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Remove fragments & holes doesn't remove small objects from the current selection #976

@petebankhead

Description

@petebankhead

Bug report

Describe the bug
Whenever Objects → Annotations... → Remove fragments & holes would result in an entire annotation being removed, it lingers in the selection until the selection is reset.

In other words, it looks like it was not deleted - and remains included in the selection model - even though it was really removed from the hierarchy.

To Reproduce
Steps to reproduce the behavior:

  1. Open an image and add some annotations of varying sizes
  2. Select all the annotations
  3. Run Objects → Annotations... → Remove fragments & holes and set thresholds that should case a subset of annotations to be removed
  4. Observe that the objects that should be removed continue to appear selected
  5. Reset the selection, e.g. by double-clicking elsewhere with the Move tool selected6.
  6. Observe that the small objects were removed after all

Expected behavior
The objects that are removed from the hierarchy are also removed from the selection.

Desktop (please complete the following information):

  • OS: All
  • QuPath Version 0.3.2 (probably earlier)

Additional context
It was reported elsewhere that Remove fragments & holes sometimes behaves inconsistently and doesn't delete fragments as expected. I'm not sure if this is the same problem or a different one.

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