Stratification fixes

Author: brandynlucca

echopop/acoustics.py

@@ -276,26 +276,12 @@ def nasc_to_biomass(
     age_group_cols = settings_dict["transect"]["age_group_columns"]
 
     # Extract the correct strata dataframe
-    # ---- Define `strata_df`
-    strata_df = input_dict["spatial"]["strata_df"].copy()
-    # ---- Determine with the default ('ks') needs to be swapped out for 'inpfc'
-    if settings_dict["transect"]["stratum"] == "inpfc":
-        # ---- Get the INPFC strata
-        inpfc_df = input_dict["spatial"]["inpfc_strata_df"].copy().set_index(["haul_bin"])
-        # ---- Offset starts
-        inpfc_df["haul_start"] = inpfc_df["haul_start"] - int(1)
-        # ---- Get the `haul_bins`
-        haul_bins = np.unique(inpfc_df.loc[:, "haul_start":"haul_end"].stack().values)
-        # NOT CORRECT BINS !
-
-        # ---- Cut `strata_df` to haul_bins
-        strata_df["haul_bin"] = pd.cut(strata_df["haul_num"], haul_bins)
-        # ---- Set index
-        strata_df.set_index(["haul_bin"], inplace=True)
-        # ---- Merge
-        strata_df["stratum_inpfc"] = inpfc_df["stratum_inpfc"]
-        # ---- Reset index
-        strata_df = strata_df.reset_index().drop(columns=["haul_bin", "stratum_num"])
+    # ---- Define `strata_df` if KS
+    if settings_dict["transect"]["stratum"] == "ks":
+        strata_df = input_dict["spatial"]["strata_df"].copy()
+    # Define `inpfc_strata_df` if INPFC
+    elif settings_dict["transect"]["stratum"] == "inpfc":
+        strata_df = input_dict["spatial"]["inpfc_strata_df"].copy()
 
     # Get group-specific column names and create conversion key
     name_conversion_key = {age_group_cols["haul_id"]: "haul_num", age_group_cols["nasc_id"]: "nasc"}

echopop/spatial/mesh.py

@@ -429,9 +429,13 @@ def stratify_mesh(input_dict: dict, kriged_mesh: pd.DataFrame, settings_dict: di
 
     # Extract the geographic-delimited strata
     if settings_dict["stratum"].lower() == "ks":
-        geo_strata = input_dict["spatial"]["geo_strata_df"]
+        geo_strata = input_dict["spatial"]["geo_strata_df"].copy().drop_duplicates(
+            "latitude_interval"
+        ).sort_values("latitude_interval")
     elif settings_dict["stratum"].lower() == "inpfc":
-        geo_strata = input_dict["spatial"]["inpfc_strata_df"]
+        geo_strata = input_dict["spatial"]["inpfc_geo_strata_df"].copy().drop_duplicates(
+            "latitude_interval"
+        ).sort_values("latitude_interval")
 
     # Define the latitude bin array
     latitude_bins = np.concatenate([[-90.0], geo_strata["northlimit_latitude"], [90.0]])
@@ -479,10 +483,14 @@ def mesh_to_transects(
     # Extract the appropriate stratum definitions/delimiters
     if settings_dict["stratum"].lower() == "inpfc":
         # ---- INPFC
-        strata = spatial_dict["inpfc_strata_df"]
+        strata = spatial_dict["inpfc_geo_strata_df"].copy().drop_duplicates(
+            "latitude_interval"
+        ).sort_values(["latitude_interval"])
     elif settings_dict["stratum"].tolower() == "ks":
         # ---- KS
-        strata = spatial_dict["geo_strata_df"]
+        strata = spatial_dict["geo_strata_df"].copy().drop_duplicates(
+            "latitude_interval"
+        ).sort_values(["latitude_interval"])
     # ---- Create latitude bins
     latitude_bins = latitude_bins = np.concatenate([[-90.0], strata["northlimit_latitude"], [90.0]])
 

echopop/utils/message.py

@@ -251,6 +251,12 @@ def kriging_results_msg(kriging_results_dict: pd.DataFrame, settings_dict: dict)
     else:
         crop_str = "Extrapolated over uncropped grid"
 
+    # Amend variable name for density
+    if "density" in settings_dict["variable"]:
+        density_var = settings_dict["variable"].replace("_", " ")
+    else:
+        density_var = settings_dict["variable"] + " density"
+
     # Generate message output
     return print(
         f"--------------------------------\n"