PyFAI-2024.09

What's Changed

• New tutorials:
  • On flatfield calculation from several detector position (ID31)
  • On discarded pixels when using sigma-clipping (ID15a)
• New feature in pilx: the tool to view diffraction map
  • Fix/unfix curves
  • Colors improved
  • Motor position can ge registered and displayed along axis
• Other new feature:
  • Expose orientation in calib2 (excluding Nexus-detectors)
  • Extra comments in PONI-file like the calibration file
  • Sigma-clipping in pure cython with hybrid error-model
  • New calibrant (Lysozyme for MX) & integration into calib2
  • Engineering notation when printing detector
  • New JSON format for integration configuration (backward compatible)
  • Import CrystFEL geom-file to generate a detector + geometry
  • GIWAXS and sigma-clip impose no pixel splitting
  • Sigma-clipping is possible from the GUI and via config files
  • Peakfinding: discard peaks with masked pixels in the local region
• New detector: Jungfrau 1M (ID09)
• Bug fixed:
  • Absorption kwarg was missing in sigma-clip
  • Close HDF5 files ASAP (risk of hitting the max number of file open)
  • Bug in medfilt (empty ensemble)
  • Several bugs fixed in worker (heavily used by ewoks)
  • Correct some tutorials for typos
  • Orientation of interate2d results legacy vs ng
  • Compatibility with Numpy2
  • Compatibility with Eiger2+Lima2 multi-threshold files
  • Compatibility with GCC14, discarded some deprecated code
• Validated with Python 3.8-3.12

New Contributors

• @pierrepaleo made their first contribution in #2207
• @mjdiff made their first contribution in #2239
• @jacobfilik made their first contribution in #2243

Full Changelog: v2024.05...v2024.09

pyFAI-2024.05

• Implemented unweighted average for 2D integration

• Integration engines now handle the boolean 'weighted_average' to switch to unweighted mean, similar to legacy methods

• Implementation of pilx (pyFAI-diffmap-view command): interactive viewer for pyFAI-diffmap files (thanks Loic Huder)
• Creation of a RingExtraction class based on multi-threading (thanks Emily Massahud)
• Flat-field and dark current corrections for pyFAI-calib2
• Tunable units and integration methods for fiber/grazing-incidence scattering
• Fix several bugs related to pyFAI-diffmap GUI/no-GUI options
• Compatibility with numpy2
• Fix numerical precision issue (spotted on MacOS/arm64)
• Build system moved from bob to cibuildwheels
  • Windows wheels are build with openmp disabled (?)

pyFAI-2024.02

• Include grazing-incidence capabilities + tutorial (thanks Edgar)
• Fix segmentation-fault in calib2 application #2047 (thanks Thomas & Edgar)
• Use the dynamic mask to mask-out dead pixels in Eiger images in calib2
• Extend Poisson+azimuthal uncertainties to all Cython integrators (+ non regression tests)
• Support for Python 3.7-3.12 & requires silx v2

pyFAI-2024.01

• Possibility to define the detector orientation:
  • It is the position of the origin of the detector at any of the 4 corner of the image
  • Uses the EXIF nomenclature where pyFAI's (default) orientation is tagged 3
  • Offers compatibility with calibration made by Diotas (where orientation=2 since images are flipped)
  • Expose the feature in the calib2 GUI for custom detectors.
  • Tutorial on the usage
  • New sub-version of the PoniFile API (2.1) for this feature
• Expose the number of corners of a detector pixel (feature unused for now)
• Refactor pyFAI-benchmark tool with better looking reults (Thanks Edgar)
• Possibility to integrate in 2D with any second dimension unit:
  • No more limited to the azimuthal angle chi
  • Several new units have been added
  • Offers the qx/qy integration as example
• Support for Detris Pilatus4 detector both with Si and CdTe sensors (thanks to Max Burian)
• Support XRDML formt (compatibility with MAUD software)
• Multigeometry gains a reset() method to free some memory with optimized garbage collection.
• Support pathlib when reading-PONI files
• Change in the build system:
  • Drop of setup.py the build system based on distutils/numpy.distutils/setuptools
  • Enforce the use of meson-python
  • Move the sources of the code into src directory
  • Support for Python 3.7-3.12 (requires silx v2 for 3.12) + Provide debian packages for debian12 but ubuntu 20.04 is too old and lack meson-python
• Facts and figures:
  • 600+ commits; 120 pull-requests
    *with the contribution of:
    Edgar Gutierrez Fernandez
    Jérôme Kieffer.

pyFAI-2023.09

• Bug fix release over 2023.08
• Fix calibrant selection in calib2 (Thanks Valentin)
• Centralized control of Random Number Generator for tests, to make non-regression test more consistent for CI.
• Correct behaviour of dynamic mask (was causing systematic crashes)
• Correct spelling of several messages.
• Compatibility with matplotlib 3.7
• New application icon and launcher under linux
• Updated notebook (addresses API changes)

pyFAI-2023.08

• Minor release, mostly bug-fixes. 87 commits.
• fix malformed headers in 1D ASCII export
• Debian packaging without setup.py (at all)
• Fix cache invalidation issue for polarization in geometry
• More compact (+scrollable) calibrant widget in Calib2 (Contribution from Valentin Valls)
• Compatibility with PyQt6 and PySide6 bacckends (Contribution from malte-storm)
• Compatibility with elder Matplotlib (<3.2)
• Fix reproducibility issue with no-split sparse matrix multiplication (all 3)
• Lower memory consumption of hexagonal detector instantiation.
• Enforce the usage of the detector_factory. Detector(**config) stops working.

v2023.05.0

• New detector: Jungfrau 8M used at SwissFEL
• new method in Geometry to guess the number of bin (and avoid oversampling)
• new method in AzimuthalIntegrator to guess the polarization factor
• CSC-integrators (1D + 2D) implemented in pure python using scipy.sparse
• Update documentation
• Minor correction (remove debugging)
• Packaging for debian12 using meson-python

pyFAI v2023.3

• Rework all 2D integrator to propagate variance, expose standard deviation and standard error of the mean.
• Support all version of python between 3.7 and 3.11
• Support Cython 3.0b1 (with performance degradation) in addition of cython 0.29.31+

pyFAI 2023.2

• Core:
  • sigma_clip_ng is not the default sigma_clip
  • expose documentation for sigma_clip_legacy in addition to sigma_clip_ng
  • Worker can now use sigma_clip_legacy in addition to sigma_clip_ng, integrate1d or integrate2d
  • New calibrant: Vanadinite (used in high-pressure, often as single crystal)
• GUI:
  • Fix labels on axes for some rarely used units
  • refactor IntegrationMethodDialog and share the IntegrationMethodTabs with pyFAI-calib2
• Test:
  • silent some noisy test (OpenCL on windows)

pyFAI 2023.1

First stable version of pyFAI: v2023.1.

Sources and binary wheels can be found at: https://pypi.org/project/pyFAI/
and at: https://github.com/silx-kit/pyFAI/releases/tag/v2023.1

One of a few ways to install this release with pip:

pip install pyFAI==2023.1.0

Release notes and important changes since 0.21:

• Developer and packager tools:
  • Switch build system from numpy.distutils to meson-python
  • Keep the former setup.py for compatibility reasons: it will be removed in a future release
  • Drop Python 3.6 (default parameters in namedtuple feature used)
  • Require silx 1.1 (for OpenCL), scipy and matplotlib
• GUI side:
  • several minor improvements in pyFAI-calib2
  • Fixed calibration in jupyter-lab
• Core improvements:
  • Refactoring of the Geometry class
  • Geometry pseudo-inversion optimization
  • Improved support from Medipix-based Lambda-detectors
  • New detectors from Dectris (Pilatus 900k and Eiger 250k)
  • Support Nexus format in output: NXmonpd and NXcansas
  • Single-threaded CSC sparse matrix multiplication engine
• Improved uncertainty propagation:
  • Refactor error model management (uses enum)
  • Hybrid error model (azimuthal for sigma-clipping but reports Poissonian noise)
  • Export peakfinder data to the CXI format (used by CrystFEL)
• Improvement in the doc:
  • Update installation instructions
  • Multi-threaded integration tutorial
  • GPU implementation tutorial
• Facts and figures:
  • 400+ commits, 100 PR
    +with the contribution of:
    Clemens Prescher,
    Elena Pascal,
    Jérôme Kieffer,
    Malte Storm,
    Marco Cammarata,
    Michael Hudson-Doyle,
    Picca Frédéric-Emmanuel,
    Rodrigo Telles,
    Thomas A Caswell,
    Tommaso Vinci,
    Valentin Valls,
    Wout de Nolf.