added foundation option flat

fsl_mrs_mce/mc_in.py

@@ -43,12 +43,27 @@ def conc_df_from_file(input_path="input/", foundation="vivo_average"):
 
     # Load foundation file, a line with e.g. in-vivo averages
     # The code expects a one-line-foundation.
+    molecule_names = ['Ala', 'Asc', 'Asp', 'Cr', 'GABA', 'GPC', 'GSH',
+                      'Glc', 'Gln', 'Glu', 'Ins', 'Lac', 'NAA', 'NAAG',
+                      'PCho', 'PCr', 'PE', 'Scyllo', 'Tau',
+                      'mm', 'Glu+Gln', 'GPC+PCho', 'Cr+PCr',
+                      'Glc+Tau', 'NAA+NAAG']
+
     if foundation == "vivo_average":
         try:
             df_foundation = pd.read_csv(
                 "basis/fit_conc_result.csv").mean().to_frame().transpose()
         except:
             print("No basis/fit_conc_result.csv file supplied")
+    # Sets all initial molecules, including some groups, to 0
+    if foundation == "flat":
+        try:
+            df_foundation = pd.read_csv(
+                "basis/fit_conc_result.csv").mean().to_frame().transpose()
+            for molecule in molecule_names:
+                df_foundation[molecule] = 0
+        except:
+            print("No basis/fit_conc_result.csv file supplied")
     else:
         print("Only foundation mode vivo_average not chosen")