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_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 _is_bval_type_b(grouped_dicoms):
"""
Check if the bvals are stored in the second of 2 currently known ways for single frame dti
"""
bval_tag = Tag(0x0018, 0x9087)
bvec_tag = Tag(0x0018, 0x9089)
for group in grouped_dicoms:
if bvec_tag in group[0] and bval_tag in group[0]:
bvec = common.get_fd_array_value(group[0][bvec_tag], 3)
bval = common.get_fd_value(group[0][bval_tag])
if _is_float(bvec[0]) and _is_float(bvec[1]) and _is_float(bvec[2]) and _is_float(bval) and bval != 0:
return True
return False
def _is_bval_type_b(grouped_dicoms):
"""
Check if the bvals are stored in the second of 2 currently known ways for single frame dti
"""
bval_tag = Tag(0x0018, 0x9087)
bvec_tag = Tag(0x0018, 0x9089)
for group in grouped_dicoms:
if bvec_tag in group[0] and bval_tag in group[0]:
bvec = common.get_fd_array_value(group[0][bvec_tag], 3)
bval = common.get_fd_value(group[0][bval_tag])
if _is_float(bvec[0]) and _is_float(bvec[1]) and _is_float(bvec[2]) and _is_float(bval) and bval != 0:
return True
return False
def _create_singleframe_bvals_bvecs(grouped_dicoms, bval_file, bvec_file,
nifti, nifti_file):
"""
Write the bvals from the sorted dicom files to a bval file
"""
# create the empty arrays
bvals = numpy.zeros([len(grouped_dicoms)], dtype=numpy.int32)
bvecs = numpy.zeros([len(grouped_dicoms), 3])
# loop over all timepoints and create a list with all bvals and bvecs
if _is_bval_type_a(grouped_dicoms):
bval_tag = Tag(0x2001, 0x1003)
bvec_x_tag = Tag(0x2005, 0x10b0)
bvec_y_tag = Tag(0x2005, 0x10b1)
bvec_z_tag = Tag(0x2005, 0x10b2)
for stack_index in range(0, len(grouped_dicoms)):
bvals[stack_index] = common.get_fl_value(
grouped_dicoms[stack_index][0][bval_tag])
bvecs[stack_index, :] = [
common.get_fl_value(
grouped_dicoms[stack_index][0][bvec_x_tag]),
common.get_fl_value(
grouped_dicoms[stack_index][0][bvec_y_tag]),
common.get_fl_value(grouped_dicoms[stack_index][0][bvec_z_tag])
]
elif _is_bval_type_b(grouped_dicoms):
bval_tag = Tag(0x0018, 0x9087)
bvec_tag = Tag(0x0018, 0x9089)
for stack_index in range(0, len(grouped_dicoms)):
bvals[stack_index] = common.get_fd_value(
grouped_dicoms[stack_index][0][bval_tag])
bvecs[stack_index, :] = common.get_fd_array_value(
grouped_dicoms[stack_index][0][bvec_tag], 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 nifti, bvals, bvecs, bval_file, bvec_file
def _create_singleframe_bvals_bvecs(grouped_dicoms, bval_file, bvec_file, nifti, nifti_file):
"""
Write the bvals from the sorted dicom files to a bval file
"""
# create the empty arrays
bvals = numpy.zeros([len(grouped_dicoms)], dtype=numpy.int32)
bvecs = numpy.zeros([len(grouped_dicoms), 3])
# loop over all timepoints and create a list with all bvals and bvecs
if _is_bval_type_a(grouped_dicoms):
bval_tag = Tag(0x2001, 0x1003)
bvec_x_tag = Tag(0x2005, 0x10b0)
bvec_y_tag = Tag(0x2005, 0x10b1)
bvec_z_tag = Tag(0x2005, 0x10b2)
for stack_index in range(0, len(grouped_dicoms)):
bvals[stack_index] = common.get_fl_value(grouped_dicoms[stack_index][0][bval_tag])
bvecs[stack_index, :] = [common.get_fl_value(grouped_dicoms[stack_index][0][bvec_x_tag]),
common.get_fl_value(grouped_dicoms[stack_index][0][bvec_y_tag]),
common.get_fl_value(grouped_dicoms[stack_index][0][bvec_z_tag])]
elif _is_bval_type_b(grouped_dicoms):
bval_tag = Tag(0x0018, 0x9087)
bvec_tag = Tag(0x0018, 0x9089)
for stack_index in range(0, len(grouped_dicoms)):
bvals[stack_index] = common.get_fd_value(grouped_dicoms[stack_index][0][bval_tag])
bvecs[stack_index, :] = common.get_fd_array_value(grouped_dicoms[stack_index][0][bvec_tag], 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 nifti, bvals, bvecs, bval_file, bvec_file
