break master = filter(lambda t: t != -1, master) if not outputFile: return master else: # write it out to disk io.saveTrk(outputFile, master, None, None, True) # # entry point # if __name__ == "__main__": parser = FNNDSCParser(description="Add or subtract TrackVis (*.trk) files.") parser.add_argument( "-i", "--input", action="append", dest="input", required=True, help="input trackvis files, f.e. -i ~/files/f01.trk -i ~/files/f02.trk -i ~/files/f03.trk ..", ) parser.add_argument( "-o", "--output", action="store", dest="output", required=True,
else: outputFileName = os.path.join( outputDirectory, currentInputFileBasenameWithoutExt) savedImage = io.saveImage(outputFileName, resampledImage) #c.info( ' new spacing: ' + str( savedImageHeader.get_zooms() ) ) c.info(' new dimensions: ' + str(savedImage.shape[:3])) c.info('All done!') # # entry point # parser = FNNDSCParser( description= 'Convert dimension, spacing and origin of input images to match a master image which gets converted to isotropic spacing' ) parser.add_argument( '-m', '--master', action='store', dest='master', required=True, help='master image to use for all input images, f.e. -m image00.img') parser.add_argument( '-i', '--input', action='append', dest='input', required=True,
def draw( self ): self.__gridWidget.clear() for i in range( self.__rows ): for j in range( self.__cols ): r, g, b = self.__world.spectrum_get( i, j ).arr_get() self.__gridWidget.draw( i, j, r, g, b ) # # entry point # if __name__ == "__main__": parser = FNNDSCParser( description='Visualize the evolution of a grid.' ) parser.add_argument( '-t', '--test', action='store_true', dest='test', required=False, help='activate a test case (101x101, initialized at 3 points along the diagonal' ) parser.add_argument( '-i', '--iterations', action='store', dest='iterations', default=-1, required=False, help='Optional number of max. iterations.' ) parser.add_argument( '-c', '--convergenceCriteria', action='store', dest='convergence', default=-1, required=False, help=""" Stopping criteria. If "corners", stop when every corner cell of the grid has become active. If a float number, stop once the number of system iterations is equal to the float multiple of the number of elements on the diagonal." """ ) parser.add_argument( '-u', '--updateAmount', action='store', dest='updateAmount', default=1, required=False,
newTrack = ( newPoints, track[1], track[2] ) # replace the old track with the newTrack tracks[t] = newTrack if not outputFile: return tracks else: # write it out to disk io.saveTrk( outputFile, tracks, None, None, True ) # # entry point # if __name__ == "__main__": parser = FNNDSCParser( description='Transform TrackVis (*.trk) files.' ) parser.add_argument( '-i', '--input', action='store', dest='input', required=True, help='input trackvis file, f.e. -i ~/files/f01.trk' ) parser.add_argument( '-o', '--output', action='store', dest='output', required=True, help='output trackvis file, f.e. -o /tmp/f_out.trk' ) parser.add_argument( '-m', '--matrix', action='store', dest='matrix', required=True, help='transformation matrix file, f.e. -m ~/files/f01.mat - a 4x4 matrix is required.' ) parser.add_argument( '-j', '--jobs', action='store', dest='jobs', default=multiprocessing.cpu_count(), help='number of parallel computations, f.e. -j 10' ) # always show the help if no arguments were specified if len( sys.argv ) == 1: parser.print_help() sys.exit( 1 ) options = parser.parse_args() logic = TrackvisTransformLogic()
break master = filter(lambda t: t != -1, master) if not outputFile: return master else: # write it out to disk io.saveTrk(outputFile, master, None, None, True) # # entry point # if __name__ == "__main__": parser = FNNDSCParser( description='Add or subtract TrackVis (*.trk) files.') parser.add_argument( '-i', '--input', action='append', dest='input', required=True, help= 'input trackvis files, f.e. -i ~/files/f01.trk -i ~/files/f02.trk -i ~/files/f03.trk ..' ) parser.add_argument('-o', '--output', action='store', dest='output', required=True,
break return inputs # ENTRYPOINT if __name__ == "__main__": # 1) scan input directory # 2) preform preprocessing # 3) perform mapping # 4) perform filtering # 5) create connectivity matrices parser = FNNDSCParser( description='fyborg - THE ULTIMATE SCALAR MAPPING FRAMEWORK FOR TRACKVIS (.TRK) FILES' ) parser.add_argument( '-i', '--input', action='store', dest='input', required=True, help='The input folder which gets scanned automatically for usable volume- and track-files.' ) parser.add_argument( '-o', '--output', action='store', dest='output', required=True, help='The output folder which gets created if it does not exit' ) parser.add_argument( '-r', '--radius', action='store', dest='radius', default=3, type=int, help='The look-a-round radius in voxels. E.g. --radius 10, DEFAULT: 3' ) parser.add_argument( '-l', '--length', action='store', dest='length', default="20 200", help='The lower and upper borders for length thresholding in mm. E.g. --length "60 100", DEFAULT "20 200" ' ) parser.add_argument( '-co', '--cortex_only', action='store_true', dest='cortex_only', help='Perform filtering for cortex specific analysis and skip sub-cortical structures.' ) parser.add_argument( '-s', '--stage', action='store', dest='stage', default=0, type=int, help='Start with a specific stage while skipping the ones before. E.g. --stage 3 directly starts the mapping without preprocessing, --stage 4 starts with the filtering' ) parser.add_argument( '-overwrite', '--overwrite', action='store_true', dest='overwrite', help='Overwrite any existing output. DANGER!!' ) parser.add_argument( '-v', '--verbose', action='store_true', dest='verbose', help='Show verbose output' ) # always show the help if no arguments were specified if len( sys.argv ) == 1: parser.print_help() sys.exit( 1 )
results = kd_tree.query_ball_point( point, radius ) if k == 1 and radius == -1: results = [results] print 'Found', len( results ), 'results!' for r in results: print vertices[r], 'vertex index:', r, 'distance:', numpy.linalg.norm( vertices[r] - point ) # # entry point # if __name__ == "__main__": parser = FNNDSCParser( description='Find nearest neighbors on a Freesurfer mesh.' ) parser.add_argument( '-i', '--input', action='store', dest='input', required=True, help='the Freesurfer mesh, f.e. -i lh.smoothwm' ) parser.add_argument( '-p', '--point', action='store', nargs=3, dest='point', type=float, required=True, help='the source point in RAS space ([mm]), f.e. -p 123.05 12.3 144.2' ) parser.add_argument( '-k', '--k', action='store', dest='k', required=False, type=int, help='number of points to find. DEFAULT: 1', default=1 ) parser.add_argument( '-r', '--radius', action='store', dest='radius', type=float, required=False, help='radius [mm] to include in point search (overrides -k/--k). DEFAULT: -1 to ignore.', default= -1 ) # always show the help if no arguments were specified if len( sys.argv ) == 1: parser.print_help() sys.exit( 1 ) options = parser.parse_args() find_nearest_neighbor( options.input, options.point, options.k, options.radius )