def section_CreateSecondBranch(self):
self.delayDisplay("Create second branch in subject hierarchy",
self.delayMs)
from vtkSlicerSubjectHierarchyModuleMRML import vtkMRMLSubjectHierarchyNode
patient2Node = vtkMRMLSubjectHierarchyNode.CreateSubjectHierarchyNode(
slicer.mrmlScene, None,
slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMLevelPatient(),
self.patient2Name)
study2Node = vtkMRMLSubjectHierarchyNode.CreateSubjectHierarchyNode(
slicer.mrmlScene, patient2Node,
slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMLevelStudy(),
self.study2Name)
seriesNode = vtkMRMLSubjectHierarchyNode.CreateSubjectHierarchyNode(
slicer.mrmlScene, study2Node,
slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMLevelSeries(),
self.testSeriesName)
subseriesNode = vtkMRMLSubjectHierarchyNode.CreateSubjectHierarchyNode(
slicer.mrmlScene, seriesNode,
slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMLevelSubseries(),
self.testSubseriesName)
# Check if the created nodes have the right parents
self.assertTrue(study2Node.GetParentNode() == patient2Node)
self.assertTrue(seriesNode.GetParentNode() == study2Node)
self.assertTrue(subseriesNode.GetParentNode() == seriesNode)
def section_MarkupRole(self):
self.delayDisplay("Markup role", self.delayMs)
# Create sample markups node
markupsNode = slicer.vtkMRMLMarkupsFiducialNode()
slicer.mrmlScene.AddNode(markupsNode)
markupsNode.SetName(self.sampleMarkupName)
fiducialPosition = [100.0, 0.0, 0.0]
markupsNode.AddFiducialFromArray(fiducialPosition)
# Add markups to subject hierarchy
from vtkSlicerSubjectHierarchyModuleMRML import vtkMRMLSubjectHierarchyNode
patientNode = vtkMRMLSubjectHierarchyNode.CreateSubjectHierarchyNode(
slicer.mrmlScene, None,
slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMLevelPatient(),
'Patient')
studyNode = vtkMRMLSubjectHierarchyNode.CreateSubjectHierarchyNode(
slicer.mrmlScene, patientNode, self.studyName,
slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMLevelStudy())
markupsShNode = vtkMRMLSubjectHierarchyNode.CreateSubjectHierarchyNode(
slicer.mrmlScene, studyNode,
slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMLevelSeries(),
self.sampleMarkupName, markupsNode)
self.assertIsNotNone(markupsShNode)
self.assertEqual(markupsShNode.GetParentNode(), studyNode)
self.assertEqual(markupsShNode.GetOwnerPluginName(), 'Markups')
def section_CreateSecondBranch(self):
self.delayDisplay("Create second branch in subject hierarchy",
self.delayMs)
from vtkSlicerSubjectHierarchyModuleMRML import vtkMRMLSubjectHierarchyNode
patientNode = vtkMRMLSubjectHierarchyNode.CreateSubjectHierarchyNode(
slicer.mrmlScene, None, 'Subject', 'Patient2')
studyNode = vtkMRMLSubjectHierarchyNode.CreateSubjectHierarchyNode(
slicer.mrmlScene, patientNode, 'Study', self.study2Name)
seriesNode = vtkMRMLSubjectHierarchyNode.CreateSubjectHierarchyNode(
slicer.mrmlScene, studyNode, 'Series', 'TestSeries_Empty')
subseriesNode = vtkMRMLSubjectHierarchyNode.CreateSubjectHierarchyNode(
slicer.mrmlScene, seriesNode, 'Subseries', 'TestSuberies_Empty')
def section_ChartRole(self):
self.delayDisplay("Chart role",self.delayMs)
# Create sample chart node
chartNode = slicer.vtkMRMLChartNode()
slicer.mrmlScene.AddNode(chartNode)
chartNode.SetName(self.sampleChartName)
# Add markups to subject hierarchy
from vtkSlicerSubjectHierarchyModuleMRML import vtkMRMLSubjectHierarchyNode
studyNode = slicer.util.getNode(self.studyName + slicer.vtkMRMLSubjectHierarchyConstants.GetSubjectHierarchyNodeNamePostfix())
self.assertTrue( studyNode != None )
chartShNode = vtkMRMLSubjectHierarchyNode.CreateSubjectHierarchyNode(slicer.mrmlScene, studyNode, slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMLevelSeries(), self.sampleChartName, chartNode)
self.assertTrue( chartShNode != None )
self.assertTrue( chartShNode.GetParentNode() == studyNode )
self.assertTrue( chartShNode.GetOwnerPluginName() == 'Charts' )
def addSeriesInSubjectHierarchy(self, loadable, dataNode):
"""Add loaded DICOM series into subject hierarchy.
The DICOM tags are read from the first file referenced by the
given loadable. The dataNode argument is associated to the created
series node and provides fallback name in case of empty series
description.
This function should be called from the load() function of
each subclass of the DICOMPlugin class.
"""
tags = {}
tags['seriesInstanceUID'] = "0020,000E"
tags['seriesModality'] = "0008,0060"
tags['seriesNumber'] = "0020,0011"
tags['studyInstanceUID'] = "0020,000D"
tags['studyID'] = "0020,0010"
tags['studyDescription'] = "0008,1030"
tags['studyDate'] = "0008,0020"
tags['studyTime'] = "0008,0030"
tags['patientID'] = "0010,0020"
tags['patientName'] = "0010,0010"
tags['patientSex'] = "0010,0040"
tags['patientBirthDate'] = "0010,0030"
tags['patientComments'] = "0010,4000"
tags['instanceUID'] = "0008,0018"
# Import and check dependencies
from vtkSlicerSubjectHierarchyModuleMRML import vtkMRMLSubjectHierarchyNode
from vtkSlicerSubjectHierarchyModuleLogic import vtkSlicerSubjectHierarchyModuleLogic
try:
vtkMRMLSubjectHierarchyNode
vtkSlicerSubjectHierarchyModuleLogic
except AttributeError:
import sys
sys.stderr.write(
'Unable to create SubjectHierarchy nodes: SubjectHierarchy module not found!'
)
return
# Validate dataNode argument
if dataNode is None or not dataNode.IsA('vtkMRMLNode'):
import sys
sys.stderr.write(
'Unable to create SubjectHierarchy nodes: invalid data node provided!'
)
return
# Get first file to access DICOM tags from it
firstFile = loadable.files[0]
# Set up subject hierarchy node
seriesNode = vtkMRMLSubjectHierarchyNode.CreateSubjectHierarchyNode(
slicer.mrmlScene, None,
slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMLevelSeries(),
slicer.util.toVTKString(loadable.name), dataNode)
# Specify details of series node
seriesInstanceUid = slicer.dicomDatabase.fileValue(
firstFile, tags['seriesInstanceUID'])
seriesNode.AddUID(
slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMUIDName(),
seriesInstanceUid)
seriesNode.SetAttribute(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMSeriesModalityAttributeName(),
slicer.dicomDatabase.fileValue(firstFile, tags['seriesModality']))
seriesNode.SetAttribute(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMSeriesNumberAttributeName(),
slicer.dicomDatabase.fileValue(firstFile, tags['seriesNumber']))
# Set instance UIDs
instanceUIDs = ""
for file in loadable.files:
uid = slicer.dicomDatabase.fileValue(file, tags['instanceUID'])
if uid == "":
uid = "Unknown"
instanceUIDs += uid + " "
instanceUIDs = instanceUIDs[:-1] # strip last space
seriesNode.AddUID(
slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMInstanceUIDName(),
instanceUIDs)
# Set referenced instance UIDs from loadable to series
referencedInstanceUIDs = ""
if hasattr(loadable, 'referencedInstanceUIDs'):
for instanceUID in loadable.referencedInstanceUIDs:
referencedInstanceUIDs += instanceUID + " "
referencedInstanceUIDs = referencedInstanceUIDs[:
-1] # strip last space
seriesNode.SetAttribute(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMReferencedInstanceUIDsAttributeName(),
referencedInstanceUIDs)
# Add series node to hierarchy under the right study and patient nodes. If they are present then used, if not, then created
patientId = slicer.dicomDatabase.fileValue(firstFile,
tags['patientID'])
patientNode = vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNodeByUID(
slicer.mrmlScene,
slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMUIDName(),
patientId)
studyInstanceUid = slicer.dicomDatabase.fileValue(
firstFile, tags['studyInstanceUID'])
studyId = slicer.dicomDatabase.fileValue(firstFile, tags['studyID'])
studyNode = vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNodeByUID(
slicer.mrmlScene,
slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMUIDName(),
studyInstanceUid)
vtkSlicerSubjectHierarchyModuleLogic.InsertDicomSeriesInHierarchy(
slicer.mrmlScene, patientId, studyInstanceUid, seriesInstanceUid)
if patientNode is None:
patientNode = vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNodeByUID(
slicer.mrmlScene,
slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMUIDName(),
patientId)
if patientNode is not None:
# Add attributes for DICOM tags
patientName = slicer.util.toVTKString(
slicer.dicomDatabase.fileValue(firstFile,
tags['patientName']))
if patientName == '':
patientName = 'No name'
patientNode.SetAttribute(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMPatientNameAttributeName(), patientName)
patientNode.SetAttribute(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMPatientIDAttributeName(),
slicer.dicomDatabase.fileValue(firstFile,
tags['patientID']))
patientNode.SetAttribute(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMPatientSexAttributeName(),
slicer.dicomDatabase.fileValue(firstFile,
tags['patientSex']))
patientNode.SetAttribute(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMPatientBirthDateAttributeName(),
slicer.dicomDatabase.fileValue(firstFile,
tags['patientBirthDate']))
patientNode.SetAttribute(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMPatientCommentsAttributeName(),
slicer.dicomDatabase.fileValue(firstFile,
tags['patientComments']))
# Set node name
patientNode.SetName(patientName +
slicer.vtkMRMLSubjectHierarchyConstants.
GetSubjectHierarchyNodeNamePostfix())
if studyNode is None:
studyNode = vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNodeByUID(
slicer.mrmlScene,
slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMUIDName(),
studyInstanceUid)
if studyNode is not None:
# Add attributes for DICOM tags
studyDescription = slicer.util.toVTKString(
slicer.dicomDatabase.fileValue(firstFile,
tags['studyDescription']))
if studyDescription == '':
studyDescription = 'No study description'
studyNode.SetAttribute(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMStudyDescriptionAttributeName(), studyDescription)
studyDate = slicer.util.toVTKString(
slicer.dicomDatabase.fileValue(firstFile,
tags['studyDate']))
studyNode.SetAttribute(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMStudyInstanceUIDTagName(), studyInstanceUid)
studyNode.SetAttribute(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMStudyIDTagName(), studyId)
studyNode.SetAttribute(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMStudyDateAttributeName(), studyDate)
studyNode.SetAttribute(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMStudyTimeAttributeName(),
slicer.dicomDatabase.fileValue(firstFile,
tags['studyTime']))
# Set node name
studyNode.SetName(studyDescription + ' (' + studyDate + ')' +
slicer.vtkMRMLSubjectHierarchyConstants.
GetSubjectHierarchyNodeNamePostfix())