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 )
