Adding AE qualification

slicerModule/iraemmBrowser.py

@@ -50,9 +50,9 @@ class iraemmBrowserWidget(ScriptedLoadableModuleWidget):
     self.project="iPNUMMretro/Study"
     self.dataset="Imaging1"
     self.reviewDataset="ImageReview"
+    self.aeDataset="PET"
+    self.segmentList=['liver','bowel','thyroid','lung','kidney','pancreas']
 
-
-    self.logic=iraemmBrowserLogic(self)
     
 
     ds=self.network.filterDataset(self.project,self.dataset,[])
@@ -69,7 +69,9 @@ class iraemmBrowserWidget(ScriptedLoadableModuleWidget):
     
     setupFormLayout = qt.QFormLayout(setupCollapsibleButton)
 
-   
+    self.participantField=qt.QLabel("PatientId")
+    setupFormLayout.addRow("Participant field:",self.participantField)
+    
     self.ctField=qt.QLabel("ctResampled")
     setupFormLayout.addRow("Data field (CT):",self.ctField)
 
@@ -78,10 +80,12 @@ class iraemmBrowserWidget(ScriptedLoadableModuleWidget):
 
     self.segmentationField=qt.QLabel("Segmentation")
     setupFormLayout.addRow("Data field (Segmentation):",self.segmentationField)
+    
+    self.logic=iraemmBrowserLogic(self)
 
 
     #
-    # Patienrs Area
+    # Patients Area
     #
     patientsCollapsibleButton = ctk.ctkCollapsibleButton()
     patientsCollapsibleButton.text = "Patients"
@@ -152,9 +156,17 @@ class iraemmBrowserWidget(ScriptedLoadableModuleWidget):
     for opt in reviewOptions:
         self.reviewResult.addItem(opt)
     
+    self.aeResult=qt.QComboBox()
+    self.reviewFormLayout.addRow("Is organ suffering from adverse effect?",\
+            self.aeResult)
+    aeOptions=['Select','Yes','No']
+    for opt in aeOptions:
+        self.aeResult.addItem(opt)
+    #self.aeResult.setCurrentIndex(0)
+
     self.updateReview=qt.QPushButton("Save")
     self.reviewFormLayout.\
-            addRow("Save segmentation decision for current segment",\
+            addRow("Save segmentation and AE decision for current segment",\
             self.updateReview)
     self.updateReview.clicked.connect(self.onUpdateReviewButtonClicked)
 
@@ -218,24 +230,34 @@ class iraemmBrowserWidget(ScriptedLoadableModuleWidget):
       #try:
       self.logic.loadImage(self.currentRow,self.keepCached.isChecked())
       segmentList=self.logic.compileSegmentation()
-      importantSegmentList=['liver','bowel','thyroid','lung','spleen']
       #also bladder,vertebraL1, stomach, heart
       for seg in segmentList:
-          if not seg in importantSegmentList:
+          if not seg in self.segmentList:
               continue
           #filter to most important ones
           self.reviewSegment.addItem(seg)
       self.logic.loadReview(self.currentRow)
+      self.logic.loadAE(self.currentRow)
+      for segment in self.segmentList:
+          rIdx=self.logic.getReviewResult(segment)
+          aIdx=self.logic.getAEResult(segment)
+          print("Segment {}: {}/{}".format(segment,rIdx,aIdx))
+          if (rIdx+aIdx)>0:
+              self.updateResult(segment,rIdx,aIdx)
+      self.reviewComment.setPlainText(self.logic.reviewComment)
+
       self.onReviewSegmentChanged()
       #except AttributeError:
       #    print("Missing current row")
       #    return
   
   def onReviewSegmentChanged(self):
+      segment=self.reviewSegment.currentText
       self.logic.hideSegments()
-      self.logic.showSegment(self.reviewSegment.currentText)
+      self.logic.showSegment(segment)
       #set reviewFlag to stored value
-      self.reviewResult.setCurrentIndex(self.logic.getReviewResult(self.reviewSegment.currentText)) 
+      self.reviewResult.setCurrentIndex(self.logic.getReviewResult(segment))
+      self.aeResult.setCurrentIndex(self.logic.getAEResult(segment))
 
   def onSubmitReviewButtonClicked(self):
       print("Submit")
@@ -244,29 +266,52 @@ class iraemmBrowserWidget(ScriptedLoadableModuleWidget):
       print("Comment:{}".format(self.reviewComment))
       self.logic.submitReview(self.currentRow,\
               self.reviewComment.plainText)
+      self.logic.submitAE(self.currentRow)
 
   def onUpdateReviewButtonClicked(self):
       print("Save")
       
-      self.logic.updateReview(self.reviewSegment.currentText,\
+      segment=self.reviewSegment.currentText
+      self.logic.updateReview(segment,\
               self.reviewResult.currentIndex)
-      
-      idx=self.findCompletedSegment(self.reviewSegment.currentText)
+
+      self.logic.updateAE(segment,\
+              self.aeResult.currentIndex)
+      self.updateResult(segment,self.reviewResult.currentIndex,\
+              self.aeResult.currentIndex)
+
+     
+  def updateResult(self,segment,reviewResult,aeResult):
+      reviewText=self.reviewResult.itemText(reviewResult)
+      aeText=self.aeResult.itemText(aeResult)
+
+      idx=self.findCompletedSegment(segment)
+
       if idx<0:
-          qReview=qt.QLabel(self.reviewResult.currentText)
-          self.submitFormLayout.insertRow(0,self.reviewSegment.currentText,qReview)
+          qReview=qt.QLabel(reviewText)
+          self.submitFormLayout.insertRow(0,segment,qReview)
+          qAE=qt.QLabel(aeText)
+          self.submitFormLayout.insertRow(1,segment+'AE',qAE)
           try:
-              self.segmentsCompleted.append(self.reviewSegment.currentText)
+              self.segmentsCompleted.append(segment)
+              self.segmentsCompleted.append(segment+'AE')
           except AttributeError:
               self.segmentsCompleted=[]
-              self.segmentsCompleted.append(self.reviewSegment.currentText)
+              self.segmentsCompleted.append(segment)
+              self.segmentsCompleted.append(segment+'AE')
       else:
           qReview=self.submitFormLayout.itemAt(idx,1).widget()
-          qReview.setText(self.reviewResult.currentText)
+          qReview.setText(reviewText)
+          qAE=self.submitFormLayout.itemAt(idx+1,1).widget()
+          qAE.setText(aeText)
+
+      reviewColors=['pink','green','yellow','orange','red']
+      qReview.setStyleSheet("background-color: "+reviewColors[reviewResult])
+      aeColors=['pink','red','green']
+      qAE.setStyleSheet("background-color: "+aeColors[aeResult])
+
+
 
-      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()):
@@ -293,6 +338,7 @@ class iraemmBrowserWidget(ScriptedLoadableModuleWidget):
       self.logic.clearVolumesAndSegmentations()
       self.reviewSegment.clear()
       self.removeCompletedSegments()
+      self.reviewComment.clear()
 
       
 
@@ -323,6 +369,8 @@ class iraemmBrowserLogic(ScriptedLoadableModuleLogic):
           self.parent=parent
           self.net=parent.network
           self.project=parent.project
+          self.participantField=parent.participantField.text
+          self.segmentList=parent.segmentList
 
       self.segLabel={'1':'liver','2':'spleen','3':'lung','4':'thyroid',\
               '5':'kidney','6':'pancreas','7':'gallbladder','8':'bladder',\
@@ -330,6 +378,8 @@ class iraemmBrowserLogic(ScriptedLoadableModuleLogic):
               '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)
@@ -449,6 +499,7 @@ class iraemmBrowserLogic(ScriptedLoadableModuleLogic):
       res=[slicer.mrmlScene.RemoveNode(f) for f in nodes] 
       self.segmentationNode=None
       self.reviewResult={}
+      self.aeList={}
 
   #reviews by segment
 
@@ -470,53 +521,58 @@ class iraemmBrowserLogic(ScriptedLoadableModuleLogic):
           return 0
   
   #load review from labkey
-  def loadReview(self,currentRow):
 
-      #see if we have already done a review
+  def getUniqueRows(self, project, dataset, fields, inputRow):
       filters=[]
-      fields=['PatientId','SequenceNum']
-
 
       for f in fields:
-          filters.append({'variable':f,'value':str(currentRow[f]),'oper':'eq'})
+          filters.append({'variable':f,'value':str(inputRow[f]),'oper':'eq'})
+      
       
-      ds=self.net.filterDataset(self.parent.project,\
-              self.parent.reviewDataset,filters)
+      ds=self.net.filterDataset(project,dataset,filters)
+      return ds['rows']
 
-      if len(ds['rows'])==0:
+  def loadReview(self,currentRow):
+
+      #see if we have already done a review
+      rows=self.getUniqueRows(self.parent.project,self.parent.reviewDataset,\
+              [self.participantField,'visitCode','Segmentation'],currentRow)
+
+      if len(rows)==0:
           return
 
-      row=ds['rows'][0]
-      for label in self.segLabel:
-          name=self.segLabel[label]+'Review'
+      row=rows[0]
+      for label in self.segmentList:
+          #name=self.segLabel[label]+'Review'
+          name=label+'Review'
           try:
-              self.updateReview(self.segLabel[label],row[name])
+              self.updateReview(label,row[name])
           except KeyError:
               continue 
-   
+      self.reviewComment=row['reviewComment']
+
   #submit review to labkey
   def submitReview(self,currentRow,comment):
-      row={}
+      fields=[self.participantField,'visitCode','Segmentation']
+      rows=self.getUniqueRows(self.parent.project,self.parent.reviewDataset,\
+              fields,currentRow)
 
-      fields=['PatientId','SequenceNum']
 
-      #see if we have to update or insert
-      filters=[]
-
-      for f in fields:
-          filters.append({'variable':f,'value':str(currentRow[f]),'oper':'eq'})
+      mode='update'
       
-      ds=self.net.filterDataset(self.parent.project,\
-              self.parent.reviewDataset,filters)
-
-      mode='insert'
-
-      if len(ds['rows'])>0:
-          row=ds['rows'][0]
-          mode='update'
-      else:
+      if len(rows)==0:
+          mode='insert'
+          row={}
           for f in fields:
               row[f]=currentRow[f]
+          
+          frows=self.getUniqueRows(self.parent.project,self.parent.reviewDataset,\
+                  [self.participantField,'visitCode'],currentRow)
+
+          row['SequenceNum']=currentRow['SequenceNum']+0.01*len(frows)
+      
+      else:     
+          row=rows[0]
       
       seg=self.segmentationNode.GetSegmentation()
  
@@ -528,12 +584,83 @@ class iraemmBrowserLogic(ScriptedLoadableModuleLogic):
 
       row['reviewComment']=comment
       row['Date']=datetime.datetime.now().ctime()
-      ds=self.net.modifyDataset(mode,self.parent.project,\
+      self.net.modifyDataset(mode,self.parent.project,\
               self.parent.reviewDataset,[row])
       
       print("review submitted")
 
 
+#AE management
+  def updateAE(self,segment,value):
+      try:
+          self.aeList[segment]=value
+      except AttributeError:
+          self.aeList={}
+          self.updateAE(segment,value)
+  
+  def getAEResult(self,segment):
+      try:
+          return self.aeList[segment]
+      except AttributeError:
+          #review result not initialized (unknown)
+          return 0
+      except KeyError:
+          #segment not done yet (unknown)
+          return 0
+  
+
+
+  def loadAE(self,currentRow):
+      fields=[self.participantField,'petResampled']
+      rows=self.getUniqueRows(self.parent.project,self.parent.aeDataset,\
+              fields,currentRow)
+      
+      if len(rows)==0:
+          return
+
+      print("Found {} rows".format(len(rows)))
+      row=rows[0]
+      
+      for seg in self.segmentList:
+          name=seg+'AE'
+          try:
+              self.updateAE(seg,row[name])
+          except AttributeError:
+              continue
+          except KeyError:
+              continue
+
+  def submitAE(self,currentRow):
+      fields=[self.participantField,'petResampled']
+      rows=self.getUniqueRows(self.parent.project,self.parent.aeDataset,\
+              fields,currentRow)
+      
+      
+      if len(rows)==0:
+          mode='insert'
+          row={}
+          for f in fields:
+              row[f]=currentRow[f]
+          
+          row['SequenceNum']=currentRow['SequenceNum']
+      
+      else:
+          mode='update'
+          row=rows[0]
+     
+      for seg in self.segmentList:
+          row[seg+'AE']=self.getAEResult(seg) 
+
+      row['Date']=datetime.datetime.now().ctime()
+      resp=self.net.modifyDataset(mode,self.parent.project,\
+              self.parent.aeDataset,[row])
+      print("Response {}".format(resp))
+      print("AE submitted")
+      
+      
+
+
+
 class irAEMMBrowserTest(ScriptedLoadableModuleTest):
 
   """