def convert_npy_to_dicom(npy_array, fname=None,
slice_thickness=None,
pixel_spacing=None,
spacing_between_slices=None,
single_file_mode=True
):
"""
convert npy array to dicom
:param npy_array: npy array
:param fname: file name
:param slice_thickness: slice thickness
:param spacing_between_slices: spacing between slices
:param pixel_spacing: pixel spacing
:param single_file_mode: if False, slice by slice dicom files are generated
:return: dcm
"""
uint16_img = np.array(npy_array).astype(float)
uint16_img = (
(uint16_img - uint16_img.min()) /
(uint16_img.max() - uint16_img.min()) * (2 ** 16 - 1)
).astype(np.uint16)
dim = len(uint16_img.shape)
if dim == 1:
raise Exception('Cannot convert 1D array to dicom')
elif dim == 2:
uint16_img = uint16_img[np.newaxis, :, :]
elif dim > 3:
raise Exception('{}D array is not supported.'.format(dim))
x_min = float(npy_array.min())
x_max = float(npy_array.max())
x_max_min = x_max - x_min
t_max = (2 ** 16) - 1
slope = x_max_min / t_max
intercept = x_min
now = datetime.now().timestamp()
file_meta = Dataset()
file_meta.MediaStorageSOPClassUID = '1.2.840.100008.5.1.4.1.1.20'
file_meta.MediaStorageSOPInstanceUID = f'333.333.0.0.0.333.333333333.{now}'
file_meta.ImplementationClassUID = '0.0.0.0'
file_meta.FileMetaInformationGroupLength = 140
dcm = FileDataset(fname, {}, file_meta=file_meta, preamble=b'\0' * 128)
dcm.Modality = 'OT'
if single_file_mode:
dcm.ImageType = ["DERIVED", "PRIMARY", "RECON TOMO", "EMISSION"]
else:
dcm.ImageType = ["DERIVED", "SECONDARY"]
dcm.ContentDate = datetime.now().strftime('%Y%m%d')
dcm.ContentTime = datetime.now().strftime('%H%M%S')
dcm.InstanceCreationDate = datetime.now().strftime('%Y%m%d')
dcm.InstanceCreationTime = datetime.now().strftime('%H%M%S')
dcm.SeriesDate = datetime.now().strftime('%Y%m%d')
dcm.SeriesTime = datetime.now().strftime('%H%M%S')
dcm.AcquisitionTime = datetime.now().strftime('%H%M%S')
dcm.PatientName = os.path.basename(fname)
dcm.PatientBirthDate = datetime.now().strftime('%Y%m%d')
dcm.PatientAge = '000Y'
dcm.PatientSize = 1
dcm.PatientWeight = 1
dcm.PatientID = os.path.basename(fname)
dcm.PatientSex = 'O'
dcm.StudyDescription = os.path.basename(fname)
dcm.StudyDate = datetime.now().strftime('%Y%m%d')
dcm.StudyTime = datetime.now().strftime('%H%M%S')
dcm.StudyID = os.path.basename(fname)
dcm.SeriesDescription = os.path.basename(fname)
dcm.SamplesPerPixel = 1
dcm.PhotometricInterpretation = 'MONOCHROME2'
dcm.PixelRepresentation = 0 # unsigned 0, signed 1
dcm.HighBit = 16
dcm.BitsStored = 16
dcm.BitsAllocated = 16
dcm.Columns = uint16_img.shape[2]
dcm.Rows = uint16_img.shape[1]
if single_file_mode:
dcm.NumberOfFrames = uint16_img.shape[0]
dcm.ImagesInAquisition = uint16_img.shape[0]
dcm.SliceVector = (np.arange(uint16_img.shape[0]) + 1).tolist()
dcm.FrameIncrementPointer = [(0x0054, 0x0080)]
else:
dcm.NumberOfTimeSlices = 1
dcm.FrameReferenceTime = 0.
dcm.ImageOrientationPatient = [1., 0., 0., 0., -1., 0.]
dcm.SeriesNumber = 0
dcm.NumberOfSlices = uint16_img.shape[0]
dcm.RescaleIntercept = intercept
dcm.RescaleSlope = slope
dcm.Units = "NONE"
dcm.DecayCorrection = "NONE"
dcm.InstanceCreatorUID = '333.333.0.0.0'
dcm.SOPClassUID = '1.2.840.10008.5.1.4.1.1.20'
dcm.SliceThickness = 1 if slice_thickness is None else slice_thickness
if spacing_between_slices is None:
dcm.SpacingBetweenSlices = 1 if slice_thickness is None else slice_thickness
else:
dcm.SpacingBetweenSlices = spacing_between_slices
ps = 1 if pixel_spacing is None else pixel_spacing
if isinstance(ps, list) or isinstance(ps, np.ndarray):
dcm.PixelSpacing = [ps[0], ps[1]]
else:
dcm.PixelSpacing = [ps, ps]
if single_file_mode:
dcm.PixelData = uint16_img.tostring()
dcm.StudyInstanceUID = f'333.333.0.0.0.{now}'
dcm.SeriesInstanceUID = f'333.333.0.0.0.{now}.3333'
dcm.FrameOfReferenceUID = dcm.StudyInstanceUID
dcm.SeriesNumber = 0
dcm.InstanceNumber = 0
dcm.BodyPartExamined = 'UNKNOWN'
dcm.Manufacturer = 'DicomConversionUtils'
dcm.DeviceSerialNumber = ''
dcm.AcquisitionTerminationCondition = 'MANU'
dcm.SoftwareVersions = f'{pydicom_ext_version}'
dcm.AccessionNumber = '{:13d}'.format(random.randint(0, 1e13))
dcm.InstitutionName = 'DicomConversionUtils'
dcm.ImagePositionPatient = [0, 0, 0]
if fname is not None:
dcm.save_as(fname, write_like_original=False)
return dcm
else:
dcms = []
for slice_idx in range(uint16_img.shape[0]):
dcm.SOPInstanceUID = f'333.333.0.0.0.{now}.{slice_idx:06d}'
dcm.PixelData = uint16_img[slice_idx].tostring()
dcm.StudyInstanceUID = f'333.333.0.0.0.{now}'
dcm.SeriesInstanceUID = f'333.333.0.0.0.{now}.3333'
dcm.FrameOfReferenceUID = dcm.StudyInstanceUID
dcm.InstanceNumber = slice_idx
dcm.BodyPartExamined = 'UNKNOWN'
dcm.Manufacturer = 'DicomConversionUtils'
dcm.DeviceSerialNumber = ''
dcm.AcquisitionTerminationCondition = 'MANU'
dcm.SoftwareVersions = f'{pydicom_ext_version}'
dcm.AccessionNumber = '{:13d}'.format(random.randint(0, 1e13))
dcm.InstitutionName = 'DicomConversionUtils'
dcm.ImageIndex = slice_idx
if spacing_between_slices is None:
if slice_thickness is None:
dcm.ImagePositionPatient = [0, 0, slice_idx]
dcm.SliceLocation = slice_idx
else:
dcm.ImagePositionPatient = [0, 0, slice_idx * slice_thickness]
dcm.SliceLocation = slice_idx * slice_thickness
else:
dcm.ImagePositionPatient = [0, 0, slice_idx * spacing_between_slices]
dcm.SliceLocation = slice_idx * spacing_between_slices
dcms.append(dcm)
if fname is not None:
f = copy.copy(fname)
if ".dcm" in f:
f = f.replace(".dcm", f"_{slice_idx:06d}.dcm")
else:
f += f"_{slice_idx:06d}.dcm"
dcm.save_as(f, write_like_original=False)
return dcms
def convert_npy_to_dicom(fname,
npy_array,
slice_thickness=None,
pixel_spacing=None):
"""
convert npy array to dicom
:param fname: file name
:param npy_array: npy array
:param slice_thickness: slice thickness
:param pixel_spacing: pixel spacing
:return: dcm
"""
uint16_img = np.array(npy_array)
uint16_img = ((uint16_img - uint16_img.min()) /
(uint16_img.max() - uint16_img.min()) * (2**16 - 1)).astype(
np.uint16)
dim = len(uint16_img.shape)
if dim == 1:
raise Exception('Cannot convert 1D array to dicom')
elif dim == 2:
uint16_img = uint16_img[np.newaxis, :, :]
elif dim > 3:
raise Exception('{}D array is not supported.'.format(dim))
x_min = npy_array.min()
x_max = npy_array.max()
x_max_min = x_max - x_min
t_max = (2**16) - 1
slope = x_max_min / t_max
intercept = x_min
file_meta = Dataset()
file_meta.MediaStorageSOPClassUID = '0.0.000.000000.0.0.0.0.0.00'
file_meta.MediaStorageSOPInstanceUID = \
'333.333.0.0.0.333.333333333.{}'.format(
datetime.now().timestamp())
file_meta.ImplementationClassUID = '0.0.0.0'
dcm = FileDataset(fname, {}, file_meta=file_meta, preamble=b'\0' * 128)
dcm.Modality = 'OT'
dcm.ImageType = ['ORIGINAL', 'PRIMARY']
dcm.ContentDate = datetime.now().strftime('%Y%m%d')
dcm.ContentTime = datetime.now().strftime('%H%M%S')
dcm.InstanceCreationDate = datetime.now().strftime('%Y%m%d')
dcm.InstanceCreationTime = datetime.now().strftime('%H%M%S')
dcm.SeriesDate = datetime.now().strftime('%Y%m%d')
dcm.SeriesTime = datetime.now().strftime('%H%M%S')
dcm.AcquisitionTime = datetime.now().strftime('%H%M%S')
dcm.PatientName = os.path.basename(fname)
dcm.PatientBirthDate = datetime.now().strftime('%Y%m%d')
dcm.PatientAge = '000Y'
dcm.PatientSize = 1
dcm.PatientWeight = 1
dcm.PatientID = os.path.basename(fname)
dcm.PatientSex = 'O'
dcm.StudyDescription = os.path.basename(fname)
dcm.StudyDate = datetime.now().strftime('%Y%m%d')
dcm.StudyTime = datetime.now().strftime('%H%M%S')
dcm.StudyID = os.path.basename(fname)
dcm.SeriesDescription = os.path.basename(fname)
dcm.SamplesPerPixel = 1
dcm.PhotometricInterpretation = 'MONOCHROME1'
dcm.PixelRepresentation = 0 # unsigned 0, signed 1
dcm.HighBit = 16
dcm.BitsStored = 16
dcm.BitsAllocated = 16
dcm.SmallestImagePixelValue = uint16_img.min()
dcm.LargestImagePixelValue = uint16_img.max()
dcm.Columns = uint16_img.shape[2]
dcm.Rows = uint16_img.shape[1]
dcm.NumberOfFrames = uint16_img.shape[0]
dcm.NumberOfSlices = uint16_img.shape[0]
dcm.ImagesInAquisition = uint16_img.shape[0]
dcm.RescaleIntercept = intercept
dcm.RescaleSlope = slope
dcm.SliceVector = (np.arange(uint16_img.shape[0]) + 1).tolist()
dcm.FrameIncrementPointer = [(0x0054, 0x0080)]
dcm.PixelData = uint16_img.tostring()
dcm.SliceThickness = 1 if slice_thickness is None else slice_thickness
ps = 1 if pixel_spacing is None else pixel_spacing
if isinstance(ps, list) or isinstance(ps, np.ndarray):
dcm.PixelSpacing = [ps[0], ps[1]]
else:
dcm.PixelSpacing = [ps, ps]
dcm.InstanceCreatorUID = '333.333.0.0.0'
dcm.SOPClassUID = '0.0.000.00000.0.0.0.0.0.00'
dcm.SOPInstanceUID = '333.333.0.0.0.{}'.format(datetime.now().timestamp())
dcm.StudyInstanceUID = '333.333.0.0.0.{}'.format(
datetime.now().timestamp())
dcm.SeriesInstanceUID = '333.333.0.0.0.{}.3333'.format(
datetime.now().timestamp())
dcm.FrameOfReferenceUID = dcm.StudyInstanceUID
dcm.SeriesNumber = 0
dcm.InstanceNumber = 0
dcm.BodyPartExamined = 'UNKNOWN'
dcm.Manufacturer = 'DicomConversionUtils'
dcm.DeviceSerialNumber = ''
dcm.AcquisitionTerminationCondition = 'MANU'
dcm.SoftwareVersions = 'UNKNOWN'
dcm.AccessionNumber = '{:13d}'.format(random.randint(0, 1e13))
dcm.InstitutionName = 'DicomConversionUtils'
dcm.save_as(fname)
return dcm
