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fix(schema): Update microscopy pixel size checks to account for error and OME convention #1920

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Aug 30, 2024
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fix(schema): Update microscopy pixel size checks to account for error and OME convention #1920

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29 changes: 23 additions & 6 deletions src/schema/rules/checks/micr.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -12,15 +12,32 @@ PixelSizeInconsistent:
- sidecar.PixelSize != null
- sidecar.PixelSizeUnits != null
checks:
# Note that OME-XML uses µm for microns and BIDS uses um
# Accept an error up to .001 of the BIDS unit, to account for floating point error
- |
ome.PhysicalSizeX * 10 ** (-3 * index(["mm", "um", "nm"], ome.PhysicalSizeXUnit))
== sidecar.PixelSize[0] * 10 ** (-3 * index(["mm", "um", "nm"], sidecar.PixelSizeUnits))
ome.PhysicalSizeX * 10 ** (-3 * index(["mm", "µm", "nm"], ome.PhysicalSizeXUnit))
- sidecar.PixelSize[0] * 10 ** (-3 * index(["mm", "um", "nm"], sidecar.PixelSizeUnits))
< 0.001 * 10 ** (-3 * index(["mm", "um", "nm"], sidecar.PixelSizeUnits))
- |
ome.PhysicalSizeY * 10 ** (-3 * index(["mm", "um", "nm"], ome.PhysicalSizeYUnit))
== sidecar.PixelSize[1] * 10 ** (-3 * index(["mm", "um", "nm"], sidecar.PixelSizeUnits))
sidecar.PixelSize[0] * 10 ** (-3 * index(["mm", "um", "nm"], sidecar.PixelSizeUnits))
- ome.PhysicalSizeX * 10 ** (-3 * index(["mm", "µm", "nm"], ome.PhysicalSizeXUnit))
< 0.001 * 10 ** (-3 * index(["mm", "um", "nm"], sidecar.PixelSizeUnits))
- |
ome.PhysicalSizeZ * 10 ** (-3 * index(["mm", "um", "nm"], ome.PhysicalSizeZUnit))
== sidecar.PixelSize[2] * 10 ** (-3 * index(["mm", "um", "nm"], sidecar.PixelSizeUnits))
ome.PhysicalSizeY * 10 ** (-3 * index(["mm", "µm", "nm"], ome.PhysicalSizeYUnit))
- sidecar.PixelSize[1] * 10 ** (-3 * index(["mm", "um", "nm"], sidecar.PixelSizeUnits))
< 0.001 * 10 ** (-3 * index(["mm", "um", "nm"], sidecar.PixelSizeUnits))
- |
sidecar.PixelSize[1] * 10 ** (-3 * index(["mm", "um", "nm"], sidecar.PixelSizeUnits))
- ome.PhysicalSizeY * 10 ** (-3 * index(["mm", "µm", "nm"], ome.PhysicalSizeYUnit))
< 0.001 * 10 ** (-3 * index(["mm", "um", "nm"], sidecar.PixelSizeUnits))
- |
ome.PhysicalSizeZ * 10 ** (-3 * index(["mm", "µm", "nm"], ome.PhysicalSizeZUnit))
- sidecar.PixelSize[2] * 10 ** (-3 * index(["mm", "um", "nm"], sidecar.PixelSizeUnits))
< 0.001 * 10 ** (-3 * index(["mm", "um", "nm"], sidecar.PixelSizeUnits))
- |
sidecar.PixelSize[2] * 10 ** (-3 * index(["mm", "um", "nm"], sidecar.PixelSizeUnits))
- ome.PhysicalSizeZ * 10 ** (-3 * index(["mm", "µm", "nm"], ome.PhysicalSizeZUnit))
< 0.001 * 10 ** (-3 * index(["mm", "um", "nm"], sidecar.PixelSizeUnits))

# 227
InconsistentTiffExtension:
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