Convert from zero- to one-based indices in output

hmsc/utils/export_rds_utils.py

@@ -33,10 +33,21 @@ def load_model_from_rds(rds_file_path):
 
 def save_chains_postList_to_rds(postList, postList_file_path, nChains, elapsedTime=-1, flag_save_eta=True):
  data = {}
- data["list"] = convert_to_numpy(postList)
- if not flag_save_eta:
- for i in range(len(data["list"])):
- for j in range(len(data["list"][i])):
- data["list"][i][j]["Eta"] = None
+ output_list = convert_to_numpy(postList)
+
+ for i in range(len(output_list)):
+ for j in range(len(output_list[i])):
+ item = output_list[i][j]
+
+ # Convert from zero- to one-based indices
+ item["rhoInd"] += 1
+ for k in range(len(item["AlphaInd"])):
+ item["AlphaInd"][k] += 1
+
+ # Remove eta if requested
+ if not flag_save_eta:
+ item["Eta"] = None
+
+ data["list"] = output_list
  data["time"] = elapsedTime
  rdata.write_rds(postList_file_path, data)