Projects:ARRA:SlicerEM:Slicer4

EMSegmenter in Slicer4

TODO

• untie KWWidgets from EMSegment base
• untie KWWidgets from EMSegment commandline tool
• create EMSegment4 as an extension for Slicer4
  • include the commandline tool in the extension (Problem: infrastructure is not ready yet)
• Merge old EMSegment4 and the new extension all in Slicer3 repository
• introduce Slicer Common Interface (SCI) which holds functionality which is different between Slicer3 and Slicer4 but provides the same API for both
  • provide EMSegment3 functionality in the SCI
  • provide EMSegment4 functionality in the SCI (work in progress)
• update EMSegment4 Qt Gui
• provide nightly extension builds

Slicer Common Interface (SCI)

The Slicer Common Interface is a class with a unified API for Slicer3 and Slicer4 which includes functionality which has to be realized differently among the two Slicer versions.

Progress

Task	Slicer3	Slicer4
GetTclInterpeter	DONE	obsolete
SourceTclFile	DONE	DONE
EvaluateTcl	DONE	DONE
GetTclNameFromPointer	DONE	DONE
RegisterObjectWithTcl	DONE	DONE
GetApplicationTclName	DONE	DONE
InitializePythonViaTcl	DONE	obsolete
EvaluatePython	DONE	DONE
GetTemporaryDirectory	DONE	DONE
GetBinDirectory	DONE	DONE
GetRepositoryRevision	DONE	DONE
SetApplicationBinDir	DONE	obsolete
GetHTTPHandler	DONE	DONE
PromptBeforeExitOff	DONE	DONE
DestroySlicerApplication	DONE	DONE
AddDataIOToScene	DONE	DONE
RemoveDataIOFromScene	DONE	DONE

EMSegment GUI in Qt

Wizard steps

• Step1: Define Task
  • create new task functionality
  • all done
• Step2: Define input channels
  • in Simple mode show dynamic frame
  • all done
• Step3: Define anatomical tree
  • qt widget does not support creating subclasses yet
  • all done
• Step4: Define Atlas
  • qt widget supports parcellation maps
  • all done
• Step5: Edit Registration parameters
  • problem: show input channels-volume map does not work yet
  • all done
• Step6: Dynamic frame
  • support for dynamic textedits
• Step7: Specify Intensity Distributions
  • manual sampling
  • all done
• Step8: Edit node-based parameters
  • advanced GUI not done yet
  • all done
• Step9: Define Misc. Parameters
  • all done

In general:

• segmentation call not hooked up yet
• Extension infrastructure
• Testing and bug fixing

Open issues reported by Kilian

• "Attempt to go to the finish step succeeded" message when clicking segment
  • this is a ctk error
• step 3: reduce size of probability map fields (not possible)
• step 7: "Plot distribution" functionality
• step 7: incorrect mean in manual sampling mode (found the cause I think)
• step 7: incorrect reset of distribution
• step 7: size of anatomical tree not optimal
• step 7: remove auto-sampling
• step 9: grey out forward button
• put emsegmenter in category segmentation
• all steps: tooltips
• order task list alphabetically