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Fix old I03 data not processing #737

Merged
merged 8 commits into from
May 23, 2024
Merged

Fix old I03 data not processing #737

merged 8 commits into from
May 23, 2024

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ndevenish
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This data did not process, because:

  • dxtbx could not find the _meta.h5 file (it was not linked from the .nxs, which was assumed). There is now a fallback that uses pure filename instead of trying to determine it from the main file.
  • The _meta.h5 file didn't have a stored "Detector bit depth" field. This now uses the per-image bitdepth field.
  • General cleanup/update to pathlib.

Fixes dials/dials#2669.

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codecov bot commented May 22, 2024

Codecov Report

Attention: Patch coverage is 81.48148% with 5 lines in your changes are missing coverage. Please review.

Project coverage is 41.73%. Comparing base (78147cc) to head (d0934b3).
Report is 25 commits behind head on main.

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #737      +/-   ##
==========================================
- Coverage   42.15%   41.73%   -0.42%     
==========================================
  Files         188      188              
  Lines       16764    16877     +113     
  Branches     3196     3232      +36     
==========================================
- Hits         7067     7044      -23     
- Misses       9052     9178     +126     
- Partials      645      655      +10     

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@graeme-winter graeme-winter left a comment

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Approve as-is because would fix the problem as reported, I assume, but looks like there is a gap woth handling foo.nxs

newsfragments/737.bugfix Outdated Show resolved Hide resolved
src/dxtbx/format/FormatNXmxDLS.py Show resolved Hide resolved
src/dxtbx/format/FormatNXmxDLS.py Show resolved Hide resolved
src/dxtbx/format/FormatNXmxDLS.py Show resolved Hide resolved
src/dxtbx/format/FormatNXmxDLS.py Show resolved Hide resolved
@ndevenish ndevenish enabled auto-merge (squash) May 23, 2024 08:02
@ndevenish ndevenish merged commit c4fc39f into cctbx:main May 23, 2024
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ndevenish added a commit that referenced this pull request May 23, 2024
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.
@dagewa
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dagewa commented May 23, 2024

Thanks, confirmed I can process that data set now 👍

toastisme pushed a commit to toastisme/dxtbx that referenced this pull request Jul 18, 2024
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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Successfully merging this pull request may close these issues.

Failure to read old (2019) I03 data
4 participants