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@@ -0,0 +1,353 @@
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+import DICOMLib
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+from slicer.ScriptedLoadableModule import *
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+import slicerNetwork
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+import qt,vtk,ctk,slicer
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+import datetime
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+import re
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+import os
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+import slicer.cli
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+
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+class exportDicom(slicer.ScriptedLoadableModule.ScriptedLoadableModule):
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+ def __init__(self,parent):
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+ slicer.ScriptedLoadableModule.ScriptedLoadableModule.__init__(self, parent)
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+ self.className="exportDicom"
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+ self.parent.title="exportDicom"
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+ self.parent.categories = ["Examples"]
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+ self.parent.dependencies = []
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+ self.parent.contributors = ["Andrej Studen (University of Ljubljana)"] # replace with "Firstname Lastname (Organization)"
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+ self.parent.helpText = """
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+ This is an example of scripted loadable module bundled in an extension.
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+ It adds hierarchy datat for reliable dicom export of a node
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+ """
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+ self.parent.helpText += self.getDefaultModuleDocumentationLink()
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+ self.parent.acknowledgementText = """
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+ This extension developed within Medical Physics research programe of ARRS
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+ """ # replace with organization, grant and thanks.
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+
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+#
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+# dataExplorerWidget
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+
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+
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+
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+class exportDicomWidget(ScriptedLoadableModuleWidget):
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+ """Uses ScriptedLoadableModuleWidget base class, available at:
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+ https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
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+ """
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+
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+ def setup(self):
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+ ScriptedLoadableModuleWidget.setup(self)
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+ self.logic=exportDicomLogic(self)
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+
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+ try:
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+ fhome=os.environ["HOME"]
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+ except:
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+ #in windows, the variable is called HOMEPATH
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+ fhome=os.environ['HOMEDRIVE']+os.environ['HOMEPATH']
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+
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+ cfgPath=os.path.join(fhome,".labkey")
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+ cfgPath=os.path.join(cfgPath,"onko-nix.json")
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+
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+ self.onkoNet=slicerNetwork.labkeyURIHandler()
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+ self.onkoNet.parseConfig(cfgPath)
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+ self.onkoNet.initRemote()
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+
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+ self.project='EMBRACE/Studija'
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+
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+ datasetCollapsibleButton = ctk.ctkCollapsibleButton()
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+ datasetCollapsibleButton.text = "Node data"
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+ self.layout.addWidget(datasetCollapsibleButton)
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+ # Layout within the dummy collapsible button
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+ datasetFormLayout = qt.QFormLayout(datasetCollapsibleButton)
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+
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+ self.volumeNode=qt.QLineEdit("Shifted_1_PTV N")
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+ datasetFormLayout.addRow("volumeNode:",self.volumeNode)
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+ self.patientId=qt.QLineEdit("LJU004")
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+ datasetFormLayout.addRow("PatientId:",self.patientId)
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+ self.studyInstanceUid=qt.QLineEdit("1.2.840.113704.1.1762661776.922.1250707615.8")
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+ datasetFormLayout.addRow("StudyInstanceUid:",self.studyInstanceUid)
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+ self.studyDescription=qt.QLineEdit("Segmentation:PTV N")
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+ datasetFormLayout.addRow("StudyDescription:",self.studyDescription)
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+
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+ self.addHierarchyButton=qt.QPushButton("Add hierarchy")
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+ self.addHierarchyButton.clicked.connect(self.onAddHierarchyButtonClicked)
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+ datasetFormLayout.addRow("Volume:",self.addHierarchyButton)
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+
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+ self.exportButton=qt.QPushButton("Export")
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+ self.exportButton.clicked.connect(self.onExportButtonClicked)
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+ datasetFormLayout.addRow("Export:",self.exportButton)
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+
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+
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+
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+ def onAddHierarchyButtonClicked(self):
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+ metadata={'patientId':self.patientId.text,
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+ 'studyDescription':self.studyDescription.text,
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+ 'studyInstanceUid':self.studyInstanceUid.text}
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+ node=slicer.util.getFirstNodeByName(self.volumeNode.text)
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+ if node==None:
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+ return
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+ self.logic.addHierarchy(node,metadata)
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+
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+ def onExportButtonClicked(self):
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+ metadata={'patientId':self.patientId.text,
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+ 'studyDescription':self.studyDescription.text,
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+ 'studyInstanceUid':self.studyInstanceUid.text,
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+ 'seriesInstanceUid':self.logic.generateSeriesUUID('volume'),
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+ 'frameOfReferenceInstanceUid':self.logic.generateFrameOfReferenceUUID('volume')}
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+ node=slicer.util.getFirstNodeByName(self.volumeNode.text)
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+ if node==None:
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+ return
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+ self.logic.exportNode(self.onkoNet,self.project,node,metadata)
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+
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+
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+
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+class exportDicomLogic(slicer.ScriptedLoadableModule.ScriptedLoadableModuleLogic):
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+ def __init__(self,parent):
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+ slicer.ScriptedLoadableModule.ScriptedLoadableModuleLogic.__init__(self, parent)
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+ self.baseUUID='1.2.826.0.1.36800.43.10.248'
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+ self.labelUUID={'series':'1','study':'2','instance':'3','frameOfReference':4}
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+ self.dataUUID={'volume':'1','segmentation':'2','transformation':'3'}
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+
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+ try:
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+ fhome=os.environ["HOME"]
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+ except:
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+ #in windows, the variable is called HOMEPATH
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+ fhome=os.environ['HOMEDRIVE']+os.environ['HOMEPATH']
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+
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+
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+ self.basePath=os.path.join(fhome,'.dicom')
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+
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+ if not os.path.isdir(self.basePath):
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+ os.mkdir(self.basePath)
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+
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+ self.itemLabel={
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+ 'patientName': slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMPatientNameAttributeName(),
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+ 'modality': slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMSeriesModalityAttributeName(),
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+ 'patientId': slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMPatientIDAttributeName(),
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+ 'patientSex': slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMPatientSexAttributeName(),
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+ 'patientBirthDate': slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMPatientBirthDateAttributeName(),
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+ 'patientComments': slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMPatientCommentsAttributeName(),
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+ 'studyDescription': slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMStudyDescriptionAttributeName(),
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+ 'studyInstanceUid': slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMStudyInstanceUIDTagName(),
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+ 'studyDate': slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMStudyDateAttributeName(),
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+ 'studyId': slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMStudyIDTagName(),
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+ 'studyTime': slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMStudyTimeAttributeName()}
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+
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+
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+
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+
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+
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+
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+
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+ def generateStudyUUID(self,type):
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+
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+ x=datetime.datetime.now()
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+ date=x.strftime("%Y%m%d")
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+ studyFile=os.path.join(self.basePath,'studyCount'+date+'.txt')
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+
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+ try:
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+ f=open(studyFile,"r")
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+ id=int(f.readline())
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+ id=id+1
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+ f.close()
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+ except:
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+ id=0
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+
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+ studyId="{}.{}.{}.{}.{}".format(self.baseUUID,self.labelUUID['study'],
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+ self.dataUUID[type],date,id)
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+
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+ f=open(studyFile,"w")
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+ f.write("{}".format(id))
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+ f.close()
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+ return studyId
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+
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+
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+
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+ def generateFrameOfReferenceUUID(self,type):
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+
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+ x=datetime.datetime.now()
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+ date=x.strftime("%Y%m%d")
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+ forFile=os.path.join(self.basePath,'frameCount'+date+'.txt')
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+
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+ try:
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+ f=open(studyFile,"r")
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+ id=int(f.readline())
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+ id=id+1
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+ f.close()
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+ except:
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+ id=0
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+
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+ forId="{}.{}.{}.{}.{}".format(self.baseUUID,self.labelUUID['frameOfReference'],
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+ self.dataUUID[type],date,id)
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+
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+ f=open(forFile,"w")
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+ f.write("{}".format(id))
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+ f.close()
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+ return forId
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+
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+ def generateSeriesUUID(self,type):
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+
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+ x=datetime.datetime.now()
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+ hour=x.strftime("%H")
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+ hour=re.sub('^0','',hour)
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+ ft=hour+x.strftime("%M%S")
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+ seriesInstanceUid=self.baseUUID+'.'+self.labelUUID['series']+'.'
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+ seriesInstanceUid+=self.dataUUID[type]+'.'+x.strftime("%Y%m%d")+'.'+ft
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+ return seriesInstanceUid
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+
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+ def setAttribute(self,shn,itemId,label,metadata):
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+ try:
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+ shn.SetItemAttribute(itemId,self.itemLabel['modality'],metadata['modality'])
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+ except KeyError:
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+ pass
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+
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+ def addHierarchy(self,dataNode,metadata):
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+ #convert dataNode to fully fledged DICOM object in hierarchy
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+
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+ #variation of addSeriesInSubjectHierarchy
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+ shn=slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)
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+ sceneItemId=shn.GetSceneItemID()
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+
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+ #add the series for the data node
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+ seriesItemId=shn.CreateItem(sceneItemId,dataNode)
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+
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+ x=datetime.datetime.now()
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+ hour=x.strftime("%H")
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+ hour=re.sub('^0','',hour)
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+ ft=hour+x.strftime("%M%S")
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+ seriesInstanceUid=self.baseUUID+'.'+self.labelUUID['series']+'.'
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+ seriesInstanceUid+=self.dataUUID['volume']+'.'+x.strftime("%Y%m%d")+'.'+ft
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+ shn.SetItemUID(seriesItemId,slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMUIDName(),
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+ seriesInstanceUid)
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+
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+ self.setAttribute(shn,seriesItemId,'modality',metadata)
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+ self.setAttribute(shn,seriesItemId,'seriesNumber',metadata)
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+
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+ #add PatientId
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+ try:
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+ patientId=metadata['patientId']
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+ except KeyError:
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+ patientId='Unknown'
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+
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+ try:
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+ studyInstanceUid=metadata['studyInstanceUid']
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+ except KeyError:
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+ studyInstanceUid=self.generateStudyUUID('volume')
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+
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+ slicer.vtkSlicerSubjectHierarchyModuleLogic.InsertDicomSeriesInHierarchy(shn,patientId,
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+ studyInstanceUid,seriesInstanceUid)
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+
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+ patientItemId=shn.GetItemByUID(slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMUIDName(),patientId)
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+
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+ self.setAttribute(shn,patientItemId,'patientName',metadata)
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+ self.setAttribute(shn,patientItemId,'patientId',metadata)
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+ self.setAttribute(shn,patientItemId,'patientSex',metadata)
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+ self.setAttribute(shn,patientItemId,'patientBirthDate',metadata)
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+ self.setAttribute(shn,patientItemId,'patientComments',metadata)
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+
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+ patientItemName=patientId
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+ shn.SetItemName(patientItemId,patientItemName)
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+
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+ studyItemId=shn.GetItemByUID(slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMUIDName(),studyInstanceUid)
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+
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+ self.setAttribute(shn,studyItemId,'studyDescription',metadata)
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+ self.setAttribute(shn,studyItemId,'studyInstanceUid',metadata)
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+ self.setAttribute(shn,studyItemId,'studyId',metadata)
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+ self.setAttribute(shn,studyItemId,'studyDate',metadata)
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+ self.setAttribute(shn,studyItemId,'studyTime',metadata)
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+
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+ studyItemName=studyInstanceUid
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+ shn.SetItemName(studyItemId,studyItemName)
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+
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+ def setTagValue(self,cliparameters,metadata,field):
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+ try:
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+ cliparameters[field]=metadata[field]
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+ except KeyError:
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+ pass
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+
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+ def setDirectoryValue(self,cliparameters,cliKey,metadata,key):
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+ try:
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+ cliparameters[cliKey]=metadata[key]
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+ except KeyError:
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+ pass
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+
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+
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+
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+ def exportNode(self,net, project,volumeNode,metadata):
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+
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+ cliparameters={}
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+ tagList=['patientName','patientComments','studyDate','studyTime','studyDescription',
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+ 'modality','manufacturer','model','seriesDescription',
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+ 'seriesNumber','seriesDate','seriesTime','contentDate','contentTime']
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+
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+ for tag in tagList:
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+ self.setTagValue(cliparameters,metadata,tag)
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+
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+ valuePairs={'patientID':'patientId',
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+ 'studyID':'studyId',
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+ 'seriesInstanceUID':'seriesInstanceUid',
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+ 'studyInstanceUID':'studyInstanceUid',
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+ 'frameOfReferenceInstanceUID':'frameOfReferenceInstanceUid'}
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+
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+ for key in valuePairs:
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+ self.setDirectoryValue(cliparameters,key,metadata,valuePairs[key])
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+
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+
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+ #buffed up exportable is now ready to be stored
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+ fdir=net.GetLocalCacheDirectory()
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+ project=project.replace('/','\\')
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+ fdir=os.path.join(fdir,project)
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+ fdir=os.path.join(fdir,'%40files')
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+ fdir=os.path.join(fdir,metadata['patientId'])
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+ fdir=os.path.join(fdir,'Registration')
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+
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+ if not os.path.isdir(fdir):
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+ os.mkdir(fdir)
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+
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+ relDir=net.GetRelativePathFromLocalPath(fdir)
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+ remoteDir=net.GetLabkeyPathFromRelativePath(relDir)
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+
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+ if not net.isRemoteDir(remoteDir):
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+ net.mkdir(remoteDir)
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+
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+
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+ dirName=volumeNode.GetName();
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+ dirName=dirName.replace(" ","_")
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+ fdir=os.path.join(fdir,dirName)
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+
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+ if not os.path.isdir(fdir):
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+ os.mkdir(fdir)
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+
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+ cliparameters['dicomDirectory']=fdir
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+ cliparameters['dicomPrefix']='IMG'
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+ cliparameters['inputVolume']=volumeNode.GetID()
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+
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+ print("[CLI]SeriesInstanceUID: {}").format(cliparameters['seriesInstanceUID'])
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+ print("[MeD]SeriesInstanceUID: {}").format(metadata['seriesInstanceUid'])
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+
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+ try:
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+ dicomWrite=slicer.modules.createdicomseries
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+ except AttributeError:
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+ print("Missing dicom exporter")
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+ return
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+
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+ cliNode=slicer.cli.run(dicomWrite,None,cliparameters,wait_for_completion=True)
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+ status=cliNode.GetStatusString()
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+ print("Status: {}").format(status)
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+ if status.find("error")>-1:
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+ print("Error: {}").format(cliNode.GetErrorText())
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+ return
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+
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+ relDir=net.GetRelativePathFromLocalPath(fdir)
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+ remoteDir=net.GetLabkeyPathFromRelativePath(relDir)
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+
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+ if not net.isRemoteDir(remoteDir):
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+ net.mkdir(remoteDir)
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+
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+ for f in os.listdir(fdir):
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+ localPath=os.path.join(fdir,f)
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+ print("localPath: {}").format(localPath)
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+ relativePath=net.GetRelativePathFromLocalPath(localPath)
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+ print("relativePath: {}").format(relativePath)
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+ remotePath=net.GetLabkeyPathFromRelativePath(relativePath)
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+ print("remotePath: {}").format(relativePath)
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+ net.copyLocalFileToRemote(localPath,remotePath)
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