Adding by-organ review

slicerModule/iraemmBrowser.py

@@ -133,26 +133,48 @@ class iraemmBrowserWidget(ScriptedLoadableModuleWidget):
     reviewCollapsibleButton.text = "Review"
     self.layout.addWidget(reviewCollapsibleButton)
     
-    reviewFormLayout = qt.QFormLayout(reviewCollapsibleButton)
+    self.reviewBoxLayout = qt.QVBoxLayout(reviewCollapsibleButton)
 
+    self.reviewFormLayout = qt.QFormLayout()
+
+
+    self.reviewSegment=qt.QComboBox()
+    self.reviewSegment.currentIndexChanged.connect(self.onReviewSegmentChanged)
+    self.reviewFormLayout.addRow("Selected region:",self.reviewSegment)
+    
    
+
     self.reviewResult=qt.QComboBox()
-    reviewFormLayout.addRow("What do you think about the segmentation:",\
+    self.reviewFormLayout.addRow("What do you think about the segmentation:",\
             self.reviewResult)
-    self.reviewResult.addItem("Excellent")
-    self.reviewResult.addItem("Minor deficiencies")
-    self.reviewResult.addItem("Major deficiencies")
-    self.reviewResult.addItem("Unusable")
+    reviewOptions=['Select','Excellent','Minor deficiencies','Major deficiencies','Unusable']
+    for opt in reviewOptions:
+        self.reviewResult.addItem(opt)
     
-    self.reviewComment=qt.QLineEdit("this is a test")
-    reviewFormLayout.addRow("Comments (optional)",\
+    self.updateReview=qt.QPushButton("Save")
+    self.reviewFormLayout.addRow("Save segmentation decision for current segment",\
+            self.updateReview)
+    self.updateReview.clicked.connect(self.onUpdateReviewButtonClicked)
+
+    self.reviewBoxLayout.addLayout(self.reviewFormLayout)
+
+    submitFrame=qt.QFrame()
+    
+    self.submitFormLayout=qt.QFormLayout()
+
+    self.reviewComment=qt.QTextEdit("this is a test")
+    self.submitFormLayout.addRow("Comments (optional)",\
             self.reviewComment)
     
     self.submitReviewButton=qt.QPushButton("Submit")
-    reviewFormLayout.addRow("Submit to database",\
+    self.submitFormLayout.addRow("Submit to database",\
             self.submitReviewButton)
     self.submitReviewButton.clicked.connect(self.onSubmitReviewButtonClicked)
-
+    submitFrame.setLayout(self.submitFormLayout)
+    submitFrame.setFrameShape(qt.QFrame.StyledPanel)
+    submitFrame.setFrameShadow(qt.QFrame.Sunken)
+    submitFrame.setStyleSheet("background-color:rgba(220,215,180,45)")
+    self.reviewBoxLayout.addWidget(submitFrame)
 
   def onPatientListChanged(self,i):
       idFilter={'variable':'PatientId','value':self.patientList.currentText,'oper':'eq'}
@@ -186,16 +208,29 @@ class iraemmBrowserWidget(ScriptedLoadableModuleWidget):
       self.ctCode.setText(row[self.ctField.text])
       self.segmentationCode.setText(row[self.segmentationField.text])
 
-
   def onPatientLoadButtonClicked(self):
       print("Load")
       #delegate loading to logic
       #try:
       self.logic.loadImage(self.currentRow,self.keepCached.isChecked())
-      self.logic.compileSegmentation()
+      segmentList=self.logic.compileSegmentation()
+      importantSegmentList=['liver','bowel','thyroid','bladder']
+      for seg in segmentList:
+          if not seg in importantSegmentList:
+              continue
+          #filter to most important ones
+          self.reviewSegment.addItem(seg)
+      self.logic.loadReview(self.currentRow)
+      self.onReviewSegmentChanged()
       #except AttributeError:
       #    print("Missing current row")
       #    return
+  
+  def onReviewSegmentChanged(self):
+      self.logic.hideSegments()
+      self.logic.showSegment(self.reviewSegment.currentText)
+      #set reviewFlag to stored value
+      self.reviewResult.setCurrentIndex(self.logic.getReviewResult(self.reviewSegment.currentText)) 
 
   def onSubmitReviewButtonClicked(self):
       print("Submit")
@@ -203,11 +238,60 @@ class iraemmBrowserWidget(ScriptedLoadableModuleWidget):
           self.reviewResult.currentText))
       print("Comment:{}".format(self.reviewComment))
       self.logic.submitReview(self.currentRow,\
-              self.reviewResult.currentIndex,\
-              self.reviewComment.text)
+              self.reviewComment.plainText)
+
+  def onUpdateReviewButtonClicked(self):
+      print("Save")
+      
+      self.logic.updateReview(self.reviewSegment.currentText,\
+              self.reviewResult.currentIndex)
+      
+      idx=self.findCompletedSegment(self.reviewSegment.currentText)
+      if idx<0:
+          qReview=qt.QLabel(self.reviewResult.currentText)
+          self.submitFormLayout.insertRow(0,self.reviewSegment.currentText,qReview)
+          try:
+              self.segmentsCompleted.append(self.reviewSegment.currentText)
+          except AttributeError:
+              self.segmentsCompleted=[]
+              self.segmentsCompleted.append(self.reviewSegment.currentText)
+      else:
+          qReview=self.submitFormLayout.itemAt(idx,1).widget()
+          qReview.setText(self.reviewResult.currentText)
+
+      colors=['pink','green','yellow','orange','red']
+      qReview.setStyleSheet("background-color: "+colors[self.reviewResult.currentIndex])
+  
+  def findCompletedSegment(self,segment):
+
+      for i in range(self.submitFormLayout.rowCount()):
+          if self.submitFormLayout.itemAt(i,0).widget().text==segment:
+              return i
+      return -1
+
+  def removeCompletedSegments(self):
+      
+      try:
+          segments=self.segmentsCompleted
+      except AttributeError:
+          return 
+
+      for seg in segments:
+          idx=self.findCompletedSegment(seg)
+          if idx>-1:
+              self.submitFormLayout.removeRow(idx)
+      
+      self.segmentsCompleted=[]
+
 
   def onPatientClearButtonClicked(self):
       self.logic.clearVolumesAndSegmentations()
+      self.reviewSegment.clear()
+      self.removeCompletedSegments()
+
+      
+
+  
 
 
 
@@ -235,6 +319,12 @@ class iraemmBrowserLogic(ScriptedLoadableModuleLogic):
           self.net=parent.network
           self.project=parent.project
 
+      self.segLabel={'1':'liver','2':'spleen','3':'lung','4':'thyroid',\
+              '5':'kidney','6':'pancreas','7':'gallbladder','8':'bladder',\
+              '9':'aorta','10':'trachea','11':'sternum','12':'vertebraL1',\
+              '13':'adrenal','14':'psoasMajor','15':'rectus',\
+              '16':'bowel','17':'stomach','18':'heart'}
+
   def setLabkeyInterface(self,net):
       #additional way of setting the labkey network interface 
       #if no parent was provided in logic initialization (stand-alone mode)
@@ -260,7 +350,7 @@ class iraemmBrowserLogic(ScriptedLoadableModuleLogic):
           p=relativePaths[f]
           labkeyPath=self.net.GetLabkeyPathFromRelativePath(p)
           rp=self.net.head(labkeyPath)
-          if not rp.code==200:
+          if not slicerNetwork.labkeyURIHandler.HTTPStatus(rp):
               print("Failed to get {}".format(labkeyPath))
               continue
 
@@ -284,6 +374,9 @@ class iraemmBrowserLogic(ScriptedLoadableModuleLogic):
       slicer.util.setSliceViewerLayers(background=self.volumeNode['CT'],\
           foreground=self.volumeNode['PET'],foregroundOpacity=0.5,fit=True)
 
+
+  #segmentations
+
   def compileSegmentation(self):
       try:
           labelmapVolumeNode = self.volumeNode['Segmentation']
@@ -291,30 +384,113 @@ class iraemmBrowserLogic(ScriptedLoadableModuleLogic):
           print("No segmentaion volumeNode available")
           return
      
-      seg = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLSegmentationNode')
+      self.segmentationNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLSegmentationNode')
       slicer.modules.segmentations.logic().\
-              ImportLabelmapToSegmentationNode(labelmapVolumeNode, seg)
+              ImportLabelmapToSegmentationNode(labelmapVolumeNode, self.segmentationNode)
       
-      segLabel={'1':'liver','2':'spleen','3':'lung','4':'thyroid',\
-              '5':'kidney','6':'pancreas','7':'gallbladder','8':'bladder',\
-              '9':'aorta','10':'trachea','11':'sternum','12':'vertebra L1',\
-              '13':'adrenal','14':'psoas major','15':'rectus',\
-              '16':'bowel','17':'stomach','18':'heart'}
       
-      for i in range(seg.GetSegmentation().GetNumberOfSegments()):
-          segment=seg.GetSegmentation().GetNthSegment(i)
-          segment.SetName(segLabel[segment.GetName()])
+      segmentList=[]
+      
+      seg=self.segmentationNode.GetSegmentation()
+
+      for i in range(seg.GetNumberOfSegments()):
+          segment=seg.GetNthSegment(i)
+          segment.SetName(self.segLabel[segment.GetName()])
+          segmentList.append(segment.GetName())
 
       #seg.CreateClosedSurfaceRepresentation()
       slicer.mrmlScene.RemoveNode(labelmapVolumeNode)
       self.volumeNode.pop('Segmentation',None)
 
+      #return list of segment names
+      return segmentList
+  
+  def hideSegments(self):
+
+      try:
+          displayNode=self.segmentationNode.GetDisplayNode()
+      except AttributeError:
+          return
+
+      seg=self.segmentationNode.GetSegmentation()
+      for i in range(seg.GetNumberOfSegments()):
+          #segment=self.segmentationNode.GetSegmentation().GetNthSegment(i)
+          segmentID=seg.GetNthSegmentID(i)
+          displayNode.SetSegmentVisibility(segmentID, False)
+      #print("Done")
+  
+  def showSegment(self,name):
+      try:
+          displayNode=self.segmentationNode.GetDisplayNode()
+      except AttributeError:
+          return
+      
+      seg=self.segmentationNode.GetSegmentation()
+      for i in range(seg.GetNumberOfSegments()):
+          segment=seg.GetNthSegment(i)
+          if not segment.GetName()==name:
+              continue
+          segmentID=seg.GetNthSegmentID(i)
+          displayNode.SetSegmentVisibility(segmentID, True)
+          break
+      #print("Done")
+  
+
+  #clear 
+
   def clearVolumesAndSegmentations(self):
       nodes=slicer.util.getNodesByClass("vtkMRMLVolumeNode")
       nodes.extend(slicer.util.getNodesByClass("vtkMRMLSegmentationNode"))
       res=[slicer.mrmlScene.RemoveNode(f) for f in nodes] 
+      self.segmentationNode=None
+      self.reviewResult={}
+
+  #reviews by segment
+
+  def updateReview(self,segment,value):
+      try:
+          self.reviewResult[segment]=value
+      except AttributeError:
+          self.reviewResult={}
+          self.updateReview(segment,value)
+  
+  def getReviewResult(self,segment):
+      try:
+          return self.reviewResult[segment]
+      except AttributeError:
+          #review result not initialized
+          return 0
+      except KeyError:
+          #segment not done yet
+          return 0
+  
+  #load review from labkey
+  def loadReview(self,currentRow):
+
+      #see if we have already done a review
+      filters=[]
+      fields=['PatientId','SequenceNum']
+
+
+      for f in fields:
+          filters.append({'variable':f,'value':str(currentRow[f]),'oper':'eq'})
+      
+      ds=self.net.filterDataset(self.parent.project,\
+              self.parent.reviewDataset,filters)
+
+      if len(ds['rows'])==0:
+          return
 
-  def submitReview(self,currentRow,idx,comment):
+      row=ds['rows'][0]
+      for label in self.segLabel:
+          name=self.segLabel[label]+'Review'
+          try:
+              self.updateReview(self.segLabel[label],row[name])
+          except KeyError:
+              continue 
+   
+  #submit review to labkey
+  def submitReview(self,currentRow,comment):
       row={}
 
       fields=['PatientId','SequenceNum']
@@ -337,7 +513,14 @@ class iraemmBrowserLogic(ScriptedLoadableModuleLogic):
           for f in fields:
               row[f]=currentRow[f]
       
-      row['reviewResult']=idx+1 #labkey has 1-based arrays
+      seg=self.segmentationNode.GetSegmentation()
+ 
+      for i in range(seg.GetNumberOfSegments()):
+          segment=seg.GetNthSegment(i)
+          fieldName=segment.GetName()+'Review'
+          value=self.getReviewResult(segment.GetName())
+          row[fieldName]=value
+
       row['reviewComment']=comment
       row['Date']=datetime.datetime.now().ctime()
       ds=self.net.modifyDataset(mode,self.parent.project,\