changelog.txt

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 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

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.

llow 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.

Replace corrupted Ru.mat attenuation data.

Solve a problem with fit configuration window size affecting MacOS computers.

Prevent the use of numbers as material names.

Prevent an endless loop in case of typing a bad matrix element in the concentrations tab.

Add the necessary scripts to build PyMca as a python library under windows.

The calibration was not properly written when converting to EDF file format.

VERSION 4.2.5

- Batch fitting.
  Save concentrations as images too.

- Advanced Fit changes.
  Previous linear fit change was missing in batch mode.
  Correct a problem showing up when Kr L lines were fitted as a group.

- ROI Imaging.
  Show the calculated principal components when using PCA.
  Useless stack background subtraction was not working.

VERSION 4.2.4
- Add ESRF Xia Correct to the Tools menu.

- ROI Imaging changes.
  Do not reset ROI image selection on ROI change.
  Add data saving capabilities to the ROI image window.
  Implement basic principal component analysis mapping.
  Support AIFIRA and SupaVisio maps.

- Advanced Fit changes.
  Improved transmission geometry support.
  User can specify the scattering angle in the fit configuration.
  Support "funny type" attenuators.
  Make better use of the available space in the McaAdvancedFit window.
  Linear fit: fix peaks to 0 area if they are outside the fitting region.

- Simplify access to binding energies by putting them in a separate ASCII file.

- Add anchors and smoothing information to the HTML reports.

- Correct a bug on the reconstruction of the chisq image when using the
multiple processes batch option.

- Correct a bug preventing the generation of HTML reports in batch mode.

- Correct a specfile compilation issue with some gcc versions.

- Suppress shared memory compilation warnings.

VERSION 4.2.3
- Possibility to use pseudo-Voigt as advanced fit function.

- Possibility to save as data and to remove selected images from
RGBCorrelator.

- Support Lucia beamline maps.

- Support Diamond I18 beamline maps.

- Correct ROI fitting option bug.

- Some other minor bugs corrected and some other minor features added.

VERSION 4.2.2

- Input/Output: Support CSV format.
  This should simplify data exchange with spreadsheets.

- Input/Output: Support 64-bit handling of EDF files.

- ScanWindow: Possibility to save all curves in a single specfile.

- McaWindow: Spectra are saved with the active calibration instead of its own.
  In other words: what you see is what you get.

- Possibility to rename graph curves.

- Possibility to save images thru matplotlib.
  This allows user customization (axes, colorbar, colormap, contours, ...)

- ROI imaging: Use file-mapped arrays for stacks of more than 2 Gbytes.
  This feature is implemented for 64-bit linux systems.

- McaAdvancedFit: The combination of linear fit and fixed pile-up was buggy.

- Calibration: Correct a crash under python 2.5 using the Auto FWHM option.

- RGB Correlator: ASCII images saved under windows can be read under linux.

- Add peak statistics information to fit reports.

- Some other minor bugs corrected and some other minor features added.

VERSION 4.2.1

- ROI image: Possibility to normalize spectra to number of pixels.

- Speed up access to specfiles containing many scans.

- Correct a bug that was making the calculation of net ROI images useless.

- Correct ESRF specific data acquisition monitoring problems.

VERSION 4.2.0

- ROI Imaging Tool: Possibility to calculate net ROI images.

- ROI Imaging Tool: Minimum width was a problem on dual screen displays.

- ROI Imaging Tool: When using two stacks, the colormaps where coupled.

- Main MCA Window old ROI markers were not erased under some conditions.

VERSION 4.1.1

- ROI Tool: Possibility to handle two stacks of same size simultaneously.
  The interest is to combine fluorescence and diffraction maps.

- Possibility to save ROI configuration directly from the table.

- ROI Tool: Stack background removal implemented.
  It may be of interest on diffraction maps. It is very slow and not worth
  for fluorescence maps. The advanced fit is much better in this later case.

- Linux: Add pymcaroitool to the binary package.
  The ROI Tool can be started as an independent application and not only from
  within PyMca.

- Corrected: Simple fit combined with an energy calibration works.

- Corrected: Scan monitoring. Last scan point was not shown.

VERSION 4.1.0

- Changed numerical library from Numeric to Numpy.

- Added a tool to convert spectra to ESRF data format.

- Improved shared memory access.

- Possibility to calculate concentrations in mM.

- Possibility to export the main MCA window in graphical format.

- MCA window inactive legends after a fit problem corrected.

- Corrected a problem in which HTML reports generated interactively
after changing the concentration parameters without passing thru the
fit configuration window could be different from those shown on the
screen.

VERSION 4.0.9

- Concentration calculated on batch mode were wrong if the fundamental
parameter method was employed and no report was generated. This bug was
introduced in version 4.0.2

- Batches were unable to start if the first file had a name with
more characters than the last one.

- Solved a random crash when showing the fit configuration dialog.

- Program was unable to start under Python 2.5

- Possibility to set anchors to the strip background. This makes the
strip background the ideal choice when the spectra present background
pile up artifacts.

- Correct a memory leak appearing when the Savitsky-Golay smoothing was one.

VERSION 4.0.8

- Upgraded underlying sip and PyQt libraries.

- Scan window operational.

- Shared memory access operational.

- Batches can profit from multiple processors (windows and linux).

- Batch deadlocks solved by the library upgrade.

VERSION 4.0.7

- Improved ergonomy.
  A lot of clicks saved ...

- Improved handling of ini files.

- A lot of work made on the scan window.
  It is quite close to being fully operational.

- Improved shared memory access.
  Almost fully operational.

- Solved funny crashes under windows.
  The program was crashing under some particular situations
  like using remote desktop, hiding the windows taskbar or
  when the screensaver was activated.

- Several minor bugs fixed.

VERSION 4.0.6

- Recover material editor functionality.

- Solve a printing issue on some systems.
  A black square was always present at the lower right corner.

- Started to add functionalities to the scan window.

VERSION 4.0.5

- Improvements in the RGB Correlator/Post Batch tool:
  Read new images.
  Perform mathematical operations with the images.

- Solve a file format identification problem.
  Some EDF files where wrongly identified as specfile.

- Correct a bug reading specfile formatted files.
  In case of multiple scans, only the mca(s) of the first scan were read.

- Clear all items from print preview working.


VERSION 4.0.4

- Add the possibility to save graphics in vectorial format (svg).

- Scale print preview to have a width equal to 50% of the page width.

- Solve a problem in specfile batches when dealing with the @CHANN entry.

- Correct ROI image colormap bug in ROI imaging tool.

- Add specfile support to the ROI imaging tool.

- Correct random crashes on startup and on specfile batches.

VERSION 4.0.3

- Correct a bug in the ROI imaging tool.
  If the first channel was different from 0, there was an offset in each ROI.

- Windows: Correct a bug making the applications crash on startup.

- Speed up fit configuration dialog. It was awfully slow since version 3.9.4 Qt4.

- Linux: Matplotlib saving of graphics working in the binary release also under (K)Ubuntu.
  (It was already the case in pymca4.0.2-linux-p1.tgz)

VERSION 4.0.2

- Allow the user to choose if the data have to be weighted during the fit.

- Correct a bug only affecting linear batches: areas and concentrations were smaller by
a factor 10000. The bug was introduced in version 4.0.0

- Faster concentrations calculation.

- Concentrations calculated on batches do not force the generation of the .fit files.

- Linux: sps library made locale independent.

VERSION 4.0.1

- Plotting under windows should be faster.

- Solved a small memory leak usign the strip background.

- Advanced fit config button reported not to work on a gentoo 64-bit system when building PyMCA from source. Corrected.

VERSION 4.0.0

- Simplify batch preparation.
  After a fit, you can load the non-linear parameters from last fit into the configuration just by pressing a button.

- Huge speed up of pure imaging batches (specially linear fits).

- Possibility to save the imaging tool generated images in ASCII and EDF formats besides pure graphical formats.

- Display (X, Y, Z) coordenates in EDF viewers.

- Mark selected peaks in fit window, not in the main McaWindow.

- The windows installation allows to keep the old 3.9.4 version (ESRF)installed.
  That windows version can be downloaded from the ESRF. It has less features but a faster interface.
  Physics is not changed and files generated by the 3.9.4 version can be used with this version.

- Repeated HTML reports were incorrectly visualized.

- Correct a memory leak in the specfile library.

- Speed up sequential mca readout in specfile library.

- Batch pause button is working now.

- Force a main McaWindow plot and calibration update after a fit.

- Solve a Windows XP specific problem.
  The peak selection buttons were not coloured under some windows theme configurations.


VERSION 3.9.4 Qt4

- Publication quality graphics thru matplotlib.
  The packages are so big in part because of matplotlib.

- Qt4 support. I will drop Qt3 in future releases.
  Latest windows versions now available from sourceforge and not from the ESRF.

- Universal support for Mac.

- Started to add imaging tools (ESRF Data Format file stacks for the time being).

- Added an RGB correlator to easily find correlations among elements.
  This tool is to be used after a batch (Qt4 only).
  It can be used with previous batch results.

- Image printing added.

- Error when working with Nd element fixed.

- Incomplete legends in plots solved (Mac-i386)

- Missing features:
  Some previous features have not been ported to PyQt4 yet.
  If you need them please, keep the older version till I add them.
  The Physics has NOT changed. I kept the 3.9.4 to make it clear..

- New tools can be accessed thru the PyMCA Tools menu.

VERSION 3.9.4

- Possibility to fit separately K-alpha and K-beta lines.

- Possibility to use alternative L shell ratios.

- Ebel's work reference corrected

- Long standing bug affecting the fit of L and M lines as a group corrected.

VERSION 3.9.3

- Add automatic x-ray tube weighted profile generation following Ebel's formulae.

- Consider scatter of more than just one excitation energy.

- Take into account peaks outside the fitting region if  at least one of its escape lines falls into the fitting region.
  Particularly important for Germanium detectors where the K escape lines are far from the excitation energy.

- Starting pile-up parameter changed from 1.0e-10 to 1.0e-8

- The rhodium density was wrong. Changed.

- Solved a problem affecting the calibration in qt 2.3.0.

- Solved a program crash in qt 2.3.0 when Matrix Spectrum of a bad or non existing matrix was requested.

- Solved a program crash loading the shell configuration files. The problem affected some Intel based Macs (not all).

VERSION 3.9.2

- It corrects a bug affecting EDF files: The ADD REMOVE REPLACE buttons were not working.

- The default short tail slope is set to 0.5

- The peaks tailing information was missing in the HTML Report. It should be there now.

- It exposes all the theoretical shell constants in ASCII files.
  This allows the end user to customize the theoretical values by editing the relevant files:
         KShellRates.dat
         KShellConstants.dat
         LShellRates.dat
         LShellConstants.dat
         MShellRates.dat
         MShellConstants.dat

VERSION 3.9.1

- Huge batch fitting speed up in case the user does not generate the .fit files

VERSION 3.9.0

- Possibility to perform linear fits. That can improve batch fitting speed.

- Solved a long standing problem with the L lines of Sb, I, Cs, Ba, La, Ce, Pr and Nd.
  Problem was due to a bad transcription of the used theoretical data.

- The elements info shows energy dependent L and M ratios.
  Nothing changes for the fit. Just the information is shown.