def methods( t1full, t2full, t2flair, options, verbose=False, debug=False, nohup=False): print('\nRunnning ants_lct.py\n') if qa.qa_input_files( input_files, False): if not os.path.exists( out_directory ): os.makedirs( out_directory ) # bash $0 -d 3 -e brainWithSkullTemplate.nii.gz -m brainPrior.nii.gz -p segmentationPriors%d.nii.gz -o output \${anatomicalImages[@]} callCommand = ['antsLongitudinalCorticalThickness.sh', '-d', '3', '-t', options['t_option'], '-w', '0.25', '-e', options['e_option'], '-m', options['m_option'], '-f', options['f_option'], '-p', options['p_option'], '-o', options['o_option'], t1full ] callCommand = callCommand + [ '-a', t1full ] if not t2full == None: callCommand = callCommand + [ '-a', t2full ] if not inArgs.t2flair == None: callCommand = callCommand + [ '-a', t2flair ] util.iw_subprocess( callCommand, verbose, debug, nohup ) else: print('\nUnable to run iwAntsCT.py. Failed input QA.') qa.qa_exist( input_files, True ) print('\n')
def methods(t1full, t2full, t2flair, options, verbose=False, debug=False, nohup=False): print('\nRunnning ants_ct.py\n') if qa.qa_input_files(input_files, False): if not os.path.exists(out_directory): os.makedirs(out_directory) callCommand = [ 'antsCorticalThickness.sh', '-d', '3', '-t', options['t_option'], '-w', '0.25', '-e', options['e_option'], '-m', options['m_option'], '-f', options['f_option'], '-p', options['p_option'], '-o', options['o_option'] ] callCommand = callCommand + ['-a', t1full] if not t2full == None: callCommand = callCommand + ['-a', t2full] if not inArgs.t2flair == None: callCommand = callCommand + ['-a', t2flair] util.iw_subprocess(callCommand, verbose, debug, nohup) else: print('\nUnable to run iwAntsCT.py. Failed input QA.') qa.qa_exist(input_files, True) print('\n')
m_option, 'f_option': f_option, 'p_option': p_option, 'p_options': [p1_option, p2_option, p3_option, p4_option, p5_option, p6_option], 'o_option': inArgs.outdir + '/' + inArgs.outprefix } # QA inputs # if 'input' in inArgs.qa: qa.qa_input_files(input_files, True, False) qa.freeview(input_files[:2], True, inArgs.verbose) qa.freeview(input_files[2:], True, inArgs.verbose) # Archive/Clean Directory if inArgs.archive: archive(out_directory, 'archive') if inArgs.clean: clean(out_directory) # Replace Mask if inArgs.mask is not None:
def main(): usage = "usage: %prog [options] arg1 arg2" parser = argparse.ArgumentParser(prog='create_sphere') parser.add_argument("in_image", help="Image") parser.add_argument("in_csv", help="CSV file containing coordinates") parser.add_argument("out_image", help="Image") parser.add_argument("--label", help="Label number", type=int, default=1000) parser.add_argument("--radius", help="Radius of ROI", type=int, default=5) parser.add_argument("--roi_prefix", help="ROI prefix added to --image", default="roi.") parser.add_argument("--roi_add", help="Display Results", action="store_true", default=False) parser.add_argument("--roi_type", help="ROI Type (sphere, point)", choices=['sphere', 'point'], default='sphere') parser.add_argument("--merge", help="Merge ROIs", action="store_true", default=True) parser.add_argument("--collapse", help="Collapse ROIs", action="store_true", default=True) parser.add_argument("-d", "--display", help="Display Results", action="store_true", default=False) 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) parser.add_argument("--method", help="Method ( 'equation', 'convolution')", choices = ('convolution, equation'), default='convolution') parser.add_argument("--qi", help="QA inputs", action="store_true", default=False) parser.add_argument("--qo", help="QA outputs", action="store_true", default=False) parser.add_argument("-r", "--run", help="Run processing pipeline", action="store_true", default=False) # group = parser.add_mutually_exclusive_group(required=True) parser.add_argument("--point", help="Input a single point", nargs=3, type=float, default=None) inArgs = parser.parse_args() input_files = [[inArgs.in_image, ':colormap=grayscale']] # output_files = [[ inArgs.image, ':colormap=grayscale'], # [ roiImage, ':colormap=jet']] if inArgs.roi_type == 'sphere': radius = inArgs.radius else: radius = 0 if inArgs.debug: print ("inArgs.in_image = " + str(inArgs.in_image)) print ("inArgs.in_csv = " + str(inArgs.in_csv)) print ("inArgs.out_image = " + str(inArgs.out_image)) print ("inArgs.radius = " + str(inArgs.radius)) print print ("radius = " + str(radius)) print print ("inArgs.display = " + str(inArgs.display)) print ("inArgs.debug = " + str(inArgs.debug)) print ("inArgs.verbose = " + str(inArgs.verbose)) print # print ("ROI image = " + roiImage) print if inArgs.qi: _qa_utilities.qa_input_files(input_files, inArgs.verbose, False) in_points = pd.read_csv(inArgs.in_csv) create_roi(inArgs.out_image, inArgs.in_image, in_points, inArgs.radius, inArgs.method, inArgs.verbose, inArgs.debug)