Improve predict batch (#876)

* run per batch, not per image per batch

src/deepforest/main.py

@@ -881,12 +881,11 @@ def predict_batch(self, images, preprocess_fn=None):
 
         #using Pytorch Ligthning's predict_step
         with torch.no_grad():
-            predictions = []
-            for idx, image in enumerate(images):
-                predictions = self.predict_step(image.unsqueeze(0), idx)
-                predictions.extend(predictions)
+            predictions = self.predict_step(images, 0)
+
         #convert predictions to dataframes
-        results = [pd.DataFrame(pred) for pred in predictions if pred is not None]
+        results = [utilities.read_file(pred) for pred in predictions if pred is not None]
+
         return results
 
     def configure_optimizers(self):

tests/test_main.py

@@ -701,107 +701,52 @@ def test_predict_tile_with_crop_model_empty():
     # Assert the result
     assert result is None
 
-# @pytest.mark.parametrize("batch_size", [1, 4, 8])
-# def test_batch_prediction(m, batch_size, raster_path):
-#    
-#     # Prepare input data
-#     tile = np.array(Image.open(raster_path))
-#     ds = dataset.TileDataset(tile=tile, patch_overlap=0.1, patch_size=100)
-#     dl = DataLoader(ds, batch_size=batch_size)
-
-#     # Perform prediction
-#     predictions = []
-#     for batch in dl:
-#         prediction = m.predict_batch(batch)
-#         predictions.append(prediction)
-
-#     # Check results
-#     assert len(predictions) == len(dl)
-#     for batch_pred in predictions:
-#         assert isinstance(batch_pred, pd.DataFrame)
-#         assert set(batch_pred.columns) == {
-#             "xmin", "ymin", "xmax", "ymax", "label", "score", "geometry"
-#         }
-
-# @pytest.mark.parametrize("batch_size", [1, 4])
-# def test_batch_training(m, batch_size, tmpdir):
-#     
-#     # Generate synthetic training data
-#     csv_file = get_data("example.csv")
-#     root_dir = os.path.dirname(csv_file)
-#     train_ds = m.load_dataset(csv_file, root_dir=root_dir)
-#     train_dl = DataLoader(train_ds, batch_size=batch_size, shuffle=True)
-
-#     # Configure the model and trainer
-#     m.config["batch_size"] = batch_size
-#     m.create_trainer()
-#     trainer = m.trainer
-
-#     # Train the model
-#     trainer.fit(m, train_dl)
-
-#     # Assertions
-#     assert trainer.current_epoch == 1
-#     assert trainer.batch_size == batch_size
-
-# @pytest.mark.parametrize("batch_size", [2, 4])
-# def test_batch_data_augmentation(m, batch_size, raster_path):
-#     
-#     tile = np.array(Image.open(raster_path))
-#     ds = dataset.TileDataset(tile=tile, patch_overlap=0.1, patch_size=100, augment=True)
-#     dl = DataLoader(ds, batch_size=batch_size)
+def test_batch_prediction(m, raster_path):
+    # Prepare input data
+    tile = np.array(Image.open(raster_path))
+    ds = dataset.TileDataset(tile=tile, patch_overlap=0.1, patch_size=300)
+    dl = DataLoader(ds, batch_size=3)
 
-#     predictions = []
-#     for batch in dl:
-#         prediction = m.predict_batch(batch)
-#         predictions.append(prediction)
+    # Perform prediction
+    predictions = []
+    for batch in dl:
+        prediction = m.predict_batch(batch)
+        predictions.append(prediction)
 
-#     assert len(predictions) == len(dl)
-#     for batch_pred in predictions:
-#         assert isinstance(batch_pred, pd.DataFrame)
-#         assert set(batch_pred.columns) == {
-#             "xmin", "ymin", "xmax", "ymax", "label", "score", "geometry"
-#         }
-
-# def test_batch_inference_consistency(m, raster_path):
-#     
-#     tile = np.array(Image.open(raster_path))
-#     ds = dataset.TileDataset(tile=tile, patch_overlap=0.1, patch_size=100)
-#     dl = DataLoader(ds, batch_size=4)
+    # Check results
+    assert len(predictions) == len(dl)
+    for batch_pred in predictions:
+        for image_pred in batch_pred:
+            assert isinstance(image_pred, pd.DataFrame)
+            assert "label" in image_pred.columns
+            assert "score" in image_pred.columns
+            assert "geometry" in image_pred.columns
+
+def test_batch_inference_consistency(m, raster_path):
+    tile = np.array(Image.open(raster_path))
+    ds = dataset.TileDataset(tile=tile, patch_overlap=0.1, patch_size=300)
+    dl = DataLoader(ds, batch_size=4)
 
-#     batch_predictions = []
-#     for batch in dl:
-#         prediction = m.predict_batch(batch)
-#         batch_predictions.append(prediction)
+    batch_predictions = []
+    for batch in dl:
+        prediction = m.predict_batch(batch)
+        batch_predictions.extend(prediction)
 
-#     single_predictions = []
-#     for image in ds:
-#         prediction = m.predict_image(image=image)
-#         single_predictions.append(prediction)
+    single_predictions = []
+    for image in ds:
+        image = image.permute(1,2,0).numpy() * 255
+        prediction = m.predict_image(image=image)
+        single_predictions.append(prediction)
 
-#     batch_df = pd.concat(batch_predictions, ignore_index=True)
-#     single_df = pd.concat(single_predictions, ignore_index=True)
+    batch_df = pd.concat(batch_predictions, ignore_index=True)
+    single_df = pd.concat(single_predictions, ignore_index=True)
 
-#     pd.testing.assert_frame_equal(batch_df, single_df)
+    # Make all xmin, ymin, xmax, ymax integers
+    for col in ["xmin", "ymin", "xmax", "ymax"]:
+        batch_df[col] = batch_df[col].astype(int)
+        single_df[col] = single_df[col].astype(int)
+    pd.testing.assert_frame_equal(batch_df[["xmin", "ymin", "xmax", "ymax"]], single_df[["xmin", "ymin", "xmax", "ymax"]], check_dtype=False)
 
-# def test_large_batch_handling(m, raster_path):
-#    
-#     tile = np.array(Image.open(raster_path))
-#     ds = dataset.TileDataset(tile=tile, patch_overlap=0.1, patch_size=100)
-#     dl = DataLoader(ds, batch_size=16)
-
-#     predictions = []
-#     for batch in dl:
-#         prediction = m.predict_batch(batch)
-#         predictions.append(prediction)
-
-#     assert len(predictions) > 0
-#     for batch_pred in predictions:
-#         assert isinstance(batch_pred, pd.DataFrame)
-#         assert set(batch_pred.columns) == {
-#             "xmin", "ymin", "xmax", "ymax", "label", "score", "geometry"
-#         }
-#         assert not batch_pred.empty
 
 def test_epoch_evaluation_end(m):
     preds = [{