': "a*x+b", "name": "linear"})
> component = getattr(components1d, component_name)(**kwargs)
hyperspy/tests/component/test_components.py:63:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_components/skew_normal.py:154: in __init__
super(SkewNormal, self).__init__(
hyperspy/_components/expression.py:158: in __init__
self.compile_function(module=module, position=position)
hyperspy/_components/expression.py:209: in compile_function
expr = _parse_substitutions(self._str_expression)
hyperspy/_components/expression.py:61: in _parse_substitutions
expr = expr.subs(t[0], sympy.sympify(t[1]))
/usr/lib/python3/dist-packages/sympy/core/sympify.py:495: in sympify
expr = parse_expr(a, local_dict=locals, transformations=transformations, evaluate=evaluate)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1105: in parse_expr
raise e from ValueError(f"Error from parse_expr with transformed code: {code!r}")
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1096: in parse_expr
rv = eval_expr(code, local_dict, global_dict)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:915: in eval_expr
expr = eval(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E TypeError: unsupported operand type(s) for *: 'function' and 'Symbol'
<string>:1: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
________________________________ test_function _________________________________
[gw3] linux -- Python 3.10.7 /usr/bin/python3.10
ValueError: Error from parse_expr with transformed code: "(Integer (1 )+erf (shape *Symbol ('t' )/sqrt (Integer (2 ))))/Integer (2 )"
The above exception was the direct cause of the following exception:
def test_function():
> g = SkewNormal()
hyperspy/tests/component/test_skewnormal.py:39:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_components/skew_normal.py:154: in __init__
super(SkewNormal, self).__init__(
hyperspy/_components/expression.py:158: in __init__
self.compile_function(module=module, position=position)
hyperspy/_components/expression.py:209: in compile_function
expr = _parse_substitutions(self._str_expression)
hyperspy/_components/expression.py:61: in _parse_substitutions
expr = expr.subs(t[0], sympy.sympify(t[1]))
/usr/lib/python3/dist-packages/sympy/core/sympify.py:495: in sympify
expr = parse_expr(a, local_dict=locals, transformations=transformations, evaluate=evaluate)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1105: in parse_expr
raise e from ValueError(f"Error from parse_expr with transformed code: {code!r}")
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1096: in parse_expr
rv = eval_expr(code, local_dict, global_dict)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:915: in eval_expr
expr = eval(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E TypeError: unsupported operand type(s) for *: 'function' and 'Symbol'
<string>:1: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
_______________ test_estimate_parameters_binned[True-True-True] ________________
[gw3] linux -- Python 3.10.7 /usr/bin/python3.10
ValueError: Error from parse_expr with transformed code: "(Integer (1 )+erf (shape *Symbol ('t' )/sqrt (Integer (2 ))))/Integer (2 )"
The above exception was the direct cause of the following exception:
only_current = True, binned = True, lazy = True
@pytest.mark.parametrize(("lazy"), (True, False))
@pytest.mark.parametrize(("only_current", "binned"), TRUE_FALSE_2_TUPLE)
def test_estimate_parameters_binned(only_current, binned, lazy):
s = Signal1D(np.empty((300,)))
s.metadata.Signal.binned = binned
axis = s.axes_manager.signal_axes[0]
axis.scale = 0.2
axis.offset = -10
> g1 = SkewNormal(A=2, x0=2, scale=10, shape=5)
hyperspy/tests/component/test_skewnormal.py:62:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_components/skew_normal.py:154: in __init__
super(SkewNormal, self).__init__(
hyperspy/_components/expression.py:158: in __init__
self.compile_function(module=module, position=position)
hyperspy/_components/expression.py:209: in compile_function
expr = _parse_substitutions(self._str_expression)
hyperspy/_components/expression.py:61: in _parse_substitutions
expr = expr.subs(t[0], sympy.sympify(t[1]))
/usr/lib/python3/dist-packages/sympy/core/sympify.py:495: in sympify
expr = parse_expr(a, local_dict=locals, transformations=transformations, evaluate=evaluate)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1105: in parse_expr
raise e from ValueError(f"Error from parse_expr with transformed code: {code!r}")
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1096: in parse_expr
rv = eval_expr(code, local_dict, global_dict)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:915: in eval_expr
expr = eval(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E TypeError: unsupported operand type(s) for *: 'function' and 'Symbol'
<string>:1: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
_______________ test_estimate_parameters_binned[True-True-False] _______________
[gw3] linux -- Python 3.10.7 /usr/bin/python3.10
ValueError: Error from parse_expr with transformed code: "(Integer (1 )+erf (shape *Symbol ('t' )/sqrt (Integer (2 ))))/Integer (2 )"
The above exception was the direct cause of the following exception:
only_current = True, binned = True, lazy = False
@pytest.mark.parametrize(("lazy"), (True, False))
@pytest.mark.parametrize(("only_current", "binned"), TRUE_FALSE_2_TUPLE)
def test_estimate_parameters_binned(only_current, binned, lazy):
s = Signal1D(np.empty((300,)))
s.metadata.Signal.binned = binned
axis = s.axes_manager.signal_axes[0]
axis.scale = 0.2
axis.offset = -10
> g1 = SkewNormal(A=2, x0=2, scale=10, shape=5)
hyperspy/tests/component/test_skewnormal.py:62:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_components/skew_normal.py:154: in __init__
super(SkewNormal, self).__init__(
hyperspy/_components/expression.py:158: in __init__
self.compile_function(module=module, position=position)
hyperspy/_components/expression.py:209: in compile_function
expr = _parse_substitutions(self._str_expression)
hyperspy/_components/expression.py:61: in _parse_substitutions
expr = expr.subs(t[0], sympy.sympify(t[1]))
/usr/lib/python3/dist-packages/sympy/core/sympify.py:495: in sympify
expr = parse_expr(a, local_dict=locals, transformations=transformations, evaluate=evaluate)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1105: in parse_expr
raise e from ValueError(f"Error from parse_expr with transformed code: {code!r}")
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1096: in parse_expr
rv = eval_expr(code, local_dict, global_dict)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:915: in eval_expr
expr = eval(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E TypeError: unsupported operand type(s) for *: 'function' and 'Symbol'
<string>:1: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
_______________ test_estimate_parameters_binned[True-False-True] _______________
[gw3] linux -- Python 3.10.7 /usr/bin/python3.10
ValueError: Error from parse_expr with transformed code: "(Integer (1 )+erf (shape *Symbol ('t' )/sqrt (Integer (2 ))))/Integer (2 )"
The above exception was the direct cause of the following exception:
only_current = True, binned = False, lazy = True
@pytest.mark.parametrize(("lazy"), (True, False))
@pytest.mark.parametrize(("only_current", "binned"), TRUE_FALSE_2_TUPLE)
def test_estimate_parameters_binned(only_current, binned, lazy):
s = Signal1D(np.empty((300,)))
s.metadata.Signal.binned = binned
axis = s.axes_manager.signal_axes[0]
axis.scale = 0.2
axis.offset = -10
> g1 = SkewNormal(A=2, x0=2, scale=10, shape=5)
hyperspy/tests/component/test_skewnormal.py:62:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_components/skew_normal.py:154: in __init__
super(SkewNormal, self).__init__(
hyperspy/_components/expression.py:158: in __init__
self.compile_function(module=module, position=position)
hyperspy/_components/expression.py:209: in compile_function
expr = _parse_substitutions(self._str_expression)
hyperspy/_components/expression.py:61: in _parse_substitutions
expr = expr.subs(t[0], sympy.sympify(t[1]))
/usr/lib/python3/dist-packages/sympy/core/sympify.py:495: in sympify
expr = parse_expr(a, local_dict=locals, transformations=transformations, evaluate=evaluate)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1105: in parse_expr
raise e from ValueError(f"Error from parse_expr with transformed code: {code!r}")
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1096: in parse_expr
rv = eval_expr(code, local_dict, global_dict)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:915: in eval_expr
expr = eval(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E TypeError: unsupported operand type(s) for *: 'function' and 'Symbol'
<string>:1: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
______________ test_estimate_parameters_binned[True-False-False] _______________
[gw3] linux -- Python 3.10.7 /usr/bin/python3.10
ValueError: Error from parse_expr with transformed code: "(Integer (1 )+erf (shape *Symbol ('t' )/sqrt (Integer (2 ))))/Integer (2 )"
The above exception was the direct cause of the following exception:
only_current = True, binned = False, lazy = False
@pytest.mark.parametrize(("lazy"), (True, False))
@pytest.mark.parametrize(("only_current", "binned"), TRUE_FALSE_2_TUPLE)
def test_estimate_parameters_binned(only_current, binned, lazy):
s = Signal1D(np.empty((300,)))
s.metadata.Signal.binned = binned
axis = s.axes_manager.signal_axes[0]
axis.scale = 0.2
axis.offset = -10
> g1 = SkewNormal(A=2, x0=2, scale=10, shape=5)
hyperspy/tests/component/test_skewnormal.py:62:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_components/skew_normal.py:154: in __init__
super(SkewNormal, self).__init__(
hyperspy/_components/expression.py:158: in __init__
self.compile_function(module=module, position=position)
hyperspy/_components/expression.py:209: in compile_function
expr = _parse_substitutions(self._str_expression)
hyperspy/_components/expression.py:61: in _parse_substitutions
expr = expr.subs(t[0], sympy.sympify(t[1]))
/usr/lib/python3/dist-packages/sympy/core/sympify.py:495: in sympify
expr = parse_expr(a, local_dict=locals, transformations=transformations, evaluate=evaluate)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1105: in parse_expr
raise e from ValueError(f"Error from parse_expr with transformed code: {code!r}")
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1096: in parse_expr
rv = eval_expr(code, local_dict, global_dict)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:915: in eval_expr
expr = eval(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E TypeError: unsupported operand type(s) for *: 'function' and 'Symbol'
<string>:1: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
_______________ test_estimate_parameters_binned[False-True-True] _______________
[gw3] linux -- Python 3.10.7 /usr/bin/python3.10
ValueError: Error from parse_expr with transformed code: "(Integer (1 )+erf (shape *Symbol ('t' )/sqrt (Integer (2 ))))/Integer (2 )"
The above exception was the direct cause of the following exception:
only_current = False, binned = True, lazy = True
@pytest.mark.parametrize(("lazy"), (True, False))
@pytest.mark.parametrize(("only_current", "binned"), TRUE_FALSE_2_TUPLE)
def test_estimate_parameters_binned(only_current, binned, lazy):
s = Signal1D(np.empty((300,)))
s.metadata.Signal.binned = binned
axis = s.axes_manager.signal_axes[0]
axis.scale = 0.2
axis.offset = -10
> g1 = SkewNormal(A=2, x0=2, scale=10, shape=5)
hyperspy/tests/component/test_skewnormal.py:62:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_components/skew_normal.py:154: in __init__
super(SkewNormal, self).__init__(
hyperspy/_components/expression.py:158: in __init__
self.compile_function(module=module, position=position)
hyperspy/_components/expression.py:209: in compile_function
expr = _parse_substitutions(self._str_expression)
hyperspy/_components/expression.py:61: in _parse_substitutions
expr = expr.subs(t[0], sympy.sympify(t[1]))
/usr/lib/python3/dist-packages/sympy/core/sympify.py:495: in sympify
expr = parse_expr(a, local_dict=locals, transformations=transformations, evaluate=evaluate)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1105: in parse_expr
raise e from ValueError(f"Error from parse_expr with transformed code: {code!r}")
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1096: in parse_expr
rv = eval_expr(code, local_dict, global_dict)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:915: in eval_expr
expr = eval(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E TypeError: unsupported operand type(s) for *: 'function' and 'Symbol'
<string>:1: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
______________ test_estimate_parameters_binned[False-True-False] _______________
[gw3] linux -- Python 3.10.7 /usr/bin/python3.10
ValueError: Error from parse_expr with transformed code: "(Integer (1 )+erf (shape *Symbol ('t' )/sqrt (Integer (2 ))))/Integer (2 )"
The above exception was the direct cause of the following exception:
only_current = False, binned = True, lazy = False
@pytest.mark.parametrize(("lazy"), (True, False))
@pytest.mark.parametrize(("only_current", "binned"), TRUE_FALSE_2_TUPLE)
def test_estimate_parameters_binned(only_current, binned, lazy):
s = Signal1D(np.empty((300,)))
s.metadata.Signal.binned = binned
axis = s.axes_manager.signal_axes[0]
axis.scale = 0.2
axis.offset = -10
> g1 = SkewNormal(A=2, x0=2, scale=10, shape=5)
hyperspy/tests/component/test_skewnormal.py:62:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_components/skew_normal.py:154: in __init__
super(SkewNormal, self).__init__(
hyperspy/_components/expression.py:158: in __init__
self.compile_function(module=module, position=position)
hyperspy/_components/expression.py:209: in compile_function
expr = _parse_substitutions(self._str_expression)
hyperspy/_components/expression.py:61: in _parse_substitutions
expr = expr.subs(t[0], sympy.sympify(t[1]))
/usr/lib/python3/dist-packages/sympy/core/sympify.py:495: in sympify
expr = parse_expr(a, local_dict=locals, transformations=transformations, evaluate=evaluate)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1105: in parse_expr
raise e from ValueError(f"Error from parse_expr with transformed code: {code!r}")
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1096: in parse_expr
rv = eval_expr(code, local_dict, global_dict)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:915: in eval_expr
expr = eval(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E TypeError: unsupported operand type(s) for *: 'function' and 'Symbol'
<string>:1: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
______________ test_estimate_parameters_binned[False-False-True] _______________
[gw3] linux -- Python 3.10.7 /usr/bin/python3.10
ValueError: Error from parse_expr with transformed code: "(Integer (1 )+erf (shape *Symbol ('t' )/sqrt (Integer (2 ))))/Integer (2 )"
The above exception was the direct cause of the following exception:
only_current = False, binned = False, lazy = True
@pytest.mark.parametrize(("lazy"), (True, False))
@pytest.mark.parametrize(("only_current", "binned"), TRUE_FALSE_2_TUPLE)
def test_estimate_parameters_binned(only_current, binned, lazy):
s = Signal1D(np.empty((300,)))
s.metadata.Signal.binned = binned
axis = s.axes_manager.signal_axes[0]
axis.scale = 0.2
axis.offset = -10
> g1 = SkewNormal(A=2, x0=2, scale=10, shape=5)
hyperspy/tests/component/test_skewnormal.py:62:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_components/skew_normal.py:154: in __init__
super(SkewNormal, self).__init__(
hyperspy/_components/expression.py:158: in __init__
self.compile_function(module=module, position=position)
hyperspy/_components/expression.py:209: in compile_function
expr = _parse_substitutions(self._str_expression)
hyperspy/_components/expression.py:61: in _parse_substitutions
expr = expr.subs(t[0], sympy.sympify(t[1]))
/usr/lib/python3/dist-packages/sympy/core/sympify.py:495: in sympify
expr = parse_expr(a, local_dict=locals, transformations=transformations, evaluate=evaluate)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1105: in parse_expr
raise e from ValueError(f"Error from parse_expr with transformed code: {code!r}")
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1096: in parse_expr
rv = eval_expr(code, local_dict, global_dict)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:915: in eval_expr
expr = eval(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E TypeError: unsupported operand type(s) for *: 'function' and 'Symbol'
<string>:1: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
______________ test_estimate_parameters_binned[False-False-False] ______________
[gw3] linux -- Python 3.10.7 /usr/bin/python3.10
ValueError: Error from parse_expr with transformed code: "(Integer (1 )+erf (shape *Symbol ('t' )/sqrt (Integer (2 ))))/Integer (2 )"
The above exception was the direct cause of the following exception:
only_current = False, binned = False, lazy = False
@pytest.mark.parametrize(("lazy"), (True, False))
@pytest.mark.parametrize(("only_current", "binned"), TRUE_FALSE_2_TUPLE)
def test_estimate_parameters_binned(only_current, binned, lazy):
s = Signal1D(np.empty((300,)))
s.metadata.Signal.binned = binned
axis = s.axes_manager.signal_axes[0]
axis.scale = 0.2
axis.offset = -10
> g1 = SkewNormal(A=2, x0=2, scale=10, shape=5)
hyperspy/tests/component/test_skewnormal.py:62:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_components/skew_normal.py:154: in __init__
super(SkewNormal, self).__init__(
hyperspy/_components/expression.py:158: in __init__
self.compile_function(module=module, position=position)
hyperspy/_components/expression.py:209: in compile_function
expr = _parse_substitutions(self._str_expression)
hyperspy/_components/expression.py:61: in _parse_substitutions
expr = expr.subs(t[0], sympy.sympify(t[1]))
/usr/lib/python3/dist-packages/sympy/core/sympify.py:495: in sympify
expr = parse_expr(a, local_dict=locals, transformations=transformations, evaluate=evaluate)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1105: in parse_expr
raise e from ValueError(f"Error from parse_expr with transformed code: {code!r}")
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1096: in parse_expr
rv = eval_expr(code, local_dict, global_dict)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:915: in eval_expr
expr = eval(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E TypeError: unsupported operand type(s) for *: 'function' and 'Symbol'
<string>:1: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
_________________________ test_function_nd[True-True] __________________________
[gw3] linux -- Python 3.10.7 /usr/bin/python3.10
ValueError: Error from parse_expr with transformed code: "(Integer (1 )+erf (shape *Symbol ('t' )/sqrt (Integer (2 ))))/Integer (2 )"
The above exception was the direct cause of the following exception:
binned = True, lazy = True
@pytest.mark.parametrize(("lazy"), (True, False))
@pytest.mark.parametrize(("binned"), (True, False))
def test_function_nd(binned, lazy):
s = Signal1D(np.empty((300,)))
axis = s.axes_manager.signal_axes[0]
axis.scale = 0.2
axis.offset = -10
> g1 = SkewNormal(A=2, x0=2, scale=10, shape=5)
hyperspy/tests/component/test_skewnormal.py:84:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_components/skew_normal.py:154: in __init__
super(SkewNormal, self).__init__(
hyperspy/_components/expression.py:158: in __init__
self.compile_function(module=module, position=position)
hyperspy/_components/expression.py:209: in compile_function
expr = _parse_substitutions(self._str_expression)
hyperspy/_components/expression.py:61: in _parse_substitutions
expr = expr.subs(t[0], sympy.sympify(t[1]))
/usr/lib/python3/dist-packages/sympy/core/sympify.py:495: in sympify
expr = parse_expr(a, local_dict=locals, transformations=transformations, evaluate=evaluate)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1105: in parse_expr
raise e from ValueError(f"Error from parse_expr with transformed code: {code!r}")
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1096: in parse_expr
rv = eval_expr(code, local_dict, global_dict)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:915: in eval_expr
expr = eval(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E TypeError: unsupported operand type(s) for *: 'function' and 'Symbol'
<string>:1: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
_________________________ test_function_nd[True-False] _________________________
[gw3] linux -- Python 3.10.7 /usr/bin/python3.10
ValueError: Error from parse_expr with transformed code: "(Integer (1 )+erf (shape *Symbol ('t' )/sqrt (Integer (2 ))))/Integer (2 )"
The above exception was the direct cause of the following exception:
binned = True, lazy = False
@pytest.mark.parametrize(("lazy"), (True, False))
@pytest.mark.parametrize(("binned"), (True, False))
def test_function_nd(binned, lazy):
s = Signal1D(np.empty((300,)))
axis = s.axes_manager.signal_axes[0]
axis.scale = 0.2
axis.offset = -10
> g1 = SkewNormal(A=2, x0=2, scale=10, shape=5)
hyperspy/tests/component/test_skewnormal.py:84:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_components/skew_normal.py:154: in __init__
super(SkewNormal, self).__init__(
hyperspy/_components/expression.py:158: in __init__
self.compile_function(module=module, position=position)
hyperspy/_components/expression.py:209: in compile_function
expr = _parse_substitutions(self._str_expression)
hyperspy/_components/expression.py:61: in _parse_substitutions
expr = expr.subs(t[0], sympy.sympify(t[1]))
/usr/lib/python3/dist-packages/sympy/core/sympify.py:495: in sympify
expr = parse_expr(a, local_dict=locals, transformations=transformations, evaluate=evaluate)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1105: in parse_expr
raise e from ValueError(f"Error from parse_expr with transformed code: {code!r}")
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1096: in parse_expr
rv = eval_expr(code, local_dict, global_dict)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:915: in eval_expr
expr = eval(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E TypeError: unsupported operand type(s) for *: 'function' and 'Symbol'
<string>:1: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
_________________________ test_function_nd[False-True] _________________________
[gw3] linux -- Python 3.10.7 /usr/bin/python3.10
ValueError: Error from parse_expr with transformed code: "(Integer (1 )+erf (shape *Symbol ('t' )/sqrt (Integer (2 ))))/Integer (2 )"
The above exception was the direct cause of the following exception:
binned = False, lazy = True
@pytest.mark.parametrize(("lazy"), (True, False))
@pytest.mark.parametrize(("binned"), (True, False))
def test_function_nd(binned, lazy):
s = Signal1D(np.empty((300,)))
axis = s.axes_manager.signal_axes[0]
axis.scale = 0.2
axis.offset = -10
> g1 = SkewNormal(A=2, x0=2, scale=10, shape=5)
hyperspy/tests/component/test_skewnormal.py:84:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_components/skew_normal.py:154: in __init__
super(SkewNormal, self).__init__(
hyperspy/_components/expression.py:158: in __init__
self.compile_function(module=module, position=position)
hyperspy/_components/expression.py:209: in compile_function
expr = _parse_substitutions(self._str_expression)
hyperspy/_components/expression.py:61: in _parse_substitutions
expr = expr.subs(t[0], sympy.sympify(t[1]))
/usr/lib/python3/dist-packages/sympy/core/sympify.py:495: in sympify
expr = parse_expr(a, local_dict=locals, transformations=transformations, evaluate=evaluate)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1105: in parse_expr
raise e from ValueError(f"Error from parse_expr with transformed code: {code!r}")
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1096: in parse_expr
rv = eval_expr(code, local_dict, global_dict)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:915: in eval_expr
expr = eval(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E TypeError: unsupported operand type(s) for *: 'function' and 'Symbol'
<string>:1: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
________________________ test_function_nd[False-False] _________________________
[gw3] linux -- Python 3.10.7 /usr/bin/python3.10
ValueError: Error from parse_expr with transformed code: "(Integer (1 )+erf (shape *Symbol ('t' )/sqrt (Integer (2 ))))/Integer (2 )"
The above exception was the direct cause of the following exception:
binned = False, lazy = False
@pytest.mark.parametrize(("lazy"), (True, False))
@pytest.mark.parametrize(("binned"), (True, False))
def test_function_nd(binned, lazy):
s = Signal1D(np.empty((300,)))
axis = s.axes_manager.signal_axes[0]
axis.scale = 0.2
axis.offset = -10
> g1 = SkewNormal(A=2, x0=2, scale=10, shape=5)
hyperspy/tests/component/test_skewnormal.py:84:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_components/skew_normal.py:154: in __init__
super(SkewNormal, self).__init__(
hyperspy/_components/expression.py:158: in __init__
self.compile_function(module=module, position=position)
hyperspy/_components/expression.py:209: in compile_function
expr = _parse_substitutions(self._str_expression)
hyperspy/_components/expression.py:61: in _parse_substitutions
expr = expr.subs(t[0], sympy.sympify(t[1]))
/usr/lib/python3/dist-packages/sympy/core/sympify.py:495: in sympify
expr = parse_expr(a, local_dict=locals, transformations=transformations, evaluate=evaluate)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1105: in parse_expr
raise e from ValueError(f"Error from parse_expr with transformed code: {code!r}")
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1096: in parse_expr
rv = eval_expr(code, local_dict, global_dict)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:915: in eval_expr
expr = eval(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E TypeError: unsupported operand type(s) for *: 'function' and 'Symbol'
<string>:1: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
______________________________ test_util_mean_get ______________________________
[gw3] linux -- Python 3.10.7 /usr/bin/python3.10
ValueError: Error from parse_expr with transformed code: "(Integer (1 )+erf (shape *Symbol ('t' )/sqrt (Integer (2 ))))/Integer (2 )"
The above exception was the direct cause of the following exception:
def test_util_mean_get():
> g1 = SkewNormal()
hyperspy/tests/component/test_skewnormal.py:98:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_components/skew_normal.py:154: in __init__
super(SkewNormal, self).__init__(
hyperspy/_components/expression.py:158: in __init__
self.compile_function(module=module, position=position)
hyperspy/_components/expression.py:209: in compile_function
expr = _parse_substitutions(self._str_expression)
hyperspy/_components/expression.py:61: in _parse_substitutions
expr = expr.subs(t[0], sympy.sympify(t[1]))
/usr/lib/python3/dist-packages/sympy/core/sympify.py:495: in sympify
expr = parse_expr(a, local_dict=locals, transformations=transformations, evaluate=evaluate)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1105: in parse_expr
raise e from ValueError(f"Error from parse_expr with transformed code: {code!r}")
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1096: in parse_expr
rv = eval_expr(code, local_dict, global_dict)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:915: in eval_expr
expr = eval(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E TypeError: unsupported operand type(s) for *: 'function' and 'Symbol'
<string>:1: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
____________________________ test_util_variance_get ____________________________
[gw3] linux -- Python 3.10.7 /usr/bin/python3.10
ValueError: Error from parse_expr with transformed code: "(Integer (1 )+erf (shape *Symbol ('t' )/sqrt (Integer (2 ))))/Integer (2 )"
The above exception was the direct cause of the following exception:
def test_util_variance_get():
> g1 = SkewNormal()
hyperspy/tests/component/test_skewnormal.py:106:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_components/skew_normal.py:154: in __init__
super(SkewNormal, self).__init__(
hyperspy/_components/expression.py:158: in __init__
self.compile_function(module=module, position=position)
hyperspy/_components/expression.py:209: in compile_function
expr = _parse_substitutions(self._str_expression)
hyperspy/_components/expression.py:61: in _parse_substitutions
expr = expr.subs(t[0], sympy.sympify(t[1]))
/usr/lib/python3/dist-packages/sympy/core/sympify.py:495: in sympify
expr = parse_expr(a, local_dict=locals, transformations=transformations, evaluate=evaluate)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1105: in parse_expr
raise e from ValueError(f"Error from parse_expr with transformed code: {code!r}")
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1096: in parse_expr
rv = eval_expr(code, local_dict, global_dict)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:915: in eval_expr
expr = eval(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E TypeError: unsupported operand type(s) for *: 'function' and 'Symbol'
<string>:1: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
____________________________ test_util_skewness_get ____________________________
[gw3] linux -- Python 3.10.7 /usr/bin/python3.10
ValueError: Error from parse_expr with transformed code: "(Integer (1 )+erf (shape *Symbol ('t' )/sqrt (Integer (2 ))))/Integer (2 )"
The above exception was the direct cause of the following exception:
def test_util_skewness_get():
> g1 = SkewNormal()
hyperspy/tests/component/test_skewnormal.py:114:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_components/skew_normal.py:154: in __init__
super(SkewNormal, self).__init__(
hyperspy/_components/expression.py:158: in __init__
self.compile_function(module=module, position=position)
hyperspy/_components/expression.py:209: in compile_function
expr = _parse_substitutions(self._str_expression)
hyperspy/_components/expression.py:61: in _parse_substitutions
expr = expr.subs(t[0], sympy.sympify(t[1]))
/usr/lib/python3/dist-packages/sympy/core/sympify.py:495: in sympify
expr = parse_expr(a, local_dict=locals, transformations=transformations, evaluate=evaluate)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1105: in parse_expr
raise e from ValueError(f"Error from parse_expr with transformed code: {code!r}")
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1096: in parse_expr
rv = eval_expr(code, local_dict, global_dict)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:915: in eval_expr
expr = eval(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E TypeError: unsupported operand type(s) for *: 'function' and 'Symbol'
<string>:1: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
______________________________ test_util_mode_get ______________________________
[gw3] linux -- Python 3.10.7 /usr/bin/python3.10
ValueError: Error from parse_expr with transformed code: "(Integer (1 )+erf (shape *Symbol ('t' )/sqrt (Integer (2 ))))/Integer (2 )"
The above exception was the direct cause of the following exception:
def test_util_mode_get():
> g1 = SkewNormal()
hyperspy/tests/component/test_skewnormal.py:122:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_components/skew_normal.py:154: in __init__
super(SkewNormal, self).__init__(
hyperspy/_components/expression.py:158: in __init__
self.compile_function(module=module, position=position)
hyperspy/_components/expression.py:209: in compile_function
expr = _parse_substitutions(self._str_expression)
hyperspy/_components/expression.py:61: in _parse_substitutions
expr = expr.subs(t[0], sympy.sympify(t[1]))
/usr/lib/python3/dist-packages/sympy/core/sympify.py:495: in sympify
expr = parse_expr(a, local_dict=locals, transformations=transformations, evaluate=evaluate)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1105: in parse_expr
raise e from ValueError(f"Error from parse_expr with transformed code: {code!r}")
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1096: in parse_expr
rv = eval_expr(code, local_dict, global_dict)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:915: in eval_expr
expr = eval(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E TypeError: unsupported operand type(s) for *: 'function' and 'Symbol'
<string>:1: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
______________________________ test_load_readonly ______________________________
[gw1] linux -- Python 3.10.7 /usr/bin/python3.10
def test_load_readonly():
s = hs.load(FILE2, lazy=True)
> k = next(filter(lambda x: isinstance(x, str) and
x.startswith("array-original"),
s.data.dask.keys()))
E StopIteration
hyperspy/tests/io/test_blockfile.py:226: StopIteration
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
------------------------------ Captured log call -------------------------------
WARNING hyperspy.io:io.py:561 `signal_type='diffraction'` not understood. See `hs.print_known_signal_types()` for a list of known signal types, and the developer guide for details on how to add new signal_types.
_____________ TestSavingMetadataContainers.test_numpy_general_type _____________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_hdf5.TestSavingMetadataContainers object at 0x9f6068f8>
tmp_path = PosixPath('/tmp/pytest-of-buildd/pytest-0/popen-gw2/test_numpy_general_type0')
@pytest.mark.xfail(sys.platform == 'win32',
reason="randomly fails in win32")
def test_numpy_general_type(self, tmp_path):
s = self.s
s.metadata.set_item('test', np.array([[1., 2], ['3', 4]]))
fname = tmp_path / 'test.hspy'
> s.save(fname)
hyperspy/tests/io/test_hdf5.py:227:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:733: in write_signal
dict2hdfgroup(metadata_dict, mapped_par, **kwds)
hyperspy/io_plugins/hspy.py:465: in dict2hdfgroup
overwrite_dataset(group, value, key, **kwds)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>
data = array([[b'1.0', b'2'],
[b'3', b'4']], dtype='|S32'), key = 'test'
signal_axes = None, chunks = True, kwds = {'compression': 'gzip'}
maxshape = (None, None), got_data = True
these_kwds = {'chunks': True, 'compression': 'gzip', 'dtype': dtype('S32'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
________________ TestAxesConfiguration.test_axes_configuration _________________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_hdf5.TestAxesConfiguration object at 0x9f5bf1c0>
def test_axes_configuration(self):
> s = load(self.filename)
hyperspy/tests/io/test_hdf5.py:409:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/io.py:405: in load
objects = [load_single_file(filename, lazy=lazy, **kwds) for filename in filenames]
hyperspy/io.py:405: in <listcomp>
objects = [load_single_file(filename, lazy=lazy, **kwds) for filename in filenames]
hyperspy/io.py:456: in load_single_file
return load_with_reader(filename=filename, reader=reader, **kwds)
hyperspy/io.py:475: in load_with_reader
file_data_list = reader.file_reader(filename, **kwds)
hyperspy/io_plugins/hspy.py:175: in file_reader
exp = hdfgroup2signaldict(exg, lazy)
hyperspy/io_plugins/hspy.py:213: in hdfgroup2signaldict
group[original_metadata], lazy=lazy),
h5py/_debian_h5py_serial/_objects.pyx:54: in h5py._debian_h5py_serial._objects.with_phil.wrapper
???
h5py/_debian_h5py_serial/_objects.pyx:55: in h5py._debian_h5py_serial._objects.with_phil.wrapper
???
/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/_hl/group.py:328: in __getitem__
oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
h5py/_debian_h5py_serial/_objects.pyx:54: in h5py._debian_h5py_serial._objects.with_phil.wrapper
???
h5py/_debian_h5py_serial/_objects.pyx:55: in h5py._debian_h5py_serial._objects.with_phil.wrapper
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E KeyError: "Unable to open object (object 'original_metadata' doesn't exist)"
h5py/_debian_h5py_serial/h5o.pyx:190: KeyError
---------------------------- Captured stdout setup -----------------------------
Overwrite '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/testfile.hdf5' (y/n)?
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
------------------------------ Captured log call -------------------------------
ERROR hyperspy.io:io.py:459 If this file format is supported, please report this error to the HyperSpy developers.
_____________________________ test_glob_wildcards ______________________________
[gw0] linux -- Python 3.10.7 /usr/bin/python3.10
def test_glob_wildcards():
s = Signal1D(np.arange(10))
with tempfile.TemporaryDirectory() as dirpath:
fnames = [os.path.join(dirpath, f"temp[1x{x}].hspy") for x in range(2)]
for f in fnames:
> s.save(f)
hyperspy/tests/io/test_io.py:99:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>, data = array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
key = 'data', signal_axes = (0,), chunks = (10,), kwds = {'compression': 'gzip'}
maxshape = (None,), got_data = True
these_kwds = {'chunks': (10,), 'compression': 'gzip', 'dtype': dtype('int32'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
____________________________ test_file_reader_error ____________________________
[gw0] linux -- Python 3.10.7 /usr/bin/python3.10
def test_file_reader_error():
# Only None, str or objects with attr "file_reader" are supported
s = Signal1D(np.arange(10))
with tempfile.TemporaryDirectory() as dirpath:
f = os.path.join(dirpath, "temp.hspy")
> s.save(f)
hyperspy/tests/io/test_io.py:153:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>, data = array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
key = 'data', signal_axes = (0,), chunks = (10,), kwds = {'compression': 'gzip'}
maxshape = (None,), got_data = True
these_kwds = {'chunks': (10,), 'compression': 'gzip', 'dtype': dtype('int32'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
___________________________ test_file_reader_warning ___________________________
[gw0] linux -- Python 3.10.7 /usr/bin/python3.10
caplog = <_pytest.logging.LogCaptureFixture object at 0x995d0628>
def test_file_reader_warning(caplog):
# Test fallback to Pillow imaging library
s = Signal1D(np.arange(10))
with tempfile.TemporaryDirectory() as dirpath:
f = os.path.join(dirpath, "temp.hspy")
> s.save(f)
hyperspy/tests/io/test_io.py:165:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>, data = array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
key = 'data', signal_axes = (0,), chunks = (10,), kwds = {'compression': 'gzip'}
maxshape = (None,), got_data = True
these_kwds = {'chunks': (10,), 'compression': 'gzip', 'dtype': dtype('int32'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
___________________________ test_file_reader_options ___________________________
[gw0] linux -- Python 3.10.7 /usr/bin/python3.10
def test_file_reader_options():
s = Signal1D(np.arange(10))
with tempfile.TemporaryDirectory() as dirpath:
f = os.path.join(dirpath, "temp.hspy")
> s.save(f)
hyperspy/tests/io/test_io.py:179:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>, data = array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
key = 'data', signal_axes = (0,), chunks = (10,), kwds = {'compression': 'gzip'}
maxshape = (None,), got_data = True
these_kwds = {'chunks': (10,), 'compression': 'gzip', 'dtype': dtype('int32'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
_____________ Test_permanent_markers_io.test_save_permanent_marker _____________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_hdf5.Test_permanent_markers_io object at 0x9f5bf1a8>
def test_save_permanent_marker(self):
s = Signal2D(np.arange(100).reshape(10, 10))
m = markers.point(x=5, y=5)
s.add_marker(m, permanent=True)
with tempfile.TemporaryDirectory() as tmp:
filename = tmp + '/testsavefile.hdf5'
> s.save(filename)
hyperspy/tests/io/test_hdf5.py:426:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>
data = array([[ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
[10, 11, 12, 13, 14, 15, 16, 17, 18, 19],
[20, 21, 22, ...75, 76, 77, 78, 79],
[80, 81, 82, 83, 84, 85, 86, 87, 88, 89],
[90, 91, 92, 93, 94, 95, 96, 97, 98, 99]])
key = 'data', signal_axes = (1, 0), chunks = (10, 10)
kwds = {'compression': 'gzip'}, maxshape = (None, None), got_data = True
these_kwds = {'chunks': (10, 10), 'compression': 'gzip', 'dtype': dtype('int32'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
___________________________ test_save_default_format ___________________________
[gw0] linux -- Python 3.10.7 /usr/bin/python3.10
def test_save_default_format():
s = Signal1D(np.arange(10))
with tempfile.TemporaryDirectory() as dirpath:
f = os.path.join(dirpath, "temp")
> s.save(f)
hyperspy/tests/io/test_io.py:199:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>, data = array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
key = 'data', signal_axes = (0,), chunks = (10,), kwds = {'compression': 'gzip'}
maxshape = (None,), got_data = True
these_kwds = {'chunks': (10,), 'compression': 'gzip', 'dtype': dtype('int32'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
_______ Test_permanent_markers_io.test_save_load_empty_metadata_markers ________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_hdf5.Test_permanent_markers_io object at 0x9f5bf6a0>
def test_save_load_empty_metadata_markers(self):
s = Signal2D(np.arange(100).reshape(10, 10))
m = markers.point(x=5, y=5)
m.name = "test"
s.add_marker(m, permanent=True)
del s.metadata.Markers.test
with tempfile.TemporaryDirectory() as tmp:
filename = tmp + '/testsavefile.hdf5'
> s.save(filename)
hyperspy/tests/io/test_hdf5.py:436:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>
data = array([[ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
[10, 11, 12, 13, 14, 15, 16, 17, 18, 19],
[20, 21, 22, ...75, 76, 77, 78, 79],
[80, 81, 82, 83, 84, 85, 86, 87, 88, 89],
[90, 91, 92, 93, 94, 95, 96, 97, 98, 99]])
key = 'data', signal_axes = (1, 0), chunks = (10, 10)
kwds = {'compression': 'gzip'}, maxshape = (None, None), got_data = True
these_kwds = {'chunks': (10, 10), 'compression': 'gzip', 'dtype': dtype('int32'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
__________ Test_permanent_markers_io.test_save_load_permanent_marker ___________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_hdf5.Test_permanent_markers_io object at 0x9f5bfc58>
def test_save_load_permanent_marker(self):
x, y = 5, 2
color = 'red'
size = 10
name = 'testname'
s = Signal2D(np.arange(100).reshape(10, 10))
m = markers.point(x=x, y=y, color=color, size=size)
m.name = name
s.add_marker(m, permanent=True)
with tempfile.TemporaryDirectory() as tmp:
filename = tmp + '/testloadfile.hdf5'
> s.save(filename)
hyperspy/tests/io/test_hdf5.py:451:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>
data = array([[ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
[10, 11, 12, 13, 14, 15, 16, 17, 18, 19],
[20, 21, 22, ...75, 76, 77, 78, 79],
[80, 81, 82, 83, 84, 85, 86, 87, 88, 89],
[90, 91, 92, 93, 94, 95, 96, 97, 98, 99]])
key = 'data', signal_axes = (1, 0), chunks = (10, 10)
kwds = {'compression': 'gzip'}, maxshape = (None, None), got_data = True
these_kwds = {'chunks': (10, 10), 'compression': 'gzip', 'dtype': dtype('int32'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
_____ Test_permanent_markers_io.test_save_load_permanent_marker_all_types ______
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_hdf5.Test_permanent_markers_io object at 0x9f5bfa18>
def test_save_load_permanent_marker_all_types(self):
x1, y1, x2, y2 = 5, 2, 1, 8
s = Signal2D(np.arange(100).reshape(10, 10))
m0_list = [
markers.point(x=x1, y=y1),
markers.horizontal_line(y=y1),
markers.horizontal_line_segment(x1=x1, x2=x2, y=y1),
markers.line_segment(x1=x1, x2=x2, y1=y1, y2=y2),
markers.rectangle(x1=x1, x2=x2, y1=y1, y2=y2),
markers.text(x=x1, y=y1, text="test"),
markers.vertical_line(x=x1),
markers.vertical_line_segment(x=x1, y1=y1, y2=y2),
]
for m in m0_list:
s.add_marker(m, permanent=True)
with tempfile.TemporaryDirectory() as tmp:
filename = tmp + '/testallmarkersfile.hdf5'
> s.save(filename)
hyperspy/tests/io/test_hdf5.py:478:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>
data = array([[ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
[10, 11, 12, 13, 14, 15, 16, 17, 18, 19],
[20, 21, 22, ...75, 76, 77, 78, 79],
[80, 81, 82, 83, 84, 85, 86, 87, 88, 89],
[90, 91, 92, 93, 94, 95, 96, 97, 98, 99]])
key = 'data', signal_axes = (1, 0), chunks = (10, 10)
kwds = {'compression': 'gzip'}, maxshape = (None, None), got_data = True
these_kwds = {'chunks': (10, 10), 'compression': 'gzip', 'dtype': dtype('int32'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
_______ Test_permanent_markers_io.test_save_load_horizontal_line_marker ________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_hdf5.Test_permanent_markers_io object at 0x9f5bfc40>
def test_save_load_horizontal_line_marker(self):
y = 8
color = 'blue'
linewidth = 2.5
name = "horizontal_line_test"
s = Signal2D(np.arange(100).reshape(10, 10))
m = markers.horizontal_line(y=y, color=color, linewidth=linewidth)
m.name = name
s.add_marker(m, permanent=True)
with tempfile.TemporaryDirectory() as tmp:
filename = tmp + '/test_save_horizontal_line_marker.hdf5'
> s.save(filename)
hyperspy/tests/io/test_hdf5.py:502:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>
data = array([[ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
[10, 11, 12, 13, 14, 15, 16, 17, 18, 19],
[20, 21, 22, ...75, 76, 77, 78, 79],
[80, 81, 82, 83, 84, 85, 86, 87, 88, 89],
[90, 91, 92, 93, 94, 95, 96, 97, 98, 99]])
key = 'data', signal_axes = (1, 0), chunks = (10, 10)
kwds = {'compression': 'gzip'}, maxshape = (None, None), got_data = True
these_kwds = {'chunks': (10, 10), 'compression': 'gzip', 'dtype': dtype('int32'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
___ Test_permanent_markers_io.test_save_load_horizontal_line_segment_marker ____
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_hdf5.Test_permanent_markers_io object at 0x9f5bfdf0>
def test_save_load_horizontal_line_segment_marker(self):
x1, x2, y = 1, 5, 8
color = 'red'
linewidth = 1.2
name = "horizontal_line_segment_test"
s = Signal2D(np.arange(100).reshape(10, 10))
m = markers.horizontal_line_segment(
x1=x1, x2=x2, y=y, color=color, linewidth=linewidth)
m.name = name
s.add_marker(m, permanent=True)
with tempfile.TemporaryDirectory() as tmp:
filename = tmp + '/test_save_horizontal_line_segment_marker.hdf5'
> s.save(filename)
hyperspy/tests/io/test_hdf5.py:519:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>
data = array([[ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
[10, 11, 12, 13, 14, 15, 16, 17, 18, 19],
[20, 21, 22, ...75, 76, 77, 78, 79],
[80, 81, 82, 83, 84, 85, 86, 87, 88, 89],
[90, 91, 92, 93, 94, 95, 96, 97, 98, 99]])
key = 'data', signal_axes = (1, 0), chunks = (10, 10)
kwds = {'compression': 'gzip'}, maxshape = (None, None), got_data = True
these_kwds = {'chunks': (10, 10), 'compression': 'gzip', 'dtype': dtype('int32'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
________ Test_permanent_markers_io.test_save_load_vertical_line_marker _________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_hdf5.Test_permanent_markers_io object at 0x9f660c88>
def test_save_load_vertical_line_marker(self):
x = 9
color = 'black'
linewidth = 3.5
name = "vertical_line_test"
s = Signal2D(np.arange(100).reshape(10, 10))
m = markers.vertical_line(x=x, color=color, linewidth=linewidth)
m.name = name
s.add_marker(m, permanent=True)
with tempfile.TemporaryDirectory() as tmp:
filename = tmp + '/test_save_vertical_line_marker.hdf5'
> s.save(filename)
hyperspy/tests/io/test_hdf5.py:535:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>
data = array([[ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
[10, 11, 12, 13, 14, 15, 16, 17, 18, 19],
[20, 21, 22, ...75, 76, 77, 78, 79],
[80, 81, 82, 83, 84, 85, 86, 87, 88, 89],
[90, 91, 92, 93, 94, 95, 96, 97, 98, 99]])
key = 'data', signal_axes = (1, 0), chunks = (10, 10)
kwds = {'compression': 'gzip'}, maxshape = (None, None), got_data = True
these_kwds = {'chunks': (10, 10), 'compression': 'gzip', 'dtype': dtype('int32'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
____ Test_permanent_markers_io.test_save_load_vertical_line_segment_marker _____
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_hdf5.Test_permanent_markers_io object at 0x9f7015b0>
def test_save_load_vertical_line_segment_marker(self):
x, y1, y2 = 2, 1, 3
color = 'white'
linewidth = 4.2
name = "vertical_line_segment_test"
s = Signal2D(np.arange(100).reshape(10, 10))
m = markers.vertical_line_segment(
x=x, y1=y1, y2=y2, color=color, linewidth=linewidth)
m.name = name
s.add_marker(m, permanent=True)
with tempfile.TemporaryDirectory() as tmp:
filename = tmp + '/test_save_vertical_line_segment_marker.hdf5'
> s.save(filename)
hyperspy/tests/io/test_hdf5.py:552:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>
data = array([[ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
[10, 11, 12, 13, 14, 15, 16, 17, 18, 19],
[20, 21, 22, ...75, 76, 77, 78, 79],
[80, 81, 82, 83, 84, 85, 86, 87, 88, 89],
[90, 91, 92, 93, 94, 95, 96, 97, 98, 99]])
key = 'data', signal_axes = (1, 0), chunks = (10, 10)
kwds = {'compression': 'gzip'}, maxshape = (None, None), got_data = True
these_kwds = {'chunks': (10, 10), 'compression': 'gzip', 'dtype': dtype('int32'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
_________ Test_permanent_markers_io.test_save_load_line_segment_marker _________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_hdf5.Test_permanent_markers_io object at 0x9f7018c8>
def test_save_load_line_segment_marker(self):
x1, x2, y1, y2 = 1, 9, 4, 7
color = 'cyan'
linewidth = 0.7
name = "line_segment_test"
s = Signal2D(np.arange(100).reshape(10, 10))
m = markers.line_segment(
x1=x1, x2=x2, y1=y1, y2=y2, color=color, linewidth=linewidth)
m.name = name
s.add_marker(m, permanent=True)
with tempfile.TemporaryDirectory() as tmp:
filename = tmp + '/test_save_line_segment_marker.hdf5'
> s.save(filename)
hyperspy/tests/io/test_hdf5.py:569:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>
data = array([[ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
[10, 11, 12, 13, 14, 15, 16, 17, 18, 19],
[20, 21, 22, ...75, 76, 77, 78, 79],
[80, 81, 82, 83, 84, 85, 86, 87, 88, 89],
[90, 91, 92, 93, 94, 95, 96, 97, 98, 99]])
key = 'data', signal_axes = (1, 0), chunks = (10, 10)
kwds = {'compression': 'gzip'}, maxshape = (None, None), got_data = True
these_kwds = {'chunks': (10, 10), 'compression': 'gzip', 'dtype': dtype('int32'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
____________ Test_permanent_markers_io.test_save_load_point_marker _____________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_hdf5.Test_permanent_markers_io object at 0x9f3f6aa8>
def test_save_load_point_marker(self):
x, y = 9, 8
color = 'purple'
name = "point test"
s = Signal2D(np.arange(100).reshape(10, 10))
m = markers.point(
x=x, y=y, color=color)
m.name = name
s.add_marker(m, permanent=True)
with tempfile.TemporaryDirectory() as tmp:
filename = tmp + '/test_save_point_marker.hdf5'
> s.save(filename)
hyperspy/tests/io/test_hdf5.py:585:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>
data = array([[ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
[10, 11, 12, 13, 14, 15, 16, 17, 18, 19],
[20, 21, 22, ...75, 76, 77, 78, 79],
[80, 81, 82, 83, 84, 85, 86, 87, 88, 89],
[90, 91, 92, 93, 94, 95, 96, 97, 98, 99]])
key = 'data', signal_axes = (1, 0), chunks = (10, 10)
kwds = {'compression': 'gzip'}, maxshape = (None, None), got_data = True
these_kwds = {'chunks': (10, 10), 'compression': 'gzip', 'dtype': dtype('int32'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
__________ Test_permanent_markers_io.test_save_load_rectangle_marker ___________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_hdf5.Test_permanent_markers_io object at 0x9f51e5b0>
def test_save_load_rectangle_marker(self):
x1, x2, y1, y2 = 2, 4, 1, 3
color = 'yellow'
linewidth = 5
name = "rectangle_test"
s = Signal2D(np.arange(100).reshape(10, 10))
m = markers.rectangle(
x1=x1, x2=x2, y1=y1, y2=y2, color=color, linewidth=linewidth)
m.name = name
s.add_marker(m, permanent=True)
with tempfile.TemporaryDirectory() as tmp:
filename = tmp + '/test_save_rectangle_marker.hdf5'
> s.save(filename)
hyperspy/tests/io/test_hdf5.py:602:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>
data = array([[ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
[10, 11, 12, 13, 14, 15, 16, 17, 18, 19],
[20, 21, 22, ...75, 76, 77, 78, 79],
[80, 81, 82, 83, 84, 85, 86, 87, 88, 89],
[90, 91, 92, 93, 94, 95, 96, 97, 98, 99]])
key = 'data', signal_axes = (1, 0), chunks = (10, 10)
kwds = {'compression': 'gzip'}, maxshape = (None, None), got_data = True
these_kwds = {'chunks': (10, 10), 'compression': 'gzip', 'dtype': dtype('int32'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
_____________ Test_permanent_markers_io.test_save_load_text_marker _____________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_hdf5.Test_permanent_markers_io object at 0x9f51eec8>
def test_save_load_text_marker(self):
x, y = 3, 9.5
color = 'brown'
name = "text_test"
text = "a text"
s = Signal2D(np.arange(100).reshape(10, 10))
m = markers.text(
x=x, y=y, text=text, color=color)
m.name = name
s.add_marker(m, permanent=True)
with tempfile.TemporaryDirectory() as tmp:
filename = tmp + '/test_save_text_marker.hdf5'
> s.save(filename)
hyperspy/tests/io/test_hdf5.py:619:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>
data = array([[ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
[10, 11, 12, 13, 14, 15, 16, 17, 18, 19],
[20, 21, 22, ...75, 76, 77, 78, 79],
[80, 81, 82, 83, 84, 85, 86, 87, 88, 89],
[90, 91, 92, 93, 94, 95, 96, 97, 98, 99]])
key = 'data', signal_axes = (1, 0), chunks = (10, 10)
kwds = {'compression': 'gzip'}, maxshape = (None, None), got_data = True
these_kwds = {'chunks': (10, 10), 'compression': 'gzip', 'dtype': dtype('int32'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
_____ Test_permanent_markers_io.test_save_load_multidim_navigation_marker ______
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_hdf5.Test_permanent_markers_io object at 0x9f51ef88>
def test_save_load_multidim_navigation_marker(self):
x, y = (1, 2, 3), (5, 6, 7)
name = 'test point'
s = Signal2D(np.arange(300).reshape(3, 10, 10))
m = markers.point(x=x, y=y)
m.name = name
s.add_marker(m, permanent=True)
with tempfile.TemporaryDirectory() as tmp:
filename = tmp + '/test_save_multidim_nav_marker.hdf5'
> s.save(filename)
hyperspy/tests/io/test_hdf5.py:633:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>
data = array([[[ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
[ 10, 11, 12, 13, 14, 15, 16, 17, 18, 19]... [280, 281, 282, 283, 284, 285, 286, 287, 288, 289],
[290, 291, 292, 293, 294, 295, 296, 297, 298, 299]]])
key = 'data', signal_axes = (2, 1), chunks = (3, 10, 10)
kwds = {'compression': 'gzip'}, maxshape = (None, None, None), got_data = True
these_kwds = {'chunks': (3, 10, 10), 'compression': 'gzip', 'dtype': dtype('int32'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
____________________________ test_compression[None] ____________________________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
compression = None
tmp_path = PosixPath('/tmp/pytest-of-buildd/pytest-0/popen-gw2/test_compression_None_0')
@pytest.mark.parametrize("compression", (None, "gzip", "lzf"))
def test_compression(compression, tmp_path):
s = Signal1D(np.ones((3,3)))
> s.save(tmp_path / 'test_compression.hspy', overwrite=True,
compression=compression)
hyperspy/tests/io/test_hdf5.py:670:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>
data = array([[1., 1., 1.],
[1., 1., 1.],
[1., 1., 1.]])
key = 'data', signal_axes = (1,), chunks = (3, 3), kwds = {'compression': None}
maxshape = (None, None), got_data = True
these_kwds = {'chunks': (3, 3), 'compression': None, 'dtype': dtype('float64'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
____________________________ test_compression[gzip] ____________________________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
compression = 'gzip'
tmp_path = PosixPath('/tmp/pytest-of-buildd/pytest-0/popen-gw2/test_compression_gzip_0')
@pytest.mark.parametrize("compression", (None, "gzip", "lzf"))
def test_compression(compression, tmp_path):
s = Signal1D(np.ones((3,3)))
> s.save(tmp_path / 'test_compression.hspy', overwrite=True,
compression=compression)
hyperspy/tests/io/test_hdf5.py:670:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>
data = array([[1., 1., 1.],
[1., 1., 1.],
[1., 1., 1.]])
key = 'data', signal_axes = (1,), chunks = (3, 3)
kwds = {'compression': 'gzip'}, maxshape = (None, None), got_data = True
these_kwds = {'chunks': (3, 3), 'compression': 'gzip', 'dtype': dtype('float64'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
____________________________ test_compression[lzf] _____________________________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
compression = 'lzf'
tmp_path = PosixPath('/tmp/pytest-of-buildd/pytest-0/popen-gw2/test_compression_lzf_0')
@pytest.mark.parametrize("compression", (None, "gzip", "lzf"))
def test_compression(compression, tmp_path):
s = Signal1D(np.ones((3,3)))
> s.save(tmp_path / 'test_compression.hspy', overwrite=True,
compression=compression)
hyperspy/tests/io/test_hdf5.py:670:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>
data = array([[1., 1., 1.],
[1., 1., 1.],
[1., 1., 1.]])
key = 'data', signal_axes = (1,), chunks = (3, 3), kwds = {'compression': 'lzf'}
maxshape = (None, None), got_data = True
these_kwds = {'chunks': (3, 3), 'compression': 'lzf', 'dtype': dtype('float64'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
________________________ test_read_protochips_gas_cell _________________________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
def test_read_protochips_gas_cell():
filename = os.path.join(dirpath, 'protochips_gas_cell.csv')
> s = hs.load(filename)
hyperspy/tests/io/test_protochips.py:46:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/io.py:405: in load
objects = [load_single_file(filename, lazy=lazy, **kwds) for filename in filenames]
hyperspy/io.py:405: in <listcomp>
objects = [load_single_file(filename, lazy=lazy, **kwds) for filename in filenames]
hyperspy/io.py:456: in load_single_file
return load_with_reader(filename=filename, reader=reader, **kwds)
hyperspy/io.py:475: in load_with_reader
file_data_list = reader.file_reader(filename, **kwds)
hyperspy/io_plugins/protochips.py:54: in file_reader
csv_file = ProtochipsCSV(filename)
hyperspy/io_plugins/protochips.py:73: in __init__
self._read_data()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <hyperspy.io_plugins.protochips.ProtochipsCSV object at 0x94ca05b0>
def _read_data(self):
names = [name.replace(' ', '_') for name in self.column_name]
# Necessary for numpy >= 1.14
kwargs = {'encoding': 'latin1'} if np.__version__ >= LooseVersion("1.14") else {
}
data = np.genfromtxt(self.filename, delimiter=',', dtype=None,
names=names,
skip_header=self.header_last_line_number,
unpack=True, **kwargs)
self._data_dictionary = dict()
for i, name, name_dtype in zip(range(len(names)), self.column_name,
names):
if name == 'Notes':
self.notes = data[name_dtype].astype(str)
elif name == 'Time':
> self.time_axis = data[name_dtype]
E TypeError: list indices must be integers or slices, not str
hyperspy/io_plugins/protochips.py:155: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
------------------------------ Captured log call -------------------------------
ERROR hyperspy.io:io.py:459 If this file format is supported, please report this error to the HyperSpy developers.
_____________________ test_loading_invalid_protochips_file _____________________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
def test_loading_invalid_protochips_file():
filename = os.path.join(dirpath, 'invalid_protochips_file.csv')
with pytest.raises(IOError) as cm:
> hs.load(filename)
hyperspy/tests/io/test_protochips.py:87:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/io.py:405: in load
objects = [load_single_file(filename, lazy=lazy, **kwds) for filename in filenames]
hyperspy/io.py:405: in <listcomp>
objects = [load_single_file(filename, lazy=lazy, **kwds) for filename in filenames]
hyperspy/io.py:456: in load_single_file
return load_with_reader(filename=filename, reader=reader, **kwds)
hyperspy/io.py:475: in load_with_reader
file_data_list = reader.file_reader(filename, **kwds)
hyperspy/io_plugins/protochips.py:54: in file_reader
csv_file = ProtochipsCSV(filename)
hyperspy/io_plugins/protochips.py:73: in __init__
self._read_data()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <hyperspy.io_plugins.protochips.ProtochipsCSV object at 0x94c2eb38>
def _read_data(self):
names = [name.replace(' ', '_') for name in self.column_name]
# Necessary for numpy >= 1.14
kwargs = {'encoding': 'latin1'} if np.__version__ >= LooseVersion("1.14") else {
}
data = np.genfromtxt(self.filename, delimiter=',', dtype=None,
names=names,
skip_header=self.header_last_line_number,
unpack=True, **kwargs)
self._data_dictionary = dict()
for i, name, name_dtype in zip(range(len(names)), self.column_name,
names):
if name == 'Notes':
self.notes = data[name_dtype].astype(str)
elif name == 'Time':
> self.time_axis = data[name_dtype]
E TypeError: list indices must be integers or slices, not str
hyperspy/io_plugins/protochips.py:155: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
------------------------------ Captured log call -------------------------------
ERROR hyperspy.io:io.py:459 If this file format is supported, please report this error to the HyperSpy developers.
_______________________ test_read_protochips_electrical ________________________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
def test_read_protochips_electrical():
filename = os.path.join(dirpath, 'protochips_electrical.csv')
> s = hs.load(filename)
hyperspy/tests/io/test_protochips.py:196:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/io.py:405: in load
objects = [load_single_file(filename, lazy=lazy, **kwds) for filename in filenames]
hyperspy/io.py:405: in <listcomp>
objects = [load_single_file(filename, lazy=lazy, **kwds) for filename in filenames]
hyperspy/io.py:456: in load_single_file
return load_with_reader(filename=filename, reader=reader, **kwds)
hyperspy/io.py:475: in load_with_reader
file_data_list = reader.file_reader(filename, **kwds)
hyperspy/io_plugins/protochips.py:54: in file_reader
csv_file = ProtochipsCSV(filename)
hyperspy/io_plugins/protochips.py:73: in __init__
self._read_data()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <hyperspy.io_plugins.protochips.ProtochipsCSV object at 0x9668b730>
def _read_data(self):
names = [name.replace(' ', '_') for name in self.column_name]
# Necessary for numpy >= 1.14
kwargs = {'encoding': 'latin1'} if np.__version__ >= LooseVersion("1.14") else {
}
data = np.genfromtxt(self.filename, delimiter=',', dtype=None,
names=names,
skip_header=self.header_last_line_number,
unpack=True, **kwargs)
self._data_dictionary = dict()
for i, name, name_dtype in zip(range(len(names)), self.column_name,
names):
if name == 'Notes':
self.notes = data[name_dtype].astype(str)
elif name == 'Time':
> self.time_axis = data[name_dtype]
E TypeError: list indices must be integers or slices, not str
hyperspy/io_plugins/protochips.py:155: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
------------------------------ Captured log call -------------------------------
ERROR hyperspy.io:io.py:459 If this file format is supported, please report this error to the HyperSpy developers.
_________________________ test_read_protochips_thermal _________________________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
def test_read_protochips_thermal():
filename = os.path.join(dirpath, 'protochips_thermal.csv')
> s = hs.load(filename)
hyperspy/tests/io/test_protochips.py:254:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/io.py:405: in load
objects = [load_single_file(filename, lazy=lazy, **kwds) for filename in filenames]
hyperspy/io.py:405: in <listcomp>
objects = [load_single_file(filename, lazy=lazy, **kwds) for filename in filenames]
hyperspy/io.py:456: in load_single_file
return load_with_reader(filename=filename, reader=reader, **kwds)
hyperspy/io.py:475: in load_with_reader
file_data_list = reader.file_reader(filename, **kwds)
hyperspy/io_plugins/protochips.py:54: in file_reader
csv_file = ProtochipsCSV(filename)
hyperspy/io_plugins/protochips.py:73: in __init__
self._read_data()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <hyperspy.io_plugins.protochips.ProtochipsCSV object at 0x968e9598>
def _read_data(self):
names = [name.replace(' ', '_') for name in self.column_name]
# Necessary for numpy >= 1.14
kwargs = {'encoding': 'latin1'} if np.__version__ >= LooseVersion("1.14") else {
}
data = np.genfromtxt(self.filename, delimiter=',', dtype=None,
names=names,
skip_header=self.header_last_line_number,
unpack=True, **kwargs)
self._data_dictionary = dict()
for i, name, name_dtype in zip(range(len(names)), self.column_name,
names):
if name == 'Notes':
self.notes = data[name_dtype].astype(str)
elif name == 'Time':
> self.time_axis = data[name_dtype]
E TypeError: list indices must be integers or slices, not str
hyperspy/io_plugins/protochips.py:155: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
------------------------------ Captured log call -------------------------------
ERROR hyperspy.io:io.py:459 If this file format is supported, please report this error to the HyperSpy developers.
_____________________ test_read_protochips_electrothermal ______________________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
def test_read_protochips_electrothermal():
filename = os.path.join(dirpath, 'protochips_electrothermal.csv')
> s = hs.load(filename)
hyperspy/tests/io/test_protochips.py:294:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/io.py:405: in load
objects = [load_single_file(filename, lazy=lazy, **kwds) for filename in filenames]
hyperspy/io.py:405: in <listcomp>
objects = [load_single_file(filename, lazy=lazy, **kwds) for filename in filenames]
hyperspy/io.py:456: in load_single_file
return load_with_reader(filename=filename, reader=reader, **kwds)
hyperspy/io.py:475: in load_with_reader
file_data_list = reader.file_reader(filename, **kwds)
hyperspy/io_plugins/protochips.py:54: in file_reader
csv_file = ProtochipsCSV(filename)
hyperspy/io_plugins/protochips.py:73: in __init__
self._read_data()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <hyperspy.io_plugins.protochips.ProtochipsCSV object at 0x98f724a8>
def _read_data(self):
names = [name.replace(' ', '_') for name in self.column_name]
# Necessary for numpy >= 1.14
kwargs = {'encoding': 'latin1'} if np.__version__ >= LooseVersion("1.14") else {
}
data = np.genfromtxt(self.filename, delimiter=',', dtype=None,
names=names,
skip_header=self.header_last_line_number,
unpack=True, **kwargs)
self._data_dictionary = dict()
for i, name, name_dtype in zip(range(len(names)), self.column_name,
names):
if name == 'Notes':
self.notes = data[name_dtype].astype(str)
elif name == 'Time':
> self.time_axis = data[name_dtype]
E TypeError: list indices must be integers or slices, not str
hyperspy/io_plugins/protochips.py:155: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
------------------------------ Captured log call -------------------------------
ERROR hyperspy.io:io.py:459 If this file format is supported, please report this error to the HyperSpy developers.
_________________________ TestDLSNexus.test_save_hspy __________________________
[gw0] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_nexus_hdf.TestDLSNexus object at 0x9f59a160>
tmp_path = PosixPath('/tmp/pytest-of-buildd/pytest-0/popen-gw0/test_save_hspy0')
def test_save_hspy(self, tmp_path):
try:
> self.s.save(tmp_path / 'test.hspy')
hyperspy/tests/io/test_nexus_hdf.py:97:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Signal1D, title: nexustest, dimensions: (10, 10|15)>
filename = PosixPath('/tmp/pytest-of-buildd/pytest-0/popen-gw0/test_save_hspy0/test.hspy')
overwrite = None, extension = None, kwds = {}
def save(self, filename=None, overwrite=None, extension=None,
**kwds):
"""Saves the signal in the specified format.
The function gets the format from the specified extension (see
:ref:`supported-formats` in the User Guide for more information):
* ``'hspy'`` for HyperSpy's HDF5 specification
* ``'rpl'`` for Ripple (useful to export to Digital Micrograph)
* ``'msa'`` for EMSA/MSA single spectrum saving.
* ``'unf'`` for SEMPER unf binary format.
* ``'blo'`` for Blockfile diffraction stack saving.
* Many image formats such as ``'png'``, ``'tiff'``, ``'jpeg'``...
If no extension is provided the default file format as defined
in the `preferences` is used.
Please note that not all the formats supports saving datasets of
arbitrary dimensions, e.g. ``'msa'`` only supports 1D data, and
blockfiles only supports image stacks with a `navigation_dimension` < 2.
Each format accepts a different set of parameters. For details
see the specific format documentation.
Parameters
----------
filename : str or None
If None (default) and `tmp_parameters.filename` and
`tmp_parameters.folder` are defined, the
filename and path will be taken from there. A valid
extension can be provided e.g. ``'my_file.rpl'``
(see `extension` parameter).
overwrite : None or bool
If None, if the file exists it will query the user. If
True(False) it does(not) overwrite the file if it exists.
extension : None or str
The extension of the file that defines the file format.
Allowable string values are: {``'hspy'``, ``'hdf5'``, ``'rpl'``,
``'msa'``, ``'unf'``, ``'blo'``, ``'emd'``, and common image
extensions e.g. ``'tiff'``, ``'png'``, etc.}
``'hspy'`` and ``'hdf5'`` are equivalent. Use ``'hdf5'`` if
compatibility with HyperSpy versions older than 1.2 is required.
If ``None``, the extension is determined from the following list in
this order:
i) the filename
ii) `Signal.tmp_parameters.extension`
iii) ``'hspy'`` (the default extension)
"""
if filename is None:
if (self.tmp_parameters.has_item('filename') and
self.tmp_parameters.has_item('folder')):
filename = Path(
self.tmp_parameters.folder,
self.tmp_parameters.filename)
extension = (self.tmp_parameters.extension
if not extension
else extension)
elif self.metadata.has_item('General.original_filename'):
filename = self.metadata.General.original_filename
else:
raise ValueError('File name not defined')
filename = Path(filename)
if extension is not None:
filename = filename.with_suffix(f".{extension}")
> io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/signal.py:2748:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = PosixPath('/tmp/pytest-of-buildd/pytest-0/popen-gw0/test_save_hspy0/test.hspy')
signal = <Signal1D, title: nexustest, dimensions: (10, 10|15)>, overwrite = None
kwds = {}, extension = '.hspy'
writer = <module 'hyperspy.io_plugins.hspy' from '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/io_plugins/hspy.py'>
plugin = <module 'hyperspy.io_plugins.hspy' from '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/io_plugins/hspy.py'>
is_file = False, write = True
def save(filename, signal, overwrite=None, **kwds):
"""Save hyperspy signal to a file.
A list of plugins supporting file saving can be found here:
http://hyperspy.org/hyperspy-doc/current/user_guide/io.html#supported-formats
Any extra keywords are passed to the corresponding save method in the
io_plugin. For available options, see their individual documentation.
Parameters
----------
filename : None or str or pathlib.Path
The filename to save the signal to.
signal : Hyperspy signal
The signal to be saved to file.
overwrite : None or bool, default None
If None and a file exists the user will be prompted to on whether to
overwrite. If False and a file exists the file will not be written.
If True and a file exists the file will be overwritten without
prompting
Returns
-------
None
"""
filename = Path(filename).resolve()
extension = filename.suffix
if extension == '':
extension = ".hspy"
filename = filename.with_suffix(extension)
writer = None
for plugin in io_plugins:
# Drop the "." separator from the suffix
if extension[1:].lower() in plugin.file_extensions:
writer = plugin
break
if writer is None:
raise ValueError(
f"{extension} does not correspond to any supported format. "
f"Supported file extensions are: {strlist2enumeration(default_write_ext)}"
)
# Check if the writer can write
sd = signal.axes_manager.signal_dimension
nd = signal.axes_manager.navigation_dimension
if writer.writes is False:
raise ValueError(
"Writing to this format is not supported. "
f"Supported file extensions are: {strlist2enumeration(default_write_ext)}"
)
if writer.writes is not True and (sd, nd) not in writer.writes:
yes_we_can = [plugin.format_name for plugin in io_plugins
if plugin.writes is True or
plugin.writes is not False and
(sd, nd) in plugin.writes]
raise IOError(
"This file format does not support this data. "
f"Please try one of {strlist2enumeration(yes_we_can)}"
)
# Create the directory if it does not exist
ensure_directory(filename.parent)
is_file = filename.is_file()
if overwrite is None:
write = overwrite_method(filename) # Ask what to do
elif overwrite is True or (overwrite is False and not is_file):
write = True # Write the file
elif overwrite is False and is_file:
write = False # Don't write the file
else:
raise ValueError(
"`overwrite` parameter can only be None, True or False."
)
if write:
# Pass as a string for now, pathlib.Path not
# properly supported in io_plugins
> writer.file_writer(str(filename), signal, **kwds)
hyperspy/io.py:756:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/tmp/pytest-of-buildd/pytest-0/popen-gw0/test_save_hspy0/test.hspy'
signal = <Signal1D, title: nexustest, dimensions: (10, 10|15)>, args = ()
kwds = {}, f = <Closed HDF5 file>, exps = <Closed HDF5 group>
group_name = 'nexustest', expg = <Closed HDF5 group>
smd = ├── binned = False
└── signal_type =
def file_writer(filename, signal, *args, **kwds):
"""Writes data to hyperspy's hdf5 format
Parameters
----------
filename: str
signal: a BaseSignal instance
*args, optional
**kwds, optional
"""
with h5py.File(filename, mode='w') as f:
f.attrs['file_format'] = "HyperSpy"
f.attrs['file_format_version'] = version
exps = f.create_group('Experiments')
group_name = signal.metadata.General.title if \
signal.metadata.General.title else '__unnamed__'
# / is a invalid character, see #942
if "/" in group_name:
group_name = group_name.replace("/", "-")
expg = exps.create_group(group_name)
# Add record_by metadata for backward compatibility
smd = signal.metadata.Signal
if signal.axes_manager.signal_dimension == 1:
smd.record_by = "spectrum"
elif signal.axes_manager.signal_dimension == 2:
smd.record_by = "image"
else:
smd.record_by = ""
try:
> write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:784:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
signal = <Signal1D, title: nexustest, dimensions: (10, 10|15)>
group = <Closed HDF5 group>, kwds = {'compression': 'gzip'}
metadata = 'metadata', original_metadata = 'original_metadata'
axis = <Unnamed 2nd axis, size: 15>
axis_dict = {'name': <undefined>, 'navigate': False, 'offset': 0.0, 'scale': 1.0, ...}
coord_group = <Closed HDF5 group>, mapped_par = <Closed HDF5 group>
metadata_dict = {'General': {'title': 'nexustest'}, 'Signal': {'binned': False, 'record_by': 'spectrum', 'signal_type': ''}, '_HyperSpy': {'Folding': {'original_axes_manager': None, 'original_shape': None, 'signal_unfolded': False, 'unfolded': False}}}
def write_signal(signal, group, **kwds):
"Writes a hyperspy signal to a hdf5 group"
group.attrs.update(get_object_package_info(signal))
if default_version < LooseVersion("1.2"):
metadata = "mapped_parameters"
original_metadata = "original_parameters"
else:
metadata = "metadata"
original_metadata = "original_metadata"
if 'compression' not in kwds:
kwds['compression'] = 'gzip'
for axis in signal.axes_manager._axes:
axis_dict = axis.get_axis_dictionary()
coord_group = group.create_group(
'axis-%s' % axis.index_in_array)
dict2hdfgroup(axis_dict, coord_group, **kwds)
mapped_par = group.create_group(metadata)
metadata_dict = signal.metadata.as_dictionary()
> overwrite_dataset(group, signal.data, 'data',
signal_axes=signal.axes_manager.signal_indices_in_array,
**kwds)
hyperspy/io_plugins/hspy.py:727:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>
data = array([[[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.],
...
[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.]]])
key = 'data', signal_axes = (2,), chunks = (10, 10, 15)
kwds = {'compression': 'gzip'}, maxshape = (None, None, None), got_data = True
these_kwds = {'chunks': (10, 10, 15), 'compression': 'gzip', 'dtype': dtype('<f8'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
During handling of the above exception, another exception occurred:
self = <hyperspy.tests.io.test_nexus_hdf.TestDLSNexus object at 0x9f59a160>
tmp_path = PosixPath('/tmp/pytest-of-buildd/pytest-0/popen-gw0/test_save_hspy0')
def test_save_hspy(self, tmp_path):
try:
self.s.save(tmp_path / 'test.hspy')
except:
> pytest.fail("unexpected error saving hdf5")
E Failed: unexpected error saving hdf5
hyperspy/tests/io/test_nexus_hdf.py:99: Failed
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
______________________ TestDLSNexusNoAxes.test_save_hspy _______________________
[gw0] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_nexus_hdf.TestDLSNexusNoAxes object at 0x9f3798b0>
tmp_path = PosixPath('/tmp/pytest-of-buildd/pytest-0/popen-gw0/test_save_hspy1')
def test_save_hspy(self, tmp_path):
try:
> self.s.save(tmp_path / 'test.hspy')
hyperspy/tests/io/test_nexus_hdf.py:142:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <BaseSignal, title: nexustest, dimensions: (15, 10, 10|)>
filename = PosixPath('/tmp/pytest-of-buildd/pytest-0/popen-gw0/test_save_hspy1/test.hspy')
overwrite = None, extension = None, kwds = {}
def save(self, filename=None, overwrite=None, extension=None,
**kwds):
"""Saves the signal in the specified format.
The function gets the format from the specified extension (see
:ref:`supported-formats` in the User Guide for more information):
* ``'hspy'`` for HyperSpy's HDF5 specification
* ``'rpl'`` for Ripple (useful to export to Digital Micrograph)
* ``'msa'`` for EMSA/MSA single spectrum saving.
* ``'unf'`` for SEMPER unf binary format.
* ``'blo'`` for Blockfile diffraction stack saving.
* Many image formats such as ``'png'``, ``'tiff'``, ``'jpeg'``...
If no extension is provided the default file format as defined
in the `preferences` is used.
Please note that not all the formats supports saving datasets of
arbitrary dimensions, e.g. ``'msa'`` only supports 1D data, and
blockfiles only supports image stacks with a `navigation_dimension` < 2.
Each format accepts a different set of parameters. For details
see the specific format documentation.
Parameters
----------
filename : str or None
If None (default) and `tmp_parameters.filename` and
`tmp_parameters.folder` are defined, the
filename and path will be taken from there. A valid
extension can be provided e.g. ``'my_file.rpl'``
(see `extension` parameter).
overwrite : None or bool
If None, if the file exists it will query the user. If
True(False) it does(not) overwrite the file if it exists.
extension : None or str
The extension of the file that defines the file format.
Allowable string values are: {``'hspy'``, ``'hdf5'``, ``'rpl'``,
``'msa'``, ``'unf'``, ``'blo'``, ``'emd'``, and common image
extensions e.g. ``'tiff'``, ``'png'``, etc.}
``'hspy'`` and ``'hdf5'`` are equivalent. Use ``'hdf5'`` if
compatibility with HyperSpy versions older than 1.2 is required.
If ``None``, the extension is determined from the following list in
this order:
i) the filename
ii) `Signal.tmp_parameters.extension`
iii) ``'hspy'`` (the default extension)
"""
if filename is None:
if (self.tmp_parameters.has_item('filename') and
self.tmp_parameters.has_item('folder')):
filename = Path(
self.tmp_parameters.folder,
self.tmp_parameters.filename)
extension = (self.tmp_parameters.extension
if not extension
else extension)
elif self.metadata.has_item('General.original_filename'):
filename = self.metadata.General.original_filename
else:
raise ValueError('File name not defined')
filename = Path(filename)
if extension is not None:
filename = filename.with_suffix(f".{extension}")
> io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/signal.py:2748:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = PosixPath('/tmp/pytest-of-buildd/pytest-0/popen-gw0/test_save_hspy1/test.hspy')
signal = <BaseSignal, title: nexustest, dimensions: (15, 10, 10|)>
overwrite = None, kwds = {}, extension = '.hspy'
writer = <module 'hyperspy.io_plugins.hspy' from '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/io_plugins/hspy.py'>
plugin = <module 'hyperspy.io_plugins.hspy' from '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/io_plugins/hspy.py'>
is_file = False, write = True
def save(filename, signal, overwrite=None, **kwds):
"""Save hyperspy signal to a file.
A list of plugins supporting file saving can be found here:
http://hyperspy.org/hyperspy-doc/current/user_guide/io.html#supported-formats
Any extra keywords are passed to the corresponding save method in the
io_plugin. For available options, see their individual documentation.
Parameters
----------
filename : None or str or pathlib.Path
The filename to save the signal to.
signal : Hyperspy signal
The signal to be saved to file.
overwrite : None or bool, default None
If None and a file exists the user will be prompted to on whether to
overwrite. If False and a file exists the file will not be written.
If True and a file exists the file will be overwritten without
prompting
Returns
-------
None
"""
filename = Path(filename).resolve()
extension = filename.suffix
if extension == '':
extension = ".hspy"
filename = filename.with_suffix(extension)
writer = None
for plugin in io_plugins:
# Drop the "." separator from the suffix
if extension[1:].lower() in plugin.file_extensions:
writer = plugin
break
if writer is None:
raise ValueError(
f"{extension} does not correspond to any supported format. "
f"Supported file extensions are: {strlist2enumeration(default_write_ext)}"
)
# Check if the writer can write
sd = signal.axes_manager.signal_dimension
nd = signal.axes_manager.navigation_dimension
if writer.writes is False:
raise ValueError(
"Writing to this format is not supported. "
f"Supported file extensions are: {strlist2enumeration(default_write_ext)}"
)
if writer.writes is not True and (sd, nd) not in writer.writes:
yes_we_can = [plugin.format_name for plugin in io_plugins
if plugin.writes is True or
plugin.writes is not False and
(sd, nd) in plugin.writes]
raise IOError(
"This file format does not support this data. "
f"Please try one of {strlist2enumeration(yes_we_can)}"
)
# Create the directory if it does not exist
ensure_directory(filename.parent)
is_file = filename.is_file()
if overwrite is None:
write = overwrite_method(filename) # Ask what to do
elif overwrite is True or (overwrite is False and not is_file):
write = True # Write the file
elif overwrite is False and is_file:
write = False # Don't write the file
else:
raise ValueError(
"`overwrite` parameter can only be None, True or False."
)
if write:
# Pass as a string for now, pathlib.Path not
# properly supported in io_plugins
> writer.file_writer(str(filename), signal, **kwds)
hyperspy/io.py:756:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = '/tmp/pytest-of-buildd/pytest-0/popen-gw0/test_save_hspy1/test.hspy'
signal = <BaseSignal, title: nexustest, dimensions: (15, 10, 10|)>, args = ()
kwds = {}, f = <Closed HDF5 file>, exps = <Closed HDF5 group>
group_name = 'nexustest', expg = <Closed HDF5 group>
smd = ├── binned = False
└── signal_type =
def file_writer(filename, signal, *args, **kwds):
"""Writes data to hyperspy's hdf5 format
Parameters
----------
filename: str
signal: a BaseSignal instance
*args, optional
**kwds, optional
"""
with h5py.File(filename, mode='w') as f:
f.attrs['file_format'] = "HyperSpy"
f.attrs['file_format_version'] = version
exps = f.create_group('Experiments')
group_name = signal.metadata.General.title if \
signal.metadata.General.title else '__unnamed__'
# / is a invalid character, see #942
if "/" in group_name:
group_name = group_name.replace("/", "-")
expg = exps.create_group(group_name)
# Add record_by metadata for backward compatibility
smd = signal.metadata.Signal
if signal.axes_manager.signal_dimension == 1:
smd.record_by = "spectrum"
elif signal.axes_manager.signal_dimension == 2:
smd.record_by = "image"
else:
smd.record_by = ""
try:
> write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:784:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
signal = <BaseSignal, title: nexustest, dimensions: (15, 10, 10|)>
group = <Closed HDF5 group>, kwds = {'compression': 'gzip'}
metadata = 'metadata', original_metadata = 'original_metadata'
axis = <Unnamed 0th axis, size: 15, index: 0>
axis_dict = {'name': <undefined>, 'navigate': True, 'offset': 0.0, 'scale': 1.0, ...}
coord_group = <Closed HDF5 group>, mapped_par = <Closed HDF5 group>
metadata_dict = {'General': {'title': 'nexustest'}, 'Signal': {'binned': False, 'record_by': '', 'signal_type': ''}, '_HyperSpy': {'Folding': {'original_axes_manager': None, 'original_shape': None, 'signal_unfolded': False, 'unfolded': False}}}
def write_signal(signal, group, **kwds):
"Writes a hyperspy signal to a hdf5 group"
group.attrs.update(get_object_package_info(signal))
if default_version < LooseVersion("1.2"):
metadata = "mapped_parameters"
original_metadata = "original_parameters"
else:
metadata = "metadata"
original_metadata = "original_metadata"
if 'compression' not in kwds:
kwds['compression'] = 'gzip'
for axis in signal.axes_manager._axes:
axis_dict = axis.get_axis_dictionary()
coord_group = group.create_group(
'axis-%s' % axis.index_in_array)
dict2hdfgroup(axis_dict, coord_group, **kwds)
mapped_par = group.create_group(metadata)
metadata_dict = signal.metadata.as_dictionary()
> overwrite_dataset(group, signal.data, 'data',
signal_axes=signal.axes_manager.signal_indices_in_array,
**kwds)
hyperspy/io_plugins/hspy.py:727:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>
data = array([[[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.],
...
[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.]]])
key = 'data', signal_axes = (), chunks = (10, 10, 15)
kwds = {'compression': 'gzip'}, maxshape = (None, None, None), got_data = True
these_kwds = {'chunks': (10, 10, 15), 'compression': 'gzip', 'dtype': dtype('<f8'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
During handling of the above exception, another exception occurred:
self = <hyperspy.tests.io.test_nexus_hdf.TestDLSNexusNoAxes object at 0x9f3798b0>
tmp_path = PosixPath('/tmp/pytest-of-buildd/pytest-0/popen-gw0/test_save_hspy1')
def test_save_hspy(self, tmp_path):
try:
self.s.save(tmp_path / 'test.hspy')
except:
> pytest.fail("unexpected error saving hdf5")
E Failed: unexpected error saving hdf5
hyperspy/tests/io/test_nexus_hdf.py:144: Failed
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
________________ TestSavingMetadataContainers.test_save_scalers ________________
[gw0] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_nexus_hdf.TestSavingMetadataContainers object at 0x9f419ef8>
tmp_path = PosixPath('/tmp/pytest-of-buildd/pytest-0/popen-gw0/test_save_scalers0')
def test_save_scalers(self, tmp_path):
s = self.s
s.original_metadata.set_item('test1', 44.0)
s.original_metadata.set_item('test2', 54.0)
s.original_metadata.set_item('test3', 64.0)
fname = tmp_path / 'test.nxs'
> s.save(fname)
hyperspy/tests/io/test_nexus_hdf.py:242:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/nexus.py:1137: in file_writer
_write_signal(sig, nxentry, signal_name, **kwds)
hyperspy/io_plugins/nexus.py:1058: in _write_signal
overwrite_dataset(nxdata, signal.data, "data", chunks=None, **kwds)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>, data = array([0.1, 0.2, 0.3]), key = 'data'
signal_axes = None, chunks = True, kwds = {'compression': 'gzip'}
maxshape = (None,), got_data = True
these_kwds = {'chunks': True, 'compression': 'gzip', 'dtype': dtype('float64'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
________________ TestSavingMetadataContainers.test_save_arrays _________________
[gw0] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_nexus_hdf.TestSavingMetadataContainers object at 0x9f419f58>
tmp_path = PosixPath('/tmp/pytest-of-buildd/pytest-0/popen-gw0/test_save_arrays0')
def test_save_arrays(self, tmp_path):
s = self.s
s.original_metadata.set_item("testarray1", ["a", 2, "b", 4, 5])
s.original_metadata.set_item("testarray2", (1, 2, 3, 4, 5))
s.original_metadata.set_item("testarray3", np.array([1, 2, 3, 4, 5]))
fname = tmp_path / 'test.nxs'
> s.save(fname)
hyperspy/tests/io/test_nexus_hdf.py:255:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/nexus.py:1137: in file_writer
_write_signal(sig, nxentry, signal_name, **kwds)
hyperspy/io_plugins/nexus.py:1058: in _write_signal
overwrite_dataset(nxdata, signal.data, "data", chunks=None, **kwds)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>, data = array([0.1, 0.2, 0.3]), key = 'data'
signal_axes = None, chunks = True, kwds = {'compression': 'gzip'}
maxshape = (None,), got_data = True
these_kwds = {'chunks': True, 'compression': 'gzip', 'dtype': dtype('float64'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
___________ TestSavingMetadataContainers.test_save_original_metadata ___________
[gw0] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.io.test_nexus_hdf.TestSavingMetadataContainers object at 0x9f419700>
tmp_path = PosixPath('/tmp/pytest-of-buildd/pytest-0/popen-gw0/test_save_original_metadata0')
def test_save_original_metadata(self, tmp_path):
s = self.s
s.original_metadata.set_item("testarray1", ["a", 2, "b", 4, 5])
s.original_metadata.set_item("testarray2", (1, 2, 3, 4, 5))
s.original_metadata.set_item("testarray3", np.array([1, 2, 3, 4, 5]))
fname = tmp_path / 'test.nxs'
> s.save(fname, save_original_metadata=False)
hyperspy/tests/io/test_nexus_hdf.py:270:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/nexus.py:1137: in file_writer
_write_signal(sig, nxentry, signal_name, **kwds)
hyperspy/io_plugins/nexus.py:1058: in _write_signal
overwrite_dataset(nxdata, signal.data, "data", chunks=None, **kwds)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>, data = array([0.1, 0.2, 0.3]), key = 'data'
signal_axes = None, chunks = True, kwds = {'compression': 'gzip'}
maxshape = (None,), got_data = True
these_kwds = {'chunks': True, 'compression': 'gzip', 'dtype': dtype('float64'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
__________________________ test_saving_multi_signals ___________________________
[gw0] linux -- Python 3.10.7 /usr/bin/python3.10
tmp_path = PosixPath('/tmp/pytest-of-buildd/pytest-0/popen-gw0/test_saving_multi_signals0')
def test_saving_multi_signals(tmp_path):
sig = hs.signals.Signal2D(np.zeros((15, 1, 40, 40)))
sig.axes_manager[0].name = "stage_y_axis"
sig.original_metadata.set_item("stage_y.value", 4.0)
sig.original_metadata.set_item("stage_y.attrs.units", "mm")
sig2 = hs.signals.Signal1D(np.zeros((30, 30, 10)))
sig2.axes_manager[0].name = "axis1"
sig2.axes_manager[1].name = "axis2"
sig2.original_metadata.set_item("stage_x.value", 8.0)
sig2.original_metadata.set_item("stage_x.attrs.units", "mm")
fname = tmp_path / 'test.nxs'
> sig.save(fname)
hyperspy/tests/io/test_nexus_hdf.py:290:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/nexus.py:1137: in file_writer
_write_signal(sig, nxentry, signal_name, **kwds)
hyperspy/io_plugins/nexus.py:1058: in _write_signal
overwrite_dataset(nxdata, signal.data, "data", chunks=None, **kwds)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>
data = array([[[[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.]... [0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.]]]])
key = 'data', signal_axes = None, chunks = True, kwds = {'compression': 'gzip'}
maxshape = (None, None, None, None), got_data = True
these_kwds = {'chunks': True, 'compression': 'gzip', 'dtype': dtype('float64'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
________________________ test_serial_date_to_ISO_format ________________________
[gw1] linux -- Python 3.10.7 /usr/bin/python3.10
def test_serial_date_to_ISO_format():
iso_1 = dtt.serial_date_to_ISO_format(serial1)
dt1_local = dt1.astimezone(tz.tzlocal())
assert iso_1[0] == dt1_local.date().isoformat()
assert iso_1[1] == dt1_local.time().isoformat()
assert iso_1[2] == dt1_local.tzname()
> iso_2 = dtt.serial_date_to_ISO_format(serial2)
hyperspy/tests/misc/test_date_time_tools.py:128:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/misc/date_time_tools.py:147: in serial_date_to_ISO_format
dt_local = dt_utc.astimezone(tz.tzlocal())
/usr/lib/python3/dist-packages/dateutil/tz/_common.py:144: in fromutc
return f(self, dt)
/usr/lib/python3/dist-packages/dateutil/tz/_common.py:261: in fromutc
_fold = self._fold_status(dt, dt_wall)
/usr/lib/python3/dist-packages/dateutil/tz/_common.py:196: in _fold_status
if self.is_ambiguous(dt_wall):
/usr/lib/python3/dist-packages/dateutil/tz/tz.py:254: in is_ambiguous
naive_dst = self._naive_is_dst(dt)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = tzlocal()
dt = datetime.datetime(2124, 3, 25, 15, 4, 48, 1, tzinfo=tzlocal())
def _naive_is_dst(self, dt):
timestamp = _datetime_to_timestamp(dt)
> return time.localtime(timestamp + time.timezone).tm_isdst
E OverflowError: timestamp out of range for platform time_t
/usr/lib/python3/dist-packages/dateutil/tz/tz.py:260: OverflowError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
________________________ test_ISO_format_to_serial_date ________________________
[gw1] linux -- Python 3.10.7 /usr/bin/python3.10
def test_ISO_format_to_serial_date():
res1 = dtt.ISO_format_to_serial_date(
dt1.date().isoformat(), dt1.time().isoformat(), timezone=dt1.tzname())
np.testing.assert_allclose(res1, serial1, atol=1E-5)
> dt = dt2.astimezone(tz.tzlocal())
hyperspy/tests/misc/test_date_time_tools.py:148:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3/dist-packages/dateutil/tz/_common.py:144: in fromutc
return f(self, dt)
/usr/lib/python3/dist-packages/dateutil/tz/_common.py:261: in fromutc
_fold = self._fold_status(dt, dt_wall)
/usr/lib/python3/dist-packages/dateutil/tz/_common.py:196: in _fold_status
if self.is_ambiguous(dt_wall):
/usr/lib/python3/dist-packages/dateutil/tz/tz.py:254: in is_ambiguous
naive_dst = self._naive_is_dst(dt)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = tzlocal()
dt = datetime.datetime(2124, 3, 25, 15, 4, 48, tzinfo=tzlocal())
def _naive_is_dst(self, dt):
timestamp = _datetime_to_timestamp(dt)
> return time.localtime(timestamp + time.timezone).tm_isdst
E OverflowError: timestamp out of range for platform time_t
/usr/lib/python3/dist-packages/dateutil/tz/tz.py:260: OverflowError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
_________ TestLoadDecompositionResults.test_load_decomposition_results _________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.learn.test_decomposition.TestLoadDecompositionResults object at 0x9d8e38c8>
def test_load_decomposition_results(self):
"""Test whether the sequence of loading learning results and then
saving the signal causes errors. See #2093.
"""
with TemporaryDirectory() as tmpdir:
self.s.decomposition()
fname1 = Path(tmpdir, "results.npz")
self.s.learning_results.save(fname1)
self.s.learning_results.load(fname1)
fname2 = Path(tmpdir, "output.hspy")
> self.s.save(fname2)
hyperspy/tests/learn/test_decomposition.py:488:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>
data = array([[1.1, 1.2, 1.4, 1.3],
[1.5, 1.5, 1.4, 1.2]]), key = 'data'
signal_axes = (1,), chunks = (2, 4), kwds = {'compression': 'gzip'}
maxshape = (None, None), got_data = True
these_kwds = {'chunks': (2, 4), 'compression': 'gzip', 'dtype': dtype('float64'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
----------------------------- Captured stdout call -----------------------------
Decomposition info:
normalize_poissonian_noise=False
algorithm=SVD
output_dimension=None
centre=None
____________________ TestModelFitBinnedGlobal.test_fit_shgo ____________________
[gw3] linux -- Python 3.10.7 /usr/bin/python3.10
self = <scipy.optimize._shgo_lib.triangulation.VertexCache object at 0x98f38af0>
x = (0, 0, 0), indexed = True
def __getitem__(self, x, indexed=True):
try:
> return self.cache[x]
E KeyError: (0, 0, 0)
/usr/lib/python3/dist-packages/scipy/optimize/_shgo_lib/triangulation.py:630: KeyError
During handling of the above exception, another exception occurred:
self = <hyperspy.tests.model.test_fitting.TestModelFitBinnedGlobal object at 0x9cc1ff58>
def test_fit_shgo(self):
pytest.importorskip("scipy", minversion="1.2.0")
> self.m.fit(optimizer="SHGO", loss_function="ls", bounded=True)
hyperspy/tests/model/test_fitting.py:290:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/model.py:1450: in fit
self.fit_output = _supported_global[optimizer](
/usr/lib/python3/dist-packages/scipy/optimize/_shgo.py:420: in shgo
shc.construct_complex()
/usr/lib/python3/dist-packages/scipy/optimize/_shgo.py:733: in construct_complex
self.iterate()
/usr/lib/python3/dist-packages/scipy/optimize/_shgo.py:876: in iterate
self.iterate_complex()
/usr/lib/python3/dist-packages/scipy/optimize/_shgo.py:895: in iterate_hypercube
self.HC = Complex(self.dim, self.func, self.args,
/usr/lib/python3/dist-packages/scipy/optimize/_shgo_lib/triangulation.py:25: in __init__
self.n_cube(dim, symmetry=symmetry)
/usr/lib/python3/dist-packages/scipy/optimize/_shgo_lib/triangulation.py:76: in n_cube
self.C0.add_vertex(self.V[origintuple])
/usr/lib/python3/dist-packages/scipy/optimize/_shgo_lib/triangulation.py:634: in __getitem__
xval = Vertex(x, bounds=self.bounds,
/usr/lib/python3/dist-packages/scipy/optimize/_shgo_lib/triangulation.py:557: in __init__
self.f = func(x_a, *func_args)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
x = array([200. , 40. , 4.5])
wrapper_args = (array([2.53283311e-14, 2.97171279e-14, 3.48524549e-14, 4.08588554e-14,
4.78812303e-14, 5.60880948e-14, 6.56753...806e-21, 1.27154683e-21, 1.04334733e-21,
8.55759529e-22, 7.01618222e-22, 5.75011139e-22, 4.71061855e-22]), None)
def function_wrapper(x, *wrapper_args):
ncalls[0] += 1
# A copy of x is sent to the user function (gh13740)
> fx = function(np.copy(x), *(wrapper_args + args))
E TypeError: BaseModel._errfunc_sq() takes from 3 to 4 positional arguments but 6 were given
/usr/lib/python3/dist-packages/scipy/optimize/_optimize.py:466: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
________ TestHistogramBinMethodsBadDataset.test_lazy_fd_logger_warning _________
[gw1] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.misc.test_hist_tools.TestHistogramBinMethodsBadDataset object at 0x9e21d5e0>
caplog = <_pytest.logging.LogCaptureFixture object at 0x98995238>
def test_fd_logger_warning(self, caplog):
with caplog.at_level(logging.WARNING):
> out = self.s1.get_histogram()
hyperspy/tests/misc/test_hist_tools.py:86:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_signals/lazy.py:448: in get_histogram
hist, bin_edges = histogram_dask(data, bins=bins, **kwargs)
hyperspy/misc/hist_tools.py:189: in histogram_dask
_, bins = _freedman_bw_dask(a, True)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
data = dask.array<reshape, shape=(32500,), dtype=float64, chunksize=(32500,), chunktype=numpy.ndarray>
return_bins = True
def _freedman_bw_dask(data, return_bins=True):
r"""Dask version of freedman_bin_width
Parameters
----------
data : dask array
the data
return_bins : bool (optional)
if True, then return the bin edges
Returns
-------
width : float
optimal bin width using Scott's rule
bins : ndarray
bin edges: returned if `return_bins` is True
Notes
-----
The optimal bin width is
.. math::
\Delta_b = \frac{2(q_{75} - q_{25})}{n^{1/3}}
where :math:`q_{N}` is the :math:`N` percent quartile of the data, and
:math:`n` is the number of data points.
"""
if not isinstance(data, da.Array):
raise TypeError("Expected a dask array")
if data.ndim != 1:
data = data.flatten()
n = data.size
v25, v75 = da.percentile(data, [25, 75])
dx = 2 * (v75 - v25) * n ** (-1.0 / 3.0)
c_dx, mx, mn = da.compute(dx, data.max(), data.min())
if return_bins:
Nbins = max(1, np.ceil((mx - mn) / c_dx))
> bins = mn + c_dx * np.arange(Nbins + 1)
E numpy.core._exceptions._ArrayMemoryError: Unable to allocate 1.36 GiB for an array with shape (182966505,) and data type float64
hyperspy/misc/hist_tools.py:312: MemoryError
---------------------------- Captured stdout setup -----------------------------
[ ] | 0% Completed | 0.0s
[########################################] | 100% Completed | 1.1s
[ ] | 0% Completed | 0.0s
[########################################] | 100% Completed | 0.1s
Initial ZLP position statistics
-------------------------------
Summary statistics
------------------
mean: 1.5e+03
std: 0
min: 1.5e+03
Q1: 1.5e+03
median: 1.5e+03
Q3: 1.5e+03
max: 1.5e+03
---------------------------- Captured stderr setup -----------------------------
0%| | 0/5 [00:00<?, ?it/s]
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
----------------------------- Captured stderr call -----------------------------
100%|██████████| 5/5 [00:00<00:00, 6.37it/s]
__ TestHistogramBinMethodsBadDataset.test_lazy_deprecation_warnings[freedman] __
[gw1] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.misc.test_hist_tools.TestHistogramBinMethodsBadDataset object at 0x9d8db700>
bins = 'freedman'
@pytest.mark.parametrize("bins", ["scotts", "freedman"])
def test_deprecation_warnings(self, bins):
with pytest.warns(
VisibleDeprecationWarning, match="has been deprecated and will be removed"
):
> _ = self.s1.get_histogram(bins=bins)
hyperspy/tests/misc/test_hist_tools.py:108:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_signals/lazy.py:448: in get_histogram
hist, bin_edges = histogram_dask(data, bins=bins, **kwargs)
hyperspy/misc/hist_tools.py:189: in histogram_dask
_, bins = _freedman_bw_dask(a, True)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
data = dask.array<reshape, shape=(32500,), dtype=float64, chunksize=(32500,), chunktype=numpy.ndarray>
return_bins = True
def _freedman_bw_dask(data, return_bins=True):
r"""Dask version of freedman_bin_width
Parameters
----------
data : dask array
the data
return_bins : bool (optional)
if True, then return the bin edges
Returns
-------
width : float
optimal bin width using Scott's rule
bins : ndarray
bin edges: returned if `return_bins` is True
Notes
-----
The optimal bin width is
.. math::
\Delta_b = \frac{2(q_{75} - q_{25})}{n^{1/3}}
where :math:`q_{N}` is the :math:`N` percent quartile of the data, and
:math:`n` is the number of data points.
"""
if not isinstance(data, da.Array):
raise TypeError("Expected a dask array")
if data.ndim != 1:
data = data.flatten()
n = data.size
v25, v75 = da.percentile(data, [25, 75])
dx = 2 * (v75 - v25) * n ** (-1.0 / 3.0)
c_dx, mx, mn = da.compute(dx, data.max(), data.min())
if return_bins:
Nbins = max(1, np.ceil((mx - mn) / c_dx))
> bins = mn + c_dx * np.arange(Nbins + 1)
E numpy.core._exceptions._ArrayMemoryError: Unable to allocate 1.36 GiB for an array with shape (182966505,) and data type float64
hyperspy/misc/hist_tools.py:312: MemoryError
---------------------------- Captured stdout setup -----------------------------
[ ] | 0% Completed | 0.0s
[########################################] | 100% Completed | 0.1s
[ ] | 0% Completed | 0.0s
[########################################] | 100% Completed | 0.1s
Initial ZLP position statistics
-------------------------------
Summary statistics
------------------
mean: 1.5e+03
std: 0
min: 1.5e+03
Q1: 1.5e+03
median: 1.5e+03
Q3: 1.5e+03
max: 1.5e+03
---------------------------- Captured stderr setup -----------------------------
0%| | 0/5 [00:00<?, ?it/s]
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
----------------------------- Captured stderr call -----------------------------
100%|██████████| 5/5 [00:00<00:00, 14.14it/s]
_________________________ TestSamfireEmpty.test_setup __________________________
[gw0] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.samfire.test_samfire.TestSamfireEmpty object at 0x9e246598>
def test_setup(self):
m = self.model
samf = m.create_samfire(workers=N_WORKERS, setup=False)
assert samf.metadata._gt_dump is None
assert samf.pool is None
> samf._setup(ipyparallel=False)
hyperspy/tests/samfire/test_samfire.py:169:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/samfire.py:226: in _setup
self.pool = SamfirePool(**kwargs)
hyperspy/samfire_utils/samfire_pool.py:122: in __init__
super(SamfirePool, self).__init__(**kwargs)
hyperspy/utils/parallel_pool.py:95: in __init__
self.setup(ipyparallel=ipyparallel)
hyperspy/utils/parallel_pool.py:164: in setup
self._setup_multiprocessing()
hyperspy/utils/parallel_pool.py:139: in _setup_multiprocessing
self.pool = Pool(processes=self.num_workers)
/usr/lib/python3.10/multiprocessing/context.py:119: in Pool
return Pool(processes, initializer, initargs, maxtasksperchild,
/usr/lib/python3.10/multiprocessing/pool.py:191: in __init__
self._setup_queues()
/usr/lib/python3.10/multiprocessing/pool.py:346: in _setup_queues
self._inqueue = self._ctx.SimpleQueue()
/usr/lib/python3.10/multiprocessing/context.py:113: in SimpleQueue
return SimpleQueue(ctx=self.get_context())
/usr/lib/python3.10/multiprocessing/queues.py:341: in __init__
self._rlock = ctx.Lock()
/usr/lib/python3.10/multiprocessing/context.py:68: in Lock
return Lock(ctx=self.get_context())
/usr/lib/python3.10/multiprocessing/synchronize.py:162: in __init__
SemLock.__init__(self, SEMAPHORE, 1, 1, ctx=ctx)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Lock(owner=unknown)>, kind = 1, value = 1, maxvalue = 1
def __init__(self, kind, value, maxvalue, *, ctx):
if ctx is None:
ctx = context._default_context.get_context()
name = ctx.get_start_method()
unlink_now = sys.platform == 'win32' or name == 'fork'
for i in range(100):
try:
> sl = self._semlock = _multiprocessing.SemLock(
kind, value, maxvalue, self._make_name(),
unlink_now)
E FileNotFoundError: [Errno 2] No such file or directory
/usr/lib/python3.10/multiprocessing/synchronize.py:57: FileNotFoundError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
___________________ TestModelSaving.test_save_and_load_model ___________________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.model.test_model_storing.TestModelSaving object at 0x9e23d760>
def test_save_and_load_model(self):
m = self.m
> m.save('tmp.hdf5', overwrite=True)
hyperspy/tests/model/test_model_storing.py:156:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/model.py:303: in save
self.signal.save(file_name, **kwargs)
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>
data = array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
17, 18, 19, 20, 21, 22, 23, 24, 25, ...72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84,
85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99])
key = 'data', signal_axes = (0,), chunks = (100,)
kwds = {'compression': 'gzip'}, maxshape = (None,), got_data = True
these_kwds = {'chunks': (100,), 'compression': 'gzip', 'dtype': dtype('int32'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
_________________ TestEELSModelSaving.test_save_and_load_model _________________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.model.test_model_storing.TestEELSModelSaving object at 0x9e23d958>
def test_save_and_load_model(self):
m = self.m
> m.save('tmp.hdf5', overwrite=True)
hyperspy/tests/model/test_model_storing.py:187:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/model.py:303: in save
self.signal.save(file_name, **kwargs)
hyperspy/signal.py:2748: in save
io.save(filename, self, overwrite=overwrite, **kwds)
hyperspy/io.py:756: in save
writer.file_writer(str(filename), signal, **kwds)
hyperspy/io_plugins/hspy.py:784: in file_writer
write_signal(signal, expg, **kwds)
hyperspy/io_plugins/hspy.py:727: in write_signal
overwrite_dataset(group, signal.data, 'data',
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
group = <Closed HDF5 group>
data = array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
17, 18, 19, 20, 21, 22, 23, 24, 25, ...72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84,
85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99])
key = 'data', signal_axes = (0,), chunks = (100,)
kwds = {'compression': 'gzip'}, maxshape = (None,), got_data = True
these_kwds = {'chunks': (100,), 'compression': 'gzip', 'dtype': dtype('int32'), 'exact': True, ...}
dset = <Closed HDF5 dataset>
def overwrite_dataset(group, data, key, signal_axes=None, chunks=None, **kwds):
if chunks is None:
if signal_axes is None:
# Use automatic h5py chunking
chunks = True
else:
# Optimise the chunking to contain at least one signal per chunk
chunks = get_signal_chunks(data.shape, data.dtype, signal_axes)
if np.issubdtype(data.dtype, np.dtype('U')):
# Saving numpy unicode type is not supported in h5py
data = data.astype(np.dtype('S'))
if data.dtype == np.dtype('O'):
# For saving ragged array
# http://docs.h5py.org/en/stable/special.html#arbitrary-vlen-data
group.require_dataset(key,
chunks,
dtype=h5py.special_dtype(vlen=data[0].dtype),
**kwds)
group[key][:] = data[:]
maxshape = tuple(None for _ in data.shape)
got_data = False
while not got_data:
try:
these_kwds = kwds.copy()
these_kwds.update(dict(shape=data.shape,
dtype=data.dtype,
exact=True,
maxshape=maxshape,
chunks=chunks,
shuffle=True,))
# If chunks is True, the `chunks` attribute of `dset` below
# contains the chunk shape guessed by h5py
dset = group.require_dataset(key, **these_kwds)
got_data = True
except TypeError:
# if the shape or dtype/etc do not match,
# we delete the old one and create new in the next loop run
del group[key]
> if dset == data:
E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
hyperspy/io_plugins/hspy.py:592: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
_______________ TestFindPeaks2D.test_find_peaks[True-dense-stat] _______________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.signal.test_find_peaks2D.TestFindPeaks2D object at 0x9c9d88e0>
method = 'stat', dataset_name = 'dense', parallel = True
@pytest.mark.parametrize('method', PEAK_METHODS)
@pytest.mark.parametrize('dataset_name', DATASETS_NAME)
@pytest.mark.parametrize('parallel', [True, False])
def test_find_peaks(self, method, dataset_name, parallel):
if method == 'stat':
pytest.importorskip("sklearn")
dataset = getattr(self, dataset_name)
# Parallel is not used in `map` for lazy signal
if parallel and dataset._lazy:
pytest.skip("Parallel=True is ignored for lazy signal.")
if method == 'template_matching':
disc = np.zeros((11, 11))
disc[2:9, 2:9] = 0.5
disc[4:7, 4:7] = 0.75
disc[5, 5] = 1
peaks = dataset.find_peaks(method=method, parallel=parallel,
interactive=False, template=disc)
else:
> peaks = dataset.find_peaks(method=method, parallel=parallel,
interactive=False)
hyperspy/tests/signal/test_find_peaks2D.py:121:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_signals/signal2d.py:925: in find_peaks
peaks = self.map(method_func, show_progressbar=show_progressbar,
hyperspy/signal.py:4508: in map
res = self._map_iterate(function, iterating_kwargs=ndkwargs,
hyperspy/signal.py:4643: in _map_iterate
for ind, res in zip(
/usr/lib/python3.10/concurrent/futures/_base.py:621: in result_iterator
yield _result_or_cancel(fs.pop())
/usr/lib/python3.10/concurrent/futures/_base.py:319: in _result_or_cancel
return fut.result(timeout)
/usr/lib/python3.10/concurrent/futures/_base.py:458: in result
return self.__get_result()
/usr/lib/python3.10/concurrent/futures/_base.py:403: in __get_result
raise self._exception
/usr/lib/python3.10/concurrent/futures/thread.py:58: in run
result = self.fn(*self.args, **self.kwargs)
hyperspy/misc/utils.py:1090: in func
return function(dat, **these_kwargs)
hyperspy/utils/peakfinders2D.py:454: in find_peaks_stat
return clean_peaks(stat_peak_finder(z, convergence_ratio))
hyperspy/utils/peakfinders2D.py:437: in stat_peak_finder
image, peaks_curr = _peak_find_once(image) # 4-7
hyperspy/utils/peakfinders2D.py:427: in _peak_find_once
peaks = separate_peaks(image) # 6
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
binarised_image = array([[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
...,
[1, 1, 0, ..., 1, 1, 1],
[0, 0, 0, ..., 1, 1, 1],
[0, 0, 0, ..., 1, 1, 1]])
def separate_peaks(binarised_image):
"""Identify adjacent 'on' coordinates via DBSCAN."""
bi = binarised_image.astype("bool")
coordinates = np.indices(bi.shape).reshape(2, -1).T[bi.flatten()]
> db = import_sklearn.sklearn.cluster.DBSCAN(2, 3)
E TypeError: DBSCAN.__init__() takes from 1 to 2 positional arguments but 3 were given
hyperspy/utils/peakfinders2D.py:415: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
----------------------------- Captured stderr call -----------------------------
0%| | 0/1 [00:00<?, ?it/s]
______ TestFindPeaks2D.test_find_peaks[True-dense-difference_of_gaussian] ______
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.signal.test_find_peaks2D.TestFindPeaks2D object at 0x9c9d8970>
method = 'difference_of_gaussian', dataset_name = 'dense', parallel = True
@pytest.mark.parametrize('method', PEAK_METHODS)
@pytest.mark.parametrize('dataset_name', DATASETS_NAME)
@pytest.mark.parametrize('parallel', [True, False])
def test_find_peaks(self, method, dataset_name, parallel):
if method == 'stat':
pytest.importorskip("sklearn")
dataset = getattr(self, dataset_name)
# Parallel is not used in `map` for lazy signal
if parallel and dataset._lazy:
pytest.skip("Parallel=True is ignored for lazy signal.")
if method == 'template_matching':
disc = np.zeros((11, 11))
disc[2:9, 2:9] = 0.5
disc[4:7, 4:7] = 0.75
disc[5, 5] = 1
peaks = dataset.find_peaks(method=method, parallel=parallel,
interactive=False, template=disc)
else:
> peaks = dataset.find_peaks(method=method, parallel=parallel,
interactive=False)
hyperspy/tests/signal/test_find_peaks2D.py:121:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_signals/signal2d.py:925: in find_peaks
peaks = self.map(method_func, show_progressbar=show_progressbar,
hyperspy/signal.py:4508: in map
res = self._map_iterate(function, iterating_kwargs=ndkwargs,
hyperspy/signal.py:4643: in _map_iterate
for ind, res in zip(
/usr/lib/python3.10/concurrent/futures/_base.py:621: in result_iterator
yield _result_or_cancel(fs.pop())
/usr/lib/python3.10/concurrent/futures/_base.py:319: in _result_or_cancel
return fut.result(timeout)
/usr/lib/python3.10/concurrent/futures/_base.py:458: in result
return self.__get_result()
/usr/lib/python3.10/concurrent/futures/_base.py:403: in __get_result
raise self._exception
/usr/lib/python3.10/concurrent/futures/thread.py:58: in run
result = self.fn(*self.args, **self.kwargs)
hyperspy/misc/utils.py:1090: in func
return function(dat, **these_kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
z = array([[0.70165162, 0.71450877, 0.72106518, ..., 0.52227921, 0.52947204,
0.54271189],
[0.76271489, 0.77...23,
0.96811211],
[0.80960236, 0.76366337, 0.71725186, ..., 0.98919486, 0.97610825,
0.95047115]])
min_sigma = 1.0, max_sigma = 50.0, sigma_ratio = 1.6, threshold = 0.2
overlap = 0.5, exclude_border = False
def find_peaks_dog(z, min_sigma=1., max_sigma=50., sigma_ratio=1.6,
threshold=0.2, overlap=0.5, exclude_border=False):
"""Method to locate peaks via the Difference of Gaussian Matrices method.
This function wraps :py:func:`skimage.feature.blob_dog` function and
sorts the results for consistency with other peak finding methods.
Parameters
----------
z : numpy.ndarray
2-d array of intensities
min_sigma, max_sigma, sigma_ratio, threshold, overlap, exclude_border :
Additional parameters to be passed to the algorithm. See `blob_dog`
documentation for details:
http://scikit-image.org/docs/dev/api/skimage.feature.html#blob-dog
Returns
-------
peaks : numpy.ndarray
(n_peaks, 2)
Peak pixel coordinates.
Notes
-----
While highly effective at finding even very faint peaks, this method is
sensitive to fluctuations in intensity near the edges of the image.
"""
z = z / np.max(z)
blobs = blob_dog(z, min_sigma=min_sigma, max_sigma=max_sigma,
sigma_ratio=sigma_ratio, threshold=threshold,
overlap=overlap, exclude_border=exclude_border)
try:
centers = np.round(blobs[:, :2]).astype(int)
except IndexError:
return NO_PEAKS
clean_centers = []
for center in centers:
if len(np.intersect1d(center, (0, 1) + z.shape + tuple(
c - 1 for c in z.shape))) > 0:
continue
clean_centers.append(center)
peaks = np.array(clean_centers)
> ind = np.lexsort((peaks[:,0], peaks[:,1]))
E IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed
hyperspy/utils/peakfinders2D.py:500: IndexError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
----------------------------- Captured stderr call -----------------------------
0%| | 0/1 [00:00<?, ?it/s][A
--------------------------- Captured stderr teardown ---------------------------
0%| | 0/1 [00:13<?, ?it/s]
___________ TestFindPeaks2D.test_find_peaks[True-sparse_nav0d-stat] ____________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.signal.test_find_peaks2D.TestFindPeaks2D object at 0x9c9d8b20>
method = 'stat', dataset_name = 'sparse_nav0d', parallel = True
@pytest.mark.parametrize('method', PEAK_METHODS)
@pytest.mark.parametrize('dataset_name', DATASETS_NAME)
@pytest.mark.parametrize('parallel', [True, False])
def test_find_peaks(self, method, dataset_name, parallel):
if method == 'stat':
pytest.importorskip("sklearn")
dataset = getattr(self, dataset_name)
# Parallel is not used in `map` for lazy signal
if parallel and dataset._lazy:
pytest.skip("Parallel=True is ignored for lazy signal.")
if method == 'template_matching':
disc = np.zeros((11, 11))
disc[2:9, 2:9] = 0.5
disc[4:7, 4:7] = 0.75
disc[5, 5] = 1
peaks = dataset.find_peaks(method=method, parallel=parallel,
interactive=False, template=disc)
else:
> peaks = dataset.find_peaks(method=method, parallel=parallel,
interactive=False)
hyperspy/tests/signal/test_find_peaks2D.py:121:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_signals/signal2d.py:925: in find_peaks
peaks = self.map(method_func, show_progressbar=show_progressbar,
hyperspy/signal.py:4508: in map
res = self._map_iterate(function, iterating_kwargs=ndkwargs,
hyperspy/signal.py:4643: in _map_iterate
for ind, res in zip(
/usr/lib/python3.10/concurrent/futures/_base.py:621: in result_iterator
yield _result_or_cancel(fs.pop())
/usr/lib/python3.10/concurrent/futures/_base.py:319: in _result_or_cancel
return fut.result(timeout)
/usr/lib/python3.10/concurrent/futures/_base.py:458: in result
return self.__get_result()
/usr/lib/python3.10/concurrent/futures/_base.py:403: in __get_result
raise self._exception
/usr/lib/python3.10/concurrent/futures/thread.py:58: in run
result = self.fn(*self.args, **self.kwargs)
hyperspy/misc/utils.py:1090: in func
return function(dat, **these_kwargs)
hyperspy/utils/peakfinders2D.py:454: in find_peaks_stat
return clean_peaks(stat_peak_finder(z, convergence_ratio))
hyperspy/utils/peakfinders2D.py:437: in stat_peak_finder
image, peaks_curr = _peak_find_once(image) # 4-7
hyperspy/utils/peakfinders2D.py:427: in _peak_find_once
peaks = separate_peaks(image) # 6
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
binarised_image = array([[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
...,
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0]])
def separate_peaks(binarised_image):
"""Identify adjacent 'on' coordinates via DBSCAN."""
bi = binarised_image.astype("bool")
coordinates = np.indices(bi.shape).reshape(2, -1).T[bi.flatten()]
> db = import_sklearn.sklearn.cluster.DBSCAN(2, 3)
E TypeError: DBSCAN.__init__() takes from 1 to 2 positional arguments but 3 were given
hyperspy/utils/peakfinders2D.py:415: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
----------------------------- Captured stderr call -----------------------------
0%| | 0/1 [00:00<?, ?it/s]
___________ TestFindPeaks2D.test_find_peaks[True-sparse_nav1d-stat] ____________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.signal.test_find_peaks2D.TestFindPeaks2D object at 0x9c9d8d60>
method = 'stat', dataset_name = 'sparse_nav1d', parallel = True
@pytest.mark.parametrize('method', PEAK_METHODS)
@pytest.mark.parametrize('dataset_name', DATASETS_NAME)
@pytest.mark.parametrize('parallel', [True, False])
def test_find_peaks(self, method, dataset_name, parallel):
if method == 'stat':
pytest.importorskip("sklearn")
dataset = getattr(self, dataset_name)
# Parallel is not used in `map` for lazy signal
if parallel and dataset._lazy:
pytest.skip("Parallel=True is ignored for lazy signal.")
if method == 'template_matching':
disc = np.zeros((11, 11))
disc[2:9, 2:9] = 0.5
disc[4:7, 4:7] = 0.75
disc[5, 5] = 1
peaks = dataset.find_peaks(method=method, parallel=parallel,
interactive=False, template=disc)
else:
> peaks = dataset.find_peaks(method=method, parallel=parallel,
interactive=False)
hyperspy/tests/signal/test_find_peaks2D.py:121:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_signals/signal2d.py:925: in find_peaks
peaks = self.map(method_func, show_progressbar=show_progressbar,
hyperspy/signal.py:4508: in map
res = self._map_iterate(function, iterating_kwargs=ndkwargs,
hyperspy/signal.py:4643: in _map_iterate
for ind, res in zip(
/usr/lib/python3.10/concurrent/futures/_base.py:621: in result_iterator
yield _result_or_cancel(fs.pop())
/usr/lib/python3.10/concurrent/futures/_base.py:319: in _result_or_cancel
return fut.result(timeout)
/usr/lib/python3.10/concurrent/futures/_base.py:458: in result
return self.__get_result()
/usr/lib/python3.10/concurrent/futures/_base.py:403: in __get_result
raise self._exception
/usr/lib/python3.10/concurrent/futures/thread.py:58: in run
result = self.fn(*self.args, **self.kwargs)
hyperspy/misc/utils.py:1090: in func
return function(dat, **these_kwargs)
hyperspy/utils/peakfinders2D.py:454: in find_peaks_stat
return clean_peaks(stat_peak_finder(z, convergence_ratio))
hyperspy/utils/peakfinders2D.py:437: in stat_peak_finder
image, peaks_curr = _peak_find_once(image) # 4-7
hyperspy/utils/peakfinders2D.py:427: in _peak_find_once
peaks = separate_peaks(image) # 6
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
binarised_image = array([[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
...,
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0]])
def separate_peaks(binarised_image):
"""Identify adjacent 'on' coordinates via DBSCAN."""
bi = binarised_image.astype("bool")
coordinates = np.indices(bi.shape).reshape(2, -1).T[bi.flatten()]
> db = import_sklearn.sklearn.cluster.DBSCAN(2, 3)
E TypeError: DBSCAN.__init__() takes from 1 to 2 positional arguments but 3 were given
hyperspy/utils/peakfinders2D.py:415: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
----------------------------- Captured stderr call -----------------------------
0%| | 0/2 [00:00<?, ?it/s][A[A
___________ TestFindPeaks2D.test_find_peaks[True-sparse_nav2d-stat] ____________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.signal.test_find_peaks2D.TestFindPeaks2D object at 0x9c9d8fa0>
method = 'stat', dataset_name = 'sparse_nav2d', parallel = True
@pytest.mark.parametrize('method', PEAK_METHODS)
@pytest.mark.parametrize('dataset_name', DATASETS_NAME)
@pytest.mark.parametrize('parallel', [True, False])
def test_find_peaks(self, method, dataset_name, parallel):
if method == 'stat':
pytest.importorskip("sklearn")
dataset = getattr(self, dataset_name)
# Parallel is not used in `map` for lazy signal
if parallel and dataset._lazy:
pytest.skip("Parallel=True is ignored for lazy signal.")
if method == 'template_matching':
disc = np.zeros((11, 11))
disc[2:9, 2:9] = 0.5
disc[4:7, 4:7] = 0.75
disc[5, 5] = 1
peaks = dataset.find_peaks(method=method, parallel=parallel,
interactive=False, template=disc)
else:
> peaks = dataset.find_peaks(method=method, parallel=parallel,
interactive=False)
hyperspy/tests/signal/test_find_peaks2D.py:121:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_signals/signal2d.py:925: in find_peaks
peaks = self.map(method_func, show_progressbar=show_progressbar,
hyperspy/signal.py:4508: in map
res = self._map_iterate(function, iterating_kwargs=ndkwargs,
hyperspy/signal.py:4643: in _map_iterate
for ind, res in zip(
/usr/lib/python3.10/concurrent/futures/_base.py:621: in result_iterator
yield _result_or_cancel(fs.pop())
/usr/lib/python3.10/concurrent/futures/_base.py:319: in _result_or_cancel
return fut.result(timeout)
/usr/lib/python3.10/concurrent/futures/_base.py:458: in result
return self.__get_result()
/usr/lib/python3.10/concurrent/futures/_base.py:403: in __get_result
raise self._exception
/usr/lib/python3.10/concurrent/futures/thread.py:58: in run
result = self.fn(*self.args, **self.kwargs)
hyperspy/misc/utils.py:1090: in func
return function(dat, **these_kwargs)
hyperspy/utils/peakfinders2D.py:454: in find_peaks_stat
return clean_peaks(stat_peak_finder(z, convergence_ratio))
hyperspy/utils/peakfinders2D.py:437: in stat_peak_finder
image, peaks_curr = _peak_find_once(image) # 4-7
hyperspy/utils/peakfinders2D.py:427: in _peak_find_once
peaks = separate_peaks(image) # 6
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
binarised_image = array([[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
...,
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0]])
def separate_peaks(binarised_image):
"""Identify adjacent 'on' coordinates via DBSCAN."""
bi = binarised_image.astype("bool")
coordinates = np.indices(bi.shape).reshape(2, -1).T[bi.flatten()]
> db = import_sklearn.sklearn.cluster.DBSCAN(2, 3)
E TypeError: DBSCAN.__init__() takes from 1 to 2 positional arguments but 3 were given
hyperspy/utils/peakfinders2D.py:415: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
----------------------------- Captured stderr call -----------------------------
0%| | 0/6 [00:00<?, ?it/s][A[A[A
______________ TestFindPeaks2D.test_find_peaks[False-dense-stat] _______________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.signal.test_find_peaks2D.TestFindPeaks2D object at 0x9c9f5208>
method = 'stat', dataset_name = 'dense', parallel = False
@pytest.mark.parametrize('method', PEAK_METHODS)
@pytest.mark.parametrize('dataset_name', DATASETS_NAME)
@pytest.mark.parametrize('parallel', [True, False])
def test_find_peaks(self, method, dataset_name, parallel):
if method == 'stat':
pytest.importorskip("sklearn")
dataset = getattr(self, dataset_name)
# Parallel is not used in `map` for lazy signal
if parallel and dataset._lazy:
pytest.skip("Parallel=True is ignored for lazy signal.")
if method == 'template_matching':
disc = np.zeros((11, 11))
disc[2:9, 2:9] = 0.5
disc[4:7, 4:7] = 0.75
disc[5, 5] = 1
peaks = dataset.find_peaks(method=method, parallel=parallel,
interactive=False, template=disc)
else:
> peaks = dataset.find_peaks(method=method, parallel=parallel,
interactive=False)
hyperspy/tests/signal/test_find_peaks2D.py:121:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_signals/signal2d.py:925: in find_peaks
peaks = self.map(method_func, show_progressbar=show_progressbar,
hyperspy/signal.py:4508: in map
res = self._map_iterate(function, iterating_kwargs=ndkwargs,
hyperspy/signal.py:4667: in _map_iterate
for ind, res in zip(range(res_data.size), map(func, zip(*iterators))):
hyperspy/misc/utils.py:1090: in func
return function(dat, **these_kwargs)
hyperspy/utils/peakfinders2D.py:454: in find_peaks_stat
return clean_peaks(stat_peak_finder(z, convergence_ratio))
hyperspy/utils/peakfinders2D.py:437: in stat_peak_finder
image, peaks_curr = _peak_find_once(image) # 4-7
hyperspy/utils/peakfinders2D.py:427: in _peak_find_once
peaks = separate_peaks(image) # 6
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
binarised_image = array([[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
...,
[1, 1, 0, ..., 1, 1, 1],
[0, 0, 0, ..., 1, 1, 1],
[0, 0, 0, ..., 1, 1, 1]])
def separate_peaks(binarised_image):
"""Identify adjacent 'on' coordinates via DBSCAN."""
bi = binarised_image.astype("bool")
coordinates = np.indices(bi.shape).reshape(2, -1).T[bi.flatten()]
> db = import_sklearn.sklearn.cluster.DBSCAN(2, 3)
E TypeError: DBSCAN.__init__() takes from 1 to 2 positional arguments but 3 were given
hyperspy/utils/peakfinders2D.py:415: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
----------------------------- Captured stderr call -----------------------------
0%| | 0/1 [00:00<?, ?it/s][A[A[A[A
_____ TestFindPeaks2D.test_find_peaks[False-dense-difference_of_gaussian] ______
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.signal.test_find_peaks2D.TestFindPeaks2D object at 0x9c9f5298>
method = 'difference_of_gaussian', dataset_name = 'dense', parallel = False
@pytest.mark.parametrize('method', PEAK_METHODS)
@pytest.mark.parametrize('dataset_name', DATASETS_NAME)
@pytest.mark.parametrize('parallel', [True, False])
def test_find_peaks(self, method, dataset_name, parallel):
if method == 'stat':
pytest.importorskip("sklearn")
dataset = getattr(self, dataset_name)
# Parallel is not used in `map` for lazy signal
if parallel and dataset._lazy:
pytest.skip("Parallel=True is ignored for lazy signal.")
if method == 'template_matching':
disc = np.zeros((11, 11))
disc[2:9, 2:9] = 0.5
disc[4:7, 4:7] = 0.75
disc[5, 5] = 1
peaks = dataset.find_peaks(method=method, parallel=parallel,
interactive=False, template=disc)
else:
> peaks = dataset.find_peaks(method=method, parallel=parallel,
interactive=False)
hyperspy/tests/signal/test_find_peaks2D.py:121:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_signals/signal2d.py:925: in find_peaks
peaks = self.map(method_func, show_progressbar=show_progressbar,
hyperspy/signal.py:4508: in map
res = self._map_iterate(function, iterating_kwargs=ndkwargs,
hyperspy/signal.py:4667: in _map_iterate
for ind, res in zip(range(res_data.size), map(func, zip(*iterators))):
hyperspy/misc/utils.py:1090: in func
return function(dat, **these_kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
z = array([[0.70165162, 0.71450877, 0.72106518, ..., 0.52227921, 0.52947204,
0.54271189],
[0.76271489, 0.77...23,
0.96811211],
[0.80960236, 0.76366337, 0.71725186, ..., 0.98919486, 0.97610825,
0.95047115]])
min_sigma = 1.0, max_sigma = 50.0, sigma_ratio = 1.6, threshold = 0.2
overlap = 0.5, exclude_border = False
def find_peaks_dog(z, min_sigma=1., max_sigma=50., sigma_ratio=1.6,
threshold=0.2, overlap=0.5, exclude_border=False):
"""Method to locate peaks via the Difference of Gaussian Matrices method.
This function wraps :py:func:`skimage.feature.blob_dog` function and
sorts the results for consistency with other peak finding methods.
Parameters
----------
z : numpy.ndarray
2-d array of intensities
min_sigma, max_sigma, sigma_ratio, threshold, overlap, exclude_border :
Additional parameters to be passed to the algorithm. See `blob_dog`
documentation for details:
http://scikit-image.org/docs/dev/api/skimage.feature.html#blob-dog
Returns
-------
peaks : numpy.ndarray
(n_peaks, 2)
Peak pixel coordinates.
Notes
-----
While highly effective at finding even very faint peaks, this method is
sensitive to fluctuations in intensity near the edges of the image.
"""
z = z / np.max(z)
blobs = blob_dog(z, min_sigma=min_sigma, max_sigma=max_sigma,
sigma_ratio=sigma_ratio, threshold=threshold,
overlap=overlap, exclude_border=exclude_border)
try:
centers = np.round(blobs[:, :2]).astype(int)
except IndexError:
return NO_PEAKS
clean_centers = []
for center in centers:
if len(np.intersect1d(center, (0, 1) + z.shape + tuple(
c - 1 for c in z.shape))) > 0:
continue
clean_centers.append(center)
peaks = np.array(clean_centers)
> ind = np.lexsort((peaks[:,0], peaks[:,1]))
E IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed
hyperspy/utils/peakfinders2D.py:500: IndexError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
----------------------------- Captured stderr call -----------------------------
0%| | 0/1 [00:00<?, ?it/s][A[A[A[A[A
___________ TestFindPeaks2D.test_find_peaks[False-sparse_nav0d-stat] ___________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.signal.test_find_peaks2D.TestFindPeaks2D object at 0x9c9f5448>
method = 'stat', dataset_name = 'sparse_nav0d', parallel = False
@pytest.mark.parametrize('method', PEAK_METHODS)
@pytest.mark.parametrize('dataset_name', DATASETS_NAME)
@pytest.mark.parametrize('parallel', [True, False])
def test_find_peaks(self, method, dataset_name, parallel):
if method == 'stat':
pytest.importorskip("sklearn")
dataset = getattr(self, dataset_name)
# Parallel is not used in `map` for lazy signal
if parallel and dataset._lazy:
pytest.skip("Parallel=True is ignored for lazy signal.")
if method == 'template_matching':
disc = np.zeros((11, 11))
disc[2:9, 2:9] = 0.5
disc[4:7, 4:7] = 0.75
disc[5, 5] = 1
peaks = dataset.find_peaks(method=method, parallel=parallel,
interactive=False, template=disc)
else:
> peaks = dataset.find_peaks(method=method, parallel=parallel,
interactive=False)
hyperspy/tests/signal/test_find_peaks2D.py:121:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_signals/signal2d.py:925: in find_peaks
peaks = self.map(method_func, show_progressbar=show_progressbar,
hyperspy/signal.py:4508: in map
res = self._map_iterate(function, iterating_kwargs=ndkwargs,
hyperspy/signal.py:4667: in _map_iterate
for ind, res in zip(range(res_data.size), map(func, zip(*iterators))):
hyperspy/misc/utils.py:1090: in func
return function(dat, **these_kwargs)
hyperspy/utils/peakfinders2D.py:454: in find_peaks_stat
return clean_peaks(stat_peak_finder(z, convergence_ratio))
hyperspy/utils/peakfinders2D.py:437: in stat_peak_finder
image, peaks_curr = _peak_find_once(image) # 4-7
hyperspy/utils/peakfinders2D.py:427: in _peak_find_once
peaks = separate_peaks(image) # 6
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
binarised_image = array([[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
...,
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0]])
def separate_peaks(binarised_image):
"""Identify adjacent 'on' coordinates via DBSCAN."""
bi = binarised_image.astype("bool")
coordinates = np.indices(bi.shape).reshape(2, -1).T[bi.flatten()]
> db = import_sklearn.sklearn.cluster.DBSCAN(2, 3)
E TypeError: DBSCAN.__init__() takes from 1 to 2 positional arguments but 3 were given
hyperspy/utils/peakfinders2D.py:415: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
----------------------------- Captured stderr call -----------------------------
0%| | 0/1 [00:00<?, ?it/s][A[A[A[A[A[A
___________ TestFindPeaks2D.test_find_peaks[False-sparse_nav1d-stat] ___________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.signal.test_find_peaks2D.TestFindPeaks2D object at 0x9c9f5688>
method = 'stat', dataset_name = 'sparse_nav1d', parallel = False
@pytest.mark.parametrize('method', PEAK_METHODS)
@pytest.mark.parametrize('dataset_name', DATASETS_NAME)
@pytest.mark.parametrize('parallel', [True, False])
def test_find_peaks(self, method, dataset_name, parallel):
if method == 'stat':
pytest.importorskip("sklearn")
dataset = getattr(self, dataset_name)
# Parallel is not used in `map` for lazy signal
if parallel and dataset._lazy:
pytest.skip("Parallel=True is ignored for lazy signal.")
if method == 'template_matching':
disc = np.zeros((11, 11))
disc[2:9, 2:9] = 0.5
disc[4:7, 4:7] = 0.75
disc[5, 5] = 1
peaks = dataset.find_peaks(method=method, parallel=parallel,
interactive=False, template=disc)
else:
> peaks = dataset.find_peaks(method=method, parallel=parallel,
interactive=False)
hyperspy/tests/signal/test_find_peaks2D.py:121:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_signals/signal2d.py:925: in find_peaks
peaks = self.map(method_func, show_progressbar=show_progressbar,
hyperspy/signal.py:4508: in map
res = self._map_iterate(function, iterating_kwargs=ndkwargs,
hyperspy/signal.py:4667: in _map_iterate
for ind, res in zip(range(res_data.size), map(func, zip(*iterators))):
hyperspy/misc/utils.py:1090: in func
return function(dat, **these_kwargs)
hyperspy/utils/peakfinders2D.py:454: in find_peaks_stat
return clean_peaks(stat_peak_finder(z, convergence_ratio))
hyperspy/utils/peakfinders2D.py:437: in stat_peak_finder
image, peaks_curr = _peak_find_once(image) # 4-7
hyperspy/utils/peakfinders2D.py:427: in _peak_find_once
peaks = separate_peaks(image) # 6
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
binarised_image = array([[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
...,
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0]])
def separate_peaks(binarised_image):
"""Identify adjacent 'on' coordinates via DBSCAN."""
bi = binarised_image.astype("bool")
coordinates = np.indices(bi.shape).reshape(2, -1).T[bi.flatten()]
> db = import_sklearn.sklearn.cluster.DBSCAN(2, 3)
E TypeError: DBSCAN.__init__() takes from 1 to 2 positional arguments but 3 were given
hyperspy/utils/peakfinders2D.py:415: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
----------------------------- Captured stderr call -----------------------------
0%| | 0/2 [00:00<?, ?it/s]
___________ TestFindPeaks2D.test_find_peaks[False-sparse_nav2d-stat] ___________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.signal.test_find_peaks2D.TestFindPeaks2D object at 0x9c9f58c8>
method = 'stat', dataset_name = 'sparse_nav2d', parallel = False
@pytest.mark.parametrize('method', PEAK_METHODS)
@pytest.mark.parametrize('dataset_name', DATASETS_NAME)
@pytest.mark.parametrize('parallel', [True, False])
def test_find_peaks(self, method, dataset_name, parallel):
if method == 'stat':
pytest.importorskip("sklearn")
dataset = getattr(self, dataset_name)
# Parallel is not used in `map` for lazy signal
if parallel and dataset._lazy:
pytest.skip("Parallel=True is ignored for lazy signal.")
if method == 'template_matching':
disc = np.zeros((11, 11))
disc[2:9, 2:9] = 0.5
disc[4:7, 4:7] = 0.75
disc[5, 5] = 1
peaks = dataset.find_peaks(method=method, parallel=parallel,
interactive=False, template=disc)
else:
> peaks = dataset.find_peaks(method=method, parallel=parallel,
interactive=False)
hyperspy/tests/signal/test_find_peaks2D.py:121:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_signals/signal2d.py:925: in find_peaks
peaks = self.map(method_func, show_progressbar=show_progressbar,
hyperspy/signal.py:4508: in map
res = self._map_iterate(function, iterating_kwargs=ndkwargs,
hyperspy/signal.py:4667: in _map_iterate
for ind, res in zip(range(res_data.size), map(func, zip(*iterators))):
hyperspy/misc/utils.py:1090: in func
return function(dat, **these_kwargs)
hyperspy/utils/peakfinders2D.py:454: in find_peaks_stat
return clean_peaks(stat_peak_finder(z, convergence_ratio))
hyperspy/utils/peakfinders2D.py:437: in stat_peak_finder
image, peaks_curr = _peak_find_once(image) # 4-7
hyperspy/utils/peakfinders2D.py:427: in _peak_find_once
peaks = separate_peaks(image) # 6
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
binarised_image = array([[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
...,
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0]])
def separate_peaks(binarised_image):
"""Identify adjacent 'on' coordinates via DBSCAN."""
bi = binarised_image.astype("bool")
coordinates = np.indices(bi.shape).reshape(2, -1).T[bi.flatten()]
> db = import_sklearn.sklearn.cluster.DBSCAN(2, 3)
E TypeError: DBSCAN.__init__() takes from 1 to 2 positional arguments but 3 were given
hyperspy/utils/peakfinders2D.py:415: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
----------------------------- Captured stderr call -----------------------------
0%| | 0/6 [00:00<?, ?it/s][A
______________ TestFindPeaks2D.test_gets_right_answer[True-stat] _______________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.signal.test_find_peaks2D.TestFindPeaks2D object at 0x9c9f5d48>
method = 'stat', parallel = True
@pytest.mark.parametrize('method', PEAK_METHODS)
@pytest.mark.parametrize('parallel', [True, False])
def test_gets_right_answer(self, method, parallel):
if method == 'stat':
pytest.importorskip("sklearn")
ans = np.empty((1,), dtype=object)
ans[0] = np.array([[self.xref, self.yref]])
if method == 'template_matching':
disc = np.zeros((5, 5))
disc[1:4, 1:4] = 0.5
disc[2,2] = 1
peaks = self.ref.find_peaks(method=method, parallel=parallel,
interactive=False, template=disc)
else:
> peaks = self.ref.find_peaks(method=method, parallel=parallel,
interactive=False)
hyperspy/tests/signal/test_find_peaks2D.py:166:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_signals/signal2d.py:925: in find_peaks
peaks = self.map(method_func, show_progressbar=show_progressbar,
hyperspy/signal.py:4508: in map
res = self._map_iterate(function, iterating_kwargs=ndkwargs,
hyperspy/signal.py:4643: in _map_iterate
for ind, res in zip(
/usr/lib/python3.10/concurrent/futures/_base.py:621: in result_iterator
yield _result_or_cancel(fs.pop())
/usr/lib/python3.10/concurrent/futures/_base.py:319: in _result_or_cancel
return fut.result(timeout)
/usr/lib/python3.10/concurrent/futures/_base.py:458: in result
return self.__get_result()
/usr/lib/python3.10/concurrent/futures/_base.py:403: in __get_result
raise self._exception
/usr/lib/python3.10/concurrent/futures/thread.py:58: in run
result = self.fn(*self.args, **self.kwargs)
hyperspy/misc/utils.py:1090: in func
return function(dat, **these_kwargs)
hyperspy/utils/peakfinders2D.py:454: in find_peaks_stat
return clean_peaks(stat_peak_finder(z, convergence_ratio))
hyperspy/utils/peakfinders2D.py:437: in stat_peak_finder
image, peaks_curr = _peak_find_once(image) # 4-7
hyperspy/utils/peakfinders2D.py:427: in _peak_find_once
peaks = separate_peaks(image) # 6
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
binarised_image = array([[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
...,
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0]])
def separate_peaks(binarised_image):
"""Identify adjacent 'on' coordinates via DBSCAN."""
bi = binarised_image.astype("bool")
coordinates = np.indices(bi.shape).reshape(2, -1).T[bi.flatten()]
> db = import_sklearn.sklearn.cluster.DBSCAN(2, 3)
E TypeError: DBSCAN.__init__() takes from 1 to 2 positional arguments but 3 were given
hyperspy/utils/peakfinders2D.py:415: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
----------------------------- Captured stderr call -----------------------------
0%| | 0/1 [00:00<?, ?it/s][A[A
______________ TestFindPeaks2D.test_gets_right_answer[False-stat] ______________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.signal.test_find_peaks2D.TestFindPeaks2D object at 0x9c9f5f88>
method = 'stat', parallel = False
@pytest.mark.parametrize('method', PEAK_METHODS)
@pytest.mark.parametrize('parallel', [True, False])
def test_gets_right_answer(self, method, parallel):
if method == 'stat':
pytest.importorskip("sklearn")
ans = np.empty((1,), dtype=object)
ans[0] = np.array([[self.xref, self.yref]])
if method == 'template_matching':
disc = np.zeros((5, 5))
disc[1:4, 1:4] = 0.5
disc[2,2] = 1
peaks = self.ref.find_peaks(method=method, parallel=parallel,
interactive=False, template=disc)
else:
> peaks = self.ref.find_peaks(method=method, parallel=parallel,
interactive=False)
hyperspy/tests/signal/test_find_peaks2D.py:166:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_signals/signal2d.py:925: in find_peaks
peaks = self.map(method_func, show_progressbar=show_progressbar,
hyperspy/signal.py:4508: in map
res = self._map_iterate(function, iterating_kwargs=ndkwargs,
hyperspy/signal.py:4667: in _map_iterate
for ind, res in zip(range(res_data.size), map(func, zip(*iterators))):
hyperspy/misc/utils.py:1090: in func
return function(dat, **these_kwargs)
hyperspy/utils/peakfinders2D.py:454: in find_peaks_stat
return clean_peaks(stat_peak_finder(z, convergence_ratio))
hyperspy/utils/peakfinders2D.py:437: in stat_peak_finder
image, peaks_curr = _peak_find_once(image) # 4-7
hyperspy/utils/peakfinders2D.py:427: in _peak_find_once
peaks = separate_peaks(image) # 6
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
binarised_image = array([[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
...,
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0]])
def separate_peaks(binarised_image):
"""Identify adjacent 'on' coordinates via DBSCAN."""
bi = binarised_image.astype("bool")
coordinates = np.indices(bi.shape).reshape(2, -1).T[bi.flatten()]
> db = import_sklearn.sklearn.cluster.DBSCAN(2, 3)
E TypeError: DBSCAN.__init__() takes from 1 to 2 positional arguments but 3 were given
hyperspy/utils/peakfinders2D.py:415: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
----------------------------- Captured stderr call -----------------------------
0%| | 0/1 [00:00<?, ?it/s][A[A[A
____________ TestFindPeaks2D.test_lazy_find_peaks[False-dense-stat] ____________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.signal.test_find_peaks2D.TestFindPeaks2D object at 0x9c9d8118>
method = 'stat', dataset_name = 'dense', parallel = False
@pytest.mark.parametrize('method', PEAK_METHODS)
@pytest.mark.parametrize('dataset_name', DATASETS_NAME)
@pytest.mark.parametrize('parallel', [True, False])
def test_find_peaks(self, method, dataset_name, parallel):
if method == 'stat':
pytest.importorskip("sklearn")
dataset = getattr(self, dataset_name)
# Parallel is not used in `map` for lazy signal
if parallel and dataset._lazy:
pytest.skip("Parallel=True is ignored for lazy signal.")
if method == 'template_matching':
disc = np.zeros((11, 11))
disc[2:9, 2:9] = 0.5
disc[4:7, 4:7] = 0.75
disc[5, 5] = 1
peaks = dataset.find_peaks(method=method, parallel=parallel,
interactive=False, template=disc)
else:
> peaks = dataset.find_peaks(method=method, parallel=parallel,
interactive=False)
hyperspy/tests/signal/test_find_peaks2D.py:121:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_signals/signal2d.py:925: in find_peaks
peaks = self.map(method_func, show_progressbar=show_progressbar,
hyperspy/signal.py:4508: in map
res = self._map_iterate(function, iterating_kwargs=ndkwargs,
hyperspy/_signals/lazy.py:578: in _map_iterate
res_data.flat[i] = pixel.compute()
/usr/lib/python3/dist-packages/dask/base.py:290: in compute
(result,) = compute(self, traverse=False, **kwargs)
/usr/lib/python3/dist-packages/dask/base.py:573: in compute
results = schedule(dsk, keys, **kwargs)
/usr/lib/python3/dist-packages/dask/threaded.py:81: in get
results = get_async(
/usr/lib/python3/dist-packages/dask/local.py:506: in get_async
raise_exception(exc, tb)
/usr/lib/python3/dist-packages/dask/local.py:314: in reraise
raise exc
/usr/lib/python3/dist-packages/dask/local.py:219: in execute_task
result = _execute_task(task, data)
/usr/lib/python3/dist-packages/dask/core.py:119: in _execute_task
return func(*(_execute_task(a, cache) for a in args))
hyperspy/misc/utils.py:1090: in func
return function(dat, **these_kwargs)
hyperspy/utils/peakfinders2D.py:454: in find_peaks_stat
return clean_peaks(stat_peak_finder(z, convergence_ratio))
hyperspy/utils/peakfinders2D.py:437: in stat_peak_finder
image, peaks_curr = _peak_find_once(image) # 4-7
hyperspy/utils/peakfinders2D.py:427: in _peak_find_once
peaks = separate_peaks(image) # 6
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
binarised_image = array([[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
...,
[1, 1, 0, ..., 1, 1, 1],
[0, 0, 0, ..., 1, 1, 1],
[0, 0, 0, ..., 1, 1, 1]])
def separate_peaks(binarised_image):
"""Identify adjacent 'on' coordinates via DBSCAN."""
bi = binarised_image.astype("bool")
coordinates = np.indices(bi.shape).reshape(2, -1).T[bi.flatten()]
> db = import_sklearn.sklearn.cluster.DBSCAN(2, 3)
E TypeError: DBSCAN.__init__() takes from 1 to 2 positional arguments but 3 were given
hyperspy/utils/peakfinders2D.py:415: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
----------------------------- Captured stdout call -----------------------------
[ ] | 0% Completed | 0.0s
[ ] | 0% Completed | 0.2s
___ TestFindPeaks2D.test_lazy_find_peaks[False-dense-difference_of_gaussian] ___
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.signal.test_find_peaks2D.TestFindPeaks2D object at 0x9c9d80e8>
method = 'difference_of_gaussian', dataset_name = 'dense', parallel = False
@pytest.mark.parametrize('method', PEAK_METHODS)
@pytest.mark.parametrize('dataset_name', DATASETS_NAME)
@pytest.mark.parametrize('parallel', [True, False])
def test_find_peaks(self, method, dataset_name, parallel):
if method == 'stat':
pytest.importorskip("sklearn")
dataset = getattr(self, dataset_name)
# Parallel is not used in `map` for lazy signal
if parallel and dataset._lazy:
pytest.skip("Parallel=True is ignored for lazy signal.")
if method == 'template_matching':
disc = np.zeros((11, 11))
disc[2:9, 2:9] = 0.5
disc[4:7, 4:7] = 0.75
disc[5, 5] = 1
peaks = dataset.find_peaks(method=method, parallel=parallel,
interactive=False, template=disc)
else:
> peaks = dataset.find_peaks(method=method, parallel=parallel,
interactive=False)
hyperspy/tests/signal/test_find_peaks2D.py:121:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_signals/signal2d.py:925: in find_peaks
peaks = self.map(method_func, show_progressbar=show_progressbar,
hyperspy/signal.py:4508: in map
res = self._map_iterate(function, iterating_kwargs=ndkwargs,
hyperspy/_signals/lazy.py:578: in _map_iterate
res_data.flat[i] = pixel.compute()
/usr/lib/python3/dist-packages/dask/base.py:290: in compute
(result,) = compute(self, traverse=False, **kwargs)
/usr/lib/python3/dist-packages/dask/base.py:573: in compute
results = schedule(dsk, keys, **kwargs)
/usr/lib/python3/dist-packages/dask/threaded.py:81: in get
results = get_async(
/usr/lib/python3/dist-packages/dask/local.py:506: in get_async
raise_exception(exc, tb)
/usr/lib/python3/dist-packages/dask/local.py:314: in reraise
raise exc
/usr/lib/python3/dist-packages/dask/local.py:219: in execute_task
result = _execute_task(task, data)
/usr/lib/python3/dist-packages/dask/core.py:119: in _execute_task
return func(*(_execute_task(a, cache) for a in args))
hyperspy/misc/utils.py:1090: in func
return function(dat, **these_kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
z = array([[0.70165162, 0.71450877, 0.72106518, ..., 0.52227921, 0.52947204,
0.54271189],
[0.76271489, 0.77...23,
0.96811211],
[0.80960236, 0.76366337, 0.71725186, ..., 0.98919486, 0.97610825,
0.95047115]])
min_sigma = 1.0, max_sigma = 50.0, sigma_ratio = 1.6, threshold = 0.2
overlap = 0.5, exclude_border = False
def find_peaks_dog(z, min_sigma=1., max_sigma=50., sigma_ratio=1.6,
threshold=0.2, overlap=0.5, exclude_border=False):
"""Method to locate peaks via the Difference of Gaussian Matrices method.
This function wraps :py:func:`skimage.feature.blob_dog` function and
sorts the results for consistency with other peak finding methods.
Parameters
----------
z : numpy.ndarray
2-d array of intensities
min_sigma, max_sigma, sigma_ratio, threshold, overlap, exclude_border :
Additional parameters to be passed to the algorithm. See `blob_dog`
documentation for details:
http://scikit-image.org/docs/dev/api/skimage.feature.html#blob-dog
Returns
-------
peaks : numpy.ndarray
(n_peaks, 2)
Peak pixel coordinates.
Notes
-----
While highly effective at finding even very faint peaks, this method is
sensitive to fluctuations in intensity near the edges of the image.
"""
z = z / np.max(z)
blobs = blob_dog(z, min_sigma=min_sigma, max_sigma=max_sigma,
sigma_ratio=sigma_ratio, threshold=threshold,
overlap=overlap, exclude_border=exclude_border)
try:
centers = np.round(blobs[:, :2]).astype(int)
except IndexError:
return NO_PEAKS
clean_centers = []
for center in centers:
if len(np.intersect1d(center, (0, 1) + z.shape + tuple(
c - 1 for c in z.shape))) > 0:
continue
clean_centers.append(center)
peaks = np.array(clean_centers)
> ind = np.lexsort((peaks[:,0], peaks[:,1]))
E IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed
hyperspy/utils/peakfinders2D.py:500: IndexError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
----------------------------- Captured stdout call -----------------------------
[ ] | 0% Completed | 0.0s
[ ] | 0% Completed | 0.1s
[ ] | 0% Completed | 0.2s
________ TestFindPeaks2D.test_lazy_find_peaks[False-sparse_nav0d-stat] _________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.signal.test_find_peaks2D.TestFindPeaks2D object at 0x9c9dea30>
method = 'stat', dataset_name = 'sparse_nav0d', parallel = False
@pytest.mark.parametrize('method', PEAK_METHODS)
@pytest.mark.parametrize('dataset_name', DATASETS_NAME)
@pytest.mark.parametrize('parallel', [True, False])
def test_find_peaks(self, method, dataset_name, parallel):
if method == 'stat':
pytest.importorskip("sklearn")
dataset = getattr(self, dataset_name)
# Parallel is not used in `map` for lazy signal
if parallel and dataset._lazy:
pytest.skip("Parallel=True is ignored for lazy signal.")
if method == 'template_matching':
disc = np.zeros((11, 11))
disc[2:9, 2:9] = 0.5
disc[4:7, 4:7] = 0.75
disc[5, 5] = 1
peaks = dataset.find_peaks(method=method, parallel=parallel,
interactive=False, template=disc)
else:
> peaks = dataset.find_peaks(method=method, parallel=parallel,
interactive=False)
hyperspy/tests/signal/test_find_peaks2D.py:121:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_signals/signal2d.py:925: in find_peaks
peaks = self.map(method_func, show_progressbar=show_progressbar,
hyperspy/signal.py:4508: in map
res = self._map_iterate(function, iterating_kwargs=ndkwargs,
hyperspy/_signals/lazy.py:578: in _map_iterate
res_data.flat[i] = pixel.compute()
/usr/lib/python3/dist-packages/dask/base.py:290: in compute
(result,) = compute(self, traverse=False, **kwargs)
/usr/lib/python3/dist-packages/dask/base.py:573: in compute
results = schedule(dsk, keys, **kwargs)
/usr/lib/python3/dist-packages/dask/threaded.py:81: in get
results = get_async(
/usr/lib/python3/dist-packages/dask/local.py:506: in get_async
raise_exception(exc, tb)
/usr/lib/python3/dist-packages/dask/local.py:314: in reraise
raise exc
/usr/lib/python3/dist-packages/dask/local.py:219: in execute_task
result = _execute_task(task, data)
/usr/lib/python3/dist-packages/dask/core.py:119: in _execute_task
return func(*(_execute_task(a, cache) for a in args))
hyperspy/misc/utils.py:1090: in func
return function(dat, **these_kwargs)
hyperspy/utils/peakfinders2D.py:454: in find_peaks_stat
return clean_peaks(stat_peak_finder(z, convergence_ratio))
hyperspy/utils/peakfinders2D.py:437: in stat_peak_finder
image, peaks_curr = _peak_find_once(image) # 4-7
hyperspy/utils/peakfinders2D.py:427: in _peak_find_once
peaks = separate_peaks(image) # 6
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
binarised_image = array([[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
...,
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0]])
def separate_peaks(binarised_image):
"""Identify adjacent 'on' coordinates via DBSCAN."""
bi = binarised_image.astype("bool")
coordinates = np.indices(bi.shape).reshape(2, -1).T[bi.flatten()]
> db = import_sklearn.sklearn.cluster.DBSCAN(2, 3)
E TypeError: DBSCAN.__init__() takes from 1 to 2 positional arguments but 3 were given
hyperspy/utils/peakfinders2D.py:415: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
----------------------------- Captured stdout call -----------------------------
[ ] | 0% Completed | 0.0s
[ ] | 0% Completed | 0.2s
[ ] | 0% Completed | 0.3s
________ TestFindPeaks2D.test_lazy_find_peaks[False-sparse_nav1d-stat] _________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.signal.test_find_peaks2D.TestFindPeaks2D object at 0x9c9dee98>
method = 'stat', dataset_name = 'sparse_nav1d', parallel = False
@pytest.mark.parametrize('method', PEAK_METHODS)
@pytest.mark.parametrize('dataset_name', DATASETS_NAME)
@pytest.mark.parametrize('parallel', [True, False])
def test_find_peaks(self, method, dataset_name, parallel):
if method == 'stat':
pytest.importorskip("sklearn")
dataset = getattr(self, dataset_name)
# Parallel is not used in `map` for lazy signal
if parallel and dataset._lazy:
pytest.skip("Parallel=True is ignored for lazy signal.")
if method == 'template_matching':
disc = np.zeros((11, 11))
disc[2:9, 2:9] = 0.5
disc[4:7, 4:7] = 0.75
disc[5, 5] = 1
peaks = dataset.find_peaks(method=method, parallel=parallel,
interactive=False, template=disc)
else:
> peaks = dataset.find_peaks(method=method, parallel=parallel,
interactive=False)
hyperspy/tests/signal/test_find_peaks2D.py:121:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_signals/signal2d.py:925: in find_peaks
peaks = self.map(method_func, show_progressbar=show_progressbar,
hyperspy/signal.py:4508: in map
res = self._map_iterate(function, iterating_kwargs=ndkwargs,
hyperspy/_signals/lazy.py:578: in _map_iterate
res_data.flat[i] = pixel.compute()
/usr/lib/python3/dist-packages/dask/base.py:290: in compute
(result,) = compute(self, traverse=False, **kwargs)
/usr/lib/python3/dist-packages/dask/base.py:573: in compute
results = schedule(dsk, keys, **kwargs)
/usr/lib/python3/dist-packages/dask/threaded.py:81: in get
results = get_async(
/usr/lib/python3/dist-packages/dask/local.py:506: in get_async
raise_exception(exc, tb)
/usr/lib/python3/dist-packages/dask/local.py:314: in reraise
raise exc
/usr/lib/python3/dist-packages/dask/local.py:219: in execute_task
result = _execute_task(task, data)
/usr/lib/python3/dist-packages/dask/core.py:119: in _execute_task
return func(*(_execute_task(a, cache) for a in args))
hyperspy/misc/utils.py:1090: in func
return function(dat, **these_kwargs)
hyperspy/utils/peakfinders2D.py:454: in find_peaks_stat
return clean_peaks(stat_peak_finder(z, convergence_ratio))
hyperspy/utils/peakfinders2D.py:437: in stat_peak_finder
image, peaks_curr = _peak_find_once(image) # 4-7
hyperspy/utils/peakfinders2D.py:427: in _peak_find_once
peaks = separate_peaks(image) # 6
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
binarised_image = array([[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
...,
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0]])
def separate_peaks(binarised_image):
"""Identify adjacent 'on' coordinates via DBSCAN."""
bi = binarised_image.astype("bool")
coordinates = np.indices(bi.shape).reshape(2, -1).T[bi.flatten()]
> db = import_sklearn.sklearn.cluster.DBSCAN(2, 3)
E TypeError: DBSCAN.__init__() takes from 1 to 2 positional arguments but 3 were given
hyperspy/utils/peakfinders2D.py:415: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
----------------------------- Captured stdout call -----------------------------
[ ] | 0% Completed | 0.0s
[############# ] | 33% Completed | 0.2s
________ TestFindPeaks2D.test_lazy_find_peaks[False-sparse_nav2d-stat] _________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.signal.test_find_peaks2D.TestFindPeaks2D object at 0x9c9de7a8>
method = 'stat', dataset_name = 'sparse_nav2d', parallel = False
@pytest.mark.parametrize('method', PEAK_METHODS)
@pytest.mark.parametrize('dataset_name', DATASETS_NAME)
@pytest.mark.parametrize('parallel', [True, False])
def test_find_peaks(self, method, dataset_name, parallel):
if method == 'stat':
pytest.importorskip("sklearn")
dataset = getattr(self, dataset_name)
# Parallel is not used in `map` for lazy signal
if parallel and dataset._lazy:
pytest.skip("Parallel=True is ignored for lazy signal.")
if method == 'template_matching':
disc = np.zeros((11, 11))
disc[2:9, 2:9] = 0.5
disc[4:7, 4:7] = 0.75
disc[5, 5] = 1
peaks = dataset.find_peaks(method=method, parallel=parallel,
interactive=False, template=disc)
else:
> peaks = dataset.find_peaks(method=method, parallel=parallel,
interactive=False)
hyperspy/tests/signal/test_find_peaks2D.py:121:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_signals/signal2d.py:925: in find_peaks
peaks = self.map(method_func, show_progressbar=show_progressbar,
hyperspy/signal.py:4508: in map
res = self._map_iterate(function, iterating_kwargs=ndkwargs,
hyperspy/_signals/lazy.py:578: in _map_iterate
res_data.flat[i] = pixel.compute()
/usr/lib/python3/dist-packages/dask/base.py:290: in compute
(result,) = compute(self, traverse=False, **kwargs)
/usr/lib/python3/dist-packages/dask/base.py:573: in compute
results = schedule(dsk, keys, **kwargs)
/usr/lib/python3/dist-packages/dask/threaded.py:81: in get
results = get_async(
/usr/lib/python3/dist-packages/dask/local.py:506: in get_async
raise_exception(exc, tb)
/usr/lib/python3/dist-packages/dask/local.py:314: in reraise
raise exc
/usr/lib/python3/dist-packages/dask/local.py:219: in execute_task
result = _execute_task(task, data)
/usr/lib/python3/dist-packages/dask/core.py:119: in _execute_task
return func(*(_execute_task(a, cache) for a in args))
hyperspy/misc/utils.py:1090: in func
return function(dat, **these_kwargs)
hyperspy/utils/peakfinders2D.py:454: in find_peaks_stat
return clean_peaks(stat_peak_finder(z, convergence_ratio))
hyperspy/utils/peakfinders2D.py:437: in stat_peak_finder
image, peaks_curr = _peak_find_once(image) # 4-7
hyperspy/utils/peakfinders2D.py:427: in _peak_find_once
peaks = separate_peaks(image) # 6
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
binarised_image = array([[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
...,
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0]])
def separate_peaks(binarised_image):
"""Identify adjacent 'on' coordinates via DBSCAN."""
bi = binarised_image.astype("bool")
coordinates = np.indices(bi.shape).reshape(2, -1).T[bi.flatten()]
> db = import_sklearn.sklearn.cluster.DBSCAN(2, 3)
E TypeError: DBSCAN.__init__() takes from 1 to 2 positional arguments but 3 were given
hyperspy/utils/peakfinders2D.py:415: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
----------------------------- Captured stdout call -----------------------------
[ ] | 0% Completed | 0.0s
[############# ] | 33% Completed | 0.1s
[############# ] | 33% Completed | 0.3s
____________ TestFindPeaks2D.test_lazy_gets_right_answer[True-stat] ____________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.signal.test_find_peaks2D.TestFindPeaks2D object at 0x9c9de4d8>
method = 'stat', parallel = True
@pytest.mark.parametrize('method', PEAK_METHODS)
@pytest.mark.parametrize('parallel', [True, False])
def test_gets_right_answer(self, method, parallel):
if method == 'stat':
pytest.importorskip("sklearn")
ans = np.empty((1,), dtype=object)
ans[0] = np.array([[self.xref, self.yref]])
if method == 'template_matching':
disc = np.zeros((5, 5))
disc[1:4, 1:4] = 0.5
disc[2,2] = 1
peaks = self.ref.find_peaks(method=method, parallel=parallel,
interactive=False, template=disc)
else:
> peaks = self.ref.find_peaks(method=method, parallel=parallel,
interactive=False)
hyperspy/tests/signal/test_find_peaks2D.py:166:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_signals/signal2d.py:925: in find_peaks
peaks = self.map(method_func, show_progressbar=show_progressbar,
hyperspy/signal.py:4508: in map
res = self._map_iterate(function, iterating_kwargs=ndkwargs,
hyperspy/_signals/lazy.py:578: in _map_iterate
res_data.flat[i] = pixel.compute()
/usr/lib/python3/dist-packages/dask/base.py:290: in compute
(result,) = compute(self, traverse=False, **kwargs)
/usr/lib/python3/dist-packages/dask/base.py:573: in compute
results = schedule(dsk, keys, **kwargs)
/usr/lib/python3/dist-packages/dask/threaded.py:81: in get
results = get_async(
/usr/lib/python3/dist-packages/dask/local.py:506: in get_async
raise_exception(exc, tb)
/usr/lib/python3/dist-packages/dask/local.py:314: in reraise
raise exc
/usr/lib/python3/dist-packages/dask/local.py:219: in execute_task
result = _execute_task(task, data)
/usr/lib/python3/dist-packages/dask/core.py:119: in _execute_task
return func(*(_execute_task(a, cache) for a in args))
hyperspy/misc/utils.py:1090: in func
return function(dat, **these_kwargs)
hyperspy/utils/peakfinders2D.py:454: in find_peaks_stat
return clean_peaks(stat_peak_finder(z, convergence_ratio))
hyperspy/utils/peakfinders2D.py:437: in stat_peak_finder
image, peaks_curr = _peak_find_once(image) # 4-7
hyperspy/utils/peakfinders2D.py:427: in _peak_find_once
peaks = separate_peaks(image) # 6
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
binarised_image = array([[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
...,
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0]])
def separate_peaks(binarised_image):
"""Identify adjacent 'on' coordinates via DBSCAN."""
bi = binarised_image.astype("bool")
coordinates = np.indices(bi.shape).reshape(2, -1).T[bi.flatten()]
> db = import_sklearn.sklearn.cluster.DBSCAN(2, 3)
E TypeError: DBSCAN.__init__() takes from 1 to 2 positional arguments but 3 were given
hyperspy/utils/peakfinders2D.py:415: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
----------------------------- Captured stdout call -----------------------------
[ ] | 0% Completed | 0.0s
[ ] | 0% Completed | 0.9s
[ ] | 0% Completed | 1.0s
[ ] | 0% Completed | 1.1s
___________ TestFindPeaks2D.test_lazy_gets_right_answer[False-stat] ____________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.signal.test_find_peaks2D.TestFindPeaks2D object at 0x9c9dee20>
method = 'stat', parallel = False
@pytest.mark.parametrize('method', PEAK_METHODS)
@pytest.mark.parametrize('parallel', [True, False])
def test_gets_right_answer(self, method, parallel):
if method == 'stat':
pytest.importorskip("sklearn")
ans = np.empty((1,), dtype=object)
ans[0] = np.array([[self.xref, self.yref]])
if method == 'template_matching':
disc = np.zeros((5, 5))
disc[1:4, 1:4] = 0.5
disc[2,2] = 1
peaks = self.ref.find_peaks(method=method, parallel=parallel,
interactive=False, template=disc)
else:
> peaks = self.ref.find_peaks(method=method, parallel=parallel,
interactive=False)
hyperspy/tests/signal/test_find_peaks2D.py:166:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_signals/signal2d.py:925: in find_peaks
peaks = self.map(method_func, show_progressbar=show_progressbar,
hyperspy/signal.py:4508: in map
res = self._map_iterate(function, iterating_kwargs=ndkwargs,
hyperspy/_signals/lazy.py:578: in _map_iterate
res_data.flat[i] = pixel.compute()
/usr/lib/python3/dist-packages/dask/base.py:290: in compute
(result,) = compute(self, traverse=False, **kwargs)
/usr/lib/python3/dist-packages/dask/base.py:573: in compute
results = schedule(dsk, keys, **kwargs)
/usr/lib/python3/dist-packages/dask/threaded.py:81: in get
results = get_async(
/usr/lib/python3/dist-packages/dask/local.py:506: in get_async
raise_exception(exc, tb)
/usr/lib/python3/dist-packages/dask/local.py:314: in reraise
raise exc
/usr/lib/python3/dist-packages/dask/local.py:219: in execute_task
result = _execute_task(task, data)
/usr/lib/python3/dist-packages/dask/core.py:119: in _execute_task
return func(*(_execute_task(a, cache) for a in args))
hyperspy/misc/utils.py:1090: in func
return function(dat, **these_kwargs)
hyperspy/utils/peakfinders2D.py:454: in find_peaks_stat
return clean_peaks(stat_peak_finder(z, convergence_ratio))
hyperspy/utils/peakfinders2D.py:437: in stat_peak_finder
image, peaks_curr = _peak_find_once(image) # 4-7
hyperspy/utils/peakfinders2D.py:427: in _peak_find_once
peaks = separate_peaks(image) # 6
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
binarised_image = array([[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
...,
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0]])
def separate_peaks(binarised_image):
"""Identify adjacent 'on' coordinates via DBSCAN."""
bi = binarised_image.astype("bool")
coordinates = np.indices(bi.shape).reshape(2, -1).T[bi.flatten()]
> db = import_sklearn.sklearn.cluster.DBSCAN(2, 3)
E TypeError: DBSCAN.__init__() takes from 1 to 2 positional arguments but 3 were given
hyperspy/utils/peakfinders2D.py:415: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
----------------------------- Captured stdout call -----------------------------
[ ] | 0% Completed | 0.0s
[ ] | 0% Completed | 0.9s
[ ] | 0% Completed | 1.1s
[ ] | 0% Completed | 1.2s
___________________ test_remove_backgound_type[Skew normal] ____________________
[gw3] linux -- Python 3.10.7 /usr/bin/python3.10
ValueError: Error from parse_expr with transformed code: "(Integer (1 )+erf (shape *Symbol ('t' )/sqrt (Integer (2 ))))/Integer (2 )"
The above exception was the direct cause of the following exception:
background_type = 'Skew normal'
@pytest.mark.parametrize('background_type',
['Doniach', 'Exponential', 'Gaussian', 'Lorentzian',
'Polynomial', 'Power law', 'Power Law', 'PowerLaw',
'Offset', 'Skew normal', 'Skew Normal', 'SkewNormal',
'Split Voigt', 'Split voigt', 'SplitVoigt',
'Voigt'])
def test_remove_backgound_type(background_type):
s = hs.signals.Signal1D(np.arange(100))
> s.remove_background(background_type=background_type,signal_range=(2,98))
hyperspy/tests/signal/test_remove_background.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_signals/signal1d.py:1218: in remove_background
background_estimator = _get_background_estimator(
hyperspy/signal_tools.py:1477: in _get_background_estimator
background_estimator = components1d.SkewNormal()
hyperspy/_components/skew_normal.py:154: in __init__
super(SkewNormal, self).__init__(
hyperspy/_components/expression.py:158: in __init__
self.compile_function(module=module, position=position)
hyperspy/_components/expression.py:209: in compile_function
expr = _parse_substitutions(self._str_expression)
hyperspy/_components/expression.py:61: in _parse_substitutions
expr = expr.subs(t[0], sympy.sympify(t[1]))
/usr/lib/python3/dist-packages/sympy/core/sympify.py:495: in sympify
expr = parse_expr(a, local_dict=locals, transformations=transformations, evaluate=evaluate)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1105: in parse_expr
raise e from ValueError(f"Error from parse_expr with transformed code: {code!r}")
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1096: in parse_expr
rv = eval_expr(code, local_dict, global_dict)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:915: in eval_expr
expr = eval(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E TypeError: unsupported operand type(s) for *: 'function' and 'Symbol'
<string>:1: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
___________________ test_remove_backgound_type[Skew Normal] ____________________
[gw3] linux -- Python 3.10.7 /usr/bin/python3.10
ValueError: Error from parse_expr with transformed code: "(Integer (1 )+erf (shape *Symbol ('t' )/sqrt (Integer (2 ))))/Integer (2 )"
The above exception was the direct cause of the following exception:
background_type = 'Skew Normal'
@pytest.mark.parametrize('background_type',
['Doniach', 'Exponential', 'Gaussian', 'Lorentzian',
'Polynomial', 'Power law', 'Power Law', 'PowerLaw',
'Offset', 'Skew normal', 'Skew Normal', 'SkewNormal',
'Split Voigt', 'Split voigt', 'SplitVoigt',
'Voigt'])
def test_remove_backgound_type(background_type):
s = hs.signals.Signal1D(np.arange(100))
> s.remove_background(background_type=background_type,signal_range=(2,98))
hyperspy/tests/signal/test_remove_background.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_signals/signal1d.py:1218: in remove_background
background_estimator = _get_background_estimator(
hyperspy/signal_tools.py:1477: in _get_background_estimator
background_estimator = components1d.SkewNormal()
hyperspy/_components/skew_normal.py:154: in __init__
super(SkewNormal, self).__init__(
hyperspy/_components/expression.py:158: in __init__
self.compile_function(module=module, position=position)
hyperspy/_components/expression.py:209: in compile_function
expr = _parse_substitutions(self._str_expression)
hyperspy/_components/expression.py:61: in _parse_substitutions
expr = expr.subs(t[0], sympy.sympify(t[1]))
/usr/lib/python3/dist-packages/sympy/core/sympify.py:495: in sympify
expr = parse_expr(a, local_dict=locals, transformations=transformations, evaluate=evaluate)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1105: in parse_expr
raise e from ValueError(f"Error from parse_expr with transformed code: {code!r}")
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1096: in parse_expr
rv = eval_expr(code, local_dict, global_dict)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:915: in eval_expr
expr = eval(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E TypeError: unsupported operand type(s) for *: 'function' and 'Symbol'
<string>:1: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
____________________ test_remove_backgound_type[SkewNormal] ____________________
[gw3] linux -- Python 3.10.7 /usr/bin/python3.10
ValueError: Error from parse_expr with transformed code: "(Integer (1 )+erf (shape *Symbol ('t' )/sqrt (Integer (2 ))))/Integer (2 )"
The above exception was the direct cause of the following exception:
background_type = 'SkewNormal'
@pytest.mark.parametrize('background_type',
['Doniach', 'Exponential', 'Gaussian', 'Lorentzian',
'Polynomial', 'Power law', 'Power Law', 'PowerLaw',
'Offset', 'Skew normal', 'Skew Normal', 'SkewNormal',
'Split Voigt', 'Split voigt', 'SplitVoigt',
'Voigt'])
def test_remove_backgound_type(background_type):
s = hs.signals.Signal1D(np.arange(100))
> s.remove_background(background_type=background_type,signal_range=(2,98))
hyperspy/tests/signal/test_remove_background.py:266:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/_signals/signal1d.py:1218: in remove_background
background_estimator = _get_background_estimator(
hyperspy/signal_tools.py:1477: in _get_background_estimator
background_estimator = components1d.SkewNormal()
hyperspy/_components/skew_normal.py:154: in __init__
super(SkewNormal, self).__init__(
hyperspy/_components/expression.py:158: in __init__
self.compile_function(module=module, position=position)
hyperspy/_components/expression.py:209: in compile_function
expr = _parse_substitutions(self._str_expression)
hyperspy/_components/expression.py:61: in _parse_substitutions
expr = expr.subs(t[0], sympy.sympify(t[1]))
/usr/lib/python3/dist-packages/sympy/core/sympify.py:495: in sympify
expr = parse_expr(a, local_dict=locals, transformations=transformations, evaluate=evaluate)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1105: in parse_expr
raise e from ValueError(f"Error from parse_expr with transformed code: {code!r}")
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:1096: in parse_expr
rv = eval_expr(code, local_dict, global_dict)
/usr/lib/python3/dist-packages/sympy/parsing/sympy_parser.py:915: in eval_expr
expr = eval(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> ???
E TypeError: unsupported operand type(s) for *: 'function' and 'Symbol'
<string>:1: TypeError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
__________________________ TestROIs.test_circle_spec ___________________________
[gw2] linux -- Python 3.10.7 /usr/bin/python3.10
self = <hyperspy.tests.utils.test_roi.TestROIs object at 0x9bebc1c0>
def test_circle_spec(self):
s = self.s_s
s.data = np.ones_like(s.data)
r = CircleROI(20, 25, 20)
r_ann = CircleROI(20, 25, 20, 15)
sr = r(s)
sr_ann = r_ann(s)
scale = s.axes_manager[0].scale
n = int(round(40 / scale))
assert sr.axes_manager.navigation_shape == (n, n)
assert sr_ann.axes_manager.navigation_shape == (n, n)
# Check that mask is same for all images:
for i in range(n):
for j in range(n):
assert (np.all(sr.data.mask[j, i, :] == True) or
np.all(sr.data.mask[j, i, :] == False))
assert (np.all(sr_ann.data.mask[j, i, :] == True) or
np.all(sr_ann.data.mask[j, i, :] == False))
# Check that the correct elements has been masked out:
mask = sr.data.mask[:, :, 0]
print(mask) # To help debugging, this shows the shape of the mask
np.testing.assert_array_equal(
np.where(mask.flatten())[0],
[0, 1, 6, 7, 8, 15, 48, 55, 56, 57, 62, 63])
mask_ann = sr_ann.data.mask[:, :, 0]
print(mask_ann) # To help debugging, this shows the shape of the mask
np.testing.assert_array_equal(
np.where(mask_ann.flatten())[0],
[0, 1, 6, 7, 8, 10, 11, 12, 13, 15, 17, 18, 19, 20, 21, 22, 25,
26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46,
48, 50, 51, 52, 53, 55, 56, 57, 62, 63])
# Check that mask works for sum
assert np.sum(sr.data) == (n**2 - 3 * 4) * 4
assert np.sum(sr_ann.data) == 4 * 5 * 4
s.plot()
r_signal = r.interactive(signal=s)
> r_ann_signal = r_ann.interactive(signal=s)
hyperspy/tests/utils/test_roi.py:294:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hyperspy/roi.py:381: in interactive
self.add_widget(navigation_signal, color=color,
hyperspy/roi.py:472: in add_widget
self._apply_roi2widget(widget)
hyperspy/roi.py:958: in _apply_roi2widget
widget.size = (self.r, inner)
hyperspy/drawing/widget.py:592: in <lambda>
size = property(lambda s: s._get_size(), lambda s, v: s._set_size(v))
hyperspy/drawing/_widgets/circle.py:71: in _set_size
self._size_changed()
hyperspy/drawing/widget.py:636: in _size_changed
self._update_patch_size()
hyperspy/drawing/_widgets/circle.py:161: in _update_patch_size
self.ax.artists.remove(self.patch[0])
/usr/lib/python3.10/_collections_abc.py:1158: in remove
del self[self.index(value)]
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Axes.ArtistList of 0 artists>
value = <matplotlib.patches.Circle object at 0x87c17250>, start = 0, stop = None
def index(self, value, start=0, stop=None):
'''S.index(value, [start, [stop]]) -> integer -- return first index of value.
Raises ValueError if the value is not present.
Supporting start and stop arguments is optional, but
recommended.
'''
if start is not None and start < 0:
start = max(len(self) + start, 0)
if stop is not None and stop < 0:
stop += len(self)
i = start
while stop is None or i < stop:
try:
v = self[i]
if v is value or v == value:
return i
except IndexError:
break
i += 1
> raise ValueError
E ValueError
/usr/lib/python3.10/_collections_abc.py:1075: ValueError
------------------------------ Captured log setup ------------------------------
WARNING matplotlib.testing:__init__.py:38 Could not set locale to English/United States. Some date-related tests may fail.
----------------------------- Captured stdout call -----------------------------
[[ True True False False False False True True]
[ True False False False False False False True]
[False False False False False False False False]
[False False False False False False False False]
[False False False False False False False False]
[False False False False False False False False]
[ True False False False False False False True]
[ True True False False False False True True]]
[[ True True False False False False True True]
[ True False True True True True False True]
[False True True True True True True False]
[False True True True True True True False]
[False True True True True True True False]
[False True True True True True True False]
[ True False True True True True False True]
[ True True False False False False True True]]
=============================== warnings summary ===============================
hyperspy/ui_registry.py:19
hyperspy/ui_registry.py:19
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/ui_registry.py:19: DeprecationWarning: invalid escape sequence '\*'
"""Registry of user interface widgets.
hyperspy/utils/__init__.py:51
hyperspy/utils/__init__.py:51
hyperspy/utils/__init__.py:51
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/utils/__init__.py:51: DeprecationWarning: invalid escape sequence '\s'
"""Print all known `signal_type`\s
hyperspy/misc/label_position.py:222
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/misc/label_position.py:222: DeprecationWarning: invalid escape sequence '\m'
formatted = element+' '+'$\mathregular{'+subshell[0]+'_'+\
hyperspy/misc/label_position.py:225
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/misc/label_position.py:225: DeprecationWarning: invalid escape sequence '\m'
formatted = element+' '+'$\mathregular{'+subshell[0]+'}$'
hyperspy/_signals/signal1d.py:29
hyperspy/_signals/signal1d.py:29
hyperspy/_signals/signal1d.py:29
hyperspy/_signals/signal1d.py:29
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_signals/signal1d.py:29: DeprecationWarning: Please use `gaussian_filter1d` from the `scipy.ndimage` namespace, the `scipy.ndimage.filters` namespace is deprecated.
from scipy.ndimage.filters import gaussian_filter1d
hyperspy/_components/pes_voigt.py:87
hyperspy/_components/pes_voigt.py:87
hyperspy/_components/pes_voigt.py:87
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_components/pes_voigt.py:87: DeprecationWarning: invalid escape sequence '\c'
"""This is the legacy Voigt profile component dedicated to photoemission
hyperspy/_components/pes_voigt.py:161
hyperspy/_components/pes_voigt.py:161
hyperspy/_components/pes_voigt.py:161
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_components/pes_voigt.py:161: DeprecationWarning: invalid escape sequence '\c'
""" Voigt component for photoemission spectroscopy data analysis.
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/component/test_components2D.py: 1 warning
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/component/test_gaussianhf.py: 1 warning
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/learn/test_cluster.py: 5 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/learn/test_lazy_decomposition.py: 10 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/learn/test_rpca.py: 18 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/model/test_fitting.py: 18 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_1D_tools.py: 22 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_eels.py: 12 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_remove_background.py: 6 warnings
/usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: <function tqdm.__del__ at 0xa2059538>
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/tqdm/std.py", line 1162, in __del__
self.close()
File "/usr/lib/python3/dist-packages/tqdm/notebook.py", line 287, in close
self.disp(bar_style='danger', check_delay=False)
AttributeError: 'tqdm_notebook' object has no attribute 'disp'
warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/component/test_components.py: 5 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/misc/test_hist_tools.py: 17 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_2D_tools.py: 29 warnings
/usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: <function tqdm.__del__ at 0xa2065658>
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/tqdm/std.py", line 1162, in __del__
self.close()
File "/usr/lib/python3/dist-packages/tqdm/notebook.py", line 287, in close
self.disp(bar_style='danger', check_delay=False)
AttributeError: 'tqdm_notebook' object has no attribute 'disp'
warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_markers.py::TestMarkers::test_get_data_shape_point
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_markers.py:114: DeprecationWarning: `np.object` is a deprecated alias for the builtin `object`. To silence this warning, use `object` by itself. Doing this will not modify any behavior and is safe.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
m4.data['x1'][()] = np.array(None, dtype=np.object)
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_markers.py::TestMarkers::test_get_data_shape_point
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_markers.py:115: DeprecationWarning: `np.object` is a deprecated alias for the builtin `object`. To silence this warning, use `object` by itself. Doing this will not modify any behavior and is safe.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
m4.data['y1'][()] = np.array(None, dtype=np.object)
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_figure.py: 19 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_markers.py: 33 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_model.py: 11 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_model1d.py: 5 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_roi_widgets.py: 15 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal.py: 199 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal2d.py: 59 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal_tools.py: 11 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal1d.py: 61 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_widgets.py: 6 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/test_hdf5.py: 13 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/model/test_edsmodel.py: 2 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/model/test_fit_component.py: 1 warning
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/model/test_model.py: 5 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_edges_range.py: 32 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_eels.py: 10 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_find_peaks2D.py: 2 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_image_contrast_editor_tool.py: 4 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_spike_removal_tool.py: 1 warning
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/utils/test_roi.py: 6 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_eds_tem.py: 3 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/drawing/utils.py:163: MatplotlibDeprecationWarning:
The set_window_title function was deprecated in Matplotlib 3.4 and will be removed two minor releases later. Use `.FigureManagerBase.set_window_title` or GUI-specific methods instead.
fig.canvas.set_window_title(window_title)
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_figure.py: 21 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_model1d.py: 1 warning
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_model.py: 5 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_markers.py: 4 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_roi_widgets.py: 1 warning
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal1d.py: 8 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal.py: 30 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/model/test_model.py: 3 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_edges_range.py: 6 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_spike_removal_tool.py: 6 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/utils/test_roi.py: 2 warnings
/usr/lib/python3.10/_collections_abc.py:1158: MatplotlibDeprecationWarning:
The modification of the Axes.lines property was deprecated in Matplotlib 3.5 and will be removed two minor releases later. Use Artist.remove() instead.
del self[self.index(value)]
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_figure.py: 6 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_model.py: 1 warning
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_markers.py: 2 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal1d.py: 5 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal.py: 17 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/model/test_model.py: 3 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_edges_range.py: 6 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/utils/test_roi.py: 1 warning
/usr/lib/python3.10/_collections_abc.py:1158: MatplotlibDeprecationWarning:
The modification of the Axes.texts property was deprecated in Matplotlib 3.5 and will be removed two minor releases later. Use Artist.remove() instead.
del self[self.index(value)]
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_model.py: 2982 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/misc/eels/hydrogenic_gos.py:196: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
u = XU[np.int(iz)]
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_roi_widgets.py: 3 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal_tools.py: 11 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_widgets.py: 7 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/model/test_fit_component.py: 1 warning
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_edges_range.py: 16 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_image_contrast_editor_tool.py: 5 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_spike_removal_tool.py: 14 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/utils/test_roi.py: 2 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/drawing/_widgets/range.py:285: MatplotlibDeprecationWarning: The 'span_stays' parameter of __init__() has been renamed 'interactive' since Matplotlib 3.5; support for the old name will be dropped two minor releases later.
SpanSelector.__init__(self, ax, onselect, direction=direction,
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_roi_widgets.py: 12 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal_tools.py: 2 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_widgets.py: 26 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_image_contrast_editor_tool.py: 2 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/utils/test_roi.py: 20 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/drawing/_widgets/range.py:366: MatplotlibDeprecationWarning:
The rect attribute was deprecated in Matplotlib 3.5 and will be removed two minor releases later.
return self.rect.get_x()
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_roi_widgets.py: 6 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal_tools.py: 11 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_widgets.py: 13 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_image_contrast_editor_tool.py: 13 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/utils/test_roi.py: 10 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/drawing/_widgets/range.py:372: MatplotlibDeprecationWarning:
The rect attribute was deprecated in Matplotlib 3.5 and will be removed two minor releases later.
return self.rect.get_width()
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_roi_widgets.py: 4 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal_tools.py: 1 warning
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_widgets.py: 8 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_image_contrast_editor_tool.py: 1 warning
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/utils/test_roi.py: 2 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/drawing/_widgets/range.py:354: MatplotlibDeprecationWarning:
The rect attribute was deprecated in Matplotlib 3.5 and will be removed two minor releases later.
self.rect.set_x(value)
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_roi_widgets.py: 4 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal_tools.py: 1 warning
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_widgets.py: 8 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_image_contrast_editor_tool.py: 1 warning
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/utils/test_roi.py: 6 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/drawing/_widgets/range.py:360: MatplotlibDeprecationWarning:
The rect attribute was deprecated in Matplotlib 3.5 and will be removed two minor releases later.
self.rect.set_width(value)
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_roi_widgets.py: 3 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal_tools.py: 1 warning
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_widgets.py: 7 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_image_contrast_editor_tool.py: 1 warning
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/utils/test_roi.py: 2 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/drawing/_widgets/range.py:395: MatplotlibDeprecationWarning:
The rect attribute was deprecated in Matplotlib 3.5 and will be removed two minor releases later.
self.rect.set_visible(True)
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_roi_widgets.py: 3 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal_tools.py: 1 warning
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_widgets.py: 7 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_image_contrast_editor_tool.py: 1 warning
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/utils/test_roi.py: 2 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/drawing/_widgets/range.py:396: MatplotlibDeprecationWarning:
The rect attribute was deprecated in Matplotlib 3.5 and will be removed two minor releases later.
self.rect.contains = self.contains
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_roi_widgets.py: 3 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_widgets.py: 5 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/utils/test_roi.py: 2 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/drawing/_widgets/range.py:89: MatplotlibDeprecationWarning:
The rect attribute was deprecated in Matplotlib 3.5 and will be removed two minor releases later.
self.patch = [self.span.rect]
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_roi_widgets.py: 6 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_widgets.py: 14 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/drawing/_widgets/range.py:368: MatplotlibDeprecationWarning:
The rect attribute was deprecated in Matplotlib 3.5 and will be removed two minor releases later.
return self.rect.get_y()
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_roi_widgets.py: 3 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_widgets.py: 7 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/drawing/_widgets/range.py:374: MatplotlibDeprecationWarning:
The rect attribute was deprecated in Matplotlib 3.5 and will be removed two minor releases later.
return self.rect.get_height()
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_roi_widgets.py::TestPlotROI::test_plot_spanroi_axis_2
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_roi_widgets.py::TestPlotROI::test_plot_spanroi_axis_2
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_widgets.py::TestPlotRangeWidget::test_plot_range_Signal2D
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_widgets.py::TestPlotRangeWidget::test_plot_range_Signal2D
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_widgets.py::TestPlotRangeWidget::test_plot_ModifiableSpanSelector
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_widgets.py::TestPlotRangeWidget::test_plot_ModifiableSpanSelector
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/drawing/_widgets/range.py:356: MatplotlibDeprecationWarning:
The rect attribute was deprecated in Matplotlib 3.5 and will be removed two minor releases later.
self.rect.set_y(value)
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_roi_widgets.py::TestPlotROI::test_plot_spanroi_axis_2
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_roi_widgets.py::TestPlotROI::test_plot_spanroi_axis_2
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_widgets.py::TestPlotRangeWidget::test_plot_range_Signal2D
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_widgets.py::TestPlotRangeWidget::test_plot_range_Signal2D
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_widgets.py::TestPlotRangeWidget::test_plot_ModifiableSpanSelector
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/drawing/_widgets/range.py:362: MatplotlibDeprecationWarning:
The rect attribute was deprecated in Matplotlib 3.5 and will be removed two minor releases later.
self.rect.set_height(value)
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_mva.py: 8 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal2d.py: 11 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/learn/test_ornmf.py: 14 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/model/test_edsmodel.py: 2 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/samfire/test_goodness_of_fit_tests.py: 2 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/samfire/test_samfire.py: 1 warning
/usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: <function tqdm.__del__ at 0xa203f460>
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/tqdm/std.py", line 1162, in __del__
self.close()
File "/usr/lib/python3/dist-packages/tqdm/notebook.py", line 287, in close
self.disp(bar_style='danger', check_delay=False)
AttributeError: 'tqdm_notebook' object has no attribute 'disp'
warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal_tools.py::test_plot_BackgroundRemoval
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/signal_tools.py:87: MatplotlibDeprecationWarning:
The rect attribute was deprecated in Matplotlib 3.5 and will be removed two minor releases later.
x0 = self.span_selector.rect.get_x()
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal_tools.py::test_plot_BackgroundRemoval
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/signal_tools.py:91: MatplotlibDeprecationWarning:
The rect attribute was deprecated in Matplotlib 3.5 and will be removed two minor releases later.
x1 = self.ss_left_value + self.span_selector.rect.get_width()
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal_tools.py: 10 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_widgets.py: 1 warning
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_image_contrast_editor_tool.py: 5 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/drawing/_widgets/range.py:285: MatplotlibDeprecationWarning: The 'rectprops' parameter of __init__() has been renamed 'props' since Matplotlib 3.5; support for the old name will be dropped two minor releases later.
SpanSelector.__init__(self, ax, onselect, direction=direction,
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_widgets.py::TestPlotRangeWidget::test_plot_range
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_widgets.py:178: MatplotlibDeprecationWarning:
The rect attribute was deprecated in Matplotlib 3.5 and will be removed two minor releases later.
assert self.range.span.rect.get_alpha() == 0.5
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_widgets.py::TestPlotRangeWidget::test_plot_range
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_widgets.py:185: MatplotlibDeprecationWarning:
The rect attribute was deprecated in Matplotlib 3.5 and will be removed two minor releases later.
assert w.span.rect.get_fc() == color_rgba
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_widgets.py::TestPlotRangeWidget::test_plot_range
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_widgets.py:186: MatplotlibDeprecationWarning:
The rect attribute was deprecated in Matplotlib 3.5 and will be removed two minor releases later.
assert w.span.rect.get_ec() == color_rgba
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_widgets.py::TestPlotRangeWidget::test_plot_ModifiableSpanSelector
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_widgets.py:242: MatplotlibDeprecationWarning:
The rect attribute was deprecated in Matplotlib 3.5 and will be removed two minor releases later.
assert span_h.rect.get_fc() == color_rgba
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_widgets.py::TestPlotRangeWidget::test_plot_ModifiableSpanSelector
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_widgets.py:243: MatplotlibDeprecationWarning:
The rect attribute was deprecated in Matplotlib 3.5 and will be removed two minor releases later.
assert span_h.rect.get_ec() == color_rgba
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal2d.py::test_plot_images_cmap_mpl_colors_w_single_cbar
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal2d.py::test_plot_images_cmap_multi_signal
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal2d.py::test_plot_images_cmap_multi_w_rgb
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/drawing/utils.py:1159: UserWarning: Trying to register the cmap 'mpl0' which already exists.
mpl.cm.register_cmap(name, cmap)
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal2d.py::test_plot_images_cmap_mpl_colors_w_single_cbar
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal2d.py::test_plot_images_cmap_multi_signal
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal2d.py::test_plot_images_cmap_multi_w_rgb
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/drawing/utils.py:1159: UserWarning: Trying to register the cmap 'mpl1' which already exists.
mpl.cm.register_cmap(name, cmap)
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal2d.py::test_plot_images_cmap_mpl_colors_w_single_cbar
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal2d.py::test_plot_images_cmap_multi_signal
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal2d.py::test_plot_images_cmap_multi_w_rgb
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/drawing/utils.py:1159: UserWarning: Trying to register the cmap 'mpl2' which already exists.
mpl.cm.register_cmap(name, cmap)
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal2d.py::test_plot_images_cmap_mpl_colors_w_single_cbar
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal2d.py::test_plot_images_cmap_multi_signal
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal2d.py::test_plot_images_cmap_multi_w_rgb
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/drawing/utils.py:1159: UserWarning: Trying to register the cmap 'mpl3' which already exists.
mpl.cm.register_cmap(name, cmap)
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal2d.py::test_plot_images_cmap_mpl_colors_w_single_cbar
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal2d.py::test_plot_images_cmap_multi_signal
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal2d.py::test_plot_images_cmap_multi_w_rgb
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/drawing/utils.py:1159: UserWarning: Trying to register the cmap 'mpl4' which already exists.
mpl.cm.register_cmap(name, cmap)
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal2d.py::test_plot_images_cmap_mpl_colors_w_single_cbar
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal2d.py::test_plot_images_cmap_multi_signal
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal2d.py::test_plot_images_cmap_multi_w_rgb
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/drawing/utils.py:1159: UserWarning: Trying to register the cmap 'mpl5' which already exists.
mpl.cm.register_cmap(name, cmap)
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal2d.py::test_plot_images_cmap_mpl_colors_w_single_cbar
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal2d.py::test_plot_images_cmap_multi_signal
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal2d.py::test_plot_images_cmap_multi_w_rgb
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/drawing/utils.py:1159: UserWarning: Trying to register the cmap 'mpl6' which already exists.
mpl.cm.register_cmap(name, cmap)
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/drawing/test_plot_signal2d.py::test_plot_images_cmap_make_cmap_bitfalse
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/drawing/utils.py:1159: UserWarning: Trying to register the cmap 'test_cmap' which already exists.
mpl.cm.register_cmap(name, cmap)
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/test_empad.py::test_read_map[False]
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/test_empad.py::test_read_map[False]
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/test_empad.py::test_read_map[True]
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/test_empad.py::test_read_map[True]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/io_plugins/empad.py:92: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
v = np.float(value) * _ureg(units)
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/test_emd.py: 245 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/io_plugins/emd.py:1483: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
v = np.float(value) * self.ureg(units)
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/test_nexus_hdf.py: 24946 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/io_plugins/nexus.py:103: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
if isinstance(toreturn, (np.int, np.float)):
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/test_nexus_hdf.py: 24946 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/io_plugins/nexus.py:103: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
if isinstance(toreturn, (np.int, np.float)):
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/test_hdf5.py::test_save_ragged_array
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/io_plugins/hspy.py:592: DeprecationWarning: elementwise comparison failed; this will raise an error in the future.
if dset == data:
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/io/test_sur.py: 10 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/io_plugins/sur.py:1267: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
_points = _points.astype(np.float) \
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/learn/test_bss.py::test_bss_FastICA_object
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/learn/test_bss.py::test_bss_pipeline
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/learn/test_bss.py::test_fastica_whiten_method[None]
/usr/lib/python3/dist-packages/sklearn/decomposition/_fastica.py:494: FutureWarning: Starting in v1.3, whiten='unit-variance' will be used by default.
warnings.warn(
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/learn/test_svd_pca.py: 13 warnings
/usr/lib/python3/dist-packages/sklearn/utils/extmath.py:370: FutureWarning: If 'random_state' is not supplied, the current default is to use 0 as a fixed seed. This will change to None in version 1.2 leading to non-deterministic results that better reflect nature of the randomized_svd solver. If you want to silence this warning, set 'random_state' to an integer seed or to None explicitly depending if you want your code to be deterministic or not.
warnings.warn(
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/learn/test_decomposition.py: 4 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/model/test_fit_component.py: 1 warning
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/model/test_model.py: 8 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_complex_signal.py: 6 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_find_peaks1D_ohaver.py: 2 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_find_peaks2D.py: 83 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_hologram_image.py: 3 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_kramers_kronig_transform.py: 6 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_map_method.py: 41 warnings
/usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: <function tqdm.__del__ at 0xa2096580>
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/tqdm/std.py", line 1162, in __del__
self.close()
File "/usr/lib/python3/dist-packages/tqdm/notebook.py", line 287, in close
self.disp(bar_style='danger', check_delay=False)
AttributeError: 'tqdm_notebook' object has no attribute 'disp'
warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/misc/test_tv_denoise.py::test_2d_tv_denoise
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/misc/test_tv_denoise.py:32: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
data = ascent().astype(np.float)
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/misc/test_tv_denoise.py::test_2d_tv_denoise
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/misc/tv_denoise.py:174: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
if im_type is not np.float:
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/misc/test_tv_denoise.py::test_2d_tv_denoise
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/misc/tv_denoise.py:175: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
im = im.astype(np.float)
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/misc/test_tv_denoise.py::test_3d_tv_denoise
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/misc/test_tv_denoise.py:47: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
data = 255 * data.astype(np.float)
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/misc/test_tv_denoise.py::test_3d_tv_denoise
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/misc/tv_denoise.py:72: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
if im_type is not np.float:
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/misc/test_tv_denoise.py::test_3d_tv_denoise
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/misc/tv_denoise.py:73: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
im = im.astype(np.float)
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/model/test_edsmodel.py: 6 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_eds_tem.py: 46 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_signals/eds_tem.py:598: DeprecationWarning: Please use `binary_dilation` from the `scipy.ndimage` namespace, the `scipy.ndimage.morphology` namespace is deprecated.
from scipy.ndimage.morphology import binary_dilation, binary_erosion
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/model/test_edsmodel.py: 6 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_eds_tem.py: 46 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_signals/eds_tem.py:598: DeprecationWarning: Please use `binary_erosion` from the `scipy.ndimage` namespace, the `scipy.ndimage.morphology` namespace is deprecated.
from scipy.ndimage.morphology import binary_dilation, binary_erosion
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_1D_tools.py: 54 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_find_peaks1D_ohaver.py: 4 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_signals/signal1d.py:136: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
peak_dt = np.dtype([('position', np.float),
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_1D_tools.py: 54 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_find_peaks1D_ohaver.py: 4 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_signals/signal1d.py:137: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
('height', np.float),
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_1D_tools.py: 54 warnings
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_find_peaks1D_ohaver.py: 4 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/_signals/signal1d.py:138: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
('width', np.float)])
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_1D_tools.py: 18 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/misc/tv_denoise.py:270: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
if im_type is not np.float:
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_1D_tools.py: 18 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/misc/tv_denoise.py:271: DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`. To silence this warning, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
im = im.astype(np.float)
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_eds_tem.py::Test_quantification::test_quant_lorimer_warning
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_eds_tem.py::Test_quantification::test_quant_lorimer_ac
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_eds_tem.py::Test_quantification::test_quant_zeta
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_eds_tem.py::Test_quantification::test_quant_cross_section_ac
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_eds_tem.py::Test_quantification::test_lazy_quant_lorimer_warning
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_eds_tem.py::Test_quantification::test_lazy_quant_lorimer_ac
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_eds_tem.py::Test_quantification::test_lazy_quant_zeta
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_eds_tem.py::Test_quantification::test_lazy_quant_cross_section_ac
/usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: <function tqdm.__del__ at 0xa203f460>
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/tqdm/std.py", line 1162, in __del__
self.close()
File "/usr/lib/python3/dist-packages/tqdm/notebook.py", line 290, in close
self.disp(bar_style='success', check_delay=False)
AttributeError: 'tqdm_notebook' object has no attribute 'disp'
warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_find_peaks2D.py: 68 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/utils/peakfinders2D.py:151: DeprecationWarning: Please use `maximum_filter` from the `scipy.ndimage` namespace, the `scipy.ndimage.filters` namespace is deprecated.
data_max = ndi.filters.maximum_filter(z, distance)
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_find_peaks2D.py: 68 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/utils/peakfinders2D.py:153: DeprecationWarning: Please use `minimum_filter` from the `scipy.ndimage` namespace, the `scipy.ndimage.filters` namespace is deprecated.
data_min = ndi.filters.minimum_filter(z, distance)
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_find_peaks2D.py: 44 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/utils/peakfinders2D.py:373: DeprecationWarning: Please use `generic_filter` from the `scipy.ndimage` namespace, the `scipy.ndimage.filters` namespace is deprecated.
stat = ndi.filters.generic_filter(image, func, footprint=kernel)
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_find_peaks2D.py: 22 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/utils/peakfinders2D.py:387: DeprecationWarning: Please use `generic_filter` from the `scipy.ndimage` namespace, the `scipy.ndimage.filters` namespace is deprecated.
smoothed_image = ndi.filters.generic_filter(image, _fast_mean, footprint=kernel)
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_find_peaks2D.py: 22 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/utils/peakfinders2D.py:402: DeprecationWarning: Please use `uniform_filter` from the `scipy.ndimage` namespace, the `scipy.ndimage.filters` namespace is deprecated.
image = ndi.filters.uniform_filter(image, size=3)
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_find_peaks2D.py: 22 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/utils/peakfinders2D.py:403: DeprecationWarning: Please use `uniform_filter` from the `scipy.ndimage` namespace, the `scipy.ndimage.filters` namespace is deprecated.
image = ndi.filters.uniform_filter(image, size=3)
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_hologram_image.py::test_reconstruct_phase_nonstandard[True]
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_hologram_image.py::test_reconstruct_phase_nonstandard[False]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_hologram_image.py:163: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.int(sb_size2.inav[0].data * 2),
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_hologram_image.py::test_reconstruct_phase_nonstandard[True]
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_hologram_image.py::test_reconstruct_phase_nonstandard[False]
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_hologram_image.py:164: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
np.int(sb_size2.inav[0].data * 2),
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_image_contrast_editor_tool.py::TestContrastEditorTool::test_reset_span_selector
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_image_contrast_editor_tool.py::TestContrastEditorTool::test_reset_span_selector
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/signal_tools.py:902: MatplotlibDeprecationWarning:
The rect attribute was deprecated in Matplotlib 3.5 and will be removed two minor releases later.
self.ss_left_value = self.span_selector.rect.get_x()
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_image_contrast_editor_tool.py::TestContrastEditorTool::test_reset_span_selector
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_image_contrast_editor_tool.py::TestContrastEditorTool::test_reset_span_selector
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/signal_tools.py:904: MatplotlibDeprecationWarning:
The rect attribute was deprecated in Matplotlib 3.5 and will be removed two minor releases later.
self.span_selector.rect.get_width()
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_image_contrast_editor_tool.py::TestContrastEditorTool::test_reset_span_selector
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/signal_tools.py:1052: MatplotlibDeprecationWarning:
The rect attribute was deprecated in Matplotlib 3.5 and will be removed two minor releases later.
if self.span_selector and self.span_selector.rect.get_x() > 0:
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_image_contrast_editor_tool.py: 1 warning
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_spike_removal_tool.py: 13 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build/hyperspy/drawing/_widgets/range.py:615: MatplotlibDeprecationWarning:
The rect attribute was deprecated in Matplotlib 3.5 and will be removed two minor releases later.
self.ax.patches.remove(self.rect)
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_image_contrast_editor_tool.py: 1 warning
.pybuild/cpython3_3.10_hyperspy/build/hyperspy/tests/signal/test_spike_removal_tool.py: 13 warnings
/usr/lib/python3.10/_collections_abc.py:1158: MatplotlibDeprecationWarning:
The modification of the Axes.patches property was deprecated in Matplotlib 3.5 and will be removed two minor releases later. Use Artist.remove() instead.
del self[self.index(value)]
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
SKIPPED [1] hyperspy/tests/io/test_mrcz.py:32: mrcz not installed
SKIPPED [1] hyperspy/tests/io/test_phenom.py:26: skipping test_phenom tests, requires imagecodecs
SKIPPED [1] hyperspy/tests/io/test_usid.py:10: pyUSID not installed
SKIPPED [1] hyperspy/tests/datasets/test_eelsdb.py:39: Unable to connect to EELSdb
SKIPPED [1] hyperspy/tests/datasets/test_eelsdb.py:95: Unable to connect to EELSdb
SKIPPED [1] hyperspy/tests/drawing/test_mpl_testing_setup.py:48: No --mpl command line option
SKIPPED [1] hyperspy/tests/io/test_bruker.py:191: could not import 'hyperspy.io_plugins.unbcf_fast': No module named 'hyperspy.io_plugins.unbcf_fast'
SKIPPED [1] hyperspy/tests/io/test_edax.py:71: download of EDAX test files failed: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /hyperspy/hyperspy/blob/e7a323a3bb9b237c24bd9267d2cc4fcb31bb99f3/hyperspy/tests/io/edax_files.zip?raw=true (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x9f5b6160>: Failed to establish a new connection: [Errno 111] Connection refused')))
SKIPPED [1] hyperspy/tests/io/test_edax.py:83: download of EDAX test files failed: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /hyperspy/hyperspy/blob/e7a323a3bb9b237c24bd9267d2cc4fcb31bb99f3/hyperspy/tests/io/edax_files.zip?raw=true (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x9f5b6160>: Failed to establish a new connection: [Errno 111] Connection refused')))
SKIPPED [1] hyperspy/tests/io/test_edax.py:114: download of EDAX test files failed: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /hyperspy/hyperspy/blob/e7a323a3bb9b237c24bd9267d2cc4fcb31bb99f3/hyperspy/tests/io/edax_files.zip?raw=true (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x9f5b6160>: Failed to establish a new connection: [Errno 111] Connection refused')))
SKIPPED [1] hyperspy/tests/io/test_edax.py:124: download of EDAX test files failed: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /hyperspy/hyperspy/blob/e7a323a3bb9b237c24bd9267d2cc4fcb31bb99f3/hyperspy/tests/io/edax_files.zip?raw=true (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x9f5b6160>: Failed to establish a new connection: [Errno 111] Connection refused')))
SKIPPED [1] hyperspy/tests/io/test_edax.py:151: download of EDAX test files failed: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /hyperspy/hyperspy/blob/e7a323a3bb9b237c24bd9267d2cc4fcb31bb99f3/hyperspy/tests/io/edax_files.zip?raw=true (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x9f5b6160>: Failed to establish a new connection: [Errno 111] Connection refused')))
SKIPPED [1] hyperspy/tests/io/test_edax.py:161: download of EDAX test files failed: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /hyperspy/hyperspy/blob/e7a323a3bb9b237c24bd9267d2cc4fcb31bb99f3/hyperspy/tests/io/edax_files.zip?raw=true (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x9f5b6160>: Failed to establish a new connection: [Errno 111] Connection refused')))
SKIPPED [1] hyperspy/tests/io/test_edax.py:190: download of EDAX test files failed: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /hyperspy/hyperspy/blob/e7a323a3bb9b237c24bd9267d2cc4fcb31bb99f3/hyperspy/tests/io/edax_files.zip?raw=true (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x9f5b6160>: Failed to establish a new connection: [Errno 111] Connection refused')))
SKIPPED [1] hyperspy/tests/io/test_edax.py:200: download of EDAX test files failed: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /hyperspy/hyperspy/blob/e7a323a3bb9b237c24bd9267d2cc4fcb31bb99f3/hyperspy/tests/io/edax_files.zip?raw=true (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x9f5b6160>: Failed to establish a new connection: [Errno 111] Connection refused')))
SKIPPED [1] hyperspy/tests/io/test_edax.py:227: download of EDAX test files failed: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /hyperspy/hyperspy/blob/e7a323a3bb9b237c24bd9267d2cc4fcb31bb99f3/hyperspy/tests/io/edax_files.zip?raw=true (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x9f5b6160>: Failed to establish a new connection: [Errno 111] Connection refused')))
SKIPPED [1] hyperspy/tests/io/test_edax.py:259: download of EDAX test files failed: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /hyperspy/hyperspy/blob/e7a323a3bb9b237c24bd9267d2cc4fcb31bb99f3/hyperspy/tests/io/edax_files.zip?raw=true (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x9f5b6160>: Failed to establish a new connection: [Errno 111] Connection refused')))
SKIPPED [1] hyperspy/tests/io/test_edax.py:287: download of EDAX test files failed: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /hyperspy/hyperspy/blob/e7a323a3bb9b237c24bd9267d2cc4fcb31bb99f3/hyperspy/tests/io/edax_files.zip?raw=true (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x9f5b6160>: Failed to establish a new connection: [Errno 111] Connection refused')))
SKIPPED [1] hyperspy/tests/io/test_edax.py:309: download of EDAX test files failed: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /hyperspy/hyperspy/blob/e7a323a3bb9b237c24bd9267d2cc4fcb31bb99f3/hyperspy/tests/io/edax_files.zip?raw=true (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x9f5b6160>: Failed to establish a new connection: [Errno 111] Connection refused')))
SKIPPED [1] hyperspy/tests/io/test_edax.py:314: download of EDAX test files failed: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /hyperspy/hyperspy/blob/e7a323a3bb9b237c24bd9267d2cc4fcb31bb99f3/hyperspy/tests/io/edax_files.zip?raw=true (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x9f5b6160>: Failed to establish a new connection: [Errno 111] Connection refused')))
SKIPPED [1] hyperspy/tests/io/test_edax.py:352: download of EDAX test files failed: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /hyperspy/hyperspy/blob/e7a323a3bb9b237c24bd9267d2cc4fcb31bb99f3/hyperspy/tests/io/edax_files.zip?raw=true (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x9f5b6160>: Failed to establish a new connection: [Errno 111] Connection refused')))
SKIPPED [1] hyperspy/tests/io/test_edax.py:384: download of EDAX test files failed: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /hyperspy/hyperspy/blob/e7a323a3bb9b237c24bd9267d2cc4fcb31bb99f3/hyperspy/tests/io/edax_files.zip?raw=true (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x9f5b6160>: Failed to establish a new connection: [Errno 111] Connection refused')))
SKIPPED [1] hyperspy/tests/io/test_edax.py:412: download of EDAX test files failed: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /hyperspy/hyperspy/blob/e7a323a3bb9b237c24bd9267d2cc4fcb31bb99f3/hyperspy/tests/io/edax_files.zip?raw=true (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x9f5b6160>: Failed to establish a new connection: [Errno 111] Connection refused')))
SKIPPED [1] hyperspy/tests/io/test_edax.py:434: download of EDAX test files failed: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /hyperspy/hyperspy/blob/e7a323a3bb9b237c24bd9267d2cc4fcb31bb99f3/hyperspy/tests/io/edax_files.zip?raw=true (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x9f5b6160>: Failed to establish a new connection: [Errno 111] Connection refused')))
SKIPPED [1] hyperspy/tests/io/test_edax.py:439: download of EDAX test files failed: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /hyperspy/hyperspy/blob/e7a323a3bb9b237c24bd9267d2cc4fcb31bb99f3/hyperspy/tests/io/edax_files.zip?raw=true (Caused by ProxyError('Cannot connect to proxy.', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x9f5b6160>: Failed to establish a new connection: [Errno 111] Connection refused')))
SKIPPED [1] hyperspy/tests/io/test_tiff.py:609: imagecodecs is required
SKIPPED [4] hyperspy/tests/signal/test_1D_tools.py:266: Ignored on non-Windows OS
SKIPPED [1] hyperspy/tests/signal/test_2D.py:337: LazySignals do not support folding
SKIPPED [1] hyperspy/tests/signal/test_2D.py:345: LazySignals do not support folding
SKIPPED [32] hyperspy/tests/signal/test_find_peaks2D.py:111: Parallel=True is ignored for lazy signal.
SKIPPED [1] hyperspy/tests/signal/test_map_method.py:339: Not compatible with lazy signal.
SKIPPED [1] hyperspy/tests/signal/test_signal_operators.py:42: Inplace not supported by LazySignals
SKIPPED [1] hyperspy/tests/signal/test_signal_operators.py:64: Inplace not supported by LazySignals
SKIPPED [1] hyperspy/tests/signal/test_signal_operators.py:107: Inplace not supported by LazySignals
SKIPPED [1] hyperspy/tests/signal/test_signal_operators.py:118: Inplace not supported by LazySignals
SKIPPED [1] hyperspy/tests/signal/test_signal_subclass_conversion.py:97: Dask array flags not supported
SKIPPED [1] hyperspy/tests/signal/test_signal_subclass_conversion.py:114: Dask array flags not supported
SKIPPED [1] hyperspy/tests/signal/test_tools.py:207: LazySignals do not support masked arrays
SKIPPED [1] hyperspy/tests/signal/test_tools.py:241: LazySignals do not support masked arrays
SKIPPED [1] hyperspy/tests/signal/test_tools.py:261: LazySignals do not support masked arrays
SKIPPED [1] hyperspy/tests/signal/test_transpose.py:119: LazySignal optimization is tested in test_lazy_tranpose_rechunk
XFAIL hyperspy/tests/drawing/test_utils.py::test_create_figure
reason: agg backend does not support on_close event.
XFAIL hyperspy/tests/io/test_hdf5.py::TestLoadingNewSavedMetadata::test_binary_string
dill is not guaranteed to load across Python versions
XFAIL hyperspy/tests/samfire/test_samfire.py::test_multiprocessed
Sometimes the number of failed pixels > 3 when using multiprocessing. Unknown reason
ERROR hyperspy/tests/io/test_io.py::TestIOOverwriting::test_io_overwriting_True
ERROR hyperspy/tests/io/test_io.py::TestIOOverwriting::test_io_overwriting_False
ERROR hyperspy/tests/io/test_io.py::TestIOOverwriting::test_io_overwriting_no_existing_file[None]
ERROR hyperspy/tests/io/test_io.py::TestIOOverwriting::test_io_overwriting_no_existing_file[True]
ERROR hyperspy/tests/io/test_io.py::TestIOOverwriting::test_io_overwriting_no_existing_file[False]
ERROR hyperspy/tests/io/test_io.py::TestIOOverwriting::test_io_overwriting_None_existing_file_y
ERROR hyperspy/tests/io/test_hdf5.py::TestLoadingOOMReadOnly::test_oom_loading
ERROR hyperspy/tests/io/test_io.py::TestIOOverwriting::test_io_overwriting_None_existing_file_n
ERROR hyperspy/tests/io/test_hdf5.py::TestPassingArgs::test_compression_opts
ERROR hyperspy/tests/io/test_protochips.py::TestProtochipsGasCellCSV::test_read_metadata
ERROR hyperspy/tests/io/test_protochips.py::TestProtochipsGasCellCSV::test_read_original_metadata
ERROR hyperspy/tests/io/test_protochips.py::TestProtochipsGasCellCSVNoUser::test_read_metadata
ERROR hyperspy/tests/io/test_protochips.py::TestProtochipsGasCellCSVNoUser::test_read_original_metadata
ERROR hyperspy/tests/io/test_protochips.py::TestProtochipsGasCellCSVReader::test_read_column_name
ERROR hyperspy/tests/io/test_protochips.py::TestProtochipsGasCellCSVReader::test_read_start_datetime
ERROR hyperspy/tests/io/test_protochips.py::TestProtochipsGasCellCSVReader::test_read_data
ERROR hyperspy/tests/io/test_protochips.py::TestProtochipsGasCellCSVReader::test_read_metadata_header
ERROR hyperspy/tests/io/test_protochips.py::TestProtochipsElectricalCSVReader::test_read_column_name
ERROR hyperspy/tests/io/test_protochips.py::TestProtochipsElectricalCSVReader::test_read_start_datetime
ERROR hyperspy/tests/io/test_protochips.py::TestProtochipsElectricalCSVReader::test_read_data
ERROR hyperspy/tests/io/test_protochips.py::TestProtochipsThermallCSVReader::test_read_column_name
ERROR hyperspy/tests/io/test_protochips.py::TestProtochipsThermallCSVReader::test_read_start_datetime
ERROR hyperspy/tests/io/test_protochips.py::TestProtochipsThermallCSVReader::test_read_data
ERROR hyperspy/tests/io/test_protochips.py::TestProtochipsElectrothermalCSVReader::test_read_column_name
ERROR hyperspy/tests/io/test_protochips.py::TestProtochipsElectrothermalCSVReader::test_read_start_datetime
ERROR hyperspy/tests/io/test_protochips.py::TestProtochipsElectrothermalCSVReader::test_read_data
ERROR hyperspy/tests/signal/test_remove_background.py::TestRemoveBackground1DSkewNormal::test_background_remove_skewnormal
ERROR hyperspy/tests/signal/test_remove_background.py::TestRemoveBackground1DSkewNormal::test_background_remove_skewnormal_full_fit
ERROR hyperspy/tests/signal/test_remove_background.py::TestRemoveBackground1DSkewNormal::test_lazy_background_remove_skewnormal
ERROR hyperspy/tests/signal/test_remove_background.py::TestRemoveBackground1DSkewNormal::test_lazy_background_remove_skewnormal_full_fit
FAILED hyperspy/tests/component/test_components.py::test_creation_components1d[SkewNormal]
FAILED hyperspy/tests/component/test_skewnormal.py::test_function - TypeError...
FAILED hyperspy/tests/component/test_skewnormal.py::test_estimate_parameters_binned[True-True-True]
FAILED hyperspy/tests/component/test_skewnormal.py::test_estimate_parameters_binned[True-True-False]
FAILED hyperspy/tests/component/test_skewnormal.py::test_estimate_parameters_binned[True-False-True]
FAILED hyperspy/tests/component/test_skewnormal.py::test_estimate_parameters_binned[True-False-False]
FAILED hyperspy/tests/component/test_skewnormal.py::test_estimate_parameters_binned[False-True-True]
FAILED hyperspy/tests/component/test_skewnormal.py::test_estimate_parameters_binned[False-True-False]
FAILED hyperspy/tests/component/test_skewnormal.py::test_estimate_parameters_binned[False-False-True]
FAILED hyperspy/tests/component/test_skewnormal.py::test_estimate_parameters_binned[False-False-False]
FAILED hyperspy/tests/component/test_skewnormal.py::test_function_nd[True-True]
FAILED hyperspy/tests/component/test_skewnormal.py::test_function_nd[True-False]
FAILED hyperspy/tests/component/test_skewnormal.py::test_function_nd[False-True]
FAILED hyperspy/tests/component/test_skewnormal.py::test_function_nd[False-False]
FAILED hyperspy/tests/component/test_skewnormal.py::test_util_mean_get - Type...
FAILED hyperspy/tests/component/test_skewnormal.py::test_util_variance_get - ...
FAILED hyperspy/tests/component/test_skewnormal.py::test_util_skewness_get - ...
FAILED hyperspy/tests/component/test_skewnormal.py::test_util_mode_get - Type...
FAILED hyperspy/tests/io/test_blockfile.py::test_load_readonly - StopIteration
FAILED hyperspy/tests/io/test_hdf5.py::TestSavingMetadataContainers::test_numpy_general_type
FAILED hyperspy/tests/io/test_hdf5.py::TestAxesConfiguration::test_axes_configuration
FAILED hyperspy/tests/io/test_io.py::test_glob_wildcards - ValueError: The tr...
FAILED hyperspy/tests/io/test_io.py::test_file_reader_error - ValueError: The...
FAILED hyperspy/tests/io/test_io.py::test_file_reader_warning - ValueError: T...
FAILED hyperspy/tests/io/test_io.py::test_file_reader_options - ValueError: T...
FAILED hyperspy/tests/io/test_hdf5.py::Test_permanent_markers_io::test_save_permanent_marker
FAILED hyperspy/tests/io/test_io.py::test_save_default_format - ValueError: T...
FAILED hyperspy/tests/io/test_hdf5.py::Test_permanent_markers_io::test_save_load_empty_metadata_markers
FAILED hyperspy/tests/io/test_hdf5.py::Test_permanent_markers_io::test_save_load_permanent_marker
FAILED hyperspy/tests/io/test_hdf5.py::Test_permanent_markers_io::test_save_load_permanent_marker_all_types
FAILED hyperspy/tests/io/test_hdf5.py::Test_permanent_markers_io::test_save_load_horizontal_line_marker
FAILED hyperspy/tests/io/test_hdf5.py::Test_permanent_markers_io::test_save_load_horizontal_line_segment_marker
FAILED hyperspy/tests/io/test_hdf5.py::Test_permanent_markers_io::test_save_load_vertical_line_marker
FAILED hyperspy/tests/io/test_hdf5.py::Test_permanent_markers_io::test_save_load_vertical_line_segment_marker
FAILED hyperspy/tests/io/test_hdf5.py::Test_permanent_markers_io::test_save_load_line_segment_marker
FAILED hyperspy/tests/io/test_hdf5.py::Test_permanent_markers_io::test_save_load_point_marker
FAILED hyperspy/tests/io/test_hdf5.py::Test_permanent_markers_io::test_save_load_rectangle_marker
FAILED hyperspy/tests/io/test_hdf5.py::Test_permanent_markers_io::test_save_load_text_marker
FAILED hyperspy/tests/io/test_hdf5.py::Test_permanent_markers_io::test_save_load_multidim_navigation_marker
FAILED hyperspy/tests/io/test_hdf5.py::test_compression[None] - ValueError: T...
FAILED hyperspy/tests/io/test_hdf5.py::test_compression[gzip] - ValueError: T...
FAILED hyperspy/tests/io/test_hdf5.py::test_compression[lzf] - ValueError: Th...
FAILED hyperspy/tests/io/test_protochips.py::test_read_protochips_gas_cell - ...
FAILED hyperspy/tests/io/test_protochips.py::test_loading_invalid_protochips_file
FAILED hyperspy/tests/io/test_protochips.py::test_read_protochips_electrical
FAILED hyperspy/tests/io/test_protochips.py::test_read_protochips_thermal - T...
FAILED hyperspy/tests/io/test_protochips.py::test_read_protochips_electrothermal
FAILED hyperspy/tests/io/test_nexus_hdf.py::TestDLSNexus::test_save_hspy - Fa...
FAILED hyperspy/tests/io/test_nexus_hdf.py::TestDLSNexusNoAxes::test_save_hspy
FAILED hyperspy/tests/io/test_nexus_hdf.py::TestSavingMetadataContainers::test_save_scalers
FAILED hyperspy/tests/io/test_nexus_hdf.py::TestSavingMetadataContainers::test_save_arrays
FAILED hyperspy/tests/io/test_nexus_hdf.py::TestSavingMetadataContainers::test_save_original_metadata
FAILED hyperspy/tests/io/test_nexus_hdf.py::test_saving_multi_signals - Value...
FAILED hyperspy/tests/misc/test_date_time_tools.py::test_serial_date_to_ISO_format
FAILED hyperspy/tests/misc/test_date_time_tools.py::test_ISO_format_to_serial_date
FAILED hyperspy/tests/learn/test_decomposition.py::TestLoadDecompositionResults::test_load_decomposition_results
FAILED hyperspy/tests/model/test_fitting.py::TestModelFitBinnedGlobal::test_fit_shgo
FAILED hyperspy/tests/misc/test_hist_tools.py::TestHistogramBinMethodsBadDataset::test_lazy_fd_logger_warning
FAILED hyperspy/tests/misc/test_hist_tools.py::TestHistogramBinMethodsBadDataset::test_lazy_deprecation_warnings[freedman]
FAILED hyperspy/tests/samfire/test_samfire.py::TestSamfireEmpty::test_setup
FAILED hyperspy/tests/model/test_model_storing.py::TestModelSaving::test_save_and_load_model
FAILED hyperspy/tests/model/test_model_storing.py::TestEELSModelSaving::test_save_and_load_model
FAILED hyperspy/tests/signal/test_find_peaks2D.py::TestFindPeaks2D::test_find_peaks[True-dense-stat]
FAILED hyperspy/tests/signal/test_find_peaks2D.py::TestFindPeaks2D::test_find_peaks[True-dense-difference_of_gaussian]
FAILED hyperspy/tests/signal/test_find_peaks2D.py::TestFindPeaks2D::test_find_peaks[True-sparse_nav0d-stat]
FAILED hyperspy/tests/signal/test_find_peaks2D.py::TestFindPeaks2D::test_find_peaks[True-sparse_nav1d-stat]
FAILED hyperspy/tests/signal/test_find_peaks2D.py::TestFindPeaks2D::test_find_peaks[True-sparse_nav2d-stat]
FAILED hyperspy/tests/signal/test_find_peaks2D.py::TestFindPeaks2D::test_find_peaks[False-dense-stat]
FAILED hyperspy/tests/signal/test_find_peaks2D.py::TestFindPeaks2D::test_find_peaks[False-dense-difference_of_gaussian]
FAILED hyperspy/tests/signal/test_find_peaks2D.py::TestFindPeaks2D::test_find_peaks[False-sparse_nav0d-stat]
FAILED hyperspy/tests/signal/test_find_peaks2D.py::TestFindPeaks2D::test_find_peaks[False-sparse_nav1d-stat]
FAILED hyperspy/tests/signal/test_find_peaks2D.py::TestFindPeaks2D::test_find_peaks[False-sparse_nav2d-stat]
FAILED hyperspy/tests/signal/test_find_peaks2D.py::TestFindPeaks2D::test_gets_right_answer[True-stat]
FAILED hyperspy/tests/signal/test_find_peaks2D.py::TestFindPeaks2D::test_gets_right_answer[False-stat]
FAILED hyperspy/tests/signal/test_find_peaks2D.py::TestFindPeaks2D::test_lazy_find_peaks[False-dense-stat]
FAILED hyperspy/tests/signal/test_find_peaks2D.py::TestFindPeaks2D::test_lazy_find_peaks[False-dense-difference_of_gaussian]
FAILED hyperspy/tests/signal/test_find_peaks2D.py::TestFindPeaks2D::test_lazy_find_peaks[False-sparse_nav0d-stat]
FAILED hyperspy/tests/signal/test_find_peaks2D.py::TestFindPeaks2D::test_lazy_find_peaks[False-sparse_nav1d-stat]
FAILED hyperspy/tests/signal/test_find_peaks2D.py::TestFindPeaks2D::test_lazy_find_peaks[False-sparse_nav2d-stat]
FAILED hyperspy/tests/signal/test_find_peaks2D.py::TestFindPeaks2D::test_lazy_gets_right_answer[True-stat]
FAILED hyperspy/tests/signal/test_find_peaks2D.py::TestFindPeaks2D::test_lazy_gets_right_answer[False-stat]
FAILED hyperspy/tests/signal/test_remove_background.py::test_remove_backgound_type[Skew normal]
FAILED hyperspy/tests/signal/test_remove_background.py::test_remove_backgound_type[Skew Normal]
FAILED hyperspy/tests/signal/test_remove_background.py::test_remove_backgound_type[SkewNormal]
FAILED hyperspy/tests/utils/test_roi.py::TestROIs::test_circle_spec - ValueError
= 85 failed, 3608 passed, 75 skipped, 3 xfailed, 55076 warnings, 30 errors in 3835.35s (1:03:55) =
E: pybuild pybuild:379: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_hyperspy/build; python3.10 -m pytest
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.10 returned exit code 13
make: *** [debian/rules:9: build-arch] Error 25
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2022-09-19T12:01:42Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 0
Build-Time: 3898
Distribution: bookworm-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 3365
Job: hyperspy_1.6.1-1
Machine Architecture: armhf
Package: hyperspy
Package-Time: 7353
Source-Version: 1.6.1-1
Space: 0
Status: failed
Version: 1.6.1-1
--------------------------------------------------------------------------------
Finished at 2022-09-19T12:01:42Z
Build needed 00:00:00, 0k disc space