Log the image template #2278
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Log the image template #2278
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Tagging @graeme-winter, @phyy-nx and @rjgildea as those who commented on #1662 |
Codecov Report
@@ Coverage Diff @@
## main #2278 +/- ##
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- Coverage 80.61% 80.54% -0.07%
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Files 587 587
Lines 67306 67320 +14
Branches 8995 8999 +4
==========================================
- Hits 54258 54223 -35
- Misses 10972 11018 +46
- Partials 2076 2079 +3 |
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Tempted to merge this, because it is an improvement for users processing scans and doesn't change the behaviour for users processing stills. Any thoughts? |
Fixes #2279 Co-authored-by: James Beilsten-Edmands <30625594+jbeilstenedmands@users.noreply.github.com>
As of wxPython 4.2.0 passing a float results in an error: Timer.Start(): argument 1 has unexpected type 'float'
* Improve comments. "Incident beam" is ambiguous as it might mean incident on the sample, or on the detector. * Add link to the relevant XDS paper * Factor is less ambiguous than fraction * Correct file name
NoQA for typing imports
* Pin boost to 1.74 conda currently picks 1.78, which requires c++14. This is failing for dxtbx/dials.
dev.dials.napari_rlv is an alternative reciprocal lattice viewer based on napari.
Don't count zero as negative. Fixes #2084
Co-authored-by: Aaron Brewster <asbrewster@lbl.gov> Co-authored-by: Iris Young <idyoung@gmail.com>
…0` (#2298) Allow `reflection_table.remove_on_experiment_identifiers` when `len==0`
Add new feature to dials.stills_process: reflection_subsampling. If reflection_subsampling.enable=True, and an image fails to index, the program will randomly subsample the reflections and try again. It keeps trying, randomly subsampling in smaller amounts until a threshold is reached or the image successfully indexes. The default is descending from 100% to 50% of the strong spots by 2% steps, randomly subsampling from the original pool of strong reflections at each step. We have observed nearly doubling the number of indexed images for some samples using this approach, and we verified that the additional lattices are high quality (ie we are not adding merely weak lattices that failed to index). * Add test for reflection_subsampling The gain of the SACLA MPCCD detector is normally 10. The new test wrong_gain changes it to 0.5 and produce more spots, which causes the 3rd image to fail to index. This is rescued by reflection_subsampling. Co-authored-by: Daniel Paley dwpaley@lbl.gov Co-authored-by: Asmit Bhowmick abhowmick@lbl.gov
… during scaling (#2312) Only triggered if a dataset being removed is near the end of the experimentlist
When selecting the odd experiments in a large reflection table from a serial dataset, this improves the time for the select statement from ~10 min to ~1 second.
This was counting number of clusters instead of size of each cluster.
Co-authored-by: Richard Gildea <rjgildea@users.noreply.github.com>
Previously UnboundLocalError was raised when absorption_correction.apply=True, but absorption_correction.algorithm was unspecified. Now, whenever algorithm= is expected but unspecified, a ValueError is raised, unless user specifically requests algorithm=other.
These functions expect ints Co-authored-by: James Beilsten-Edmands <30625594+jbeilstenedmands@users.noreply.github.com>
Prevent dials.combine_experiments from raising TypeError in cases where clustering.use=True but the default clustering.max_clusters=None. Instead, interpret max_clusters=None as requesting all of the clusters.
Using C++14 by default exposes dials to failures on windows because of the standard library overrides in cctbx, so remove those when building dials libraries. Using C++14 means that we can use Boost::Geometry in boost 1.78, which dropped support for older versions. This means that we can build against the January 2023 release of cctbx, which requires boost 1.78. Additionally, dxtbx directly links to zlib but this was only ever pulled into the conda environments implicitly, but on some configurations of building dials on windows this is no longer the case - so make the dependency explicit here. Fixes #2291.
subprocess.Popen docs recommend passing a fully-qualified path to the executable, as resolving the path of the executable is platform dependent. https://docs.python.org/3/library/subprocess.html#subprocess.Popen This was causing test failures in some windows configurations.
We expect a C++11 compiler, so we may as well use standard C++11 features where available instead of legacy boost equivalents. - Use std::atomic instead of boost::atomic - Use std::shared_ptr instead of boost::shared_ptr - Use std::make_shared instead of boost::make_shared - Use standard <random> instead of boost equivalent - Use std::dynamic_pointer_cast - Remove unused boost includes
towncrier --name=DIALS --version='3.13.0'
Historically this has been allowed to lag. We should try to move towards a more consistently updated value for future releases.
If calling phil.extract() raises an exception (for example because the provided value is of the wrong type or out of range) then catch the error and call parser.error() which results in a call to sys.exit().
…in dials.ssx_integrate. (#2337)
* Move a block from run to run_dials_refine * Ensure sys.exit only appears under run, not under run_dials_refine * forgot the news * Rename newsfragments/xxx.bugfix to newsfragments/2325.bugfix --------- Co-authored-by: DiamondLightSource-build-server <DiamondLightSource-build-server@users.noreply.github.com>
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Sigh. Implicit rebase when I did a |
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Ok with me. Sorry I haven't had a chance to work on it. |
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Just to note, this is also relevant for #2072, though that request is also to put this information in spot-finding and integration logs, so this does not strictly close it. @jbeilstenedmands I think you said you might look at this for stills? If not soon, I'd be keen to merge this. |
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WIP for #1662
This works for scans, but not for stills. Could somebody who works with stills please add in the appropriate code path? I don't know how to get a template out of an
ImageSetand anyway I don't know how you want to report the possibly cherry-picked image numbers.