DIALS 3.17.1 #193
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DIALS 3.17.1 #193
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This attempted to import some code from experiment_list before printing the warning, but used an incorrect import path. This didn't get tested because this was added in the commit otherwise removing datablock completely.
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Added properties to Scan to allow for more diverse experiment types (e.g. 3D time-of-flight data).
Add oscillation fix for Scan.set_image_range.
For mrcfile>=1.5.0 use the indexed_extended_header. Attempt to process the extended header only if its length is equal to the number of images. Ignore extended header values if the pixel size is set to zero.
New parameter and updated behavior to account for occasional dropped spectra in the XTC stream, when spectra a used to produce a calibrated average wavelength. If spectrum_required=True, and the FEE spectrometer is not found in an event, get_spectrum will raise a RuntimeError. If spectrum_required = False and spectra calibration constants (spectrum_eV_per_pixel and spectrum_eV_offset) are provided, wavelength_offset can be used to apply a general correction for any events with a dropped spectrum. If the spectrum is present and calibration constants are provided, wavelength_offset is ignored.
Basic readers for Bruker Format-100 and miniCBF images from the ELDICO ED-1 instrument.
…#683) * Always mask out the central cross of pixels, as even if these have got reasonable intensity values, they do not correctly represent the reflection profiles. This also means handling between the 4- panel 512*512 pixel model (which excludes the edge pixels between the panels) and the 516*516 pixel model are now consistent. Both versions now exclude these special edge pixels.
New file writer image dimensions Reported now as slow, fast i.e. correct rather than historical fast, slow which we have always had to invert Fixes cctbx#657 Much more sensible fix suggested by @biochem-fan - checks firmware version using packaging.version as a sane comparitor. Thanks to @spmeisburger for pointing out errors. Co-authored-by: Takanori Nakane <nakane.t@gmail.com>
Added a missing test for this. Fixes 2606.
Time of flight data does not fully fit in either still or sweeps camp, but in most cases the check is used to distinguish between 2D and 3D data. Within DIALS, time of flight data is being treated as 3D data, with the third dimension being time of flight rather than rotation. Update this check to reflect that.
There were non-regression tests in dials_regression that were not included in the online testing. This reverts commit 80f81f5.
Allow rotation angles to be < 0 i.e. crystals rocking back and forth in the beam for efficiency.
This complements 39e463e. Twirling, always twirling.
* Be tolerant of fast and slow axis values in `test_FormatISISSXD.test_import` that may vary in the least significant digits.
* Fixed bug in `Scan.from_dict` where some properties were not correctly parsed.
Add natural sorting This will allow dials.import to behave as a user would expect, as it naturally sorts rather than strictly sorts input values (i.e. 2 comes before 11) Fixes dials/dials#2302 * Rename newsfragments/XXX.bugfix to newsfragments/697.bugfix * azure conda env update --------- Co-authored-by: DiamondLightSource-build-server <DiamondLightSource-build-server@users.noreply.github.com>
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Allow distance override for multi-panel detectors. If a multi-panel detector has a hierarchy, it will have its root node distance set. If there is no hierarchy then each panel will individually have distance set, but only if those panels are coplanar and already at the same distance.
…too! (why?!) In such cases it seems that hierarchy is useless, and has origin at 0,0,0. When we have a single panel, ensure that it is the panel itself that has its distance updated. Only change the hierarchy for multi-panel detectors, where it is assumed that it has a sensible origin.
…-detectors-with-hierarchy Set distance for single panel detectors with hierarchy
Add format class to understand Jungfrau4M serial data from ID29, ESRF
…cctbx#701) * Relax conditions when creating time of flight interpolators to allow time of flight frames to start from zero.
* Added FormatMANDI.py
Fix recently added JF4M format class. Avoids matching to dataset h5 files
* Bugfix: need to avoid None * News * Rename newsfragments/xxx.bugfix to newsfragments/710.bugfix --------- Co-authored-by: DiamondLightSource-build-server <DiamondLightSource-build-server@users.noreply.github.com>
* Add wavelength range to polychromatic beams.
* Add getstate and setstate for PolychromaticBeam.
* Add missing argument in PolychromaticBeamPickleSuite.
* Add tof_helpers.tof_from_wavelength.
Defaults for detz_offset and cent_mm were calibrated using mfxl032222 (April 2024)
towncrier --name=dxtbx --version='3.19.0'
This behaviour has changed in cctbx, however has not been backported to the release.
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Some data taken with the Eiger pre-2020 was written: - With a 64-bit VDS pointing to 32-bit data arrays, - Without the metafile being linked in the main file, - Without the eiger self-reported data type being in the metafile. Solving these allows DIALS to know that the VDS is wrong, and that it is safe to convert down to 32-bit. Soves dials/dials#2669.
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Bugfixes
dxtbx.datablockmodule failed to display warning properly. (Update removed datablock warning cctbx/dxtbx#665)Misc
#672 <https://github.com/cctbx/dxtbx/issues/672>_