def main():
usage = "usage: %prog [options] arg1 arg2"
parser = argparse.ArgumentParser(prog='label_connected_components')
parser.add_argument("in_nii", help="Filename of NIFTI input label ")
parser.add_argument(
"--out_nii",
help="Filename of NIFTI output label. (default = label.<in> ) ",
default=None)
parser.add_argument('-l',
'--lower',
help="Lower threshold. (-infinity)",
type=float,
default=-numpy.inf)
parser.add_argument('-u',
'--upper',
help="Upper threshold. (+infinity) ",
type=float,
default=numpy.inf)
inArgs = parser.parse_args()
if inArgs.out_nii == None:
out_filename = _utilities.add_prefix_to_filename(
inArgs.in_nii, 'label.')
else:
out_filename = inArgs.out_nii
label_connected_components(inArgs.in_nii, out_filename, inArgs.lower,
inArgs.upper)
return 0
def main():
## Parsing Arguments
usage = "usage: %prog [options] arg1 arg2"
parser = argparse.ArgumentParser(prog='remove')
parser.add_argument("in_nii", help="Filename of NIFTI input label ")
parser.add_argument(
"--out_nii",
help=
"Filename of NIFTI output label. If <out_nii> is set to in then overwrite "
"input file (default = remove.<in_nii> )")
parser.add_argument('-r',
"--remove",
help="Labels to remove",
type=float,
nargs="*",
default=[])
parser.add_argument("--csv",
help="CSV filename containing labels to remove",
default=[])
parser.add_argument("-v",
"--verbose",
help="Verbose flag",
action="store_true",
default=False)
inArgs = parser.parse_args()
# Set output filename
if inArgs.out_nii == None:
out_filename = util.add_prefix_to_filename(inArgs.in_nii, 'remove.')
elif inArgs.out_nii == 'in':
out_filename = inArgs.in_nii
else:
out_filename = inArgs.out_nii
remove(inArgs.in_nii, inArgs.remove, inArgs.csv, out_filename)
def main():
## Parsing Arguments
#
#
usage = "usage: %prog [options] arg1 arg2"
parser = argparse.ArgumentParser(prog='keep')
parser.add_argument("in_nii", help="Filename of NIFTI input label ")
parser.add_argument(
"--out_nii",
help="Filename of NIFTI output label. (default = keep.<in_nii> )")
parser.add_argument('-k',
"--keep",
help="Labels to remove",
type=float,
nargs="*",
default=[])
parser.add_argument("--csv",
help="CSV filename containing labels to remove",
default=[])
parser.add_argument("-v",
"--verbose",
help="Verbose flag",
action="store_true",
default=False)
inArgs = parser.parse_args()
if inArgs.out_nii == None:
out_filename = util.add_prefix_to_filename(inArgs.in_nii, 'keep.')
elif inArgs.out_nii == 'same':
out_filename = inArgs.in_nii
else:
out_filename = inArgs.out_nii
keep(inArgs.in_nii, inArgs.keep, inArgs.csv, out_filename)
"--out_nii",
help="Filename of NIFTI output label. (default = extract.<in> ) ",
default=None)
parser.add_argument('-v',
'--verbose',
help='Verbose flag',
action='store_true',
default=False)
inArgs = parser.parse_args()
# Read NIFTI File
in_nii = nibabel.load(inArgs.in_nii)
df_bvals = pandas.read_csv(inArgs.bvals,
delim_whitespace=True,
header=None,
index_col=False)
bvals = df_bvals.transpose()[0].values
bvals_index = numpy.where(bvals == 0)
out_nii = tools.extract_volumes(in_nii, bvals_index, inArgs.verbose)
if inArgs.out_nii is None:
out_nii_filename = util.add_prefix_to_filename(inArgs.in_nii, 'b0.')
else:
out_nii_filename = inArgs.out_nii
nibabel.save(out_nii, out_nii_filename)
help="CSV Filename (default=imageFile.csv).",
default=None)
parser.add_argument('-s',
'--sort',
help='Labels to sort',
type=str,
nargs=1,
default='phase/freq')
parser.add_argument('-v',
'--verbose',
help='Verbose flag',
action='store_true',
default=False)
inArgs = parser.parse_args()
df_phase_ghosts = calculate_phase_ghosts(inArgs.in_csv, inArgs.verbose)
# Save results to file
if inArgs.out is not None:
if inArgs.out == 'prefix':
out_filename = util.add_prefix_to_filename(inArgs.in_csv,
'phase_ghosts.')
else:
out_filename = inArgs.out
df_phase_ghosts.to_csv(out_filename, index=False)
parser.add_argument(
"--out_nii",
help="Filename of NIFTI output label. (default = cumsum_nii.<in> ) ",
default=None)
parser.add_argument('-s',
'--scale',
help='Multiply NIFTI output array by scale factor ',
type=float,
default=1.0)
parser.add_argument('-v',
'--verbose',
help='Verbose flag',
action='store_true',
default=False)
inArgs = parser.parse_args()
# Read NIFTI File
in_nii = nibabel.load(inArgs.in_nii)
out_nii = cumsum_nii(in_nii, inArgs.scale)
if inArgs.out_nii is None:
out_nii_filename = util.add_prefix_to_filename(inArgs.in_nii,
'cumsum_nii.')
else:
out_nii_filename = inArgs.out_nii
nibabel.save(out_nii, out_nii_filename)
'Filename of NIFTI QA background label. (qa_background_label.<in_nii> )',
default=None)
parser.add_argument(
'--labels',
help="QA labels for phase, frequency and other. (100,200,300)",
nargs=3,
type=int,
default=[100, 200, 300])
parser.add_argument('--swap',
help="Swap phase and frequency labels. (false)",
action="store_true",
default=False)
parser.add_argument("-v",
"--verbose",
help="Verbose flag",
action="store_true",
default=False)
inArgs = parser.parse_args()
if inArgs.out_nii is None:
out_nii_filename = util.add_prefix_to_filename(inArgs.in_nii,
'qa_background_label.')
else:
out_nii_filename = inArgs.out_nii
create_qa_labels(inArgs.in_nii, inArgs.labels, out_nii_filename,
inArgs.swap, inArgs.verbose)
def create_mask(in_image, n4_flag=True, imopen_flag=True, thr=0, thrp=25, scale=1, imopen_iterations=0, imclose_iterations=0,
verbose=False, debug=False, noglc_flag=True):
inMask = in_image
# N4 Bias Correction
if n4_flag:
outMask = util.add_prefix_to_filename( in_image, 'n4')
if not os.path.isfile( outMask ):
util.iw_subprocess( ["N4BiasFieldCorrection","-d","3", "-i", inMask, "-r", "-s", "-o", outMask], verbose)
inMask = outMask
# Threshold
iiMask = 1
outMask = util.add_prefix_to_filename( in_image, str(iiMask) + ".create_mask.")
util.iw_subprocess( ["fslmaths", inMask, "-mul", str(scale), "-thrp",
str(thrp), "-thr", str(thr), "-bin",outMask ], verbose, debug)
# Fill Holes
inMask = outMask
iiMask = iiMask + 1
outMask = util.add_prefix_to_filename( in_image, str(iiMask) + ".create_mask.")
util.iw_subprocess( ["ImageMath","3", outMask, "FillHoles", inMask ], verbose, debug)
# Opening image operation
inMask = outMask
if imopen_iterations > 0:
iiMask = iiMask + 1
outMask = util.add_prefix_to_filename( in_image, str(iiMask) + ".create_mask.")
util.iw_subprocess( ["fslmaths", inMask, "-kernel", "2D"] +
["-ero"]*imopen_iterations +["-dilM"]*imopen_iterations + [outMask], verbose, debug)
# Close image operation
inMask = outMask
if imclose_iterations > 0:
iiMask = iiMask + 1
outMask = util.add_prefix_to_filename( in_image, str(iiMask) + ".create_mask.")
util.iw_subprocess( ["fslmaths", inMask, "-kernel", "2D"] +
["-dilM"]*imclose_iterations +["-ero"]*imclose_iterations + [outMask], verbose, debug)
# Don't grab greatest larges component
inMask = outMask
if not noglc_flag:
iiMask = iiMask + 1
outMask = util.add_prefix_to_filename( in_image, str(iiMask) + ".create_mask.")
util.iw_subprocess(["ImageMath","3", outMask, "GetLargestComponent", inMask],verbose, debug)
# Active Contour
inMask = outMask
out_mask_filename = util.add_prefix_to_filename( in_image, "mask.")
# if inArgs.active_contour and False: # Active contour no longer works. Talk to Craig
#
# util.iw_subprocess( ["matlab", "-nodisplay", "-noFigureWindows", "-nosplash", "-r",
# "iw_calculate_boundary('"+inMask+"',[ " + str(inArgs.smoothing) + "," +
# str(inArgs.iterations) + " ],'ch."+outMask+"', 'ac." + outMask + "'); exit"], verbose)
# shutil.copyfile("ac."+outMask, out_mask_filename)
#
# else:
shutil.copyfile(outMask, out_mask_filename)
util.iw_subprocess( ["fslcpgeom", in_image, out_mask_filename], verbose)
return out_mask_filename