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Add the "atldld dataset preview" command #66

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Merged
merged 34 commits into from
Aug 31, 2021
Merged

Add the "atldld dataset preview" command #66

merged 34 commits into from
Aug 31, 2021

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Stannislav
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It determines the locations of all section images in the reference space and saves a plot to disk.

I tested with

  • coronal: atldld dataset preview 479
  • sagittal: atldld dataset preview 75492803

but feel free to test with other datasets, maybe you'll discover some bugs.

Stanislav Schmidt added 15 commits August 26, 2021 10:27
@Stannislav Stannislav marked this pull request as draft August 26, 2021 13:41
@Stannislav Stannislav self-assigned this Aug 27, 2021
@Stannislav Stannislav marked this pull request as ready for review August 27, 2021 09:05
EmilieDel
EmilieDel approved these changes Aug 27, 2021
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I tried the CLI and I really like it 😍 Thanks for the PR, @Stannislav !

One small thing, it seems sometimes corners can be out of the boundaries of the reference shape, especially for the coronal axis. See for example atldld dataset preview 77371835
image. Maybe we can extend the boundary of the coronal axis for those datasets ?

jankrepl
jankrepl reviewed Aug 27, 2021
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Cool feature:) Thank you:) I read through the code quickly and left some comments:)

@Stannislav
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I tried the CLI and I really like it 😍 Thanks for the PR, @Stannislav !

One small thing, it seems sometimes corners can be out of the boundaries of the reference shape, especially for the coronal axis. See for example atldld dataset preview 77371835
image. Maybe we can extend the boundary of the coronal axis for those datasets ?

Nice catch! I removed the ylim and added the full reference space outline in 143d267, what do you think?

dataset-id-77371835-preview

Stanislav Schmidt added 4 commits August 28, 2021 08:35
Fix sphinx warnings
c36250e
Add the --output-dir option to dataset preview
eeef51f
Fix bandit bug
cb7e9a7
Revert "Fix bandit bug"
add2f4f 
This reverts commit cb7e9a7.

The bug-causing library importlib-metadata==4.8.0 was yanked
from PyPI.
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EmilieDel commented Aug 30, 2021 •
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Nice catch! I removed the ylim and added the full reference space outline in 143d267, what do you think?

Sounds great! Thanks for changing this!

@Stannislav Stannislav mentioned this pull request Aug 30, 2021
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@Stannislav Stannislav mentioned this pull request Aug 30, 2021
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@EmilieDel EmilieDel self-requested a review August 31, 2021 15:32
@Stannislav Stannislav merged commit 2ad46b0 into main Aug 31, 2021
@Stannislav Stannislav deleted the add-preview-dataset branch August 31, 2021 16:05
@jankrepl jankrepl mentioned this pull request Oct 7, 2021
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@Stannislav @EmilieDel @jankrepl