added foundation option some_molecules

fsl_mrs_mce/mc_in.py

@@ -29,11 +29,13 @@ def load_config(input_folder="input/", section="default"):
         print(f"No {configFilePath} provided.")
 
 
-def conc_df_from_file(input_path="input/", foundation="vivo_average"):
+def conc_df_from_file(input_path="input/", foundation="vivo_average",
+                      include_molecules=[]):
     sections = load_config(input_path, "")
     """Generates concentration dataframe for mc method.
     Supports different variation types (absolute/delta/relative)
-    Returns data_frame of different concentrations"""
+    Returns data_frame of different concentrations.
+    include_molecules needed for option some_molecules"""
     # Load all relevant sections
     list_parser_parameter = []
 
@@ -64,6 +66,15 @@ def conc_df_from_file(input_path="input/", foundation="vivo_average"):
                 df_foundation[molecule] = 0
         except:
             print("No basis/fit_conc_result.csv file supplied")
+    if foundation == "some_molecules":
+        try:
+            df_foundation = pd.read_csv(
+                "basis/fit_conc_result.csv").mean().to_frame().transpose()
+            for molecule in molecule_names:
+                if molecule not in include_molecules:
+                    df_foundation[molecule] = 0
+        except:
+            print("No basis/fit_conc_result.csv file supplied")
     else:
         print("Only foundation mode vivo_average not chosen")