def _get_window(dicom_file: pydicom.FileDataset, window='default', unit=None):
if isinstance(window, dict):
wc = window.get('window_center')
ww = window.get('window_width')
elif window == 'default' or unit is None:
try:
wc = dicom_file.WindowCenter
ww = dicom_file.WindowWidth
if isinstance(wc, pydicom.multival.MultiValue):
wc = wc[0]
if isinstance(ww, pydicom.multival.MultiValue):
ww = ww[0]
except:
BitsStored = dicom_file.get('BitsStored')
wc = 2**(BitsStored - 1)
ww = 2**BitsStored
elif isinstance(window, str) and unit in ['HU', 'Hounsfield Unit']:
wc, ww = get_ct_window(window)
else:
try:
wc = dicom_file.WindowCenter
ww = dicom_file.WindowWidth
if isinstance(wc, pydicom.multival.MultiValue):
wc = wc[0]
if isinstance(ww, pydicom.multival.MultiValue):
ww = ww[0]
except:
wc = None
ww = None
if wc is None or ww is None:
raise ValueError('Either window center or window width not found')
return wc, ww
def voi_lut_trans(dicom_file: pydicom.FileDataset,
image_data: numpy.ndarray,
depth,
window='default',
unit: str = None):
VOILUTSequence = getattr(dicom_file, 'VOILUTSequence', [{}])[0]
lut_descriptor = VOILUTSequence.get('LUTDescriptor')
if lut_descriptor is None:
lut_descriptor = VOILUTSequence.get('LUTDescriptor')
if isinstance(lut_descriptor, bytes):
PixelRepresentation = int(dicom_file.get('PixelRepresentation'))
if modality_classifier(
dicom_file) is None and PixelRepresentation == 0:
dtype = numpy.ushort
else:
dtype = numpy.short
lut_descriptor = numpy.frombuffer(lut_descriptor, dtype)
lut_data = VOILUTSequence.get('LUTData')
if isinstance(lut_data, bytes):
if lut_descriptor[2] == 8:
dtype = numpy.uint8
elif lut_descriptor[2] == 16:
dtype = numpy.uint16
else:
raise ValueError(
f'LUTDescriptor[2] should be 8 or 16. Got {lut_descriptor[2]}')
lut_data = numpy.frombuffer(lut_data, dtype)
scale_factor = depth / int(2**getattr(dicom_file, 'BitsStored', 12))
return lut_trans(image_data, lut_descriptor, lut_data, scale_factor)
def voi_classifier(dicom_file: pydicom.FileDataset):
"""
Get value of interest (voi) transform method name from dicom object
:param dicom_file: object read from pydicom
:return: voi transform method name. Includes
'LINEAR', 'LINEAR_EXACT', 'SIGMOID', 'TABLE', or None
"""
VOILUTFunction = dicom_file.get('VOILUTFunction')
VOILUTSequence = dicom_file.get('VOILUTSequence')
WindowCenter = dicom_file.get('WindowCenter')
if (VOILUTSequence is not None) and (WindowCenter is None):
return 'TABLE'
elif WindowCenter is not None:
if VOILUTFunction is None:
return 'LINEAR'
else:
return VOILUTFunction
else:
return 'LINEAR'
def modality_lut_trans(dicom_file: pydicom.FileDataset, image_data: numpy.ndarray):
ModalityLUTSequence = dicom_file.get('ModalityLUTSequence')[0]
lut_descriptor = ModalityLUTSequence.get('LUTDescriptor')
if lut_descriptor is None: # debug
lut_descriptor = ModalityLUTSequence.get('LUTDescriptor') # if don't do this line, line 40 will be None
if isinstance(lut_descriptor, bytes):
PixelRepresentation = int(dicom_file.get('PixelRepresentation'))
dtype = numpy.ushort if PixelRepresentation == 0 else numpy.short
lut_descriptor = numpy.frombuffer(lut_descriptor, dtype)
lut_data = ModalityLUTSequence.get('LUTData')
if isinstance(lut_data, bytes):
if lut_descriptor[2] == 8:
dtype = numpy.uint8
elif lut_descriptor[2] == 16:
dtype = numpy.uint16
else:
raise ValueError(f'LUTDescriptor[2] should be 8 or 16. Got {lut_descriptor[2]}')
lut_data = numpy.frombuffer(lut_data, dtype)
unit = ModalityLUTSequence.get('ModalityLUTType')
return lut_trans(image_data, lut_descriptor, lut_data), unit
def get_dcm_filed(__dcm: pydicom.FileDataset, __field_name: str):
__field = __dcm.get(__field_name)
if type(__field) == pydicom.multival.MultiValue:
return int(__field[0])
else:
return int(__field)