Merge branch 'master' into measurement-import

DICOMPlugins/DICOMParametricMapPlugin.py

@@ -105,7 +105,7 @@ def load(self,loadable):
       self.cleanup()
       return False
 
-    (_,pmNode) = slicer.util.loadVolume(os.path.join(self.tempDir,"pmap.nrrd"), returnNode=True)
+    pmNode = slicer.util.loadVolume(os.path.join(self.tempDir,"pmap.nrrd"))
 
     # load the metadata JSON to retrieve volume semantics (quantity stored and units)
     with open(os.path.join(self.tempDir,"meta.json")) as metafile:

DICOMPlugins/DICOMSegmentationPlugin.py

@@ -1,3 +1,4 @@
+from __future__ import absolute_import
 import glob
 import os
 import json
@@ -12,6 +13,7 @@
 
 from SlicerDevelopmentToolboxUtils.mixins import ModuleLogicMixin
 from SlicerDevelopmentToolboxUtils.constants import DICOMTAGS
+from six.moves import range
 
 
 #
@@ -48,15 +50,12 @@ def examineFiles(self,files):
       if isDicomSeg:
         loadable = DICOMLoadable()
         loadable.files = [cFile]
-        loadable.name = desc + ' - as a DICOM SEG object'
-        loadable.tooltip = loadable.name
+        loadable.name = desc
+        loadable.tooltip = loadable.name + ' - as a DICOM SEG object'
         loadable.selected = True
         loadable.confidence = 0.95
         loadable.uid = uid
         self.addReferences(loadable)
-        refName = self.referencedSeriesName(loadable)
-        if refName != "":
-          loadable.name = refName + " " + desc + " - Segmentations"
 
         loadables.append(loadable)
 
@@ -145,13 +144,13 @@ def load(self,loadable):
         for segment in segmentAttributes:
           try:
             rgb255 = segment["recommendedDisplayRGBValue"]
-            rgb = map(lambda c: float(c) / 255., rgb255)
+            rgb = [float(c) / 255. for c in rgb255]
           except KeyError:
             rgb = (0., 0., 0.)
 
           segmentId = segment["labelID"]
 
-          defaults = ['T-D0050', 'Tissue', 'SRT']
+          defaults = ['85756007', 'Tissue', 'SCT']
           categoryCode, categoryCodingScheme, categoryCodeMeaning = \
             self.getValuesFromCodeSequence(segment, "SegmentedPropertyCategoryCodeSequence", defaults)
 
@@ -161,7 +160,7 @@ def load(self,loadable):
           typeModCode, typeModCodingScheme, typeModCodeMeaning = \
             self.getValuesFromCodeSequence(segment, "SegmentedPropertyTypeModifierCodeSequence")
 
-          anatomicRegionDefaults = ['T-D0010', 'SRT', 'Entire Body']
+          anatomicRegionDefaults = ['38266002', 'SCT', 'Entire Body']
           regionCode, regionCodingScheme, regionCodeMeaning = \
             self.getValuesFromCodeSequence(segment, "AnatomicRegionSequence", anatomicRegionDefaults)
 
@@ -183,11 +182,12 @@ def load(self,loadable):
 
           # load the segmentation volume file and name it for the reference series and segment color
           labelFileName = os.path.join(self.tempDir, str(segmentId) + ".nrrd")
-          segmentName = seriesName + "-" + typeCodeMeaning + "-label"
-          success, labelNode = slicer.util.loadLabelVolume(labelFileName,properties={'name': segmentName},
-                                                           returnNode=True)
-          if not success:
-            raise ValueError("{} could not be loaded into Slicer!".format(labelFileName))
+          if segment["SegmentDescription"] is None:
+            segmentName = seriesName + "-" + typeCodeMeaning + "-label"
+          else:
+            segmentName = segment["SegmentDescription"]
+
+          labelNode = slicer.util.loadLabelVolume(labelFileName,properties={'name': segmentName})
 
           # Set terminology properties as attributes to the label node (which is a temporary node)
           #TODO: This is a quick solution, maybe there is a better one
@@ -248,7 +248,7 @@ def _removeLabelNode(self, labelNode):
 
   def _initializeSegmentation(self, loadable):
     segmentationNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode")
-    segmentationNode.SetName(self.referencedSeriesName(loadable))
+    segmentationNode.SetName(loadable.name)
 
     segmentationDisplayNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationDisplayNode")
     segmentationNode.SetAndObserveDisplayNodeID(segmentationDisplayNode.GetID())
@@ -315,7 +315,7 @@ def _setupExportable(self, exportable, subjectHierarchyItemID):
     exportable.subjectHierarchyItemID = subjectHierarchyItemID
     exportable.pluginClass = self.__module__
     # Define common required tags and default values
-    exportable.setTag('SeriesDescription', 'No series description')
+    exportable.setTag('SeriesDescription', 'Segmentation')
     exportable.setTag('SeriesNumber', '1')
     return [exportable]
 
@@ -337,14 +337,20 @@ def export(self, exportables):
 
       exporter = DICOMSegmentationExporter(segmentationNode)
 
+      metadata = {}
+      for attr in ["SeriesDescription", "ContentCreatorName", "ClinicalTrialSeriesID", "ClinicalTrialTimePointID",
+        "ClinicalTrialCoordinatingCenterName"]:
+        if exportable.tag(attr) != "":
+          metadata[attr] = exportable.tag(attr)
+
       try:
         segFileName = "subject_hierarchy_export.SEG" + exporter.currentDateTime + ".dcm"
         segFilePath = os.path.join(exportable.directory, segFileName)
         try:
-          exporter.export(exportable.directory, segFileName)
+          exporter.export(exportable.directory, segFileName, metadata)
         except DICOMSegmentationExporter.EmptySegmentsFoundError as exc:
           if slicer.util.confirmYesNoDisplay(exc.message):
-            exporter.export(exportable.directory, segFileName, skipEmpty=True)
+            exporter.export(exportable.directory, segFileName, metadata, skipEmpty=True)
           else:
             raise ValueError("Export canceled")
         slicer.dicomDatabase.insert(segFilePath)
@@ -448,12 +454,21 @@ def export(self, outputDirectory, segFileName, metadata, segmentIDs=None, skipEm
     data = self.getSeriesAttributes()
     data.update(metadata)
 
-    try:
-      for attr in ["SeriesDescription", "ContentCreatorName", "ClinicalTrialSeriesID", "ClinicalTrialTimePointID",
+    metadataDefaults = {}
+    metadataDefaults["SeriesDescription"] = "Segmentation"
+    metadataDefaults["ContentCreatorName"] = self.contentCreatorName
+    metadataDefaults["ClinicalTrialSeriesID"] = "1"
+    metadataDefaults["ClinicalTrialTimePointID"] = "1"
+    metadataDefaults["ClinicalTrialCoordinatingCenterName"] = "QIICR"
+
+    for attr in ["SeriesDescription", "ContentCreatorName", "ClinicalTrialSeriesID", "ClinicalTrialTimePointID",
                    "ClinicalTrialCoordinatingCenterName"]:
-        data[attr]
-    except KeyError as exc:
-      raise self.MissingAttributeError(str(exc))
+      try:
+        if data[attr] == "":
+          data[attr] = metadataDefaults[attr]
+
+      except KeyError as exc:
+        data[attr] = metadataDefaults[attr]
 
     self.formatMetaDataDICOMConform(data)
 

DICOMPlugins/DICOMTID1500Plugin.py

@@ -4,9 +4,11 @@
 import vtk
 import datetime
 from collections import Counter
-import dicom
+
 import numpy
 import random
+import pydicom
+
 
 import slicer
 from DICOMLib import DICOMLoadable
@@ -41,7 +43,7 @@ def examineFiles(self, files):
     loadables = []
 
     for cFile in files:
-      dataset = dicom.read_file(cFile)
+      dataset = pydicom.read_file(cFile)
 
       uid = self.getDICOMValue(dataset, "SOPInstanceUID")
       if uid == "":
@@ -140,20 +142,20 @@ def sortReportsByDateTime(self, uids):
 
   def getDateTime(self, uid):
     filename = slicer.dicomDatabase.fileForInstance(uid)
-    dataset = dicom.read_file(filename)
+    dataset = pydicom.read_file(filename)
     if hasattr(dataset, 'SeriesDate') and hasattr(dataset, "SeriesTime"):
       date = dataset.SeriesDate
       time = dataset.SeriesTime
     elif hasattr(dataset, 'StudyDate') and hasattr(dataset, "StudyTime"):
       date = dataset.StudyDate
       time = dataset.StudyDate
     else:
-      date = "19630524"
-      time = "000000"
+      date = ""
+      time = ""
     try:
       dateTime = datetime.datetime.strptime(date+time, '%Y%m%d%H%M%S')
     except ValueError:
-      dateTime = "19630524000000"
+      dateTime = ""
     return dateTime
 
   def load(self, loadable):
@@ -216,6 +218,10 @@ def load(self, loadable):
 
       table = self.metadata2vtkTableNode(outputFile)
       if table:
+        with open(outputFile, 'r') as srMetadataFile:
+          srMetadataJSON = json.loads(srMetadataFile.read())
+          table.SetName(srMetadataJSON["SeriesDescription"])
+
         # TODO: think about the following...
         if len(slicer.util.getNodesByClass('vtkMRMLSegmentationNode')) > 0:
           segmentationNode = slicer.util.getNodesByClass('vtkMRMLSegmentationNode')[-1]
@@ -268,7 +274,7 @@ def determineAndApplyRWVMToReferencedSeries(self, loadable, segLoadable):
       rwvmPlugin = slicer.modules.dicomPlugins["DICOMRWVMPlugin"]()
       rwvmFile = rwvmFiles[0]
       logging.debug("Reading RWVM from " + rwvmFile)
-      rwvmDataset = dicom.read_file(rwvmFile)
+      rwvmDataset = pydicom.read_file(rwvmFile)
       if hasattr(rwvmDataset, "ReferencedSeriesSequence"):
         if hasattr(rwvmDataset.ReferencedSeriesSequence[0], "SeriesInstanceUID"):
           if rwvmDataset.ReferencedSeriesSequence[0].SeriesInstanceUID == segLoadable.referencedSeriesUID:
@@ -445,7 +451,7 @@ def examineFiles(self, files):
     loadables = []
 
     for cFile in files:
-      dataset = dicom.read_file(cFile)
+      dataset = pydicom.read_file(cFile)
 
       uid = self.getDICOMValue(dataset, "SOPInstanceUID")
       if uid == "":
@@ -485,7 +491,7 @@ def getRelatedSRs(self, dataset):
       foundSRs = []
       for s in series:
         srFile = self.fileForSeries(s)
-        tempDCM = dicom.read_file(srFile)
+        tempDCM = pydicom.read_file(srFile)
         if self.isDICOMTID1500(tempDCM):
           foundSRs.append(srFile)
           otherSRDatasets.append(tempDCM)

DICOMPlugins/base/DICOMPluginBase.py

@@ -1,5 +1,5 @@
 import slicer
-import dicom
+import pydicom
 import logging
 from datetime import datetime
 from DICOMLib import DICOMPlugin
@@ -59,7 +59,7 @@ def examineForImport(self, fileLists):
   def addReferences(self, loadable):
     """Puts a list of the referenced UID into the loadable for use
     in the node if this is loaded."""
-    dcm = dicom.read_file(loadable.files[0])
+    dcm = pydicom.read_file(loadable.files[0])
     loadable.referencedInstanceUIDs = []
     self._addReferencedSeries(loadable, dcm)
     self._addReferencedImages(loadable, dcm)
@@ -69,7 +69,7 @@ def _addReferencedSeries(self, loadable, dcm):
     if hasattr(dcm, "ReferencedSeriesSequence"):
       if hasattr(dcm.ReferencedSeriesSequence[0], "SeriesInstanceUID"):
         for f in slicer.dicomDatabase.filesForSeries(dcm.ReferencedSeriesSequence[0].SeriesInstanceUID):
-          refDCM = dicom.read_file(f)
+          refDCM = pydicom.read_file(f)
           loadable.referencedInstanceUIDs.append(refDCM.SOPInstanceUID)
         loadable.referencedSeriesUID = dcm.ReferencedSeriesSequence[0].SeriesInstanceUID
 
@@ -79,4 +79,4 @@ def _addReferencedImages(self, loadable, dcm):
         if hasattr(item, "ReferencedSOPInstanceUID"):
           loadable.referencedInstanceUIDs.append(item.ReferencedSOPInstanceUID)
           # TODO: what to do with the SeriesInstanceUID?
-          # refDCM = dicom.read_file(slicer.dicomDatabase.fileForInstance(item.ReferencedSOPInstanceUID))
+          # refDCM = pydicom.read_file(slicer.dicomDatabase.fileForInstance(item.ReferencedSOPInstanceUID))

QuantitativeReporting/CMakeLists.txt

@@ -2,7 +2,6 @@
 
 set(MODULE_PYTHON_SCRIPTS
   QRCustomizations/__init__.py
-  QRCustomizations/CustomDICOMDetailsWidget.py
   QRCustomizations/CustomSegmentEditor.py
   QRCustomizations/CustomSegmentStatistics.py
   QRCustomizations/SegmentEditorAlgorithmTracker.py

QuantitativeReporting/QRCustomizations/CustomSegmentEditor.py

@@ -1,6 +1,8 @@
+from __future__ import absolute_import
 import qt
 import slicer
 import vtk
+import os
 
 
 from QRCustomizations.CustomSegmentStatistics import CustomSegmentStatisticsLogic
@@ -11,6 +13,7 @@
 from SegmentEditor import SegmentEditorWidget
 
 import vtkSegmentationCorePython as vtkSegmentationCore
+from six.moves import range
 
 
 class CustomSegmentEditorWidget(SegmentEditorWidget, ModuleWidgetMixin):
@@ -46,14 +49,19 @@ def __init__(self, parent):
     SegmentEditorWidget.__init__(self, parent)
     self.logic = CustomSegmentEditorLogic()
 
+  def resourcePath(self, filename):
+    scriptedModulesPath = os.path.dirname(slicer.util.modulePath("QuantitativeReporting"))
+    return os.path.join(scriptedModulesPath, 'Resources', filename)
+
   def setup(self):
     super(CustomSegmentEditorWidget, self).setup()
-    if self.developerMode:
-      self.reloadCollapsibleButton.hide()
     self.editor.switchToSegmentationsButtonVisible = False
     self.editor.segmentationNodeSelectorVisible = False
     self.editor.setEffectButtonStyle(qt.Qt.ToolButtonIconOnly)
     self.clearSegmentationEditorSelectors()
+
+  def setupDeveloperSection(self):
+    return
 
   def onSegmentSelected(self, selectedRow):
     try:
@@ -182,4 +190,4 @@ def calculateSegmentStatistics(self, segNode, grayscaleNode, visibleSegmentsOnly
       self.segmentStatisticsLogic.getParameterNode().UnsetParameter("ScalarVolume")
     self.segmentStatisticsLogic.computeStatistics()
     tableNode = self.segmentStatisticsLogic.exportToTable(tableNode)
-    return tableNode
+    return tableNode

QuantitativeReporting/QRCustomizations/CustomSegmentStatistics.py

@@ -1,3 +1,4 @@
+from __future__ import absolute_import
 import logging
 import slicer
 import qt
@@ -121,7 +122,7 @@ def generateJSON4DcmSR(self, dcmSegmentationFile, sourceVolumeNode):
 
       data["Finding"] = self.createJSONFromTerminologyContext(terminologyEntry)["SegmentedPropertyTypeCodeSequence"]
       anatomicContext = self.createJSONFromAnatomicContext(terminologyEntry)
-      if anatomicContext.has_key("AnatomicRegionSequence"):
+      if "AnatomicRegionSequence" in anatomicContext:
         data["FindingSite"] = anatomicContext["AnatomicRegionSequence"]
       data["measurementItems"] = self.createMeasurementItemsForLabelValue(segmentID)
       measurements.append(data)
@@ -137,7 +138,7 @@ def createMeasurementItemsForLabelValue(self, segmentValue):
         item["value"] = str(self.statistics[segmentValue, key])
         item["quantity"] = self._createCodeSequence(measurementInfo["DICOM.QuantityCode"])
         item["units"] = self._createCodeSequence(measurementInfo["DICOM.UnitsCode"])
-        if measurementInfo.has_key("DICOM.DerivationCode"):
+        if "DICOM.DerivationCode" in measurementInfo:
           item["derivationModifier"] = self._createCodeSequence(measurementInfo["DICOM.DerivationCode"])
         measurementItems.append(item)
     return measurementItems

QuantitativeReporting/QRCustomizations/SegmentEditorAlgorithmTracker.py

@@ -1,6 +1,8 @@
+from __future__ import absolute_import
 import slicer
 import vtk
 import vtkSegmentationCorePython as vtkSegmentationCore
+from six.moves import range
 
 
 class SegmentEditorAlgorithmTracker(object):