def export(self,exportables):
for exportable in exportables:
# Get node to export
node = slicer.mrmlScene.GetNodeByID(exportable.nodeID)
if node.GetAssociatedNode() == None or not node.GetAssociatedNode().IsA('vtkMRMLScalarVolumeNode'):
error = "Series '" + node.GetNameWithoutPostfix() + "' cannot be exported!"
print(error)
return error
# Get output directory and create a subdirectory. This is necessary
# to avoid overwriting the files in case of multiple exportables, as
# naming of the DICOM files is static
directoryDir = qt.QDir(exportable.directory)
directoryDir.mkdir(exportable.nodeID)
directoryDir.cd(exportable.nodeID)
directory = directoryDir.absolutePath()
print("Export scalar volume '" + node.GetAssociatedNode().GetName() + "' to directory " + directory)
# Get study and patient nodes
studyNode = node.GetParentNode()
if studyNode == None:
error = "Unable to get study node for series '" + node.GetAssociatedNode().GetName() + "'"
print(error)
return error
patientNode = studyNode.GetParentNode()
if patientNode == None:
error = "Unable to get patient node for series '" + node.GetAssociatedNode().GetName() + "'"
print(error)
return error
# Assemble tags dictionary for volume export
from vtkSlicerSubjectHierarchyModuleMRMLPython import vtkMRMLSubjectHierarchyConstants
tags = {}
tags['Patient Name'] = exportable.tag(vtkMRMLSubjectHierarchyConstants.GetDICOMPatientNameTagName())
tags['Patient ID'] = exportable.tag(vtkMRMLSubjectHierarchyConstants.GetDICOMPatientIDTagName())
tags['Patient Comments'] = exportable.tag(vtkMRMLSubjectHierarchyConstants.GetDICOMPatientCommentsTagName())
tags['Study ID'] = self.defaultStudyID
tags['Study Date'] = exportable.tag(vtkMRMLSubjectHierarchyConstants.GetDICOMStudyDateTagName())
tags['Study Description'] = exportable.tag(vtkMRMLSubjectHierarchyConstants.GetDICOMStudyDescriptionTagName())
tags['Modality'] = exportable.tag('Modality')
tags['Manufacturer'] = exportable.tag('Manufacturer')
tags['Model'] = exportable.tag('Model')
tags['Series Description'] = exportable.tag('SeriesDescription')
tags['Series Number'] = exportable.tag('SeriesNumber')
# Validate tags
if tags['Modality'] == "":
error = "Empty modality for series '" + node.GetAssociatedNode().GetName() + "'"
print(error)
return error
#TODO: more tag checks
# Perform export
exporter = DICOMExportScalarVolume(tags['Study ID'], node.GetAssociatedNode(), tags, directory)
exporter.export()
# Success
return ""
def export(self,exportables):
for exportable in exportables:
# Get node to export
node = slicer.mrmlScene.GetNodeByID(exportable.nodeID)
if node.GetAssociatedNode() is None or not node.GetAssociatedNode().IsA('vtkMRMLScalarVolumeNode'):
error = "Series '" + node.GetNameWithoutPostfix() + "' cannot be exported!"
logging.error(error)
return error
# Get output directory and create a subdirectory. This is necessary
# to avoid overwriting the files in case of multiple exportables, as
# naming of the DICOM files is static
directoryDir = qt.QDir(exportable.directory)
directoryDir.mkdir(exportable.nodeID)
directoryDir.cd(exportable.nodeID)
directory = directoryDir.absolutePath()
logging.info("Export scalar volume '" + node.GetAssociatedNode().GetName() + "' to directory " + directory)
# Get study and patient nodes
studyNode = node.GetParentNode()
if studyNode is None:
error = "Unable to get study node for series '" + node.GetAssociatedNode().GetName() + "'"
logging.error(error)
return error
patientNode = studyNode.GetParentNode()
if patientNode is None:
error = "Unable to get patient node for series '" + node.GetAssociatedNode().GetName() + "'"
logging.error(error)
return error
# Assemble tags dictionary for volume export
tags = {}
tags['Patient Name'] = exportable.tag(slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMPatientNameTagName())
tags['Patient ID'] = exportable.tag(slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMPatientIDTagName())
tags['Patient Comments'] = exportable.tag(slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMPatientCommentsTagName())
tags['Study ID'] = self.defaultStudyID
tags['Study Date'] = exportable.tag(slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMStudyDateTagName())
tags['Study Description'] = exportable.tag(slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMStudyDescriptionTagName())
tags['Modality'] = exportable.tag('Modality')
tags['Manufacturer'] = exportable.tag('Manufacturer')
tags['Model'] = exportable.tag('Model')
tags['Series Description'] = exportable.tag('SeriesDescription')
tags['Series Number'] = exportable.tag('SeriesNumber')
# Validate tags
if tags['Modality'] == "":
error = "Empty modality for series '" + node.GetAssociatedNode().GetName() + "'"
logging.error(error)
return error
#TODO: more tag checks
# Perform export
exporter = DICOMExportScalarVolume(tags['Study ID'], node.GetAssociatedNode(), tags, directory)
exporter.export()
# Success
return ""
def export(self, exportables):
for exportable in exportables:
# Get volume node to export
shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(
slicer.mrmlScene)
if shNode is None:
error = "Invalid subject hierarchy"
logging.error(error)
return error
volumeNode = shNode.GetItemDataNode(
exportable.subjectHierarchyItemID)
if volumeNode is None or not volumeNode.IsA(
'vtkMRMLScalarVolumeNode'):
error = "Series '" + shNode.GetItemName(
exportable.subjectHierarchyItemID
) + "' cannot be exported as volume sequence"
logging.error(error)
return error
sequenceBrowserNode = self.getSequenceBrowserNodeForMasterOutputNode(
volumeNode)
if not sequenceBrowserNode:
error = "Series '" + shNode.GetItemName(
exportable.subjectHierarchyItemID
) + "' cannot be exported as volume sequence"
logging.error(error)
return error
volumeSequenceNode = sequenceBrowserNode.GetSequenceNode(
volumeNode)
if not volumeSequenceNode:
error = "Series '" + shNode.GetItemName(
exportable.subjectHierarchyItemID
) + "' cannot be exported as volume sequence"
logging.error(error)
return error
# Get study and patient items
studyItemID = shNode.GetItemParent(
exportable.subjectHierarchyItemID)
if not studyItemID:
error = "Unable to get study for series '" + volumeNode.GetName(
) + "'"
logging.error(error)
return error
patientItemID = shNode.GetItemParent(studyItemID)
if not patientItemID:
error = "Unable to get patient for series '" + volumeNode.GetName(
) + "'"
logging.error(error)
return error
# Assemble tags dictionary for volume export
tags = {}
tags['Patient Name'] = exportable.tag(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMPatientNameTagName())
tags['Patient ID'] = exportable.tag(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMPatientIDTagName())
tags['Patient Comments'] = exportable.tag(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMPatientCommentsTagName())
if slicer.app.majorVersion >= 5 or (slicer.app.majorVersion == 4
and
slicer.app.minorVersion >= 11):
tags['Study Instance UID'] = pydicom.uid.generate_uid()
else:
tags['Study Instance UID'] = dicom.UID.generate_uid()
tags['Study ID'] = exportable.tag(
slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMStudyIDTagName(
))
tags['Study Date'] = exportable.tag(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMStudyDateTagName())
tags['Study Time'] = exportable.tag(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMStudyTimeTagName())
tags['Study Description'] = exportable.tag(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMStudyDescriptionTagName())
tags['Modality'] = exportable.tag('Modality')
tags['Manufacturer'] = exportable.tag('Manufacturer')
tags['Model'] = exportable.tag('Model')
tags['Series Description'] = exportable.tag('SeriesDescription')
tags['Series Number'] = exportable.tag('SeriesNumber')
tags['Series Date'] = exportable.tag("SeriesDate")
tags['Series Time'] = exportable.tag("SeriesTime")
if slicer.app.majorVersion >= 5 or (slicer.app.majorVersion == 4
and
slicer.app.minorVersion >= 11):
tags['Series Instance UID'] = pydicom.uid.generate_uid()
tags[
'Frame of Reference Instance UID'] = pydicom.uid.generate_uid(
)
else:
tags['Series Instance UID'] = dicom.UID.generate_uid()
tags[
'Frame of Reference Instance UID'] = dicom.UID.generate_uid(
)
# Validate tags
if tags['Modality'] == "":
error = "Empty modality for series '" + volumeNode.GetName(
) + "'"
logging.error(error)
return error
#TODO: more tag checks
sequenceItemCount = sequenceBrowserNode.GetMasterSequenceNode(
).GetNumberOfDataNodes()
originalSelectedSequenceItemNumber = sequenceBrowserNode.GetSelectedItemNumber(
)
masterVolumeNode = sequenceBrowserNode.GetMasterSequenceNode()
# initialize content datetime from series datetime
contentStartDate = exportable.tag("SeriesDate")
contentStartTime = exportable.tag("SeriesTime")
import datetime
datetimeNow = datetime.datetime.now()
if not contentStartDate:
contentStartDate = datetimeNow.strftime("%Y%m%d")
if not contentStartTime:
contentStartTime = datetimeNow.strftime("%H%M%S.%f")
contentStartDatetime = self.datetimeFromDicom(
contentStartDate, contentStartTime)
# Get output directory and create a subdirectory. This is necessary
# to avoid overwriting the files in case of multiple exportables, as
# naming of the DICOM files is static
directoryName = 'VolumeSequence_' + str(
exportable.subjectHierarchyItemID)
directoryDir = qt.QDir(exportable.directory)
directoryDir.mkdir(directoryName)
directoryDir.cd(directoryName)
directory = directoryDir.absolutePath()
logging.info("Export scalar volume '" + volumeNode.GetName() +
"' to directory " + directory)
for sequenceItemIndex in range(sequenceItemCount):
# Switch to next item in the series
sequenceBrowserNode.SetSelectedItemNumber(sequenceItemIndex)
slicer.app.processEvents()
# Compute content date&time
# TODO: verify that unit in sequence node is "second" (and convert to seconds if not)
timeOffsetSec = float(
masterVolumeNode.GetNthIndexValue(sequenceItemIndex)
) - float(masterVolumeNode.GetNthIndexValue(0))
contentDatetime = contentStartDatetime + datetime.timedelta(
seconds=timeOffsetSec)
tags['Content Date'] = contentDatetime.strftime("%Y%m%d")
tags['Content Time'] = contentDatetime.strftime("%H%M%S.%f")
# Perform export
filenamePrefix = f"IMG_{sequenceItemIndex:04d}_"
exporter = DICOMExportScalarVolume(tags['Study ID'],
volumeNode, tags, directory,
filenamePrefix)
exporter.export()
# Success
return ""
def export(self, exportables):
for exportable in exportables:
# Get volume node to export
shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(
slicer.mrmlScene)
if shNode is None:
error = "Invalid subject hierarchy"
logging.error(error)
return error
volumeNode = shNode.GetItemDataNode(
exportable.subjectHierarchyItemID)
if volumeNode is None or not volumeNode.IsA(
'vtkMRMLScalarVolumeNode'):
error = "Series '" + shNode.GetItemName(
exportable.subjectHierarchyItemID) + "' cannot be exported"
logging.error(error)
return error
# Get output directory and create a subdirectory. This is necessary
# to avoid overwriting the files in case of multiple exportables, as
# naming of the DICOM files is static
directoryName = 'ScalarVolume_' + str(
exportable.subjectHierarchyItemID)
directoryDir = qt.QDir(exportable.directory)
directoryDir.mkdir(directoryName)
directoryDir.cd(directoryName)
directory = directoryDir.absolutePath()
logging.info("Export scalar volume '" + volumeNode.GetName() +
"' to directory " + directory)
# Get study and patient items
studyItemID = shNode.GetItemParent(
exportable.subjectHierarchyItemID)
if not studyItemID:
error = "Unable to get study for series '" + volumeNode.GetName(
) + "'"
logging.error(error)
return error
patientItemID = shNode.GetItemParent(studyItemID)
if not patientItemID:
error = "Unable to get patient for series '" + volumeNode.GetName(
) + "'"
logging.error(error)
return error
# Assemble tags dictionary for volume export
tags = {}
tags['Patient Name'] = exportable.tag(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMPatientNameTagName())
tags['Patient ID'] = exportable.tag(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMPatientIDTagName())
tags['Patient Comments'] = exportable.tag(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMPatientCommentsTagName())
tags['Study ID'] = self.defaultStudyID
tags['Study Date'] = exportable.tag(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMStudyDateTagName())
tags['Study Time'] = exportable.tag(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMStudyTimeTagName())
tags['Study Description'] = exportable.tag(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMStudyDescriptionTagName())
tags['Modality'] = exportable.tag('Modality')
tags['Manufacturer'] = exportable.tag('Manufacturer')
tags['Model'] = exportable.tag('Model')
tags['Series Description'] = exportable.tag('SeriesDescription')
tags['Series Number'] = exportable.tag('SeriesNumber')
tags['Series Date'] = exportable.tag('SeriesDate')
tags['Series Time'] = exportable.tag('SeriesTime')
tags['Content Date'] = exportable.tag('ContentDate')
tags['Content Time'] = exportable.tag('ContentTime')
tags['Study Instance UID'] = exportable.tag('StudyInstanceUID')
tags['Series Instance UID'] = exportable.tag('SeriesInstanceUID')
tags['Frame of Reference Instance UID'] = exportable.tag(
'FrameOfReferenceInstanceUID')
# Validate tags
if tags['Modality'] == "":
error = "Empty modality for series '" + volumeNode.GetName(
) + "'"
logging.error(error)
return error
#TODO: more tag checks
# Perform export
exporter = DICOMExportScalarVolume(tags['Study ID'], volumeNode,
tags, directory)
exporter.export()
# Success
return ""
def export(self,exportables):
for exportable in exportables:
# Get volume node to export
shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)
if shNode is None:
error = "Invalid subject hierarchy"
logging.error(error)
return error
volumeNode = shNode.GetItemDataNode(exportable.subjectHierarchyItemID)
if volumeNode is None or not volumeNode.IsA('vtkMRMLScalarVolumeNode'):
error = "Series '" + shNode.GetItemName(exportable.subjectHierarchyItemID) + "' cannot be exported"
logging.error(error)
return error
# Get output directory and create a subdirectory. This is necessary
# to avoid overwriting the files in case of multiple exportables, as
# naming of the DICOM files is static
directoryName = 'ScalarVolume_' + str(exportable.subjectHierarchyItemID)
directoryDir = qt.QDir(exportable.directory)
directoryDir.mkdir(directoryName)
directoryDir.cd(directoryName)
directory = directoryDir.absolutePath()
logging.info("Export scalar volume '" + volumeNode.GetName() + "' to directory " + directory)
# Get study and patient items
studyItemID = shNode.GetItemParent(exportable.subjectHierarchyItemID)
if not studyItemID:
error = "Unable to get study for series '" + volumeNode.GetName() + "'"
logging.error(error)
return error
patientItemID = shNode.GetItemParent(studyItemID)
if not patientItemID:
error = "Unable to get patient for series '" + volumeNode.GetName() + "'"
logging.error(error)
return error
# Assemble tags dictionary for volume export
tags = {}
tags['Patient Name'] = exportable.tag(slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMPatientNameTagName())
tags['Patient ID'] = exportable.tag(slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMPatientIDTagName())
tags['Patient Comments'] = exportable.tag(slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMPatientCommentsTagName())
tags['Study ID'] = self.defaultStudyID
tags['Study Date'] = exportable.tag(slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMStudyDateTagName())
tags['Study Time'] = exportable.tag(slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMStudyTimeTagName())
tags['Study Description'] = exportable.tag(slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMStudyDescriptionTagName())
tags['Modality'] = exportable.tag('Modality')
tags['Manufacturer'] = exportable.tag('Manufacturer')
tags['Model'] = exportable.tag('Model')
tags['Series Description'] = exportable.tag('SeriesDescription')
tags['Series Number'] = exportable.tag('SeriesNumber')
tags['Series Date'] = exportable.tag('SeriesDate')
tags['Series Time'] = exportable.tag('SeriesTime')
tags['Content Date'] = exportable.tag('ContentDate')
tags['Content Time'] = exportable.tag('ContentTime')
tags['Study Instance UID'] = exportable.tag('StudyInstanceUID')
tags['Series Instance UID'] = exportable.tag('SeriesInstanceUID')
tags['Frame of Reference Instance UID'] = exportable.tag('FrameOfReferenceInstanceUID')
# Validate tags
if tags['Modality'] == "":
error = "Empty modality for series '" + volumeNode.GetName() + "'"
logging.error(error)
return error
#TODO: more tag checks
# Perform export
exporter = DICOMExportScalarVolume(tags['Study ID'], volumeNode, tags, directory)
exporter.export()
# Success
return ""
def export(self, exportables):
for exportable in exportables:
# Get volume node to export
shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(
slicer.mrmlScene)
if shNode is None:
error = "Invalid subject hierarchy"
logging.error(error)
return error
volumeNode = shNode.GetItemDataNode(
exportable.subjectHierarchyItemID)
if volumeNode is None or not volumeNode.IsA(
'vtkMRMLScalarVolumeNode'):
error = "Series '" + shNode.GetItemName(
exportable.subjectHierarchyItemID) + "' cannot be exported"
logging.error(error)
return error
# Get output directory and create a subdirectory. This is necessary
# to avoid overwriting the files in case of multiple exportables, as
# naming of the DICOM files is static
directoryName = 'ScalarVolume_' + str(
exportable.subjectHierarchyItemID)
directoryDir = qt.QDir(exportable.directory)
directoryDir.mkpath(directoryName)
directoryDir.cd(directoryName)
directory = directoryDir.absolutePath()
logging.info("Export scalar volume '" + volumeNode.GetName() +
"' to directory " + directory)
# Get study and patient items
studyItemID = shNode.GetItemParent(
exportable.subjectHierarchyItemID)
if not studyItemID:
error = "Unable to get study for series '" + volumeNode.GetName(
) + "'"
logging.error(error)
return error
patientItemID = shNode.GetItemParent(studyItemID)
if not patientItemID:
error = "Unable to get patient for series '" + volumeNode.GetName(
) + "'"
logging.error(error)
return error
# Assemble tags dictionary for volume export
tags = {}
tags['Patient Name'] = exportable.tag(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMPatientNameTagName())
tags['Patient ID'] = exportable.tag(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMPatientIDTagName())
tags['Patient Birth Date'] = exportable.tag(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMPatientBirthDateTagName())
tags['Patient Sex'] = exportable.tag(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMPatientSexTagName())
tags['Patient Comments'] = exportable.tag(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMPatientCommentsTagName())
tags['Study ID'] = exportable.tag(
slicer.vtkMRMLSubjectHierarchyConstants.GetDICOMStudyIDTagName(
))
tags['Study Date'] = exportable.tag(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMStudyDateTagName())
tags['Study Time'] = exportable.tag(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMStudyTimeTagName())
tags['Study Description'] = exportable.tag(
slicer.vtkMRMLSubjectHierarchyConstants.
GetDICOMStudyDescriptionTagName())
tags['Modality'] = exportable.tag('Modality')
tags['Manufacturer'] = exportable.tag('Manufacturer')
tags['Model'] = exportable.tag('Model')
tags['Series Description'] = exportable.tag('SeriesDescription')
tags['Series Number'] = exportable.tag('SeriesNumber')
tags['Series Date'] = exportable.tag('SeriesDate')
tags['Series Time'] = exportable.tag('SeriesTime')
tags['Content Date'] = exportable.tag('ContentDate')
tags['Content Time'] = exportable.tag('ContentTime')
tags['Study Instance UID'] = exportable.tag('StudyInstanceUID')
tags['Series Instance UID'] = exportable.tag('SeriesInstanceUID')
tags['Frame of Reference UID'] = exportable.tag(
'FrameOfReferenceUID')
# Generate any missing but required UIDs
if not tags['Study Instance UID']:
import pydicom as dicom
tags['Study Instance UID'] = dicom.uid.generate_uid()
if not tags['Series Instance UID']:
import pydicom as dicom
tags['Series Instance UID'] = dicom.uid.generate_uid()
if not tags['Frame of Reference UID']:
import pydicom as dicom
tags['Frame of Reference UID'] = dicom.uid.generate_uid()
# Use the default Study ID if none is specified
if not tags['Study ID']:
tags['Study ID'] = self.defaultStudyID
# Validate tags
if tags['Modality'] == "":
error = "Empty modality for series '" + volumeNode.GetName(
) + "'"
logging.error(error)
return error
seriesInstanceUID = tags['Series Instance UID']
if seriesInstanceUID:
# Make sure we don't use a series instance UID that already exists (it would mix in more slices into an existing series,
# which is very unlikely that users would want).
db = slicer.dicomDatabase
studyInstanceUID = db.studyForSeries(seriesInstanceUID)
if studyInstanceUID:
# This seriesInstanceUID is already found in the database
if len(seriesInstanceUID) > 25:
seriesInstanceUID = seriesInstanceUID[:20] + "..."
error = f"A series already exists in the database by SeriesInstanceUID {seriesInstanceUID}."
logging.error(error)
return error
# TODO: more tag checks
# Perform export
exporter = DICOMExportScalarVolume(tags['Study ID'], volumeNode,
tags, directory)
if not exporter.export():
return "Creating DICOM files from scalar volume failed. See the application log for details."
# Success
return ""
