def run_main(args):
import sct_utils as sct
from spinalcordtoolbox.mtsat import mtsat
sct.start_stream_logger()
fname_mtsat, fname_t1map = mtsat.compute_mtsat_from_file(
args.mt,
args.pd,
args.t1,
args.trmt,
args.trpd,
args.trt1,
args.famt,
args.fapd,
args.fat1,
fname_b1map=args.b1map,
fname_mtsat=args.omtsat,
fname_t1map=args.ot1map,
verbose=1)
sct.display_viewer_syntax([fname_mtsat, fname_t1map],
colormaps=['gray', 'gray'],
minmax=['-10,10', '0, 3'],
opacities=['1', '1'],
verbose=args.v)
# ==========================================================================================
def main(args=None):
# initialization
verbose = 1
# check user arguments
if not args:
args = sys.argv[1:]
# Get parser info
parser = get_parser()
arguments = parser.parse(sys.argv[1:])
di = arguments['-di']
da = arguments['-da']
db = arguments['-db']
# Compute MSCC
MSCC = mscc(di, da, db)
# Display results
sct.printv('\nMSCC = ' + str(MSCC) + '\n', verbose, 'info')
# START PROGRAM
# ==========================================================================================
if __name__ == "__main__":
sct.start_stream_logger()
# call main function
main()
def main(args):
import io
import sct_utils as sct
import pickle
import numpy as np
import matplotlib.pyplot as plt
sct.start_stream_logger()
# make sure number of inputs and labels are the same
if len(arguments.input) != len(arguments.label):
raise RuntimeError("Mismatch between # of files and labels")
# fs = 10 # font size
nb_plots = args.input.__len__()
list_data = []
text_results = [] # numerical results to display inside the figure
for fname_pickle in args.input:
df = pickle.load(io.open(fname_pickle, "rb"))
# filter lines based on status. For status definition, see sct_pipeline
# Note: the > 0 test is to filter out NaN
df_dice = df.query(
"(status != 200) & (status != 201) & (dice > 0 )")["dice"]
list_data.append(df_dice.get_values())
# compute statistics
count_passed = df.status[df.status == 0].count()
count_failed = df.status[df.status == 99].count()
count_crashed_run = df.status[df.status == 1].count()
count_crashed_integrity = df.status[df.status == 2].count()
count_total = count_passed + count_failed + count_crashed_run + count_crashed_integrity
text_results.append('\n'.join([
"PASS: {}/{}".format(count_passed,
count_total), "FAIL: {}".format(count_failed),
"CRASH_RUN: " + str(count_crashed_run),
"CRASH_INTEGRITY: " + str(count_crashed_integrity)
]))
pos = np.arange(nb_plots)
# plot fig
fig, ax = plt.subplots(1)
plt.violinplot(list_data,
pos,
points=100,
widths=0.8,
showmeans=True,
showextrema=True,
showmedians=True,
bw_method=0.5)
plt.grid(axis='y')
plt.ylabel('Dice coefficient')
plt.xticks(pos, args.label)
ax.spines['right'].set_visible(False)
ax.spines['left'].set_visible(False)
ax.spines['top'].set_visible(False)
ylim = ax.get_ylim()
for i in range(nb_plots):
plt.text(i + 0.02,
ylim[0] + 0.01,
text_results[i],
horizontalalignment='left',
verticalalignment='bottom')
plt.savefig('violin_plot.png')
def run_main():
sct.start_stream_logger()
parser = get_parser()
args = sys.argv[1:]
arguments = parser.parse(args)
# Input filename
fname_input_data = arguments["-i"]
fname_data = os.path.abspath(fname_input_data)
# Method used
method = 'optic'
if "-method" in arguments:
method = arguments["-method"]
# Contrast type
contrast_type = ''
if "-c" in arguments:
contrast_type = arguments["-c"]
if method == 'optic' and not contrast_type:
# Contrast must be
error = 'ERROR: -c is a mandatory argument when using Optic method.'
sct.printv(error, type='error')
return
# Ga between slices
interslice_gap = 10.0
if "-gap" in arguments:
interslice_gap = float(arguments["-gap"])
# Output folder
if "-ofolder" in arguments:
folder_output = sct.slash_at_the_end(arguments["-ofolder"], slash=1)
else:
folder_output = './'
# Remove temporary files
remove_temp_files = True
if "-r" in arguments:
remove_temp_files = bool(int(arguments["-r"]))
# Outputs a ROI file
output_roi = False
if "-roi" in arguments:
output_roi = bool(int(arguments["-roi"]))
# Verbosity
verbose = 0
if "-v" in arguments:
verbose = int(arguments["-v"])
if method == 'viewer':
path_data, file_data, ext_data = sct.extract_fname(fname_data)
# create temporary folder
temp_folder = sct.TempFolder()
temp_folder.copy_from(fname_data)
temp_folder.chdir()
# make sure image is in SAL orientation, as it is the orientation used by the viewer
image_input = Image(fname_data)
image_input_orientation = orientation(image_input,
get=True,
verbose=False)
reoriented_image_filename = sct.add_suffix(file_data + ext_data,
"_SAL")
cmd_image = 'sct_image -i "%s" -o "%s" -setorient SAL -v 0' % (
fname_data, reoriented_image_filename)
sct.run(cmd_image, verbose=False)
# extract points manually using the viewer
fname_points = viewer_centerline(image_fname=reoriented_image_filename,
interslice_gap=interslice_gap,
verbose=verbose)
if fname_points is not None:
image_points_RPI = sct.add_suffix(fname_points, "_RPI")
cmd_image = 'sct_image -i "%s" -o "%s" -setorient RPI -v 0' % (
fname_points, image_points_RPI)
sct.run(cmd_image, verbose=False)
image_input_reoriented = Image(image_points_RPI)
# fit centerline, smooth it and return the first derivative (in physical space)
x_centerline_fit, y_centerline_fit, z_centerline, x_centerline_deriv, y_centerline_deriv, z_centerline_deriv = smooth_centerline(
image_points_RPI,
algo_fitting='nurbs',
nurbs_pts_number=3000,
phys_coordinates=True,
verbose=verbose,
all_slices=False)
centerline = Centerline(x_centerline_fit, y_centerline_fit,
z_centerline, x_centerline_deriv,
y_centerline_deriv, z_centerline_deriv)
# average centerline coordinates over slices of the image
x_centerline_fit_rescorr, y_centerline_fit_rescorr, z_centerline_rescorr, x_centerline_deriv_rescorr, y_centerline_deriv_rescorr, z_centerline_deriv_rescorr = centerline.average_coordinates_over_slices(
image_input_reoriented)
# compute z_centerline in image coordinates for usage in vertebrae mapping
voxel_coordinates = image_input_reoriented.transfo_phys2pix([[
x_centerline_fit_rescorr[i], y_centerline_fit_rescorr[i],
z_centerline_rescorr[i]
] for i in range(len(z_centerline_rescorr))])
x_centerline_voxel = [coord[0] for coord in voxel_coordinates]
y_centerline_voxel = [coord[1] for coord in voxel_coordinates]
z_centerline_voxel = [coord[2] for coord in voxel_coordinates]
# compute z_centerline in image coordinates with continuous precision
voxel_coordinates = image_input_reoriented.transfo_phys2continuouspix(
[[
x_centerline_fit_rescorr[i], y_centerline_fit_rescorr[i],
z_centerline_rescorr[i]
] for i in range(len(z_centerline_rescorr))])
x_centerline_voxel_cont = [coord[0] for coord in voxel_coordinates]
y_centerline_voxel_cont = [coord[1] for coord in voxel_coordinates]
z_centerline_voxel_cont = [coord[2] for coord in voxel_coordinates]
# Create an image with the centerline
image_input_reoriented.data *= 0
min_z_index, max_z_index = int(round(
min(z_centerline_voxel))), int(round(max(z_centerline_voxel)))
for iz in range(min_z_index, max_z_index + 1):
image_input_reoriented.data[
int(round(x_centerline_voxel[iz - min_z_index])),
int(round(y_centerline_voxel[iz - min_z_index])),
int(
iz
)] = 1 # if index is out of bounds here for hanning: either the segmentation has holes or labels have been added to the file
# Write the centerline image
sct.printv('\nWrite NIFTI volumes...', verbose)
fname_centerline_oriented = file_data + '_centerline' + ext_data
image_input_reoriented.setFileName(fname_centerline_oriented)
image_input_reoriented.changeType('uint8')
image_input_reoriented.save()
sct.printv('\nSet to original orientation...', verbose)
sct.run('sct_image -i ' + fname_centerline_oriented +
' -setorient ' + image_input_orientation + ' -o ' +
fname_centerline_oriented)
# create a txt file with the centerline
fname_centerline_oriented_txt = file_data + '_centerline.txt'
file_results = open(fname_centerline_oriented_txt, 'w')
for i in range(min_z_index, max_z_index + 1):
file_results.write(
str(int(i)) + ' ' +
str(round(x_centerline_voxel_cont[i - min_z_index], 2)) +
' ' +
str(round(y_centerline_voxel_cont[i - min_z_index], 2)) +
'\n')
file_results.close()
fname_centerline_oriented_roi = optic.centerline2roi(
fname_image=fname_centerline_oriented,
folder_output='./',
verbose=verbose)
# return to initial folder
temp_folder.chdir_undo()
# copy result to output folder
shutil.copy(temp_folder.get_path() + fname_centerline_oriented,
folder_output)
shutil.copy(temp_folder.get_path() + fname_centerline_oriented_txt,
folder_output)
if output_roi:
shutil.copy(
temp_folder.get_path() + fname_centerline_oriented_roi,
folder_output)
centerline_filename = folder_output + fname_centerline_oriented
else:
centerline_filename = 'error'
# delete temporary folder
if remove_temp_files:
temp_folder.cleanup()
else:
# condition on verbose when using OptiC
if verbose == 1:
verbose = 2
# OptiC models
path_script = os.path.dirname(__file__)
path_sct = os.path.dirname(path_script)
optic_models_path = os.path.join(path_sct, 'data/optic_models',
'{}_model'.format(contrast_type))
# Execute OptiC binary
_, centerline_filename = optic.detect_centerline(
image_fname=fname_data,
contrast_type=contrast_type,
optic_models_path=optic_models_path,
folder_output=folder_output,
remove_temp_files=remove_temp_files,
output_roi=output_roi,
verbose=verbose)
sct.printv('\nDone! To view results, type:', verbose)
sct.printv(
"fslview " + fname_input_data + " " + centerline_filename +
" -l Red -b 0,1 -t 0.7 &\n", verbose, 'info')
fname_sc=fname_sc,
fname_ref=fname_ref,
path_template=path_template,
path_ofolder=path_results,
verbose=verbose)
# run the analyze
lesion_obj.analyze()
# remove tmp_dir
if rm_tmp:
shutil.rmtree(lesion_obj.tmp_dir)
printv(
'\nDone! To view the labeled lesion file (one value per lesion), type:',
verbose)
if fname_ref is not None:
printv(
'fslview ' + fname_mask + ' ' + path_results +
lesion_obj.fname_label + ' -l Red-Yellow -t 0.7 & \n', verbose,
'info')
else:
printv(
'fslview ' + path_results + lesion_obj.fname_label +
' -l Red-Yellow -t 0.7 & \n', verbose, 'info')
if __name__ == "__main__":
start_stream_logger()
main()
def test(path_data='', parameters=''):
verbose = 0
dice_threshold = 0.9
add_path_for_template = False # if absolute path or no path to template is provided, then path to data should not be added.
# initializations
dice_template2anat = float('NaN')
dice_anat2template = float('NaN')
output = ''
if not parameters:
parameters = '-i t2/t2.nii.gz -l t2/labels.nii.gz -s t2/t2_seg.nii.gz ' \
'-param step=1,type=seg,algo=centermassrot,metric=MeanSquares:step=2,type=seg,algo=bsplinesyn,iter=5,metric=MeanSquares ' \
'-t template/ -r 0'
add_path_for_template = True # in this case, path to data should be added
parser = sct_register_to_template.get_parser()
dict_param = parser.parse(parameters.split(), check_file_exist=False)
if add_path_for_template:
dict_param_with_path = parser.add_path_to_file(deepcopy(dict_param),
path_data,
input_file=True)
else:
dict_param_with_path = parser.add_path_to_file(deepcopy(dict_param),
path_data,
input_file=True,
do_not_add_path=['-t'])
param_with_path = parser.dictionary_to_string(dict_param_with_path)
# Check if input files exist
if not (os.path.isfile(dict_param_with_path['-i'])
and os.path.isfile(dict_param_with_path['-l'])
and os.path.isfile(dict_param_with_path['-s'])):
status = 200
output = 'ERROR: the file(s) provided to test function do not exist in folder: ' + path_data
return status, output, DataFrame(data={
'status': int(status),
'output': output
},
index=[path_data])
# return status, output, DataFrame(
# data={'status': status, 'output': output,
# 'dice_template2anat': float('nan'), 'dice_anat2template': float('nan')},
# index=[path_data])
# if template is not specified, use default
# if not os.path.isdir(dict_param_with_path['-t']):
# status, path_sct = commands.getstatusoutput('echo $SCT_DIR')
# dict_param_with_path['-t'] = path_sct + default_template
# param_with_path = parser.dictionary_to_string(dict_param_with_path)
# get contrast folder from -i option.
# We suppose we can extract it as the first object when spliting with '/' delimiter.
contrast_folder = ''
input_filename = ''
if dict_param['-i'][0] == '/':
dict_param['-i'] = dict_param['-i'][1:]
input_split = dict_param['-i'].split('/')
if len(input_split) == 2:
contrast_folder = input_split[0] + '/'
input_filename = input_split[1]
else:
input_filename = input_split[0]
if not contrast_folder: # if no contrast folder, send error.
status = 201
output = 'ERROR: when extracting the contrast folder from input file in command line: ' + dict_param[
'-i'] + ' for ' + path_data
return status, output, DataFrame(data={
'status': int(status),
'output': output
},
index=[path_data])
# return status, output, DataFrame(
# data={'status': status, 'output': output, 'dice_template2anat': float('nan'), 'dice_anat2template': float('nan')}, index=[path_data])
# create output path
# TODO: create function for that
import time, random
subject_folder = path_data.split('/')
if subject_folder[-1] == '' and len(subject_folder) > 1:
subject_folder = subject_folder[-2]
else:
subject_folder = subject_folder[-1]
path_output = sct.slash_at_the_end(
'sct_register_to_template_' + subject_folder + '_' +
time.strftime("%y%m%d%H%M%S") + '_' + str(random.randint(1, 1000000)),
slash=1)
param_with_path += ' -ofolder ' + path_output
sct.create_folder(path_output)
# log file
# TODO: create function for that
import sys
fname_log = path_output + 'output.log'
sct.pause_stream_logger()
file_handler = sct.add_file_handler_to_logger(filename=fname_log,
mode='w',
log_format="%(message)s")
#
# stdout_log = file(fname_log, 'w')
# redirect to log file
# stdout_orig = sys.stdout
# sys.stdout = stdout_log
cmd = 'sct_register_to_template ' + param_with_path
output += '\n====================================================================================================\n' + cmd + '\n====================================================================================================\n\n' # copy command
time_start = time.time()
try:
status, o = sct.run(cmd, verbose)
except:
status, o = 1, 'ERROR: Function crashed!'
output += o
duration = time.time() - time_start
# if command ran without error, test integrity
if status == 0:
# get filename_template_seg
fname_template_seg = get_file_label(
sct.slash_at_the_end(dict_param_with_path['-t'], 1) + 'template/',
'spinal cord',
output='filewithpath')
# apply transformation to binary mask: template --> anat
sct.run(
'sct_apply_transfo -i ' + fname_template_seg + ' -d ' +
dict_param_with_path['-s'] + ' -w ' + path_output +
'warp_template2anat.nii.gz' + ' -o ' + path_output +
'test_template2anat.nii.gz -x nn', verbose)
# apply transformation to binary mask: anat --> template
sct.run(
'sct_apply_transfo -i ' + dict_param_with_path['-s'] + ' -d ' +
fname_template_seg + ' -w ' + path_output +
'warp_anat2template.nii.gz' + ' -o ' + path_output +
'test_anat2template.nii.gz -x nn', verbose)
# compute dice coefficient between template segmentation warped into anat and segmentation from anat
cmd = 'sct_dice_coefficient -i ' + dict_param_with_path[
'-s'] + ' -d ' + path_output + 'test_template2anat.nii.gz'
status1, output1 = sct.run(cmd, verbose)
# parse output and compare to acceptable threshold
dice_template2anat = float(
output1.split('3D Dice coefficient = ')[1].split('\n')[0])
if dice_template2anat < dice_threshold:
status1 = 99
# compute dice coefficient between segmentation from anat warped into template and template segmentation
# N.B. here we use -bmax because the FOV of the anat is smaller than the template
cmd = 'sct_dice_coefficient -i ' + fname_template_seg + ' -d ' + path_output + 'test_anat2template.nii.gz -bmax 1'
status2, output2 = sct.run(cmd, verbose)
# parse output and compare to acceptable threshold
dice_anat2template = float(
output2.split('3D Dice coefficient = ')[1].split('\n')[0])
if dice_anat2template < dice_threshold:
status2 = 99
# check if at least one integrity status was equal to 99
if status1 == 99 or status2 == 99:
status = 99
# concatenate outputs
output = output + output1 + output2
# transform results into Pandas structure
results = DataFrame(data={
'status': int(status),
'output': output,
'dice_template2anat': dice_template2anat,
'dice_anat2template': dice_anat2template,
'duration [s]': duration
},
index=[path_data])
sct.log.info(output)
sct.remove_handler(file_handler)
sct.start_stream_logger()
return status, output, results