def _create_bvals_bvecs(multiframe_dicom, bval_file, bvec_file, nifti, nifti_file):
"""
Write the bvals from the sorted dicom files to a bval file
Inspired by https://github.com/IBIC/ibicUtils/blob/master/ibicBvalsBvecs.py
"""
# create the empty arrays
number_of_stack_slices = common.get_ss_value(multiframe_dicom[Tag(0x2001, 0x105f)][0][Tag(0x2001, 0x102d)])
number_of_stacks = int(int(multiframe_dicom.NumberOfFrames) / number_of_stack_slices)
bvals = numpy.zeros([number_of_stacks], dtype=numpy.int32)
bvecs = numpy.zeros([number_of_stacks, 3])
# loop over all timepoints and create a list with all bvals and bvecs
for stack_index in range(0, number_of_stacks):
stack = multiframe_dicom[Tag(0x5200, 0x9230)][stack_index]
if str(stack[Tag(0x0018, 0x9117)][0][Tag(0x0018, 0x9075)].value) == 'DIRECTIONAL':
bvals[stack_index] = common.get_fd_value(stack[Tag(0x0018, 0x9117)][0][Tag(0x0018, 0x9087)])
bvecs[stack_index, :] = common.get_fd_array_value(stack[Tag(0x0018, 0x9117)][0]
[Tag(0x0018, 0x9076)][0][Tag(0x0018, 0x9089)], 3)
# truncate nifti if needed
nifti, bvals, bvecs = _fix_diffusion_images(bvals, bvecs, nifti, nifti_file)
# save the found bvecs to the file
if numpy.count_nonzero(bvals) > 0 or numpy.count_nonzero(bvecs) > 0:
common.write_bval_file(bvals, bval_file)
common.write_bvec_file(bvecs, bvec_file)
else:
bval_file = None
bvec_file = None
bvals = None
bvecs = None
return bvals, bvecs, bval_file, bvec_file
def _create_affine_multiframe(multiframe_dicom):
"""
Function to create the affine matrix for a siemens mosaic dataset
This will work for siemens dti and 4D if in mosaic format
"""
first_frame = multiframe_dicom[Tag(0x5200, 0x9230)][0]
last_frame = multiframe_dicom[Tag(0x5200, 0x9230)][-1]
# Create affine matrix (http://nipy.sourceforge.net/nibabel/dicom/dicom_orientation.html#dicom-slice-affine)
image_orient1 = numpy.array(first_frame.PlaneOrientationSequence[0].ImageOrientationPatient)[0:3].astype(float)
image_orient2 = numpy.array(first_frame.PlaneOrientationSequence[0].ImageOrientationPatient)[3:6].astype(float)
normal = numpy.cross(image_orient1, image_orient2)
delta_r = float(first_frame[0x2005, 0x140f][0].PixelSpacing[0])
delta_c = float(first_frame[0x2005, 0x140f][0].PixelSpacing[1])
image_pos = numpy.array(first_frame.PlanePositionSequence[0].ImagePositionPatient).astype(float)
last_image_pos = numpy.array(last_frame.PlanePositionSequence[0].ImagePositionPatient).astype(float)
number_of_stack_slices = int(common.get_ss_value(multiframe_dicom[Tag(0x2001, 0x105f)][0][Tag(0x2001, 0x102d)]))
delta_s = abs(numpy.linalg.norm(last_image_pos - image_pos)) / (number_of_stack_slices - 1)
return numpy.array(
[[-image_orient1[0] * delta_c, -image_orient2[0] * delta_r, -delta_s * normal[0], -image_pos[0]],
[-image_orient1[1] * delta_c, -image_orient2[1] * delta_r, -delta_s * normal[1], -image_pos[1]],
[image_orient1[2] * delta_c, image_orient2[2] * delta_r, delta_s * normal[2], image_pos[2]],
[0, 0, 0, 1]])
def _create_bvals_bvecs(multiframe_dicom, bval_file, bvec_file, nifti, nifti_file):
"""
Write the bvals from the sorted dicom files to a bval file
Inspired by https://github.com/IBIC/ibicUtils/blob/master/ibicBvalsBvecs.py
"""
# create the empty arrays
number_of_stack_slices = common.get_ss_value(multiframe_dicom[Tag(0x2001, 0x105f)][0][Tag(0x2001, 0x102d)])
number_of_stacks = int(int(multiframe_dicom.NumberOfFrames) / number_of_stack_slices)
bvals = numpy.zeros([number_of_stacks], dtype=numpy.int32)
bvecs = numpy.zeros([number_of_stacks, 3])
# loop over all timepoints and create a list with all bvals and bvecs
for stack_index in range(0, number_of_stacks):
stack = multiframe_dicom[Tag(0x5200, 0x9230)][stack_index]
if str(stack[Tag(0x0018, 0x9117)][0][Tag(0x0018, 0x9075)].value) == 'DIRECTIONAL':
bvals[stack_index] = common.get_fd_value(stack[Tag(0x0018, 0x9117)][0][Tag(0x0018, 0x9087)])
bvecs[stack_index, :] = common.get_fd_array_value(stack[Tag(0x0018, 0x9117)][0]
[Tag(0x0018, 0x9076)][0][Tag(0x0018, 0x9089)], 3)
# truncate nifti if needed
nifti, bvals, bvecs = _fix_diffusion_images(bvals, bvecs, nifti, nifti_file)
# save the found bvecs to the file
if numpy.count_nonzero(bvals) > 0 or numpy.count_nonzero(bvecs) > 0:
common.write_bval_file(bvals, bval_file)
common.write_bvec_file(bvecs, bvec_file)
else:
bval_file = None
bvec_file = None
bvals = None
bvecs = None
return bvals, bvecs, bval_file, bvec_file
def _create_affine_multiframe(multiframe_dicom):
"""
Function to create the affine matrix for a siemens mosaic dataset
This will work for siemens dti and 4D if in mosaic format
"""
first_frame = multiframe_dicom[Tag(0x5200, 0x9230)][0]
last_frame = multiframe_dicom[Tag(0x5200, 0x9230)][-1]
# Create affine matrix (http://nipy.sourceforge.net/nibabel/dicom/dicom_orientation.html#dicom-slice-affine)
image_orient1 = numpy.array(first_frame.PlaneOrientationSequence[0].ImageOrientationPatient)[0:3].astype(float)
image_orient2 = numpy.array(first_frame.PlaneOrientationSequence[0].ImageOrientationPatient)[3:6].astype(float)
normal = numpy.cross(image_orient1, image_orient2)
delta_r = float(first_frame[0x2005, 0x140f][0].PixelSpacing[0])
delta_c = float(first_frame[0x2005, 0x140f][0].PixelSpacing[1])
image_pos = numpy.array(first_frame.PlanePositionSequence[0].ImagePositionPatient).astype(float)
last_image_pos = numpy.array(last_frame.PlanePositionSequence[0].ImagePositionPatient).astype(float)
number_of_stack_slices = int(common.get_ss_value(multiframe_dicom[Tag(0x2001, 0x105f)][0][Tag(0x2001, 0x102d)]))
delta_s = abs(numpy.linalg.norm(last_image_pos - image_pos)) / (number_of_stack_slices - 1)
return numpy.array(
[[-image_orient1[0] * delta_c, -image_orient2[0] * delta_r, -delta_s * normal[0], -image_pos[0]],
[-image_orient1[1] * delta_c, -image_orient2[1] * delta_r, -delta_s * normal[1], -image_pos[1]],
[image_orient1[2] * delta_c, image_orient2[2] * delta_r, delta_s * normal[2], image_pos[2]],
[0, 0, 0, 1]])
def _multiframe_to_block(multiframe_dicom):
"""
Generate a full datablock containing all stacks
"""
# Calculate the amount of stacks and slices in the stack
number_of_stack_slices = int(common.get_ss_value(multiframe_dicom[Tag(0x2001, 0x105f)][0][Tag(0x2001, 0x102d)]))
number_of_stacks = int(int(multiframe_dicom.NumberOfFrames) / number_of_stack_slices)
# We create a numpy array
size_x = multiframe_dicom.pixel_array.shape[2]
size_y = multiframe_dicom.pixel_array.shape[1]
size_z = number_of_stack_slices
size_t = number_of_stacks
# get the format
format_string = common.get_numpy_type(multiframe_dicom)
# get header info needed for ordering
frame_info = multiframe_dicom[0x5200, 0x9230]
data_4d = numpy.zeros((size_z, size_y, size_x, size_t), dtype=format_string)
# loop over each slice and insert in datablock
t_location_index = _get_t_position_index(multiframe_dicom)
for slice_index in range(0, size_t * size_z):
z_location = frame_info[slice_index].FrameContentSequence[0].InStackPositionNumber - 1
if t_location_index is None:
t_location = frame_info[slice_index].FrameContentSequence[0].TemporalPositionIndex - 1
else:
t_location = frame_info[slice_index].FrameContentSequence[0].DimensionIndexValues[t_location_index] - 1
block_data = multiframe_dicom.pixel_array[slice_index, :, :]
# apply scaling
rescale_intercept = frame_info[slice_index].PixelValueTransformationSequence[0].RescaleIntercept
rescale_slope = frame_info[slice_index].PixelValueTransformationSequence[0].RescaleSlope
block_data = common.do_scaling(block_data,
rescale_slope, rescale_intercept)
# switch to float if needed
if block_data.dtype != data_4d.dtype:
data_4d = data_4d.astype(block_data.dtype)
data_4d[z_location, :, :, t_location] = block_data
full_block = numpy.zeros((size_x, size_y, size_z, size_t), dtype=data_4d.dtype)
# loop over each stack and reorganize the data
for t_index in range(0, size_t):
# transpose the block so the directions are correct
data_3d = numpy.transpose(data_4d[:, :, :, t_index], (2, 1, 0))
# add the block the the full data
full_block[:, :, :, t_index] = data_3d
return full_block
def _multiframe_to_block(multiframe_dicom):
"""
Generate a full datablock containing all stacks
"""
# Calculate the amount of stacks and slices in the stack
number_of_stack_slices = int(common.get_ss_value(multiframe_dicom[Tag(0x2001, 0x105f)][0][Tag(0x2001, 0x102d)]))
number_of_stacks = int(int(multiframe_dicom.NumberOfFrames) / number_of_stack_slices)
# We create a numpy array
size_x = multiframe_dicom.pixel_array.shape[2]
size_y = multiframe_dicom.pixel_array.shape[1]
size_z = number_of_stack_slices
size_t = number_of_stacks
# get the format
format_string = common.get_numpy_type(multiframe_dicom)
# get header info needed for ordering
frame_info = multiframe_dicom[0x5200, 0x9230]
data_4d = numpy.zeros((size_z, size_y, size_x, size_t), dtype=format_string)
# loop over each slice and insert in datablock
t_location_index = _get_t_position_index(multiframe_dicom)
for slice_index in range(0, size_t * size_z):
z_location = frame_info[slice_index].FrameContentSequence[0].InStackPositionNumber - 1
if t_location_index is None:
t_location = frame_info[slice_index].FrameContentSequence[0].TemporalPositionIndex - 1
else:
t_location = frame_info[slice_index].FrameContentSequence[0].DimensionIndexValues[t_location_index] - 1
block_data = multiframe_dicom.pixel_array[slice_index, :, :]
# apply scaling
rescale_intercept = frame_info[slice_index].PixelValueTransformationSequence[0].RescaleIntercept
rescale_slope = frame_info[slice_index].PixelValueTransformationSequence[0].RescaleSlope
block_data = common.do_scaling(block_data,
rescale_slope, rescale_intercept)
# switch to float if needed
if block_data.dtype != data_4d.dtype:
data_4d = data_4d.astype(block_data.dtype)
data_4d[z_location, :, :, t_location] = block_data
full_block = numpy.zeros((size_x, size_y, size_z, size_t), dtype=data_4d.dtype)
# loop over each stack and reorganize the data
for t_index in range(0, size_t):
# transpose the block so the directions are correct
data_3d = numpy.transpose(data_4d[:, :, :, t_index], (2, 1, 0))
# add the block the the full data
full_block[:, :, :, t_index] = data_3d
return full_block
def shrink_multiframe(input_file, output_file=None, slice_count=8, timepoint_count=4):
if output_file is None:
output_file = input_file
# Load dicom_file_in
dicom_in = compressed_dicom.read_file(input_file)
if _is_multiframe_diffusion_imaging([dicom_in]) or _is_multiframe_4d([dicom_in]):
number_of_stack_slices = int(common.get_ss_value(dicom_in[(0x2001, 0x105f)][0][(0x2001, 0x102d)]))
number_of_stacks = int(int(dicom_in.NumberOfFrames) / number_of_stack_slices)
# We create a numpy array
size_x = dicom_in.pixel_array.shape[2]
size_y = dicom_in.pixel_array.shape[1]
size_t = number_of_stacks
frame_info = dicom_in.PerFrameFunctionalGroupsSequence
data_4d = numpy.zeros((slice_count * timepoint_count, size_x, size_y), dtype=common.get_numpy_type(dicom_in))
new_frame_info = [None] * slice_count * timepoint_count
for index_z in range(0, slice_count):
for index_t in range(0, timepoint_count):
slice_index = int(size_t * index_z + index_t)
new_slice_index = int(timepoint_count * index_z + index_t)
z_location = frame_info[slice_index].FrameContentSequence[0].InStackPositionNumber - 1
new_frame_info[new_slice_index] = frame_info[slice_index]
logging.info('Importing slice on position %s %s %s' % (slice_index, z_location, index_t))
data_4d[new_slice_index, :, :] = dicom_in.pixel_array[slice_index, :, :]
dicom_in.PixelData = data_4d.tostring()
common.set_ss_value(dicom_in[(0x2001, 0x105f)][0][(0x2001, 0x102d)], slice_count)
setattr(dicom_in, 'NumberOfFrames', slice_count * timepoint_count)
setattr(dicom_in, 'PerFrameFunctionalGroupsSequence', new_frame_info)
else:
# truncate the data
dicom_in.PixelData = dicom_in.pixel_array[:slice_count, :, :].tostring()
# set number of frames
common.set_ss_value(dicom_in[(0x2001, 0x105f)][0][(0x2001, 0x102d)], slice_count)
setattr(dicom_in, 'NumberOfFrames', slice_count)
# truncate the pre frame groups sequence
setattr(dicom_in, 'PerFrameFunctionalGroupsSequence', dicom_in.PerFrameFunctionalGroupsSequence[:slice_count])
# Save the file
dicom_in.save_as(output_file)
def _is_multiframe_4d(dicom_input):
"""
Use this function to detect if a dicom series is a philips multiframe 4D dataset
"""
# check if it is multi frame dicom
if not common.is_multiframe_dicom(dicom_input):
return False
header = dicom_input[0]
# check if there are multiple stacks
number_of_stack_slices = common.get_ss_value(header[Tag(0x2001, 0x105f)][0][Tag(0x2001, 0x102d)])
number_of_stacks = int(int(header.NumberOfFrames) / number_of_stack_slices)
if number_of_stacks <= 1:
return False
return True
def _is_multiframe_4d(dicom_input):
"""
Use this function to detect if a dicom series is a philips multiframe 4D dataset
"""
# check if it is multi frame dicom
if not common.is_multiframe_dicom(dicom_input):
return False
header = dicom_input[0]
# check if there are multiple stacks
number_of_stack_slices = common.get_ss_value(header[Tag(0x2001, 0x105f)][0][Tag(0x2001, 0x102d)])
number_of_stacks = int(int(header.NumberOfFrames) / number_of_stack_slices)
if number_of_stacks <= 1:
return False
return True
def _is_multiframe_anatomical(dicom_input):
"""
Use this function to detect if a dicom series is a philips multiframe anatomical dataset
NOTE: Only the first slice will be checked so you can only provide an already sorted dicom directory
(containing one series)
"""
# check if it is multi frame dicom
if not common.is_multiframe_dicom(dicom_input):
return False
header = dicom_input[0]
# check if there are multiple stacks
number_of_stack_slices = common.get_ss_value(header[Tag(0x2001, 0x105f)][0][Tag(0x2001, 0x102d)])
number_of_stacks = int(int(header.NumberOfFrames) / number_of_stack_slices)
if number_of_stacks > 1:
return False
return True
def _is_multiframe_anatomical(dicom_input):
"""
Use this function to detect if a dicom series is a philips multiframe anatomical dataset
NOTE: Only the first slice will be checked so you can only provide an already sorted dicom directory
(containing one series)
"""
# check if it is multi frame dicom
if not common.is_multiframe_dicom(dicom_input):
return False
header = dicom_input[0]
# check if there are multiple stacks
number_of_stack_slices = common.get_ss_value(header[Tag(0x2001, 0x105f)][0][Tag(0x2001, 0x102d)])
number_of_stacks = int(int(header.NumberOfFrames) / number_of_stack_slices)
if number_of_stacks > 1:
return False
return True
def shrink_multiframe(input_file,
output_file=None,
slice_count=8,
timepoint_count=4):
if output_file is None:
output_file = input_file
# Load dicom_file_in
dicom_in = compressed_dicom.read_file(input_file)
if _is_multiframe_diffusion_imaging([dicom_in]) or _is_multiframe_4d(
[dicom_in]):
number_of_stack_slices = int(
common.get_ss_value(dicom_in[(0x2001, 0x105f)][0][(0x2001,
0x102d)]))
number_of_stacks = int(
int(dicom_in.NumberOfFrames) / number_of_stack_slices)
# We create a numpy array
size_x = dicom_in.pixel_array.shape[2]
size_y = dicom_in.pixel_array.shape[1]
size_t = number_of_stacks
frame_info = dicom_in.PerFrameFunctionalGroupsSequence
data_4d = numpy.zeros((slice_count * timepoint_count, size_x, size_y),
dtype=common.get_numpy_type(dicom_in))
new_frame_info = [None] * slice_count * timepoint_count
for index_z in range(0, slice_count):
for index_t in range(0, timepoint_count):
slice_index = int(size_t * index_z + index_t)
new_slice_index = int(timepoint_count * index_z + index_t)
z_location = frame_info[slice_index].FrameContentSequence[
0].InStackPositionNumber - 1
new_frame_info[new_slice_index] = frame_info[slice_index]
logging.info('Importing slice on position %s %s %s' %
(slice_index, z_location, index_t))
data_4d[new_slice_index, :, :] = dicom_in.pixel_array[
slice_index, :, :]
dicom_in.PixelData = data_4d.tostring()
common.set_ss_value(dicom_in[(0x2001, 0x105f)][0][(0x2001, 0x102d)],
slice_count)
setattr(dicom_in, 'NumberOfFrames', slice_count * timepoint_count)
setattr(dicom_in, 'PerFrameFunctionalGroupsSequence', new_frame_info)
else:
# truncate the data
dicom_in.PixelData = dicom_in.pixel_array[:slice_count, :, :].tostring(
)
# set number of frames
common.set_ss_value(dicom_in[(0x2001, 0x105f)][0][(0x2001, 0x102d)],
slice_count)
setattr(dicom_in, 'NumberOfFrames', slice_count)
# truncate the pre frame groups sequence
setattr(dicom_in, 'PerFrameFunctionalGroupsSequence',
dicom_in.PerFrameFunctionalGroupsSequence[:slice_count])
# Save the file
dicom_in.save_as(output_file)