Add functionality to convert images to labelmaps #444

floryst · 2023-10-04T17:37:02Z

Improve image space comparison to check physical spacing
Add support to convert an image to a labelmap for painting
Update the labelmap store API
- support the aforementioned functionality and future metadata
- explicitly store ordering of labelmaps per image
Update the UX around layering to instead be accessed via a dropdown menu

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floryst · 2023-10-04T17:39:07Z

I'm open to workflow suggestions surrounding labelmap conversion. Right now this does not support converting DICOM datasets to labelmaps.

src/utils/imageSpace.ts

src/store/datasets-labelmaps.ts

PaulHax

Geting TypeError when:

Load Fetus
Immediately click Annotations tab

When converting image to labelmap, it disapears from DataBrowser. 🥹 No going back?

Nice to have an icon or something indicate when a image is a Layer on another image.

When do we do the great layer and labelmap unification? First step unifies the Labelmap stack on the Annotations tab with the Layers stack on the Rendering tab?

src/components/LabelmapList.vue

aylward · 2023-10-04T20:23:02Z

Painted labels appear as very thin lines in orthogonal slices, and they should represent the resolution in the orthogonal direction.

Steps to reproduce:

Load Prostate data
Draw in any slice
Error: in the other windows only a thin line is drawn.

aylward · 2023-10-04T20:26:29Z

Instead of presenting items at the labelmap level, they should be presented at the paint-color level. Or maybe this should be under the labelmap grouping. That is, if a color appears in a labelmap, it should appear as an item under that labelmap in the annotations tab, and it should be possible to rename, generate a 3D rendering, convert to contour, etc for that specific paint color. The idea is that we're generating objects (annotations) and they can be rendered in different ways in the 2D and 3D views. But things are presented at the object level, not at the labelmap level.

floryst · 2023-10-04T20:50:11Z

Painted labels appear as very thin lines in orthogonal slices...

If you zoom in, those lines do correspond to the thickness of the painted slice.

Instead of presenting items at the labelmap level, they should be presented at the paint-color level.

Good point. The next step is to expose an API that operates at the segmentation level. This is closely related to configurable default segmentation labels (paint labels) and how those affect labelmaps.

aylward · 2023-10-04T21:21:47Z

You're right! We need to include resolution (voxel size) info in the information box and give physical position of the cursor in the corner annotations. Additionally, for the brush size we need to give physical units. I was mistakenly thinking it was corresponding to 1 voxel, but it does not.

This gets hard to grok when drawing things with a brush size of 1 in the different planes. In the following I draw with brush size 1 as follows

Green square box was drawn in axial and correctly shows as a square box in that isotropic plane
Red boxes were drawn in the coronal and sagittal planes, and I expected them to produce a square box in the axial plane (reflecting one voxel being painted) - but it is approximating a in-plane circle, not drawing 1 voxel. So, I think everything is ok, but we need to convey the physical size of the brush. We should also have the option to turn off texture interpolation when rendering the slice data, so that voxel edges become more apparent and the data's resolution becomes appropriately represented.

floryst · 2023-10-12T16:28:35Z

When converting image to labelmap, it disapears from DataBrowser. 🥹 No going back?

I'll be adding a means of going from labelmap -> image.

Nice to have an icon or something indicate when a image is a Layer on another image.

Agreed. I can add an icon indicating that an image is a layer. We can worry about indicating which images its a layer of when we need it.

When do we do the great layer and labelmap unification? First step unifies the Labelmap stack on the Annotations tab with the Layers stack on the Rendering tab?

Layer + labelmap unification is more tricky, so we won't touch on it in this work. For one, overlaying other images is a purely rendering thing, while labelmaps are an annotation thing. Their colormap requirements are different (you can edit labelmap colormaps), and same with the opacity. Right now their data models are distinct enough that we should keep them apart. We can revisit this down the line.

- Add a new onImageDeleted listener to delete labelmaps when the parent image is gone. - Explicitly store labelmap insertion order. - Add new APIs for adding and deleting labelmaps. Existing APIs are preserved.

Instead of comparing image spaces via metadata comparison, we instead check to see that the volume corners are the same (module rotations and flips).

The IsolatedDialog currently stops certain keys from propagating out of the dialog.

floryst · 2023-10-13T19:35:22Z

I've added the segment editor. Please try it out and let me know if there are any bugs/basic issues, e.g. the eraser isn't available yet.

PaulHax · 2023-10-17T13:16:55Z

Segment editor is snazy. Basic stuff:

Should opacity be per labelmap like layers?
Should new labelmap copy all of last labelmap segments?
Saving a session.zip has error.
Should we call segments -> labels? Or vice versa...
Should the label editor UI match the segment editor UI or vice versa?

floryst · 2023-10-18T17:40:56Z

Should opacity be per labelmap like layers?

Yes, that's a good idea to consider. I'm thinking we can even make opacity be applied per-segment, but I'm not sure how useful that is.

Should new labelmap copy all of last labelmap segments?

I like that behavior. I'll add it unless we have good reasons to not do such a thing otherewise.

Saving a session.zip has error.

Thanks, will look into it.

Should we call segments -> labels? Or vice versa...

This naming is mostly going off of Slicer, where a labelmap is a type of segmentation, and segments are just a particular label. I'm keeping with segments for now to reflect that, but if labels is more intuitive then we can call them labels.

Should the label editor UI match the segment editor UI or vice versa?

Good point, I haven't considered that. I think I'll try using the label editor UI for the segment editor UI.

aylward · 2023-10-25T21:44:10Z

How do you give a name to a ruler, square, or polyline annotation. Much each new name have a new label? Can I have multiple things labeled and painted as "tumor" and yet name each one independently, e.g., tumor 1, tumor big, maybe-its-a-tumor tumor...

floryst · 2023-10-26T17:53:44Z

Let's discuss the behaviors for annotation labels, since I think there are some conflicting expectations.

floryst · 2023-10-31T20:14:15Z

Updated:

measurements and labelmaps are now organized into tabs. Selecting certain annotation tools will focus the tab.

I do not plan on addressing the expected behavior of labels in this PR because this is intended to only be related to labelmaps.

floryst · 2023-11-03T20:15:39Z

Update:

add eraser
merged main into this branch

@aylward @finetjul how does the following naming seem to you?

Labelmap -> SegmentGroup
Label/Segment -> SegmentMask (runner-up suggestion: Segment)

Once the naming is locked down, I will begin renaming various parts of VolView to reflect the terminology change.

floryst · 2023-11-06T22:59:40Z

Updated:

eraser is now global and available via a tool mode swatch in the paint controls
user is prompted for a new name when a labelmap is created
dropdown menu has been replaced in favor of a radio list of labelmaps

floryst · 2023-11-07T21:36:21Z

@aylward @PaulHax this is ready for functional evaluation again. Ignore the naming for now.

refactor: rename labelmaps to segment groups

floryst · 2023-11-13T17:35:27Z

I'll probably merge this soon and we can iterate on it after the fact.

floryst requested a review from PaulHax October 4, 2023 17:38

PaulHax reviewed Oct 4, 2023

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src/utils/imageSpace.ts Show resolved Hide resolved

PaulHax reviewed Oct 4, 2023

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src/store/datasets-labelmaps.ts Outdated Show resolved Hide resolved

PaulHax reviewed Oct 4, 2023

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floryst added 12 commits October 13, 2023 11:07

feat(labelmap): improve labelmap store API

54ecd91

- Add a new onImageDeleted listener to delete labelmaps when the parent image is gone. - Explicitly store labelmap insertion order. - Add new APIs for adding and deleting labelmaps. Existing APIs are preserved.

feat(LabelmapList): select active paint labelmap

c717a98

fix(types): export proper vtk types

438283d

fix(ImageListCard): remove unnecessary div

6fcca71

feat(compareImageSpace): better space comparison

6f25f78

Instead of comparing image spaces via metadata comparison, we instead check to see that the volume corners are the same (module rotations and flips).

feat: add buttons to convert to labelmap

eff8bde

fix(LabelmapList): guard against empty labelmaps

045f8f7

refactor(LabelEditor): make label editor generic

465ca26

feat(IsolatedDialog): event-isolated dialog

79cf60a

The IsolatedDialog currently stops certain keys from propagating out of the dialog.

feat(LabelEditor): add cancel capability

8135d43

fix(shortcuts): modifiers trigger no-mod shortcuts

ddeb75c

feat: add initial segment editor

3b68ef7

floryst force-pushed the convert-to-labelmap branch from ee10b65 to 3b68ef7 Compare October 13, 2023 19:28

floryst added 3 commits October 23, 2023 16:35

refactor(labelmap): component renaming

c58e526

fix(ToolLabelEditor): emit strokeWidth event

674ddd0

feat: unify label and segment editable list UX

4aad7de

feat(AnnotationsModule): use tabs for annotations

a8987f3

floryst added 2 commits November 3, 2023 14:38

feat(paint): add eraser

70220e8

Merge remote-tracking branch 'origin/main' into convert-to-labelmap

5ccc1cf

PaulHax mentioned this pull request Nov 6, 2023

fix(LayerProperties): handle long layer names #479

Merged

floryst added 4 commits November 6, 2023 11:41

fix(ImageDataBrowser): remove labelmap convert btn

0d10237

feat(paint): add eraser mode

d5785ed

feat(labelmaps): ask for name upon creation

c685ade

feat(LabelmapControls): radio button list

2f7f8a4

feat(LabelmapControls): better styling

4a34db6

floryst force-pushed the convert-to-labelmap branch from bccd0db to 4a34db6 Compare November 6, 2023 23:05

floryst added 2 commits November 6, 2023 18:08

feat(AnnotationsModule): visual separator

ea697a1

feat(LabelmapControls): enforce name uniqueness

a1d279e

refactor: rename labelmaps to segment groups

3c20960

floryst mentioned this pull request Nov 8, 2023

refactor: rename labelmaps to segment groups #494

Merged

floryst and others added 4 commits November 9, 2023 11:27

Merge pull request #494 from Kitware/rename-labelmaps-to-segment-groups

9598381

refactor: rename labelmaps to segment groups

Merge remote-tracking branch 'origin/main' into convert-to-labelmap

6c5633e

fix(datasets-dicom): duplicate cleanupName

9cc82e1

feat(SegmentGroupControls): improve new group UI

2936961

floryst added this pull request to the merge queue Nov 13, 2023

Merged via the queue into main with commit cbd3d93 Nov 13, 2023
6 checks passed

PaulHax mentioned this pull request Nov 27, 2023

Backwards compatibility of session.volview.zip files #521

Closed

floryst deleted the convert-to-labelmap branch March 21, 2024 16:26

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Add functionality to convert images to labelmaps #444

Add functionality to convert images to labelmaps #444

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Add functionality to convert images to labelmaps #444

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