Add images from .qpproj file always import annotations even if option is not selected

[Rdornier]

Bug report

Describe the bug
We try to add a qpproj file in another one to import all images. The checkbox "Import objects" was unchecked but all objects have been imported.

To Reproduce

1. Open a new QuPath project
2. Click on Add Images
3. Drag-drop another QuPath project (.qpproj file) containing annotations on images
4. Uncheck the "Import Objects" checkbox
5. Click on Import
6. After importation, if you open a image coming from the imported project, then you should see annotations.

Expected behavior
If the checkbox is unticked, no annotations should be imported.

Desktop

• OS: Windows 11
• QuPath Version: 0.4.3

[petebankhead]

Very good point, I hadn't ever really considered those two things together.

In my mind, 'Import objects' was always associated with trying to read objects that are somehow associated with the source image (e.g. ROIs stored as an overlay for ImageJ TIFF, objects from an OMERO image).

The ability to add images from another project, on the other hand, was developed separately and intended to always import all the data from that project. This means the entire image data, including stain vectors etc. The object hierarchy comes along with that.

I imagined that, if anyone wanted to add the images without objects, they would just add the images in the 'normal way' and not via a project. But I suppose that assumes that projects don't contain very many images scattered across different disks, or accessed via OMERO or elsewhere.

In any case, I agree that the current behavior is confusing in the case you describe, and should probably be changed. But I'm not sure if it should be a change of behavior, or a change of documentation + the addition of a new command?

Some ideas:

1. Don't import any specific ImageData from a project when the "Import objects" checkbox is unselected. This would exclude objects and everything else. Potentially also including custom metadata, channel names, stain vectors etc.
   • In this case, it would probably be best to rename the checkbox and document this behavior
2. Keep the behavior as it is, but document it better. A user can always run a one-line script to delete all the objects later.
   • I can imagine there might be use cases where someone wants to create a new project with the same images, but no associated data. Exporting the image list and reimporting it should support those cases.
   • There is a related issue to this
     • 'Export image list' uses a different format to 'Add images' #1177
3. Add an entirely separate command to import images from another project and/or prompt the users when importing from a project. This would give more control over what exactly should be import, but it's another menu item in already quite crowded menus.

Keen to know what you and any interested others think.

[Rdornier]

Hello,

Thanks for your explanations and suggestions.

Don't import any specific ImageData from a project when the "Import objects" checkbox is unselected. This would exclude objects and everything else. Potentially also including custom metadata, channel names, stain vectors etc.

This is a suitable option to import only raw image files and I think it should work. But it may be a bit restrictive regarding metadata and stain vectors.

In this case, it would probably be best to rename the checkbox and document this behavior

Yes

Add an entirely separate command to import images from another project and/or prompt the users when importing from a project. This would give more control over what exactly should be import, but it's another menu item in already quite crowded menus.

I like this option but it's also true that added a new menu is not optimal. One way to do could be to add a popup menu only if a project will be imported. The import window will remain the same, with the "import object" option. If this option is unticked, then no objects are imported, regardless of the what will be imported (same behavior as the first option). If it is ticked, then it checks if there is a project to import and in case, a popup menu appears to select what ImageData should be imported.

Keep the behavior as it is, but document it better. A user can always run a one-line script to delete all the objects later.

For me, it will still be a bit confusing ; I really prefer the two other options but this is only my point of view.