forked from linupi/pymca
-
Notifications
You must be signed in to change notification settings - Fork 3
/
changelog.txt
1404 lines (767 loc) · 39.6 KB
/
changelog.txt
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
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
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
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
VERSION 5.9.2
-------------
- XRF. Prevent considering twice the same element when using the SingleLayerStrategy.
- Packaging. Compatibility with PyInstaller 6.x
- GUI. Improved PyQt6 compatibility.
- GUI. Compatibility with current silx master branch.
- GUI. Add histogram of pixel intensities to image views (requires silx).
VERSION 5.9.1
-------------
- ROI Imaging. It is now possible to apply NNMA on stacks of images.
- ROI Imaging. HDF5 stacks of images could not be selected due to a bug introduced in 5.8.2.
- MCA. Correct ID18 calibration issues.
VERSION 5.9.0
-------------
- IO. Compatibility with h5py 2.10 (Ubuntu 20.04)
- GUI. Compatibility with Matplotlib 3.8
VERSION 5.8.9
-------------
- FastXRF. Restore compatibility with dynamically loaded HDF5 data
VERSION 5.8.8
-------------
- GUI. Compatibility with matplotlib 3.7.x
VERSION 5.8.7
-------------
- ROI Imaging. Correct plugin threading issues introduced in version 5.8.2
VERSION 5.8.6
-------------
- XRF. Correct threading issue on MacOS introduced in version 5.8.2
VERSION 5.8.5
-------------
- RGB Correlator. Add the possibility to calculate the mean ratio and the median ratio of selected pixels.
- Packaging. Correct issue preventing packaging for Ubuntu 20.04
VERSION 5.8.4
-------------
- XRF. Correct configuration error when number of energies is more than 4 but less than 10.
- RGB Correlator. Add the possibility to calculate the correlation coefficient of selected pixels.
VERSION 5.8.3
-------------
- Adapt to conda-forge.https://github.com/conda-forge/pymca-feedstock/pull/34
VERSION 5.8.2
-------------
- XRF. Allow multithreading with fisx > 1.3.0
- GUI. Save user preferences concerning default actions.
- GUI. Recover loading of user-saved HDF5 selection tables.
- GUI. Synchronize index-based Signal selections with Monitor and Axes on HDF5 files.
- GUI. Compatibility with PyQt6 shipped with Qt 6.4.3
- 1d-Plots. When one plot axis is frozen, reset zoom based on displayed portion of the active curve.
- Packaging. Add cx_Freeze support.
VERSION 5.8.1
-------------
- GUI. Add PyQt6 support.
- GUI. Adapt to PySide 6.4.x
- GUI. Add link to documentation pages under the Help menu.
- RGB Correlator. Add mask statistics calculator.
- ROI Imaging. Calculate maximum spectrum of masked region.
- ROI Imaging. Do not remove spaces from user specified output path in Fast XRF linear fit plugin.
- ScanWindow. Calculate derivative when dealing with strictly decreasing and full-negative X axis values.
- Python. Remove dependency on deprecated distutils module.
VERSION 5.8.0
-------------
- 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+
VERSION 5.7.6
-------------
- 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.
VERSION 5.7.5
-------------
- 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.
VERSION 5.7.4
-------------
- 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.
VERSION 5.7.3
-------------
- 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.
VERSION 5.7.2
-------------
- 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
VERSION 5.7.1
-------------
- Correct GUI issue with the combination Python 3.10 and PyQt5
VERSION 5.7.0
-------------
- Support PySide2 and PySide6.
- Drop Qt4 support (PyQt4 and PySide)
- Drop Object3D module.
VERSION 5.6.7
-------------
- Graphics. Fast XRF fitting results visualization not working with matplotlib 3.5.0
VERSION 5.6.6
-------------
- 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
VERSION 5.6.5
-------------
- 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.
VERSION 5.6.4
-------------
- 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.
VERSION 5.6.3
-------------
- XRF. Allow to take user supplied transmission tables as attenuators.
- IO. Allow sorting of entries in NeXus files by title.
VERSION 5.6.2
-------------
- IO. h5py 3.0.0 compatibility
- Double-check OpenGL availability on startup
- Allow building of PyMca under linux without OpenGL
VERSION 5.6.1
-------------
- 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.
VERSION 5.6.0
-------------
- 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.
VERSION 5.5.5
-------------
- 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.
VERSION 5.5.4
-------------
- 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.
VERSION 5.5.3
-------------
- HDF5. Handle broken toplevel external links
- XRF. The fit configuration window was too high when using large font scaling.
- Enable ICA calculations on HDF5 stacks.
VERSION 5.5.2
-------------
- HDF5: Make the code compatible with new h5py default file opening mode.
VERSION 5.5.1
-------------
- 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 start crash using PySide2.
VERSION 5.5.0
-------------
- 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 as hard dependency. Keep it as optional dependency.
- Default to silx (if present) for 3D and scatter plots.
VERSION 5.4.3
-------------
- Fix SPEC shared memory update during scans bug introduced in 5.4.0
- Make default binding PyQt4 under Python 2
VERSION 5.4.2
-------------
- 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
VERSION 5.4.1
-------------
- 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.
VERSION 5.4.0
-------------
- Add training exercises to the tutorials
- Support quantification accounting for live time when using HDF5 files
- Add higher order excitations example to the training data
- Use silx toolkit for graphics
- Allow the user to select a particular Qt binding (--binding option, default is PyQt5)
- 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
VERSION 5.3.2
-------------
- Fix build issues under Python 3.7
- Fix numpy 1.14.x deprecation warnings
- Continue the documentation improvements
VERSION 5.3.1
-------------
- 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)
VERSION 5.3.0
-------------
- XRF
Correct several Single Layer Strategy issues.
Support calibration readout using HDF5 files.
Support time readout and use of time information from HDF5 files.
- HDF5
Simplify HDF5 data selection handling by generatic automatic data selection tables besides the user defined one (requires use of a measurement group)
Support readout of motor positions together with curve data when following ESRF and Sardana standards.
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.
- Adopt MIT license for SpecFile library
VERSION 5.2.0
-------------
- RGB Correlator can now export the data as a single TIFF file or as multiple TIFF files.
- 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.
- Extend the command line usage of the FastXRFLinearFit module to HDF5 datasets.
- ROI Imaging.
- Improved external images plugin. It requires silx.
- Plugin to display per pixel information (motors and others). It requires silx.
- Allow to sum the master and the slave stack. It can be used to sum an arbitrary number of stacks.
- Selecting multiple HDF5 datasets as signal generates a stack that is the sum of all of the datasets.
- 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.
- 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
-------------
- Correct the generation of the efficiency plot in the ATTENUATORS tab when BeamFilter0 was selected. That problem only affected the plot, not anything else.
- Adapt to latest SPEC version
- Correct compatibility issues with matplotlib 1.5
- Improved compatibility with Qt 5
- Update to fisx 1.0.9 for windows compatibility under Python 3.5
- 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 from 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
-------------
- Correct bug reading HDF5 top level datasets.
- Improved handling of Bruker/Tracer CSV files
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.
VERSION 4.6.2
-------------
- Fix calculation of the MCA associated to a region when using dynamically loaded 1D stacks.
- Fix scan XANES normalization. All curves normalized instead of just the active one.
VERSION 4.6.1
-------------
- Support GZIP compressed EDF files (extensions: edf.gz, ccd.gz, raw.gz)
- Fix annoying issue of having to select the left side of a pixel in order to have the pixel actually selected.
- Fix windows problem of PyMca not starting when the "My Documents" folder has been relocated (issue number 3537267)
- Fix Debian hurd-i386 build from source problem.
VERSION 4.6.0
-------------
- Add an X-ray fluorescence spectrum for training purposes.
- Improved unicode support.
- Added a simple stack normalization plugin to the ROI tool.
- Added a simple XANES normalization plugins to the ROI tool and the scan window.
- Adapt installation script to simplify linux distribution maintainers task.
- Add a minimalistic set of post-installation tests.
- Add man pages.
- Correct variance information displayed in the terminal window.
- Restore functionality of colormap-based mask calculation.
- Add a progress bar to the stack simple fitting plugin.
- Possibility to perform simple fitting of masked stack regions.
VERSION 4.5.0
-------------
- Support h5py version 2.x
- Support OMNIC 8.x .map file format
- Support TIFF format. Uncompressed and packbits.
- Support a couple of ASCII based file formats of beamlines of Diamond and APS.
- Preliminary Python 3.2 support.
- Support principal components analysis of dynamically loaded stacks.
- Improved HDF5 file format handling.
- Possibility to visualize variable width line profiles on images.
- Add split Gauss, split Lorentz and split Pseudo-Voigt as fitting functions.
- Do not automatically sort the list of files to be treated in batch mode. The program will respect the order provided by the user.
- Allow visualized 3D objects to share the same colormap.
- Lower the energy threshold in order to consider Boron K X rays.
- Correct Arsenic density.
- Allow to customize the saving of Scan window curves using matplotlib.
- Allow multiple processes in MacOS X when using a non frozen PyMca version.
VERSION 4.4.1
-------------
- Allow detailed customization of 1D output.
- Add simple normalization plugins to the Scan window.
- Implement a plugin system for the ROI Imaging tool.
- Implement a generic batch fitting of stacks as a stack plugin. The functions are totally specified by the user.
- Implement simple background removal tools as stack plugins.
- Implement an alternative ROI window as a stack plugin.
- Support convertion of big EDF image stacks to HDF5.
- Visualization of large image stacks via dynamic loading and use of HDF5.
- Support MDP based PCA and ICA on user selected regions.
- Read calibration from OMNIC 7.x .map files.
- Support Bruker Opus maps exported in DPT format.
- Improve the reading speed of TwinMic .dta files.
- Add simple MarCCD support.
- Add very simple support for some flavours of Pilatus CBF.
- Show file header information.
- Properly handle Amptek MCA calibration when more than two points or ROIs have been used.
- Allow Savitzky-Golay (SG) filtering of stacks.
- Correct problem affecting odd order SG derivatives.
- Very primitive HDF5 2D Visualization.
- Possibility to visualize HDF5 3D datasets as series of images.
- Implement a context menu on the main window HDF5 browser.
- Table visualization of non-numerical HDF5 datasets.
- Support segmented HDF5 files using default segmentation.
- Allow the use of several processes when batch fitting a single HDF5 file.
- Allow reading of pure image formats in the RGB correlator.
- The fit configuration window was too high for Mac computers having exactly 800 pixels vertical resolution.
- Workaround a windows problem when trying to select thousands of files in the batch file dialog by using Qt file dialogs.
- Minor visualization and data handling improvements.
- Prevent a crash when the excitation energy is below 1 keV.
- Add a script to build PyMca from source on Debian or Ubuntu systems.
- Make specfile LC_NUMERIC locale independent to solve Debian bug report 602471.
- Unify the sps library used by PyMca and the one used by Certified Scientific Software package SPEC. Use a BSD like license for the associated code.
VERSION 4.4.0
-------------
- Extend the usability of the code down to 100 eV extending XCOM mass attenuation coefficients with EPDL97 data when energies are below 1 keV.
- Alternative background subtraction algorithm (SNIP) implemented.
- Support of HDF5 file format.
- Possibility to export ROI imaging tool data stack in HDF5.
- Workaround 32-bit limit when handling huge EDF maps in 32-bit machines.
- Better customization capabilities when saving images through matplotlib.
- Support Fit2D .chi files.
- Simple support of ADSC files wrapping them as EDF files.
- Possibility to save images as 32-bit floats for people using the ImageJ EDF plugin.
- Support combined PCA when using two data stacks.
- Support Independent Component Analysis via MDP if installed.
- Support non-negative Matrix Approximation Analysis using Uwe Schmitt modules (http://public.procoders.net/nnma/)
- Add multivariate analysis capabilities to the RGBCorrelator.
- Implement a mechanism to add plugins to 1D plots.
- Implement simple 3D visualization capabilities.
- Solve X-ray tube profile generation problems at tube voltages below 20 kV.
- Allow a greater number of energies defining the X-ray tube emission profile.
- Correct logarithmic colormap handling.
- Correct colormap problems in 64-bit platforms.
- Correct problem preventing data calibration in some 64-bit platforms.
- Minor bugs corrected and minor features added.
VERSION 4.3.0
-------------
- Speed up fit configuration when using multiple energies.
- Import/export the multiple energies beam description as CSV files.
- Possibility to calculate transmission curves added to the tools menu.
- Offer the possibility to use an additional filter in the x-ray tube setup.
- Visualization of the absorption and the detector contribution to the efficiency.
- Prevent the use of trailing spaces in the definition of materials.
- Implement zoomed window panning (press CTRL key and desired arrow key simultaneously).
- Offer contour plot customization when saving images though matplotlib.
- Possibility to flip external images used for selection in the ROI imaging tool.
- Numpy 1.2 runtime deprecation warnings suppressed.
- Interpolated mass attenuation coefficients were between 0 and 3 % overestimated.
- Correct a bug appearing when trying to fit separate Ka and Kb lines of elements above Rb.
VERSION 4.2.6
-------------
- Add very basic spx file format support.
- Improved SPE file format support.
- Improved semilogarithmic Y axis toggling.
- Correct a problem appearing when adding curves to the scan window in show points only mode.
- Offer the possibility to choose between Qt and native file dialogs through the PyMca command line argument --nativefiledialogs=1.
- Allow overwriting ROI definition files.
- Two column ASCII files were not read in the ROI Imaging.
- Implement the ROI Imaging --fileindex=1 command line option to deal with the case the EDF map was column oriented instead of row oriented.
- Add the possibility to transpose the resulting images of a batch fitting by passing the --fileindex=1 option to PyMcaPostBatch.
- Add threshold selection methods.
- Implement selections from external images.
- Correct a bug affecting saving of McaAdvancedFit data in CSV format.