def examineFiles(self, files):
loadables = []
for currentFile in files:
dataset = pydicom.read_file(currentFile)
uid = self.getDICOMValue(dataset, "SOPInstanceUID")
if uid == "":
return []
seriesDescription = self.getDICOMValue(dataset,
"SeriesDescription",
"Unknown")
if self.isQIICRX(dataset):
loadable = DICOMLoadable()
loadable.selected = True
loadable.confidence = 0.95
loadable.files = [currentFile]
loadable.name = '{} - as a DICOM {} object'.format(
seriesDescription, self.TEMPLATE_ID)
loadable.tooltip = loadable.name
loadable.selected = True
loadable.confidence = 0.95
loadable.uids = [uid]
loadables.append(loadable)
logging.debug('DICOM SR {} modality found'.format(
self.TEMPLATE_ID))
return loadables
def examineFiles(self,files):
""" Returns a list of DICOMLoadable instances
corresponding to ways of interpreting the
files parameter.
Look for the special private creator tags that indicate
a slicer data bundle
Note that each data bundle is in a unique series, so
if 'files' is a list of more than one element, then this
is not a data bundle.
"""
loadables = []
if len(files) == 1:
f = files[0]
# get the series description to use as base for volume name
name = slicer.dicomDatabase.fileValue(f, self.tags['seriesDescription'])
if name == "":
name = "Unknown"
candygramValue = slicer.dicomDatabase.fileValue(f, self.tags['candygram'])
if candygramValue:
# default loadable includes all files for series
loadable = DICOMLoadable()
loadable.files = [f]
loadable.name = name + ' - as Slicer Scene'
loadable.selected = True
loadable.tooltip = 'Appears to contain a slicer scene'
loadables.append(loadable)
return loadables
def examineFiles(self, files):
""" Returns a list of DICOMLoadable instances
corresponding to ways of interpreting the
files parameter.
"""
self.detailedLogging = slicer.util.settingsValue('DICOM/detailedLogging', False, converter=slicer.util.toBool)
supportedSOPClassUIDs = [
'1.2.840.10008.5.1.4.1.1.6.2', # Enhanced US Volume Storage
]
# The only sample data set that we received from GE LOGIQE10 (software version R1.5.1).
# It added all volumes into a single series, even though they were acquired minutes apart.
# Therefore, instead of loading the volumes into a sequence, we load each as a separate volume.
loadables = []
for filePath in files:
# Quick check of SOP class UID without parsing the file...
sopClassUID = slicer.dicomDatabase.fileValue(filePath, self.tags['sopClassUID'])
if not (sopClassUID in supportedSOPClassUIDs):
# Unsupported class
continue
instanceNumber = slicer.dicomDatabase.fileValue(filePath, self.tags['instanceNumber'])
modality = slicer.dicomDatabase.fileValue(filePath, self.tags['modality'])
seriesNumber = slicer.dicomDatabase.fileValue(filePath, self.tags['seriesNumber'])
seriesDescription = slicer.dicomDatabase.fileValue(filePath, self.tags['seriesDescription'])
photometricInterpretation = slicer.dicomDatabase.fileValue(filePath, self.tags['photometricInterpretation'])
name = ''
if seriesNumber:
name = f'{seriesNumber}:'
if modality:
name = f'{name} {modality}'
if seriesDescription:
name = f'{name} {seriesDescription}'
else:
name = f'{name} volume'
if instanceNumber:
name = f'{name} [{instanceNumber}]'
loadable = DICOMLoadable()
loadable.singleSequence = False # put each instance in a separate sequence
loadable.files = [filePath]
loadable.name = name.strip() # remove leading and trailing spaces, if any
loadable.warning = "Loading of this image type is experimental. Please verify image geometry and report any problem is found."
loadable.tooltip = f"Ultrasound volume"
loadable.selected = True
# Confidence is slightly larger than default scalar volume plugin's (0.5)
# and DICOMVolumeSequencePlugin (0.7)
# but still leaving room for more specialized plugins.
loadable.confidence = 0.8
loadable.grayscale = ('MONOCHROME' in photometricInterpretation)
loadables.append(loadable)
return loadables
def createLoadableAndAddReferences(self, datasets):
loadable = DICOMLoadable()
loadable.selected = True
loadable.confidence = 0.95
loadable.referencedSegInstanceUIDs = []
# store lists of UIDs separately to avoid re-parsing later
loadable.ReferencedSegmentationInstanceUIDs = {}
loadable.ReferencedRWVMSeriesInstanceUIDs = []
loadable.ReferencedOtherInstanceUIDs = []
loadable.referencedInstanceUIDs = []
segPlugin = slicer.modules.dicomPlugins["DICOMSegmentationPlugin"]()
for dataset in datasets:
uid = self.getDICOMValue(dataset, "SOPInstanceUID")
loadable.ReferencedSegmentationInstanceUIDs[uid] = []
if hasattr(dataset, "CurrentRequestedProcedureEvidenceSequence"):
for refSeriesSequence in dataset.CurrentRequestedProcedureEvidenceSequence:
for referencedSeriesSequence in refSeriesSequence.ReferencedSeriesSequence:
for refSOPSequence in referencedSeriesSequence.ReferencedSOPSequence:
if refSOPSequence.ReferencedSOPClassUID == self.UID_SegmentationStorage:
logging.debug("Found referenced segmentation")
loadable.ReferencedSegmentationInstanceUIDs[uid].append(referencedSeriesSequence.SeriesInstanceUID)
elif refSOPSequence.ReferencedSOPClassUID == self.UID_RealWorldValueMappingStorage: # handle SUV mapping
logging.debug("Found referenced RWVM")
loadable.ReferencedRWVMSeriesInstanceUIDs.append(referencedSeriesSequence.SeriesInstanceUID)
else:
# TODO: those are not used at all
logging.debug( "Found other reference")
loadable.ReferencedOtherInstanceUIDs.append(refSOPSequence.ReferencedSOPInstanceUID)
for segSeriesInstanceUID in loadable.ReferencedSegmentationInstanceUIDs[uid]:
segLoadables = segPlugin.examine([slicer.dicomDatabase.filesForSeries(segSeriesInstanceUID)])
for segLoadable in segLoadables:
loadable.referencedInstanceUIDs += segLoadable.referencedInstanceUIDs
loadable.referencedInstanceUIDs = list(set(loadable.referencedInstanceUIDs))
if len(loadable.ReferencedSegmentationInstanceUIDs[uid])>1:
logging.warning("SR references more than one SEG. This has not been tested!")
for segUID in loadable.ReferencedSegmentationInstanceUIDs:
loadable.referencedSegInstanceUIDs.append(segUID)
if len(loadable.ReferencedRWVMSeriesInstanceUIDs)>1:
logging.warning("SR references more than one RWVM. This has not been tested!")
# not adding RWVM instances to referencedSeriesInstanceUIDs
return loadable
def examineFiles(self, files):
""" Returns a list of DICOMLoadable instances
corresponding to ways of interpreting the
files parameter.
"""
loadables = []
# just read the modality type; need to go to reporting logic, since DCMTK
# is not wrapped ...
for file in files:
uid = slicer.dicomDatabase.fileValue(file,
self.tags['instanceUID'])
if uid == '':
return []
desc = slicer.dicomDatabase.fileValue(
file, self.tags['seriesDescription'])
if desc == "":
name = "Unknown"
number = slicer.dicomDatabase.fileValue(file,
self.tags['seriesNumber'])
if number == '':
number = "Unknown"
reportingLogic = None
reportingLogic = slicer.modules.reporting.logic()
isDicomSeg = (slicer.dicomDatabase.fileValue(
file, self.tags['modality']) == 'SEG')
if isDicomSeg:
loadable = DICOMLoadable()
loadable.files = [file]
loadable.name = desc + ' - as a DICOM SEG object'
loadable.tooltip = loadable.name
loadable.selected = True
loadable.confidence = 0.95
loadable.uid = uid
self.addReferences(loadable)
refName = self.referencedSeriesName(loadable)
if refName != "":
loadable.name = refName + " " + desc + " - Segmentations"
loadables.append(loadable)
print('DICOM SEG modality found')
return loadables
def examineFiles(self, files):
""" Returns a list of DICOMLoadable instances
corresponding to ways of interpreting the
files parameter.
Look for the special private creator tags that indicate
a slicer data bundle
Note that each data bundle is in a unique series, so
if 'files' is a list of more than one element, then this
is not a data bundle.
"""
loadables = []
if len(files) == 1:
f = files[0]
# get the series description to use as base for volume name
name = slicer.dicomDatabase.fileValue(f, self.tags['seriesDescription'])
if name == "":
name = "Unknown"
candygramValue = slicer.dicomDatabase.fileValue(f, self.tags['candygram'])
if candygramValue:
# default loadable includes all files for series
loadable = DICOMLoadable()
loadable.files = [f]
loadable.name = name + ' - as Slicer Scene'
loadable.selected = True
loadable.tooltip = 'Contains a Slicer scene'
loadable.confidence = 0.9
loadables.append(loadable)
return loadables
def createLoadableAndAddReferences(self, dataset):
loadable = DICOMLoadable()
loadable.selected = True
loadable.confidence = 0.95
if hasattr(dataset, "CurrentRequestedProcedureEvidenceSequence"):
loadable.referencedSeriesInstanceUIDs = []
loadable.referencedSOPInstanceUIDs = []
for refSeriesSequence in dataset.CurrentRequestedProcedureEvidenceSequence:
for referencedSeriesSequence in refSeriesSequence.ReferencedSeriesSequence:
for refSOPSequence in referencedSeriesSequence.ReferencedSOPSequence:
if refSOPSequence.ReferencedSOPClassUID == self.UID_SegmentationStorage: # TODO: differentiate between SR, SEG and other volumes
logging.debug("Found referenced segmentation")
loadable.referencedSeriesInstanceUIDs.append(referencedSeriesSequence.SeriesInstanceUID)
else:
logging.debug( "Found other reference")
for sopInstanceUID in slicer.dicomDatabase.fileForInstance(refSOPSequence.ReferencedSOPInstanceUID):
loadable.referencedSOPInstanceUIDs.append(sopInstanceUID)
# loadable.referencedSOPInstanceUID = refSOPSequence.ReferencedSOPInstanceUID
return loadable
def examineFiles(self, files):
""" Returns a list of DICOMLoadable instances
corresponding to ways of interpreting the
files parameter.
Process is to look for 'known' private tags corresponding
to the types of diffusion datasets that the DWIConvert utility
should be able to process. We look at the first three
headers because some vendors don't write gradient information
in the B0.
For testing:
dv = slicer.modules.dicomPlugins['DICOMDiffusionVolumePlugin']()
dv.examineForImport([['/media/extra650/data/DWI-examples/SiemensTrioTimB17-DWI/63000-000025-000001.dcm']])
"""
# get the series description to use as base for volume name
name = slicer.dicomDatabase.fileValue(files[0],
self.tags['seriesDescription'])
if name == "":
name = "Unknown"
validDWI = False
loadables = []
# The only valid modality is MR
modality = slicer.dicomDatabase.fileValue(files[0],
self.tags['modality'])
if (modality.upper() != "MR"):
return loadables
vendorName = ""
matchingVendors = []
for vendor in self.diffusionTags:
for tag in self.diffusionTags[vendor]:
# Check the first three files because some tags may
# not be present in the b0 image (e.g. for Siemens)
for i in range(0, 3 if (len(files) > 2) else len(files)):
value = slicer.dicomDatabase.fileValue(files[i], tag)
hasTag = value != ""
if hasTag and not vendor in matchingVendors:
matchingVendors.append(vendor)
if len(matchingVendors) > 0:
validDWI = True
if validDWI:
# default loadable includes all files for series
loadable = DICOMLoadable()
loadable.files = files
loadable.name = name + ' - as DWI Volume'
loadable.selected = True
loadable.tooltip = "Matches DICOM tags for the following vendor(s): %s" % (
", ".join(matchingVendors))
loadable.confidence = 0.6
loadables = [loadable]
return loadables
def examine(self,fileLists):
""" Returns a list of DICOMLoadable instances
corresponding to ways of interpreting the
fileLists parameter.
"""
petCtStudies = self.__scanForValidPETCTStudies(fileLists)
mainLoadable = DICOMLoadable()
mainLoadable.tooltip = "PET/CT Studies for Longitudinal PET/CT Report"
studyplrlsing = "Studies" if len(petCtStudies) != 1 else "Study"
mainLoadable.name = str(len(petCtStudies))+" PET/CT "+ studyplrlsing
mainLoadable.selected = True
mainLoadable.confidence = 1.0
petImageSeries = 0
ctImageSeries = 0
for fileList in fileLists:
petSeries = self.__getSeriesInformation(fileList, self.tags['seriesModality']) == self.petTerm
ctSeries = self.__getSeriesInformation(fileList, self.tags['seriesModality']) == self.ctTerm
fromPetCtStudy = self.__getSeriesInformation(fileList, self.tags['studyInstanceUID']) in petCtStudies
if (petSeries | ctSeries) & fromPetCtStudy:
loadables = self.getCachedLoadables(fileList)
if not loadables:
loadables = self.scalarVolumePlugin.examineFiles(fileList)
self.cacheLoadables(fileList, loadables)
for ldbl in loadables:
if ldbl.selected:
imageType = ""
if petSeries:
petImageSeries += 1
imageType = "PT"
elif ctSeries:
ctImageSeries += 1
imageType = "CT"
mainLoadable.files += ldbl.files
ldbl.name = imageType +"_"+self.__getSeriesInformation(ldbl.files, self.tags['studyDate'])+"_"+self.__getSeriesInformation(ldbl.files, self.tags['seriesTime'])
self.cacheLoadables(ldbl.files, [ldbl])
if ldbl.warning:
mainLoadable.warning += ldbl.warning +" "
break # break for loop because only one loadable needed
loadables = []
if mainLoadable.files:
mainLoadable.name = mainLoadable.name + " containing " + str(petImageSeries) + " PET and " + str(ctImageSeries) + " CT image series"
loadables = [mainLoadable]
return loadables
def examineFiles(self, files):
""" Returns a list of DICOMLoadable instances
corresponding to ways of interpreting the
files parameter.
"""
loadables = []
# just read the modality type; need to go to reporting logic, since DCMTK
# is not wrapped ...
for cFile in files:
uid = slicer.dicomDatabase.fileValue(cFile,
self.tags['instanceUID'])
if uid == '':
return []
desc = slicer.dicomDatabase.fileValue(
cFile, self.tags['seriesDescription'])
if desc == '':
desc = "Unknown"
isDicomPM = (slicer.dicomDatabase.fileValue(
cFile, self.tags['classUID']) == '1.2.840.10008.5.1.4.1.1.30')
if isDicomPM:
loadable = DICOMLoadable()
loadable.files = [cFile]
loadable.name = desc + ' - as a DICOM Parametric Map object'
loadable.tooltip = loadable.name
loadable.selected = True
loadable.confidence = 0.95
loadable.uid = uid
self.addReferences(loadable)
refName = self.referencedSeriesName(loadable)
if refName != "":
loadable.name = refName + " " + desc + " - ParametricMap"
loadables.append(loadable)
logging.debug('DICOM Parametric Map found')
return loadables
def examineFiles(self,files):
""" Returns a list of DICOMLoadable instances
corresponding to ways of interpreting the
files parameter.
"""
loadables = []
# just read the modality type; need to go to reporting logic, since DCMTK
# is not wrapped ...
for file in files:
uid = slicer.dicomDatabase.fileValue(file, self.tags['instanceUID'])
if uid == '':
return []
desc = slicer.dicomDatabase.fileValue(file, self.tags['seriesDescription'])
if desc == "":
name = "Unknown"
number = slicer.dicomDatabase.fileValue(file, self.tags['seriesNumber'])
if number == '':
number = "Unknown"
isDicomSeg = (slicer.dicomDatabase.fileValue(file, self.tags['modality']) == 'SEG')
if isDicomSeg:
loadable = DICOMLoadable()
loadable.files = [file]
loadable.name = desc + ' - as a DICOM SEG object'
loadable.tooltip = loadable.name
loadable.selected = True
loadable.confidence = 0.95
loadable.uid = uid
self.addReferences(loadable)
refName = self.referencedSeriesName(loadable)
if refName != "":
loadable.name = refName + " " + desc + " - Segmentations"
loadables.append(loadable)
print('DICOM SEG modality found')
return loadables
def examineFiles(self, files):
""" Returns a list of DICOMLoadable instances
corresponding to ways of interpreting the
files parameter.
Process is to look for 'known' private tags corresponding
to the types of diffusion datasets that the DicomToNrrd utility
should be able to process. Only need to look at one header
in the series since all should be the same with respect
to this check.
For testing:
dv = slicer.modules.dicomPlugins['DICOMDiffusionVolumePlugin']()
dv.examineForImport([['/media/extra650/data/DWI-examples/SiemensTrioTimB17-DWI/63000-000025-000001.dcm']])
"""
# get the series description to use as base for volume name
name = slicer.dicomDatabase.fileValue(files[0],
self.tags['seriesDescription'])
if name == "":
name = "Unknown"
validDWI = False
vendorName = ""
for vendor in self.diffusionTags:
matchesVendor = True
for tag in self.diffusionTags[vendor]:
# Check the first three files because some tags may
# not be present in the b0 image (e.g. for Siemens)
for i in xrange(0, 3 if (len(files) > 2) else len(files)):
value = slicer.dicomDatabase.fileValue(files[i], tag)
hasTag = value != ""
if hasTag:
matchesVendor &= hasTag
if matchesVendor:
validDWI = True
vendorName = vendor
loadables = []
if validDWI:
# default loadable includes all files for series
loadable = DICOMLoadable()
loadable.files = files
loadable.name = name + ' - as DWI Volume'
loadable.selected = True
loadable.tooltip = "Appears to be DWI from vendor %s" % vendorName
loadable.confidence = 0.4
loadables = [loadable]
return loadables
def examineFiles(self,files):
""" Returns a list of DICOMLoadable instances
corresponding to ways of interpreting the
files parameter.
"""
loadables = []
# just read the modality type; need to go to reporting logic, since DCMTK
# is not wrapped ...
for cFile in files:
uid = slicer.dicomDatabase.fileValue(cFile, self.tags['instanceUID'])
if uid == '':
return []
desc = slicer.dicomDatabase.fileValue(cFile, self.tags['seriesDescription'])
if desc == '':
desc = "Unknown"
isDicomPM = (slicer.dicomDatabase.fileValue(cFile, self.tags['classUID']) == '1.2.840.10008.5.1.4.1.1.30')
if isDicomPM:
loadable = DICOMLoadable()
loadable.files = [cFile]
loadable.name = desc + ' - as a DICOM Parametric Map object'
loadable.tooltip = loadable.name
loadable.selected = True
loadable.confidence = 0.95
loadable.uid = uid
self.addReferences(loadable)
refName = self.referencedSeriesName(loadable)
if refName != "":
loadable.name = refName + " " + desc + " - ParametricMap"
loadables.append(loadable)
logging.debug('DICOM Parametric Map found')
return loadables
def examineFiles(self, files):
""" Returns a list of DICOMLoadable instances
corresponding to ways of interpreting the
files parameter.
"""
loadables = []
# just read the modality type; need to go to reporting logic, since DCMTK
# is not wrapped ...
for cFile in files:
uid = slicer.dicomDatabase.fileValue(cFile,
self.tags['instanceUID'])
if uid == '':
return []
desc = slicer.dicomDatabase.fileValue(
cFile, self.tags['seriesDescription'])
if desc == '':
desc = "Unknown"
isDicomSeg = (slicer.dicomDatabase.fileValue(
cFile, self.tags['modality']) == 'SEG')
if isDicomSeg:
loadable = DICOMLoadable()
loadable.files = [cFile]
loadable.name = desc
loadable.tooltip = loadable.name + ' - as a DICOM SEG object'
loadable.selected = True
loadable.confidence = 0.95
loadable.uid = uid
self.addReferences(loadable)
loadables.append(loadable)
logging.debug('DICOM SEG modality found')
return loadables
def examineFiles(self,files):
""" Returns a list of DICOMLoadable instances
corresponding to ways of interpreting the
files parameter.
Process is to look for 'known' private tags corresponding
to the types of diffusion datasets that the DicomToNrrd utility
should be able to process. Only need to look at one header
in the series since all should be the same with respect
to this check.
For testing:
dv = slicer.modules.dicomPlugins['DICOMDiffusionVolumePlugin']()
dv.examineForImport([['/media/extra650/data/DWI-examples/SiemensTrioTimB17-DWI/63000-000025-000001.dcm']])
"""
# get the series description to use as base for volume name
name = slicer.dicomDatabase.fileValue(files[0], self.tags['seriesDescription'])
if name == "":
name = "Unknown"
validDWI = False
vendorName = ""
for vendor in self.diffusionTags:
matchesVendor = True
for tag in self.diffusionTags[vendor]:
# Check the first three files because some tags may
# not be present in the b0 image (e.g. for Siemens)
for i in xrange(0, 3 if (len(files) > 2) else len(files)):
value = slicer.dicomDatabase.fileValue(files[i], tag)
hasTag = value != ""
if hasTag:
matchesVendor &= hasTag
if matchesVendor:
validDWI = True
vendorName = vendor
loadables = []
if validDWI:
# default loadable includes all files for series
loadable = DICOMLoadable()
loadable.files = files
loadable.name = name + ' - as DWI Volume'
loadable.selected = True
loadable.tooltip = "Appears to be DWI from vendor %s" % vendorName
loadable.confidence = 0.4
loadables = [loadable]
return loadables
def convertUltrasoundDicomToNrrd(self, inputDicomFilePath,
outputNrrdFilePath):
# Load from DICOM
from DICOMLib import DICOMLoadable
loadable = DICOMLoadable()
loadable.files = [inputDicomFilePath]
loadable.name = os.path.basename(inputDicomFilePath)
loadable.tooltip = ''
loadable.selected = True
loadable.confidence = 1.
loadable.createBrowserNode = False # don't create browser nodes (it would clutter the scene when batch processing)
dicomPlugin = slicer.modules.dicomPlugins['DicomUltrasoundPlugin']()
sequenceNode = dicomPlugin.load(loadable)
# Write to NRRD
storageNode = sequenceNode.GetStorageNode()
storageNode.SetFileName(outputNrrdFilePath)
success = storageNode.WriteData(sequenceNode)
# Clean up
slicer.mrmlScene.RemoveNode(sequenceNode)
return success
def examineFiles(self, files):
""" Returns a list of DICOMLoadable instances
corresponding to ways of interpreting the
files parameter.
Process is to look for 'known' private tags corresponding
to the types of diffusion datasets that the DicomToNrrd utility
should be able to process. Only need to look at one header
in the series since all should be the same with respect
to this check.
For testing:
dv = slicer.modules.dicomPlugins['DICOMTractographyPlugin']()
dv.examineForImport([['/media/extra650/data/DWI-examples/SiemensTrioTimB17-DWI/63000-000025-000001.dcm']])
"""
# get the series description to use as base for volume name
name = slicer.dicomDatabase.fileValue(files[0],
self.tags['seriesDescription'])
if name == "":
name = "Unknown"
validTractObject = False
for tag in self.tags.keys():
value = slicer.dicomDatabase.fileValue(files[0], tag)
hasTag = (value != "")
validTractObject = True
vendorName = slicer.dicomDatabase.fileValue(files[0], "0008,0070")
loadables = []
if validTractObject:
# default loadable includes all files for series
loadable = DICOMLoadable()
loadable.files = files
loadable.name = name + ' - as DWI Volume'
loadable.selected = False
loadable.tooltip = "Appears to be DWI from vendor %s" % vendorName
loadable.confidence = 0.75
loadables = [loadable]
return loadables
def convertUltrasoundDicomToNrrd(self, inputDicomFilePath, outputNrrdFilePath):
# Load from DICOM
from DICOMLib import DICOMLoadable
loadable = DICOMLoadable()
loadable.files = [inputDicomFilePath]
loadable.name = os.path.basename(inputDicomFilePath)
loadable.tooltip = ''
loadable.selected = True
loadable.confidence = 1.
loadable.createBrowserNode = False # don't create browser nodes (it would clutter the scene when batch processing)
dicomPlugin = slicer.modules.dicomPlugins['DicomUltrasoundPlugin']()
sequenceNode = dicomPlugin.load(loadable)
# Write to NRRD
storageNode = sequenceNode.GetStorageNode()
storageNode.SetFileName(outputNrrdFilePath)
success = storageNode.WriteData(sequenceNode)
# Clean up
slicer.mrmlScene.RemoveNode(sequenceNode)
return success
def examineFiles(self,files):
""" Returns a list of DICOMLoadable instances
corresponding to ways of interpreting the
files parameter.
"""
loadables = []
# just read the modality type; need to go to reporting logic, since DCMTK
# is not wrapped ...
for cFile in files:
uid = slicer.dicomDatabase.fileValue(cFile, self.tags['instanceUID'])
if uid == '':
return []
desc = slicer.dicomDatabase.fileValue(cFile, self.tags['seriesDescription'])
if desc == '':
desc = "Unknown"
isDicomSeg = (slicer.dicomDatabase.fileValue(cFile, self.tags['modality']) == 'SEG')
if isDicomSeg:
loadable = DICOMLoadable()
loadable.files = [cFile]
loadable.name = desc
loadable.tooltip = loadable.name + ' - as a DICOM SEG object'
loadable.selected = True
loadable.confidence = 0.95
loadable.uid = uid
self.addReferences(loadable)
loadables.append(loadable)
logging.debug('DICOM SEG modality found')
return loadables
def examineFiles(self,files):
""" Returns a list of DICOMLoadable instances
corresponding to ways of interpreting the
files parameter.
Process is to look for 'known' private tags corresponding
to the types of diffusion datasets that the DicomToNrrd utility
should be able to process. Only need to look at one header
in the series since all should be the same with respect
to this check.
For testing:
dv = slicer.modules.dicomPlugins['DICOMTractographyPlugin']()
dv.examineForImport([['/media/extra650/data/DWI-examples/SiemensTrioTimB17-DWI/63000-000025-000001.dcm']])
"""
# get the series description to use as base for volume name
name = slicer.dicomDatabase.fileValue(files[0], self.tags['seriesDescription'])
if name == "":
name = "Unknown"
validTractObject = False
for tag in self.tags.keys():
value = slicer.dicomDatabase.fileValue(files[0], tag)
hasTag = (value != "")
validTractObject = True
vendorName = slicer.dicomDatabase.fileValue(files[0], "0008,0070")
loadables = []
if validTractObject:
# default loadable includes all files for series
loadable = DICOMLoadable()
loadable.files = files
loadable.name = name + ' - as DWI Volume'
loadable.selected = False
loadable.tooltip = "Appears to be DWI from vendor %s" % vendorName
loadable.confidence = 0.75
loadables = [loadable]
return loadables
def createLoadableAndAddReferences(self, dataset):
loadable = DICOMLoadable()
loadable.selected = True
loadable.confidence = 0.95
if hasattr(dataset, "CurrentRequestedProcedureEvidenceSequence"):
loadable.referencedSeriesInstanceUIDs = []
loadable.referencedSOPInstanceUIDs = []
for refSeriesSequence in dataset.CurrentRequestedProcedureEvidenceSequence:
for referencedSeriesSequence in refSeriesSequence.ReferencedSeriesSequence:
for refSOPSequence in referencedSeriesSequence.ReferencedSOPSequence:
if refSOPSequence.ReferencedSOPClassUID == self.UID_SegmentationStorage: # TODO: differentiate between SR, SEG and other volumes
logging.debug("Found referenced segmentation")
loadable.referencedSeriesInstanceUIDs.append(
referencedSeriesSequence.SeriesInstanceUID)
else:
logging.debug("Found other reference")
for sopInstanceUID in slicer.dicomDatabase.fileForInstance(
refSOPSequence.ReferencedSOPInstanceUID):
loadable.referencedSOPInstanceUIDs.append(
sopInstanceUID)
# loadable.referencedSOPInstanceUID = refSOPSequence.ReferencedSOPInstanceUID
return loadable
def examineFiles(self, files):
""" Returns a list of DICOMLoadable instances
corresponding to ways of interpreting the
files parameter.
"""
seriesUID = slicer.dicomDatabase.fileValue(files[0],
self.tags['seriesUID'])
seriesName = self.defaultSeriesNodeName(seriesUID)
# default loadable includes all files for series
loadable = DICOMLoadable()
loadable.files = files
loadable.name = seriesName
loadable.tooltip = "%d files, first file: %s" % (len(
loadable.files), loadable.files[0])
loadable.selected = True
# add it to the list of loadables later, if pixel data is available in at least one file
# make subseries volumes based on tag differences
subseriesTags = [
"seriesInstanceUID",
"imageOrientationPatient",
"diffusionGradientOrientation",
]
if self.allowLoadingByTime():
subseriesTags.append("contentTime")
subseriesTags.append("triggerTime")
#
# first, look for subseries within this series
# - build a list of files for each unique value
# of each tag
#
subseriesFiles = {}
subseriesValues = {}
for file in loadable.files:
# check for subseries values
for tag in subseriesTags:
value = slicer.dicomDatabase.fileValue(file, self.tags[tag])
value = value.replace(
",", "_") # remove commas so it can be used as an index
if tag not in subseriesValues:
subseriesValues[tag] = []
if not subseriesValues[tag].__contains__(value):
subseriesValues[tag].append(value)
if (tag, value) not in subseriesFiles:
subseriesFiles[tag, value] = []
subseriesFiles[tag, value].append(file)
loadables = []
# Pixel data is available, so add the default loadable to the output
loadables.append(loadable)
#
# second, for any tags that have more than one value, create a new
# virtual series
#
for tag in subseriesTags:
if len(subseriesValues[tag]) > 1:
for valueIndex, value in enumerate(subseriesValues[tag]):
# default loadable includes all files for series
loadable = DICOMLoadable()
loadable.files = subseriesFiles[tag, value]
# value can be a long string (and it will be used for generating node name)
# therefore use just an index instead
loadable.name = seriesName + " - %s %d" % (tag,
valueIndex + 1)
loadable.tooltip = "%d files, grouped by %s = %s. First file: %s" % (
len(loadable.files), tag, value, loadable.files[0])
loadable.selected = False
loadables.append(loadable)
# remove any files from loadables that don't have pixel data (no point sending them to ITK for reading)
# also remove DICOM SEG, since it is not handled by ITK readers
newLoadables = []
for loadable in loadables:
newFiles = []
excludedLoadable = False
for file in loadable.files:
if slicer.dicomDatabase.fileValue(
file, self.tags['pixelData']) != '':
newFiles.append(file)
if slicer.dicomDatabase.fileValue(
file, self.tags['sopClassUID']
) == '1.2.840.10008.5.1.4.1.1.66.4':
excludedLoadable = True
logging.error(
'Please install Quantitative Reporting extension to enable loading of DICOM Segmentation objects'
)
elif slicer.dicomDatabase.fileValue(
file, self.tags['sopClassUID']
) == '1.2.840.10008.5.1.4.1.1.481.3':
excludedLoadable = True
logging.error(
'Please install SlicerRT extension to enable loading of DICOM RT Structure Set objects'
)
if len(newFiles) > 0 and not excludedLoadable:
loadable.files = newFiles
newLoadables.append(loadable)
elif excludedLoadable:
continue
else:
# here all files in have no pixel data, so they might be
# secondary capture images which will read, so let's pass
# them through with a warning and low confidence
loadable.warning += "There is no pixel data attribute for the DICOM objects, but they might be readable as secondary capture images. "
loadable.confidence = 0.2
newLoadables.append(loadable)
loadables = newLoadables
#
# now for each series and subseries, sort the images
# by position and check for consistency
#
for loadable in loadables:
loadable.files, distances, loadable.warning = DICOMUtils.getSortedImageFiles(
loadable.files, self.epsilon)
return loadables
def examineFiles(self,files):
""" Returns a list of DICOMLoadable instances
corresponding to ways of interpreting the
files parameter.
"""
loadables = []
if len(files) > 1:
# there should only be one instance per 4D volume
return []
filePath = files[0]
# currently only this one (bogus, non-standard) Philips 4D US format is supported
supportedSOPClassUID = '1.2.840.113543.6.6.1.3.10002'
# Quick check of SOP class UID without parsing the file...
try:
sopClassUID = slicer.dicomDatabase.fileValue(filePath,self.tags['sopClassUID'])
if sopClassUID != supportedSOPClassUID:
# Unsupported class
return []
except Exception as e:
# Quick check could not be completed (probably Slicer DICOM database is not initialized).
# No problem, we'll try to parse the file and check the SOP class UID then.
pass
try:
ds = dicom.read_file(filePath, stop_before_pixels=True)
except Exception as e:
logging.debug("Failed to parse DICOM file: {0}".format(e.message))
return []
if ds.SOPClassUID != supportedSOPClassUID:
# Unsupported class
return []
if ds.PhotometricInterpretation != 'MONOCHROME2':
logging.warning('Warning: unsupported PhotometricInterpretation')
loadable.confidence = .4
if ds.BitsAllocated != 8 or ds.BitsStored != 8 or ds.HighBit != 7:
logging.warning('Warning: Bad scalar type (not unsigned byte)')
loadable.confidence = .4
if ds.PhysicalUnitsXDirection != 3 or ds.PhysicalUnitsYDirection != 3:
logging.warning('Warning: Units not in centimeters')
loadable.confidence = .4
if ds.SamplesPerPixel != 1:
logging.warning('Warning: multiple samples per pixel')
loadable.confidence = .4
name = ''
if hasattr(ds,'SeriesNumber') and ds.SeriesNumber:
name = '{0}:'.format(ds.SeriesNumber)
if hasattr(ds,'Modality') and ds.Modality:
name = '{0} {1}'.format(name, ds.Modality)
if hasattr(ds,'SeriesDescription') and ds.SeriesDescription:
name = '{0} {1}'.format(name, ds.SeriesDescription)
if hasattr(ds,'InstanceNumber') and ds.InstanceNumber:
name = '{0} [{1}]'.format(name, ds.InstanceNumber)
loadable = DICOMLoadable()
loadable.files = files
loadable.name = name.strip() # remove leading and trailing spaces, if any
loadable.tooltip = "Philips 4D Ultrasound"
loadable.selected = True
loadable.confidence = 1.
loadables.append(loadable)
return loadables
def examineFiles(self, files):
""" Returns a list of DICOMLoadable instances
corresponding to ways of interpreting the
files parameter.
"""
# get the series description to use as base for volume name
name = slicer.dicomDatabase.fileValue(files[0],
self.tags['seriesDescription'])
if name == "":
name = "Unknown"
num = slicer.dicomDatabase.fileValue(files[0],
self.tags['seriesNumber'])
if num != "":
name = num + ": " + name
# default loadable includes all files for series
loadable = DICOMLoadable()
loadable.files = files
loadable.name = name
loadable.tooltip = "%d files, first file: %s" % (len(
loadable.files), loadable.files[0])
loadable.selected = True
# add it to the list of loadables later, if pixel data is available in at least one file
# while looping through files, keep track of their
# position and orientation for later use
positions = {}
orientations = {}
# make subseries volumes based on tag differences
subseriesTags = [
"seriesInstanceUID",
"contentTime",
"triggerTime",
"diffusionGradientOrientation",
"imageOrientationPatient",
]
# it will be set to true if pixel data is found in any of the files
pixelDataAvailable = False
#
# first, look for subseries within this series
# - build a list of files for each unique value
# of each tag
#
subseriesFiles = {}
subseriesValues = {}
for file in loadable.files:
# save position and orientation
positions[file] = slicer.dicomDatabase.fileValue(
file, self.tags['position'])
if positions[file] == "":
positions[file] = None
orientations[file] = slicer.dicomDatabase.fileValue(
file, self.tags['orientation'])
if orientations[file] == "":
orientations[file] = None
# check for subseries values
for tag in subseriesTags:
value = slicer.dicomDatabase.fileValue(file, self.tags[tag])
value = value.replace(
",", "_") # remove commas so it can be used as an index
if not subseriesValues.has_key(tag):
subseriesValues[tag] = []
if not subseriesValues[tag].__contains__(value):
subseriesValues[tag].append(value)
if not subseriesFiles.has_key((tag, value)):
subseriesFiles[tag, value] = []
subseriesFiles[tag, value].append(file)
loadables = []
# Pixel data is available, so add the default loadable to the output
loadables.append(loadable)
#
# second, for any tags that have more than one value, create a new
# virtual series
#
for tag in subseriesTags:
if len(subseriesValues[tag]) > 1:
for value in subseriesValues[tag]:
# default loadable includes all files for series
loadable = DICOMLoadable()
loadable.files = subseriesFiles[tag, value]
loadable.name = name + " for %s of %s" % (tag, value)
loadable.tooltip = "%d files, first file: %s" % (len(
loadable.files), loadable.files[0])
loadable.selected = False
loadables.append(loadable)
# remove any files from loadables that don't have pixel data (no point sending them to ITK for reading)
newLoadables = []
for loadable in loadables:
newFiles = []
for file in loadable.files:
if slicer.dicomDatabase.fileValue(
file, self.tags['pixelData']) != '':
newFiles.append(file)
if len(newFiles) > 0:
loadable.files = newFiles
newLoadables.append(loadable)
else:
# here all files in have no pixel data, so they might be
# secondary capture images which will read, so let's pass
# them through with a warning and low confidence
loadable.warning += "There is no pixel data attribute for the DICOM objects, but they might be readable as secondary capture images. "
loadable.confidence = 0.2
newLoadables.append(loadable)
loadables = newLoadables
#
# now for each series and subseries, sort the images
# by position and check for consistency
#
# TODO: more consistency checks:
# - is there gantry tilt?
# - are the orientations the same for all slices?
for loadable in loadables:
#
# use the first file to get the ImageOrientationPatient for the
# series and calculate the scan direction (assumed to be perpendicular
# to the acquisition plane)
#
value = slicer.dicomDatabase.fileValue(loadable.files[0],
self.tags['numberOfFrames'])
if value != "":
loadable.warning += "Multi-frame image. If slice orientation or spacing is non-uniform then the image may be displayed incorrectly. Use with caution. "
validGeometry = True
ref = {}
for tag in [self.tags['position'], self.tags['orientation']]:
value = slicer.dicomDatabase.fileValue(loadable.files[0], tag)
if not value or value == "":
loadable.warning += "Reference image in series does not contain geometry information. Please use caution. "
validGeometry = False
loadable.confidence = 0.2
break
ref[tag] = value
if not validGeometry:
continue
# get the geometry of the scan
# with respect to an arbitrary slice
sliceAxes = [
float(zz) for zz in ref[self.tags['orientation']].split('\\')
]
x = sliceAxes[:3]
y = sliceAxes[3:]
scanAxis = self.cross(x, y)
scanOrigin = [
float(zz) for zz in ref[self.tags['position']].split('\\')
]
#
# for each file in series, calculate the distance along
# the scan axis, sort files by this
#
sortList = []
missingGeometry = False
for file in loadable.files:
if not positions[file]:
missingGeometry = True
break
position = [float(zz) for zz in positions[file].split('\\')]
vec = self.difference(position, scanOrigin)
dist = self.dot(vec, scanAxis)
sortList.append((file, dist))
if missingGeometry:
loadable.warning += "One or more images is missing geometry information. "
else:
sortedFiles = sorted(sortList, key=lambda x: x[1])
distances = {}
loadable.files = []
for file, dist in sortedFiles:
loadable.files.append(file)
distances[file] = dist
#
# confirm equal spacing between slices
# - use variable 'epsilon' to determine the tolerance
#
spaceWarnings = 0
if len(loadable.files) > 1:
file0 = loadable.files[0]
file1 = loadable.files[1]
dist0 = distances[file0]
dist1 = distances[file1]
spacing0 = dist1 - dist0
n = 1
for fileN in loadable.files[1:]:
fileNminus1 = loadable.files[n - 1]
distN = distances[fileN]
distNminus1 = distances[fileNminus1]
spacingN = distN - distNminus1
spaceError = spacingN - spacing0
if abs(spaceError) > self.epsilon:
spaceWarnings += 1
loadable.warning += "Images are not equally spaced (a difference of %g in spacings was detected). Slicer will load this series as if it had a spacing of %g. Please use caution. " % (
spaceError, spacing0)
break
n += 1
if spaceWarnings != 0:
logging.warning(
"Geometric issues were found with %d of the series. Please use caution."
% spaceWarnings)
return loadables
def examineFiles(self,files):
""" Returns a list of DICOMLoadable instances
corresponding to ways of interpreting the
files parameter.
"""
seriesUID = slicer.dicomDatabase.fileValue(files[0],self.tags['seriesUID'])
seriesName = self.defaultSeriesNodeName(seriesUID)
# default loadable includes all files for series
loadable = DICOMLoadable()
loadable.files = files
loadable.name = seriesName
loadable.tooltip = "%d files, first file: %s" % (len(loadable.files), loadable.files[0])
loadable.selected = True
# add it to the list of loadables later, if pixel data is available in at least one file
# make subseries volumes based on tag differences
subseriesTags = [
"seriesInstanceUID",
"imageOrientationPatient",
"diffusionGradientOrientation",
]
if self.allowLoadingByTime():
subseriesTags.append("contentTime")
subseriesTags.append("triggerTime")
#
# first, look for subseries within this series
# - build a list of files for each unique value
# of each tag
#
subseriesFiles = {}
subseriesValues = {}
for file in loadable.files:
# check for subseries values
for tag in subseriesTags:
value = slicer.dicomDatabase.fileValue(file,self.tags[tag])
value = value.replace(",","_") # remove commas so it can be used as an index
if tag not in subseriesValues:
subseriesValues[tag] = []
if not subseriesValues[tag].__contains__(value):
subseriesValues[tag].append(value)
if (tag,value) not in subseriesFiles:
subseriesFiles[tag,value] = []
subseriesFiles[tag,value].append(file)
loadables = []
# Pixel data is available, so add the default loadable to the output
loadables.append(loadable)
#
# second, for any tags that have more than one value, create a new
# virtual series
#
for tag in subseriesTags:
if len(subseriesValues[tag]) > 1:
for valueIndex, value in enumerate(subseriesValues[tag]):
# default loadable includes all files for series
loadable = DICOMLoadable()
loadable.files = subseriesFiles[tag,value]
# value can be a long string (and it will be used for generating node name)
# therefore use just an index instead
loadable.name = seriesName + " - %s %d" % (tag,valueIndex+1)
loadable.tooltip = "%d files, grouped by %s = %s. First file: %s" % (len(loadable.files), tag, value, loadable.files[0])
loadable.selected = False
loadables.append(loadable)
# remove any files from loadables that don't have pixel data (no point sending them to ITK for reading)
# also remove DICOM SEG, since it is not handled by ITK readers
newLoadables = []
for loadable in loadables:
newFiles = []
excludedLoadable = False
for file in loadable.files:
if slicer.dicomDatabase.fileValue(file,self.tags['pixelData'])!='':
newFiles.append(file)
if slicer.dicomDatabase.fileValue(file,self.tags['sopClassUID'])=='1.2.840.10008.5.1.4.1.1.66.4':
excludedLoadable = True
logging.error('Please install Quantitative Reporting extension to enable loading of DICOM Segmentation objects')
elif slicer.dicomDatabase.fileValue(file,self.tags['sopClassUID'])=='1.2.840.10008.5.1.4.1.1.481.3':
excludedLoadable = True
logging.error('Please install SlicerRT extension to enable loading of DICOM RT Structure Set objects')
if len(newFiles) > 0 and not excludedLoadable:
loadable.files = newFiles
newLoadables.append(loadable)
elif excludedLoadable:
continue
else:
# here all files in have no pixel data, so they might be
# secondary capture images which will read, so let's pass
# them through with a warning and low confidence
loadable.warning += "There is no pixel data attribute for the DICOM objects, but they might be readable as secondary capture images. "
loadable.confidence = 0.2
newLoadables.append(loadable)
loadables = newLoadables
#
# now for each series and subseries, sort the images
# by position and check for consistency
#
for loadable in loadables:
loadable.files, distances, loadable.warning = DICOMUtils.getSortedImageFiles(loadable.files, self.epsilon)
return loadables
def examineEigenArtemis3DUS(self, filePath):
supportedSOPClassUID = '1.2.840.10008.5.1.4.1.1.3.1' # UltrasoundMultiframeImageStorage
# Quick check of SOP class UID without parsing the file...
try:
sopClassUID = slicer.dicomDatabase.fileValue(
filePath, self.tags['sopClassUID'])
if sopClassUID != supportedSOPClassUID:
# Unsupported class
#logging.debug("Not EigenArtemis3DUS: sopClassUID "+sopClassUID+" != supportedSOPClassUID "+supportedSOPClassUID)
return []
except Exception as e:
# Quick check could not be completed (probably Slicer DICOM database is not initialized).
# No problem, we'll try to parse the file and check the SOP class UID then.
pass
try:
ds = dicom.read_file(filePath, stop_before_pixels=True)
except Exception as e:
logging.debug("Failed to parse DICOM file: {0}".format(str(e)))
return []
if ds.SOPClassUID != supportedSOPClassUID:
# Unsupported class
logging.debug("Not EigenArtemis3DUS: sopClassUID " +
ds.SOPClassUID + " != supportedSOPClassUID " +
supportedSOPClassUID)
return []
if not (ds.Manufacturer == "Eigen"
and ds.ManufacturerModelName == "Artemis"):
return []
confidence = 0.9
if ds.PhotometricInterpretation != 'MONOCHROME2':
logging.warning('Warning: unsupported PhotometricInterpretation')
confidence = .4
if ds.BitsAllocated != 8 or ds.BitsStored != 8 or ds.HighBit != 7:
logging.warning('Warning: Bad scalar type (not unsigned byte)')
confidence = .4
if ds.SamplesPerPixel != 1:
logging.warning('Warning: multiple samples per pixel')
confidence = .4
"""Use manufacturer-specific conventions, per communication
from Rajesh Venkateraman (email to Andrey Fedorov et al on Feb 10, 2020):
> please take the PixelAspectRatio tag divide by 1000 and that would be your isotropic resolution for display in all 3 dimensions.
>
> Image Patient Orientation would be [1 0 0; 0 1 0] for each frame
>
> The origin of the volume is the center of the 3D cube and the span would be
>
> For X: [-0.5*Rows*PixelAspectRatio[0]/1000, -0.5*Rows*PixelAspectRatio[0]/1000 ]
>
> For Y: [-0.5*Columns*PixelAspectRatio[0]/1000, -0.5*Columns*PixelAspectRatio[0]/1000 ]
>
> For Z: [-0.5*NumberOfSlices*PixelAspectRatio[0]/1000, -0.5* NumberOfSlices *PixelAspectRatio[0]/1000 ]
Also, cross-check with the private attributes, if those are available.
"""
pixelSpacingPrivate = None
pixelSpacingPublic = None
try:
pixelSpacingPrivateTag = findPrivateTag(ds, 0x1129, 0x16,
"Eigen, Inc")
if pixelSpacingPrivateTag is None:
pixelSpacingPrivateTag = findPrivateTag(
ds, 0x1129, 0x16, "Eigen Artemis")
if pixelSpacingPrivateTag is not None:
pixelSpacingPrivate = float(ds[pixelSpacingPrivateTag].value)
except KeyError:
logging.warning(
"examineEigenArtemis3DUS: spacing not available in private tag"
)
if hasattr(ds, "PixelAspectRatio"):
if ds.PixelAspectRatio[0] != ds.PixelAspectRatio[1]:
logging.warning(
"examineEigenArtemis3DUS: PixelAspectRatio items are not equal!"
)
pixelSpacingPublic = float(ds.PixelAspectRatio[0]) / 1000.
if pixelSpacingPrivate is not None and pixelSpacingPrivate != pixelSpacingPublic:
logging.warning(
"examineEigenArtemis3DUS: private tag based spacing does not match computed spacing"
)
else:
if pixelSpacingPrivate is None:
logging.debug(
"examineEigenArtemis3DUS: unable to find spacing information"
)
return []
# prefer private, if available
outputSpacing = pixelSpacingPrivate if pixelSpacingPrivate is not None else pixelSpacingPublic
outputOrigin = [
0.5 * float(ds.Rows) * outputSpacing,
0.5 * float(ds.Columns) * outputSpacing,
-0.5 * float(ds.NumberOfSlices) * outputSpacing
]
logging.debug("examineEigenArtemis3DUS: assumed pixel spacing: %s" %
str(outputSpacing))
name = ''
if hasattr(ds, 'SeriesNumber') and ds.SeriesNumber:
name = '{0}:'.format(ds.SeriesNumber)
if hasattr(ds, 'Modality') and ds.Modality:
name = '{0} {1}'.format(name, ds.Modality)
if hasattr(ds, 'SeriesDescription') and ds.SeriesDescription:
name = '{0} {1}'.format(name, ds.SeriesDescription)
else:
name = name + " Eigen Artemis 3D US"
if hasattr(ds, 'InstanceNumber') and ds.InstanceNumber:
name = '{0} [{1}]'.format(name, ds.InstanceNumber)
loadable = DICOMLoadable()
loadable.files = [filePath]
loadable.name = name.strip(
) # remove leading and trailing spaces, if any
loadable.tooltip = "Eigen Artemis 3D ultrasound"
loadable.selected = True
loadable.confidence = confidence
loadable.spacing = outputSpacing
loadable.origin = outputOrigin
return [loadable]
def examineFiles(self, files):
""" Returns a list of DICOMLoadable instances
corresponding to ways of interpreting the
files parameter.
"""
self.detailedLogging = slicer.util.settingsValue(
'DICOM/detailedLogging', False, converter=slicer.util.toBool)
supportedSOPClassUIDs = [
'1.2.840.10008.5.1.4.1.1.12.1', # X-Ray Angiographic Image Storage
'1.2.840.10008.5.1.4.1.1.12.2', # X-Ray Fluoroscopy Image Storage
'1.2.840.10008.5.1.4.1.1.3.1', # Ultrasound Multiframe Image Storage
'1.2.840.10008.5.1.4.1.1.6.1', # Ultrasound Image Storage
'1.2.840.10008.5.1.4.1.1.7', # Secondary Capture Image Storage (only accepted for modalities that typically acquire 2D image sequences)
'1.2.840.10008.5.1.4.1.1.4', # MR Image Storage (will be only accepted if cine-MRI)
]
# Modalities that typically acquire 2D image sequences:
suppportedSecondaryCaptureModalities = ['US', 'XA', 'RF', 'ES']
# Each instance will be a loadable, that will result in one sequence browser node
# and usually one sequence (except simultaneous biplane acquisition, which will
# result in two sequences).
# Each pedal press on the XA/RF acquisition device creates a new instance number,
# but if the device has two imaging planes (biplane) then two sequences
# will be acquired, which have the same instance number. These two sequences
# are synchronized in time, therefore they have to be assigned to the same
# browser node.
instanceNumberToLoadableIndex = {}
loadables = []
canBeCineMri = True
cineMriTriggerTimes = set()
cineMriInstanceNumberToFilenameIndex = {}
for filePath in files:
# Quick check of SOP class UID without parsing the file...
try:
sopClassUID = slicer.dicomDatabase.fileValue(
filePath, self.tags['sopClassUID'])
if not (sopClassUID in supportedSOPClassUIDs):
# Unsupported class
continue
# Only accept MRI if it looks like cine-MRI
if sopClassUID != '1.2.840.10008.5.1.4.1.1.4': # MR Image Storage (will be only accepted if cine-MRI)
canBeCineMri = False
if not canBeCineMri and sopClassUID == '1.2.840.10008.5.1.4.1.1.4': # MR Image Storage
continue
except Exception as e:
# Quick check could not be completed (probably Slicer DICOM database is not initialized).
# No problem, we'll try to parse the file and check the SOP class UID then.
pass
instanceNumber = slicer.dicomDatabase.fileValue(
filePath, self.tags['instanceNumber'])
if sopClassUID == '1.2.840.10008.5.1.4.1.1.4': # MR Image Storage
if not instanceNumber:
# no instance number, probably not cine-MRI
canBeCineMri = False
if self.detailedLogging:
logging.debug(
"No instance number attribute found, the series will not be considered as a cine MRI"
)
continue
cineMriInstanceNumberToFilenameIndex[int(
instanceNumber)] = filePath
cineMriTriggerTimes.add(
slicer.dicomDatabase.fileValue(filePath,
self.tags['triggerTime']))
else:
modality = slicer.dicomDatabase.fileValue(
filePath, self.tags['modality'])
if sopClassUID == '1.2.840.10008.5.1.4.1.1.7': # Secondary Capture Image Storage
if modality not in suppportedSecondaryCaptureModalities:
# practice of dumping secondary capture images into the same series
# is only prevalent in US and XA/RF modalities
continue
if not (instanceNumber
in instanceNumberToLoadableIndex.keys()):
# new instance number
seriesNumber = slicer.dicomDatabase.fileValue(
filePath, self.tags['seriesNumber'])
seriesDescription = slicer.dicomDatabase.fileValue(
filePath, self.tags['seriesDescription'])
photometricInterpretation = slicer.dicomDatabase.fileValue(
filePath, self.tags['photometricInterpretation'])
name = ''
if seriesNumber:
name = f'{seriesNumber}:'
if modality:
name = f'{name} {modality}'
if seriesDescription:
name = f'{name} {seriesDescription}'
if instanceNumber:
name = f'{name} [{instanceNumber}]'
loadable = DICOMLoadable()
loadable.singleSequence = False # put each instance in a separate sequence
loadable.files = [filePath]
loadable.name = name.strip(
) # remove leading and trailing spaces, if any
loadable.warning = "Image spacing may need to be calibrated for accurate size measurements."
loadable.tooltip = f"{modality} image sequence"
loadable.selected = True
# Confidence is slightly larger than default scalar volume plugin's (0.5)
# but still leaving room for more specialized plugins.
loadable.confidence = 0.7
loadable.grayscale = ('MONOCHROME'
in photometricInterpretation)
# Add to loadables list
loadables.append(loadable)
instanceNumberToLoadableIndex[instanceNumber] = len(
loadables) - 1
else:
# existing instance number, add this file
loadableIndex = instanceNumberToLoadableIndex[
instanceNumber]
loadables[loadableIndex].files.append(filePath)
loadable.tooltip = f"{modality} image sequence ({len(loadables[loadableIndex].files)} planes)"
if canBeCineMri and len(cineMriInstanceNumberToFilenameIndex) > 1:
# Get description from first
ds = dicom.read_file(cineMriInstanceNumberToFilenameIndex[next(
iter(cineMriInstanceNumberToFilenameIndex))],
stop_before_pixels=True)
name = ''
if hasattr(ds, 'SeriesNumber') and ds.SeriesNumber:
name = f'{ds.SeriesNumber}:'
if hasattr(ds, 'Modality') and ds.Modality:
name = f'{name} {ds.Modality}'
if hasattr(ds, 'SeriesDescription') and ds.SeriesDescription:
name = f'{name} {ds.SeriesDescription}'
loadable = DICOMLoadable()
loadable.singleSequence = True # put all instances in a single sequence
loadable.instanceNumbers = sorted(
cineMriInstanceNumberToFilenameIndex)
loadable.files = [
cineMriInstanceNumberToFilenameIndex[instanceNumber]
for instanceNumber in loadable.instanceNumbers
]
loadable.name = name.strip(
) # remove leading and trailing spaces, if any
loadable.tooltip = f"{ds.Modality} image sequence"
loadable.selected = True
if len(cineMriTriggerTimes) > 3:
if self.detailedLogging:
logging.debug("Several different trigger times found (" +
repr(cineMriTriggerTimes) +
") - assuming this series is a cine MRI")
# This is likely a cardiac cine acquisition.
# Multivolume importer sets confidence=1.0, so we need to set a bit higher confidence to be selected by default
loadable.confidence = 1.05
else:
# This may be a 3D acquisition,so set lower confidence than scalar volume's default (0.5)
if self.detailedLogging:
logging.debug(
"Only one or few different trigger times found (" +
repr(cineMriTriggerTimes) +
") - assuming this series is not a cine MRI")
loadable.confidence = 0.4
loadable.grayscale = ('MONOCHROME' in ds.PhotometricInterpretation)
# Add to loadables list
loadables.append(loadable)
return loadables
def examineFiles(self,files):
""" Returns a list of DICOMLoadable instances
corresponding to ways of interpreting the
files parameter.
"""
seriesUID = slicer.dicomDatabase.fileValue(files[0],self.tags['seriesUID'])
seriesName = self.defaultSeriesNodeName(seriesUID)
# default loadable includes all files for series
loadable = DICOMLoadable()
loadable.files = files
loadable.name = seriesName
loadable.tooltip = "%d files, first file: %s" % (len(loadable.files), loadable.files[0])
loadable.selected = True
# add it to the list of loadables later, if pixel data is available in at least one file
# while looping through files, keep track of their
# position and orientation for later use
positions = {}
orientations = {}
# make subseries volumes based on tag differences
subseriesTags = [
"seriesInstanceUID",
"contentTime",
"triggerTime",
"diffusionGradientOrientation",
"imageOrientationPatient",
]
#
# first, look for subseries within this series
# - build a list of files for each unique value
# of each tag
#
subseriesFiles = {}
subseriesValues = {}
for file in loadable.files:
# save position and orientation
positions[file] = slicer.dicomDatabase.fileValue(file,self.tags['position'])
if positions[file] == "":
positions[file] = None
orientations[file] = slicer.dicomDatabase.fileValue(file,self.tags['orientation'])
if orientations[file] == "":
orientations[file] = None
# check for subseries values
for tag in subseriesTags:
value = slicer.dicomDatabase.fileValue(file,self.tags[tag])
value = value.replace(",","_") # remove commas so it can be used as an index
if not subseriesValues.has_key(tag):
subseriesValues[tag] = []
if not subseriesValues[tag].__contains__(value):
subseriesValues[tag].append(value)
if not subseriesFiles.has_key((tag,value)):
subseriesFiles[tag,value] = []
subseriesFiles[tag,value].append(file)
loadables = []
# Pixel data is available, so add the default loadable to the output
loadables.append(loadable)
#
# second, for any tags that have more than one value, create a new
# virtual series
#
for tag in subseriesTags:
if len(subseriesValues[tag]) > 1:
for value in subseriesValues[tag]:
# default loadable includes all files for series
loadable = DICOMLoadable()
loadable.files = subseriesFiles[tag,value]
loadable.name = seriesName + " for %s of %s" % (tag,value)
loadable.tooltip = "%d files, first file: %s" % (len(loadable.files), loadable.files[0])
loadable.selected = False
loadables.append(loadable)
# remove any files from loadables that don't have pixel data (no point sending them to ITK for reading)
newLoadables = []
for loadable in loadables:
newFiles = []
for file in loadable.files:
if slicer.dicomDatabase.fileValue(file,self.tags['pixelData'])!='':
newFiles.append(file)
if len(newFiles) > 0:
loadable.files = newFiles
newLoadables.append(loadable)
else:
# here all files in have no pixel data, so they might be
# secondary capture images which will read, so let's pass
# them through with a warning and low confidence
loadable.warning += "There is no pixel data attribute for the DICOM objects, but they might be readable as secondary capture images. "
loadable.confidence = 0.2
newLoadables.append(loadable)
loadables = newLoadables
#
# now for each series and subseries, sort the images
# by position and check for consistency
#
# TODO: more consistency checks:
# - is there gantry tilt?
# - are the orientations the same for all slices?
for loadable in loadables:
#
# use the first file to get the ImageOrientationPatient for the
# series and calculate the scan direction (assumed to be perpendicular
# to the acquisition plane)
#
value = slicer.dicomDatabase.fileValue(loadable.files[0], self.tags['numberOfFrames'])
if value != "":
loadable.warning += "Multi-frame image. If slice orientation or spacing is non-uniform then the image may be displayed incorrectly. Use with caution. "
validGeometry = True
ref = {}
for tag in [self.tags['position'], self.tags['orientation']]:
value = slicer.dicomDatabase.fileValue(loadable.files[0], tag)
if not value or value == "":
loadable.warning += "Reference image in series does not contain geometry information. Please use caution. "
validGeometry = False
loadable.confidence = 0.2
break
ref[tag] = value
if not validGeometry:
continue
# get the geometry of the scan
# with respect to an arbitrary slice
sliceAxes = [float(zz) for zz in ref[self.tags['orientation']].split('\\')]
x = sliceAxes[:3]
y = sliceAxes[3:]
scanAxis = self.cross(x,y)
scanOrigin = [float(zz) for zz in ref[self.tags['position']].split('\\')]
#
# for each file in series, calculate the distance along
# the scan axis, sort files by this
#
sortList = []
missingGeometry = False
for file in loadable.files:
if not positions[file]:
missingGeometry = True
break
position = [float(zz) for zz in positions[file].split('\\')]
vec = self.difference(position, scanOrigin)
dist = self.dot(vec, scanAxis)
sortList.append((file, dist))
if missingGeometry:
loadable.warning += "One or more images is missing geometry information. "
else:
sortedFiles = sorted(sortList, key=lambda x: x[1])
distances = {}
loadable.files = []
for file,dist in sortedFiles:
loadable.files.append(file)
distances[file] = dist
#
# confirm equal spacing between slices
# - use variable 'epsilon' to determine the tolerance
#
spaceWarnings = 0
if len(loadable.files) > 1:
file0 = loadable.files[0]
file1 = loadable.files[1]
dist0 = distances[file0]
dist1 = distances[file1]
spacing0 = dist1 - dist0
n = 1
for fileN in loadable.files[1:]:
fileNminus1 = loadable.files[n-1]
distN = distances[fileN]
distNminus1 = distances[fileNminus1]
spacingN = distN - distNminus1
spaceError = spacingN - spacing0
if abs(spaceError) > self.epsilon:
spaceWarnings += 1
loadable.warning += "Images are not equally spaced (a difference of %g vs %g in spacings was detected). Slicer will try to load this series with a transform to compensate. Please use caution. " % (spaceError, spacing0)
break
n += 1
if spaceWarnings != 0:
logging.warning("Geometric issues were found with %d of the series. Please use caution." % spaceWarnings)
return loadables
def examineFiles(self, files):
""" Returns a list of DICOMLoadable instances
corresponding to ways of interpreting the
files parameter.
"""
seriesUID = slicer.dicomDatabase.fileValue(files[0],
self.tags['seriesUID'])
seriesName = self.defaultSeriesNodeName(seriesUID)
# default loadable includes all files for series
allFilesLoadable = DICOMLoadable()
allFilesLoadable.files = files
allFilesLoadable.name = self.cleanNodeName(seriesName)
allFilesLoadable.tooltip = "%d files, first file: %s" % (len(
allFilesLoadable.files), allFilesLoadable.files[0])
allFilesLoadable.selected = True
# add it to the list of loadables later, if pixel data is available in at least one file
# make subseries volumes based on tag differences
subseriesTags = [
"seriesInstanceUID",
"acquisitionNumber",
# GE volume viewer and Siemens Axiom CBCT systems put an overview (localizer) slice and all the reconstructed slices
# in one series, using two different image types. Splitting based on image type allows loading of these volumes
# (loading the series without localizer).
"imageType",
"imageOrientationPatient",
"diffusionGradientOrientation",
]
if self.allowLoadingByTime():
subseriesTags.append("contentTime")
subseriesTags.append("triggerTime")
# Values for these tags will only be enumerated (value itself will not be part of the loadable name)
# because the vale itself is usually too long and complicated to be displayed to users
subseriesTagsToEnumerateValues = [
"seriesInstanceUID",
"imageOrientationPatient",
"diffusionGradientOrientation",
]
#
# first, look for subseries within this series
# - build a list of files for each unique value
# of each tag
#
subseriesFiles = {}
subseriesValues = {}
for file in allFilesLoadable.files:
# check for subseries values
for tag in subseriesTags:
value = slicer.dicomDatabase.fileValue(file, self.tags[tag])
value = value.replace(
",", "_") # remove commas so it can be used as an index
if tag not in subseriesValues:
subseriesValues[tag] = []
if not subseriesValues[tag].__contains__(value):
subseriesValues[tag].append(value)
if (tag, value) not in subseriesFiles:
subseriesFiles[tag, value] = []
subseriesFiles[tag, value].append(file)
loadables = []
# Pixel data is available, so add the default loadable to the output
loadables.append(allFilesLoadable)
#
# second, for any tags that have more than one value, create a new
# virtual series
#
subseriesCount = 0
# List of loadables that look like subseries that contain the full series except a single frame
probableLocalizerFreeLoadables = []
for tag in subseriesTags:
if len(subseriesValues[tag]) > 1:
subseriesCount += 1
for valueIndex, value in enumerate(subseriesValues[tag]):
# default loadable includes all files for series
loadable = DICOMLoadable()
loadable.files = subseriesFiles[tag, value]
# value can be a long string (and it will be used for generating node name)
# therefore use just an index instead
if tag in subseriesTagsToEnumerateValues:
loadable.name = seriesName + " - %s %d" % (
tag, valueIndex + 1)
else:
loadable.name = seriesName + " - %s %s" % (tag, value)
loadable.name = self.cleanNodeName(loadable.name)
loadable.tooltip = "%d files, grouped by %s = %s. First file: %s. %s = %s" % (
len(loadable.files), tag, value, loadable.files[0],
tag, value)
loadable.selected = False
loadables.append(loadable)
if len(subseriesValues[tag]) == 2:
otherValue = subseriesValues[tag][1 - valueIndex]
if len(subseriesFiles[tag, value]) > 1 and len(
subseriesFiles[tag, otherValue]) == 1:
# this looks like a subseries without a localizer image
probableLocalizerFreeLoadables.append(loadable)
# remove any files from loadables that don't have pixel data (no point sending them to ITK for reading)
# also remove DICOM SEG, since it is not handled by ITK readers
newLoadables = []
for loadable in loadables:
newFiles = []
excludedLoadable = False
for file in loadable.files:
if slicer.dicomDatabase.fileValueExists(
file, self.tags['pixelData']):
newFiles.append(file)
if slicer.dicomDatabase.fileValue(
file, self.tags['sopClassUID']
) == '1.2.840.10008.5.1.4.1.1.66.4':
excludedLoadable = True
if 'DICOMSegmentationPlugin' not in slicer.modules.dicomPlugins:
logging.warning(
'Please install Quantitative Reporting extension to enable loading of DICOM Segmentation objects'
)
elif slicer.dicomDatabase.fileValue(
file, self.tags['sopClassUID']
) == '1.2.840.10008.5.1.4.1.1.481.3':
excludedLoadable = True
if 'DicomRtImportExportPlugin' not in slicer.modules.dicomPlugins:
logging.warning(
'Please install SlicerRT extension to enable loading of DICOM RT Structure Set objects'
)
if len(newFiles) > 0 and not excludedLoadable:
loadable.files = newFiles
loadable.grayscale = (
'MONOCHROME' in slicer.dicomDatabase.fileValue(
newFiles[0], self.tags['photometricInterpretation']))
newLoadables.append(loadable)
elif excludedLoadable:
continue
else:
# here all files in have no pixel data, so they might be
# secondary capture images which will read, so let's pass
# them through with a warning and low confidence
loadable.warning += "There is no pixel data attribute for the DICOM objects, but they might be readable as secondary capture images. "
loadable.confidence = 0.2
loadable.grayscale = (
'MONOCHROME' in slicer.dicomDatabase.fileValue(
loadable.files[0],
self.tags['photometricInterpretation']))
newLoadables.append(loadable)
loadables = newLoadables
#
# now for each series and subseries, sort the images
# by position and check for consistency
# then adjust confidence values based on warnings
#
for loadable in loadables:
loadable.files, distances, loadable.warning = DICOMUtils.getSortedImageFiles(
loadable.files, self.epsilon)
loadablesBetterThanAllFiles = []
if allFilesLoadable.warning != "":
for probableLocalizerFreeLoadable in probableLocalizerFreeLoadables:
if probableLocalizerFreeLoadable.warning == "":
# localizer-free loadables are better then all files, if they don't have warning
loadablesBetterThanAllFiles.append(
probableLocalizerFreeLoadable)
if not loadablesBetterThanAllFiles and subseriesCount == 1:
# there was a sorting warning and
# only one kind of subseries, so it's probably correct
# to have lower confidence in the default all-files version.
for loadable in loadables:
if loadable != allFilesLoadable and loadable.warning == "":
loadablesBetterThanAllFiles.append(loadable)
# if there are loadables that are clearly better then all files, then use those (otherwise use all files loadable)
preferredLoadables = loadablesBetterThanAllFiles if loadablesBetterThanAllFiles else [
allFilesLoadable
]
# reduce confidence and deselect all non-preferred loadables
for loadable in loadables:
if loadable in preferredLoadables:
loadable.selected = True
else:
loadable.selected = False
if loadable.confidence > .45:
loadable.confidence = .45
return loadables
def examinePhilips4DUS(self, filePath):
# currently only this one (bogus, non-standard) Philips 4D US format is supported
supportedSOPClassUID = '1.2.840.113543.6.6.1.3.10002'
# Quick check of SOP class UID without parsing the file...
try:
sopClassUID = slicer.dicomDatabase.fileValue(
filePath, self.tags['sopClassUID'])
if sopClassUID != supportedSOPClassUID:
# Unsupported class
return []
except Exception as e:
# Quick check could not be completed (probably Slicer DICOM database is not initialized).
# No problem, we'll try to parse the file and check the SOP class UID then.
pass
try:
ds = dicom.read_file(filePath, stop_before_pixels=True)
except Exception as e:
logging.debug("Failed to parse DICOM file: {0}".format(e.msg))
return []
if ds.SOPClassUID != supportedSOPClassUID:
# Unsupported class
return []
confidence = 0.9
if ds.PhotometricInterpretation != 'MONOCHROME2':
logging.warning('Warning: unsupported PhotometricInterpretation')
confidence = .4
if ds.BitsAllocated != 8 or ds.BitsStored != 8 or ds.HighBit != 7:
logging.warning('Warning: Bad scalar type (not unsigned byte)')
confidence = .4
if ds.PhysicalUnitsXDirection != 3 or ds.PhysicalUnitsYDirection != 3:
logging.warning('Warning: Units not in centimeters')
confidence = .4
if ds.SamplesPerPixel != 1:
logging.warning('Warning: multiple samples per pixel')
confidence = .4
name = ''
if hasattr(ds, 'SeriesNumber') and ds.SeriesNumber:
name = '{0}:'.format(ds.SeriesNumber)
if hasattr(ds, 'Modality') and ds.Modality:
name = '{0} {1}'.format(name, ds.Modality)
if hasattr(ds, 'SeriesDescription') and ds.SeriesDescription:
name = '{0} {1}'.format(name, ds.SeriesDescription)
if hasattr(ds, 'InstanceNumber') and ds.InstanceNumber:
name = '{0} [{1}]'.format(name, ds.InstanceNumber)
loadable = DICOMLoadable()
loadable.files = [filePath]
loadable.name = name.strip(
) # remove leading and trailing spaces, if any
loadable.tooltip = "Philips 4D Ultrasound"
loadable.selected = True
loadable.confidence = confidence
return [loadable]
def createLoadableAndAddReferences(self, datasets):
loadable = DICOMLoadable()
loadable.selected = True
loadable.confidence = 0.95
loadable.referencedSegInstanceUIDs = []
# store lists of UIDs separately to avoid re-parsing later
loadable.ReferencedSegmentationInstanceUIDs = {}
loadable.ReferencedRWVMSeriesInstanceUIDs = []
loadable.ReferencedOtherInstanceUIDs = []
loadable.referencedInstanceUIDs = []
segPlugin = slicer.modules.dicomPlugins["DICOMSegmentationPlugin"]()
for dataset in datasets:
uid = self.getDICOMValue(dataset, "SOPInstanceUID")
loadable.ReferencedSegmentationInstanceUIDs[uid] = []
if hasattr(dataset, "CurrentRequestedProcedureEvidenceSequence"):
for refSeriesSequence in dataset.CurrentRequestedProcedureEvidenceSequence:
for referencedSeriesSequence in refSeriesSequence.ReferencedSeriesSequence:
for refSOPSequence in referencedSeriesSequence.ReferencedSOPSequence:
if refSOPSequence.ReferencedSOPClassUID == self.UID_SegmentationStorage:
logging.debug("Found referenced segmentation")
loadable.ReferencedSegmentationInstanceUIDs[uid].append(referencedSeriesSequence.SeriesInstanceUID)
elif refSOPSequence.ReferencedSOPClassUID == self.UID_RealWorldValueMappingStorage: # handle SUV mapping
logging.debug("Found referenced RWVM")
loadable.ReferencedRWVMSeriesInstanceUIDs.append(referencedSeriesSequence.SeriesInstanceUID)
else:
# TODO: those are not used at all
logging.debug( "Found other reference")
loadable.ReferencedOtherInstanceUIDs.append(refSOPSequence.ReferencedSOPInstanceUID)
for segSeriesInstanceUID in loadable.ReferencedSegmentationInstanceUIDs[uid]:
segLoadables = segPlugin.examine([slicer.dicomDatabase.filesForSeries(segSeriesInstanceUID)])
for segLoadable in segLoadables:
loadable.referencedInstanceUIDs += segLoadable.referencedInstanceUIDs
loadable.referencedInstanceUIDs = list(set(loadable.referencedInstanceUIDs))
if len(loadable.ReferencedSegmentationInstanceUIDs[uid])>1:
logging.warning("SR references more than one SEG. This has not been tested!")
for segUID in loadable.ReferencedSegmentationInstanceUIDs:
loadable.referencedSegInstanceUIDs.append(segUID)
if len(loadable.ReferencedRWVMSeriesInstanceUIDs)>1:
logging.warning("SR references more than one RWVM. This has not been tested!")
# not adding RWVM instances to referencedSeriesInstanceUIDs
return loadable
def examineGeUSMovie(self, filePath):
supportedSOPClassUIDs = [
'1.2.840.10008.5.1.4.1.1.6.1' # UltrasoundImageStorage
]
# Quick check of SOP class UID without parsing the file...
try:
sopClassUID = slicer.dicomDatabase.fileValue(
filePath, self.tags['sopClassUID'])
if not sopClassUID in supportedSOPClassUIDs:
# Unsupported class
return []
except Exception as e:
# Quick check could not be completed (probably Slicer DICOM database is not initialized).
# No problem, we'll try to parse the file and check the SOP class UID then.
pass
try:
ds = dicom.read_file(
filePath,
defer_size=30) # use defer_size to not load large fields
except Exception as e:
logging.debug("Failed to parse DICOM file: {0}".format(e.msg))
return []
if not ds.SOPClassUID in supportedSOPClassUIDs:
# Unsupported class
return []
geUsMovieGroupRootTag = dicom.tag.Tag('0x7fe1', '0x0010')
geUsMovieGroupRootItem = ds.get(geUsMovieGroupRootTag)
if not geUsMovieGroupRootItem:
return []
if geUsMovieGroupRootItem.name != 'Private Creator':
return []
if geUsMovieGroupRootItem.value != 'GEMS_Ultrasound_MovieGroup_001':
return []
confidence = 0.8
name = ''
if hasattr(ds, 'SeriesNumber') and ds.SeriesNumber:
name = '{0}:'.format(ds.SeriesNumber)
if hasattr(ds, 'Modality') and ds.Modality:
name = '{0} {1}'.format(name, ds.Modality)
if hasattr(ds, 'SeriesDescription') and ds.SeriesDescription:
name = '{0} {1}'.format(name, ds.SeriesDescription)
if hasattr(ds, 'InstanceNumber') and ds.InstanceNumber:
name = '{0} [{1}]'.format(name, ds.InstanceNumber)
loadable = DICOMLoadable()
loadable.files = [filePath]
loadable.name = name.strip(
) # remove leading and trailing spaces, if any
loadable.tooltip = "GE ultrasound image sequence"
loadable.warning = "Importing of this file format is experimental: images may be distorted, size measurements may be inaccurate."
loadable.selected = True
loadable.confidence = confidence
return [loadable]
def examineGeKretzUS(self, filePath):
# E Kretz uses 'Ultrasound Image Storage' SOP class UID
supportedSOPClassUID = '1.2.840.10008.5.1.4.1.1.6.1'
# Quick check of SOP class UID without parsing the file...
try:
sopClassUID = slicer.dicomDatabase.fileValue(
filePath, self.tags['sopClassUID'])
if sopClassUID != supportedSOPClassUID:
# Unsupported class
return []
except Exception as e:
# Quick check could not be completed (probably Slicer DICOM database is not initialized).
# No problem, we'll try to parse the file and check the SOP class UID then.
pass
try:
ds = dicom.read_file(
filePath,
defer_size=50) # use defer_size to not load large fields
except Exception as e:
logging.debug("Failed to parse DICOM file: {0}".format(e.msg))
return []
if ds.SOPClassUID != supportedSOPClassUID:
# Unsupported class
return []
# Check if these expected DICOM tags are available:
# (7fe1,0011) LO [KRETZ_US] # 8, 1 PrivateCreator
# (7fe1,1101) OB 4b\52\45\54\5a\46\49\4c\45\20\31\2e\30\20\20\20\00\00\01\00\02\00... # 3471038, 1 Unknown Tag & Data
kretzUsTag = dicom.tag.Tag('0x7fe1', '0x11')
kretzUsDataTag = dicom.tag.Tag('0x7fe1', '0x1101')
if kretzUsTag not in ds.keys():
return []
if kretzUsDataTag not in ds.keys():
return []
confidence = 0.9
# These manufacturers values have been found in successfully loadable files:
# - Kretztechnik
# - GE Healthcare
# - GE Healthcare Austria GmbH & Co OG
if (ds.Manufacturer != 'Kretztechnik') and (
ds.Manufacturer.find('GE Healthcare') < 0):
logging.warning('Warning: unknown manufacturer: ' +
ds.Manufacturer)
confidence = .4
name = ''
if hasattr(ds, 'SeriesNumber') and ds.SeriesNumber:
name = '{0}:'.format(ds.SeriesNumber)
if hasattr(ds, 'Modality') and ds.Modality:
name = '{0} {1}'.format(name, ds.Modality)
if hasattr(ds, 'SeriesDescription') and ds.SeriesDescription:
name = '{0} {1}'.format(name, ds.SeriesDescription)
if hasattr(ds, 'InstanceNumber') and ds.InstanceNumber:
name = '{0} [{1}]'.format(name, ds.InstanceNumber)
name = name.strip() # remove leading and trailing spaces, if any
loadable = DICOMLoadable()
loadable.files = [filePath]
loadable.name = name
loadable.tooltip = "GE Kretz 3D Ultrasound"
loadable.warning = "Importing of this file format is experimental: images may be distorted, size measurements may be inaccurate."
loadable.selected = True
loadable.confidence = confidence
loadableHighRes1 = DICOMLoadable()
loadableHighRes1.files = loadable.files
loadableHighRes1.name = loadable.name + " (LR)"
loadableHighRes1.tooltip = loadable.tooltip + " (low-resolution)"
loadableHighRes1.warning = loadable.warning
loadableHighRes1.selected = False
loadableHighRes1.confidence = confidence
loadableHighRes2 = DICOMLoadable()
loadableHighRes2.files = loadable.files
loadableHighRes2.name = loadable.name + " (HR)"
loadableHighRes2.tooltip = loadable.tooltip + " (high-resolution)"
loadableHighRes2.warning = loadable.warning
loadableHighRes2.selected = False
loadableHighRes2.confidence = confidence
return [loadable, loadableHighRes1, loadableHighRes2]
def examinePhilipsAffinity3DUS(self, filePath):
supportedSOPClassUID = '1.2.840.10008.5.1.4.1.1.3.1' # UltrasoundMultiframeImageStorage
# Quick check of SOP class UID without parsing the file...
try:
sopClassUID = slicer.dicomDatabase.fileValue(
filePath, self.tags['sopClassUID'])
if sopClassUID != supportedSOPClassUID:
# Unsupported class
logging.error("sopClassUID " + sopClassUID +
" != supportedSOPClassUID " +
supportedSOPClassUID)
return []
except Exception as e:
# Quick check could not be completed (probably Slicer DICOM database is not initialized).
# No problem, we'll try to parse the file and check the SOP class UID then.
pass
try:
ds = dicom.read_file(filePath, stop_before_pixels=True)
except Exception as e:
logging.debug("Failed to parse DICOM file: {0}".format(e.msg))
return []
if ds.SOPClassUID != supportedSOPClassUID:
# Unsupported class
logging.error("sopClassUID " + ds.SOPClassUID +
" != supportedSOPClassUID " + supportedSOPClassUID)
return []
voxelSpacingTag = findPrivateTag(ds, 0x200d, 0x03,
"Philips US Imaging DD 036")
if not voxelSpacingTag:
# this is most likely not a PhilipsAffinity image
return []
if voxelSpacingTag not in ds.keys():
return []
confidence = 0.9
if ds.PhotometricInterpretation != 'MONOCHROME2':
logging.warning('Warning: unsupported PhotometricInterpretation')
confidence = .4
if ds.BitsAllocated != 8 or ds.BitsStored != 8 or ds.HighBit != 7:
logging.warning('Warning: Bad scalar type (not unsigned byte)')
confidence = .4
if ds.SamplesPerPixel != 1:
logging.warning('Warning: multiple samples per pixel')
confidence = .4
name = ''
if hasattr(ds, 'SeriesNumber') and ds.SeriesNumber:
name = '{0}:'.format(ds.SeriesNumber)
if hasattr(ds, 'Modality') and ds.Modality:
name = '{0} {1}'.format(name, ds.Modality)
if hasattr(ds, 'SeriesDescription') and ds.SeriesDescription:
name = '{0} {1}'.format(name, ds.SeriesDescription)
if hasattr(ds, 'InstanceNumber') and ds.InstanceNumber:
name = '{0} [{1}]'.format(name, ds.InstanceNumber)
loadable = DICOMLoadable()
loadable.files = [filePath]
loadable.name = name.strip(
) # remove leading and trailing spaces, if any
loadable.tooltip = "Philips Affinity 3D ultrasound"
loadable.selected = True
loadable.confidence = confidence
return [loadable]
def examineFiles(self, files):
""" Returns a list of DICOMLoadable instances
corresponding to ways of interpreting the
files parameter.
"""
loadables = []
import tempfile
from subprocess import Popen, PIPE, CalledProcessError
with tempfile.TemporaryDirectory(
dir=slicer.app.temporaryPath) as tempDir:
# write DICOM file list to text file
inputDicomFileListFilename = os.path.join(tempDir,
"input-dicom-files.txt")
with open(inputDicomFileListFilename, 'w') as fp:
for filename in files:
fp.write("{0}\n".format(filename))
# examine using dcm2niix
cmdPath = os.path.join(
os.path.dirname(slicer.modules.dcm2niixgui.path), "Resources",
"bin", "dcm2niix")
command_line = [
cmdPath,
"-n",
"-1", # examine only, do not write output files
"-s",
"y", # input is a single filelist
"-f",
"%p_%t_%s", # output file name (difference compared to the default is that folder name is removed)
"-i",
"y", # ignore derived, localizer and 2D images
"-o",
str(tempDir), # set output folder
str(inputDicomFileListFilename)
]
logging.debug(repr(command_line))
try:
# launch dcm2niix
proc = slicer.util.launchConsoleProcess(command_line)
# process output
loadableInitialized = False
for line in proc.stdout:
line = line.rstrip()
if not loadableInitialized:
# Default scalar volume reader has confidence of 0.5, so this value will not
# make dcm2niix used by default but the user has to select it
confidence = 0.45
warningMessages = []
infoMessages = []
loadableInitialized = True
logging.debug(line)
#slicer.app.processEvents() # give a chance the application to refresh GUI
if (line.startswith("Compression will be faster with pigz")
or line.startswith("Chris Rorden's dcm2niiX")
or line.startswith("Conversion required")):
# general information, ignore
pass
elif (line.startswith(" ") or line.startswith("dx=")
or line.startswith("instance=")):
# debug message, ignore
pass
elif (line.startswith("Warning:")
or line.startswith("Unsupported transfer syntax")
or line.startswith("Unable to determine")):
if line not in warningMessages:
warningMessages.append(line)
# Reduce confidence if there was a warning.
# This value is higher than scalar volume's confidence of 0.2 when no pixel data is found.
confidence = 0.3
elif line.startswith("\t"):
# found a loadable file
[dummy, seriesNumber, filepath] = line.split('\t')
loadable = DICOMLoadable()
loadable.files = files
seriesUID = slicer.dicomDatabase.fileValue(
files[0], self.tags['seriesUID'])
seriesName = self.defaultSeriesNodeName(seriesUID)
loadable.name = seriesName
loadable.warning = ('\n').join(warningMessages)
dcm2niixGeneratedName = os.path.basename(filepath)
loadable.tooltip = (
'\n').join([dcm2niixGeneratedName] + infoMessages)
loadable.selected = True
loadable.confidence = confidence
loadable.seriesNumber = seriesNumber
loadables.append(loadable)
loadableInitialized = False
else:
infoMessages.append(line)
proc.wait()
retcode = proc.returncode
if retcode != 0:
raise CalledProcessError(retcode,
proc.args,
output=proc.stdout,
stderr=proc.stderr)
except CalledProcessError as e:
logging.debug(
"Failed to examine files using dcm2niix: {0}".format(
e.message))
return loadables
def examineFiles(self, files):
""" Returns a list of DICOMLoadable instances
corresponding to ways of interpreting the
files parameter.
"""
detailedLogging = self.isDetailedLogging()
supportedSOPClassUIDs = [
'1.2.840.10008.5.1.4.1.1.3.1', # Ultrasound Multiframe Image Storage
]
loadables = []
for filePath in files:
# Quick check of SOP class UID without parsing the file...
try:
sopClassUID = slicer.dicomDatabase.fileValue(
filePath, self.tags['sopClassUID'])
if not (sopClassUID in supportedSOPClassUIDs):
# Unsupported class
continue
manufacturerModelName = slicer.dicomDatabase.fileValue(
filePath, self.tags['manufacturerModelName'])
if manufacturerModelName != "Invenia":
if detailedLogging:
logging.debug(
"ManufacturerModelName is not Invenia, the series will not be considered as an ABUS image"
)
continue
except Exception as e:
# Quick check could not be completed (probably Slicer DICOM database is not initialized).
# No problem, we'll try to parse the file and check the SOP class UID then.
pass
try:
ds = dicom.read_file(filePath, stop_before_pixels=True)
except Exception as e:
logging.debug("Failed to parse DICOM file: {0}".format(str(e)))
continue
# check if probeCurvatureRadius is available
probeCurvatureRadiusFound = False
for privateCreator in self.privateCreators:
if self.findPrivateTag(ds, 0x0021, 0x40, privateCreator):
probeCurvatureRadiusFound = True
break
if not probeCurvatureRadiusFound:
if detailedLogging:
logging.debug(
"Probe curvature radius is not found, the series will not be considered as an ABUS image"
)
continue
name = ''
if hasattr(ds, 'SeriesNumber') and ds.SeriesNumber:
name = '{0}:'.format(ds.SeriesNumber)
if hasattr(ds, 'Modality') and ds.Modality:
name = '{0} {1}'.format(name, ds.Modality)
if hasattr(ds, 'SeriesDescription') and ds.SeriesDescription:
name = '{0} {1}'.format(name, ds.SeriesDescription)
if hasattr(ds, 'InstanceNumber') and ds.InstanceNumber:
name = '{0} [{1}]'.format(name, ds.InstanceNumber)
loadable = DICOMLoadable()
loadable.files = [filePath]
loadable.name = name.strip(
) # remove leading and trailing spaces, if any
loadable.tooltip = "GE Invenia ABUS"
loadable.warning = "Loading of this image type is experimental. Please verify image size and orientation and report any problem is found."
loadable.selected = True
loadable.confidence = 0.9 # this has to be higher than 0.7 (ultrasound sequence)
# Add to loadables list
loadables.append(loadable)
return loadables
def examineFiles(self,files):
""" Returns a list of DICOMLoadable instances
corresponding to ways of interpreting the
files parameter.
"""
supportedSOPClassUIDs = [
'1.2.840.10008.5.1.4.1.1.12.1', # X-Ray Angiographic Image Storage
'1.2.840.10008.5.1.4.1.1.3.1', # Ultrasound Multiframe Image Storage
]
# Each instance will be a loadable, that will result in one sequence browser node
# and usually one sequence (except simultaneous biplane acquisition, which will
# result in two sequences).
# Each pedal press on the XA acquisition device creates a new instance number,
# but if the device has two imaging planes (biplane) then two sequences
# will be acquired, which have the same instance number. These two sequences
# are synchronized in time, therefore they have to be assigned to the same
# browser node.
instanceNumberToLoadableIndex = {}
loadables = []
# Confidence is slightly larger than default scalar volume plugin's (0.5)
# but still leaving room for more specialized plugins.
confidence = 0.7
for filePath in files:
# Quick check of SOP class UID without parsing the file...
try:
sopClassUID = slicer.dicomDatabase.fileValue(filePath, self.tags['sopClassUID'])
if not (sopClassUID in supportedSOPClassUIDs):
# Unsupported class
return []
except Exception as e:
# Quick check could not be completed (probably Slicer DICOM database is not initialized).
# No problem, we'll try to parse the file and check the SOP class UID then.
pass
try:
ds = dicom.read_file(filePath, stop_before_pixels=True)
except Exception as e:
logging.debug("Failed to parse DICOM file: {0}".format(str(e)))
return []
if not (ds.SOPClassUID in supportedSOPClassUIDs):
# Unsupported class
return []
if not (ds.InstanceNumber in instanceNumberToLoadableIndex.keys()):
# new instance number
name = ''
if hasattr(ds, 'SeriesNumber') and ds.SeriesNumber:
name = '{0}:'.format(ds.SeriesNumber)
if hasattr(ds, 'Modality') and ds.Modality:
name = '{0} {1}'.format(name, ds.Modality)
if hasattr(ds, 'SeriesDescription') and ds.SeriesDescription:
name = '{0} {1}'.format(name, ds.SeriesDescription)
if hasattr(ds, 'InstanceNumber') and ds.InstanceNumber:
name = '{0} [{1}]'.format(name, ds.InstanceNumber)
loadable = DICOMLoadable()
loadable.files = [filePath]
loadable.name = name.strip() # remove leading and trailing spaces, if any
loadable.warning = "Image spacing may need to be calibrated for accurate size measurements."
loadable.tooltip = "{0} image sequence".format(ds.Modality)
loadable.selected = True
loadable.confidence = confidence
loadable.grayscale = ('MONOCHROME' in ds.PhotometricInterpretation)
# Add to loadables list
loadables.append(loadable)
instanceNumberToLoadableIndex[ds.InstanceNumber] = len(loadables)-1
else:
# existing instance number, add this file
loadableIndex = instanceNumberToLoadableIndex[ds.InstanceNumber]
loadables[loadableIndex].files.append(filePath)
loadable.tooltip = "{0} image sequence ({1} planes)".format(ds.Modality, len(loadables[loadableIndex].files))
return loadables
def examineGeImage3dApi(self, filePath):
if not hasattr(slicer.modules, 'ultrasoundimage3dreader'):
return []
supportedSOPClassUIDs = [
'1.2.840.10008.5.1.4.1.1.3.1', # Ultrasound Multi-frame Image IOD
'1.2.840.10008.5.1.4.1.1.6.1', # Ultrasound Image IOD
]
# Quick check of SOP class UID without parsing the file...
try:
sopClassUID = slicer.dicomDatabase.fileValue(
filePath, self.tags['sopClassUID'])
if not sopClassUID in supportedSOPClassUIDs:
# Unsupported class
return []
except Exception as e:
# Quick check could not be completed (probably Slicer DICOM database is not initialized).
# No problem, we'll try to parse the file and check the SOP class UID then.
pass
try:
ds = dicom.read_file(
filePath,
defer_size=30) # use defer_size to not load large fields
except Exception as e:
logging.debug("Failed to parse DICOM file: {0}".format(str(e)))
return []
if not ds.SOPClassUID in supportedSOPClassUIDs:
# Unsupported class
return []
try:
# Check if '3D' data type is present (for example "Trace+3D")
#
# (7fe1,0010) LO [GEMS_Ultrasound_MovieGroup_001] # 30, 1 PrivateCreator
# (7fe1,1001) SQ (Sequence with explicit length #=1) # 76006288, 1 Unknown Tag & Data
# (fffe,e000) na (Item with explicit length #=6) # 76006280, 1 Item
# (7fe1,0010) LO [GEMS_Ultrasound_MovieGroup_001] # 30, 1 PrivateCreator
# (7fe1,1002) LO [Trace+3D] # 8, 1 Unknown Tag & Data
# Get private tags
movieGroupTag = findPrivateTag(ds, 0x7fe1, 0x01,
'GEMS_Ultrasound_MovieGroup_001')
imageTypeTag = findPrivateTag(ds, 0x7fe1, 0x02,
'GEMS_Ultrasound_MovieGroup_001')
contains3D = False
movieGroup = ds[movieGroupTag].value
for movieGroupItem in movieGroup:
if imageTypeTag in movieGroupItem:
if '3D' in movieGroupItem[imageTypeTag].value:
contains3D = True
break
if not contains3D:
# Probably 2D file
return []
except:
# Not a GE MovieGroup file
return []
# It looks like a GE 3D ultrasound file
import UltrasoundImage3dReader
reader = UltrasoundImage3dReader.UltrasoundImage3dReaderFileReader(
None)
try:
reader.getLoader(filePath)
except Exception as e:
logging.debug("3D ultrasound loader not found error: {0}".format(
str(e)))
logging.info(
"File {0} looks like a GE 3D ultrasound file. Installing Image3dAPI reader may make the file loadable (https://github.com/MedicalUltrasound/Image3dAPI)."
)
return []
# GE generic moviegroup reader has confidence=0.8
# this one is much better than that, so use much higher value
confidence = 0.90
name = ''
if hasattr(ds, 'SeriesNumber') and ds.SeriesNumber:
name = '{0}:'.format(ds.SeriesNumber)
if hasattr(ds, 'Modality') and ds.Modality:
name = '{0} {1}'.format(name, ds.Modality)
if hasattr(ds, 'SeriesDescription') and ds.SeriesDescription:
name = '{0} {1}'.format(name, ds.SeriesDescription)
if hasattr(ds, 'InstanceNumber') and ds.InstanceNumber:
name = '{0} [{1}]'.format(name, ds.InstanceNumber)
loadable = DICOMLoadable()
loadable.files = [filePath]
loadable.name = name.strip(
) # remove leading and trailing spaces, if any
loadable.tooltip = "GE 3D ultrasound image sequence (using Image3dAPI)"
loadable.selected = True
loadable.confidence = confidence
return [loadable]
