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Deleting a TMA grid deletes all regions #646

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SoerenXD opened this issue Nov 27, 2020 · 3 comments
Closed
4 tasks done

Deleting a TMA grid deletes all regions #646

SoerenXD opened this issue Nov 27, 2020 · 3 comments
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@SoerenXD
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SoerenXD commented Nov 27, 2020

IMPORTANT!

This section is only for bug reports, which must follow the template below.

Please post any other questions to the official QuPath forum at https://forum.image.sc/tags/qupath

If in doubt, use image.sc. This helps us keep things organized.

Before we begin...

Before submitting your bug report, please check the following:

  • I've definitely found a bug (it you're not sure, please use image.sc instead)
  • I've checked https://qupath.github.io for a new release that might already have fixed the issue
  • I've checked the Changelog to see if the bug has already been fixed in the next release
  • I've checked for existing GitHub issues describing the same problem

Bug report

Describe the bug
If a TMA grid has been assigned using the TMA dearrayer and the TMA grid is removed later, it will remove all regions along with it, regardless of whether they have been placed n the hierachy or not.

To Reproduce
Steps to reproduce the behavior:

  1. Open a TMA image
  2. Draw some regions in the TMA cores
  3. Run the TMA de-arrayer
  4. Delete the TMA-grid
  5. All manually drawn regions are gone.

Expected behavior
The TMA grid should be removed and the other regions should be kept.

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

  • OS: Windows
  • QuPath Version 0.2.3

Additional context
Add any other context about the problem here.

@petebankhead
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Thanks, I can reproduce the behavior - the entire object hierarchy is removed.
Furthermore, clearTMAGrid() no longer works from a script.

@petebankhead
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This script may be useful as a workaround, but I haven't checked if it has any unwelcome side-effects. The bug will need fixed in a later release.

def hierarchy = getCurrentHierarchy()
hierarchy.clearTMAGrid()
hierarchy.tmaGrid = null
fireHierarchyUpdate()

@petebankhead petebankhead added this to the v0.3.0 milestone Apr 4, 2021
petebankhead added a commit to petebankhead/qupath that referenced this issue Apr 6, 2021
@petebankhead
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The changes in petebankhead@deea6c7 have hopefully resolved the issue, and will be available in v0.3.
Please do reopen this if you find that it hasn't been fixed after all.

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