Click'n'Join-Mode extension to ITK-SNAP incuding global, dynamic watershed segmentation #1
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…SegementationToJdst
…of the interaction modes
needed manual modifications, these still need testing of GWS_ROI_MODE Conflicts: Common/SNAPCommon.h GUI/Qt/Windows/MainControlPanel.cxx GUI/Qt/Windows/MainControlPanel.ui GUI/Qt/Windows/MainImageWindow.cxx GUI/Qt/Windows/MainImageWindow.h GUI/Qt/Windows/MainImageWindow.ui Logic/Framework/IRISApplication.cxx
…only in SNAKE_ROI_MODE but also in GLOBALWS_ROI_MODE
…o fixed intensity range
…ScalarToRGBPixelFunctor
Conflicts: GUI/Qt/Components/CursorInspector.ui
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I managed to get 64bit "Join Source Image" (Jsrc) working, now even with itkScalarToRGBPixelFunctor. 64bit is essential for proper function of gWS, as otherwise casting to 16bit causes multiple regions to be added to Jdst even though only a single label is clicked on in Jsrc. However, with 64bit the LUT usually used for the label/segmentation image is too short an not suitable for Jsrc any more. Therefore itkScalarToRGBPixelFunctor (can be regarded as an infinite LUT) is now used to colour Jsrc. This works very well for gWS but its colours for small label IDs are quite similar. This is a disadvantage when using plain CnJ. Ideally, the user should be given an option which type of colouring should be used, or should be made dependent on the mode. gWS in stage 3 showing the overlayed "Join Source Image" colored with itkScalarToRGBPixelFunctor: |
…ing results; WsrcImage not visible in Slice-View yet
Conflicts: Logic/ImageWrapper/CommonRepresentationPolicy.cxx
This is a little unconventional, but I decided that the changes in the master branch are really ready for primetime in release 3.4, especially since I tested them for the RSNA course.
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Got closed due to branch renaming. |
Official Release 3.4.0 Conflicts: GUI/Model/GlobalUIModel.cxx GUI/Model/PaintbrushModel.cxx GUI/Model/PaintbrushModel.h GUI/Model/UIState.h GUI/Qt/Components/SliceViewPanel.ui GUI/Qt/Windows/MainControlPanel.cxx GUI/Qt/Windows/MainControlPanel.h GUI/Qt/Windows/MainControlPanel.ui GUI/Qt/Windows/MainImageWindow.cxx GUI/Qt/Windows/MainImageWindow.h GUI/Qt/Windows/MainImageWindow.ui Logic/Slicing/IRISSlicer.txx
…but has no apparent effect)
…fault any more, filter executes but has no effect
This reverts commit 30a80e2.
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Parallelized itkJoinCopyFilter now working in CnJ mode, which about halves the time needed for processing each CnJ-click. The other half is apparently spent on a single-threaded process (which could possibly be avoided, needs further investigation). |
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The single-threaded process that took up time was StoreUndoPoint, which is not working for CnJ in v3.4 any way. |
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These extensions to ITK-SNAP implement a global watershed segmentation mode (gWS). The extensions incorporate a Click'n'Join mode (CnJ) as the intended usage of gWS is related to the SegmentationEditor (http://www.itk.org/ITK/applications/segmentationeditor.html, demo video: SegmentationEditor.avi of http://www.insight-journal.org/browse/publication/70).
In CnJ mode, the user can add or remove labels from a source label image to a destination label image. The source image can either be the currently loaded segmentation, one from a file or the output of gWS. The over or under segmentation can be dynamically controlled during CnJ+gWS avoiding a complete recomputation of the watershed segementation.
There is also an extension to the "adaptive" brush of ITK-SNAP to make use of this dynamic WS (dWS) relevelling which can then be adjusted with the mouse wheel.
CnJ on the output of a morphological watershed (with borders):
CnJ+gWS:
