Fixing issue SlicerProstate#358.

SliceTracker/SliceTrackerRegistration.py

@@ -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/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

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):
@@ -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
@@ -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/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/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

SliceTracker/SliceTrackerUtils/steps/zFrameRegistration.py

@@ -9,7 +9,7 @@
 
 from ..algorithms.zFrameRegistration import LineMarkerRegistration, OpenSourceZFrameRegistration
 from ..constants import SliceTrackerConstants
-from base import SliceTrackerLogicBase, SliceTrackerStep
+from .base import SliceTrackerLogicBase, SliceTrackerStep
 
 from SlicerDevelopmentToolboxUtils.decorators import onModuleSelected
 from SlicerDevelopmentToolboxUtils.helpers import SliceAnnotation
@@ -537,4 +537,4 @@ def onApproveZFrameRegistrationButtonClicked(self):
   def onRetryZFrameRegistrationButtonClicked(self):
     self.removeZFrameInstructionAnnotation()
     self.annotationLogic.SetAnnotationVisibility(self.coverTemplateROI.GetID())
-    self.initiateZFrameRegistrationStep()
+    self.initiateZFrameRegistrationStep()

SliceTracker/SliceTrackerUtils/watch.py

@@ -32,7 +32,7 @@ def watch(self, secondsToWait=1):
     while True:
       currentFiles = self.listdirRecursive(self.directory)
       if len(self.files) < len(currentFiles):
-        print "Number of files changed"
+        print("Number of files changed")
         for newFile in self.getNewFiles(currentFiles):
           self.storeSCU(newFile)
       time.sleep(secondsToWait)
@@ -46,7 +46,7 @@ def getNewFiles(self, files):
 
   def storeSCU(self, fileName):
     cmd = ('storescu ' + self.host + ' ' + self.port + ' ' + fileName)
-    print cmd
+    print(cmd)
     os.system(cmd)
     self.files.add(fileName)
 
@@ -58,11 +58,11 @@ def main(argv):
    try:
       opts, args = getopt.getopt(argv,"i:d:h:p:?",["help","directory=","host=","port=","interval="])
    except getopt.GetoptError:
-      print 'watch.py -d <watchDirectory> -h <host> -p <port> -i <interval [in seconds]>'
+      print('watch.py -d <watchDirectory> -h <host> -p <port> -i <interval [in seconds]>')
       sys.exit(2)
    for opt, arg in opts:
       if opt in ("-?", "--help"):
-         print 'watch.py -d <watchDirectory> -h <host> -p <port>'
+         print('watch.py -d <watchDirectory> -h <host> -p <port>')
          sys.exit()
       elif opt in ("-d", "--directory"):
          watchDirectory = arg
@@ -73,12 +73,12 @@ def main(argv):
       elif opt in ("-i", "--interval"):
          interval = int(arg)
    if watchDirectory and host and port:
-     print 'Directory to watch is: ', watchDirectory
-     print 'Host to send DICOM files to is: ', host
-     print 'Port to send DICOM files to is: ', port
+     print('Directory to watch is: ', watchDirectory)
+     print('Host to send DICOM files to is: ', host)
+     print('Port to send DICOM files to is: ', port)
 
      watcher = DICOMDirectoryObserver(directory=watchDirectory, host=host, port=port)
-     print "Will watch!"
+     print("Will watch!")
      watcher.watch(interval)
 
 if __name__ == "__main__":