Addressed the comments from the PR

Author: David Cleres

src/stratigraphy/benchmark/metrics.py

@@ -61,7 +61,7 @@ def get_metrics_list(self) -> list[Metrics]:
 class OverallMetricsCatalog:
     """Keeps track of all different relevant metrics that are computed for a dataset."""
 
-    def __init__(self, languages: list[str]):
+    def __init__(self, languages: set[str]):
         self.layer_metrics = OverallMetrics()
         self.depth_interval_metrics = OverallMetrics()
         self.groundwater_metrics = OverallMetrics()

src/stratigraphy/benchmark/score.py

@@ -10,7 +10,6 @@
 from dotenv import load_dotenv
 from stratigraphy import DATAPATH
 from stratigraphy.annotations.draw import draw_predictions
-from stratigraphy.benchmark.ground_truth import GroundTruth
 from stratigraphy.evaluation.evaluation_dataclasses import BoreholeMetadataMetrics
 from stratigraphy.util.predictions import OverallFilePredictions
 
@@ -21,39 +20,6 @@
 logger = logging.getLogger(__name__)
 
 
-def create_predictions_objects(
-    predictions: OverallFilePredictions,
-    ground_truth_path: Path | None,
-) -> tuple[OverallFilePredictions, dict]:
-    """Create predictions objects from the predictions and evaluate them against the ground truth.
-
-    Args:
-        predictions (OverallFilePredictions): The predictions objects.
-        ground_truth_path (Path | None): The path to the ground truth file.
-
-    Returns:
-        tuple[OverallFilePredictions, dict]: The predictions objects and the number of ground truth values per
-                                                 file.
-    """
-    if ground_truth_path and ground_truth_path.exists():  # for inference no ground truth is available
-        ground_truth = GroundTruth(ground_truth_path)
-        ground_truth_is_present = True
-    else:
-        logging.warning("Ground truth file not found.")
-        ground_truth_is_present = False
-        return predictions, {}
-
-    number_of_truth_values = {}
-    for file_predictions in predictions.file_predictions_list:
-        if ground_truth_is_present:
-            ground_truth_for_file = ground_truth.for_file(file_predictions.file_name)
-            if ground_truth_for_file:
-                file_predictions.evaluate(ground_truth_for_file)
-                number_of_truth_values[file_predictions.file_name] = len(ground_truth_for_file["layers"])
-
-    return predictions, number_of_truth_values
-
-
 def evaluate(
     predictions: OverallFilePredictions,
     ground_truth_path: Path,

src/stratigraphy/evaluation/groundwater_evaluator.py

@@ -121,7 +121,7 @@ def evaluate(self) -> OverallGroundwaterMetrics:
                 groundwater_elevation_metrics=groundwater_elevation_metrics,
                 groundwater_date_metrics=groundwater_date_metrics,
                 filename=filename,
-            )  # TODO: This clashes with the OverallMetrics object
+            )
 
             overall_groundwater_metrics.add_groundwater_metrics(file_groundwater_metrics)
 

src/stratigraphy/main.py

@@ -233,11 +233,11 @@ def start_pipeline(
 
                 if part == "all":
                     # Extract the groundwater levels
-                    groundwater_in_document = GroundwaterInDocument.from_document(doc, metadata.elevation)
+                    groundwater_entries = GroundwaterInDocument.from_document(doc, metadata.elevation)
 
                     # Extract the layers
-                    layer_predictions_list = LayersInDocument([], filename)
-                    depths_materials_column_pairs_list = []
+                    layers = LayersInDocument([], filename)
+                    depths_materials_columns_pairs = []
                     for page_index, page in enumerate(doc):
                         page_number = page_index + 1
                         logger.info("Processing page %s", page_number)
@@ -253,7 +253,7 @@ def start_pipeline(
                             layer_predictions = remove_duplicate_layers(
                                 previous_page=doc[page_index - 1],
                                 current_page=page,
-                                previous_layers=layer_predictions_list,
+                                previous_layers=layers,
                                 current_layers=process_page_results.predictions,
                                 img_template_probability_threshold=matching_params[
                                     "img_template_probability_threshold"
@@ -262,8 +262,8 @@ def start_pipeline(
                         else:
                             layer_predictions = process_page_results.predictions
 
-                        layer_predictions_list.add_layers_on_page(layer_predictions)
-                        depths_materials_column_pairs_list.extend(process_page_results.depth_material_pairs)
+                        layers.add_layers_on_page(layer_predictions)
+                        depths_materials_columns_pairs.extend(process_page_results.depth_material_pairs)
 
                         if draw_lines:  # could be changed to if draw_lines and mflow_tracking:
                             if not mlflow_tracking:
@@ -276,10 +276,6 @@ def start_pipeline(
                                 )
                                 mlflow.log_image(img, f"pages/{filename}_page_{page.number + 1}_lines.png")
 
-                    groundwater_entries = groundwater_in_document
-                    layers = layer_predictions_list
-                    depths_materials_columns_pairs = depths_materials_column_pairs_list
-
                 # Add file predictions
                 predictions.add_file_predictions(
                     FilePredictions(