MIT version of the PyMca XRF Toolkit

Last update: Nov 23, 2022

Related tags

Miscellaneous pymca

Overview

PyMca

This is the MIT version of the PyMca XRF Toolkit. Please read the LICENSE file for details.

Installation

Ready-to-use packages are available for the most common platforms.

PyMca frozen binaries for MacOS and Windows can be obtained from Sourceforge

Unofficial Debian packages are also available, but you should check if official pacakges are available for your distribution.

Please continue reading if you want to use PyMca with your existing Python installation.

The simplest solution is to use pip:

pip install PyMca5

You can add the usual --user qualifier to install only for your local user rather than system-wide:

pip install PyMca5 --user

If you want to build from the source distribution or from a git repository checkout, you may want to have Cython installed on your system.

Examples of source installation

In your default system-wide python installation, run one or the other of the two (not both) commands below (may require root/administrator access):

# Run one of the following (not both); pip is preferred
python setup.py install    # use python setuptools
pip install .              # use the pip package manager

Or, to install just in your local user account:

# Run one of the following (not both); pip is preferred
python setup.py install --user   # use python setuptool
pip install . --user               # use the pip package manager

You will need the following dependencies installed:

python (3.6 or higher recommended)
numpy
fisx
h5py

If you want to use the graphical interface provided, you will need a running python installation with one of the following combinations:

PyQt5 + matplotlib (PyMca license will be GPL unless you have a commercial PyQt5 license)
PySide2 + matplotlib (PyMca license will be MIT because PySide2 is LGPL)

If you want to embed PyMca in your own graphical applications, I recommend you to use the McaAdvancedFit.py module. It is very easy to embed.

Testing

To run the tests after installation run:

python -m PyMca5.tests.TestAll

Development Plans

Use the fisx library for all Physics calculations and not just for corrections.
Compound fitting.

If you have any questions or comments (or contributions!), please feel free to contact me or submit a pull request.

Enjoy,

V. Armando Sole

Comments

[debian] 5.5.0 problem with tests

Hello armando,

while preparing the Debian package, I got this error. it seems that pymca tests mandata an X connection now.

I: pybuild base:217: cd /builds/science-team/pymca/debian/output/pymca-5.5.0+dfsg/.pybuild/cpython2_2.7_pymca5/build && PYMCA_DATA_DIR=/builds/science-team/pymca/debian/output/pymca-5.5.0+dfsg/PyMca5/PyMcaData/ PYMCA_DOC_DIR=/builds/science-team/pymca/debian/output/pymca-5.5.0+dfsg/PyMca5/PyMcaData/ python2.7 PyMca5/tests/TestAll.py
: cannot connect to X server 
WARNING: Taking PYMCA_DATA_DIR from environment.
Use it at your own risk.
WARNING: Taking PYMCA_DOC_DIR from environement.
Use it at your own risk.
E: pybuild pybuild:341: test: plugin custom failed with: exit code=1: cd /builds/science-team/pymca/debian/output/pymca-5.5.0+dfsg/.pybuild/cpython2_2.7_pymca5/build && PYMCA_DATA_DIR=/builds/science-team/pymca/debian/output/pymca-5.5.0+dfsg/PyMca5/PyMcaData/ PYMCA_DOC_DIR=/builds/science-team/pymca/debian/output/pymca-5.5.0+dfsg/PyMca5/PyMcaData/ python2.7 PyMca5/tests/TestAll.py
dh_auto_test: pybuild --test -i python{version} -p 2.7 returned exit code 13
make[1]: *** [debian/rules:66: override_dh_auto_test] Error 255
make[1]: Leaving directory '/builds/science-team/pymca/debian/output/pymca-5.5.0+dfsg'
make: *** [debian/rules:27: build] Error 2
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
+ cleanup
+ docker rm -f c097b8161a88827305348e74a1b26bf7c3d468e7595daea5162f55facc536da7
c097b8161a88827305348e74a1b26bf7c3d468e7595daea5162f55facc536da7
gbp:error: 'docker-build.sh registry.salsa.debian.org/salsa-ci-team/images/dockerbuilder:unstable' failed: it exited with 1
section_end:1563458464:build_script
[0Ksection_start:1563458464:after_script
[0Ksection_end:1563458465:after_script
[0Ksection_start:1563458465:upload_artifacts_on_failure
[0Ksection_end:1563458467:upload_artifacts_on_failure
[0K[31;1mERROR: Job failed: exit code 1
[0;m
``

So I added xvfb and got these errors:

https://salsa.debian.org/science-team/pymca/-/jobs/225871/raw

does it means something for you ?

opened by picca 43

Batchfit hdf5
The main purpose of this PR is to homogenize batch fitting and fast fitting in terms of output. Most interesting additions are .h5 output and saving of diagnostics (e.g. fit residuals). Apologies for the extensive refactoring.

Comparing GUI for batch and fast fit that provides identical output (in terms of structure):

Changes from a user perspective:

optional output formats like for fast-fitting (most importantly .h5) .csv and .tif are disabled for multiprocessing because merging hasn't been implemented for those

.edf output results in a single multi-image (like in fast-fitting) OutputBuffer has the option to save single-image edf's but this is not exposed by the GUI

concentrations.txt file is only saved when fit files are saved

Some comments on implementation:

Both batch fitting and fast fitting now share the same OutputBuffer (class that takes care of memory allocation and saving)

McaAdvancedFitBatch._processList seems to support multiple non-HDF5 stacks but judging from McaAdvancedFitBatch.__processStack this cannot work I think

The fit configuration is saved in .h5. However only one configuration can be saved while McaAdvancedFitBatch supports multiple configurations.

PyMcaBatch has been refactored (e.g. to support bootstrap). This has only been tested on win32 and debian (non-frozen). Binaries on Mac seem to pass only roifit options, seems strange.

McaAdvancedFitBatch has an _obsolete parameter to preserve the way data was saved before (testing purposes, currently disabled). Keep it or remove?

The files McaAdvancedFitBatch and PyMcaBacth contain several TODO's which indicate some doubts I have on existing functionality (not introduced by this PR).
opened by woutdenolf 26
numpy.ndarray' object has no attribute 'split'

Hello Armando, with 5.4.0, I get this error message each time I click on a hdf5 node.

numpy.ndarray' object has no attribute 'split' File "/usr/lib/python3/dist-packages/PyMca5/PyMcaGui/io/hdf5/QNexusWidget.py", line 618, in hdf5Slot ddict['name']) File "/usr/lib/python3/dist-packages/PyMca5/PyMcaCore/NexusTools.py", line 467, in getScannedPositioners tokens = title.split()

opened by picca 23
External images plugin
ExternalImagesPlugin version based on a silx PlotWidget.

The external image is not reduced in size to fit the stack image size (the scales are simply recalculated).

TODO:

[ ] RGBWidget needs to be modified to accept any image size. Currently an error is raised when two images of different sizes are added.

[x] Handle origin different from (0, 0)
opened by PiRK 22
bunch of files with no licenses header and copyright owner

Hello Armando,

I am preparing the pymca5 package. So once again Ineed to do the license check. Since I will create new binary package

python3-pymca5 etc... this package will be reviewed by the ftpmaster team. They are using this tool also to check for non free files.

So could you fix all these files. This will ease the review at the end.

thanks

Frederic

[email protected]:~/Debian/main/pymca/pymca$ licensecheck -r . | grep UNKN ./PyMca5/PyMcaGraph/ctools/_ctools/cython/MinMax.pyx: No copyright UNKNOWN ./PyMca5/PyMcaGraph/ctools/_ctools/cython/_ctools.py: No copyright UNKNOWN ./PyMca5/PyMcaGraph/ctools/_ctools/cython/InsidePolygonWithBounds.pyx: No copyright UNKNOWN ./PyMca5/PyMcaGraph/ctools/_ctools/cython/_ctools.pyx: No copyright UNKNOWN ./PyMca5/PyMcaGraph/ctools/_ctools/cython/ColormapLUT.pyx: No copyright UNKNOWN ./PyMca5/PyMcaGraph/ctools/_ctools/include/MinMax.h: No copyright UNKNOWN ./PyMca5/PyMcaGraph/ctools/_ctools/include/ColormapLUT.h: No copyright UNKNOWN ./PyMca5/PyMcaGraph/ctools/_ctools/include/InsidePolygonWithBounds.h: No copyright UNKNOWN ./PyMca5/PyMcaGraph/ctools/_ctools/setup.py: No copyright UNKNOWN ./PyMca5/PyMcaGraph/ctools/_ctools/src/InsidePolygonWithBounds.c: No copyright UNKNOWN ./PyMca5/PyMcaGraph/ctools/_ctools/src/MinMaxImpl.c: No copyright UNKNOWN ./PyMca5/PyMcaGraph/ctools/_ctools/src/ColormapLUT.c: No copyright UNKNOWN ./PyMca5/PyMcaGraph/ctools/init.py: No copyright UNKNOWN ./PyMca5/Object3D/Object3DQhull/Object3DQhull.c: No copyright UNKNOWN ./PyMca5/Object3D/Object3DCTools/MarchingCubes.c: No copyright UNKNOWN ./PyMca5/Object3D/Object3DCTools/setup.py: No copyright UNKNOWN ./PyMca5/Object3D/Object3DCTools/marchingsource.cpp: No copyright UNKNOWN ./PyMca5/Object3D/init.py: No copyright UNKNOWN ./PyMca5/EPDL97/GenerateEADLShellNonradiativeRates.py: No copyright UNKNOWN ./PyMca5/EPDL97/EADLParser.py: No copyright UNKNOWN ./PyMca5/EPDL97/EPDL97Parser.py: No copyright UNKNOWN ./PyMca5/EPDL97/GenerateEPDL97TotalCrossSections.py: No copyright UNKNOWN ./PyMca5/EPDL97/GenerateEADLBindingEnergies.py: No copyright UNKNOWN ./PyMca5/EPDL97/EADLSubshells.py: No copyright UNKNOWN ./PyMca5/EPDL97/GenerateEADLShellRadiativeRates.py: No copyright UNKNOWN ./PyMca5/EPDL97/init.py: No copyright UNKNOWN ./PyMca5/EPDL97/GenerateEADLShellConstants.py: No copyright UNKNOWN ./PyMca5/EPDL97/GenerateEPDL97CrossSections.py: No copyright UNKNOWN ./PyMca5/PyMcaIO/specfile/setup.py: No copyright UNKNOWN ./PyMca5/PyMcaIO/edf/setup.py: No copyright UNKNOWN ./PyMca5/PyMcaIO/sps/setup.py: No copyright UNKNOWN ./PyMca5/PyMcaIO/sps/Include/sps.h: UNKNOWN ./PyMca5/PyMcaIO/sps/Include/blissmalloc.h: UNKNOWN ./PyMca5/PyMcaIO/sps/Include/spec_shm.h: UNKNOWN ./PyMca5/PyMcaIO/sps/Src/sps.c: UNKNOWN ./PyMca5/PyMcaIO/sps/Src/sps_py.c: UNKNOWN ./PyMca5/PyMcaIO/MEDFile.py: UNKNOWN ./PyMca5/PyMcaGui/misc/QIPythonWidget.py: No copyright UNKNOWN ./PyMca5/PyMcaPlugins/CalculationThread.py: No copyright UNKNOWN ./PyMca5/PyMcaMath/mva/Lanczos.py: UNKNOWN ./PyMca5/PyMcaMath/mva/py_nnma/setup.py: No copyright UNKNOWN ./PyMca5/PyMcaMath/mva/py_nnma/nnma.py: UNKNOWN ./PyMca5/PyMcaMath/mva/py_nnma/init.py: No copyright UNKNOWN ./PyMca5/PyMcaMath/mva/NNMAModule.py: UNKNOWN ./PyMca5/PyMcaMath/PyMcaSciPy/signal/mediantools.c: UNKNOWN ./PyMca5/PyMcaMath/PyMcaSciPy/signal/median.py: No copyright UNKNOWN ./PyMca5/PyMcaMath/PyMcaSciPy/signal/medianfilter.c: No copyright UNKNOWN ./PyMca5/PyMcaMath/PyMcaSciPy/signal/init.py: No copyright UNKNOWN ./PyMca5/PyMcaMath/linalg.py: UNKNOWN ./PyMca5/PyMcaMath/sift/interpolation.py: No copyright UNKNOWN ./PyMca5/PyMcaMath/sift/sift.py: No copyright UNKNOWN ./PyMca5/PyMcaMath/sift/param.py: No copyright UNKNOWN ./PyMca5/PyMcaMath/sift/init.py: No copyright UNKNOWN

opened by picca 21

[debian] please use setuptools requires in order to provide the build dependencies

Hello,

In order to build pymca and run the tests during the build, I needed to add all these dependencies. It is possible to automatically generate the Debian binary dependency from the setup.py (like for pyFAI or silx). It would be great if you could provide this for pymca.

Then I could maintain a patch on top of this for Debian, in order to deal with the pyqt5 (dependency). I am not sure thaht pyqt5 provide eggs infor for this purpose.

I got these informations looking at the autodoc sphinx part during the build.

Cheers

                python-fisx-dbg <!nocheck>,
+               python-h5py <!nocheck> <!nodoc>,
+               python-h5py-dbg <!nocheck> <!nodoc>,
+               python-ipython,
+               python-matplotlib <!nodoc>,
+               python-matplotlib-dbg <!nodoc>,
                python-numpy,
                python-numpy-dbg,
+               python-opengl,
+               python-pyqt5 <!nodoc>,
+               python-pyqt5-dbg <!nodoc>,
+               python-pyqt5.qtopengl <!nodoc>,
+               python-pyqt5.qtopengl-dbg <!nodoc>,
+               python-pyqtgraph,
+               python-qtconsole,
                python-setuptools,
                python-sphinx,
                python-typing,
                python3-all-dbg,
                python3-all-dev,
                python3-fisx <!nocheck>,
                python3-fisx-dbg <!nocheck>,
+               python3-h5py <!nocheck> <!nodoc>,
+               python3-h5py-dbg <!nocheck> <!nodoc>,
+               python3-ipython,
+               python3-matplotlib <!nodoc>,
+               python3-matplotlib-dbg <!nodoc>,
                python3-numpy,
                python3-numpy-dbg,
+               python3-opengl,
+               python3-pyqt5 <!nodoc>,
+               python3-pyqt5-dbg <!nodoc>,
+               python3-pyqt5.qtopengl <!nodoc>,
+               python3-pyqt5.qtopengl-dbg <!nodoc>,
+               python3-pyqtgraph,
+               python3-qtconsole,
                python3-setuptools,
                python3-sphinx

opened by picca 14

Windows build lacks HDF5 SWMR support

Hi Armando,

We have noticed that we cannot open our NXS files that were produced in SWMR mode with the currently available Windows build of PyMca. Since it works fine on our Linux systems which have access to HDF5 1.10.0, I guess the Windows build contains HDF5 1.8.x?

Thanks for looking into this,

Tom

opened by tschoonj 13
Fix rounding within OmnicMap's getPositionFromIndexAndInfo
This PR aims to fix an intermittent issue in reading positions from maps.

@clsandt sent me a map where:

deltaX = 49.97058868408203

x0 = -815.0

x1 = 884.0

The number of jumps (intervals) in X is ((x1 - x0) / deltaX) which is 33.9999996946446, which means that the number of measurements nX is 33.9999996946446 + 1.

The old code wrongly rounded this down. This is what the consequences look like:

The new code rounds before converting to int so it is more robust to numeric inaccuracies. I think the change is self-explanatory. After the change (also as Omnic's software shows it):
opened by markotoplak 10
CentOS6 'QPainterPath' object has no attribute 'translate'

When I start pymca on a CentOS6 (2.6.32-431.29.2.el6.x86_64) system, I get the following error messages.

$pymca

the GUI start popup appears for abt. 1sec, then quits and there are the following messages in the terminal:

Traceback (most recent call last): File "./pymca", line 10, in execfile(fname) File "/usr/lib64/python2.6/site-packages/PyMca5/PyMcaGui/pymca/PyMcaMain.py", line 163, in from PyMca5.PyMcaGui.pymca import ScanWindow File "/usr/lib64/python2.6/site-packages/PyMca5/PyMcaGui/pymca/ScanWindow.py", line 44, in from PyMca5.PyMcaGui.plotting import PlotWindow File "/usr/lib64/python2.6/site-packages/PyMca5/PyMcaGui/plotting/PlotWindow.py", line 43, in from . import LegendSelector File "/usr/lib64/python2.6/site-packages/PyMca5/PyMcaGui/plotting/LegendSelector.py", line 80, in Symbols['x'].translate(qt.QPointF(-0.5,-0.5)) AttributeError: 'QPainterPath' object has no attribute 'translate'

The installation was without error messages and dependencies should be met. Any idea?

Thanks Jan

opened by jangobash 9
can't open pymca after installation

Hi I installed pymca 5.5.0 on my laptop, but after installation is finished, I clicked open then a black screen pops out. I barely have time to read what is on before it dissappears itself. Anyone has the same issues? What I should do? Thanks!

opened by XinFeng222 8
[debian] AttributeError: 'module' object has no attribute 'QGLWidget'

Hello, whne building pymca, I get this error

WARNING: autodoc: failed to import module u'PyMca5.Object3D.SceneGLWidget'; the following exception was raised: Traceback (most recent call last): File "/usr/lib/python2.7/dist-packages/sphinx/ext/autodoc/importer.py", line 140, in import_module import(modname) File "/<>/pymca-5.3.0+dfsg/.pybuild/cpython2_2.7_pymca5/build/PyMca5/Object3D/SceneGLWidget.py", line 36, in from . import Object3DRedBookFont File "/<>/pymca-5.3.0+dfsg/.pybuild/cpython2_2.7_pymca5/build/PyMca5/Object3D/Object3DRedBookFont.py", line 153, in class TestWidget(qt.QGLWidget): AttributeError: 'module' object has no attribute 'QGLWidget'

on Debian unstable the Qt5 available is 5.10. It seems that the pyqt5 removed this old compatibility layer...

opened by picca 8
[IO] [HDF5][ROI Imaging] Offser subsampling when working with huge HDF5 files

Currently HDF5Stack1D proceeds to load dynamically the data if they do not fit into memory.

It would be convenient to offer the user the alternative to sub-sample the data.

Monitor and positions would have to be sub-sampled too.

opened by vasole 0

Import from blissdata instead of bliss

The blissdata package is a much lighter dependency than bliss. It is available on pypi and anaconda.

# PyMca5/PyMcaCore/RedisTools.py

from bliss.config import get_sessions_list
from bliss.config.settings import scan as rdsscan
from bliss.data.node import get_node, get_nodes

# PyMca5/PyMcaCore/RedisTools.py

from bliss.config import get_sessions_list  # TODO
from blissdata.settings import scan as rdsscan
from blissdata.data.node import get_node, get_nodes

get_sessions_list is unfortunately not in blissdata. I'll try to make that happen.

FYI: soon blissdata will also work without gevent.

opened by woutdenolf 0

[HDF5] Change double-click behavior?
To access show info via the context menu seems counter-intuitive.

To change the behavior would imply:

Double-click as a short-cut to Show Information (equivalent to silx)

Single-click to show the context menu

Right-click unchanged (identical to context menu)

For datasets it seems fine, I am not so sure about groups.
opened by vasole 6

Releases(v5.8.0)

v5.8.0(Nov 14, 2022)
IO. Add support of Bruker bcf files

ROI Imaging. Allow spatial downsampling of EDF stacks not fitting into memory.

Graphics. Correct bug affecting visualization of large images with Matplotlib 6.0+

Source code(tar.gz)
Source code(zip)
v5.7.6(Sep 30, 2022)
HDF5. Correct error when selecting a monitor.

HDF5. Correct handling of broken links.

XRF. Raise the maximum number of matrix iterations.

ROI Imaging. Correct calculation of spectrum of the maximum at each channel.

GUI. Make sure QSize uses integers and not floats.

IO. Correct shape calculation of Omnic maps.

Source code(tar.gz)
Source code(zip)
v5.7.5(Aug 19, 2022)
Packaging. Correct PyInstaller packaging.

HDF5. Correct Show Info not working with PySide 6.

ROI Imaging. Add spectrum of the maximum at each channel.

GUI. Elements Info update line emission ratios when changing energy without need to ckick on the periodic table.

Source code(tar.gz)
Source code(zip)
v5.7.4(Aug 2, 2022)
HDF5. Improved support of external links PR #891.

HDF5. Single MCA selections accompanied by associated motor positions (if any).

XRF. Make more explicit the Fast XRF fit is a linear fit.

ROI Imaging. Clearer tool tips.

Source code(tar.gz)
Source code(zip)
v5.7.3(Jul 22, 2022)
Allow project build and test under Python 3.11

HDF5. Improved support of external links.

HDF5. Simplify single MCA selection in multidimensional datasets.

XRF. Enable copy to clipboard from the tables.

GUI. Add -log(y/yactive) to the list of normalization options.

IO. Support LabSpec6 exported maps.

Source code(tar.gz)
Source code(zip)
v5.7.2(Apr 8, 2022)
IO. Robust access to HDF5 files while being written.

IO. Support ProSpect v1.1.36

ROI Imaging. Double click on Stack Window adds spectrum to MCA window.

Support building of frozen binaries with PyInstaller

Source code(tar.gz)
Source code(zip)
v5.7.1(Jan 18, 2022)

Correct GUI issue with the combination Python 3.10 and PyQt5
Source code(tar.gz)
Source code(zip)
v5.7.0(Jan 13, 2022)
Add PySide2 and PySide6 support

Drop PySide and PyQt4

Drop PyMca's internal OpenGL backend (Object3D module)

Source code(tar.gz)
Source code(zip)
v5.6.7(Nov 25, 2021)

Minor release to fix compatibility with matplotlib 3.5.0
Source code(tar.gz)
Source code(zip)
v5.6.6(Nov 23, 2021)
This is a minor release motivated by the incompatibility with recent Matplotlib versions.

Graphics. Recent versions of Matplotlib do not support picker=None.

IO. Support AXAS-D format independently of using "," or "." as decimal separator.

IO. Calculate live time as elapsed time * OCR/ICR in AXAS-D format

Source code(tar.gz)
Source code(zip)
v5.6.5(Apr 9, 2021)
PyMcaBatch. Prevent the use of the input directory as output directory when the input file list is a single HDF5 file.

PyMcaBatch. Allow XRF batch fitting of a single entry in an HDF5 file containing multiple maps.

PCA. Deal with NaNs in stacks of spectra.

SPS. Correct SPEC shared memory access under Python 3.8

Adapt XIA Correct tool to python 3.

K-means. Filter non-finite numbers.

GUI. Allow the user to choose derivative order and algorithm.

IO. Read live time from KETEK AXAS-D.

IO. Deal with Renishaw files containing a single line header.

Source code(tar.gz)
Source code(zip)
v5.6.3(Nov 9, 2020)
XRF. Allow to take user supplied transmission tables as attenuators.

IO. Allow sorting of entries in NeXus files by title.

Source code(tar.gz)
Source code(zip)
v5.6.2(Oct 23, 2020)
IO. h5py 3.0.0 compatibility

Double-check OpenGL availability on startup

Allow building from source under linux without OpenGL

Source code(tar.gz)
Source code(zip)
v5.6.1(Oct 14, 2020)
K-Means. Subtract minimum of each feature prior to scaling.

IO. Improved user experience using HDF5 files.

IO. More robust access to redis.

IO. Automatic update of data from redis when last scan is selected.

Source code(tar.gz)
Source code(zip)
v5.6.0(Sep 24, 2020)
RGB Correlator. Implement K-means clustering on user selected images.

RGB Correlator. Provide a shape command line argument to simplify reading of HDF5 groups.

ROI Imaging. Support mask selections from the RGB correlator.

ROI Imaging. Save stacks with calibration, live times and positioners.

IO. Provide access to bliss data via redis.

GUI. Deal with matplotlib warnings.

Plugins. Correct numpy 1.19.x related issues.

Source code(tar.gz)
Source code(zip)
v5.5.5(Apr 13, 2020)
XRF. Allow to use up to 15 elements to refine the sample matrix.

IO. Support ARTAX files in PyMca Main window.

IO. Read motor positions from ARTAX files.

IO. Correct issues reading ARTAX and Olympus files in MacOS.

ROI Imaging. Allow to choose to perform PCA on standardized data.

ROI Imaging. Allow multiple slaves.

ROI Imaging. Do not close application when deleting slave stacks.

Plugins. Correct MotorInfo problem of table containing duplicates.

Source code(tar.gz)
Source code(zip)
v5.5.4(Jan 10, 2020)
XRF. Make PyMca compatible with recent XMI-MSIM versions

XRF. Handle the use of the % character when defining materials

ROI Imaging. Add action to export all PCA and NNMA vectors.

ROI Imaging. Support the use of regions with NNMA.

Source code(tar.gz)
Source code(zip)
v5.5.3(Oct 21, 2019)
HDF5. Handle broken top level external links.

XRF. The fit configuration was not fitting into desktop when using large font scaling.

Enable ICA calculations on HDF5 stacks.

Source code(tar.gz)
Source code(zip)
v5.5.2(Oct 3, 2019)
Add compatibility with the new h5py default file opening mode.

Source code(tar.gz)
Source code(zip)
v5.5.1(Aug 26, 2019)
Qt binding selection tries PyQt5, PySide2, PyQt4 and PySide in that order.

PyMcaBatch: Deal with spaces in the path to the fit configuration file.

Prevent starting crash using some versions of PySide2.

Source code(tar.gz)
Source code(zip)
v5.5.0(Jul 11, 2019)
XRF: Include full-analysis provenance in HDF5 output files.

Improved support of HDF5

Improved testing suite.

ROI Imaging: Improved memory handling when reading multiple HDF5 detectors as input.

ROI Imaging: Support PerkinElmer FSM file format

ROI Imaging: Correct reading OMNIC files under Python 3 in non-windows platforms.

Support PySide2

Support Matplotlib 3.1.x

Preliminary support of Python 3.8

Drop silx dependency.

Source code(tar.gz)
Source code(zip)
v5.4.3(Jan 7, 2019)
Fix SPEC shared memory update during scans bug introduced in 5.4.0

Make default binding PyQt4 under Python 2

Source code(tar.gz)
Source code(zip)
v5.4.2(Dec 20, 2018)
More robust reading of positioners from NeXus files

Respect the nativefiledialogs flag in McaAdvancedFit

Deal with underscore when sorting NeXus files by entry name

RGBCorrelator: Correct attribute error reading .dat files under Python 3

Source code(tar.gz)
Source code(zip)
v5.4.1(Nov 15, 2018)
Support NeXus default attribute at any level

Fix problems in systems where both PyQt4 and PyQt5 are installed.

Fix ScanFit print

Fix mask visibility on monocrome colormaps.

Prevent problems accessing NeXus files when title is incorrectly written as an array instead of being a string.

Enable multiple processes batch fitting a single HDF5 file.

Source code(tar.gz)
Source code(zip)
v5.4.0(Sep 19, 2018)
Add training exercises to the tutorials

Support quantification accounting for live time when using HDF5 files

Add higher order excitation example to the training data

Use silx toolkit for graphics

Allow the user to select a particular Qt binding (--binding option, default is PyQt5 use --binding=PyQt4 for old binding)

Implement a user selectable logging level (--logging option, default is warning)

Correct handling of repeated elements in the sample matrix

Correct readout of lispix data

Source code(tar.gz)
Source code(zip)
v5.3.2(Jul 11, 2018)
This is a minor release motivated by the difficulties encountered to build PyMca under Python 3.7 due to the presence of generated, incompatible, cython code.

Fix build issues under Python 3.7

Fix numpy 1.14.x deprecation warnings

Continue the documentation improvements

Source code(tar.gz)
Source code(zip)
v5.3.1(Apr 27, 2018)
PyMcaMainWindow. Correct error trying to use HDF5 files with only top level datasets.

PyMcaBatch. Correct error when opening HDF5 files as input.

Use QOpenGLWidget when available instead of QGLWidget. It solves a Debian packaging issue.

Prepare web pages using sphinx to be ready for easy deployment of improved documentation (accessible from http://www.silx.org)

Source code(tar.gz)
Source code(zip)
v5.3.0(Apr 9, 2018)
XRF. Correct several Single Layer Strategy issues.

XRF. Support calibration readout using HDF5 files.

XRF. Support time readout and use of time information from HDF5 files.

HDF5. Simplify HDF5 data selection handling by generating automatic data selection tables besides the user defined one (requires use of a measurement group)

HDF5. Support readout of motor positions together with curve data when following ESRF and Sardana standards.

HDF5. Support NXdata and default plots (requires silx)

Add plugin to fit all curves present in a 1D window (requires h5py)

ROI Imaging. No limit on the number of slaves.

Add tomographic reconstruction capabilities (requires freeART and tomoGUI)

Allow to build PyMca using GLIBC 2.26

Activate Continuous Integration.

Source code(tar.gz)
Source code(zip)
v5.2.2(Nov 23, 2017)
ROI Imaging. Correct problem normalizing integer data by integer monitor.

HDF5 Widget. Use PyMca plugins on silx data viewer.

HDF5 Batch. Correct error when all the entries in an HDF5 file do not present the same structure.

SPEC shared memory. Correct counter labeling order in case of using 10 or more counters and motors in a scan.

NeXus. Interpret new style NXdata groups using silx NXdataViewer if silx is installed.

Add script to build debian packages

Source code(tar.gz)
Source code(zip)
v5.2.0(Sep 1, 2017)
XRF: Enforces the use of fisx library 1.1.4 or above. Calculation of secondary excitation corrections with previous versions could give wrong results when using monochromatic excitation with energy very close to the absorption edge of the element primarily excited.

XRF: Deal with the case the mass fraction is zero in one of the compounds of a material. It can arrive when applying a Strategy.

RGB Correlator can now export the data as a single TIFF file or as multiple TIFF files.

Extend the command line usage of the FastXRFLinearFit module to HDF5 datasets.

ROI Imaging. Improved external images plugin. It requires silx.

ROI Imaging. Plugin to display per pixel information (motors and others). It requires silx.

ROI Imaging. Allow to sum the master and the slave stack. It can be used to sum an arbitrary number of stacks.

Implement a calculation cache to speed up secondary excitation calculations.

Allow to use fisx library for the calculation of escape peaks. Default is disabled.

Improved support of OMDAQ lmf format.

Correct bug affecting the calculation of ROIs when the x axis coordinates are negative

MacOS. Correct bug on startup when reading the default configuration.

Source code(tar.gz)
Source code(zip)

Owner

V. Armando Solé

GitHub Repository

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MIT version of the PyMca XRF Toolkit

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Comments

the GUI start popup appears for abt. 1sec, then quits and there are the following messages in the terminal:

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