To fix this we need the changes from T16019.
The parameter controls should be disabled on start up and use the same approach as in the bug mentioned above.

When clearing the seeds the pointset is completely renewed. So there are no callback functions for adding and deleting points. Can be solved by adding the SimpleMemberCommands again.

Can be fixed with T16019

Fixed with T16019

[705e4e]: Merge branch 'bug-16019-disable-fastmarching-confirm-button'

Merged commits:

2013-09-11 16:24:06 Tobias Schroeder [63cf59]
Fixed 3D FastMarching

New remote branch pushed: bug-16019-disable-fastmarching-confirm-button

It will be easy to disable the button, but the GUI must somehow get notified to enable the button again. The tools shoul emit a message if the segmentation is ready to be confirmed.

New remote branch pushed: bug-16006-ContourModelSet-integration

[4280bd]: Merge branch 'bug-16006-ContourModelSet-integration'

Merged commits:

2013-09-11 09:57:43 Tobias Schroeder [e239ab]
Check access inside bounds.

[b7e6c3]: Merge branch 'bug-16005-ContourUtils-integration'

Merged commits:

2014-02-13 15:35:06 Tobias Schroeder [27e0d5]
Removed unused code

Added mitkContourModelSet containing a std::deque of ContourModel objects.

[068da8]: Merge branch 'bug-16006-fix'

Merged commits:

2013-10-18 11:04:47 Tobias Schroeder [25d5a4]
COMP: fix use of TimeGeometry.

Since T15982 was fixed there is no more ipSegmentation dependency for utility function FillContourInSlice. ContourUtils has been moved to ContourModel module and was renamed to ContourModelUtils to avoid naming conflicts. All methods are now static member functions so no instance of ContourModelUtils is needed.
We are still keeping a legacy support of ContourUtils for class mitk::Contour in Segmentation module.

[f4f4d9]: Merge branch 'bug-16005-fix-windows-build-error'

Merged commits:

2014-02-14 11:16:45 Tobias Schroeder [3a08d9]
COMP: fix missing ContourModel_EXPORT in ContourModelUtils.

New remote branch pushed: bug-16006-ContourModelSet

Controller class is responsible for handling the result of segmentation tools and also the working and the reference image. So far only AcceptSegmetation methods have been implemented. All methods from SegTool2D were extracted and marked as deprecated. The handling of the image has been moved to T16212

Waiting for interaction testing framework to test tools with segmentation controller.

Controller handles segmentation image data (reference and working image). ToolManager gets a controller as member and passes all image requests to controller object. Thus the application can use several different ToolManager and SegmentationController instances at the same time.

New remote branch pushed: bug-16004-SegmentationController

Reopen bug.
Controller is not working as intended.
Storing of contours has been moved to segmentation data type so AcceptSegmentation methods of SegmentationController have to be redesigned.

New remote branch pushed: bug-16004-SegmentationController-integration

We are now using some VTK based filters to fill a contour in a 2D binary image.

• vtkPolyDataToImageStencil
• vtkImageStencil

• SegmentationInterpolationController uses mitkShapeBasedInterpolationAlgorithm.cpp

Occurs on MacOS too.

[b85ffc]: Merge branch 'bug-15880-Debug-assertion-ContourModelSubdivisionFilter'

Merged commits:

2013-08-19 11:32:04 Tobias Schroeder [81006a]
Use SetNthOutput

New remote branch pushed: bug-15880-Debug-assertion-ContourModelSubdivisionFilter

New remote branch pushed: bug-15876-threshold-tool-with-float-images

[0c119d]: Merge branch 'bug-15876-ThresholdTool-fix-for-float-images'

Merged commits:

2013-10-18 11:50:18 Tobias Schroeder [d509a3]
Merge branch 'bug-15876-threshold-tool-with-float-images' into bug-15876-ThresholdTool-fix-for-float-images

Thresholding tool is working with single threshold value (mitkBinaryThresholTool). The issue with the tool that uses two thresholds (mitkBinaryThresholdULTool) is due to casting the slider values to int. A solution would be to use the same appraoch as BinaryThresholdTool for its slider.

Contour cut gone wrong.

Contour appears projected on axial view in instead of cut.

[c96ae3]: Merge branch 'bug-15870-contour-in-oblique-planes'

Merged commits:

2013-08-26 13:50:09 Tobias Schroeder [ee0417]
Perfomance issues in UpDateOutputInformation fixed.

Moved contour cut issue to T15918

New remote branch pushed: bug-15870-contour-in-oblique-planes

If current point is close enough to the current rendering plane a bool flag was set to true. This flag was never changed to false for the following points. So all points were drawn no matter if they were far away from the plane.

Note:
This only affects the use of ToolManager within Segmentation plugin, nothing will be changed in ToolManager class. There will also be no changes to the current interaction implementation (Tool framework). The migration will be done with T14943.

I have introduced a module activator (mitk::SegmentationModuleActivator) that registers services for the Segmentation Module. It now registers a ToolManagerProvider service that can be called to get an instance of mitk::ToolManager. As the service itself is a singleton there will be only one object of ToolManager. So if the service is used within Segmentation plugin it is ensured that everybody uses the instance.

[2902dc]: Merge branch 'bug-15828-ToolManagerProvider-integration'

Merged commits:

2013-08-23 13:34:57 Tobias Schroeder [ddb1fa]
Fix namespace.

New remote branch pushed: bug-15828-ToolManagerProvider-integration

.bmp:

• It only occurs for 2D images that are saved as 3D with single slice.
• It works for images that also have a 2D Geometry.

*no chance to edit a comment*

[659952]: Merge branch 'bug-15820-save-2D-images-as-bmp'

Merged commits:

2013-08-14 16:28:11 Tobias Schroeder [d4d730]
Check all support picture formats.

New remote branch pushed: bug-15820-save-2D-images-as-bmp

We also changed the mitkImageWriterTest to cover all supported picture formats.
During the implementation we've noticed that PixelType comparison won't work for this. Not all of the bit sizes can be used. E.g. PNGs max bit size for grayscale images is 16. So the images won't have the same PixelType after saving and loading again.

Issue moved to T16497.
Feature will be introduced with new segmentation data type.

New remote branch pushed: bug-15808-ContourManager-integration

New remote branch pushed: bug-15808-ContourManager-integration-2

New remote branch pushed: bug-15808-keep-contours-for-segmentation

New remote branch pushed: bug-15808-ContourManager-store-contours

Requirements

Has already been fixed

New remote branch pushed: bug-15779-LiveWire-tool-description

[65d3ed]: Merge branch 'bug-15779-LiveWire-tool-description'

Merged commits:

2013-08-06 11:50:38 Tobias Schroeder [3f80e3]
Changed max size of description text.

The IpSegmentation free ContourUtils is found in T15982

New remote branch pushed: bug-15763-ContourModel-Modul

[cff5b5]: Merge branch 'bug-15763-move-classes-into-new-module'

Merged commits:

2013-09-09 15:30:21 Andreas Fetzer [60a45d]
Renamed Module in the CMakeLists

Added a ContourObjectFactory for Mappers and IO classes and fixed some of the filters. (Changes were done in bug-15763-move-classes-into-new-module).

Renamed module to ContourModel.
mitk::ContourUtils needs to be moved to ContourModel module as soon as it has no dependency to IpSegmentation (see T15982 and T16005).

This bug occured after T15676 was fixed. Changed severity because the application is in corrupt state afterwards.

New remote branch pushed: bug-15687-feedback-contour-for-4D-segmentations

All access functions to contour vertices had to be adapted within the tools. Also ContourUntils had to be extented for FillContourInSlice to specify the time step due to 2D slice .

Time steps greater than 1 could only be tested after T15676 was fixed.
The contour is not visible because all segmentations tools are adding vertices at the default time step, which is 0.

The problem was that memset has accessed memory that was not allocated for the image itself. The volumes for each time step seem not to be continuous in memory. memset is now executed separately for each volume in case of 4D data.

Switched to mitkContourModel for Tools using contour to visualize segmentation result. All classes that inherit from mitkFeedbackContourTool are using mitkContourModel.

Fixed by integration of UI redesign branch

Seems to be fixed in current master

Set volume at current time step by SetVolume(void*, t) with itk filter output data.

New remote branch pushed: bug-15391-FastMarching3D-deletes-time-steps

Fixed with UI redesign of segmentation plugin. A RegionGrowing view is no longer available. We have tested the mentioned steps with current master.

Reopen bug - compiler errors on linux

New remote branch pushed: bug-15282-3D-RegionGrower

Added a dummy Tool class to be handled by ToolManager and changed the RegionGrower widget class to act as a Tool GUI. So activating AdaptiveRegionGrowingTool now shows up the the UI above the tool button in the 3D ToolGUIArea of QmitkSegmentationView. Also some changes had to be done to combine the binary segmentation image with the RegionGrowing preview.

Fix compiler errors - missing typename

Added a Tool to work on 2D slice to perform FastMarching segmentation.

New remote branch pushed: bug-15149-FastMarching-2D