[Validate] Added all segmentation to poly metrics (#292)

* Added all segmentation to poly metrics

* Clean up init

* Add segmentation configs

Author: gatli

nucleus/metrics/__init__.py

@@ -15,3 +15,11 @@
     PolygonPrecision,
     PolygonRecall,
 )
+from .segmentation_metrics import (
+    SegmentationMaskToPolyMetric,
+    SegmentationToPolyAveragePrecision,
+    SegmentationToPolyIOU,
+    SegmentationToPolyMAP,
+    SegmentationToPolyPrecision,
+    SegmentationToPolyRecall,
+)

nucleus/metrics/cuboid_utils.py

@@ -6,7 +6,7 @@
 try:
     from shapely.geometry import Polygon
 except ModuleNotFoundError:
-    from .shapely_not_installed import ShapelyNotInstalled
+    from ..shapely_not_installed import ShapelyNotInstalled
 
     Polygon = ShapelyNotInstalled
 

nucleus/metrics/polygon_metrics.py

@@ -541,8 +541,11 @@ def eval(
         ) = get_true_false_positives_confidences(
             annotations_filtered, predictions_filtered, self.iou_threshold
         )
-        idxes = np.argsort(-confidences)
-        true_false_positives_sorted = true_false_positives[idxes]
+        if np.all(confidences):
+            idxes = np.argsort(-confidences)
+            true_false_positives_sorted = true_false_positives[idxes]
+        else:
+            true_false_positives_sorted = true_false_positives
         cumulative_true_positives = np.cumsum(true_false_positives_sorted)
         total_predictions = np.arange(1, len(true_false_positives) + 1)
         precisions = cumulative_true_positives / total_predictions

nucleus/metrics/polygon_utils.py

@@ -13,7 +13,7 @@
 try:
     from shapely.geometry import Polygon
 except ModuleNotFoundError:
-    from .shapely_not_installed import ShapelyNotInstalled
+    from ..shapely_not_installed import ShapelyNotInstalled
 
     Polygon = ShapelyNotInstalled
 

nucleus/metrics/segmentation_metrics.py

@@ -0,0 +1,48 @@
+import numpy as np
+from rasterio import features
+
+from nucleus import Point, PolygonPrediction
+
+try:
+    from shapely import geometry
+except ModuleNotFoundError:
+    from nucleus.shapely_not_installed import (  # pylint: disable=ungrouped-imports
+        ShapelyNotInstalled,
+    )
+
+    geometry = ShapelyNotInstalled
+
+
+def instance_mask_to_polys(instance_mask: np.ndarray, background_code=None):
+    mask_values = []
+    all_polygons = []
+    not_background_mask = (
+        (instance_mask != background_code) if background_code else None
+    )
+    for shape, value in features.shapes(
+        instance_mask.astype(np.int16),
+        mask=not_background_mask,
+    ):
+        poly = geometry.shape(shape)
+        all_polygons.append(poly)
+        mask_values.append(int(value))
+
+    return mask_values, all_polygons
+
+
+def transform_poly_codes_to_poly_preds(
+    dataset_item_id: str, pred_value, pred_polys, code_to_label
+):
+    polygon_predictions = []
+    for code, poly in zip(pred_value, pred_polys):
+        if poly.type != "Polygon":
+            continue
+        label = code_to_label[code]
+        x_stack, y_stack = poly.exterior.coords.xy
+        pred = PolygonPrediction(
+            label,
+            vertices=[Point(x, y) for x, y in zip(x_stack, y_stack)],
+            reference_id=dataset_item_id,
+        )
+        polygon_predictions.append(pred)
+    return polygon_predictions