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CZI: Use CreationDate as alternate AcquisitionDate #3430

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commented Sep 5, 2019

This is a follow up to the thread: https://forum.image.sc/t/omero-does-not-import-acquisition-date-from-czi-file-metadata/28910/3
A sample file is available in QA-27807

When the usual Information > Image > AcquisitionDateAndTime metadata is not set then also check Information > Document > CreationDate and use it to populate Image Acquisition Date.

@dgault dgault added this to the 6.3.0 milestone Sep 5, 2019

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commented Sep 6, 2019

A very quick auditing of a few CZI files in the curated QA repository seems to reveal that Information > Document > CreationDate is always present whenInformation > Image > AcquisitionDateAndTime exists but the reverse statement is not true.

For most examples, the values of both dates are very close if not identical:

$ find /data/public/ -iname *.czi -exec sh -c "echo {} && /bio-formats-build/bioformats/tools/showinf -nopix {} | grep Date" \;
...
/data/public/idr0011/Plate1-Blue-A_TS-Stinger/Plate1-Blue-A-36-Scene-3-P1-D7-03.czi
Information|Document|CreationDate #1: 2013-12-10T17:46:40.7586388+00:00
Information|Image|AcquisitionDateAndTime #1: 2013-12-10T17:46:40.7596389Z
Scaling|AutoScaling|CreationDateTime #1: 01/01/0001 00:00:00

Unless there is a reason to consider Information > Document > CreationDate as the ground truth for all filesets, falling back to Information|Document|CreationDate if Information|Image|AcquisitionDateAndTime if present looks like a safe addition.

Configuration files should probably be reviewed across the curated QA repository accordingly.

@dgault dgault added the exclude label Sep 9, 2019

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commented Sep 9, 2019

Excluding for now due to a number of failures: https://merge-ci.openmicroscopy.org/jenkins/job/BIOFORMATS-test-folder/22937/consoleFull

The deltaT failures are likely to be mostly valid, but they will each need to be reviewed a decision taken to either update all the configs or ignore CreationDate for the deltaT purposes. There are also a number of CreationDates found with values such as: 1899-12-30T00:00:00 which fail the sanity test. These could be special cased to ignore these instances.

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