- config file separation script and sct_run_batch

- yaml parser must point towards required yaml file with flag -i

config.yaml

@@ -28,9 +28,9 @@ transfo:
   bounds:
     angle_bound: 5
     shift_bound: 2.5
-    
+
 # config file for sct_run_batch
-path_data   : "data"
-path_output : "csa_atrophy_results_t2"
-script      : "process_data.sh"
-jobs        : -1
+#path_data   : "data"
+#path_output : "csa_atrophy_results_t2"
+#script      : "process_data.sh"
+#jobs        : -1

config_sct_run_batch.yml

@@ -0,0 +1,5 @@
+# config file for sct_run_batch
+path_data   : "data"
+path_output : "csa_atrophy_results_t2"
+script      : "process_data.sh"
+jobs        : -1

process_data.sh

@@ -25,18 +25,18 @@ SUBJECT=$1
 # The following global variables are retrieved from config.yaml file
 # set n_transfo to the desired number of transformed images of same subject for segmentation,
 # n_transfo also represents the number of iterations of the transformation, segmentation and labeling process
-n_transfo=$(yaml_parser -o n_transfo)
+n_transfo=$(yaml_parser -o n_transfo -i config.yaml)
 # define rescaling coefficients (always keep value 1 for reference)
-rescaling=$(yaml_parser -o rescaling)
+rescaling=$(yaml_parser -o rescaling -i config.yaml)
 R_COEFS=$(echo $rescaling | tr '[]' ' ' | tr ',' ' ' | tr "'" ' ')
-contrast=$(yaml_parser -o contrast)
+contrast=$(yaml_parser -o contrast -i config.yaml)
 if [ $contrast == "t2" ]; then
   contrast_str="T2w"
 fi
 if [ $contrast == "t1" ]; then
   contrast_str="T1w"
 fi
-path_output=$(yaml_parser -o path_output)
+path_output=$(yaml_parser -o path_output -i config_sct_run_batch.yml)
 
 
 # FUNCTIONS

yaml_parser.py

@@ -28,6 +28,11 @@ def get_parser():
         required=True,
         help="parameters to output from config.yaml",
     )
+    mandatory.add_argument(
+        "-i",
+        required=True,
+        help="input path to configuration of file",
+    )
     optional = parser.add_argument_group("\nOPTIONAL ARGUMENTS")
     optional.add_argument(
         '-h',
@@ -43,7 +48,7 @@ def main():
     parser = get_parser()
     arguments = parser.parse_args(args=None if sys.argv[0:] else ['--help'])
     # Read yaml file
-    with open("config.yaml", 'r') as config_var:
+    with open(arguments.i, 'r') as config_var:
         data_loaded = yaml.safe_load(config_var)
     # print yaml file parameters to be read by bash script
     print(data_loaded[arguments.o])