DIALS 3.18.2 #58
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DIALS 3.18.2 #58
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DiamondLightSource-build-server
commented
Apr 10, 2024
DiamondLightSource-build-server
commented
- gltbx: preserve previous behavior if pyopengl is not available
- gltbx: remove keywords from argument lists in gl_managed.py
- gltbx: switch OpenGL imports to pyopengl
- Consolidate some code - Add case for phaser_voyager [skip ci]
- Update PATH in dispatchers - When moving dispatchers to a new location, make sure that LIBTBX_PREFIX is the original location [skip ci]
…straints. Also fixes a failing test
- Attributes added to the hierarchy class in Python will require additional changes to the pickling code
- EnergyTab is a new tab in the GUI where the user can use the FEE calibration tools, generate and view associated plots, and export a phil file with the results. The phil can be imported into rungroups directly, avoiding manual transcription errors. This includes the FEE spectrometer calibration from the notch scan as well as visualizing and calculating the Ebeam offset -- that is, spectrum_eV_offset, spectrum_eV_per_pixel, and wavelength_offset. (Note, we really should consider renaming these and doing all adjustments in eV.) - CalibWorker is a new thread running in the background, executing any requested calibration tasks (so far just for EnergyTab). - ebeam_plotter.py is the plotting tool to replace the command line script thing.py for use in the GUI. - Small necessary changes were made to existing calibration and visualization scripts to make them able to accept an existing matplotlib figure and add plots to it, and to write out results. - Note of caution, window resizing seems to be crash-prone. Not entirely sure why, but given this fact, I haven't put work into making things resize nicely for different screen sizes. This is all optimized for the control room at MFX.
…ds code duplication. Note: will break the GUI. Working on that next.
* Adding initial copied scaffolding for clashscore as clashscore2. Passing the model rather than the PDB hierarchy down into clashscore2 because we'll need that for Reduce2 * Simplifying by reducing code no longer needed * Removing more code that we don't need for clashscore2 * Remove the keepExistingH parameters from mmtbx.reduce.Optimizers.Optimizer because it no longer has an impact here. The hydrogens are added in a separate step. * Switching clashscore2 over to using mmtbx.reduce from command-line reduce. * Making copies of the total model and then subsetting them for each submodel run of probe2. Fixing up models without crystal symmetry * Removing obsolete calls * Adding back in required variable * Constructing a new model from the hierarchy before copying it in clashscore2 so that all of the model elements are correct. * Trimming some unused code * Changing the plumbing so that we can pass all that we need through the system * Fixing output formatting in probe2 to match probe * Cleaning up calculation * Switching initial call to probe to use probe2 * Using correct command-line argument to determine whether probe2 should print dot count. Clarifying order of operations. * Switching second call to probe into probe2 for clashscore2 * Bumped probe minor version prior to merging into main branch * Replacing remaining calls in clashscore2 to probe program with inspection of the hierarchy * Removing redundant definition of get_results_as_JSON * Removing unused imports from clashscore2 * Removing trailing whitespace from an HTML file I didn't edit so we can pass the clutter check
Test passes now, but will later require the API to simulate shoebox pixels with ~10-fold lower memory consumption and thus fail until the fix is in.
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