PIA work: select only relevant experiments #1665
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For hdf5 grid scans, the length of the experiment is equal to the number of images in the grid scan. This results in a loop over every experiments in some places of the code, which can add significant overhead.
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Test code: Using With the changes in this PR, spotfinding now takes ~1-1.25s per image: |
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I can see how the difference is substantial for big grid scans, but I would welcome a similar analysis (for documentation) of e.g. an 80 image scan. Will test the change set in a moment and verify that it makes no difference beyond time saving. |
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For a 25 x 20 ROI gridscan (500 images) there is still an appreciable speedup: |
ndevenish
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For hdf5 grid scans, the length of the experiment is equal to the number of images in the grid scan. This results in a loop over every experiments in some places of the code, which can add significant overhead. Bikesheds-by: Nicholas Devenish <ndevenish@gmail.com> Bikesheds-by: Markus Gerstel <markus.gerstel@diamond.ac.uk>
DiamondLightSource-build-server
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Bugfixes -------- - ``dials.scale``: Fix crash when full-matrix minimisation is unsuccessful due to indeterminate normal equations. (#1653) - ``dials.scale``: Fix crash when no reflections remain after initial filtering. (#1654) - ``dials.export``: Fix error observed with ``format=mmcif`` for narrow sweeps with low symmetry (#1656) - Fix image numbering inconsistency in ascii histogram of per-image spot counts (#1660) - ``dials.find_spots_server``: Significant performance improvement for HDF5 grid scans. (#1665)
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Bugfixes -------- - ``dials.scale``: Fix crash when full-matrix minimisation is unsuccessful due to indeterminate normal equations. (#1653) - ``dials.scale``: Fix crash when no reflections remain after initial filtering. (#1654) - ``dials.export``: Fix error observed with ``format=mmcif`` for narrow sweeps with low symmetry (#1656) - Fix image numbering inconsistency in ascii histogram of per-image spot counts (#1660) - ``dials.find_spots_server``: Significant performance improvement for HDF5 grid scans. (#1665)
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For hdf5 grid scans, the length of the experiment is equal to the number of images in the grid scan. This results in a loop over every experiment which can add significant overhead:
dials/array_family/flex_ext.py
Lines 1205 to 1220 in a66ee17
called via:
dials/command_line/find_spots_server.py
Line 117 in a66ee17