def main(): parser = ArgumentParser(description=DESCRIP, epilog=EPILOG, formatter_class=RawDescriptionHelpFormatter) parser.add_argument('filename', type=str, help='4D image filename') parser.add_argument('--out-path', type=str, help='path for output image files') parser.add_argument('--out-fname-label', type=str, help='mid part of output image filenames') parser.add_argument('--ncomponents', type=int, default=10, help='number of PCA components to write') # parse the command line args = parser.parse_args() # process inputs filename = args.filename out_path = args.out_path out_root = args.out_fname_label ncomps = args.ncomponents # collect extension for output images froot, ext, gz = splitext_addext(filename) pth, fname = os.path.split(froot) if out_path is None: out_path = pth if out_root is None: out_root = fname img = nipy.load_image(filename) res = nads.screen(img, ncomps) nads.write_screen_res(res, out_path, out_root, ext + gz)
def main(): try: DATA_PATH = sys.argv[1] except IndexError: raise RuntimeError("Pass data path on command line") for name, subject in get_subjects(DATA_PATH).items(): for run in subject['functionals']: fname = run['filename'] print("Diagnosing functional " + fname) img = nipy.load_image(fname) res = screens.screen(img, slice_axis=0) pth, fname = os.path.split(fname) froot, ext = os.path.splitext(fname) if ext in ('.gz', '.bz2'): # discard compressed exts froot, ext = os.path.splitext(froot) screens.write_screen_res(res, pth, froot)
import os import nipy from nipy.algorithms.diagnostics import screens from openfmri import get_subjects for name, subject in get_subjects('ds105').items(): for run in subject['functionals']: fname = run['filename'] img = nipy.load_image(fname) res = screens.screen(img, slice_axis=0) pth, fname = os.path.split(fname) froot, ext = os.path.splitext(fname) screens.write_screen_res(res, pth, froot)
import os import nipy from nipy.algorithms.diagnostics import screens from openfmri import get_visits for name, visit in get_visits('ds105').items(): for functional in visit['functionals']: filename = functional['filename'] img = nipy.load_image(filename) res = screens.screen(img, slice_axis=0) pth, fname = os.path.split(filename) froot, ext = os.path.splitext(fname) screens.write_screen_res(res, pth, froot)