ENH: add latecrop-late detection

.gitignore

@@ -14,6 +14,7 @@ local/
 
 .vs/*
 .vscode/*
+.mypy_cache/*
 
 # Local History for Visual Studio Code
 .history/

cropclassification/preprocess/_prepare_input_BEFL.py

@@ -54,6 +54,13 @@
 ndvi_latecrop_count = "latecrop_ndvi_count"
 ndvi_latecrop_median = "latecrop_ndvi_median"
 
+# TODO: should be in REFE instead of hardcoded!!!
+late_main_crops = {
+    "MAINCROP_BEETS": ["71", "91", "8532", "9532"],
+    "MAINCROP_MAIZE": ["201", "202"],
+    "IGNORE_LATE_MAINCROP": ["396"],
+}
+
 
 def prepare_input(
     input_parcel_path: Path,
@@ -318,18 +325,16 @@
             min_parcels_in_class=min_parcels_in_class,
             is_groundtruth=True,
         )
-    elif classtype_to_prepare == "LATECROP-EARLY":
-        parceldata_df = prepare_input_latecrop_early(
-            parceldata_df=parceldata_df,
-            column_BEFL_latecrop=column_BEFL_latecrop,
-            column_BEFL_latecrop2=column_BEFL_latecrop2,
-            column_BEFL_maincrop=column_BEFL_crop,
-            column_output_class=conf.columns["class"],
-            classes_refe_path=classes_refe_path,
-            min_parcels_in_class=min_parcels_in_class,
-            is_groundtruth=False,
-        )
-    elif classtype_to_prepare == "LATECROP":
+    elif classtype_to_prepare.startswith("LATECROP"):
+        if classtype_to_prepare.startswith("LATECROP-EARLY"):
+            scope = "EARLY_MAINCROP"
+        elif classtype_to_prepare.startswith("LATECROP-LATE"):
+            scope = "LATE_MAINCROP"
+        else:
+            scope = "ALL"
+
+        is_groundtruth = classtype_to_prepare.endswith("-GROUNDTRUTH")
+
         parceldata_df = prepare_input_latecrop(
             parceldata_df=parceldata_df,
             column_BEFL_latecrop=column_BEFL_latecrop,
@@ -338,29 +343,8 @@
             column_output_class=conf.columns["class"],
             classes_refe_path=classes_refe_path,
             min_parcels_in_class=min_parcels_in_class,
-            is_groundtruth=False,
-        )
-    elif classtype_to_prepare == "LATECROP-EARLY-GROUNDTRUTH":
-        parceldata_df = prepare_input_latecrop_early(
-            parceldata_df=parceldata_df,
-            column_BEFL_latecrop=column_BEFL_latecrop_gt_verified,
-            column_BEFL_latecrop2=None,
-            column_BEFL_maincrop=column_BEFL_crop,
-            column_output_class=conf.columns["class_groundtruth"],
-            classes_refe_path=classes_refe_path,
-            min_parcels_in_class=min_parcels_in_class,
-            is_groundtruth=True,
-        )
-    elif classtype_to_prepare == "LATECROP-GROUNDTRUTH":
-        parceldata_df = prepare_input_latecrop(
-            parceldata_df=parceldata_df,
-            column_BEFL_latecrop=column_BEFL_latecrop_gt_verified,
-            column_BEFL_latecrop2=None,
-            column_BEFL_maincrop=column_BEFL_crop,
-            column_output_class=conf.columns["class_groundtruth"],
-            classes_refe_path=classes_refe_path,
-            min_parcels_in_class=min_parcels_in_class,
-            is_groundtruth=True,
+            is_groundtruth=is_groundtruth,
+            scope=scope,
         )
     elif classtype_to_prepare == "FABACEAE":
         parceldata_df = prepare_input_fabaceae(
@@ -1091,6 +1075,7 @@
     classes_refe_path: Path,
     min_parcels_in_class: int,
     is_groundtruth: bool,
+    scope: str,
 ):
     """Prepare input file for use in the latecrop marker.
 
@@ -1105,7 +1090,9 @@
     # Check if parameters are OK and init some extra params
     # -----------------------------------------------------
     if not classes_refe_path.exists():
-        raise Exception(f"Input classes file doesn't exist: {classes_refe_path}")
+        raise ValueError(f"Input classes file doesn't exist: {classes_refe_path}")
+    if scope is None or scope not in ["ALL", "EARLY_MAINCROP", "LATE_MAINCROP"]:
+        raise ValueError(f"Invalid value for scope: {scope}")
 
     # Convert the crops to unicode, in case the input is int
     if column_BEFL_latecrop in parceldata_df.columns:
@@ -1207,6 +1194,40 @@
             value=parceldata_df[f"{column_output_class_orig}_LATECROP2"],
         )
 
+    # If limited scope, apply it
+    if scope == "EARLY_MAINCROP":
+        # Only process parcels with an early main crop.
+        # Hence, set parcels with a main crop that stays late on the field to an IGNORE
+        # class.
+        for class_name, cropcodes in late_main_crops.items():
+            parceldata_df.loc[
+                parceldata_df[column_BEFL_maincrop].isin(cropcodes), column_output_class
+            ] = class_name
+            if not is_groundtruth:
+                parceldata_df.loc[
+                    parceldata_df[column_BEFL_maincrop].isin(cropcodes),
+                    conf.columns["class_declared"],
+                ] = class_name
+
+    elif scope == "LATE_MAINCROP":
+        # Only process parcels with a late main crop.
+        # Hence, set parcels with a main crop that is remove early to an IGNORE class.
+        early_maincrop_classname = "IGNORE_EARLY_MAINCROP"
+
+        early_maincrops = []
+        for _, cropcodes in late_main_crops.items():
+            early_maincrops.extend(cropcodes)
+
+        parceldata_df.loc[
+            ~parceldata_df[column_BEFL_maincrop].isin(early_maincrops),
+            column_output_class,
+        ] = early_maincrop_classname
+        if not is_groundtruth:
+            parceldata_df.loc[
+                ~parceldata_df[column_BEFL_maincrop].isin(early_maincrops),
+                conf.columns["class_declared"],
+            ] = early_maincrop_classname
+
     # For rows with no class, set to UNKNOWN
     parceldata_df.fillna(value={column_output_class: "UNKNOWN"}, inplace=True)
 
@@ -1355,57 +1376,6 @@
     return parceldata_df
 
 
-def prepare_input_latecrop_early(
-    parceldata_df,
-    column_BEFL_latecrop: str,
-    column_BEFL_latecrop2: Optional[str],
-    column_BEFL_maincrop: str,
-    column_output_class: str,
-    classes_refe_path: Path,
-    min_parcels_in_class: int,
-    is_groundtruth: bool,
-):
-    """Prepare input file for use in the latecrop_early marker.
-
-    Prepare a classname column to classify the crop groups for early detection of
-    late crops. During this early detection, some main crops will still be on the field
-    during the entire perios. For these cases, replace the class with a class based on
-    the main crop.
-    """
-    # First run the standard latecrop prepare
-    parceldata_df = prepare_input_latecrop(
-        parceldata_df=parceldata_df,
-        column_BEFL_latecrop=column_BEFL_latecrop,
-        column_BEFL_latecrop2=column_BEFL_latecrop2,
-        column_BEFL_maincrop=column_BEFL_maincrop,
-        column_output_class=column_output_class,
-        classes_refe_path=classes_refe_path,
-        min_parcels_in_class=min_parcels_in_class,
-        is_groundtruth=is_groundtruth,
-    )
-
-    # Set parcels having a main crop that stays late on the field to another class, as
-    # the main crop will still be on the field:
-    # TODO: should be in REFE instead of hardcoded!!!
-    late_main_crops = {
-        "MAINCROP_BEETS": ["71", "91", "8532", "9532"],
-        "MAINCROP_MAIZE": ["201", "202"],
-        "IGNORE_LATE_MAINCROP": ["396"],
-    }
-
-    for class_name, cropcodes in late_main_crops.items():
-        parceldata_df.loc[
-            parceldata_df[column_BEFL_maincrop].isin(cropcodes), column_output_class
-        ] = class_name
-        if not is_groundtruth:
-            parceldata_df.loc[
-                parceldata_df[column_BEFL_maincrop].isin(cropcodes),
-                conf.columns["class_declared"],
-            ] = class_name
-
-    return parceldata_df
-
-
 def prepare_input_cropgroup_early(
     parceldata_df,
     column_BEFL_cropcode: str,