def test_is_philips(self):
assert convert_philips.is_philips(
read_dicom_directory(test_data.PHILIPS_ANATOMICAL))
assert not convert_philips.is_philips(
read_dicom_directory(test_data.SIEMENS_ANATOMICAL))
assert not convert_philips.is_philips(
read_dicom_directory(test_data.GE_ANATOMICAL))
assert not convert_philips.is_philips(
read_dicom_directory(test_data.GENERIC_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 convert_philips.is_philips([dicom_header]):
if convert_philips.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 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 convert_philips.is_philips(dicom_input):
if convert_philips.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 _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 frmi
if convert_siemens.is_siemens(dicom_input):
print('Found manufacturer: SIEMENS')
return Vendor.SIEMENS
# check if it is ge frmi
if convert_ge.is_ge(dicom_input):
print('Found manufacturer: GE')
return Vendor.GE
# check if it is ge frmi
if convert_philips.is_philips(dicom_input):
print('Found manufacturer: PHILIPS')
return Vendor.PHILIPS
# check if it is siemens dti
print('WARNING: Assuming generic vendor conversion (ANATOMICAL)')
return Vendor.GENERIC
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)
