<s> import numpy <EOL> import os <EOL> from math import sqrt <EOL> from scipy import ndimage <EOL> import commands <EOL> import nibabel <EOL> from mpl_toolkits . mplot3d import Axes3D <EOL> import matplotlib . pyplot as plt <EOL> from sct_nurbs_modif import * <EOL> import make_centerline as centerline <EOL> import sct_utils as sct <EOL> import sys <EOL> import linear_fitting <EOL> def main ( file_name , smooth = <NUM_LIT:3> ) : <EOL> div = [ <NUM_LIT> ] <EOL> path , fname , ext_fname = sct . extract_fname ( file_name ) <EOL> exit = <NUM_LIT:0> <EOL> print '<STR_LIT>' , file_name <EOL> print '<STR_LIT>' <EOL> fname_centerline = fname + '<STR_LIT>' <EOL> cmd = '<STR_LIT>' + file_name + '<STR_LIT>' <EOL> sct . run ( cmd ) <EOL> print '<STR_LIT>' <EOL> fname_smooth = fname_centerline + '<STR_LIT>' <EOL> print '<STR_LIT>' , smooth <EOL> cmd = '<STR_LIT>' + fname_centerline + '<STR_LIT>' + str ( smooth ) + '<STR_LIT:U+0020>' + fname_smooth + ext_fname <EOL> sct . run ( cmd ) <EOL> for d in div : <EOL> add = d - <NUM_LIT:1> <EOL> e = <NUM_LIT:1> <EOL> print '<STR_LIT>' <EOL> while e == <NUM_LIT:1> : <EOL> add += <NUM_LIT:1> <EOL> e = centerline . check_nurbs ( add , None , None , fname_smooth + ext_fname ) <EOL> if add > <NUM_LIT:30> : <EOL> exit = <NUM_LIT:1> <EOL> break <EOL> if exit == <NUM_LIT:1> : <EOL> break <EOL> d = add <EOL> size = e <EOL> nurbs_ctl_points = int ( size ) / d <EOL> print '<STR_LIT>' , str ( d ) <EOL> cmd = '<STR_LIT>' + file_name + '<STR_LIT>' + fname_smooth + ext_fname + '<STR_LIT>' + str ( nurbs_ctl_points ) <EOL> sct . run ( cmd ) <EOL> '''<STR_LIT>''' <EOL> print '<STR_LIT>' <EOL> final_file_name = fname + '<STR_LIT>' + ext_fname <EOL> cmd = '<STR_LIT>' + fname_smooth + ext_fname + '<STR_LIT:U+0020>' + final_file_name + '<STR_LIT>' <EOL> sct . run ( cmd ) <EOL> print '<STR_LIT>' <EOL> linear_fitting . returnSquaredErrors ( final_file_name , d , size ) <EOL> os . remove ( fname_centerline + ext_fname ) <EOL> os . remove ( fname_smooth + ext_fname ) <EOL> os . remove ( '<STR_LIT>' ) <EOL> os . remove ( '<STR_LIT>' ) <EOL> def returnCenterline ( fname , div ) : <EOL> if centerline . returnCenterline ( fname , <NUM_LIT:1> , div ) == <NUM_LIT:1> : <EOL> div += <NUM_LIT:1> <EOL> returnCenterline ( fname , div ) <EOL> else : <EOL> return div <EOL> if __name__ == "<STR_LIT:__main__>" : <EOL> file_name = sys . argv [ <NUM_LIT:1> ] <EOL> print file_name <EOL> main ( file_name ) </s>
