def main(args=None):
if args is None:
args = sys.argv[1:]
# create param objects
param_seg = ParamSeg()
param_data = ParamData()
param_model = ParamModel()
param = Param()
# get parser
parser = get_parser()
arguments = parser.parse(args)
# set param arguments ad inputted by user
param_seg.fname_im = arguments["-i"]
param_seg.fname_im_original = arguments["-i"]
param_seg.fname_seg = arguments["-s"]
if '-vertfile' in arguments:
if extract_fname(arguments['-vertfile'])[1].lower() == "none":
param_seg.fname_level = None
elif os.path.isfile(arguments['-vertfile']):
param_seg.fname_level = arguments['-vertfile']
else:
param_seg.fname_level = None
printv('WARNING: -vertfile input file: "' + arguments['-vertfile'] + '" does not exist.\nSegmenting GM without using vertebral information', 1, 'warning')
if '-denoising' in arguments:
param_data.denoising = bool(int(arguments['-denoising']))
if '-normalization' in arguments:
param_data.normalization = bool(int(arguments['-normalization']))
if '-p' in arguments:
param_data.register_param = arguments['-p']
if '-w-levels' in arguments:
param_seg.weight_level = arguments['-w-levels']
if '-w-coordi' in arguments:
param_seg.weight_coord = arguments['-w-coordi']
if '-thr-sim' in arguments:
param_seg.thr_similarity = arguments['-thr-sim']
if '-model' in arguments:
param_model.path_model_to_load = os.path.abspath(arguments['-model'])
if '-res-type' in arguments:
param_seg.type_seg = arguments['-res-type']
if '-ratio' in arguments:
param_seg.ratio = arguments['-ratio']
if '-ref' in arguments:
param_seg.fname_manual_gmseg = arguments['-ref']
if '-ofolder' in arguments:
param_seg.path_results = arguments['-ofolder']
if '-qc' in arguments:
param_seg.qc = bool(int(arguments['-qc']))
if '-r' in arguments:
param.rm_tmp = bool(int(arguments['-r']))
if '-v' in arguments:
param.verbose = arguments['-v']
start_time = time.time()
seg_gm = SegmentGM(param_seg=param_seg, param_data=param_data, param_model=param_model, param=param)
seg_gm.segment()
elapsed_time = time.time() - start_time
printv('\nFinished! Elapsed time: ' + str(int(round(elapsed_time))) + 's', param.verbose)
# save quality control and sct.printv(info)
if param_seg.type_seg == 'bin':
wm_col = 'Red'
gm_col = 'Blue'
b = '0,1'
else:
wm_col = 'Blue-Lightblue'
gm_col = 'Red-Yellow'
b = '0.4,1'
if param_seg.qc:
# output QC image
printv('\nSave quality control images...', param.verbose, 'normal')
im = Image(seg_gm.tmp_dir + param_seg.fname_im)
im.save_quality_control(plane='axial', n_slices=5, seg=seg_gm.im_res_gmseg, thr=float(b.split(',')[0]),
cmap_col='red-yellow', path_output=param_seg.path_results)
if param.rm_tmp:
# remove tmp_dir
shutil.rmtree(seg_gm.tmp_dir)
printv('\nDone! To view results, type:', param.verbose)
printv('fslview ' + param_seg.fname_im_original + ' ' + seg_gm.fname_res_gmseg + ' -b ' + b + ' -l ' + gm_col + ' -t 0.7 ' + seg_gm.fname_res_wmseg + ' -b ' + b + ' -l ' + wm_col + ' -t 0.7 & \n', param.verbose, 'info')
def main(args=None):
if args is None:
args = sys.argv[1:]
# create param objects
param_seg = ParamSeg()
param_data = ParamData()
param_model = ParamModel()
param = Param()
# get parser
parser = get_parser()
arguments = parser.parse(args)
# set param arguments ad inputted by user
param_seg.fname_im = arguments["-i"]
param_seg.fname_im_original = arguments["-i"]
param_seg.fname_seg = arguments["-s"]
if '-vertfile' in arguments:
if extract_fname(arguments['-vertfile'])[1].lower() == "none":
param_seg.fname_level = None
elif os.path.isfile(arguments['-vertfile']):
param_seg.fname_level = arguments['-vertfile']
else:
param_seg.fname_level = None
printv('WARNING: -vertfile input file: "' + arguments['-vertfile'] + '" does not exist.\nSegmenting GM without using vertebral information', 1, 'warning')
if '-denoising' in arguments:
param_data.denoising = bool(int(arguments['-denoising']))
if '-normalization' in arguments:
param_data.normalization = bool(int(arguments['-normalization']))
if '-p' in arguments:
param_data.register_param = arguments['-p']
if '-w-levels' in arguments:
param_seg.weight_level = arguments['-w-levels']
if '-w-coordi' in arguments:
param_seg.weight_coord = arguments['-w-coordi']
if '-thr-sim' in arguments:
param_seg.thr_similarity = arguments['-thr-sim']
if '-model' in arguments:
param_model.path_model_to_load = os.path.abspath(arguments['-model'])
if '-res-type' in arguments:
param_seg.type_seg = arguments['-res-type']
if '-ref' in arguments:
param_seg.fname_manual_gmseg = arguments['-ref']
if '-ofolder' in arguments:
param_seg.path_results = os.path.abspath(arguments['-ofolder'])
param_seg.qc = arguments.get("-qc", None)
if '-r' in arguments:
param.rm_tmp = bool(int(arguments['-r']))
param.verbose = int(arguments.get('-v'))
sct.init_sct(log_level=param.verbose, update=True) # Update log level
start_time = time.time()
seg_gm = SegmentGM(param_seg=param_seg, param_data=param_data, param_model=param_model, param=param)
seg_gm.segment()
elapsed_time = time.time() - start_time
printv('\nFinished! Elapsed time: ' + str(int(np.round(elapsed_time))) + 's', param.verbose)
# save quality control and sct.printv(info)
if param_seg.type_seg == 'bin':
wm_col = 'red'
gm_col = 'blue'
b = '0,1'
else:
wm_col = 'blue-lightblue'
gm_col = 'red-yellow'
b = '0.4,1'
if param_seg.qc is not None:
generate_qc(param_seg.fname_im_original, seg_gm.fname_res_gmseg,
seg_gm.fname_res_wmseg, param_seg, args, os.path.abspath(param_seg.qc))
if param.rm_tmp:
# remove tmp_dir
sct.rmtree(seg_gm.tmp_dir)
sct.display_viewer_syntax([param_seg.fname_im_original, seg_gm.fname_res_gmseg, seg_gm.fname_res_wmseg], colormaps=['gray', gm_col, wm_col], minmax=['', b, b], opacities=['1', '0.7', '0.7'], verbose=param.verbose)
def main(args=None):
if args is None:
args = sys.argv[1:]
# create param objects
param_seg = ParamSeg()
param_data = ParamData()
param_model = ParamModel()
param = Param()
# get parser
parser = get_parser()
arguments = parser.parse(args)
# set param arguments ad inputted by user
param_seg.fname_im = arguments["-i"]
param_seg.fname_im_original = arguments["-i"]
param_seg.fname_seg = arguments["-s"]
if '-vertfile' in arguments:
if extract_fname(arguments['-vertfile'])[1].lower() == "none":
param_seg.fname_level = None
elif os.path.isfile(arguments['-vertfile']):
param_seg.fname_level = arguments['-vertfile']
else:
param_seg.fname_level = None
printv(
'WARNING: -vertfile input file: "' + arguments['-vertfile'] +
'" does not exist.\nSegmenting GM without using vertebral information',
1, 'warning')
if '-denoising' in arguments:
param_data.denoising = bool(int(arguments['-denoising']))
if '-normalization' in arguments:
param_data.normalization = bool(int(arguments['-normalization']))
if '-p' in arguments:
param_data.register_param = arguments['-p']
if '-w-levels' in arguments:
param_seg.weight_level = arguments['-w-levels']
if '-w-coordi' in arguments:
param_seg.weight_coord = arguments['-w-coordi']
if '-thr-sim' in arguments:
param_seg.thr_similarity = arguments['-thr-sim']
if '-model' in arguments:
param_model.path_model_to_load = os.path.abspath(arguments['-model'])
if '-res-type' in arguments:
param_seg.type_seg = arguments['-res-type']
if '-ratio' in arguments:
param_seg.ratio = arguments['-ratio']
if '-ref' in arguments:
param_seg.fname_manual_gmseg = arguments['-ref']
if '-ofolder' in arguments:
param_seg.path_results = os.path.abspath(arguments['-ofolder'])
param_seg.qc = arguments.get("-qc", None)
if '-r' in arguments:
param.rm_tmp = bool(int(arguments['-r']))
if '-v' in arguments:
param.verbose = arguments['-v']
start_time = time.time()
seg_gm = SegmentGM(param_seg=param_seg,
param_data=param_data,
param_model=param_model,
param=param)
seg_gm.segment()
elapsed_time = time.time() - start_time
printv(
'\nFinished! Elapsed time: ' + str(int(np.round(elapsed_time))) + 's',
param.verbose)
# save quality control and sct.printv(info)
if param_seg.type_seg == 'bin':
wm_col = 'red'
gm_col = 'blue'
b = '0,1'
else:
wm_col = 'blue-lightblue'
gm_col = 'red-yellow'
b = '0.4,1'
if param_seg.qc is not None:
generate_qc(param_seg.fname_im_original, seg_gm.fname_res_gmseg,
seg_gm.fname_res_wmseg, param_seg, args,
os.path.abspath(param_seg.qc))
if param.rm_tmp:
# remove tmp_dir
sct.rmtree(seg_gm.tmp_dir)
sct.display_viewer_syntax([
param_seg.fname_im_original, seg_gm.fname_res_gmseg,
seg_gm.fname_res_wmseg
],
colormaps=['gray', gm_col, wm_col],
minmax=['', b, b],
opacities=['1', '0.7', '0.7'],
verbose=param.verbose)
def main(args=None):
if args is None:
args = sys.argv[1:]
# create param objects
param_seg = ParamSeg()
param_data = ParamData()
param_model = ParamModel()
param = Param()
# get parser
parser = get_parser()
arguments = parser.parse(args)
# set param arguments ad inputted by user
param_seg.fname_im = arguments["-i"]
param_seg.fname_im_original = arguments["-i"]
param_seg.fname_seg = arguments["-s"]
if '-vertfile' in arguments:
if sct.extract_fname(arguments['-vertfile'])[1].lower() == "none":
param_seg.fname_level = None
elif os.path.isfile(arguments['-vertfile']):
param_seg.fname_level = arguments['-vertfile']
else:
sct.printv(parser.usage.generate(error='ERROR: -vertfile input file: "'+arguments['-vertfile']+'" does not exist.'))
if '-denoising' in arguments:
param_data.denoising = bool(int(arguments['-denoising']))
if '-normalization' in arguments:
param_data.normalization = arguments['-normalization']
if '-p' in arguments:
param_data.register_param = arguments['-p']
if '-w-levels' in arguments:
param_seg.weight_level = arguments['-w-levels']
if '-w-coordi' in arguments:
param_seg.weight_coord = arguments['-w-coordi']
if '-thr-sim' in arguments:
param_seg.thr_similarity = arguments['-thr-sim']
if '-model' in arguments:
param_model.path_model_to_load = os.path.abspath(arguments['-model'])
if '-res-type' in arguments:
param_seg.type_seg= arguments['-res-type']
if '-ratio' in arguments:
param_seg.ratio = arguments['-ratio']
if '-ref' in arguments:
param_seg.fname_manual_gmseg = arguments['-ref']
if '-ofolder' in arguments:
param_seg.path_results= arguments['-ofolder']
if '-qc' in arguments:
param_seg.qc = bool(int(arguments['-qc']))
if '-r' in arguments:
param.rm_tmp= bool(int(arguments['-r']))
if '-v' in arguments:
param.verbose= arguments['-v']
seg_gm = SegmentGM(param_seg=param_seg, param_data=param_data, param_model=param_model, param=param)
start = time.time()
seg_gm.segment()
end = time.time()
t = end - start
printv('Done in ' + str(int(round(t / 60))) + ' min, ' + str(round(t % 60,1)) + ' sec', param.verbose, 'info')