Fix stratified and kriging analysis INPFC bugs (OSOceanAcoustics#312)

* Create test file script * Tweaks to `kriging_analysis` to correctly use `stratum_inpfc` as a valid column name for internal dataframes * Fix to transect coordinate storage and removing duplication of `stratum_inpfc` * Remove test file script * Pre-commit changes
rebeccathomas-NOAA · Dec 5, 2024 · 3067a55 · 3067a55
1 parent 1492a53
commit 3067a55
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Showing 2 changed files with 13 additions and 6 deletions.
diff --git a/echopop/spatial/transect.py b/echopop/spatial/transect.py
@@ -70,8 +70,16 @@ def save_transect_coordinates(transect_data: pd.DataFrame, settings_dict: dict):
     # Get the correct haul and stratum names
     age_group_cols = settings_dict["age_group_columns"]
 
+    # Get stratum definition
+    stratum_def = settings_dict["stratum"]
+
     # Get stratum column name
     stratum_col = settings_dict["stratum_name"]
+    # ---- Set up the column renaming scheme
+    if stratum_def == "inpfc":
+        stratum_rename = "stratum_num"
+    else:
+        stratum_rename = stratum_col
 
     # Extract transect numbers, coordinates, and strata
     transect_data_extract = transect_data.filter(
@@ -88,7 +96,10 @@ def save_transect_coordinates(transect_data: pd.DataFrame, settings_dict: dict):
 
     # Rename the group-specific columns and return the output
     return transect_data_extract.rename(
-        columns={age_group_cols["haul_id"]: "haul_num", age_group_cols["stratum_id"]: stratum_col}
+        columns={
+            age_group_cols["haul_id"]: "haul_num",
+            age_group_cols["stratum_id"]: stratum_rename,
+        }
     )
 
 

diff --git a/echopop/survey.py b/echopop/survey.py
@@ -887,17 +887,13 @@ def kriging_analysis(
                 # ---- From `self.transect_analysis` settings
                 "exclude_age1": self.analysis["settings"]["transect"]["exclude_age1"],
                 "stratum": self.analysis["settings"]["transect"]["stratum"],
+                "stratum_name": self.analysis["settings"]["transect"]["stratum_name"],
             },
         )
 
         # Calculate additional keys for the settings
         self.analysis["settings"]["kriging"].update(
             {
-                "stratum_name": (
-                    "stratum_num"
-                    if self.analysis["settings"]["kriging"]["stratum"] == "ks"
-                    else "inpfc"
-                ),
                 "variogram_parameters": (
                     {
                         **self.input["statistics"]["variogram"]["model_config"],