Fixing issue #358.

SliceTracker/Resources/zframe/zframe-model.vtk

@@ -1,5 +1,5 @@
-# vtk DataFile Version 3.0
-vtk output
+# vtk DataFile Version 4.2
+3D Slicer output. SPACE=RAS
 ASCII
 DATASET POLYDATA
 POINTS 168 float
@@ -60,6 +60,9 @@ POINTS 168 float
 -29.25 28.701 -30 -30.75 28.701 -30 -31.5 30 -30 
 -30.75 31.299 -30 -29.25 31.299 -30 -28.5 30 -30 
 
+METADATA
+INFORMATION 0
+
 POLYGONS 56 308
 4 0 1 3 2 
 4 2 3 5 4 

SliceTracker/SliceTrackerRegistration.py

@@ -125,7 +125,7 @@ def runRegistration(self):
   @onReturnProcessEvents
   def updateProgressBar(self, **kwargs):
     if self.progress:
-      for key, value in kwargs.iteritems():
+      for key, value in kwargs.items():
         if hasattr(self.progress, key):
           setattr(self.progress, key, value)
 
@@ -237,7 +237,7 @@ def doRigidRegistration(self, **kwargs):
                    'outputVolume': self.registrationResult.volumes.rigid.GetID(),
                    'maskProcessingMode': "ROI",
                    'useRigid': True}
-    for key, value in kwargs.iteritems():
+    for key, value in kwargs.items():
       paramsRigid[key] = value
     slicer.cli.run(slicer.modules.brainsfit, None, paramsRigid, wait_for_completion=True)
     self.registrationResult.cmdArguments += "Rigid Registration Parameters: %s" % str(paramsRigid) + "\n\n"
@@ -273,7 +273,7 @@ def doBSplineRegistration(self, initialTransform, **kwargs):
                      'costFunctionConvergenceFactor': "1.00E+09",
                      'maskProcessingMode': "ROI",
                      'initialTransform': initialTransform}
-    for key, value in kwargs.iteritems():
+    for key, value in kwargs.items():
       paramsBSpline[key] = value
 
     slicer.cli.run(slicer.modules.brainsfit, None, paramsBSpline, wait_for_completion=True)
@@ -306,7 +306,7 @@ def main(argv):
 
     for inputFile in [args.fixed_label, args.moving_label, args.fixed_volume, args.moving_volume]:
       if not os.path.isfile(inputFile):
-        raise AttributeError, "File not found: %s" % inputFile
+        raise AttributeError("File not found: %s" % inputFile)
 
     success, fixedLabel = slicer.util.loadLabelVolume(args.fixed_label, returnNode=True)
     success, movingLabel = slicer.util.loadLabelVolume(args.moving_label, returnNode=True)
@@ -325,8 +325,8 @@ def main(argv):
     if args.output_directory != "-":
       logic.registrationResult.save(args.output_directory)
 
-  except Exception, e:
-    print e
+  except Exception as e:
+    print(e)
   sys.exit(0)
 
 if __name__ == "__main__":

SliceTracker/SliceTrackerUtils/configuration.py

@@ -1,7 +1,7 @@
-import ConfigParser
+import configparser
 import inspect, os
 from SlicerDevelopmentToolboxUtils.mixins import ModuleWidgetMixin
-from constants import SliceTrackerConstants as constants
+from .constants import SliceTrackerConstants as constants
 
 
 class SliceTrackerConfiguration(ModuleWidgetMixin):
@@ -13,7 +13,7 @@ def __init__(self, moduleName, configFile):
 
   def loadConfiguration(self):
 
-    config = ConfigParser.RawConfigParser()
+    config = configparser.RawConfigParser()
     config.read(self.configFile)
 
     if not self.getSetting("ZFrame_Registration_Class_Name"):
@@ -69,4 +69,4 @@ def replaceOldValues(self):
 
     for other in ['OTHER_IMAGE', 'Rating_Enabled', 'Maximum_Rating_Score']:
       if self.getSetting(other):
-        self.removeSetting(other)
+        self.removeSetting(other)

SliceTracker/SliceTrackerUtils/helpers.py

@@ -6,7 +6,7 @@
 import re
 import slicer
 
-from constants import SliceTrackerConstants as constants
+from .constants import SliceTrackerConstants as constants
 
 from SlicerDevelopmentToolboxUtils.decorators import logmethod
 from SlicerDevelopmentToolboxUtils.widgets import ExtendedQMessageBox
@@ -275,4 +275,4 @@ def updateTooltipAndIcon(self, series):
       icon = Icons.edit
       tooltip = self.listWidget.currentItem().text() if self.listWidget.currentItem() else ""
     self.setIcon(icon)
-    self.setToolTip(tooltip)
+    self.setToolTip(tooltip)

SliceTracker/SliceTrackerUtils/preopHandler.py

@@ -95,7 +95,7 @@ def _runPreProcessing(self):
 
     @onReturnProcessEvents
     def updateProgressBar(**kwargs):
-      for key, value in kwargs.iteritems():
+      for key, value in kwargs.items():
         if hasattr(progress, key):
           setattr(progress, key, value)
 
@@ -303,4 +303,4 @@ def getMostRecentWholeGlandSegmentation(self, path):
     return self.getMostRecentFile(path, FileExtension.NRRD, filter="WholeGland")
 
   def getMostRecentTargetsFile(self, path):
-    return self.getMostRecentFile(path, FileExtension.FCSV)
+    return self.getMostRecentFile(path, FileExtension.FCSV)

SliceTracker/SliceTrackerUtils/session.py

@@ -3,10 +3,10 @@
 import qt
 
 import slicer
-from sessionData import SessionData, RegistrationResult, RegistrationTypeData
-from constants import SliceTrackerConstants
-from helpers import SeriesTypeManager
-from preopHandler import PreopDataHandler
+from .sessionData import SessionData, RegistrationResult, RegistrationTypeData
+from .constants import SliceTrackerConstants
+from .helpers import SeriesTypeManager
+from .preopHandler import PreopDataHandler
 
 from SlicerDevelopmentToolboxUtils.constants import DICOMTAGS, STYLE
 from SlicerDevelopmentToolboxUtils.events import SlicerDevelopmentToolboxEvents
@@ -441,7 +441,7 @@ def verifyPatientIDEquality(self, receivedFiles):
     currentInfo = self.getPatientInformation(dicomFileName)
     currentID = currentInfo["PatientID"]
     patientName = currentInfo["PatientName"]
-    for seriesNumber, receivedInfo in seriesNumberPatientID.iteritems():
+    for seriesNumber, receivedInfo in seriesNumberPatientID.items():
       patientID = receivedInfo["PatientID"]
       if patientID is not None and patientID != currentID:
         m = 'WARNING:\n' \
@@ -457,8 +457,7 @@ def verifyPatientIDEquality(self, receivedFiles):
 
   def getPatientIDValidationSource(self):
     if len(self.loadableList.keys()) > 1:
-      keys = self.loadableList.keys()
-      keys.sort(key=lambda x: RegistrationResult.getSeriesNumberFromString(x))
+      keys = sorted(self.loadableList.keys())
       return self.loadableList[keys[0]][0]
     else:
       return None
@@ -670,7 +669,7 @@ def onInvokeRegistration(self, initial=True, retryMode=False, segmentationData=N
   @onReturnProcessEvents
   def updateProgressBar(self, **kwargs):
     if self.progress:
-      for key, value in kwargs.iteritems():
+      for key, value in kwargs.items():
         if hasattr(self.progress, key):
           setattr(self.progress, key, value)
 

SliceTracker/SliceTrackerUtils/sessionData.py

@@ -9,8 +9,8 @@
 from SlicerDevelopmentToolboxUtils.decorators import onExceptionReturnNone, logmethod
 from SlicerDevelopmentToolboxUtils.widgets import CustomStatusProgressbar
 
-from constants import SliceTrackerConstants
-from helpers import SeriesTypeManager
+from .constants import SliceTrackerConstants
+from .helpers import SeriesTypeManager
 
 
 class SessionData(ModuleLogicMixin):
@@ -168,7 +168,7 @@ def loadResults(self, data, directory):
       self.customProgressBar.updateStatus("Loading series registration result %s" % result.name, index)
       slicer.app.processEvents()
 
-      for attribute, value in jsonResult.iteritems():
+      for attribute, value in jsonResult.items():
         logging.debug("found %s: %s" % (attribute, value))
         if attribute == 'volumes':
           self._loadResultFileData(value, directory, slicer.util.loadVolume, result.setVolume)
@@ -206,7 +206,7 @@ def loadResults(self, data, directory):
         self.customProgressBar.text = "Finished loading registration results"
 
   def _loadResultFileData(self, dictionary, directory, loadFunction, setFunction):
-    for regType, filename in dictionary.iteritems():
+    for regType, filename in dictionary.items():
       data = self._loadOrGetFileData(directory, filename, loadFunction)
       setFunction(regType, data)
 
@@ -323,7 +323,7 @@ def getLocalGITRevisionInformation():
         from git import Repo, InvalidGitRepositoryError
         repo = Repo(dirname, search_parent_directories=True)
         branch = repo.active_branch
-        print branch.name
+        print(branch.name)
         return {
           "GIT_WC_URL": repo.remote().url,
           "GIT_COMMIT_HASH": repo.head.object.hexsha
@@ -476,7 +476,7 @@ def getFileNameByAttributeName(self, name):
 
   def getAllFileNames(self):
     fileNames = {}
-    for regType, node in self.asDict().iteritems():
+    for regType, node in self.asDict().items():
       if node:
         fileNames[regType] = self.getFileName(node)
     return fileNames
@@ -501,7 +501,7 @@ def createFromJSON(data):
 
   def toJSON(self):
     output = {}
-    for key, value in self.__dict__.iteritems():
+    for key, value in self.__dict__.items():
       if any(key.startswith(starter) for starter in ["_", "__"]) or value is None or value == "":
         continue
       output[key] = value.toJSON() if hasattr(value, "toJSON") else value
@@ -667,7 +667,7 @@ def isGoingToBeMoved(self, targetList, index):
     self.modifiedTargets[regType][index] = True
 
   def getRegistrationTypeForTargetList(self, targetList):
-    for regType, currentTargetList in self.asDict().iteritems():
+    for regType, currentTargetList in self.asDict().items():
       if targetList is currentTargetList:
         return regType
     return None
@@ -984,4 +984,4 @@ def save(self, outputDir):
     success, name = self.saveNodeData(self.volume, outputDir, FileExtension.NRRD)
     dictionary["volume"] = name + FileExtension.NRRD
     self.handleSaveNodeDataReturn(success, name, savedSuccessfully, failedToSave)
-    return dictionary
+    return dictionary

SliceTracker/SliceTrackerUtils/steps/evaluation.py

@@ -2,11 +2,11 @@
 import qt
 import vtk
 import slicer
-from base import SliceTrackerLogicBase, SliceTrackerStep
+from .base import SliceTrackerLogicBase, SliceTrackerStep
 from ..constants import SliceTrackerConstants as constants
-from plugins.results import SliceTrackerRegistrationResultsPlugin
-from plugins.targets import SliceTrackerTargetTablePlugin
-from plugins.charts import SliceTrackerDisplacementChartPlugin
+from .plugins.results import SliceTrackerRegistrationResultsPlugin
+from .plugins.targets import SliceTrackerTargetTablePlugin
+from .plugins.charts import SliceTrackerDisplacementChartPlugin
 
 from SlicerDevelopmentToolboxUtils.icons import Icons
 
@@ -142,4 +142,4 @@ def onNoRegistrationResultsAvailable(self, caller, event):
 
   def onRegistrationResultsAvailable(self, caller, event):
     self.approveRegistrationResultButton.enabled = True
-    self.targetTablePlugin.enabled = True
+    self.targetTablePlugin.enabled = True

SliceTracker/SliceTrackerUtils/steps/overview.py

@@ -4,12 +4,12 @@
 import slicer
 import vtk
 
-from base import SliceTrackerLogicBase, SliceTrackerStep
-from plugins.case import SliceTrackerCaseManagerPlugin
-from plugins.results import SliceTrackerRegistrationResultsPlugin
-from plugins.targets import SliceTrackerTargetTablePlugin
-from plugins.training import SliceTrackerTrainingPlugin
-from plugins.charts import SliceTrackerDisplacementChartPlugin
+from .base import SliceTrackerLogicBase, SliceTrackerStep
+from .plugins.case import SliceTrackerCaseManagerPlugin
+from .plugins.results import SliceTrackerRegistrationResultsPlugin
+from .plugins.targets import SliceTrackerTargetTablePlugin
+from .plugins.training import SliceTrackerTrainingPlugin
+from .plugins.charts import SliceTrackerDisplacementChartPlugin
 from ..constants import SliceTrackerConstants as constants
 from ..sessionData import RegistrationResult
 from ..helpers import IncomingDataMessageBox, SeriesTypeToolButton, SeriesTypeManager
@@ -368,4 +368,4 @@ def promptUserAndApplyBiasCorrectionIfNeeded(self):
           currentModule.parent().enabled = True
       customProgressbar.updateStatus("Bias correction done!")
 
-    self.session.data.preopData.usedERC = usedERC
+    self.session.data.preopData.usedERC = usedERC

SliceTracker/SliceTrackerUtils/steps/plugins/charts.py

@@ -36,7 +36,7 @@ def isTargetDisplacementChartDisplayable(self, selectedSeries):
     approvedResults = sorted([r for r in self.session.data.registrationResults.values() if r.approved],
                              key=lambda result: result.seriesNumber)
     nonSelectedApprovedResults = filter(lambda x: x.seriesNumber != selectedSeriesNumber, approvedResults)
-    if len(nonSelectedApprovedResults) == 0 or self.session.currentResult is None:
+    if len(list(nonSelectedApprovedResults)) == 0 or self.session.currentResult is None:
       return False
     return True
 
@@ -244,4 +244,4 @@ def createPlot(self, color, plotNumber):
     plotSeriesNode.SetMarkerSize(3 * plotSeriesNode.GetLineWidth())
 
     self._plotSeriesNodes.append(plotSeriesNode)
-    self._plotChartNode.AddAndObservePlotSeriesNodeID(plotSeriesNode.GetID())
+    self._plotChartNode.AddAndObservePlotSeriesNodeID(plotSeriesNode.GetID())

SliceTracker/SliceTrackerUtils/steps/plugins/segmentation/automatic.py

@@ -1,6 +1,6 @@
 import vtk
 
-from base import SliceTrackerSegmentationPluginBase
+from .base import SliceTrackerSegmentationPluginBase
 from ....algorithms.automaticProstateSegmentation import AutomaticSegmentationLogic
 
 class SliceTrackerAutomaticSegmentationPlugin(SliceTrackerSegmentationPluginBase):
@@ -44,4 +44,4 @@ def _onSegmentationFinished(self, caller, event, labelNode):
   #   import ast
   #   status = ast.literal_eval(str(callData))
   #   self.updateProgressBar(progress=statusBar, text=status["text"].replace("\n", ""), value=status["value"],
-  #                          maximum = 100)
+  #                          maximum = 100)

SliceTracker/SliceTrackerUtils/steps/plugins/segmentation/manual.py

@@ -4,7 +4,7 @@
 
 from ...base import SliceTrackerPlugin, SliceTrackerLogicBase
 from ....constants import SliceTrackerConstants as constants
-from base import SliceTrackerSegmentationPluginBase
+from .base import SliceTrackerSegmentationPluginBase
 from SurfaceCutToLabel import SurfaceCutToLabelWidget
 
 from SlicerDevelopmentToolboxUtils.decorators import onModuleSelected
@@ -120,4 +120,4 @@ def _onSegmentationFinished(self, caller, event, labelNode):
     displayNode = labelNode.GetDisplayNode()
     displayNode.SetAndObserveColorNodeID(self.session.mpReviewColorNode.GetID())
     self.surfaceCutToLabelWidget.colorSpin.setValue(self.session.segmentedLabelValue)
-    super(SliceTrackerManualSegmentationPlugin, self)._onSegmentationFinished(caller, event, labelNode)
+    super(SliceTrackerManualSegmentationPlugin, self)._onSegmentationFinished(caller, event, labelNode)

SliceTracker/SliceTrackerUtils/steps/plugins/targeting.py

@@ -1,7 +1,7 @@
 import qt
 from ...constants import SliceTrackerConstants as constants
 from ..base import SliceTrackerPlugin, SliceTrackerLogicBase
-from targets import SliceTrackerTargetTablePlugin
+from .targets import SliceTrackerTargetTablePlugin
 
 from SlicerDevelopmentToolboxUtils.helpers import SliceAnnotation
 from SlicerDevelopmentToolboxUtils.widgets import TargetCreationWidget
@@ -143,4 +143,4 @@ def _onTargetingFinished(self, caller, event):
       if not self.preopAvailableAndTargetsDefined():
         self.session.movingTargets = None
 
-    self.invokeEvent(self.TargetingFinishedEvent)
+    self.invokeEvent(self.TargetingFinishedEvent)

SliceTracker/SliceTrackerUtils/steps/plugins/targets.py

@@ -448,7 +448,7 @@ def disableTargetMovingMode(self):
     self.moveTargetMode = False
 
   def clearTargetMovementObserverAndAnnotations(self):
-    for widget, (observer, annotation) in self.mouseReleaseEventObservers.iteritems():
+    for widget, (observer, annotation) in self.mouseReleaseEventObservers.items():
       sliceView = widget.sliceView()
       interactor = sliceView.interactorStyle().GetInteractor()
       interactor.RemoveObserver(observer)

SliceTracker/SliceTrackerUtils/steps/plugins/training.py

@@ -95,7 +95,7 @@ def unzipFileAndCopyToDirectory(self, filepath, copyToDirectory):
       self.clearData()
 
   def copyDirectory(self, source, destination, recursive=True):
-    print source
+    print(source)
     assert os.path.isdir(source)
     for listObject in os.listdir(source):
       current = os.path.join(source, listObject)
@@ -118,4 +118,4 @@ def onCaseClosed(self, caller, event, callData):
     self.simulateIntraopPhaseButton.enabled = False
 
   def onPreprocessingSuccessful(self, caller, event):
-    self.simulateIntraopPhaseButton.enabled = self.session.trainingMode
+    self.simulateIntraopPhaseButton.enabled = self.session.trainingMode

SliceTracker/SliceTrackerUtils/steps/segmentation.py

@@ -3,13 +3,13 @@
 import slicer
 import vtk
 
-from base import SliceTrackerLogicBase, SliceTrackerStep
+from .base import SliceTrackerLogicBase, SliceTrackerStep
 from ..constants import SliceTrackerConstants as constants
 from ..sessionData import SegmentationData
 
-from plugins.targeting import SliceTrackerTargetingPlugin
-from plugins.segmentation.manual import SliceTrackerManualSegmentationPlugin
-from plugins.segmentation.automatic import SliceTrackerAutomaticSegmentationPlugin
+from .plugins.targeting import SliceTrackerTargetingPlugin
+from .plugins.segmentation.manual import SliceTrackerManualSegmentationPlugin
+from .plugins.segmentation.automatic import SliceTrackerAutomaticSegmentationPlugin
 
 from SlicerDevelopmentToolboxUtils.helpers import SliceAnnotation
 from SlicerDevelopmentToolboxUtils.decorators import onModuleSelected
@@ -358,4 +358,4 @@ def _onTargetingStarted(self, caller, event):
   def _onTargetingFinished(self, caller, event):
     self.finishStepButton.setEnabled(1 if self.logic.inputsAreSet() else 0)
     self.manualSegmentationPlugin.enabled = True
-    self.backButton.enabled = True
+    self.backButton.enabled = True