def run(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 input_files
print
util.verify_inputs(input_files)
in_points = ctf.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 = ctf.scale_points(out_points, scale, debug_flag)
# Fix Comment Column
out_points['comment'] = in_points['comment']
#
ctf.write_points(out_filename, out_points, verbose_flag)
def main():
## Parsing Arguments
#
#
parser = argparse.ArgumentParser(prog='iwCtf_where')
parser.add_argument("in_image", help="Input image")
parser.add_argument("out_filename", help="CSV output points")
parser.add_argument("-v",
"--verbose",
help="Verbose flag",
action="store_true",
default=False)
parser.add_argument("--debug",
help="Debug flag",
action="store_true",
default=False)
inArgs = parser.parse_args()
#
#
#
image = nb.load(inArgs.in_image)
data = image.get_data()
nshape = image.shape + (1, 1, 1)
step_01 = np.where(data > 0)
label = np.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_image], inArgs.debug)
tmp = pd.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])
ctf.write_points(inArgs.out_filename, iras_points, inArgs.verbose)
if __name__ == "__main__":
## Parsing Arguments
#
#
parser = argparse.ArgumentParser(prog='iwCtf_icsa_to_wlps')
parser.add_argument("in_filename", help="CSV input points")
parser.add_argument("out_filename", help="CSV output points")
parser.add_argument("-t", "--transform", help="Transform")
parser.add_argument("-v",
"--verbose",
help="Verbose flag",
action="store_true",
default=False)
parser.add_argument("--debug",
help="Debug flag",
action="store_true",
default=False)
inArgs = parser.parse_args()
input_files = [inArgs.in_filename, inArgs.transform]
util.verify_inputs(input_files, inArgs.debug)
ctf.wlps_to_icsa(inArgs.in_filename, inArgs.out_filename, inArgs.transform,
inArgs.verbose, inArgs.debug)
if __name__ == "__main__":
## Parsing Arguments
#
#
parser = argparse.ArgumentParser(prog='iwCtf_matrices')
parser.add_argument("in_filename", help="CSV input points")
parser.add_argument("out_filename", help="CSV output points")
parser.add_argument("-t", "--transforms", help="Transform")
parser.add_argument("-v",
"--verbose",
help="Verbose flag",
action="store_true",
default=False)
inArgs = parser.parse_args()
#
#
#
input_files = [inArgs.in_filename, inArgs.transforms]
util.verify_inputs(input_files)
ctf.wras_to_wlps(inArgs.in_filename, inArgs.out_filename,
inArgs.transforms, inArgs.verbose)
## Parsing Arguments
#
#
parser = argparse.ArgumentParser(prog='iwCtf_iras_to_wlps')
parser.add_argument("in_filename", help="CSV input points")
parser.add_argument("out_filename", help="CSV output points")
parser.add_argument("-t",
"--transform",
help="Affine image transform",
nargs=1)
parser.add_argument("-v",
"--verbose",
help="Verbose flag",
action="store_true",
default=False)
parser.add_argument("--debug",
help="Debug flag",
action="store_true",
default=False)
inArgs = parser.parse_args()
util.verify_inputs([inArgs.in_filename] + inArgs.transform, inArgs.debug)
ctf.iras_to_wlps(inArgs.in_filename, inArgs.out_filename, inArgs.transform,
inArgs.verbose, inArgs.debug)
import iwUtilities as util
import iwCtf as ctf
#
# Main Function
#
if __name__ == "__main__":
## Parsing Arguments
#
#
parser = argparse.ArgumentParser(prog='iwCtf_icsa_to_wlps')
parser.add_argument("in_fiducials", help="CSV input points" )
parser.add_argument("out_ctf_matrix", help="CSV output points" )
parser.add_argument("--ctf_scale", help="CTF scale factor", type=float, default=1)
parser.add_argument("-v","--verbose", help="Verbose flag", action="store_true", default=False )
parser.add_argument("--debug", help="Debug flag", action="store_true", default=False )
inArgs = parser.parse_args()
util.verify_inputs( [ inArgs.in_fiducials ], inArgs.debug)
ctf.calc_matrix( inArgs.in_fiducials, inArgs.out_ctf_matrix, inArgs.ctf_scale, inArgs.verbose)
step_01 = np.where(data > 0)
label = np.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_image], inArgs.debug)
tmp = pd.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])
ctf.write_points(inArgs.out_filename, iras_points, inArgs.verbose)
print
print output_directory
print stage_directory
print
#
# Check input files
#
util.print_stage("Verifying inputs", inArgs.verbose )
input_files = [ os.path.abspath( os.path.join( input_directory, inArgs.image )),
os.path.abspath( os.path.join( input_directory, inArgs.in_icsa ))
]
util.verify_inputs( input_files, inArgs.verbose)
image_filename = input_files[0]
icsa_fiducials = input_files[1]
#
# Check inputs
#
if inArgs.in_icsa.count('.') > 1:
print
print inArgs.in_icsa + " must contain only one \".\" "
print
exit()
input_files = [ image_native,
fiducials_native,
util.path_relative_to( input_directory, inArgs.native_to_template[0] ),
util.path_relative_to( input_directory, inArgs.native_to_template[1] ),
util.path_relative_to( input_directory, inArgs.template_to_native[0] ),
util.path_relative_to( input_directory, inArgs.template_to_native[1] )
]
if os.path.exists(reference_template):
input_files = input_files + [ reference_template ]
if inArgs.run or inArgs.qi:
util.print_stage("Verifying inputs", inArgs.verbose )
util.verify_inputs( input_files, inArgs.verbose)
if inArgs.qi:
util.fslview([image_native], inArgs.verbose)
#
# Stage 0 - Rename files to a common name by linking
#
stage0_directory = stage_directory[0];
stage0_input_files = input_files
print "inArgs.ants_affine = " + str(inArgs.ants_affine)
print "inArgs.ants_warp = " + str(inArgs.ants_warp)
print "inArgs.wlps_to_wctf = " + str(inArgs.wlps_to_wctf)
print "inArgs.verbose = " + str(inArgs.verbose)
#
# Check inputs
#
input_files = [
inArgs.in_ctf, inArgs.ants_affine, inArgs.ants_warp,
inArgs.wlps_to_wctf
]
iwUtilities.verify_inputs(input_files)
#
# Transform CTF points to Native Space
#
cmd = [
"antsApplyTransformsToPoints", "-d", "3", "-i", inArgs.in_ctf, "-o",
inArgs.out_native, "-t", "[", inArgs.wlps_to_wctf, ",", "1", "]"
]
iwUtilities.iw_subprocess(cmd, inArgs.verbose, inArgs.verbose)
clean_nan(inArgs.out_native)
#
if __name__ == "__main__":
## Parsing Arguments
#
#
parser = argparse.ArgumentParser(prog='iwCtf_extract_affine')
parser.add_argument("in_image", help="Input image")
parser.add_argument("out_affine", help="Filename of affine matrix")
parser.add_argument(
"--ras",
help="Multiply affine by lps affine matrix before saving",
action="store_true",
default=False)
parser.add_argument("-v",
"--verbose",
help="Verbose flag",
action="store_true",
default=False)
inArgs = parser.parse_args()
util.verify_inputs([inArgs.in_image], inArgs.verbose)
ctf.extract_affine(inArgs.in_image, inArgs.out_affine, not inArgs.ras,
inArgs.verbose)
