def trk_fixer(trkpath, trk_newpath, verbose=False):
if verbose:
t1 = time()
txt = f'Beginning to load {trkpath}'
trkdata = load_trk_spe(trkpath, 'same')
if verbose:
t2 = time()
txt = f'It took {str(t2-t1)} seconds to load {trkpath}'
print(txt)
if hasattr(trkdata, 'space_attribute'):
header = trkdata.space_attribute
elif hasattr(trkdata, 'space_attributes'):
header = trkdata.space_attributes
remove, keep = trkdata.remove_invalid_streamlines()
if verbose:
t3 = time()
duration = t3 - t2
txt = f"it took {duration} to do the test on {trkpath}, and {np.size(remove)} streamlines were removed. saving it to {trk_newpath}"
print(txt)
if np.size(remove)==0:
shutil.copy(trkpath, trk_newpath)
else:
new_streamlines = trkdata.streamlines
save_trk_header(trk_newpath, new_streamlines, header, verbose=verbose)
if verbose:
t4 = time()
txt = f'It took {str(t4-t3)} seconds to save {trk_newpath}'
print(txt)
def trk_fixer_old(trkpath, trk_newpath, verbose = False):
if verbose:
t1 = time()
txt = f'Beginning to load {trkpath}'
trkdata = load_trk_spe(trkpath, 'same')
trk_streamlines = trkdata.streamlines
if hasattr(trkdata, 'space_attribute'):
header = trkdata.space_attribute
elif hasattr(trkdata, 'space_attributes'):
header = trkdata.space_attributes
voxdim = trkdata.dimensions
if verbose:
t2 = time()
txt = f'It took {str(t2-t1)} seconds to load {trkpath}'
print(txt)
vverbose=True
orig_size = np.shape(trk_streamlines)[0]
trk_streamlines[:] = (x for x in trk_streamlines if streamline_checker(x, voxdim,vverbose))
"""
for i, streamline in enumerate(trk_streamlines):
mymin = np.min(trk_streamlines, axis=0)
mymax = np.max(trk_streamlines, axis=0)
np.asarray(list(product(*zip(mymin, mymax))))
bbox_min = np.min(trk_streamlines, axis=0)
bbox_max = np.max(trk_streamlines, axis=0)
bbox_corners = np.asarray(list(product(*zip(bbox_min, bbox_max))))
if np.any(bbox_corners[:, 0] > voxdim[0]) or \
np.any(bbox_corners[:, 1] > voxdim[1]) or \
np.any(bbox_corners[:, 2] > voxdim[2]):
np.pop()
"""
new_size = np.shape(trk_streamlines)[0]
cut_streamlines = orig_size - new_size
if verbose:
t3 = time()
duration = t3 - t2
txt = f"it took {duration} to do the test on {trkpath}, and {str(cut_streamlines)} streamlines were removed. saving it to {trk_newpath}"
print(txt)
#np.asarray(list(product(*zip(bbox_min, bbox_max))))
if cut_streamlines!=0:
save_trk_header(trk_newpath, trk_streamlines, header, verbose = verbose)
else:
shutil.copy(trkpath, trk_newpath)
if verbose:
t4 = time()
txt = f'It took {str(t4-t3)} seconds to save {trk_newpath}'
print(txt)
groupstreamlines[group])[0]:
raise Exception('happened from there')
if os.path.exists(
streamline_file_path) and overwrite and write_streamlines:
os.remove(streamline_file_path)
if not os.path.exists(streamline_file_path) and write_streamlines:
if verbose:
print(
f'Summarized the streamlines for group {group} at {streamline_file_path}'
)
pickle.dump(groupstreamlines[group],
open(streamline_file_path, "wb"))
save_trk_header(filepath=streamline_file_path,
streamlines=groupstreamlines[group],
header=header,
affine=np.eye(4),
verbose=verbose)
"""
if not os.path.exists(streamline_file_path_orig) and write_streamlines:
if verbose:
print(f'Summarized the streamlines for group {group} at {streamline_file_path}')
pickle.dump(groupstreamlines_orig[group], open(streamline_file_path, "wb"))
save_trk_header(filepath= streamline_file_path, streamlines = groupstreamlines_orig[group], header = header, affine=np.eye(4), verbose=verbose)
"""
for ref in references:
if overwrite:
if os.path.exists(grouping_files[ref, 'lines']):
os.remove(grouping_files[ref, 'lines'])
if os.path.exists(grouping_files[ref, 'points']):
#rigid = os.path.join(work_dir, "dwi", f"{subj}_rigid.mat")
#affine = os.path.join(work_dir, "dwi", f"{subj}_affine.mat")
#runno_to_MDT = os.path.join(work_dir, f'dwi/SyN_0p5_3_0p5_fa/faMDT_NoNameYet_n37_i6/reg_diffeo/{subj}_to_MDT_warp.nii.gz')
_, exists = check_files([trans, rigid, affine, runno_to_MDT])
if np.any(exists==0):
raise Exception('missing transform file')
affine_map_test = get_affine_transform(reference, subj_dwi)
streamlines, header = unload_trk(subj_trk)
tmp2_streamlines = transform_streamlines(streamlines, np.linalg.inv(affine_map_test), in_place=False)
if (not os.path.exists(trk_filepath_tmp2) or overwrite) and save_temp_files:
save_trk_header(filepath= trk_filepath_tmp2, streamlines = tmp2_streamlines, header = header, affine=np.eye(4), verbose=verbose)
#tmp2_streamlines, header_new = unload_trk(trk_filepath_tmp2)
affine_transform, newaffine = get_flip_affine(orientation_in, orientation_out)
affine_transform_new = affine_transform
#affine_transform[:3,3] = affine_transform.diagonal()[:3]* header[0][:3,3] - header[0][:3,3]
center1 = header[0][:3, 3]
center2 = affine_transform.diagonal()[:3] * center1[:3]
affine_transform_new[:3, 3] = center1 - center2
affine_transform_new[1, 3] = affine_transform[0, 3]
#affine_transform_new = np.eye(4)
#affine_transform_new[:3,:3] = np.dot(affine_transform[:3,:3], affine_map_test[:3,:3])
project_input_streamlines = transform_streamlines(tmp2_streamlines, np.linalg.inv(affine_transform_new))
new_transmat = np.eye(4)
vox_dim = [1, 1, -1]
#new_transmat[:3, 3] = np.squeeze(later_trans_mat[3:6]) * vox_dim
new_transmat[:3, 3] = np.squeeze(
np.matmul(subj_affine[:3, :3], later_trans_mat[3:6])
) #should be the AFFINE of the current image, to make sure the slight difference in orientation is ACCOUNTED FOR!!!!!!!!!!
new_transmat[2, 3] = 0
print(new_transmat)
streamlines_posttrans = transform_streamlines(streamlines_prepro,
(new_transmat))
if (not os.path.exists(trk_preprocess_posttrans)
or overwrite) and save_temp_files:
save_trk_header(filepath=trk_preprocess_posttrans,
streamlines=streamlines_posttrans,
header=header,
affine=np.eye(4),
verbose=verbose)
rigid_struct = loadmat(rigid)
var_name = list(rigid_struct.keys())[0]
rigid_ants = rigid_struct[var_name]
rigid_mat = convert_ants_vals_to_affine(rigid_ants)
#streamlines_posttrans, header_posttrans = unload_trk(trk_preprocess_posttrans)
streamlines_postrigid = transform_streamlines(streamlines_posttrans,
np.linalg.inv(rigid_mat))
if (not os.path.exists(trk_preprocess_postrigid)
or overwrite) and save_temp_files:
save_trk_header(filepath=trk_preprocess_postrigid,