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@@ -1,516 +0,0 @@
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-import slicer
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-import os
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-import subprocess
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-import re
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-import slicerNetwork
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-import ctk,qt
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-import json
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-
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-dicomModify=os.getenv("HOME")
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-if not dicomModify==None:
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- dicomModify+="/software/install/"
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- dicomModify+="dicomModify/bin/dicomModify"
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-
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-class loadDicom(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="loadDicom"
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- self.parent.title="loadDicom"
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- self.parent.categories = ["LabKey"]
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- self.parent.dependencies = []
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- self.parent.contributors = ["Andrej Studen (UL/FMF)"] # replace with "Firstname Lastname (Organization)"
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- self.parent.helpText = """
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- utilities for parsing dicom entries
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- """
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- self.parent.acknowledgementText = """
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- Developed within the medical physics research programme of the Slovenian research agency.
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- """ # replace with organization, grant and thanks.
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-
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-class loadDicomWidget(slicer.ScriptedLoadableModule.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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- slicer.ScriptedLoadableModule.ScriptedLoadableModuleWidget.setup(self)
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- self.logic=loadDicomLogic(self)
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- self.network=slicerNetwork.labkeyURIHandler()
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-
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- connectionCollapsibleButton = ctk.ctkCollapsibleButton()
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- connectionCollapsibleButton.text = "Connection"
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- self.layout.addWidget(connectionCollapsibleButton)
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-
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- connectionFormLayout = qt.QFormLayout(connectionCollapsibleButton)
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-
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- self.loadConfigButton=qt.QPushButton("Load configuration")
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- self.loadConfigButton.toolTip="Load configuration"
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- self.loadConfigButton.connect('clicked(bool)',self.onLoadConfigButtonClicked)
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- connectionFormLayout.addRow("Connection:",self.loadConfigButton)
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-
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- self.DICOMDirectory=qt.QLineEdit("Test/Temp/%40files/TEST/MLEM")
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- connectionFormLayout.addRow("LabKey directory:",self.DICOMDirectory)
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-
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-
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- loadDICOMButton=qt.QPushButton("Load")
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- loadDICOMButton.toolTip="Load DICOM"
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- loadDICOMButton.clicked.connect(self.onLoadDICOMButtonClicked)
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- connectionFormLayout.addRow("DICOM:",loadDICOMButton)
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-
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- self.DICOMFilter=qt.QLineEdit('{"seriesNumber":"SeriesLabel"}')
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- connectionFormLayout.addRow("Filter(JSON):",self.DICOMFilter)
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-
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- loadDICOMFilterButton=qt.QPushButton("Load with filter")
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- loadDICOMFilterButton.toolTip="Load DICOM with filter"
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- loadDICOMFilterButton.clicked.connect(self.onLoadDICOMFilterButtonClicked)
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- connectionFormLayout.addRow("DICOM:",loadDICOMFilterButton)
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-
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- loadDICOMSegmentationFilterButton=qt.QPushButton("Load segmentation with filter")
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- loadDICOMSegmentationFilterButton.toolTip="Load DICOM (RT contour) with filter"
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- loadDICOMSegmentationFilterButton.clicked.connect(self.onLoadDICOMSegmentationFilterButtonClicked)
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- connectionFormLayout.addRow("DICOM:",loadDICOMSegmentationFilterButton)
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-
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-
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- def onLoadConfigButtonClicked(self):
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- filename=qt.QFileDialog.getOpenFileName(None,'Open configuration file (JSON)',
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- os.path.join(os.path.expanduser('~'),'.labkey'), '*.json')
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- self.network.parseConfig(filename)
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- self.network.initRemote()
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- self.loadConfigButton.setText(os.path.basename(filename))
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-
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- def onLoadDICOMFilterButtonClicked(self):
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- filter=json.loads(self.DICOMFilter.text)
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- #print("Filter is {}".format(filter))
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- self.logic.loadVolumes(self.network,self.DICOMDirectory.text,filter)
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-
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- def onLoadDICOMSegmentationFilterButtonClicked(self):
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- filter=json.loads(self.DICOMFilter.text)
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- #print("Filter is {}".format(filter))
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- self.logic.loadSegmentations(self.network,self.DICOMDirectory.text,filter)
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-
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- def onLoadDICOMButtonClicked(self):
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- self.logic.load(self.network,self.DICOMDirectory.text)
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-
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-
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-class loadDicomLogic(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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-
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- self.tag={
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- 'sopInstanceUid' : {'tag':"0008,0018",'VR':'UI'},
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- 'studyDate': {'tag':"0008,0020",'VR':'DA'},
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- 'studyTime': {'tag':"0008,0030",'VR':'TM'},
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- 'seriesTime': {'tag':"0008,0031",'VR':'TM'},
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- 'modality': {'tag':"0008,0060",'VR':'CS'},
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- 'presentationIntentType': {'tag':"0008,0068",'VR':'CS'},
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- 'manufacturer': {'tag':"0008,0070",'VR':'LO'},
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- 'institutionName': {'tag':"0008,0080",'VR':'LO'},
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- 'studyDescription': {'tag':"0008,1030",'VR':'LO'},
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- 'seriesDescription': {'tag':"0008,103e",'VR':'LO'},
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- 'manufacturerModelName': {'tag':"0008,1090",'VR':'LO'},
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- 'patientName': {'tag':"0010,0010",'VR':'PN'},
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- 'patientId': {'tag':"0010,0020",'VR':'LO'},
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- 'patientBirthDate': {'tag':"0010,0030",'VR':'DA'},
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- 'patientSex': {'tag':"0010,0040",'VR':'CS'},
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- 'patientAge': {'tag':"0010,1010",'VR':'AS'},
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- 'patientComments': {'tag':"0010,4000",'VR':'LT'},
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- 'sequenceName': {'tag':"0018,0024",'VR':'SH'},
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- 'kVP': {'tag':"0018,0060",'VR':'DS'},
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- 'percentPhaseFieldOfView': {'tag':"0018,0094",'VR':'DS'},
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- 'xRayTubeCurrent': {'tag':"0018,1151",'VR':'IS'},
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- 'exposure': {'tag':"0018,1152",'VR':'IS'},
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- 'imagerPixelSpacing': {'tag':"0018,1164",'VR':'DS'},
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- 'bodyPartThickness': {'tag':"0018,11a0",'VR':'DS'},
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- 'compressionForce': {'tag':"0018,11a2",'VR':'DS'},
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- 'viewPosition': {'tag':"0018,5101",'VR':'CS'},
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- 'fieldOfViewHorizontalFlip': {'tag':"0018,7034",'VR':'CS'},
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- 'studyInstanceUid': {'tag':"0020,000d",'VR':'UI'},
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- 'seriesInstanceUid': {'tag':"0020,000e",'VR':'UI'},
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- 'studyId': {'tag':"0020,0010",'VR':'SH'},
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- 'seriesNumber': {'tag':"0020,0011",'VR':'IS'},
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- 'instanceNumber': {'tag':"0020,0013",'VR':'IS'},
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- 'frameOfReferenceInstanceUid': {'tag':"0020,0052",'seqTag':"3006,0010",'VR':'UI'},
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- 'imageLaterality': {'tag':"0020,0062",'VR':'CS'},
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- 'imagesInAcquisition': {'tag':"0020,1002",'VR':'IS'},
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- 'photometricInterpretation': {'tag':"0028,0004",'VR':'CS'},
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- 'reconstructionMethod': {'tag':"0054,1103",'VR':'LO'}
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- }
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- self.tagPyDicom={
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- 'studyDate': 0x00080020,
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- 'studyTime': 0x00080030,
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- 'modality': 0x00080060,
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- 'presentationIntentType': 0x00080068,
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- 'manufacturer': 0x00080070,
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- 'studyDescription': 0x00081030,
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- 'seriesDescription': 0x0008103e,
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- 'patientName': 0x00100010,
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- 'patientId': 0x00100020,
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- 'patientBirthDate': 0x00100030,
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- 'patientSex': 0x00100040,
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- 'patientComments': 0x00104000,
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- 'sequenceName': 0x00180024,
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- 'kVP': 0x00180060,
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- 'percentPhaseFieldOfView': 0x00180094,
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- 'xRayTubeCurrent': 0x00181151,
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- 'exposure': 0x00181152,
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- 'imagerPixelSpacing': 0x00181164,
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- 'bodyPartThickness': 0x001811a0,
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- 'compressionForce': 0x001811a2,
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- 'viewPosition': 0x00185101,
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- 'studyInstanceUid': 0x0020000d,
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- 'seriesInstanceUid': 0x0020000e,
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- 'studyId': 0x00200010,
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- 'seriesNumber': 0x00200011,
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- 'instanceNumber': 0x00200013,
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- 'frameOfReferenceInstanceUid': 0x00200052
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- }
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- #new_dict_items={
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- # 0x001811a0: ('DS','BodyPartThickness','Body Part Thickness')
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- #}
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- #dicom.datadict.add_dict_entries(new_dict_items)
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- self.local=False
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- self.useDicomModify=False
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-
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- def enableDicomModify(self):
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- self.useDicomModify=True
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-
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- def setLocal(self,basePath):
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- self.local=True
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- self.basePath=basePath
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-
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-
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- def getHex(self,key):
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- #convert string to hex key;
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- fv=key.split(",")
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- return int(fv[0],16)*0x10000+int(fv[1],16)
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-
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- def load(self,sNet,dir,doRemove=True):
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- #load directory using DICOMLib tools
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-
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- print("Loading dir {}").format(dir)
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- dicomFiles=self.listdir(sNet,dir)
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-
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- filelist=[]
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- for f in dicomFiles:
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- localPath=self.getfile(sNet,f)
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- filelist.append(localPath)
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- if not self.useDicomModify:
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- continue
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- if dicomModify==None:
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- continue
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- f0=localPath
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- f1=f0+"1"
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- try:
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- subprocess.call(\
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- dicomModify+" "+f0+" "+f1+" && mv "+f1+" "+f0+";",
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- shell=True)
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- except OSError:
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- print("dicomModify failed")
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-
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- try:
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- loadables=self.volumePlugin.examineForImport([filelist])
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- except AttributeError:
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- self.volumePlugin=slicer.modules.dicomPlugins['DICOMScalarVolumePlugin']()
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- loadables=self.volumePlugin.examineForImport([filelist])
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-
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-
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- for loadable in loadables:
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- #check if it makes sense to load a particular loadable
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-
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- if loadable.name.find('imageOrientationPatient')>-1:
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- continue
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- filter={}
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- filter['seriesNumber']=None
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- metadata={}
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- if not self.applyFilter(loadable,filter,metadata):
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- continue
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- volumeNode=self.volumePlugin.load(loadable)
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- if volumeNode != None:
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- vName='Series'+metadata['seriesNumber']
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- volumeNode.SetName(vName)
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-
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- try:
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- loadableRTs=self.RTPlugin.examineForImport([filelist])
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- except:
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- self.RTPlugin=plugin=slicer.modules.dicomPlugins['DicomRtImportExportPlugin']()
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- loadableRTs=self.RTPlugin.examineForImport([filelist])
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-
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- for loadable in loadableRTs:
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- segmentationNode=self.RTPlugin.load(loadable)
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-
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- if not doRemove:
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- return
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-
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- for f in filelist:
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- self.removeLocal(f)
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-
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- def applyFilter(self,loadable,filter,nodeMetadata):
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- #apply filter to loadable.file[0]. Return true if file matches prescribed filter and
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- #false otherwise
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-
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- #filter is a directory with keys equal to pre-specified values listed above
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- #if value associated to key equals None, that value gets set in nodeMetadata
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- #if value is set, a match is attempted and result reported in return value
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- #all filters should match for true output
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-
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- return self.applyFilterFile(loadable.files[0],filter,nodeMetadata)
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-
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- def applyFilterFile(self,file,filter,nodeMetadata,shell=False):
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- #apply filter to file. Return true if file matches prescribed filter and
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- #false otherwise
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-
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- #filter is a directory with keys equal to pre-specified values listed above
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- #if value associated to key equals None, that value gets set in nodeMetadata
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- #if value is set, a match is attempted and result reported in return value
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- #all filters should match for true output
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-
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- filterOK=True
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-
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- for key in filter:
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- try:
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- fileValue=dicomValue(file,self.tag[key]['tag'],self.tag[key]['seqTag'],shell=shell)
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- except KeyError:
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- fileValue=dicomValue(file,self.tag[key]['tag'],shell=shell)
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-
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-
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- if filter[key]=="SeriesLabel":
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- nodeMetadata['seriesLabel']=fileValue
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- continue
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-
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- if not filter[key]==None:
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- if not fileValue==filter[key]:
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- #print("File {} failed for tag {}: {}/{}").format(\
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- # file,key,fileValue,filter[key])
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- filterOK=False
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- break
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-
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- nodeMetadata[key]=fileValue
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-
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-
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- return filterOK
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-
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- def listdir(self,sNet,dir):
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- #list remote directory
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- if self.local:
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- dir1=os.path.join(self.basePath,dir)
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- dirs=os.listdir(dir1)
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- return [os.path.join(dir1,f) for f in dirs]
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- return sNet.listRelativeDir(dir)
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-
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- def getfile(self,sNet,file):
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- #get remote file
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- if self.local:
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- return file
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- return sNet.DownloadFileToCache(file)
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-
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- def removeLocal(self,localFile):
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- if self.local:
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- return
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- os.remove(localFile)
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-
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-
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- def loadVolumes(self,sNet,dir,filter,doRemove=True):
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- #returns all series from the directory, each as a separate node in a node list
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- #filter is a dictionary of speciifed dicom values, if filter(key)=None, that values
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- #get set, if it isn't, the file gets checked for a match
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-
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- print("Loading dir {}").format(dir)
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- dicomFiles=self.listdir(sNet,dir)
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- #filelist=[os.path.join(dir,f) for f in os.listdir(dir)]
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- filelist=[]
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- for f in dicomFiles:
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- localPath=self.getfile(sNet,f)
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- f0=localPath
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- f1=f0+"1"
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- if not dicomModify==None:
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- try:
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- subprocess.call(dicomModify+" "+f0+" "+f1+" && mv "+f1+" "+f0+";", shell=False)
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- except OSError:
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- print("dicomModify failed")
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- filelist.append(localPath)
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-
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- try:
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- loadables=self.volumePlugin.examineForImport([filelist])
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- except AttributeError:
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- self.volumePlugin=slicer.modules.dicomPlugins['DICOMScalarVolumePlugin']()
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- loadables=self.volumePlugin.examineForImport([filelist])
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-
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-
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- volumeNodes=[]
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- print("Number of loadables:{}").format(len(loadables))
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- for loadable in loadables:
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- #TODO check if it makes sense to load a particular loadable
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-
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- print("{}: Checking number of files: {}".format(\
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- loadable.name,len(loadable.files)))
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-
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- #perform checks
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- fileMetadata={}
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- loadable.files[:]=[f for f in loadable.files \
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- if self.applyFilterFile(f,filter,fileMetadata)]
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-
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- if len(loadable.files)<1:
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- #skip this loadable
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- continue
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-
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- print("{}: Final number of files: {}".format(\
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- loadable.name,len(loadable.files)))
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-
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- nodeMetadata={}
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- self.applyFilterFile(loadable.files[0],filter,nodeMetadata)
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-
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-
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-
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- volumeNode=self.volumePlugin.load(loadable,"DCMTK")
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- if volumeNode != None:
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- vName='Series'+nodeMetadata['seriesLabel']
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- volumeNode.SetName(vName)
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- volume={'node':volumeNode,'metadata':nodeMetadata}
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- volumeNodes.append(volume)
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-
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- if self.local:
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- return volumeNodes
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|
-
|
|
|
- if doRemove:
|
|
|
- for f in filelist:
|
|
|
- self.removeLocal(f)
|
|
|
-
|
|
|
- return volumeNodes
|
|
|
-
|
|
|
- def loadSegmentations(self,net,dir,filter,doRemove=True):
|
|
|
-
|
|
|
- print("Loading dir {}").format(dir)
|
|
|
- dicomFiles=self.listdir(net,dir)
|
|
|
- filelist=[self.getfile(net,f) for f in dicomFiles]
|
|
|
- segmentationNodes=[]
|
|
|
-
|
|
|
- try:
|
|
|
- loadableRTs=self.RTPlugin.examineForImport([filelist])
|
|
|
- except:
|
|
|
- self.RTPlugin=plugin=slicer.modules.dicomPlugins['DicomRtImportExportPlugin']()
|
|
|
- loadableRTs=self.RTPlugin.examineForImport([filelist])
|
|
|
-
|
|
|
- for loadable in loadableRTs:
|
|
|
-
|
|
|
- nodeMetadata={}
|
|
|
- filterOK=self.applyFilter(loadable,filter,nodeMetadata)
|
|
|
-
|
|
|
- if not filterOK:
|
|
|
- continue
|
|
|
-
|
|
|
- success=self.RTPlugin.load(loadable)
|
|
|
-
|
|
|
- if not success:
|
|
|
- print("Could not load RT structure set")
|
|
|
- return
|
|
|
-
|
|
|
- segNodes=slicer.util.getNodesByClass("vtkMRMLSegmentationNode")
|
|
|
- segmentationNode=segNodes[0]
|
|
|
- #assume we loaded the first node in list
|
|
|
-
|
|
|
- if segmentationNode != None:
|
|
|
- sName='Segmentation'+nodeMetadata['seriesLabel']
|
|
|
- segmentationNode.SetName(sName)
|
|
|
- segmentation={'node':segmentationNode,'metadata':nodeMetadata}
|
|
|
- segmentationNodes.append(segmentation)
|
|
|
-
|
|
|
- if not doRemove:
|
|
|
- return segmentationNodes
|
|
|
-
|
|
|
- for f in filelist:
|
|
|
- self.removeLocal(f)
|
|
|
-
|
|
|
- return segmentationNodes
|
|
|
-
|
|
|
-def isDicom(file):
|
|
|
- #check if file is a dicom file
|
|
|
- try:
|
|
|
- f=open(file,'rb')
|
|
|
- except IOError:
|
|
|
- return False
|
|
|
-
|
|
|
- f.read(128)
|
|
|
- dt=f.read(4)
|
|
|
- f.close()
|
|
|
- return dt=='DICM'
|
|
|
-
|
|
|
-
|
|
|
-def dicomValue(fileName,tag,seqTag=None,shell=False):
|
|
|
- #query dicom value of file using dcmdump (DCMTK routine)
|
|
|
-
|
|
|
- #shell must be false for *nix
|
|
|
- if os.name=="posix":
|
|
|
- shell=False
|
|
|
-
|
|
|
- debug=False
|
|
|
- dcmdump=os.path.join(os.environ['SLICER_HOME'],"bin","dcmdump")
|
|
|
-
|
|
|
- try:
|
|
|
- if debug:
|
|
|
- print("Calling {}".format(dcmdump))
|
|
|
- out=subprocess.check_output([dcmdump,'+p','+P',tag,fileName],shell=shell)
|
|
|
- if debug:
|
|
|
- print("Got {}".format(out))
|
|
|
- except subprocess.CalledProcessError as e:
|
|
|
- return None
|
|
|
-
|
|
|
-
|
|
|
- if debug:
|
|
|
- print("Tag {} Line '{}'").format(tag,out)
|
|
|
- if len(out)==0:
|
|
|
- return out
|
|
|
-
|
|
|
- #parse multi-match outputs which appear as several lines
|
|
|
- lst=out.split('\n')
|
|
|
- return getTagValue(lst,tag,seqTag)
|
|
|
-
|
|
|
-def getTagValue(lst,tag,seqTag=None):
|
|
|
- #report tag value from a list lst of lines reported by dcmdump
|
|
|
-
|
|
|
- debug=False
|
|
|
-
|
|
|
- #parse output
|
|
|
- longTag="^\({}\)".format(tag)
|
|
|
- #combine sequence and actual tags to long tags
|
|
|
- if not seqTag==None:
|
|
|
- if debug:
|
|
|
- print("Tag:{} seqTag:{}").format(tag,seqTag)
|
|
|
- longTag="^\({}\).\({}\)".format(seqTag,tag)
|
|
|
-
|
|
|
- #pick the values
|
|
|
- pattern=r'^.*\[(.*)\].*$'
|
|
|
-
|
|
|
- #extract tag values
|
|
|
- rpl=[re.sub(pattern,r'\1',f) for f in lst]
|
|
|
-
|
|
|
- #logical whether the line can be matched to typical dcmdump output
|
|
|
- mtchPattern=[re.match(pattern,f) for f in lst]
|
|
|
- #find matching tags
|
|
|
- mtchTag=[re.match(longTag,f) for f in lst]
|
|
|
-
|
|
|
- #weed out non-matching lines and lines not matching longTag
|
|
|
- mtch=[None if x==None or y==None else x \
|
|
|
- for x,y in zip(mtchTag,mtchPattern)]
|
|
|
- #set values
|
|
|
- out=[x for y,x in zip(mtch,rpl) if not y==None]
|
|
|
- if len(out)==0:
|
|
|
- return ''
|
|
|
- #return first match
|
|
|
- out=out[0]
|
|
|
-
|
|
|
- if debug:
|
|
|
- print("Tag {} Parsed value {}").format(tag,out)
|
|
|
- #split output to lists if values are DICOM lists
|
|
|
- if out.find('\\')>-1:
|
|
|
- out=out.split('\\')
|
|
|
-
|
|
|
- return out
|
|
|
-
|
|
|
-
|
|
|
-def clearNodes():
|
|
|
- nodes=[]
|
|
|
- nodes.extend(slicer.util.getNodesByClass("vtkMRMLScalarVolumeNode"))
|
|
|
- nodes.extend(slicer.util.getNodesByClass("vtkMRMLScalarVolumeDisplayNode"))
|
|
|
- nodes.extend(slicer.util.getNodesByClass("vtkMRMLSegmentationNode"))
|
|
|
- nodes.extend(slicer.util.getNodesByClass("vtkMRMLSegmentationDisplayNode"))
|
|
|
- for node in nodes:
|
|
|
- slicer.mrmlScene.RemoveNode(node)
|
