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pymca 2018-04-09
README 2018-04-09 9.9 kB
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Instead of the default download, you may find better suited downloads for your platform under the folder containing the latest release: Notes: See the changes section below for new features. Tutorials can be found at: Ready to use binaries for: - MacOS X: File - Windows 64 bit: File pymca5.3.0-win64.exe Users of other platforms should either: - Build from the source code. - Use PyMca as supplied by your linux distribution. PyMca can also be installed from PyPI. For that just 'pip install pymca' The mimimal dependencies are PyQt4 (or PyQt5 or PySide), numpy, fisx and matplotlib. The package h5py is needed if HDF5 file format support is desired. Changes: VERSION 5.3.0 - 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 generating automatic data selection tables - 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. VERSION 5.2.2 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 labelling 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. VERSION 5.2.1 Correct annoying error message appearing when background is not defined. Update SpecFile license to MIT VERSION 5.2.0 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. MacOS. Frozen binary uses now HDF5 1.10.1 to support SWMR files. VERSION 5.1.4 ROI Imaging tool can add multiple detector signals present in an HDF5 file. Support multiple JCAMP-DX blocks in a file. Support stacks exported by OPUS in JCAMP-DX format. Add basic support of OMDAQ lmf data format. Make sure main window menu options are available under MacOS and Qt5. Support matplotlib 2.0 Correct factor of two error when fitting step up or step down functions. VERSION 5.1.3 Correct minor Qt5 related bugs. Simplify embedding batch fitting in custom workflows. ROI Imaging: Exporting the stack in TIFF format did not respect zoomed region limits Allow exporting the x-ray tube emission continuum from the plot. Implement a "copy-selection-to-clipboard" of the concentrations table via CTRL-C. Fix error message when moving mouse on SCAN window after having used the regular mesh plugin Correct coordinate display on image window. Solve issue calculating shell photoelectric cross-sections close to edges. VERSION 5.1.2 - Adapt to latest SPEC version - Correct compatibility issues with matplotlib 1.5 - Much improved compatibility with Qt 5 - Update to fisx 1.1.0 for windows compatibility under Python 3.5 - Correct the generation of the efficiency plot in the ATTENUATORS tab when BeamFilter0 was selected. That problem only affected the plot, not anything else. - Enable OpenGL window under Python 3 - Implement Kaiser window option for XAS Fourier transform. - Reimplement curve renaming. - Recover interactive console functionality. - Correct the density of H and He. - Add more keywords for QXAS format support. - Allow ADD functionality on customized fit background (allowing multiple atan functions) - Allow the use of the regular mesh plugin on incomplete mesh scans. - Add kinetics related plugins (Rate Laws and Arrhenius-like plots). VERSION 5.1.1 Update to fisx 1.0.4 to workaround issue calculating secondary excitation corrections when the incident beam is normal to the sample surface. Restore pre-5.0.0 behavior in the scan window when displaying mouse coordinates without the crosshair cursor. Correct multiple curve averaging when input arrays are reversed. Add the possibility to save the Monte Carlo generated matrix spectra in the fit window. Correct problem of reapplying the calibration when toggling log and linear axes while already using a calibration. Restore saving of images in png and jpg in the main window. Restore data projection on PCA eigenvectors calculated using the covariance method to the same way as when using the other methods. VERSION 5.1.0 Automatic loading of user plugins. Allow the use of user specified physical constants across different installed versions. Add stack plugin to calculate multiple ROIs in one go. Add basic JCAMP-DX reading support. Add crosshair cursor option to the plot options menu. Add EXAFS extraction capabilities to the Main Window and the ROI Imaging Tool. Improved right axis autoscaling. Panning with the keyboard arrow keys implemented in most 1D plots. Correct bug on customized fit when using anchors. Correct bug saving MCA spectra when using the Taurus plugin. Correct swap of red and blue components when saving via matplotlib. Correct regular mesh plotting. VERSION 5.0.3 Recover Advanced fit graphics saving in logarithmic mode. Slower but correct reading of SPE files. Correctly handle Energy and Channel plot labels. Calculate tertiary excitation in diagnostics tab. Allow stack normalization by an external image. Correct saving of curves in the SCAN window. Add OSMesa backend to the list of available plot backends. Add crosshair cursor option. VERSION 5.0.2 Fast XRF fitting: Correct concentrations calculation. Make license information detectable by licensecheck. VERSION 5.0.1 Fast XRF fitting: Give the user the option not to check for negative peak contributions in order to maximize speed. The default behavior is unchanged. Add copyright information to files missing it. Correct bug: Windows frozen binary could not start batch from main window. Correct bug: Fast XRF fit was not working on dynamically loaded stacks when negative peak contributions were detected. Correct bug: Save action was not active on some plots. VERSION 5.0.0 Analytical secondary excitation corrections. Approximated tertiary excitation corrections. Automatic matrix update. Support .rtx file format stacks Support .rpl + .raw described stacks (Lispix file format) Support SPEC 6.02+ shared memory Possibility to generate PCA scores plot. Incorporate a new repository layout. Most of the source code can be used under MIT or LGPL licenses. Dependency on Qwt (via PyQwt) removed. Possibility to keep image aspect ratio. Improved print preview. MCA Window accepts plugins. Automatic download of user plugins. Any plot accepts ROI selection. VERSION 4.7.4 Support readout of top level datasets in HDF5 files. Improved handling of Tracer csv files. Correct problems reading spec 6.02.07+ shared memory. VERSION 4.7.3 Correct bug using SNIP background with the Fast XRF linear fit stack plugin. Better handling of screen resolutions with 768 vertical pixels. VERSION 4.7.2 Allow fitting of all Cr L lines Correct bug saving image alignment data to disk. Correct bug using linear polynomial background with the Fast XRF linear fit stack plugin VERSION 4.7.1 Support SOLEIL multiple-file different-scan-number maps. Support batch fitting of multiple HDF5 files. Fast XRF linear fit stack plugin. Possibility to load image shifts in the image alignment stack plugin. Basic support of MRC file format. Add ID08 advanced alignment scan plugin. VERSION 4.7.0 Add basic support for calculating multiple excitation corrections via the XMI-MSIM Monte Carlo code. Add Image alignment capabilities to the ROI Imaging tool. Improved handling of HDF5 external links. Solve printing issue when printing from the File menu while the SCAN window is active Recover reading support of SPE files from SLAC Correct reading of .chi files maps Extend the maximum number of counters supported in a specfile. Prevent endless loop in specfile when the last character limiting a scan is '#' Correct bug plotting a set of MCAs as one image when the number of MCA detectors is more than one. Background subtraction methods also work on stack browsers. Handling of scales in image plots. Add ID26 RIXS plugin as part of MultiScanToMesh plugins. Add XMCD and XAS plugins from ID08 and ID12. Add plugin to align curves. Stacks of DESY fio files readable by windows binary. Reduce memory usage when working with large in-memory stacks. Decide to load dynamically the data based on the amount of physical memory installed instead of based on a fixed data size.
Source: README, updated 2018-04-09