format essnmx #780
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format essnmx #780
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Are the now-commented out code blocks useful to keep around? I'd rather remove them and use the file history if it's just a reference to the way it used to work. Also, could you add a |
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Yes, the format is constantly changing (for now) so it's useful to keep that code just in case. I will remove it when the format is solifidied.
Sure. |
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Switched the main-rebase-onto-this to a merge, and merged in latest changes |
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May 20, 2025 12:57
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Adds sensor_material and sensor_thickness as options for when they are not available on the dxtbx detector model.
Managing wavelength calibration: - wavelength_scale: optional scalar to apply to each wavelength - spectrum_index_offset: optional offset if the spectrometer and images are not in sync in XTC stream - check_spectrum: mechanism for screening out shots where the spectrum is not above a minimum Plus an adjustment to the minimum trusted range for the ePix. Co-authored-by: Daniel Paley <dwpaley@lbl.gov> Co-authored-by David Moreau <dwmoreau@lbl.gov>
Support for the DECTRIS-ELA detector in Bruker SFRM format
towncrier --name=dxtbx --version='3.23.0'
towncrier --name=dxtbx --version='3.24.0'
… src (cctbx#807) See dials/dials#2902 and dials/dials#2906 Co-authored-by: Nicholas Devenish <ndevenish@gmail.com>
* Allow construction of a basic crystal model from PHIL parameters. For dials/dials#416
Hatch/Hatchling (https://hatch.pypa.io/) Uses standard pyproject.toml [project] table settings, like setuptools, but provides more places for extensibility. That's used here to automatically generate the `dxtbx.format` and `console_scripts` entry-points on build. Opportunity take to do some more pyproject.toml consolidations. This patch originally had issues and was backed out because of DIALS using old packaging approaches. This was solved in 8ecaa44 so this should be safe to put back.
* Replace uses of np.string_ with np.bytes * Fix uses of numpy.float → numpy.float64 * Explicit conversion of numpy types to python floats * Unrestrict numpy in dxtbx CI * Bump nxmx dependency to numpy-2 compatible * Flumpy: Fix miller_array test for new numpy rules Most issues: Numpy used to treat the default int as 32-bit on 64-bit platforms. Now it is always 64-bit; but because miller_index is only bound to the C-sized int, we need to update this test otherwise it fails on windows.
* Increase precision of displayed crystal matrix elements
* Make DECTRIS Singla NeXus files to work with xia2-XDS
Mainly, remove upper bound for python version. This is ignored in various places, but also prevents testing easily. If it isn't known broken then we probably shouldn't pin?
…ass is not available. (cctbx#825) In order to make sure the xds.to_imageset function returns an imageset of the correct length for h5 image files.
* A couple of fixes for CrystalFactory.from_phil, for dials.modify_experiments - Set expert_level to 2. This matches the expert_level of the other geometry PHIL parameters - Bug fix: if the PHIL parameters are to do nothing, return the reference crystal model (if present) rather than None * news
Essentially no changes, just accept the value for DETTYPE. No attempt is made yet (for Photon-III and -IV) to do anything differently depending on whether counting or integrating mode was used.
towncrier --name=dxtbx --version='3.25.0'
Co-authored-by: Aaron Brewster <asbrewster@lbl.gov>
…ctbx#816) * Working towards History as an object that can be shared between experiments * Make History pickleable * Add History to Experiment as a shareable object * Function to get unique set of history objects in the experiment list * Add append_history_item function that controls the format of the history string, and includes a UTC timestamp * bug fix * Add functions to (de)serialize and consolidate history. At the moment, consolidation is just sorting by timestamp. We could start combining history items though for cases including parallel file writes (dials.stills_process) * Change constructor to require history lines * Test for history * tidying * Add a type annotation and a docstring * News * Rename newsfragments/xxx.feature to newsfragments/816.feature * Bugfix for experiment lists with zero length history * Tidy up consolidation of histories This is better as a method of the ExperimentList class, providing an easier interface to history management. When you want to append a new history line to each experiment, just call el.consolidate_histories(), which gives you the now unique History object attached to each experiment and append the line to that object. * Missed line in SConscript * Fix issue when an ExperimentList is saved in an interactive session * Fix idiotic error in 7f1f770 * Changes based on @phyy-nx's suggestion to: - correctly get dispatcher names for libtbx builds - get script name when run as main --------- Co-authored-by: DiamondLightSource-build-server <DiamondLightSource-build-server@users.noreply.github.com>
Add missing index param for FormatMANDI.get_detector
cctbx#841) Fix typo in FormatMANDILaue when calling generate_laue_data_for_panel.
Add tof_helpers.InstrumentDefinitionReader to read instrument information directly from xml data, and update FormatMANDI to use this by default.
Fix typo in tof_helpers.InstrumentDefinitionReader.
Modify the panel hierarchy of FormatMANDI, FormatISISSXD, and FormatESSNMX to enable individual panel positions to be optimised in refinement.
Preserve an imageset's reject list through pickling. Fixes dials/dials#2998
Support mini CBF images from Pilatus and Eiger detectors at SSRF beamlines BL17U1, BL18U1, and BL19U1, which have inverted rotation axes.
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update for format essnmx