Module Import alias identifier Import alias Assign NameStore Str Assign NameStore Str Assign NameStore Str Assign NameStore Str Assign NameStore Str FunctionDef arguments args NameParam NameParam defaults Num body Expr Str Assign TupleStore NameStore NameStore TupleLoad ListLoad ListLoad For NameStore Call AttributeLoad NameLoad attr NameLoad body If BoolOpAnd UnaryOpNot Call AttributeLoad NameLoad attr Str Call AttributeLoad AttributeLoad NameLoad attr attr BinOpAdd NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr BinOpAdd BinOpAdd NameLoad NameLoad Str Expr Call AttributeLoad NameLoad attr NameLoad If UnaryOpNot NameLoad body Expr Call AttributeLoad NameLoad attr BinOpAdd BinOpAdd Str NameLoad Str keyword NameLoad keyword Str Return TupleLoad NameLoad NameLoad decorator_list Assign TupleStore NameStore NameStore Call NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr For NameStore NameLoad body Print NameLoad Expr Call AttributeLoad NameLoad attr BinOpAdd NameLoad NameLoad Expr Call AttributeLoad NameLoad attr BinOpAdd BinOpAdd BinOpAdd BinOpAdd BinOpAdd BinOpAdd BinOpAdd BinOpAdd BinOpAdd BinOpAdd Str NameLoad Str NameLoad Str NameLoad Str NameLoad Str NameLoad Str keyword Num Expr Call AttributeLoad NameLoad attr NameLoad
N/A N/A sct_utils sct N/A os N/A contrast t2 N/A path /Users/benjamindeleener/data/data_testing/test/ N/A path_output_seg /Users/benjamindeleener/data/spinal_cord_segmentation_data/test/labels/ N/A path_output_im /Users/benjamindeleener/data/spinal_cord_segmentation_data/test/data/ N/A size 80 generate_data_list N/A N/A folder_dataset verbose N/A 1 N/A N/A 
    Construction of the data list from the data set
    This function return a list of directory (in folder_dataset) in which the contrast is present.
    :return data:
     N/A N/A data_subjects subjects_dir N/A N/A N/A N/A subject_dir N/A N/A os listdir folder_dataset N/A N/A N/A N/A N/A N/A subject_dir startswith . N/A N/A N/A os path isdir N/A folder_dataset subject_dir N/A N/A N/A N/A data_subjects append N/A N/A folder_dataset subject_dir / N/A N/A N/A subjects_dir append subject_dir N/A N/A data_subjects N/A N/A N/A N/A sct printv N/A N/A ERROR: No subject data were found in  folder_dataset . Please organize your data correctly or provide a correct dataset. verbose verbose type error N/A N/A data_subjects subjects_dir N/A N/A N/A data_subjects subjects_name N/A generate_data_list path N/A current_folder N/A N/A os getcwd N/A subject_folder data_subjects N/A N/A subject_folder N/A N/A N/A os chdir N/A subject_folder contrast N/A N/A N/A sct run N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A sct_seg_utility.py -i  contrast .nii.gz -seg  contrast _manual_segmentation.nii.gz -ofolder-im  path_output_im  -ofolder-seg  path_output_seg  -size  size  -v 2 verbose 2 N/A N/A N/A os chdir current_folder