<s> import os <EOL> import numpy as np <EOL> import sys <EOL> import sct_utils as sct <EOL> from msct_image import Image <EOL> from msct_parser import Parser <EOL> from msct_gmseg_utils import resample_image , get_key_from_val <EOL> def amu_processing ( data_path ) : <EOL> """<STR_LIT>""" <EOL> im_ext = '<STR_LIT>' <EOL> if data_path [ - <NUM_LIT:1> ] == '<STR_LIT:/>' : <EOL> data_path = data_path [ : - <NUM_LIT:1> ] <EOL> original_path = os . path . abspath ( '<STR_LIT:.>' ) <EOL> os . chdir ( data_path ) <EOL> for subject_dir in os . listdir ( '<STR_LIT:.>' ) : <EOL> subject_path = data_path + '<STR_LIT:/>' + subject_dir <EOL> if os . path . isdir ( subject_dir ) : <EOL> os . chdir ( subject_dir ) <EOL> sc_seg_list = [ ] <EOL> gm_seg_list = [ ] <EOL> im_list = [ ] <EOL> for file_name in os . listdir ( '<STR_LIT:.>' ) : <EOL> ext = sct . extract_fname ( file_name ) [ <NUM_LIT:2> ] <EOL> if '<STR_LIT>' in file_name and ext != '<STR_LIT>' : <EOL> mask_im = Image ( file_name ) <EOL> sc_seg_im = mask_im . copy ( ) <EOL> sc_seg_im . file_name = sct . extract_fname ( file_name ) [ <NUM_LIT:1> ] [ : - <NUM_LIT:5> ] + '<STR_LIT>' <EOL> sc_seg_im . ext = '<STR_LIT>' <EOL> sc_seg_im . data = ( sc_seg_im . data > <NUM_LIT:1> ) . astype ( int ) <EOL> sc_seg_im . save ( ) <EOL> sc_seg_list . append ( sc_seg_im . file_name + sc_seg_im . ext ) <EOL> gm_seg_im = mask_im . copy ( ) <EOL> gm_seg_im . file_name = sct . extract_fname ( file_name ) [ <NUM_LIT:1> ] [ : - <NUM_LIT:5> ] + '<STR_LIT>' <EOL> gm_seg_im . ext = '<STR_LIT>' <EOL> gm_seg_im . data = ( gm_seg_im . data > <NUM_LIT:2> ) . astype ( int ) <EOL> gm_seg_im . save ( ) <EOL> gm_seg_list . append ( gm_seg_im . file_name + gm_seg_im . ext ) <EOL> im_list . append ( file_name [ : <NUM_LIT:2> ] + im_ext ) <EOL> im_list . reverse ( ) <EOL> gm_seg_list . reverse ( ) <EOL> sc_seg_list . reverse ( ) <EOL> cmd_merge = '<STR_LIT>' <EOL> im_name = subject_dir + '<STR_LIT>' <EOL> cmd_merge_im = cmd_merge + im_name <EOL> gmseg_name = subject_dir + '<STR_LIT>' <EOL> cmd_merge_gm_seg = cmd_merge + gmseg_name <EOL> scseg_name = subject_dir + '<STR_LIT>' <EOL> cmd_merge_sc_seg = cmd_merge + scseg_name <EOL> for im_i , gm_i , sc_i in zip ( im_list , gm_seg_list , sc_seg_list ) : <EOL> cmd_merge_im += im_i + '<STR_LIT:U+0020>' <EOL> cmd_merge_gm_seg += gm_i + '<STR_LIT:U+0020>' <EOL> cmd_merge_sc_seg += sc_i + '<STR_LIT:U+0020>' <EOL> sct . run ( cmd_merge_im ) <EOL> sct . run ( cmd_merge_gm_seg ) <EOL> sct . run ( cmd_merge_sc_seg ) <EOL> level_label = { <NUM_LIT:0> : '<STR_LIT>' , <NUM_LIT:1> : '<STR_LIT>' , <NUM_LIT:2> : '<STR_LIT>' , <NUM_LIT:3> : '<STR_LIT>' , <NUM_LIT:4> : '<STR_LIT>' , <NUM_LIT:5> : '<STR_LIT>' , <NUM_LIT:6> : '<STR_LIT>' , <NUM_LIT:7> : '<STR_LIT>' , <NUM_LIT:8> : '<STR_LIT>' , <NUM_LIT:9> : '<STR_LIT>' , <NUM_LIT:10> : '<STR_LIT>' , <NUM_LIT:11> : '<STR_LIT>' , <NUM_LIT:12> : '<STR_LIT>' , <NUM_LIT> : '<STR_LIT>' } <EOL> level_dat = np . zeros ( ( mask_im . data . shape [ <NUM_LIT:0> ] , mask_im . data . shape [ <NUM_LIT:1> ] , len ( im_list ) ) ) <EOL> for i , im_i_name in enumerate ( im_list ) : <EOL> level_dat . T [ : ] [ : ] [ i ] = get_key_from_val ( level_label , im_i_name [ : <NUM_LIT:2> ] . upper ( ) ) <EOL> Image ( param = level_dat , absolutepath = subject_dir + '<STR_LIT>' ) . save ( ) <EOL> resample_image ( im_name ) <EOL> resample_image ( gmseg_name , binary = True , thr = <NUM_LIT> ) <EOL> resample_image ( scseg_name , binary = True , thr = <NUM_LIT> ) <EOL> sct . run ( '<STR_LIT>' ) <EOL> sct . run ( '<STR_LIT>' ) <EOL> sct . run ( '<STR_LIT>' ) <EOL> sct . run ( '<STR_LIT>' ) <EOL> for file_name in os . listdir ( '<STR_LIT:.>' ) : <EOL> if '<STR_LIT>' in file_name : <EOL> sct . run ( '<STR_LIT>' + file_name + '<STR_LIT>' ) <EOL> elif '<STR_LIT>' in file_name and '<STR_LIT>' not in file_name : <EOL> sct . run ( '<STR_LIT>' + file_name + '<STR_LIT>' ) <EOL> elif '<STR_LIT>' in file_name : <EOL> sct . run ( '<STR_LIT>' + file_name + '<STR_LIT>' ) <EOL> elif '<STR_LIT>' in file_name : <EOL> sct . run ( '<STR_LIT>' + file_name + '<STR_LIT>' ) <EOL> elif not os . path . isdir ( os . path . abspath ( '<STR_LIT:.>' ) + '<STR_LIT:/>' + file_name ) : <EOL> sct . run ( '<STR_LIT>' + file_name + '<STR_LIT>' ) <EOL> os . chdir ( '<STR_LIT:..>' ) <EOL> os . chdir ( original_path ) <EOL> def vanderbilt_processing ( data_path ) : <EOL> """<STR_LIT>""" <EOL> im_ext = '<STR_LIT>' <EOL> if data_path [ - <NUM_LIT:1> ] == '<STR_LIT:/>' : <EOL> data_path = data_path [ : - <NUM_LIT:1> ] <EOL> original_path = os . path . abspath ( '<STR_LIT:.>' ) <EOL> os . chdir ( data_path ) <EOL> for subject_dir in os . listdir ( '<STR_LIT:.>' ) : <EOL> if os . path . isdir ( subject_dir ) : <EOL> os . chdir ( subject_dir ) <EOL> sc_seg_list = [ ] <EOL> gm_seg_list = [ ] <EOL> im_list = [ ] <EOL> for file_name in os . listdir ( '<STR_LIT:.>' ) : <EOL> if '<STR_LIT>' in file_name : <EOL> mask_im = Image ( file_name ) <EOL> sc_seg_im = mask_im . copy ( ) <EOL> sc_seg_im . file_name = sct . extract_fname ( file_name ) [ <NUM_LIT:1> ] [ : - <NUM_LIT:4> ] + '<STR_LIT>' <EOL> sc_seg_im . ext = '<STR_LIT>' <EOL> sc_seg_im . data = ( sc_seg_im . data > <NUM_LIT:0> ) . astype ( int ) <EOL> sc_seg_im . save ( ) <EOL> sc_seg_list . append ( sc_seg_im . file_name + sc_seg_im . ext ) <EOL> gm_seg_im = mask_im . copy ( ) <EOL> gm_seg_im . file_name = sct . extract_fname ( file_name ) [ <NUM_LIT:1> ] [ : - <NUM_LIT:4> ] + '<STR_LIT>' <EOL> gm_seg_im . ext = '<STR_LIT>' <EOL> gm_seg_im . data = ( gm_seg_im . data > <NUM_LIT:1> ) . astype ( int ) <EOL> gm_seg_im . save ( ) <EOL> gm_seg_list . append ( gm_seg_im . file_name + gm_seg_im . ext ) <EOL> im_list . append ( file_name [ : <NUM_LIT> ] + im_ext ) <EOL> cmd_merge = '<STR_LIT>' <EOL> im_name = subject_dir + '<STR_LIT>' <EOL> cmd_merge_im = cmd_merge + im_name <EOL> gmseg_name = subject_dir + '<STR_LIT>' <EOL> cmd_merge_gm_seg = cmd_merge + gmseg_name <EOL> scseg_name = subject_dir + '<STR_LIT>' <EOL> cmd_merge_sc_seg = cmd_merge + scseg_name <EOL> for im_i , gm_i , sc_i in zip ( im_list , gm_seg_list , sc_seg_list ) : <EOL> cmd_merge_im += '<STR_LIT:U+0020>' + im_i <EOL> cmd_merge_gm_seg += '<STR_LIT:U+0020>' + gm_i <EOL> cmd_merge_sc_seg += '<STR_LIT:U+0020>' + sc_i <EOL> sct . run ( cmd_merge_im ) <EOL> sct . run ( cmd_merge_gm_seg ) <EOL> sct . run ( cmd_merge_sc_seg ) <EOL> label_slices = [ im_slice . split ( '<STR_LIT:_>' ) [ - <NUM_LIT:1> ] [ <NUM_LIT:2> : <NUM_LIT:4> ] for im_slice in im_list ] <EOL> i_slice_to_level = { <NUM_LIT:0> : <NUM_LIT:6> , <NUM_LIT:1> : <NUM_LIT:6> , <NUM_LIT:2> : <NUM_LIT:6> , <NUM_LIT:3> : <NUM_LIT:6> , <NUM_LIT:4> : <NUM_LIT:6> , <NUM_LIT:5> : <NUM_LIT:5> , <NUM_LIT:6> : <NUM_LIT:5> , <NUM_LIT:7> : <NUM_LIT:5> , <NUM_LIT:8> : <NUM_LIT:5> , <NUM_LIT:9> : <NUM_LIT:5> , <NUM_LIT:10> : <NUM_LIT:4> , <NUM_LIT:11> : <NUM_LIT:4> , <NUM_LIT:12> : <NUM_LIT:4> , <NUM_LIT> : <NUM_LIT:4> , <NUM_LIT> : <NUM_LIT:4> , <NUM_LIT:15> : <NUM_LIT:3> , <NUM_LIT:16> : <NUM_LIT:3> , <NUM_LIT> : <NUM_LIT:3> , <NUM_LIT> : <NUM_LIT:3> , <NUM_LIT> : <NUM_LIT:3> , <NUM_LIT:20> : <NUM_LIT:3> , <NUM_LIT> : <NUM_LIT:2> , <NUM_LIT> : <NUM_LIT:2> , <NUM_LIT> : <NUM_LIT:2> , <NUM_LIT> : <NUM_LIT:2> , <NUM_LIT> : <NUM_LIT:1> , <NUM_LIT> : <NUM_LIT:1> , <NUM_LIT> : <NUM_LIT:1> , <NUM_LIT> : <NUM_LIT:1> , <NUM_LIT> : <NUM_LIT:1> } <EOL> level_dat = np . zeros ( ( mask_im . data . shape [ <NUM_LIT:0> ] , mask_im . data . shape [ <NUM_LIT:1> ] , len ( im_list ) ) ) <EOL> for i , l_slice in enumerate ( label_slices ) : <EOL> i_slice = int ( l_slice ) - <NUM_LIT:1> <EOL> level_dat . T [ : ] [ : ] [ i ] = i_slice_to_level [ i_slice ] <EOL> Image ( param = level_dat , absolutepath = subject_dir + '<STR_LIT>' ) . save ( ) <EOL> resample_image ( im_name ) <EOL> resample_image ( gmseg_name , binary = True ) <EOL> resample_image ( scseg_name , binary = True ) <EOL> sct . run ( '<STR_LIT>' ) <EOL> sct . run ( '<STR_LIT>' ) <EOL> sct . run ( '<STR_LIT>' ) <EOL> sct . run ( '<STR_LIT>' ) <EOL> sct . run ( '<STR_LIT>' ) <EOL> for file_name in os . listdir ( '<STR_LIT:.>' ) : <EOL> if '<STR_LIT>' in file_name and '<STR_LIT>' in file_name : <EOL> sct . run ( '<STR_LIT>' + file_name + '<STR_LIT>' ) <EOL> sct . run ( '<STR_LIT>' + file_name [ : - <NUM_LIT> ] + '<STR_LIT>' ) <EOL> for file_name in os . listdir ( '<STR_LIT:.>' ) : <EOL> if '<STR_LIT>' in file_name and '<STR_LIT>' not in file_name : <EOL> sct . run ( '<STR_LIT>' + file_name + '<STR_LIT>' ) <EOL> elif '<STR_LIT>' in file_name and '<STR_LIT>' in file_name : <EOL> sct . run ( '<STR_LIT>' + file_name + '<STR_LIT>' ) <EOL> elif '<STR_LIT>' in file_name : <EOL> sct . run ( '<STR_LIT>' + file_name + '<STR_LIT>' ) <EOL> elif '<STR_LIT>' not in file_name and not os . path . isdir ( os . path . abspath ( '<STR_LIT:.>' ) + '<STR_LIT:/>' + file_name ) or '<STR_LIT>' in file_name : <EOL> sct . run ( '<STR_LIT>' + file_name + '<STR_LIT>' ) <EOL> elif not os . path . isdir ( os . path . abspath ( '<STR_LIT:.>' ) + '<STR_LIT:/>' + file_name ) : <EOL> sct . run ( '<STR_LIT>' + file_name + '<STR_LIT>' ) <EOL> os . chdir ( '<STR_LIT:..>' ) <EOL> os . chdir ( original_path ) <EOL> if __name__ == "<STR_LIT:__main__>" : <EOL> parser = Parser ( __file__ ) <EOL> parser . usage . set_description ( '<STR_LIT>' ) <EOL> parser . add_option ( name = "<STR_LIT>" , <EOL> type_value = "<STR_LIT>" , <EOL> description = "<STR_LIT>" , <EOL> mandatory = False , <EOL> example = '<STR_LIT>' ) <EOL> parser . add_option ( name = "<STR_LIT>" , <EOL> type_value = "<STR_LIT>" , <EOL> description = "<STR_LIT>" , <EOL> mandatory = False , <EOL> example = '<STR_LIT>' ) <EOL> arguments = parser . parse ( sys . argv [ <NUM_LIT:1> : ] ) <EOL> if "<STR_LIT>" in arguments : <EOL> amu_processing ( arguments [ '<STR_LIT>' ] ) <EOL> if "<STR_LIT>" in arguments : <EOL> vanderbilt_processing ( arguments [ '<STR_LIT>' ] ) </s>
