Move config directory outside of package

And rename it to dataset_config

invokers/invoker_create_trialwise_data.py

@@ -5,7 +5,7 @@
 
 # noinspection DuplicatedCode
 def main():
-    config = load_config(str(Path(Path(__file__).parent.parent, "kymata", "config", "dataset4.yaml")))
+    config = load_config(str(Path(Path(__file__).parent.parent, "dataset_config", "dataset4.yaml")))
 
     create_trialwise_data(
         dataset_directory_name=config['dataset_directory_name'],

invokers/invoker_estimate_noise_cov_matrix.py

@@ -6,7 +6,7 @@
 
 # noinspection DuplicatedCode
 def main():
-    config = load_config(str(Path(Path(__file__).parent.parent, "kymata", "config", "dataset4.yaml")))
+    config = load_config(str(Path(Path(__file__).parent.parent, "dataset_config", "dataset4.yaml")))
 
     if config['data_location'] == "local":
         data_root_dir = str(Path(Path(__file__).parent.parent, "kymata-toolbox-data", "emeg_study_data")) + "/"
@@ -15,7 +15,7 @@ def main():
     elif config['data_location'] == "cbu-local":
         data_root_dir = '//cbsu/data/imaging/projects/cbu/kymata/data/'
     else:
-        raise Exception("The 'data_location' parameter in the config file must be either 'cbu' or 'local' or 'cbu-local'.")
+        raise Exception("The 'data_location' parameter in the dataset_config file must be either 'cbu' or 'local' or 'cbu-local'.")
 
     estimate_noise_cov( data_root_dir = data_root_dir,
                        emeg_machine_used_to_record_data = config['emeg_machine_used_to_record_data'],

invokers/invoker_run_data_cleansing.py

@@ -8,7 +8,7 @@
 
 # noinspection DuplicatedCode
 def main():
-    config = load_config(str(Path(Path(__file__).parent.parent, "kymata", "config", "dataset4.yaml")))
+    config = load_config(str(Path(Path(__file__).parent.parent, "dataset_config", "dataset4.yaml")))
 
     if config['data_location'] == "local":
         data_root_dir = str(Path(Path(__file__).parent.parent, "kymata-toolbox-data", "emeg_study_data")) + "/"
@@ -17,7 +17,7 @@ def main():
     elif config['data_location'] == "cbu-local":
         data_root_dir = '//cbsu/data/imaging/projects/cbu/kymata/data/'
     else:
-        raise Exception("The 'data_location' parameter in the config file must be either 'cbu' or 'local' or 'cbu-local'.")
+        raise Exception("The 'data_location' parameter in the dataset_config file must be either 'cbu' or 'local' or 'cbu-local'.")
 
     run_first_pass_cleansing_and_maxwell_filtering(
         data_root_dir = data_root_dir,

invokers/invoker_run_hexel_current_estimation.py

@@ -8,7 +8,7 @@
 
 # noinspection DuplicatedCode
 def main():
-    config = load_config(str(Path(Path(__file__).parent.parent, "kymata", "config", "dataset4.yaml")))
+    config = load_config(str(Path(Path(__file__).parent.parent, "dataset_config", "dataset4.yaml")))
 
     if config['data_location'] == "local":
         data_root_dir = str(Path(Path(__file__).parent.parent, "kymata-toolbox-data", "emeg_study_data")) + "/"
@@ -17,7 +17,7 @@ def main():
     elif config['data_location'] == "cbu-local":
         data_root_dir = '//cbsu/data/imaging/projects/cbu/kymata/data/'
     else:
-        raise Exception("The 'data_location' parameter in the config file must be either 'cbu' or 'local' or 'cbu-local'.")
+        raise Exception("The 'data_location' parameter in the dataset_config file must be either 'cbu' or 'local' or 'cbu-local'.")
 
     # create_current_estimation_prerequisites(data_root_dir, config=config)
 

invokers/run_gridsearch.py

@@ -63,7 +63,7 @@ def main():
     args = parser.parse_args()
 
     # TODO: use config for ppt lists etc
-    #config = load_config(str(Path(Path(__file__).parent.parent, "kymata", "config", "dataset4.yaml")))
+    #dataset_config = load_config(str(Path(Path(__file__).parent.parent, "dataset_config", "dataset4.yaml")))
 
     participants = [
         'pilot_01',

kymata/io/yaml.py

@@ -2,13 +2,13 @@
 
 
 def load_config(config_location: str):
-    """Load config parameters"""
+    """Load dataset_config parameters"""
     with open(config_location, "r") as stream:
         return yaml.safe_load(stream)
 
 def modify_param_config(config_location: str, key: str, value):
     with open(config_location, 'r') as stream:
-        """Load config parameter"""
+        """Load dataset_config parameter"""
         data = yaml.safe_load(stream)
         data[key] = value
     yaml.emitter.Emitter.process_tag = lambda self, *args, **kw: None

kymata/preproc/data_cleansing.py

@@ -674,10 +674,10 @@ def apply_automatic_bad_channel_detection(raw_fif_data: mne.io.Raw, machine_used
     raw_check = raw_fif_data.copy()
 
     fine_cal_file = Path(Path(__file__).parent.parent,
-                         'config', 'cbu_specific_files',
+                         'kymata-toolbox-data', 'cbu_specific_files',
                          'sss_cal' + machine_used + '.dat')
     crosstalk_file = Path(Path(__file__).parent.parent,
-                          'config', 'cbu_specific_files',
+                          'kymata-toolbox-data', 'cbu_specific_files',
                           'ct_sparse' + machine_used + '.fif')
 
     auto_noisy_chs, auto_flat_chs, auto_scores = mne.preprocessing.find_bad_channels_maxwell(

kymata/preproc/hexel_current_estimation.py

@@ -192,7 +192,7 @@ def create_forward_model_and_inverse_solution(data_root_dir, config: dict):
          elif config['eeg']:
              mne.write_forward_solution(Path(intrim_preprocessing_directory_name, "4_hexel_current_reconstruction","forward_sol_files", participant + '-fwd-eegonly.fif'), fwd)
          else:
-             raise Exception('eeg and meg in the config file cannot be both False')
+             raise Exception('eeg and meg in the dataset_config file cannot be both False')
 
     # Compute inverse operator