Migrating to python3 and labkeyInterface

slicerModules/cardiacSPECT.py

@@ -4,7 +4,6 @@ import unittest
 import vtk, qt, ctk, slicer
 from slicer.ScriptedLoadableModule import *
 import logging
-import vtkInterface as vi
 import slicer
 import numpy as np
 import json
@@ -52,7 +51,26 @@ class cardiacSPECTWidget(ScriptedLoadableModuleWidget):
               '.cardiacSPECT','cardiacSPECT.json')
     with open(configFile) as f:
           self.cfg=json.load(f)
-    
+
+    #need labkey browser here
+    sconfig=os.path.join(os.path.expanduser('~'),'.labkey','setup.json')
+    with open(sconfig) as f:
+            setup=json.load(f)
+    sys.path.append(setup['paths']['labkeyInterface'])
+    import labkeyInterface
+    import labkeyDatabaseBrowser
+    import labkeyFileBrowser
+
+    self.net=labkeyInterface.labkeyInterface()
+    fconfig=os.path.join(os.path.expanduser('~'),'.labkey','network.json')
+    self.net.init(fconfig)
+    self.db=labkeyDatabaseBrowser.labkeyDB(self.net)
+      
+    ds=self.db.selectRows(self.cfg['project'],self.cfg['schemaName'],\
+            self.cfg['queryName'],[])
+
+    patients=list(set([row['aliasID'] for row in ds['rows']]))
+
     # Instantiate and connect widgets ...
     dataButton = ctk.ctkCollapsibleButton()
     dataButton.text = "Data"
@@ -63,10 +81,12 @@ class cardiacSPECTWidget(ScriptedLoadableModuleWidget):
 
 
 
-    self.patientId=qt.QLineEdit();
+    self.patientId=qt.QComboBox()
+    self.patientId.insertItems(0,patients)
     dataFormLayout.addRow('Patient ID', self.patientId)
 
-    self.refPatientId=qt.QLineEdit();
+    self.refPatientId=qt.QComboBox();
+    self.refPatientId.insertItems(0,patients)
     dataFormLayout.addRow('Reference Patient ID', self.refPatientId)
 
 
@@ -263,7 +283,7 @@ class cardiacSPECTWidget(ScriptedLoadableModuleWidget):
        it=self.time_frame_select.value
        selectionNode = slicer.app.applicationLogic().GetSelectionNode()
        print("Propagating CT volume")
-       nodeName=self.patientId.text+'CT'
+       nodeName=self.patientId.currentText+'CT'
        node=slicer.mrmlScene.GetFirstNodeByName(nodeName)
        selectionNode.SetReferenceActiveVolumeID(node.GetID())
        if self.resetPosition==1:
@@ -272,7 +292,7 @@ class cardiacSPECTWidget(ScriptedLoadableModuleWidget):
        else:
           slicer.app.applicationLogic().PropagateVolumeSelection(0)
        print("Propagating SPECT volume")
-       nodeName=self.patientId.text+'Volume'+str(it)
+       nodeName=self.patientId.currentText+'Volume'+str(it)
        node=slicer.mrmlScene.GetFirstNodeByName(nodeName)
        selectionNode.SetSecondaryVolumeID(node.GetID())
        slicer.app.applicationLogic().PropagateForegroundVolumeSelection(0)
@@ -309,12 +329,12 @@ class cardiacSPECTWidget(ScriptedLoadableModuleWidget):
             dn = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
 
             dn.SetSize(n)
-            dn.SetName(self.patientId.text+'_'+self.logic.getSegmentName(j))
+            dn.SetName(self.patientId.currentText+'_'+self.logic.getSegmentName(j))
 
             dt=0;
             t0=0;
             for i in range(0,n):
-                vol=self.patientId.text+"Volume"+str(i)
+                vol=self.patientId.currentText+"Volume"+str(i)
                 fx=ft[i]
                 fy=self.logic.meanROI(vol,j)
                 dt=2*ft[i]-t0
@@ -342,37 +362,37 @@ class cardiacSPECTWidget(ScriptedLoadableModuleWidget):
         cvn.SetChartNodeID(cn.GetID())
 
   def onCountSegmentsClicked(self):
-      self.countSegmentsDisplay.setText(self.logic.countSegments())
-
+      self.countSegmentsDisplay.setText(self.logic.countSegments)
+  
   def onPatientLoadButtonClicked(self):
-      self.logic.loadPatient(self.patientId.text)
+      self.logic.loadPatient(self.patientId.currentText)
       self.time_frame_select.setMaximum(self.logic.frame_data.shape[3]-1)
 
   def onPatientLoadNRRDButtonClicked(self):
-      self.logic.loadPatientNRRD(self.patientId.text)
+      self.logic.loadPatientNRRD(self.patientId.currentText)
       self.time_frame_select.setMaximum(len(self.logic.frame_time))
 
   def onLoadSegmentationButtonClicked(self):
-      self.logic.loadSegmentation(self.patientId.text)
+      self.logic.loadSegmentation(self.patientId.currentText)
 
   def onLoadModelButtonClicked(self):
-      self.logic.loadModelVolume(self.patientId.text,self.modelParameter.text)
+      self.logic.loadModelVolume(self.patientId.currentText,self.modelParameter.text)
 
   def onSaveVolumeButtonClicked(self):
-      self.logic.storeVolumeNodes(self.patientId.text,
+      self.logic.storeVolumeNodes(self.patientId.currentText,
             self.time_frame_select.minimum,self.time_frame_select.maximum)
 
   def onSaveSegmentationButtonClicked(self):
-      self.logic.storeSegmentation(self.patientId.text)
+      self.logic.storeSegmentation(self.patientId.currentText)
 
   def onSaveTransformationButtonClicked(self):
-      self.logic.storeTransformation(self.patientId.text)
+      self.logic.storeTransformation(self.patientId.currentText)
 
   def onSaveInputFunctionButtonClicked(self):
-      self.logic.storeInputFunction(self.patientId.text)
+      self.logic.storeInputFunction(self.patientId.currentText)
 
   def onTransformNodeButtonClicked(self):
-      self.logic.applyTransform(self.patientId.text, self.refPatientId.text,
+      self.logic.applyTransform(self.patientId.currentText, self.refPatientId.currentText,
           self.time_frame_select.minimum,self.time_frame_select.maximum)
 
 
@@ -418,20 +438,25 @@ class cardiacSPECTLogic(ScriptedLoadableModuleLogic):
       self.pd=parseDicom.parseDicomLogic(self)
       self.pd.setFileBrowser(self.fb)
       
+      self.tempPath=os.path.join(os.path.expanduser('~'),\
+              'temp','cardiacSPECT')
+      if not os.path.isdir(self.tempPath):
+          os.makedirs(self.tempPath)
+      
+      self.pd.setTempBase(self.tempPath)
+      
       sys.path.append(setup['paths']['resample'])
       import resample
       self.resampler=resample.resampleLogic(None)
       
+      sys.path.append(setup['paths']['vtkInterface'])
       
-      self.tempPath=os.path.join(os.path.expanduser('~'),\
-              'temp','cardiacSPECT')
-      if not os.path.isdir(self.tempPath):
-          os.makedirs(self.tempPath)
+
       
       self.cfg=config
       
   def loadData(self,widget):
-
+    import vtkInterface
     #calculate inputDir from data on form
     inputDir=str(widget.dataPath.text)
     self.pd.readMasterDirectory(inputDir)
@@ -442,8 +467,8 @@ class cardiacSPECTLogic(ScriptedLoadableModuleLogic):
     self.ct_data,self.ct_origin,self.ct_pixel_size, \
         self.ct_orientation=self.pd.readCTDirectory(inputDir)
 
-    self.ct_orientation=vi.completeOrientation(self.ct_orientation)
-    self.frame_orientation=vi.completeOrientation(self.frame_orientation)
+    self.ct_orientation=vtkInterface.completeOrientation(self.ct_orientation)
+    self.frame_orientation=vtkInterface.completeOrientation(self.frame_orientation)
 
     self.addCT('test')
     self.addFrames('test')
@@ -458,19 +483,22 @@ class cardiacSPECTLogic(ScriptedLoadableModuleLogic):
 
   def getFilespecPath(self,r):
       if self.cfg["remote"]==True:
-          return self.fb.formatPathURL(self.cfg['project'],\
-                  '/'.join(self.cfg['imageDir'],r['Study'],r['Series']))
+          return self.fb.formatPathURL(self.cfg['transfer']['project'],\
+                  '/'.join([self.cfg['dicomDir'],r['Study'],r['Series']]))
       else:
           path=os.path.join(self.cfg["dicomPath"],r["Study"],r["Series"])
           return path
 
   def loadPatient(self,patientId):
-      print("Loading {}").format(patientId)
+      
+      import vtkInterface
+      print("Loading {}".format(patientId))
+      idFilter={'variable':'aliasID','value':patientId,'oper':'eq'}
       ds=self.db.selectRows(self.cfg['project'],self.cfg['schemaName'],
-              self.cfg['queryName'])
-      visit=[r for r in ds['rows'] if r['aliasID']==patientId][0]
+              self.cfg['queryName'],[idFilter])
+      visit=ds['rows'][0]
 
-      print visit
+      print(visit)
       idFilter={'variable':'PatientId','value':visit['aliasID'],'oper':'eq'}
       dicoms=self.db.selectRows(self.cfg['transfer']['project'],
               self.cfg['transfer']['schemaName'],
@@ -491,19 +519,20 @@ class cardiacSPECTLogic(ScriptedLoadableModuleLogic):
 
       self.pd.readMasterDirectory(masterPath)
       self.frame_data, self.frame_time, self.frame_duration,self.frame_origin, \
-          self.frame_pixel_size, self.frame_orientation=self.pd.readNMDirectory(nmPath)
+          self.frame_pixel_size, self.frame_orientation=\
+          self.pd.readNMDirectory(nmPath)
       self.ct_data,self.ct_origin,self.ct_pixel_size, \
          self.ct_orientation=self.pd.readCTDirectory(ctPath)
 
-      self.ct_orientation=vi.completeOrientation(self.ct_orientation)
-      self.frame_orientation=vi.completeOrientation(self.frame_orientation)
+      self.ct_orientation=vtkInterface.completeOrientation(self.ct_orientation)
+      self.frame_orientation=vtkInterface.completeOrientation(self.frame_orientation)
 
       self.addCT(patientId)
       self.addFrames(patientId)
 
 
   def loadPatientNRRD(self,patientId):
-      print("Loading NRRD {}").format(patientId)
+      print("Loading NRRD {}".format(patientId))
 
       self.loadDummyInputFunction(patientId)
       dnsNode=slicer.util.getFirstNodeByName(patientId+'_Dummy')
@@ -545,10 +574,13 @@ class cardiacSPECTLogic(ScriptedLoadableModuleLogic):
       remotePath=self.fb.formatPathURL(self.cfg['project'],
               '/'.join([patientId]))
       labkeyFile=remotePath+'/'+fName+suffix
-      localFile=os.path.join(self.tempPath+fName+suffix)
+      localFile=os.path.join(self.tempPath,fName+suffix)
       self.fb.readFileToFile(labkeyFile,localFile)
-      print ("Remote: {}").format(labkeyFile)
-      node=slicer.util.loadNodeFromFile(localFile,type)
+      print("Remote: {}".format(labkeyFile))
+      try:
+          node=slicer.util.loadNodeFromFile(localFile,type)
+      except RuntimeError:
+          return None    
       os.remove(localFile)
       return node
       
@@ -590,24 +622,26 @@ class cardiacSPECTLogic(ScriptedLoadableModuleLogic):
        slicer.mrmlScene.AddNode(newNode)
 
   def addFrames(self,patientId):
+       import vtkInterface
        #convert data from numpy.array to vtkImageData
        #use time point it
-       print "NFrames: {}".format(self.frame_data.shape[3])
+       print("NFrames: {}".format(self.frame_data.shape[3]))
        for it in range(0,self.frame_data.shape[3]):
            frame_data=self.frame_data[:,:,:,it];
            nodeName=patientId+'Volume'+str(it)
            self.addNode(nodeName,
-              vi.numpyToVTK(frame_data,frame_data.shape),
+              vtkInterface.numpyToVTK(frame_data,frame_data.shape),
               self.frame_origin,
               self.frame_pixel_size,
               self.frame_orientation,1)
 
   def addCT(self,patientId):
+       import vtkInterface
        nodeName=patientId+'CT'
        self.addNode(nodeName,
             #vi.numpyToVTK3D(self.ct_data,
             #    self.ct_origin,self.ct_pixel_size),
-            vi.numpyToVTK(self.ct_data,self.ct_data.shape),
+            vtkInterface.numpyToVTK(self.ct_data,self.ct_data.shape),
             self.ct_origin,self.ct_pixel_size,
             self.ct_orientation,0)
 
@@ -654,7 +688,7 @@ class cardiacSPECTLogic(ScriptedLoadableModuleLogic):
 
     #get the segmentation mask
     fNode=slicer.mrmlScene.GetNodesByClass("vtkMRMLSegmentationNode").GetItemAsObject(0)
-    print "Found segmentation node: {}".format(fNode.GetName())
+    print("Found segmentation node: {}".format(fNode.GetName()))
     segNode=slicer.vtkMRMLSegmentationNode.SafeDownCast(fNode)
 
     #no python bindings for vtkSegmentation
@@ -665,12 +699,14 @@ class cardiacSPECTLogic(ScriptedLoadableModuleLogic):
 
     #edit here to change for more segments
     segment=segNode.GetSegmentation().GetNthSegmentID(int(i))
-    mask = segNode.GetBinaryLabelmapRepresentation(segment)
+    print('Computing for segment {}'.format(segment))
+    mask=slicer.vtkOrientedImageData()
+    segNode.GetBinaryLabelmapRepresentation(segment,mask)
     if mask==None:
         print("Segment {} not found".format(segment))
         return s
 
-    print "Got mask for segment {}, npts {}".format(segment,mask.GetNumberOfPoints())
+    print("Got mask for segment {}, npts {}".format(segment,mask.GetNumberOfPoints()))
     #get mask at (x,y,z)
     #mask.GetPointData().GetScalars().GetTuple1(mask.FindPoint([x,y,z]))
 
@@ -748,7 +784,7 @@ class cardiacSPECTLogic(ScriptedLoadableModuleLogic):
     
     node=slicer.mrmlScene.GetFirstNodeByName(nodeName)
     if node==None:
-        print("Node {} not found").format(nodeName)
+        print("Node {} not found".format(nodeName))
         return
 
     suffix=".nrrd"
@@ -762,12 +798,11 @@ class cardiacSPECTLogic(ScriptedLoadableModuleLogic):
 
     localPath=os.path.join(self.tempPath,fileName)
 
-    file=os.path.join(localPath,fileName)
-    slicer.util.saveNode(node,file)
-    print("Stored to: {}").format(file)
+    slicer.util.saveNode(node,localPath)
+    print("Stored to: {}".format(localPath))
     if self.cfg["remote"]:
         labkeyPath=self.fb.buildPathURL(self.cfg['project'],pathList)
-        print ("Remote: {}").format(labkeyPath)
+        print ("Remote: {}".format(labkeyPath))
         #checks if exists
         remoteFile=labkeyPath+'/'+fileName
         self.fb.writeFileToFile(localPath,remoteFile)
@@ -788,7 +823,7 @@ class cardiacSPECTLogic(ScriptedLoadableModuleLogic):
         nodeName=nodeName+"_RS"
         self.storeNodeRemote(pathList,nodeName)
 
-    print("Storing NM from {} to {}").format(n1,n2)
+    print("Storing NM from {} to {}".format(n1,n2))
     n=n2-n1+1
     for i in range(n):
         it=i+n1
@@ -833,7 +868,7 @@ class cardiacSPECTLogic(ScriptedLoadableModuleLogic):
       transformNodeName=patientId+"_DF"
       transformNode=slicer.util.getFirstNodeByName(transformNodeName)
       if transformNode==None:
-          print("Transform node [{}] not found").format(transformNodeName)
+          print("Transform node [{}] not found".format(transformNodeName))
           return
 
 
@@ -850,7 +885,7 @@ class cardiacSPECTLogic(ScriptedLoadableModuleLogic):
           refNode=slicer.util.getFirstNodeByName(refNodeName)
           if refNode!=None:
               self.resampler.rebinNode(node,refNode)
-          print("Completed transformation {}").format(it)
+          print("Completed transformation {}".format(it))
           #unset transformation
           node.SetAndObserveTransformNodeID('NONE')
 
@@ -905,7 +940,7 @@ class cardiacSPECTLogic(ScriptedLoadableModuleLogic):
                break
 
        if juse<0:
-           print 'Failed to find Ventricle segment'
+           print('Failed to find Ventricle segment')
            return
 
        dt=0;