Deleted branch from rMITK MITK: bugfix/T28936-RemoveMultilabelSegmentationPlugin.

In general with {D744} being landed the multilabel utilities do not exist anymore so this task is obsolete.
We could discuss how to handle multiple labels for the single segmentation utilities, though, but I opened a new task for this: T29369: [Segmentation Utilities] Handle / select different labels independently.

The way the masking is done inside the QmitkImageMaskingWidget of the segmentation-plugin is different but it works as expected and is easy to understand.
As written in the task description the QmitkImageMaskingWidget of the multilabelsegmentation-plugin provided different options, but they were not used so I think we are safe here.

So far only the minimum was implemented as transparent. So I would not change anything right now.
And before changing it in one color palet, I would tend to think of making it a general feature of the LookupTable class, to say that its visualization is clamp (thus everything outside the lut window gets transparent. (but that would be a new feature request/idea).

From testing, it seems to work correctly in one direction. Everything below the level window is transparent (i.e. black) while everything above the level window is dark red, as the maximum end of the colormap. If this is the desired behavior, it works for me. If we want the upper part to also be transparent, then it is not quite right yet.

With {D744} being landed we can finally move the widgets to the SegmentationUI module.

With {D744 } being landed we need to check if this also applies for the single remaining Segmentation Utilities view.

I added a task in the "smoothed polygon" section:
Task

extend one segmentation to multiple neighboring slices to create a “3D” segmentation

Result

The segmentation mask is rendered on multiple neighboring slices.

I removed the „Smoothed surface creation“ Preference section from the Segmentation - Options checklist.

We discussed this and we decided to remove the options from the preferences completely. This will be done in the mentioned task T28793: [Segmentation][Multilabel][Options] Changing only decimation rate has no visible effect in "Create smoothed polygon model".

Pushed new branch to rMITK MITK: bugfix/T28936-RemoveMultilabelSegmentationPlugin.

I think there may have been a misunderstanding in this task. With the current description, I am not able to reproduce the problem (zoomed in image when loading).
From the mentioned checklist, I understand it that the tester zoomed in himself, as the checklist recommends, to see if the crosshair is aligned with the pixels. The comment only says "Problem with the brain image. The other are working. Attachment 1", so I assume the image is only to illustrate this.
So the only problem is that brain.nrrd is not pixel-aligned automatically when loaded, only after doing a reinit. I think this step in the checklist is worded a bit unclear anyway, so it's probably best to just improve that instruction and I think that's it.

We discussed this and we decided to remove the options from the preferences completely. That means, that

• the user cannot change the smoothing hint / value
• the user cannot change the decimation rate
• the checklists don't need to ask for changing these values
• the smoothing will use the default values (set inside QmitkCreatePolygonModelAction::Run)
  • "smoothing hint" = true (will always use image spacing as hint)
  • "smoothing value" = 1.0
  • "decimation rate" = 0.5
  • "closing ratio" was not used at all
  • note that different default values are given in ShowSegmentationAsSurface::Initialize (and other functions of this class), but are overwritten / reset by the polygon action.

Will take a look.

I modified the 2D Segmentation checklist accordingly, taking also T29349: [SEG] Improve/correct button names of live wire/lasso tool. into account:

• UI element strings were updated
• section for "Lasso" tool was added

I hope it's okay that I took over D687? Please have a look at it and try to understand the solution as well as the difference to the previously suggested solution.

Deleted branch from rMITK MITK: bugfix/T29342-FixReportOfProcessMemory.

Maybe I can clarify a few things:

1. I think it is important to also show helper nodes. In the basic simple case this leads to only showing the widget planes but in other scenarios helper nodes might be important to inspect. However, we could think about adding a checkbox inside a node-selection dialog to show / hide helper nodes, if the list of nodes is too long in scenarios with many helper nodes.

While I was looking into T29352: Segmentation Options Checklist - "Create Smoothed Polygon" Seems Not to Work I remembered this task. A small differential for this task has been added. The purpose is to clean the interface for those classes that don't need the extra functions / properties and provide an additional interface solely (for now) for the QmitkCreatePolygonModelAction.

I looked into this and can verify that there is no visible effect when changing the decimation rate. The property "Decimation rate" is correctly used inside ShowSegmentationAsSurface::ConvertBinaryImageToSurface as reductionRate. It is then used as an argument for ImageToSurfaceFilter::SetTargetReduction. The brief description of this parameter is:

I tested this and the smoothing works but as stated in the description it should be made more obvious what to do.
As @kislinsk wrote we will not tackle this issue here but instead remove the options from the preferences. However, this is more about the context menu action "Create smoothed polygon model". Should the whole action be removed? Or are we only talking about the additional preferences for "Smoothed surface creation"? If only the preferences should be removed we still need to adapt the checklist to make it more clear how a smoothed polygon should be created.

Deleted branch from rMITK MITK: feature/T29366-TurboColorMap.

Pushed new branch to rMITK MITK: feature/T29366-TurboColorMap.

The confirm string should not be changed. Result of the discussion was only to change the clear string.

A short but clear description of the interaction types is given in the MITK StdMultiWidget Editor help page (F1 on "StandardDisplay"):

I changed the strings according to the suggestions in this task.
However, your last comment only stated to rename the "Clear Segmentation" button.

I updated the "Checklist Segmentation – 3D Segmentation_EN":

• updated tool-image (no region growing, new icon for Picking and GrowCut)
• removed region growing test section, changed order of tool sections
• updated Otsu-tool GUI image
• added description of "Transfer ..." checkboxes
• modified description of "GrowCut"-tool

Pushed new branch to rMITK MITK: bugfix/T29363-mitk-processexecutor-bugfix.

The segmentation fault apparently happens in build/ep/src/ITK/Modules/ThirdParty/KWSys/src/KWSys/ProcessUNIX.c, kwsysProcess_Kill method where an array of non-existent PIDs are accessed. The PIDs are declared as volatile, causing race conditions. See the variable declaration below:

Deleted branch from rMITK MITK: bugfix/T29357-FixToolButtonsEnabledCheck.

Pushed new branch to rMITK MITK: bugfix/T29357-FixToolButtonsEnabledCheck.

Deleted branch from rMITK MITK: bugfix/T29353-InvalidSegmentationViewStates.