Merge pull request #456 from RasmusOrsoe/simplify_examples

Simplify examples

examples/04_training/01_train_model.py

@@ -19,11 +19,6 @@
 from graphnet.utilities.logging import Logger
 
 
-# Make sure W&B output directory exists
-WANDB_DIR = "./wandb/"
-os.makedirs(WANDB_DIR, exist_ok=True)
-
-
 def main(
     dataset_config_path: str,
     model_config_path: str,
@@ -34,18 +29,23 @@ def main(
     num_workers: int,
     prediction_names: Optional[List[str]],
     suffix: Optional[str] = None,
+    wandb: bool = False,
 ) -> None:
     """Run example."""
     # Construct Logger
     logger = Logger()
 
     # Initialise Weights & Biases (W&B) run
-    wandb_logger = WandbLogger(
-        project="example-script",
-        entity="graphnet-team",
-        save_dir=WANDB_DIR,
-        log_model=True,
-    )
+    if wandb:
+        # Make sure W&B output directory exists
+        wandb_dir = "./wandb/"
+        os.makedirs(wandb_dir, exist_ok=True)
+        wandb_logger = WandbLogger(
+            project="example-script",
+            entity="graphnet-team",
+            save_dir=wandb_dir,
+            log_model=True,
+        )
 
     # Build model
     model_config = ModelConfig.load(model_config_path)
@@ -80,7 +80,7 @@ def main(
     # Log configurations to W&B
     # NB: Only log to W&B on the rank-zero process in case of multi-GPU
     #     training.
-    if rank_zero_only.rank == 0:
+    if wandb and rank_zero_only.rank == 0:
         wandb_logger.experiment.config.update(config)
         wandb_logger.experiment.config.update(model_config.as_dict())
         wandb_logger.experiment.config.update(dataset_config.as_dict())
@@ -98,7 +98,7 @@ def main(
         dataloaders["train"],
         dataloaders["validation"],
         callbacks=callbacks,
-        logger=wandb_logger,
+        logger=wandb_logger if wandb else None,
         **config.fit,
     )
 
@@ -166,6 +166,12 @@ def main(
         default=None,
     )
 
+    parser.add_argument(
+        "--wandb",
+        action="store_true",
+        help="If True, Weights & Biases are used to track the experiment.",
+    )
+
     args = parser.parse_args()
 
     main(
@@ -178,4 +184,5 @@ def main(
         args.num_workers,
         args.prediction_names,
         args.suffix,
+        args.wandb,
     )

examples/04_training/02_train_model_without_configs.py

@@ -25,10 +25,6 @@
 features = FEATURES.PROMETHEUS
 truth = TRUTH.PROMETHEUS
 
-# Make sure W&B output directory exists
-WANDB_DIR = "./wandb/"
-os.makedirs(WANDB_DIR, exist_ok=True)
-
 
 def main(
     path: str,
@@ -40,18 +36,23 @@ def main(
     early_stopping_patience: int,
     batch_size: int,
     num_workers: int,
+    wandb: bool = False,
 ) -> None:
     """Run example."""
     # Construct Logger
     logger = Logger()
 
     # Initialise Weights & Biases (W&B) run
-    wandb_logger = WandbLogger(
-        project="example-script",
-        entity="graphnet-team",
-        save_dir=WANDB_DIR,
-        log_model=True,
-    )
+    if wandb:
+        # Make sure W&B output directory exists
+        wandb_dir = "./wandb/"
+        os.makedirs(wandb_dir, exist_ok=True)
+        wandb_logger = WandbLogger(
+            project="example-script",
+            entity="graphnet-team",
+            save_dir=wandb_dir,
+            log_model=True,
+        )
 
     logger.info(f"features: {features}")
     logger.info(f"truth: {truth}")
@@ -72,9 +73,9 @@ def main(
 
     archive = os.path.join(EXAMPLE_OUTPUT_DIR, "train_model_without_configs")
     run_name = "dynedge_{}_example".format(config["target"])
-
-    # Log configuration to W&B
-    wandb_logger.experiment.config.update(config)
+    if wandb:
+        # Log configuration to W&B
+        wandb_logger.experiment.config.update(config)
 
     (
         training_dataloader,
@@ -137,17 +138,16 @@ def main(
         training_dataloader,
         validation_dataloader,
         callbacks=callbacks,
-        logger=wandb_logger,
+        logger=wandb_logger if wandb else None,
         **config["fit"],
     )
 
     # Get predictions
-    prediction_columns = [config["target"] + "_pred"]
-    additional_attributes = [config["target"]]
+    additional_attributes = model.target_labels
+    assert isinstance(additional_attributes, list)  # mypy
 
     results = model.predict_as_dataframe(
         validation_dataloader,
-        prediction_columns=prediction_columns,
         additional_attributes=additional_attributes + ["event_no"],
     )
 
@@ -206,6 +206,12 @@ def main(
         "num-workers",
     )
 
+    parser.add_argument(
+        "--wandb",
+        action="store_true",
+        help="If True, Weights & Biases are used to track the experiment.",
+    )
+
     args = parser.parse_args()
 
     main(
@@ -218,4 +224,5 @@ def main(
         args.early_stopping_patience,
         args.batch_size,
         args.num_workers,
+        args.wandb,
     )

src/graphnet/models/coarsening.py

@@ -28,7 +28,7 @@
 from torch_geometric.utils import degree
 
 # NOTE: From [https://github.com/pyg-team/pytorch_geometric/pull/4903]
-# TODO: Remove once bumping to torch_geometric>=2.1.0
+# TODO:  Remove once bumping to torch_geometric>=2.1.0
 #       See [https://github.com/pyg-team/pytorch_geometric/blob/master/CHANGELOG.md]
 
 

src/graphnet/models/model.py

@@ -10,6 +10,7 @@
 import pandas as pd
 from pytorch_lightning import Trainer, LightningModule
 from pytorch_lightning.callbacks.callback import Callback
+from pytorch_lightning.callbacks import EarlyStopping
 from pytorch_lightning.loggers.logger import Logger as LightningLogger
 import torch
 from torch import Tensor
@@ -18,6 +19,7 @@
 
 from graphnet.utilities.logging import Logger
 from graphnet.utilities.config import Configurable, ModelConfig
+from graphnet.training.callbacks import ProgressBar
 
 
 class Model(Logger, Configurable, LightningModule, ABC):
@@ -88,8 +90,17 @@ def fit(
         **trainer_kwargs: Any,
     ) -> None:
         """Fit `Model` using `pytorch_lightning.Trainer`."""
-        self.train(mode=True)
+        # Checks
+        if callbacks is None:
+            callbacks = self._create_default_callbacks(
+                val_dataloader=val_dataloader,
+            )
+        elif val_dataloader is not None:
+            callbacks = self._add_early_stopping(
+                val_dataloader=val_dataloader, callbacks=callbacks
+            )
 
+        self.train(mode=True)
         self._construct_trainers(
             max_epochs=max_epochs,
             gpus=gpus,
@@ -110,6 +121,38 @@ def fit(
             self.warning("[ctrl+c] Exiting gracefully.")
             pass
 
+    def _create_default_callbacks(self, val_dataloader: DataLoader) -> List:
+        callbacks = [ProgressBar()]
+        callbacks = self._add_early_stopping(
+            val_dataloader=val_dataloader, callbacks=callbacks
+        )
+        return callbacks
+
+    def _add_early_stopping(
+        self, val_dataloader: DataLoader, callbacks: List
+    ) -> List:
+        if val_dataloader is None:
+            return callbacks
+        has_early_stopping = False
+        assert isinstance(callbacks, list)
+        for callback in callbacks:
+            if isinstance(callback, EarlyStopping):
+                has_early_stopping = True
+
+        if not has_early_stopping:
+            callbacks.append(
+                EarlyStopping(
+                    monitor="val_loss",
+                    patience=5,
+                )
+            )
+            self.warning_once(
+                "Got validation dataloader but no EarlyStopping callback. An "
+                "EarlyStopping callback has been added automatically with "
+                "patience=5 and monitor = 'val_loss'."
+            )
+        return callbacks
+
     def predict(
         self,
         dataloader: DataLoader,
@@ -178,6 +221,7 @@ def predict_as_dataframe(
                 "doesn't resample batches; or do not request "
                 "`additional_attributes`."
             )
+        self.info(f"Column names for predictions are: \n {prediction_columns}")
         predictions_torch = self.predict(
             dataloader=dataloader,
             gpus=gpus,

src/graphnet/models/standard_model.py

@@ -8,6 +8,7 @@
 from torch.optim import Adam
 from torch.utils.data import DataLoader
 from torch_geometric.data import Data
+import pandas as pd
 
 from graphnet.models.coarsening import Coarsening
 from graphnet.utilities.config import save_model_config
@@ -62,6 +63,18 @@ def __init__(
         self._scheduler_kwargs = scheduler_kwargs or dict()
         self._scheduler_config = scheduler_config or dict()
 
+    @property
+    def target_labels(self) -> List[str]:
+        """Return target label."""
+        return [label for task in self._tasks for label in task._target_labels]
+
+    @property
+    def prediction_labels(self) -> List[str]:
+        """Return prediction labels."""
+        return [
+            label for task in self._tasks for label in task._prediction_labels
+        ]
+
     def configure_optimizers(self) -> Dict[str, Any]:
         """Configure the model's optimizer(s)."""
         optimizer = self._optimizer_class(
@@ -175,3 +188,31 @@ def predict(
             gpus=gpus,
             distribution_strategy=distribution_strategy,
         )
+
+    def predict_as_dataframe(
+        self,
+        dataloader: DataLoader,
+        prediction_columns: Optional[List[str]] = None,
+        *,
+        node_level: bool = False,
+        additional_attributes: Optional[List[str]] = None,
+        index_column: str = "event_no",
+        gpus: Optional[Union[List[int], int]] = None,
+        distribution_strategy: Optional[str] = None,
+    ) -> pd.DataFrame:
+        """Return predictions for `dataloader` as a DataFrame.
+
+        Include `additional_attributes` as additional columns in the output
+        DataFrame.
+        """
+        if prediction_columns is None:
+            prediction_columns = self.prediction_labels
+        return super().predict_as_dataframe(
+            dataloader=dataloader,
+            prediction_columns=prediction_columns,
+            node_level=node_level,
+            additional_attributes=additional_attributes,
+            index_column=index_column,
+            gpus=gpus,
+            distribution_strategy=distribution_strategy,
+        )