Convert a loaded image to segment group

[jadh4v]

Convert a loaded image into a labelmap / segment group.
Choosing this option will remove the image from the list of loaded datasets, and create a new segment group under annotations tab using the image as a segmentation/labelmap.
This operation can fail if the segmentation image does not match the bounds of the selected primary image (base image on which the segmentation is to be applied).

WIP, additional points that need fixing:

• Currently, reading .nrrd file doesn't pick the metadata related to segment names and colors that are saved in a slicer compatible .nrrd segmentation. I would be a good idea to support this metadata by updating @itk-wasm/image-io to load this metadata and subsequently handling this information on the VolView side. This is added as a separate issue to be addressed later in a different PR. Reading NRRD files doesn't pick the metadata related to segment names and colors #530
• Currently tested with .vti and .nrrd segmentation images.
• These changes should also support conversion of a dicom segmentation to labelmap, but testing this will require a fix in itk-wasm for this issue: readImageDicomFileSeries doesn't read segmentation dicom correctly InsightSoftwareConsortium/ITK-Wasm#991

Snapshots

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[PaulHax]

Good stuff.

What do you think about having an "Add segmentation group from loaded image" button under the Annotation Tab->Segment Groups?

After removing the converted image from the Data Browser how can I:

• "undo" the conversion if I clicked mistakenly
• load the converted image as the "primary" image?

[jadh4v]

Good stuff.

What do you think about having an "Add segmentation group from loaded image" button under the Annotation Tab->Segment Groups?

After removing the converted image from the Data Browser how can I:

• "undo" the conversion if I clicked mistakenly
• load the converted image as the "primary" image?

Current way to undo is to simply delete the segment group and re-open the file as image again. Do you think it is a frequent use-case to go back-and-forth between image and labelmap representations?

Yes, we can also add the option "Add segmentation group from loaded image" in the annotations tab. I will add that.

[floryst]

Current way to undo is to simply delete the segment group and re-open the file as image again. Do you think it is a frequent use-case to go back-and-forth between image and labelmap representations?

I don't think there is much of a reason to have a dedicated undo functionality yet. Let's get one direction working and then we can add the other direction when there is sufficient interest/reason to do so.

[PaulHax]

DICOM Seg images make sense to convert to segment groups yeah? I guess we should just recongize that DICOM Seg objects have a base DICOM image and we just apply them to that image automatily? Is it common for this metadata matchup to fail and it would be useful to allow user to convert manually?

[jadh4v]

DICOM Seg images make sense to convert to segment groups yeah? I guess we should just recongize that DICOM Seg objects have a base DICOM image and we just apply them to that image automatily? Is it common for this metadata matchup to fail and it would be useful to allow user to convert manually?

I think we can address this when working on explicitly handling SEG DICOM objects (basically when implementing the automatic part).

[PaulHax]

Works good. Good to merge?

[jadh4v]

Works good. Good to merge?

Yes, please merge. No further changes in queue.