def main(argv=None):
parser = get_parser()
arguments = parser.parse_args(argv)
verbose = arguments.v
set_loglevel(verbose=verbose)
fname_bval_list = arguments.i
# Build fname_out
if arguments.o is not None:
fname_out = arguments.o
else:
path_in, file_in, ext_in = extract_fname(fname_bval_list[0])
fname_out = path_in + 'bvals_concat' + ext_in
# Open bval files and concatenate
bvals_concat = ''
# for file_i in fname_bval_list:
# f = open(file_i, 'r')
# for line in f:
# bvals_concat += line
# f.close()
from dipy.data.fetcher import read_bvals_bvecs
for i_fname in fname_bval_list:
bval_i, bvec_i = read_bvals_bvecs(i_fname, None)
bvals_concat += ' '.join(str(v) for v in bval_i)
bvals_concat += ' '
# Write new bval
new_f = open(fname_out, 'w')
new_f.write(bvals_concat)
new_f.close()
def main(argv=None):
"""
Main function
:param argv:
:return:
"""
parser = get_parser()
arguments = parser.parse_args(argv)
verbose = arguments.v
set_global_loglevel(verbose=verbose)
# check number of input args
if not len(arguments.i) == len(arguments.order):
raise Exception(
"Number of items between flags '-i' and '-order' should be the same."
)
if not len(arguments.bval) == len(arguments.bvec):
raise Exception(
"Number of files for bval and bvec should be the same.")
# Concatenate NIFTI files
im_list = [Image(fname) for fname in arguments.i]
im_concat = concat_data(im_list, dim=3, squeeze_data=False)
im_concat.save(arguments.o)
printv("Generated file: {}".format(arguments.o))
# Concatenate bvals and bvecs
bvals_concat = ''
bvecs_concat = ['', '', '']
i_dwi = 0 # counter for DWI files, to read in bvec/bval files
for i_item in range(len(arguments.order)):
if arguments.order[i_item] == 'b0':
# count number of b=0
n_b0 = Image(arguments.i[i_item]).dim[3]
bval = np.array([0.0] * n_b0)
bvec = np.array([[0.0, 0.0, 0.0]] * n_b0)
elif arguments.order[i_item] == 'dwi':
# read bval/bvec files
bval, bvec = read_bvals_bvecs(arguments.bval[i_dwi],
arguments.bvec[i_dwi])
i_dwi += 1
# Concatenate bvals
bvals_concat += ' '.join(str(v) for v in bval)
bvals_concat += ' '
# Concatenate bvecs
for i in (0, 1, 2):
bvecs_concat[i] += ' '.join(
str(v) for v in map(lambda n: '%.16f' % n, bvec[:, i]))
bvecs_concat[i] += ' '
bvecs_concat = '\n'.join(
str(v) for v in bvecs_concat) # transform list into lines of strings
# Write files
new_f = open(arguments.obval, 'w')
new_f.write(bvals_concat)
new_f.close()
printv("Generated file: {}".format(arguments.obval))
new_f = open(arguments.obvec, 'w')
new_f.write(bvecs_concat)
new_f.close()
printv("Generated file: {}".format(arguments.obvec))
def main():
# Get parser info
parser = get_parser()
arguments = parser.parse(sys.argv[1:])
fname_bval_list = arguments["-i"]
# Build fname_out
if "-o" in arguments:
fname_out = arguments["-o"]
else:
path_in, file_in, ext_in = extract_fname(fname_bval_list[0])
fname_out = path_in + 'bvals_concat' + ext_in
# Open bval files and concatenate
bvals_concat = ''
# for file_i in fname_bval_list:
# f = open(file_i, 'r')
# for line in f:
# bvals_concat += line
# f.close()
for i_fname in fname_bval_list:
bval_i, bvec_i = read_bvals_bvecs(i_fname, None)
bvals_concat += ' '.join(str(v) for v in bval_i)
bvals_concat += ' '
# Write new bval
new_f = open(fname_out, 'w')
new_f.write(bvals_concat)
new_f.close()
def main():
# Get parser info
parser = get_parser()
arguments = parser.parse(sys.argv[1:])
fname_bval_list = arguments["-i"]
# Build fname_out
if "-o" in arguments:
fname_out = arguments["-o"]
else:
path_in, file_in, ext_in = extract_fname(fname_bval_list[0])
fname_out = path_in+'bvals_concat'+ext_in
# Open bval files and concatenate
bvals_concat = ''
# for file_i in fname_bval_list:
# f = open(file_i, 'r')
# for line in f:
# bvals_concat += line
# f.close()
for i_fname in fname_bval_list:
bval_i, bvec_i = read_bvals_bvecs(i_fname, None)
bvals_concat += ' '.join(str(v) for v in bval_i)
bvals_concat += ' '
# Write new bval
new_f = open(fname_out, 'w')
new_f.write(bvals_concat)
new_f.close()
def dmri_single_volumes(tmp_path):
"""
Create .nii.gz, bvals, and bvecs files for individual dMRI volumes.
This prep is necessary because `sct_testing_data` lacks individual bvals
and bvecs files for the `dmri_T000#.nii.gz` files, and
sct_dmri_separate_b0_and_dwi won't generate new bvals/bvecs file either.
"""
# Get all bvals/bvecs corresponding to individual dMRI volumes
bvals, bvecs = read_bvals_bvecs(sct_test_path('dmri', 'bvals.txt'),
sct_test_path('dmri', 'bvecs.txt'))
fname_dmri_imgs, fname_bvals, fname_bvecs = [], [], []
for i, (bval, bvec) in enumerate(zip(bvals, bvecs)):
# 1. Use existing single-volume dMRI files from sct_testing_data
fname_dmri_imgs.append(sct_test_path('dmri', f'dmri_T000{i}.nii.gz'))
# 2. Copy bval into single-volume bvals file
fname_bval = str(tmp_path / f'bvals_T000{i}.txt')
fname_bvals.append(fname_bval)
with open(fname_bval, 'w') as f:
f.write(str(bval))
# 3. Copy bvec into single-volume bvecs file
fname_bvec = str(tmp_path / f'bvecs_T000{i}.txt')
fname_bvecs.append(fname_bvec)
with open(fname_bvec, 'w') as f:
f.write(' '.join(map(str, bvec)))
return fname_dmri_imgs, fname_bvals, fname_bvecs
def main(argv=None):
parser = get_parser()
arguments = parser.parse_args(argv if argv else ['--help'])
verbose = arguments.v
set_global_loglevel(verbose=verbose)
fname_bvecs_list = arguments.i
# Build fname_out
if arguments.o is not None:
fname_out = arguments.o
else:
path_in, file_in, ext_in = extract_fname(fname_bvecs_list[0])
fname_out = path_in + 'bvecs_concat' + ext_in
# # Open bvec files and collect values
# nb_files = len(fname_bvecs_list)
# bvecs_all = []
# for i_fname in fname_bvecs_list:
# bvecs = []
# with open(i_fname) as f:
# for line in f:
# bvec_line = map(float, line.split())
# bvecs.append(bvec_line)
# bvecs_all.append(bvecs)
# f.close()
# # Concatenate
# bvecs_concat = ''
# for i in range(0, 3):
# for j in range(0, nb_files):
# bvecs_concat += ' '.join(str(v) for v in bvecs_all[j][i])
# bvecs_concat += ' '
# bvecs_concat += '\n'
#
# Open bvec files and collect values
bvecs_all = ['', '', '']
for i_fname in fname_bvecs_list:
from dipy.data.fetcher import read_bvals_bvecs
bval_i, bvec_i = read_bvals_bvecs(None, i_fname)
for i in range(0, 3):
bvecs_all[i] += ' '.join(
str(v) for v in map(lambda n: '%.16f' % n, bvec_i[:, i]))
bvecs_all[i] += ' '
# Concatenate
bvecs_concat = '\n'.join(str(v) for v in bvecs_all)
# Write new bvec
new_f = open(fname_out, 'w')
new_f.write(bvecs_concat)
new_f.close()
def main():
# Get parser info
parser = get_parser()
arguments = parser.parse(sys.argv[1:])
fname_bvecs_list = arguments["-i"]
# Build fname_out
if "-o" in arguments:
fname_out = arguments["-o"]
else:
path_in, file_in, ext_in = extract_fname(fname_bvecs_list[0])
fname_out = path_in + 'bvecs_concat' + ext_in
# # Open bvec files and collect values
# nb_files = len(fname_bvecs_list)
# bvecs_all = []
# for i_fname in fname_bvecs_list:
# bvecs = []
# with open(i_fname) as f:
# for line in f:
# bvec_line = map(float, line.split())
# bvecs.append(bvec_line)
# bvecs_all.append(bvecs)
# f.close()
# # Concatenate
# bvecs_concat = ''
# for i in range(0, 3):
# for j in range(0, nb_files):
# bvecs_concat += ' '.join(str(v) for v in bvecs_all[j][i])
# bvecs_concat += ' '
# bvecs_concat += '\n'
#
# Open bvec files and collect values
bvecs_all = ['', '', '']
for i_fname in fname_bvecs_list:
bval_i, bvec_i = read_bvals_bvecs(None, i_fname)
for i in range(0, 3):
bvecs_all[i] += ' '.join(
str(v) for v in map(lambda n: '%.16f' % n, bvec_i[:, i]))
bvecs_all[i] += ' '
# Concatenate
bvecs_concat = '\n'.join(str(v) for v in bvecs_all)
# Write new bvec
new_f = open(fname_out, 'w')
new_f.write(bvecs_concat)
new_f.close()
def main():
# Get parser info
parser = get_parser()
arguments = parser.parse(sys.argv[1:])
fname_bvecs_list = arguments["-i"]
# Build fname_out
if "-o" in arguments:
fname_out = arguments["-o"]
else:
path_in, file_in, ext_in = extract_fname(fname_bvecs_list[0])
fname_out = path_in + 'bvecs_concat' + ext_in
# # Open bvec files and collect values
# nb_files = len(fname_bvecs_list)
# bvecs_all = []
# for i_fname in fname_bvecs_list:
# bvecs = []
# with open(i_fname) as f:
# for line in f:
# bvec_line = map(float, line.split())
# bvecs.append(bvec_line)
# bvecs_all.append(bvecs)
# f.close()
# # Concatenate
# bvecs_concat = ''
# for i in range(0, 3):
# for j in range(0, nb_files):
# bvecs_concat += ' '.join(str(v) for v in bvecs_all[j][i])
# bvecs_concat += ' '
# bvecs_concat += '\n'
#
# Open bvec files and collect values
bvecs_all = ['', '', '']
for i_fname in fname_bvecs_list:
bval_i, bvec_i = read_bvals_bvecs(None, i_fname)
for i in range(0, 3):
bvecs_all[i] += ' '.join(str(v) for v in map(lambda n: '%.16f'%n, bvec_i[:, i]))
bvecs_all[i] += ' '
# Concatenate
bvecs_concat = '\n'.join(str(v) for v in bvecs_all)
# Write new bvec
new_f = open(fname_out, 'w')
new_f.write(bvecs_concat)
new_f.close()
def main():
# Get parser info
parser = get_parser()
arguments = parser.parse(sys.argv[1:])
fname_bvecs = arguments['-bvec']
# Read bvecs
bvecs = read_bvals_bvecs(fname_bvecs, None)
bvecs = bvecs[0]
# if first dimension is not equal to 3 (x,y,z), transpose bvecs file
if not bvecs.shape[0] == 3:
bvecs = bvecs.transpose()
x, y, z = bvecs[0], bvecs[1], bvecs[2]
# Get total number of directions
n_dir = len(x)
# Get effective number of directions
bvecs_eff = []
n_b0 = 0
for i in range(0, n_dir):
add_direction = True
# check if b=0
if abs(x[i]) < bzero and abs(x[i]) < bzero and abs(x[i]) < bzero:
n_b0 += 1
add_direction = False
else:
# loop across bvecs_eff
for j in range(0, len(bvecs_eff)):
# if bvalue already present, then do not add to bvecs_eff
if bvecs_eff[j] == [x[i], y[i], z[i]]:
add_direction = False
if add_direction:
bvecs_eff.append([x[i], y[i], z[i]])
n_dir_eff = len(bvecs_eff)
# Display scatter plot
fig = plt.figure(facecolor='white', figsize=(9, 8))
fig.suptitle('Number of b=0: ' + str(n_b0) + ', Number of b!=0: ' +
str(n_dir - n_b0) +
', Number of effective directions (without duplicates): ' +
str(n_dir_eff))
# plt.ion()
# Display three views
plot_2dscatter(fig_handle=fig,
subplot=221,
x=bvecs[0][:],
y=bvecs[1][:],
xlabel='X',
ylabel='Y')
plot_2dscatter(fig_handle=fig,
subplot=222,
x=bvecs[0][:],
y=bvecs[2][:],
xlabel='X',
ylabel='Z')
plot_2dscatter(fig_handle=fig,
subplot=223,
x=bvecs[1][:],
y=bvecs[2][:],
xlabel='Y',
ylabel='Z')
# 3D
ax = fig.add_subplot(224, projection='3d')
# ax.auto_scale_xyz([-1, 1], [-1, 1], [-1, 1])
for i in range(0, n_dir):
# x, y, z = bvecs[0], bvecs[1], bvecs[2]
# if b=0, do not plot
if not (abs(x[i]) < bzero and abs(x[i]) < bzero and abs(x[i]) < bzero):
ax.scatter(x[i], y[i], z[i])
ax.set_xlim3d(-1, 1)
ax.set_ylim3d(-1, 1)
ax.set_zlim3d(-1, 1)
plt.title('3D view (use mouse to rotate)')
plt.axis('off')
# plt.draw()
# Save image
sct.printv("Saving figure: bvecs.png\n")
plt.savefig('bvecs.png')
plt.show()
def main():
# Get parser info
parser = get_parser()
arguments = parser.parse(sys.argv[1:])
fname_bvecs = arguments['-bvec']
# Read bvecs
bvecs = read_bvals_bvecs(fname_bvecs, None)
bvecs = bvecs[0]
# if first dimension is not equal to 3 (x,y,z), transpose bvecs file
if not bvecs.shape[0] == 3:
bvecs = bvecs.transpose()
x, y, z = bvecs[0], bvecs[1], bvecs[2]
# Get total number of directions
n_dir = len(x)
# Get effective number of directions
bvecs_eff = []
n_b0 = 0
for i in range(0, n_dir):
add_direction = True
# check if b=0
if abs(x[i]) < bzero and abs(x[i]) < bzero and abs(x[i]) < bzero:
n_b0 += 1
add_direction = False
else:
# loop across bvecs_eff
for j in range(0, len(bvecs_eff)):
# if bvalue already present, then do not add to bvecs_eff
if bvecs_eff[j] == [x[i], y[i], z[i]]:
add_direction = False
if add_direction:
bvecs_eff.append([x[i], y[i], z[i]])
n_dir_eff = len(bvecs_eff)
# Display scatter plot
fig = plt.figure(facecolor='white', figsize=(9, 8))
fig.suptitle('Number of b=0: '+str(n_b0)+', Number of b!=0: '+str(n_dir-n_b0)+', Number of effective directions (without duplicates): '+str(n_dir_eff))
# plt.ion()
# Display three views
plot_2dscatter(fig_handle=fig, subplot=221, x=bvecs[0][:], y=bvecs[1][:], xlabel='X', ylabel='Y')
plot_2dscatter(fig_handle=fig, subplot=222, x=bvecs[0][:], y=bvecs[2][:], xlabel='X', ylabel='Z')
plot_2dscatter(fig_handle=fig, subplot=223, x=bvecs[1][:], y=bvecs[2][:], xlabel='Y', ylabel='Z')
# 3D
ax = fig.add_subplot(224, projection='3d')
# ax.auto_scale_xyz([-1, 1], [-1, 1], [-1, 1])
for i in range(0, n_dir):
# x, y, z = bvecs[0], bvecs[1], bvecs[2]
# if b=0, do not plot
if not(abs(x[i]) < bzero and abs(x[i]) < bzero and abs(x[i]) < bzero):
ax.scatter(x[i], y[i], z[i])
ax.set_xlim3d(-1, 1)
ax.set_ylim3d(-1, 1)
ax.set_zlim3d(-1, 1)
plt.title('3D view (use mouse to rotate)')
plt.axis('off')
# plt.draw()
# Save image
sct.printv("Saving figure: bvecs.png\n")
plt.savefig('bvecs.png')
plt.show()
def main(argv=None):
parser = get_parser()
arguments = parser.parse_args(argv)
verbose = arguments.v
set_loglevel(verbose=verbose)
fname_bvecs = arguments.bvec
fname_bvals = arguments.bval
# Read bvals and bvecs files (if arguments.bval is not passed, bvals will be None)
bvals, bvecs = read_bvals_bvecs(fname_bvals, fname_bvecs)
# if first dimension is not equal to 3 (x,y,z), transpose bvecs file
if bvecs.shape[0] != 3:
bvecs = bvecs.transpose()
# if bvals file was not passed, create dummy unit bvals array (necessary fot scatter plots)
if bvals is None:
bvals = np.repeat(1, bvecs.shape[1])
# multiply unit b-vectors by b-values
x, y, z = bvecs[0] * bvals, bvecs[1] * bvals, bvecs[2] * bvals
# Set different color for each shell (bval)
shell_colors = {}
# Create iterator with different colors from brg palette
colors = iter(cm.nipy_spectral(np.linspace(0, 1, len(np.unique(bvals)))))
for unique_bval in np.unique(bvals):
# skip b=0
if unique_bval < BZERO_THRESH:
continue
shell_colors[unique_bval] = next(colors)
# Get total number of directions
n_dir = len(x)
# Get effective number of directions
bvecs_eff = []
n_b0 = 0
for i in range(0, n_dir):
add_direction = True
# check if b=0
if abs(x[i]) < BZERO_THRESH and abs(x[i]) < BZERO_THRESH and abs(
x[i]) < BZERO_THRESH:
n_b0 += 1
add_direction = False
else:
# loop across bvecs_eff
for j in range(0, len(bvecs_eff)):
# if bvalue already present, then do not add to bvecs_eff
if bvecs_eff[j] == [x[i], y[i], z[i]]:
add_direction = False
if add_direction:
bvecs_eff.append([x[i], y[i], z[i]])
n_dir_eff = len(bvecs_eff)
# Display scatter plot
fig = plt.figure(facecolor='white', figsize=(9, 8))
fig.suptitle('Number of b=0: ' + str(n_b0) + ', Number of b!=0: ' +
str(n_dir - n_b0) +
', Number of effective directions (without duplicates): ' +
str(n_dir_eff))
# Display three views
plot_2dscatter(fig_handle=fig,
subplot=221,
x=x,
y=y,
xlabel='X',
ylabel='Y',
bvals=bvals,
colors=shell_colors)
plot_2dscatter(fig_handle=fig,
subplot=222,
x=x,
y=z,
xlabel='X',
ylabel='Z',
bvals=bvals,
colors=shell_colors)
plot_2dscatter(fig_handle=fig,
subplot=223,
x=y,
y=z,
xlabel='Y',
ylabel='Z',
bvals=bvals,
colors=shell_colors)
# 3D
ax = fig.add_subplot(224, projection='3d')
# ax.auto_scale_xyz([-1, 1], [-1, 1], [-1, 1])
for i in range(0, n_dir):
# x, y, z = bvecs[0], bvecs[1], bvecs[2]
# if b=0, do not plot
if not (abs(x[i]) < BZERO_THRESH and abs(x[i]) < BZERO_THRESH
and abs(x[i]) < BZERO_THRESH):
ax.scatter(x[i],
y[i],
z[i],
color=shell_colors[bvals[i]],
alpha=0.7)
ax.set_xlim3d(-max(bvals), max(bvals))
ax.set_ylim3d(-max(bvals), max(bvals))
ax.set_zlim3d(-max(bvals), max(bvals))
ax.set_xlabel('X')
ax.set_ylabel('Y')
ax.set_zlabel('Z')
plt.title('3D view (use mouse to rotate)')
plt.axis('on')
# plt.draw()
plt.tight_layout()
# add legend with b-values if bvals file was passed
if arguments.bval is not None:
create_custom_legend(fig, shell_colors, bvals)
# Save image
printv("Saving figure: bvecs.png\n")
plt.savefig('bvecs.png')
