JonathanRamos · lassoan · Jun 18, 2022 · Jul 6, 2022 · Jul 6, 2022 · Jul 6, 2022
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -4,12 +4,12 @@ project(CleverSeg)
 
 #-----------------------------------------------------------------------------
 # Extension meta-information
-set(EXTENSION_HOMEPAGE "http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/CleverSeg")
+set(EXTENSION_HOMEPAGE "https://github.com/lassoan/SlicerCleverSegmentation#cleversegmentation")
 set(EXTENSION_CATEGORY "Segmentation")
-set(EXTENSION_CONTRIBUTORS "Jonathan Ramos (University of São Paulo)")
-set(EXTENSION_DESCRIPTION "This is an example of a simple extension")
-set(EXTENSION_ICONURL "http://www.example.com/Slicer/Extensions/CleverSeg.png")
-set(EXTENSION_SCREENSHOTURLS "http://www.example.com/Slicer/Extensions/CleverSeg/Screenshots/1.png")
+set(EXTENSION_CONTRIBUTORS "Jonathan Ramos (ICMC, University of São Paulo - USP)")
+set(EXTENSION_DESCRIPTION "This is the implementation of the CleverSeg method that supports multi-label segmentations")
+set(EXTENSION_ICONURL "https://raw.githubusercontent.com/lassoan/SlicerCleverSegmentation/master/CleverSegmentation/Resources/Icons/CleverSegmentation.png")
+set(EXTENSION_SCREENSHOTURLS "https://user-images.githubusercontent.com/3834596/66679138-d7dc1700-ec43-11e9-8c36-51976a1121d3.png" "https://user-images.githubusercontent.com/3834596/66679174-f215f500-ec43-11e9-84f1-85f8b5c4d568.png")
 set(EXTENSION_DEPENDS "NA") # Specified as a space separated string, a list or 'NA' if any
 
 #-----------------------------------------------------------------------------

diff --git a/CleverSegmentation/Resources/Icons/CleverSegmentation.png b/CleverSegmentation/Resources/Icons/CleverSegmentation.png
diff --git a/CleverSegmentation/SegmentEditorCleverSegmentationLib/SegmentEditorEffect.py b/CleverSegmentation/SegmentEditorCleverSegmentationLib/SegmentEditorEffect.py
@@ -1,79 +1,82 @@
-import os
-import vtk, qt, ctk, slicer
-import logging
-from SegmentEditorEffects import *
-
-class SegmentEditorEffect(AbstractScriptedSegmentEditorAutoCompleteEffect):
-  """ AutoCompleteEffect is an effect that can create a full segmentation
-      from a partial segmentation (not all slices are segmented or only
-      part of the target structures are painted).
-  """
-
-  def __init__(self, scriptedEffect):
-    AbstractScriptedSegmentEditorAutoCompleteEffect.__init__(self, scriptedEffect)
-    scriptedEffect.name = 'CleverSegmentation'
-    self.minimumNumberOfSegments = 2
-    self.clippedMasterImageDataRequired = True # master volume intensities are used by this effect
-    self.clippedMaskImageDataRequired = True # masking is used
-    self.cleverSegFilter = None
-
-  def clone(self):
-    import qSlicerSegmentationsEditorEffectsPythonQt as effects
-    clonedEffect = effects.qSlicerSegmentEditorScriptedEffect(None)
-    clonedEffect.setPythonSource(__file__.replace('\\','/'))
-    return clonedEffect
-
-  def icon(self):
-    iconPath = os.path.join(os.path.dirname(__file__), 'SegmentEditorEffect.png')
-    if os.path.exists(iconPath):
-      return qt.QIcon(iconPath)
-    return qt.QIcon()
-
-  def helpText(self):
-    return """<html>Growing segments to create complete segmentation<br>.
-Location, size, and shape of initial segments and content of master volume are taken into account.
-Final segment boundaries will be placed where master volume brightness changes abruptly. Instructions:<p>
-<ul style="margin: 0">
-<li>Use Paint or other offects to draw seeds in each region that should belong to a separate segment.
-Paint each seed with a different segment. Minimum two segments are required.</li>
-<li>Click <dfn>Initialize</dfn> to compute preview of full segmentation.</li>
-<li>Browse through image slices. If previewed segmentation result is not correct then switch to
-Paint or other effects and add more seeds in the misclassified region. Full segmentation will be
-updated automatically within a few seconds</li>
-<li>Click <dfn>Apply</dfn> to update segmentation with the previewed result.</li>
-</ul><p>
-If segments overlap, segment higher in the segments table will have priority.
-The effect uses fast clever-segmentation method</a>.
-<p></html>"""
-
-
-  def reset(self):
-    self.cleverSegFilter = None
-    AbstractScriptedSegmentEditorAutoCompleteEffect.reset(self)
-    self.updateGUIFromMRML()
-
-  def computePreviewLabelmap(self, mergedImage, outputLabelmap):
-    import vtkCleverSegModuleLogicPython as vtkCleverSeg
-
-
-
-    if not self.cleverSegFilter:
-      self.cleverSegFilter = vtkCleverSeg.vtkCleverSeg()
-      self.cleverSegFilter.SetIntensityVolume(self.clippedMasterImageData)
-      self.cleverSegFilter.SetMaskVolume(self.clippedMaskImageData)
-      maskExtent = self.clippedMaskImageData.GetExtent() if self.clippedMaskImageData else None
-      if maskExtent is not None and maskExtent[0] <= maskExtent[1] and maskExtent[2] <= maskExtent[3] and maskExtent[4] <= maskExtent[5]:
-        # Mask is used.
-        # Grow the extent more, as background segment does not surround region of interest.
-        self.extentGrowthRatio = 0.50
-      else:
-        # No masking is used.
-        # Background segment is expected to surround region of interest, so narrower margin is enough.
-        self.extentGrowthRatio = 0.20
-
-      self.extentGrowthRatio
-
-    self.cleverSegFilter.SetSeedLabelVolume(mergedImage)
-    self.cleverSegFilter.Update()
-
-    outputLabelmap.DeepCopy( self.cleverSegFilter.GetOutput() )
+import os
+import vtk, qt, ctk, slicer
+import logging
+from SegmentEditorEffects import *
+
+class SegmentEditorEffect(AbstractScriptedSegmentEditorAutoCompleteEffect):
+  """ AutoCompleteEffect is an effect that can create a full segmentation
+      from a partial segmentation (not all slices are segmented or only
+      part of the target structures are painted).
+  """
+
+  def __init__(self, scriptedEffect):
+    AbstractScriptedSegmentEditorAutoCompleteEffect.__init__(self, scriptedEffect)
+    scriptedEffect.name = 'CleverSegmentation'
+    self.minimumNumberOfSegments = 2
+    self.clippedMasterImageDataRequired = True # master volume intensities are used by this effect
+    self.clippedMaskImageDataRequired = True # masking is used
+    self.cleverSegFilter = None
+
+  def clone(self):
+    import qSlicerSegmentationsEditorEffectsPythonQt as effects
+    clonedEffect = effects.qSlicerSegmentEditorScriptedEffect(None)
+    clonedEffect.setPythonSource(__file__.replace('\\','/'))
+    return clonedEffect
+
+  def icon(self):
+    iconPath = os.path.join(os.path.dirname(__file__), 'SegmentEditorEffect.png')
+    if os.path.exists(iconPath):
+      return qt.QIcon(iconPath)
+    return qt.QIcon()
+
+  def helpText(self):
+    return """<html>Growing segments to create complete segmentation<br>.
+Location, size, and shape of initial segments and content of master volume are taken into account.
+Final segment boundaries will be placed where master volume brightness changes abruptly. Instructions:<p>
+<ul style="margin: 0">
+<li>Use Paint or other offects to draw seeds in each region that should belong to a separate segment.
+Paint each seed with a different segment. Minimum two segments are required.</li>
+<li>Click <dfn>Initialize</dfn> to compute preview of full segmentation.</li>
+<li>Browse through image slices. If previewed segmentation result is not correct then switch to
+Paint or other effects and add more seeds in the misclassified region. Full segmentation will be
+updated automatically within a few seconds</li>
+<li>Click <dfn>Apply</dfn> to update segmentation with the previewed result.</li>
+</ul><p>
+If segments overlap, segment higher in the segments table will have priority.
+The effect uses fast clever-segmentation method</a>.
+<p></html>"""
+
+
+  def reset(self):
+    self.cleverSegFilter = None
+    AbstractScriptedSegmentEditorAutoCompleteEffect.reset(self)
+    self.updateGUIFromMRML()
+
+  def computePreviewLabelmap(self, mergedImage, outputLabelmap):
+    import vtkCleverSegModuleLogicPython as vtkCleverSeg
+
+
+
+    if not self.cleverSegFilter:
+      self.cleverSegFilter = vtkCleverSeg.vtkCleverSeg()
+      self.cleverSegFilter.SetIntensityVolume(self.clippedMasterImageData)
+      self.cleverSegFilter.SetMaskVolume(self.clippedMaskImageData)
+      maskExtent = self.clippedMaskImageData.GetExtent() if self.clippedMaskImageData else None
+      if maskExtent is not None and maskExtent[0] <= maskExtent[1] and maskExtent[2] <= maskExtent[3] and maskExtent[4] <= maskExtent[5]:
+        # Mask is used.
+        # Grow the extent more, as background segment does not surround region of interest.
+        self.extentGrowthRatio = 0.50
+      else:
+        # No masking is used.
+        # Background segment is expected to surround region of interest, so narrower margin is enough.
+        self.extentGrowthRatio = 0.20
+
+      self.extentGrowthRatio
+
+    self.cleverSegFilter.SetSeedLabelVolume(mergedImage)
+    self.cleverSegFilter.Update()
+
+    outputLabelmap.DeepCopy( self.cleverSegFilter.GetOutput() )
+    imageToWorld = vtk.vtkMatrix4x4()
+    mergedImage.GetImageToWorldMatrix(imageToWorld)
+    outputLabelmap.SetImageToWorldMatrix(imageToWorld)