Removing utils folder and absorbing rest in hrvmeg

src/docs/hrvmeg/utils.md

-::: hrvmeg.utils
\ No newline at end of file

src/hrvmeg/data.py

@@ -25,7 +25,7 @@ class GetRpeaks:
         self.output_sub_dir = output_sub_dir
         self.ICA_value = ICA_value
 
-    def get_RR_intervals(self):
+    def get_R_peaks(self):
         """
         The function takes in a .CSV file containing a time and a trace, and then uses
         the scipy peak detection function to find peaks in the component value.

src/hrvmeg/main.py

@@ -10,21 +10,21 @@ from config import config
 from config.config import logger
 from hrvmeg import predict, compare
 from py_utils import config_utils, get_files, print_info
-from utils import meg_to_ica
+from hrvmeg import meg_to_ica
 
 # Initialize Typer CLI app
 app = typer.Typer()
 warnings.filterwarnings("ignore")
 
 @app.command()
-def extract_ica_from_meg(
+def extract_ic_from_meg(
     args_fp: str = "config/args.json",
     experiment_name: str = "Test 1",
     run_name: str = "Run1",
     test_run: bool = False,
 ) -> None:
     """
-    `extract_ica_from_meg` takes in a `scan_file` (a .ds file), and outputs a .csv file with the ICA
+    `extract_ic_from_meg` takes in a `scan_file` (a .ds file), and outputs a .csv file with the ICA
     components
 
     :param args_fp: str = "config/args.json", defaults to config/args.json
@@ -130,7 +130,7 @@ def label_cardiac_ic(
 
 
 @app.command
-def compare_ica_and_ecg(
+def compare_meg_and_ecg(
     args_rr: str="config/args_rr.json",
     experiment_name: str= "compare ECG + MEG",
     run_name: str="comparison 1"

src/utils/meg_to_ica.py → src/hrvmeg/meg_to_ica.py

@@ -70,7 +70,7 @@ class MNE_Processor:
         elif self.args["ica_method"] == "picard":
             fit_params = dict(extended=True)
         else:
-            print("Invalid ICA method must be either 'infomax', 'fastica', or 'picard'")
+            print("Invalid ICA method; it must be either 'infomax', 'fastica', or 'picard'")
             raise (NotImplementedError)
 
         # reject = dict(mag=5e-12, grad=4000e-13)

src/hrvmeg/predict.py

@@ -4,7 +4,7 @@ import tensorflow_addons as tfa
 from tensorflow import keras
 
 from config import config
-from utils import predict_and_vote
+from hrvmeg import predict_and_vote
 
 
 class label_ICA_components: