segmentation

Segmentation(config, num_viz_samples=5, checkpoint_path=None, run_test=False, evaluate=None, report=False)

Bases: Generic[SegmentationDataModuleT], LightningTask[SegmentationDataModuleT]

Task for segmentation.

Parameters:

• config (DictConfig) –

  Config object

• num_viz_samples (int, default: 5 ) –

  Number of samples to visualize. Defaults to 5.

• checkpoint_path (Optional[str], default: None ) –

  Path to the checkpoint to load the model from. Defaults to None.

• run_test (bool, default: False ) –

  If True, run test after training. Defaults to False.

• evaluate (Optional[DictConfig], default: None ) –

  Dict with evaluation parameters. Defaults to None.

• report (bool, default: False ) –

  If True, create report after training. Defaults to False.

Source code in quadra/tasks/segmentation.py

def __init__(
    self,
    config: DictConfig,
    num_viz_samples: int = 5,
    checkpoint_path: Optional[str] = None,
    run_test: bool = False,
    evaluate: Optional[DictConfig] = None,
    report: bool = False,
):
    super().__init__(
        config=config,
        checkpoint_path=checkpoint_path,
        run_test=run_test,
        report=report,
    )
    self.evaluate = evaluate
    self.num_viz_samples = num_viz_samples
    self.export_folder: str = "deployment_model"
    self.exported_model_path: Optional[str] = None
    if self.evaluate and any(self.evaluate.values()):
        if (
            self.config.export is None
            or len(self.config.export.types) == 0
            or "torchscript" not in self.config.export.types
        ):
            log.info(
                "Evaluation is enabled, but training does not export a deployment model. Automatically export the "
                "model as torchscript."
            )
            if self.config.export is None:
                self.config.export = DictConfig({"types": ["torchscript"]})
            else:
                self.config.export.types.append("torchscript")

        if not self.report:
            log.info("Evaluation is enabled, but reporting is disabled. Enabling reporting automatically.")
            self.report = True

module: SegmentationModel property writable

Get the module.

export()

Generate a deployment model for the task.

Source code in quadra/tasks/segmentation.py

def export(self) -> None:
    """Generate a deployment model for the task."""
    log.info("Exporting model ready for deployment")

    # Get best model!
    if (
        self.trainer.checkpoint_callback is not None
        and hasattr(self.trainer.checkpoint_callback, "best_model_path")
        and self.trainer.checkpoint_callback.best_model_path is not None
        and len(self.trainer.checkpoint_callback.best_model_path) > 0
    ):
        best_model_path = self.trainer.checkpoint_callback.best_model_path
        log.info("Loaded best model from %s", best_model_path)

        module = self.module.load_from_checkpoint(
            best_model_path,
            model=self.module.model,
            loss_fun=None,
            optimizer=self.module.optimizer,
            lr_scheduler=self.module.schedulers,
        )
    else:
        log.warning("No checkpoint callback found in the trainer, exporting the last model weights")
        module = self.module

    if "idx_to_class" not in self.config.datamodule:
        log.info("No idx_to_class key")
        idx_to_class = {0: "good", 1: "bad"}  # TODO: Why is this the default value?
    else:
        log.info("idx_to_class is present")
        idx_to_class = self.config.datamodule.idx_to_class

    if self.config.export is None:
        raise ValueError(
            "No export type specified. This should not happen, please check if you have set "
            "the export_type or assign it to a default value."
        )

    half_precision = "16" in self.trainer.precision

    input_shapes = self.config.export.input_shapes

    model_json, export_paths = export_model(
        config=self.config,
        model=module.model,
        export_folder=self.export_folder,
        half_precision=half_precision,
        input_shapes=input_shapes,
        idx_to_class=idx_to_class,
    )

    if len(export_paths) == 0:
        return

    # Pick one model for evaluation, it should be independent of the export type as the model is wrapped
    self.exported_model_path = next(iter(export_paths.values()))

    with open(os.path.join(self.export_folder, "model.json"), "w") as f:
        json.dump(model_json, f, cls=utils.HydraEncoder)

generate_report()

Generate a report for the task.

Source code in quadra/tasks/segmentation.py

def generate_report(self) -> None:
    """Generate a report for the task."""
    if self.evaluate is not None:
        log.info("Generating evaluation report!")
        eval_tasks: List[SegmentationEvaluation] = []
        if self.evaluate.analysis:
            if self.exported_model_path is None:
                raise ValueError(
                    "Exported model path is not set yet but the task tries to do an analysis evaluation"
                )
            eval_task = SegmentationAnalysisEvaluation(
                config=self.config,
                model_path=self.exported_model_path,
            )
            eval_tasks.append(eval_task)
        for task in eval_tasks:
            task.execute()

        if len(self.logger) > 0:
            mflow_logger = get_mlflow_logger(trainer=self.trainer)
            tensorboard_logger = utils.get_tensorboard_logger(trainer=self.trainer)

            if mflow_logger is not None and self.config.core.get("upload_artifacts"):
                for task in eval_tasks:
                    for file in task.metadata["report_files"]:
                        mflow_logger.experiment.log_artifact(
                            run_id=mflow_logger.run_id, local_path=file, artifact_path=task.report_path
                        )

            if tensorboard_logger is not None and self.config.core.get("upload_artifacts"):
                for task in eval_tasks:
                    for file in task.metadata["report_files"]:
                        ext = os.path.splitext(file)[1].lower()

                        if ext in [".png", ".jpg", ".jpeg", ".bmp", ".tiff", ".tif", ".gif"]:
                            try:
                                img = cv2.imread(file)
                                img = cv2.cvtColor(img, cv2.COLOR_BGR2RGB)
                            except cv2.error:
                                log.info("Could not upload artifact image %s", file)
                                continue

                            tensorboard_logger.experiment.add_image(
                                os.path.basename(file), img, 0, dataformats="HWC"
                            )
                        else:
                            utils.upload_file_tensorboard(file, tensorboard_logger)

prepare()

Prepare the task.

Source code in quadra/tasks/segmentation.py

def prepare(self) -> None:
    """Prepare the task."""
    super().prepare()
    self.module = self.config.model

SegmentationAnalysisEvaluation(config, model_path, device='cpu')

Bases: SegmentationEvaluation

Segmentation Analysis Evaluation Task Args: config: The experiment configuration model_path: The model path. device: Device to use for evaluation. If None, the device is automatically determined.

Source code in quadra/tasks/segmentation.py

def __init__(
    self,
    config: DictConfig,
    model_path: str,
    device: Optional[str] = "cpu",
):
    super().__init__(config=config, model_path=model_path, device=device)
    self.test_output: Dict[str, Any] = {}

generate_report()

Generate a report.

Source code in quadra/tasks/segmentation.py

def generate_report(self) -> None:
    """Generate a report."""
    log.info("Generating analysis report")

    for stage, output in self.test_output.items():
        image_mean = OmegaConf.to_container(self.config.transforms.mean)
        if not isinstance(image_mean, list) or any(not isinstance(x, (int, float)) for x in image_mean):
            raise ValueError("Image mean is not a list of float or integer values, please check your config")
        image_std = OmegaConf.to_container(self.config.transforms.std)
        if not isinstance(image_std, list) or any(not isinstance(x, (int, float)) for x in image_std):
            raise ValueError("Image std is not a list of float or integer values, please check your config")
        reports = create_mask_report(
            stage=stage,
            output=output,
            report_path="analysis_report",
            mean=image_mean,
            std=image_std,
            analysis=True,
            nb_samples=10,
            apply_sigmoid=True,
            show_orj_predictions=True,
        )
        self.metadata["report_files"].extend(reports)
        log.info("%s analysis report completed.", stage)

prepare()

Prepare the evaluation task.

Source code in quadra/tasks/segmentation.py

def prepare(self) -> None:
    """Prepare the evaluation task."""
    super().prepare()
    self.datamodule.setup(stage="fit")
    self.datamodule.setup(stage="test")

test()

Run testing.

Source code in quadra/tasks/segmentation.py

@automatic_datamodule_batch_size(batch_size_attribute_name="batch_size")
def test(self) -> None:
    """Run testing."""
    log.info("Starting inference for analysis.")

    stages: List[str] = []
    dataloaders: List[torch.utils.data.DataLoader] = []

    if self.datamodule.train_dataset_available:
        stages.append("train")
        dataloaders.append(self.datamodule.train_dataloader())
        if self.datamodule.val_dataset_available:
            stages.append("val")
            dataloaders.append(self.datamodule.val_dataloader())
    if self.datamodule.test_dataset_available:
        stages.append("test")
        dataloaders.append(self.datamodule.test_dataloader())
    for stage, dataloader in zip(stages, dataloaders):
        log.info("Running inference on %s set with batch size: %d", stage, dataloader.batch_size)
        image_list, mask_list, mask_pred_list, label_list = [], [], [], []
        for batch in dataloader:
            images, masks, labels = batch
            images = images.to(self.device)
            if len(masks.shape) == 3:  # BxHxW -> Bx1xHxW
                masks = masks.unsqueeze(1)
            with torch.no_grad():
                image_list.append(images.cpu())
                mask_list.append(masks.cpu())
                mask_pred_list.append(self.deployment_model(images.to(self.device)).cpu())
                label_list.append(labels.cpu())

        output = {
            "image": torch.cat(image_list, dim=0),
            "mask": torch.cat(mask_list, dim=0),
            "label": torch.cat(label_list, dim=0),
            "mask_pred": torch.cat(mask_pred_list, dim=0),
        }
        self.test_output[stage] = output

train()

Skip training.

Source code in quadra/tasks/segmentation.py

def train(self) -> None:
    """Skip training."""

SegmentationEvaluation(config, model_path, device='cpu')

Bases: Evaluation[SegmentationDataModuleT]

Segmentation Evaluation Task with deployment models.

Parameters:

• config (DictConfig) –

  The experiment configuration

• model_path (str) –

  The experiment path.

• device (Optional[str], default: 'cpu' ) –

  Device to use for evaluation. If None, the device is automatically determined.

Raises:

• ValueError –

  If the model path is not provided

Source code in quadra/tasks/segmentation.py

def __init__(
    self,
    config: DictConfig,
    model_path: str,
    device: Optional[str] = "cpu",
):
    super().__init__(config=config, model_path=model_path, device=device)
    self.config = config

inference(dataloader, deployment_model, device)

Run inference on the dataloader and return the output.

Parameters:

• dataloader (DataLoader) –

  The dataloader to run inference on

• deployment_model (BaseEvaluationModel) –

  The deployment model to use

• device (device) –

  The device to run inference on

Source code in quadra/tasks/segmentation.py

@torch.no_grad()
def inference(
    self, dataloader: DataLoader, deployment_model: BaseEvaluationModel, device: torch.device
) -> Dict[str, torch.Tensor]:
    """Run inference on the dataloader and return the output.

    Args:
        dataloader: The dataloader to run inference on
        deployment_model: The deployment model to use
        device: The device to run inference on
    """
    image_list, mask_list, mask_pred_list, label_list = [], [], [], []
    for batch in dataloader:
        images, masks, labels = batch
        images = images.to(device)
        masks = masks.to(device)
        labels = labels.to(device)
        image_list.append(images.cpu())
        mask_list.append(masks.cpu())
        mask_pred_list.append(deployment_model(images.to(device)).cpu())
        label_list.append(labels.cpu())
    output = {
        "image": torch.cat(image_list, dim=0),
        "mask": torch.cat(mask_list, dim=0),
        "label": torch.cat(label_list, dim=0),
        "mask_pred": torch.cat(mask_pred_list, dim=0),
    }
    return output

prepare()

Prepare the evaluation.

Source code in quadra/tasks/segmentation.py

def prepare(self) -> None:
    """Prepare the evaluation."""
    super().prepare()
    # TODO: Why we propagate mean and std only in Segmentation?
    self.config.transforms.mean = self.model_data["mean"]
    self.config.transforms.std = self.model_data["std"]
    # Setup datamodule
    if hasattr(self.config.datamodule, "idx_to_class"):
        idx_to_class = self.model_data["classes"]  # dict {index: class}
        self.config.datamodule.idx_to_class = idx_to_class
    self.datamodule = self.config.datamodule
    # prepare_data() must be explicitly called because there is no lightning training
    self.datamodule.prepare_data()

save_config()

Skip saving the config.

Source code in quadra/tasks/segmentation.py

def save_config(self) -> None:
    """Skip saving the config."""