Adding clear

slicerModule/iraemmBrowser.py

@@ -5,6 +5,7 @@ from slicer.ScriptedLoadableModule import *
 import slicerNetwork
 import loadDicom
 import json
+import datetime
 
 #
 # labkeySlicerPythonExtension
@@ -43,11 +44,12 @@ class iraemmBrowserWidget(ScriptedLoadableModuleWidget):
     # Instantiate and connect widgets ...
     self.network=slicerNetwork.labkeyURIHandler()
 
-    fconfig=os.path.join(os.path.expanduser('~'),'.labkey','onko-nix.json')
+    fconfig=os.path.join(os.path.expanduser('~'),'.labkey','network.json')
     self.network.parseConfig(fconfig)
     self.network.initRemote()
     self.project="iPNUMMretro/Study"
-    self.dataset="Imaging1"
+    self.dataset="Imaging"
+    self.reviewDataset="ImageReview"
 
 
     self.logic=iraemmBrowserLogic(self)
@@ -59,42 +61,99 @@ class iraemmBrowserWidget(ScriptedLoadableModuleWidget):
 
     
     #
-    # Parameters Area
+    # Setup Area
     #
-    connectionCollapsibleButton = ctk.ctkCollapsibleButton()
-    connectionCollapsibleButton.text = "Patients"
-    self.layout.addWidget(connectionCollapsibleButton)
+    setupCollapsibleButton = ctk.ctkCollapsibleButton()
+    setupCollapsibleButton.text = "Setup"
+    self.layout.addWidget(setupCollapsibleButton)
+    
+    setupFormLayout = qt.QFormLayout(setupCollapsibleButton)
+
+   
+    self.ctField=qt.QLabel("ctResampled")
+    setupFormLayout.addRow("Data field (CT):",self.ctField)
+
+    self.petField=qt.QLabel("petResampled")
+    setupFormLayout.addRow("Data field (PET):",self.petField)
+
+    self.segmentationField=qt.QLabel("Segmentation")
+    setupFormLayout.addRow("Data field (Segmentation):",self.segmentationField)
+
 
-    connectionFormLayout = qt.QFormLayout(connectionCollapsibleButton)
+    #
+    # Patienrs Area
+    #
+    patientsCollapsibleButton = ctk.ctkCollapsibleButton()
+    patientsCollapsibleButton.text = "Patients"
+    self.layout.addWidget(patientsCollapsibleButton)
+
+    patientsFormLayout = qt.QFormLayout(patientsCollapsibleButton)
 
 
     self.patientList=qt.QComboBox()
     for id in ids:
         self.patientList.addItem(id)
     self.patientList.currentIndexChanged.connect(self.onPatientListChanged)
-    connectionFormLayout.addRow("Patient:",self.patientList)
+    patientsFormLayout.addRow("Patient:",self.patientList)
 
     self.visitList=qt.QComboBox()
     self.visitList.currentIndexChanged.connect(self.onVisitListChanged)
-    connectionFormLayout.addRow("Visit:",self.visitList)
+    patientsFormLayout.addRow("Visit:",self.visitList)
 
-    self.ctCode=qt.QLabel("ctCode")
-    connectionFormLayout.addRow("CT:",self.ctCode)
 
+    self.ctCode=qt.QLabel("ctCode")
+    patientsFormLayout.addRow("CT:",self.ctCode)
+    
     self.petCode=qt.QLabel("petCode")
-    connectionFormLayout.addRow("PET:",self.petCode)
+    patientsFormLayout.addRow("PET:",self.petCode)
+
+    self.segmentationCode=qt.QLabel("segmentationCode")
+    patientsFormLayout.addRow("Segmentation",self.segmentationCode)
 
     self.patientLoad=qt.QPushButton("Load")
     self.patientLoad.clicked.connect(self.onPatientLoadButtonClicked)
-    connectionFormLayout.addRow("Load patient",self.patientLoad)
+    patientsFormLayout.addRow("Load patient",self.patientLoad)
 
+    self.patientClear=qt.QPushButton("Clear")
+    self.patientClear.clicked.connect(self.onPatientClearButtonClicked)
+    patientsFormLayout.addRow("Clear patient",self.patientClear)
+    
     self.keepCached=qt.QCheckBox("keep Cached")
     self.keepCached.setChecked(1)
-    connectionFormLayout.addRow("Keep cached",self.keepCached)
+    patientsFormLayout.addRow("Keep cached",self.keepCached)
     
     #set to a defined state
     self.onPatientListChanged(0)
 
+
+    #
+    # Review Area
+    #
+    reviewCollapsibleButton = ctk.ctkCollapsibleButton()
+    reviewCollapsibleButton.text = "Review"
+    self.layout.addWidget(reviewCollapsibleButton)
+    
+    reviewFormLayout = qt.QFormLayout(reviewCollapsibleButton)
+
+   
+    self.reviewResult=qt.QComboBox()
+    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")
+    
+    self.reviewComment=qt.QLineEdit("this is a test")
+    reviewFormLayout.addRow("Comments (optional)",\
+            self.reviewComment)
+    
+    self.submitReviewButton=qt.QPushButton("Submit")
+    reviewFormLayout.addRow("Submit to database",\
+            self.submitReviewButton)
+    self.submitReviewButton.clicked.connect(self.onSubmitReviewButtonClicked)
+
+
   def onPatientListChanged(self,i):
       idFilter={'variable':'PatientId','value':self.patientList.currentText,'oper':'eq'}
       ds=self.network.filterDataset(self.project,self.dataset, [idFilter])
@@ -111,18 +170,21 @@ class iraemmBrowserWidget(ScriptedLoadableModuleWidget):
       except IndexError:
         return
       print("Visit: Selected item: {}->{}".format(i,s))
-      idFilter={'variable':'PatientId','value':self.patientList.currentText,'oper':'eq'}
+      idFilter={'variable':'PatientId',\
+              'value':self.patientList.currentText,'oper':'eq'}
       sFilter={'variable':'SequenceNum','value':s,'oper':'eq'}
       ds=self.network.filterDataset(self.project,self.dataset,[idFilter,sFilter])
       if not len(ds['rows'])==1:
-          print("Found incorrect number {} of matches for [{}]/[{}]".format(len(ds['rows']),\
+          print("Found incorrect number {} of matches for [{}]/[{}]".\
+                  format(len(ds['rows']),\
                   self.patientList.currentText,s))
       row=ds['rows'][0]
 
       #copy row properties for data access
       self.currentRow=row
-      self.petCode.setText(row['petResampled'])
-      self.ctCode.setText(row['ctResampled'])
+      self.petCode.setText(row[self.petField.text])
+      self.ctCode.setText(row[self.ctField.text])
+      self.segmentationCode.setText(row[self.segmentationField.text])
 
 
   def onPatientLoadButtonClicked(self):
@@ -134,6 +196,20 @@ class iraemmBrowserWidget(ScriptedLoadableModuleWidget):
       #    print("Missing current row")
       #    return
 
+  def onSubmitReviewButtonClicked(self):
+      print("Submit")
+      print("Selected review:{}/{}".format(self.reviewResult.currentIndex,
+          self.reviewResult.currentText))
+      print("Comment:{}".format(self.reviewComment))
+      self.logic.submitReview(self.currentRow,\
+              self.reviewResult.currentIndex,\
+              self.reviewComment.text)
+
+  def onPatientClearButtonClicked(self):
+      self.logic.clearVolumesAndSegmentations()
+
+
+
   def cleanup(self):
     pass
 
@@ -170,11 +246,13 @@ class iraemmBrowserLogic(ScriptedLoadableModuleLogic):
       
       
       #fields={'ctResampled':True,'petResampled':False}
-      fields=['ctResampled','petResampled']
+      fields={"CT":self.parent.ctField.text,\
+              "PET":self.parent.petField.text,\
+              "Segmentation":self.parent.segmentationField.text}
 
       relativePaths={x:self.project+'/@files/preprocessedImages/'\
-             +row['patientCode']+'/'+row['visitCode']+'/'+row[x]\
-             for x in fields}
+             +row['patientCode']+'/'+row['visitCode']+'/'+row[y]\
+             for (x,y) in fields.items()}
 
       volumeNode={}
       for f in relativePaths:
@@ -186,13 +264,56 @@ class iraemmBrowserLogic(ScriptedLoadableModuleLogic):
               continue
 
           #pushes it to background
-          volumeNode[f]=self.net.loadNode(p,'VolumeFile',returnNode=True,keepCached=keepCached)
+          properties={}
+          #make sure segmentation gets loaded as a labelmap
+          if f=="Segmentation":
+              properties["labelmap"]=1
+
+          volumeNode[f]=self.net.loadNode(p,'VolumeFile',\
+                  properties=properties,returnNode=True,keepCached=keepCached)
           
-      slicer.util.setSliceViewerLayers(background=volumeNode['ctResampled'],\
-          foreground=volumeNode['petResampled'],foregroundOpacity=0.5,fit=True)
+      slicer.util.setSliceViewerLayers(background=volumeNode['CT'],\
+          foreground=volumeNode['PET'],foregroundOpacity=0.5,fit=True)
+
+  def clearVolumesAndSegmentations(self):
+      nodes=slicer.util.getNodesByClass("vtkMRMLVolumeNode")
+      nodes.extend(slicer.util.getNodesByClass("vtkMRMLSegmentationNode"))
+      res=[slicer.mrmlScene.RemoveNode(f) for f in nodes] 
+
+  def submitReview(self,currentRow,idx,comment):
+      row={}
+
+      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'})
+      
+      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:
+          for f in fields:
+              row[f]=currentRow[f]
+      
+      row['reviewResult']=idx+1 #labkey has 1-based arrays
+      row['reviewComment']=comment
+      row['Date']=datetime.datetime.now().ctime()
+      ds=self.net.modifyDataset(mode,self.parent.project,\
+              self.parent.reviewDataset,[row])
+      
+      print("review submitted")
 
 
 class irAEMMBrowserTest(ScriptedLoadableModuleTest):
+
   """
   This is the test case for your scripted module.
   Uses ScriptedLoadableModuleTest base class, available at: