def transform_image(in_filename, out_filename, reference_filename,
in_transforms, interpolation_method, verbose_flag,
debug_flag):
if type(in_filename) is list:
filename = in_filename
else:
filename = [in_filename]
if type(in_transforms) is list:
transforms = in_transforms
else:
transforms = [in_transforms]
input_files = filename + reference_filename + transforms
if debug_flag:
print('\n')
print('!!! ctf.transform_image ')
print(input_files)
print('\n')
util.verify_inputs(filename)
cmd = [
"antsApplyTransforms", "-d", "3", "-i", in_filename[0], "-o",
out_filename[0], "-r", reference_filename[0], "-n",
interpolation_method, "-t"
] + transforms
util.iw_subprocess(cmd, debug_flag, debug_flag)
def transform_points(in_filename, out_filename, in_transforms, scale,
verbose_flag, debug_flag):
if type(in_filename) is list:
filename = in_filename
else:
filename = [in_filename]
if type(in_transforms) is list:
transforms = in_transforms
else:
transforms = [in_transforms]
input_files = filename + transforms
if debug_flag:
print('\n')
print('!!! ctf.transform_points ')
print(input_files)
print('\n')
util.verify_inputs(filename)
in_points = print_points_from_file(in_filename, verbose_flag)
cmd = [
"antsApplyTransformsToPoints", "-d", "3", "-i", in_filename, "-o",
out_filename, "-t"
] + transforms
util.iw_subprocess(cmd, debug_flag, debug_flag)
# Perform scaling
out_points = pd.read_csv(out_filename, sep=',', header=0)
out_points = scale_points(out_points, scale, debug_flag)
# Fix Comment Column
out_points['label'] = in_points['label']
out_points['comment'] = in_points['comment']
#
write_points(out_filename, out_points, verbose_flag)
step_01 = numpy.where(data > 0)
label = numpy.extract(data > 0, data)
x = step_01[0].tolist()
y = step_01[1].tolist()
z = step_01[2].tolist()
if nshape[3] > 1:
t = step_01[3].tolist()
else:
t = 0 * len(x)
comment = [' '] * len(x)
util.verify_inputs([inArgs.in_label], inArgs.debug)
tmp = pandas.DataFrame(
{
'x': x,
'y': y,
'z': z,
't': t,
'label': label,
'comment': comment
},
columns=['x', 'y', 'z', 't', 'label', 'comment'])
iras_points = tmp.sort_values(['label', 'x', 'y', 'z', 't'],
ascending=[1, 1, 1, 1, 1])
labels.write_points(out_filename, iras_points, inArgs.verbose)