Skip empty slicegroups to avoid creating blank rows in output metric CSV file #4487
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For data where an image is split into multiple chunks, you may want to call the same command on multiple chunks spanning a range of vertlevels (e.g. -vert 1:12). But, not all chunks will span all levels. In this case, there is a bug where a table entry will be created for the slicegroup "()", i.e. a group containing no slices. This is a useless row containing no data. This commit adds a test that reproduces the condition and fails. As soon as the empty slicegroup row is removed, the test will pass.
joshuacwnewton
added
bug
The `if slicegroups`/`if not slicegroups` check is duplicated, which I don't love. An alternative could be to remove empty slicegroups from `slicegroups` entirely. But, then we wouldn't be able to use `vertgroups[slicegroups.index(slicegroup)]`, since vertgroups and slicegroups would be different sizes. In general, this code really needs a refactor. See this already open issue: - #4005
This is a slight tidy up as a follow-up to the comment in the previous commit.
jcohenadad
approved these changes
May 17, 2024
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I have not tested the code, but the change makes sense, there is now a test, so i'm approving. Thank you @joshuacwnewton
mguaypaq
approved these changes
May 21, 2024
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Description
For data where an image is split into multiple chunks, you may want to call the same
sct_extract_metriccommand on multiple chunks spanning a range of vertlevels (e.g.-vert 1:12). But, not all chunks will contain all of the specified levels.For this case, there is a bug where an
agg_metricentry will be created for the slicegroup "()", i.e. a group containing no slices. This will result in an empty row containing no data.This PR adds a test that reproduces the condition and fails. As soon as the empty slicegroup row is removed, the test will pass.
Linked issues
Fixes sct-pipeline/spine-park#35.