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MRC file format bug and compatibility fixes. #4019

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merged 3 commits into from
Apr 24, 2023

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blowekamp
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Addresses issues with the system stamp, 0 -spacing, and remove dead code creating warnings.

This PR is also based on the release branch so that it can also be back patched.

The computed values are unused and MRC extended headers are not
fully supported.
@blowekamp blowekamp requested review from dzenanz and zivy April 19, 2023 18:35
@github-actions github-actions bot added type:Infrastructure Infrastructure/ecosystem related changes, such as CMake or buildbots type:Testing Ensure that the purpose of a class is met/the results on a wide set of test cases are correct area:IO Issues affecting the IO module labels Apr 19, 2023
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The MRC input image file didn't get magically converted to a hash file. It will need to be manually updated.

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@zivy zivy left a comment

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LGTM

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@dzenanz dzenanz left a comment

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That file needs to be replaced by the hash (and uploaded data.kitware.com), otherwise looks fine.

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dzenanz commented Apr 20, 2023

I uploaded the test file here: https://data.kitware.com/#folder/64413821cffd1a074ef04595

Here is the hash file to be put into the repository:
tilt_uint8.mrc.sha512.zip

@github-actions github-actions bot added the type:Data Changes to testing data label Apr 21, 2023
MRC image collected as a tilt series had spacing being computed a
zero. This causes the image to be unreadable but ITK. Set the spacing
to 1 in the case.
The MRC2014 specification updated/clarifed the spec that the first two
bytes should contain the specified value to determine endian. This
appears to be enforced with Python mrcfile. This patch enables
compatibility.
@dzenanz dzenanz merged commit cac4e26 into InsightSoftwareConsortium:master Apr 24, 2023
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dzenanz commented Apr 24, 2023

Sorry, I merged these via rebase (without a merge commit). I now realize that will prevent same hashes from being used in release branch (#4023).

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4 participants