Deleted branch from rMITK MITK: release/T29075-2022-Week-17.

Pushed new branch to rMITK MITK: release/T29075-2022-Week-17.

Deleted branch from rMITK MITK: release/T29075-2022-Week-17.

Pushed new branch to rMITK MITK: release/T29075-2022-Week-17.

Deleted branch from rMITK MITK: release/T29075-v2022.04.

Deleted branch from rMPT MITK-ProjectTemplate: release/T29075-v2022.04.

This task is resolved in the current release branch.

TODOs:

• Reference all "external" data in README files
• In particular, check DICOM data if we have consent and if it really is anonymous regarding DICOM tags etc.

Merged into current release branch.

There are two contour mappers. An OpenGL version using low-level OpenGL API calls through VTK, messing around with contexts and paint devices, and a pure VTK version using PolyData. The former one is currently in use. I switched to the VTK-version which is preferable in principle and it works except for a few minor things like color.

Oh, in debug mode, I still get an error output at least:

It probably is an issue in the contour mapper or maybe even an internal issue in VTK that is triggered by the contour mapper. I noticed crashes in the Nvidia driver and OpenGL error outputs before I updated my driver that also goes into the same direction, even though the crashes are now gone. I want to check if we introduced this issue with the latest minor VTK upgrade in which case we should downgrade again.

I edited the task description since it is a general issue regarding data node removal, not restricted to image cropper bounding boxes. The rational for that is that (1) the scene adapts/focusses on the left overs so that the scene is always as tight as possible in its extents and (2) the global geometry is in sync with the remaining geometries which is for example important for segmentation which may require you to do manual reinits on images to sync with their geometry.

• Erase works on the whole slice (for the currently selected label) when clicking on the background label and the clicked region touches every single border pixel.
• Erase works only for the selected label but still the preview snaps to other labels if clicked into them resulting basically in a no-op.

Oh, I forgot, we should probably rename this task to reflect the things that are missing from the list above. Both label naming and color assignment are the ones that are fixed already.

BTW, if you are working on this, regarding the color updates that were reported not to be immediate, I can confirm that it only happens on layers != 0.

Also see rMITKb73c37478dbe: Improved generic naming and coloring of newly created labels in T29089. I added the commit link there as suggested. :)

Good idea, done.

Naming and coloring is now fixed in the release branch. Names and colors of new labels will be unique across all layers.

Also: Changing the color of a label in layer != 0, requires a click in a render window to make the changed color visible.

I guess the wrong signal of the widget is connected here as the number should only be applied after it is completely entered. The correct signal should be editingFinished().

Request for discussion: The green color is chosen deliberately as it is the typical preview color in MITK segmentation. We should discuss it should be different here and what are the implications regarding overriding/merging with existing labels.

Since we will have changes regarding the number of tools and the number of tools is even different for different operating systems (for example nnUNet is only available on Linux), we should probably not write a specific number into the checklist.

After this was merged, we should add a note to the label set preset section about the newly introduced default label set preset T29107 (I didn't want to create more merge-conflicts than necessary for you). :-)

Merged into the current release branch.

Reordered palette from above to see similar colors next to each other to simulate the worst case:

Since all colors in the widget are tuned to be in front of a white background I explicitly set the help search results background to be white.

I already started to implement a new plugin generator (T27701) but it still is delayed because of priority reasons. When the plugin generator is back, step 9 should be revised/fixed.

I used the opportunity to get rid of some unused legacy classes and properties regarding volume visualization. According to our minimum requirements of the rendering backend, I removed the rendering mode combobox (GPU vs CPU) as we can assume capable GPUs. The blend mode combobox is now labeled and its items are fully spelled.

Was mentioned again in the current testing cycle by other testers.

This is my shot at it mainly based on the palettes above with extra effort regarding neighboring color contrasts (top-left to bottom-right). But it is impossible to get 25 perfectly distinguishable colors. Also I took into account that the human eye has the highest sensitivity in the green spectrum.

Kelly is nice because it is not overly saturated as most other palettes, but I think the most useful is indeed glasbey, when the two black-ish and one grey-ish colors are removed for our context. Red and magenta both appears pretty similar twice. Also, the colors should be a reordered a little bit and for the sake of compatibility/expectations start with red. More or less the same for polychrome but there we would also need to get rid of more grey colors.

I procrastinated on the colors tonight for quite some time and finally found something that really stood out - the standard distinguishable color palettes of R:

Same for F2 regarding renaming of labels. I would also say double-click, but as it turned out, double-click is already used to jump to the center of the label.

The first two comments should be targeted for this release. The last comment is something that also happens sometimes with the new implementation of the polygon tool that uses the same base class. But fixing is too complex to be worth spending time before the release, so whoever grabs this task, focus on the first two comments.

Pushed new branch to rMPT MITK-ProjectTemplate: release/T29075-v2022.04.