Merged branch into bug-15068-segmentation-UI-redesign

New remote branch pushed: bug-15144-FastMarching-3D

There are two QmitkToolSelectionBoxes sharing the instance of ToolManager. One is associated 2D tools and the other one with 3D tools.

[d0f6fe]: Merge branch 'bug-15068-fix-ContourModelTest'

Merged commits:

2013-08-06 12:58:14 Tobias Schroeder [65585f]
COMP: Fix ContourModelTest.

There is still a need to perform a reinit on the desired 3D image.

New remote branch pushed: bug-15060-reslice-example-integration

New remote branch pushed: bug-15060-reslice-example

The reason for the 0.5 might be due some inconsistent properties of the plane that is used for the rendering. The plane has a center based origin but the flag for IsImageGeometry is set to false. Within reslicing this flag is checked during the creation of the output image. The geometry of the new slice is created from the plane that is used to resample from the image volume. If the plane is not an image-geometry (i.e. flag not set) the origin of the slice will be adapted. For our rendering planes this means the origin is no longer center based!

widget plane is center based but NO image geometry!!

Added rendering tests for rotated MRI images. One is using a 'global reinit' by default and the other one performs a 'reinit' on render window.

The image shift can be solved this way. SegmentationInterpolationTest passes for the first slice. Unfortunately SegmentationInterpolationTest still fails after that. It seems that within the test the plane for reslicing is not changed. I checked the interpolation manually in mitkWorkbench and works fine in all plane without any shift. Therefore SegmentationInterpolationTest issue was moved to T15041

bug-15013-wrong-Geometry-in-ExtractSliceFilter
contains the consideration of image geometry property within GenerateData. The reslice origin is adapted if a bounding geometry is used.

SetResliceTransformByGeometry was removed. The transformation is now always used to reslice bya given plane. So the resample grid is rotated within extraction step. That what was set manually by rendering so far and had to be done by any user of ExtractSliceFilter for rotated images.

New remote branch pushed: bug-15013-wrong-Geometry-in-ExtractSliceFilter

Cloning issue can be found in T15038

The cause for the crash is an issue with cloning a Geometry2D. The IndexToWorldTransform is somehow corrupted.
My approach is to consider the ImageGeometry property within GenerateData and adapt the origin and extend on the fly.

[b45706]: Merge branch 'bug-14893-ResliceInerpolationProperty-cubic-has-no-effec

Merged commits:

2013-05-17 09:29:34 Tobias Schroeder [3e31db]
COMP: ImageError threshold was too small.

Added a rendering test to check interpolation modes.

[39eeb3]: Merge branch 'bug-14893-ResliceInerpolationProperty-cubic-has-no-effec

Merged commits:

2013-05-03 09:42:35 Tobias Schroeder [52b67f]
Chanded revision tag of MITK-Data.

New remote branch pushed: bug-14893-ResliceInerpolationProperty-cubic-has-no-effect

A break was missing in switch statement causing to use the default nearest interpolation.

This leads to the annoying fact that the control point can't be moved if the window/ zoom level is small. It seems like always adding some new point to the contour.

Fixed with T12703

The fix seems to be ok so far. Using a default extent would be the solution i prefer too.

I had a closer look to the proposed fix. Looks ok.

It is in fact incorrect, but only for the 3d render window. The effect is not visible in 2d planes. It seems that the updated textures from the 2d planes are set at 3d.
The effect also shows up with two objects of same datatype (e.g. two images).

Have you checked if it is an updating issue? Is the texture still visible after e.g. scrolling a slice away?

I would prefer a save accessor too if one exist that is as fast as accessing the pixels by a pointer.
But actually I don't think that the usage of is a problem as only read access is performed. The worst case would be that in another thread someone changes some values inside the image volume. What causes the outline to be somehow wrong. Keep in mind that only the volume can be changed by someone else. The slice (within CreateOutlinePolyData) extracted within GenerateData is a COPY and thus nobody will ever have the object. So after next update was performed everything is fine again.

fixed with T13012

Check for image is not always valid.
The listener to delete event was not removed when a ToolManager object was deleted. Add RemoveNodeEvent.RemoveListener(*delegate*)

Added a check in callback funcion if the node contains an image.

[2a1f13]: Merge branch 'bug-13012-crash-after-closing-segmentation'

Merged commits:

2012-09-05 16:17:16 Tobias Schroeder [8cb9d6]
remove node removed event listener in destructor

• crash happens in mitkToolmanager at line 211

crash happens in mitkToolmanager at line 211

We've worked on this some time ago. There's bug branch 'bug-12954-initialize-world-geometry'. According to the comments only a callback function for AddNodeEvent was introduced but nothing else was implemented.

[970d4d]: Merge branch 'bug-12943-segmentation-bundle-doesnt-work'

Merged commits:

2012-08-29 16:41:07 Tobias Schroeder [843fbe]
check for reference or working node included

This was related to changes of node removed callback within QmitkSegmentationView (see T12917).
this->SetToolManagerSelection(NULL, NULL) was call every time.
Now checking if the removed node is one of the woking or reference nodes.

[a7a3dd]: Merge branch 'bug-12917-ToolManager-keeps-reference'

Merged commits:

2012-08-22 16:05:39 Tobias Schroeder [4435d5]
added observer and callback on toolmanager

[6c2f2e]: Merge branch 'bug-12887-connect-actions-in-subclasses-of-segtool2d'

Merged commits:

2012-08-16 14:10:31 Tobias Schroeder [b141a1]
connections to actions are now done within the tools

A new method was introduced in SegTool2D checking if the statemachine can handle the event. Removed connecting actions in constructor too.
Now the tools are responsible for connecting there methods with the appropriate action ids.

[7bbe4c]: Merge branch 'bug-12877-wrong-memory-warning-for-3d-interpolation'

Merged commits:

2012-08-15 14:14:08 Tobias Schroeder [cd6079]
fixed wrong memory warning

New remote branch pushed: bug-12704-implemant-contourModel-final-integration

[099462]: Merge branch 'bug-12704-ContourModel'

Merged commits:

2013-01-09 12:31:42 Tobias Schroeder [441150]
fixed rendering

The migration of the segmentation tool state machines will be done with T14943

[e91373]: Merge branch 'bug-12703-LiveWire-Tool-Integration'

Merged commits:

2013-03-22 09:14:21 Tobias Schroeder [64aaf3]
documentation for LiveWire Tool.

Integrated mitkContourModel with comment 2.

[4de6c2]: Merge branch 'bug-12703-LiveWire-Tool'

Merged commits:

2013-04-05 11:36:23 Tobias Schroeder [6f21e2]
COMP Changed selection method of vertices.

[b2e855]: Merge branch 'bug-12703-LiveWire-Tool'

Merged commits:

2013-04-05 10:50:32 Tobias Schroeder [535844]
COMP Fixed falsely merged file.

New remote branch pushed: bug-12703-LiveWire-Tool-Integration

Yes i have talked to Christian. And the tool will be based on the new interaction design. But since all Tools in the segmentation module are based on the old version it will be done separatelly. Jasmin is working on this.

example from TurtleSeg application

Realizes a Segmentation Tool based on LiveWire approach using mitkContourModel to visualize the segmentation progress.
Acts like magnetic lasso tool known from Photoshop. Also introduces new Interactor for mitk::ContourModel objects with LiveWire functionality.

changed to mitk default header

[203574]: Merge branch 'bug-12655-wrong-copyright-header'

Merged commits:

2012-07-18 13:36:34 Tobias Schroeder [40f120]
fixed copyright headers in sliceOperation and applier

A member m_timestep had been used in segTool2D::WritebackSegmentationResult which wasn't set. Using the positionEvent now to get the timeStep.

[7b8bb7]: Merge branch 'bug-12579-segmentation-in-4d-images'

Merged commits:

2012-07-16 11:02:26 Tobias Schroeder [c7a749]
get timestep from position event

[f16300]: Merge branch 'bug-12556-segmentation-crash'

Merged commits:

2012-08-15 14:17:04 Tobias Schroeder [9a8109]
fixed segmentation crash on start up

Will be fixed with T13321

I'm able to reproduce this bug without any special treatment. I've just performed the steps above.
It still occurs after switching branches.

Reopen bug because it occurs again on MacOS with current master.

Crash was fixed. The problem described in previous
comment is still there. See T13392.

[5d9bcf]: Merge branch 'bug-12340-overwriteslicefiltertest-fix'

Merged commits:

2012-08-01 17:41:11 Tobias Schroeder [51cd40]
created two separate tests for orthogonal and oblique planes. oblique plane test is still disabled

Fixed with [5d9bcf]: Merge branch 'bug-12340-overwriteslicefiltertest-fix'

Passed on my machine today.
It only failed on some machines and also only the test for oblique planes. I assume it was due to a rounding issue. I'll check that and change the test to a more robust version.

The issue is related to the clone method of mitk::PlaneGeometry. The referenceGeometry is not cloned, the Pointer is just set to the Geometry of 'other'.
Thus to secure the that the reference geometry will not be deleted, a SmartPointer was added. Note that this is just a quick fix and needs to be changed after T13392 will be fixed.

[20f6d6]: Merge branch 'bug-12338-crash-after-undo-segmentation'

Merged commits:

2012-10-10 17:27:31 Tobias Schroeder [8274c9]
commented changed lines

The results from the dartclients seem to be equal but a part of the image (Alfred) is somehow shifted. This is what gimp shows as diff. (level window adjusted)

DiffImage between Caspars and Alfreds Dartclient

mitk::ImageVtkMapper2D::ApplyColor line 486

Chaged the copyright text of the files mentioned above.

[b9ab0c]: Merge branch 'bug-12085-wrong-copyright-header'

Merged commits:

2012-05-31 13:43:59 Tobias Schroeder [2dcc44]
changed copyright header to new version

Values inbetween 0 and 1 can be set. And the opacity is displayed correctly for everything but the line itself. Tested with MITK-2012.06.99_r5d2306

Andreas and I found two locations where the image writing as well as the reading
of 2D images are going wrong.

We found something that might cause the bug.

Crosshair not in center of pixel

Crosshair in center of Outline

Crosshair not in center of pixel

Crosshair in center of Outline

We noticed that outline for a selected region behaves in a very strange way.
For oblique planes the outline does not fit to the selected pixels, but the shifting can't be predicted at all. So far we can not find any logical reason for that.