ENH: add capability to init from existing segmentations

Added an attribute on the finding node to pass along the id of a
prior segemented label map volume to use when adding a finding.
The module workflow is split up across multiple small functions
so the passing of the prior volume information isn't as clean
as it could be with a redesign.

Issue QIICR#1

Py/qSlicerLongitudinalPETCTModuleWidget.py

@@ -6,6 +6,7 @@
 from SlicerLongitudinalPETCTModuleSegmentationHelper import SlicerLongitudinalPETCTModuleSegmentationHelper as SegmentationHelper
 
 from Editor import EditorWidget
+from LabelStatistics import LabelStatisticsLogic
 
 import sys as SYS
 
@@ -919,11 +920,26 @@ def onFindingNodeAdded(self, finding):
 
     name = dialog.property("findingName")
     colorid = dialog.property("findingColorID")
+    priorLabelMapID = dialog.property("findingPriorSegmentationID")
 
     if (len(name) > 0) & (colorid != -1):
       finding.SetName(name)
       finding.SetColorID(colorid)
 
+      if (len(priorLabelMapID) > 0):
+        print 'Initializing segmentation from prior'
+        study = self.getActiveStudy()
+        segmentationNode = finding.GetSegmentationMappedByStudyNodeID(study.GetID())
+        # Can init from a prior label map if no segmentation node has been
+        # defined yet, or it has but it doesn't already point to the prior
+        # label map
+        if (segmentationNode == None or
+            segmentationNode.GetLabelVolumeID() == None or
+            (segmentationNode.GetLabelVolumeID() != None and segmentationNode.GetLabelVolumeID() != priorLabelMapID)):
+          finding.SetAttribute("AssociatedNodeID", priorLabelMapID)
+        else:
+          print 'Unable to initialize from prior label map with id',priorLabelMapID,', segmentationNode = ',segmentationNode
+
       self.activeReportNode.AddFindingNodeID(finding.GetID())
       self.reportOverviewWidget.selectFindingRow(self.activeReportNode.GetIndexOfFindingNodeID(finding.GetID()))
 
@@ -1321,7 +1337,47 @@ def __prepareVolumesForSegmentation(self,caller,event):
     if self.__tempLabelVol == None:
       self.__createTempLabelVolume()
 
+    if finding.GetAttribute("AssociatedNodeID"):
+      # init from the prior segmentation, then unset
+      priorSegmentationID = finding.GetAttribute("AssociatedNodeID")
+      print 'prepareVolumesForSegmentation: Finding has an associated prior: ',priorSegmentationID
+      priorSegmentationNode = slicer.mrmlScene.GetNodeByID(priorSegmentationID)
+      if priorSegmentationNode:
+        # threshold the prior to the finding value
+        findingColor = finding.GetColorID()
+        print 'Threshold the prior to the finding color',findingColor
+        threshold = vtk.vtkImageThreshold()
+        threshold.SetInputData(priorSegmentationNode.GetImageData())
+        threshold.SetReplaceOut(0)
+        threshold.SetReplaceIn(1)
+        threshold.SetInValue(findingColor)
+        # set all non zero values to the finding color
+        scalarRange = [0,0]
+        priorSegmentationNode.GetImageData().GetScalarRange(scalarRange)
+        print '\tprior scalarRange = ',scalarRange
+        threshold.ThresholdBetween(1, scalarRange[1])
+        threshold.Update()
+        threshold.ReleaseDataFlagOn()
+        priorSegmentationNode.SetAndObserveImageData(threshold.GetOutputDataObject(0))
+        # put the prior into the PET label volume so that it will be in
+        # the pipeine for segmentation
+        if (study.GetPETLabelVolumeNode().GetImageData() != None):
+          # check that the geometry matches
+          volumesLogic = slicer.modules.volumes.logic()
+          geometryCheckString = volumesLogic.CheckForLabelVolumeValidity(study.GetPETLabelVolumeNode(), priorSegmentationNode)
+          if geometryCheckString != "":
+            print 'Resampling prior due to geometry mismatch:\n',geometryCheckString
+            resampledSegmentationNode = volumesLogic.ResampleVolumeToReferenceVolume(priorSegmentationNode, study.GetPETLabelVolumeNode())
+            study.GetPETLabelVolumeNode().Copy(resampledSegmentationNode)
+          else:
+            # geometry matches
+            study.GetPETLabelVolumeNode().Copy(priorSegmentationNode)
+        else:
+          # just copy to init it
+          study.GetPETLabelVolumeNode().Copy(priorSegmentationNode)
+
     self.__tempLabelVol.Copy(study.GetPETLabelVolumeNode())
+
     self.__tempLabelVol.SetName("LongitudinalPETCT_CroppedLabelVolume")
     self.__tempLabelVol.SetSaveWithScene(False)
 
@@ -1386,6 +1442,12 @@ def onAddSegmentationToFinding(self):
     SegmentationHelper.removeSegmentationFromVolume(seg.GetLabelVolumeNode(), finding.GetColorID())
 
     pasted = SegmentationHelper.pasteFromCroppedToMainLabelVolume(self.__tempLabelVol, seg.GetLabelVolumeNode(), finding.GetColorID())
+
+    # if there was a prior, unset it now (if done before this, it can get
+    # over written or cropped out)
+    if finding.GetAttribute("AssociatedNodeID"):
+      finding.RemoveAttribute("AssociatedNodeID")
+
     #set coordinates and extent of roi used for segmentation
     c = [0.,0.,0.]
     r = [0.,0.,0.]
@@ -1445,7 +1507,7 @@ def calculateSUVsAndStatistics(self, study, finding):
     if (study == None) | (finding == None):
       return
 
-    stats = LabelStatisticsLogic(study.GetPETVolumeNode(), study.GetPETLabelVolumeNode())
+    stats = LabelStatistics.LabelStatisticsLogic(study.GetPETVolumeNode(), study.GetPETLabelVolumeNode())
 
     if finding.GetColorID() in stats.labelStats["Labels"]:
       idx = stats.labelStats["Labels"].index(finding.GetColorID())

Resources/UI/qMRMLLongitudinalPETCTFindingSettingsDialog.ui

@@ -7,7 +7,7 @@
     <x>0</x>
     <y>0</y>
     <width>374</width>
-    <height>209</height>
+    <height>317</height>
    </rect>
   </property>
   <property name="sizePolicy">
@@ -294,6 +294,56 @@ Node</string>
      </property>
     </widget>
    </item>
+   <item>
+    <widget class="ctkCollapsibleButton" name="InitializeFromPriorSegmentationCollapsibleButton">
+     <property name="toolTip">
+      <string>Select a segmented volume from the scene, resample and threshold</string>
+     </property>
+     <property name="text">
+      <string>Initialize from Prior Segmentation</string>
+     </property>
+     <property name="collapsed">
+      <bool>true</bool>
+     </property>
+     <property name="contentsFrameShape">
+      <enum>QFrame::StyledPanel</enum>
+     </property>
+     <layout class="QFormLayout" name="formLayout_3">
+      <property name="fieldGrowthPolicy">
+       <enum>QFormLayout::FieldsStayAtSizeHint</enum>
+      </property>
+      <item row="0" column="0">
+       <widget class="QLabel" name="PriorSegmentationLabel">
+        <property name="text">
+         <string>Segmentations:</string>
+        </property>
+       </widget>
+      </item>
+      <item row="0" column="1">
+       <widget class="qMRMLNodeComboBox" name="PriorSegmentationMRMLNodeComboBox">
+        <property name="toolTip">
+         <string>Select a label map volume from the scene. It will be resampled and thresholded if necessary to match the current image geometry. If there are multiple values present, they will be thresholded to the selected finding color.</string>
+        </property>
+        <property name="nodeTypes">
+         <stringlist>
+          <string>vtkMRMLLabelMapVolumeNode</string>
+         </stringlist>
+        </property>
+        <property name="noneEnabled">
+         <bool>true</bool>
+        </property>
+       </widget>
+      </item>
+     </layout>
+    </widget>
+   </item>
+   <item>
+    <widget class="Line" name="line_3">
+     <property name="orientation">
+      <enum>Qt::Horizontal</enum>
+     </property>
+    </widget>
+   </item>
    <item>
     <widget class="QDialogButtonBox" name="ButtonBox">
      <property name="standardButtons">
@@ -306,10 +356,27 @@ Node</string>
  <customwidgets>
   <customwidget>
    <class>qMRMLLabelComboBox</class>
-   <extends>QWidget</extends>
+   <extends>qMRMLWidget</extends>
    <header>qMRMLLabelComboBox.h</header>
    <container>1</container>
   </customwidget>
+  <customwidget>
+   <class>qMRMLNodeComboBox</class>
+   <extends>QWidget</extends>
+   <header>qMRMLNodeComboBox.h</header>
+  </customwidget>
+  <customwidget>
+   <class>qMRMLWidget</class>
+   <extends>QWidget</extends>
+   <header>qMRMLWidget.h</header>
+   <container>1</container>
+  </customwidget>
+  <customwidget>
+   <class>ctkCollapsibleButton</class>
+   <extends>QWidget</extends>
+   <header>ctkCollapsibleButton.h</header>
+   <container>1</container>
+  </customwidget>
  </customwidgets>
  <resources>
   <include location="../qSlicerLongitudinalPETCTModule.qrc"/>