print "To check usage, run: python extract.py"
sys.exit()
SulciThld = float(p)
else:
print "[ERROR] Option", o, "is unrecognized. Please check usage."
sys.exit()
return SurfFile, ThickFile, CurvFile, ConvFile,\
FundiVTK, PitsVTK, SulciVTK, Use, SulciThld
if __name__ == "__main__":
import sys, getopt # this line imports pulic libraries
import libfundi
try:
opts, args = getopt.getopt(sys.argv[1:],"",["thick=","conv=","fundi=", "pits=","sulci=", "curv=", "use=", "sulciThld="])
except getopt.GetoptError, err:
print str(err) # will print something like "option -a not recognized"
# print_help()
print "To check usage, run: python extract.py"
print "If you use options like --second, --pits2, --fundi2, --sulci2,",
"please note that we have disabled mapping features onto secondary surface.",
"Please check maps_to_second_surface.py under utils directory to do so."
sys.exit(2)
check_opt(opts, args)
InputFiles = process_opt(opts, args)
# new unified extraction function Forrest 2011-10-08
libfundi.getFeatures(InputFiles, 'FreeSurfer', '')
# print " [Output] Sulci on 2nd surface in:" + OutputColor + Sulci2VTK + EndColor
return VTKFile, ThickFile, ConvexFile, MeanCurvVTK, GaussCurvVTK,\
FundiVTK, PitsVTK, SulciVTK,\
SulciThld, Clouchoux
if __name__ == "__main__":
# this script extracts fundi/pits/sulci from a VTK file from the output from Joachim's code
import libfundi # this line imports my own library
try:
opts, args = getopt.getopt(sys.argv[1:],"h",
["clouchoux", "help","thick=", "convex=","fundi=","pits=","sulci=","sulciThld=","meancurv=", "gausscurv="])
except getopt.GetoptError, err:
print str(err) # will print something like "option -a not recognized"
print " Please run [python vtk_extract.py -h] or [python vtk_extract.py --help] to get the usage."
print "If you use options like --second, --pits2, --fundi2, --sulci2,",
"please note that we have disabled mapping features onto secondary surface.",
"Please check maps_to_second_surface.py under utils directory to do so."
sys.exit(2)
check_opt(opts, args)
InputArguments = process_opt(opts, args)
libfundi.getFeatures(InputArguments, 'vtk','')
