def test_is_philips(self):
assert common.is_philips(
read_dicom_directory(test_data.PHILIPS_ANATOMICAL))
assert not common.is_philips(
read_dicom_directory(test_data.SIEMENS_ANATOMICAL))
assert not common.is_philips(
read_dicom_directory(test_data.GE_ANATOMICAL))
assert not common.is_philips(
read_dicom_directory(test_data.GENERIC_ANATOMICAL))
assert not common.is_philips(
read_dicom_directory(test_data.HITACHI_ANATOMICAL))
def _is_valid_imaging_dicom(dicom_header):
"""
Function will do some basic checks to see if this is a valid imaging dicom
"""
# if it is philips and multiframe dicom then we assume it is ok
try:
if common.is_philips([dicom_header]):
if common.is_multiframe_dicom([dicom_header]):
return True
if "SeriesInstanceUID" not in dicom_header:
return False
if "InstanceNumber" not in dicom_header:
return False
if "ImageOrientationPatient" not in dicom_header or len(dicom_header.ImageOrientationPatient) < 6:
return False
if "ImagePositionPatient" not in dicom_header or len(dicom_header.ImagePositionPatient) < 3:
return False
# for all others if there is image position patient we assume it is ok
if Tag(0x0020, 0x0037) not in dicom_header:
return False
return True
except (KeyError, AttributeError):
return False
def _is_valid_imaging_dicom(dicom_header):
"""
Function will do some basic checks to see if this is a valid imaging dicom
"""
# if it is philips and multiframe dicom then we assume it is ok
try:
if common.is_philips([dicom_header]):
if common.is_multiframe_dicom([dicom_header]):
return True
if "SeriesInstanceUID" not in dicom_header:
return False
if "InstanceNumber" not in dicom_header:
return False
if "ImageOrientationPatient" not in dicom_header or len(dicom_header.ImageOrientationPatient) < 6:
return False
if "ImagePositionPatient" not in dicom_header or len(dicom_header.ImagePositionPatient) < 3:
return False
# for all others if there is image position patient we assume it is ok
if Tag(0x0020, 0x0037) not in dicom_header:
return False
return True
except (KeyError, AttributeError):
return False
def dicom_to_nifti(dicom_input, output_file=None):
"""
This is the main dicom to nifti conversion fuction for philips images.
As input philips images are required. It will then determine the type of images and do the correct conversion
Examples: See unit test
:param output_file: file path to the output nifti
:param dicom_input: directory with dicom files for 1 scan
"""
assert common.is_philips(dicom_input)
if common.is_multiframe_dicom(dicom_input):
_assert_explicit_vr(dicom_input)
logger.info('Found multiframe dicom')
if _is_multiframe_4d(dicom_input):
logger.info('Found sequence type: MULTIFRAME 4D')
return _multiframe_to_nifti(dicom_input, output_file)
if _is_multiframe_anatomical(dicom_input):
logger.info('Found sequence type: MULTIFRAME ANATOMICAL')
return _multiframe_to_nifti(dicom_input, output_file)
else:
logger.info('Found singleframe dicom')
grouped_dicoms = _get_grouped_dicoms(dicom_input)
if _is_singleframe_4d(dicom_input):
logger.info('Found sequence type: SINGLEFRAME 4D')
return _singleframe_to_nifti(grouped_dicoms, output_file)
logger.info('Assuming anatomical data')
return convert_generic.dicom_to_nifti(dicom_input, output_file)
def dicom_to_nifti(dicom_input, output_file=None):
"""
This is the main dicom to nifti conversion fuction for philips images.
As input philips images are required. It will then determine the type of images and do the correct conversion
Examples: See unit test
:param output_file: file path to the output nifti
:param dicom_input: directory with dicom files for 1 scan
"""
assert common.is_philips(dicom_input)
if common.is_multiframe_dicom(dicom_input):
_assert_explicit_vr(dicom_input)
logger.info('Found multiframe dicom')
if _is_multiframe_4d(dicom_input):
logger.info('Found sequence type: MULTIFRAME 4D')
return _multiframe_to_nifti(dicom_input, output_file)
if _is_multiframe_anatomical(dicom_input):
logger.info('Found sequence type: MULTIFRAME ANATOMICAL')
return _multiframe_to_nifti(dicom_input, output_file)
else:
logger.info('Found singleframe dicom')
grouped_dicoms = _get_grouped_dicoms(dicom_input)
if _is_singleframe_4d(dicom_input):
logger.info('Found sequence type: SINGLEFRAME 4D')
return _singleframe_to_nifti(grouped_dicoms, output_file)
logger.info('Assuming anatomical data')
return convert_generic.dicom_to_nifti(dicom_input, output_file)
def are_imaging_dicoms(dicom_input):
"""
This function will check the dicom headers to see which type of series it is
Possibilities are fMRI, DTI, Anatomical (if no clear type is found anatomical is used)
:param dicom_input: directory with dicom files or a list of dicom objects
"""
# if it is philips and multiframe dicom then we assume it is ok
if common.is_philips(dicom_input):
if common.is_multiframe_dicom(dicom_input):
return True
# for all others if there is image position patient we assume it is ok
header = dicom_input[0]
return Tag(0x0020, 0x0037) in header
def are_imaging_dicoms(dicom_input):
"""
This function will check the dicom headers to see which type of series it is
Possibilities are fMRI, DTI, Anatomical (if no clear type is found anatomical is used)
:param dicom_input: directory with dicom files or a list of dicom objects
"""
# if it is philips and multiframe dicom then we assume it is ok
if common.is_philips(dicom_input):
if common.is_multiframe_dicom(dicom_input):
return True
# for all others if there is image position patient we assume it is ok
header = dicom_input[0]
return Tag(0x0020, 0x0037) in header
def dicom_to_nifti(dicom_input, output_file=None):
"""
This is the main dicom to nifti conversion fuction for philips images.
As input philips images are required. It will then determine the type of images and do the correct conversion
Examples: See unit test
:param output_file: file path to the output nifti
:param dicom_input: directory with dicom files for 1 scan
"""
assert common.is_philips(dicom_input)
# remove duplicate slices based on position and data
dicom_input = convert_generic.remove_duplicate_slices(dicom_input)
# remove localizers based on image type
dicom_input = convert_generic.remove_localizers_by_imagetype(dicom_input)
# remove_localizers based on image orientation (only valid if slicecount is validated)
dicom_input = convert_generic.remove_localizers_by_orientation(dicom_input)
# if no dicoms remain raise exception
if not dicom_input:
raise ConversionValidationError('TOO_FEW_SLICES/LOCALIZER')
if common.is_multiframe_dicom(dicom_input):
_assert_explicit_vr(dicom_input)
logger.info('Found multiframe dicom')
if _is_multiframe_4d(dicom_input):
logger.info('Found sequence type: MULTIFRAME 4D')
return _multiframe_to_nifti(dicom_input, output_file)
if _is_multiframe_anatomical(dicom_input):
logger.info('Found sequence type: MULTIFRAME ANATOMICAL')
return _multiframe_to_nifti(dicom_input, output_file)
else:
logger.info('Found singleframe dicom')
grouped_dicoms = _get_grouped_dicoms(dicom_input)
if _is_singleframe_4d(dicom_input):
logger.info('Found sequence type: SINGLEFRAME 4D')
return _singleframe_to_nifti(grouped_dicoms, output_file)
logger.info('Assuming anatomical data')
return convert_generic.dicom_to_nifti(dicom_input, output_file)
def _get_vendor(dicom_input):
"""
This function will check the dicom headers to see which type of series it is
Possibilities are fMRI, DTI, Anatomical (if no clear type is found anatomical is used)
"""
# check if it is siemens
if common.is_siemens(dicom_input):
logger.info('Found manufacturer: SIEMENS')
return Vendor.SIEMENS
# check if it is ge
if common.is_ge(dicom_input):
logger.info('Found manufacturer: GE')
return Vendor.GE
# check if it is philips
if common.is_philips(dicom_input):
logger.info('Found manufacturer: PHILIPS')
return Vendor.PHILIPS
# check if it is philips
if common.is_hitachi(dicom_input):
logger.info('Found manufacturer: HITACHI')
return Vendor.HITACHI
# generic by default
logger.info('WARNING: Assuming generic vendor conversion (ANATOMICAL)')
return Vendor.GENERIC
def _get_vendor(dicom_input):
"""
This function will check the dicom headers to see which type of series it is
Possibilities are fMRI, DTI, Anatomical (if no clear type is found anatomical is used)
"""
# check if it is siemens
if common.is_siemens(dicom_input):
logger.info('Found manufacturer: SIEMENS')
return Vendor.SIEMENS
# check if it is ge
if common.is_ge(dicom_input):
logger.info('Found manufacturer: GE')
return Vendor.GE
# check if it is philips
if common.is_philips(dicom_input):
logger.info('Found manufacturer: PHILIPS')
return Vendor.PHILIPS
# check if it is philips
if common.is_hitachi(dicom_input):
logger.info('Found manufacturer: HITACHI')
return Vendor.HITACHI
# generic by default
logger.info('WARNING: Assuming generic vendor conversion (ANATOMICAL)')
return Vendor.GENERIC
def test_is_philips(self):
assert common.is_philips(read_dicom_directory(test_data.PHILIPS_ANATOMICAL))
assert not common.is_philips(read_dicom_directory(test_data.SIEMENS_ANATOMICAL))
assert not common.is_philips(read_dicom_directory(test_data.GE_ANATOMICAL))
assert not common.is_philips(read_dicom_directory(test_data.GENERIC_ANATOMICAL))
assert not common.is_philips(read_dicom_directory(test_data.HITACHI_ANATOMICAL))
def anonymize_directory(input_directory, output_directory=None):
if output_directory is None:
output_directory = input_directory
study_uid = pydicom.uid.generate_uid()
series_uid = pydicom.uid.generate_uid()
date = datetime.datetime.now().strftime("%Y%m%d")
time = datetime.datetime.now().strftime("%H%M%S.000000")
fields_to_keep = {
'SpecificCharacterSet':
None,
'ImageType':
None,
'AcquisitionMatrix':
None,
'SOPClassUID':
None,
'SOPInstanceUID':
None, # Will be replaced by file-unique UID
'StudyDate':
date,
'SeriesDate':
date,
'AcquisitionDate':
date,
'ContentDate':
date,
'StudyTime':
time,
'AcquisitionTime':
time,
'AcquisitionNumber':
None,
'Modality':
None,
'Manufacturer':
None,
'ManufacturersModelName':
None,
'PatientName':
'dicom2nifti',
'PatientID':
'dicom2nifti',
'PatientsBirthDate':
date,
'PatientsSex':
None,
'PatientsAge':
'0Y',
'PatientPosition':
None,
'ScanningSequence':
None,
'SequenceVariant':
None,
'MRAcquisitionType':
None,
'SequenceName':
'dicom2nifti',
'RepetitionTime':
None,
'EchoTime':
None,
'InversionTime':
None,
'DeviceSerialNumber':
'1234',
'StudyInstanceUID':
study_uid,
'SeriesInstanceUID':
series_uid,
'StudyID':
'dicom2nifti',
'SeriesNumber':
None,
'InstanceNumber':
None,
'ImagePositionPatient':
None,
'ImageOrientationPatient':
None,
'SliceLocation':
None,
'PhotometricInterpretation':
None,
'Rows':
None,
'Columns':
None,
'PixelSpacing':
None,
'BitsAllocated':
None,
'BitsStored':
None,
'HighBit':
None,
'RescaleSlope':
None,
'RescaleIntercept':
None,
'PixelRepresentation':
None,
'NumberOfFrames':
None,
'SamplesPerPixel':
None,
'SpacingBetweenSlices':
None,
# Pixel Data must be specified with hex code as it will not work for compressed dicoms
(0x7fe0, 0x0010):
None
}
if is_philips(read_dicom_directory(input_directory)):
philips_fields = {
(0x2001, 0x100a): None,
(0x2001, 0x1003): None,
(0x2001, 0x105f): None,
(0x2005, 0x100d): None,
(0x2005, 0x100e): None,
(0x2005, 0x10b0): None,
(0x2005, 0x10b1): None,
(0x2005, 0x10b2): None,
(0x0018, 0x9087): None,
(0x0018, 0x9089): None,
(0x5200, 0x9230): None,
'SharedFunctionalGroupsSequence': None
}
fields_to_keep.update(philips_fields)
if is_siemens(read_dicom_directory(input_directory)):
siemens_fields = {
(0x0019, 0x100c): None,
(0x0029, 0x1020): None,
(0x0051, 0x100b): None,
(0x0019, 0x100e): None
}
fields_to_keep.update(siemens_fields)
if is_ge(read_dicom_directory(input_directory)):
ge_fields = {
(0x0020, 0x9056): None,
(0x0020, 0x9057): None,
(0x0043, 0x1039): None,
(0x0019, 0x10bb): None,
(0x0019, 0x10bc): None,
(0x0019, 0x10bd): None
}
fields_to_keep.update(ge_fields)
_anonymize_files(input_directory, output_directory, fields_to_keep)
