octopi 1.0__py3-none-any.whl

octopi/pytorch/trainer.py

@@ -0,0 +1,438 @@
+from octopi import visualization_tools as viz
+from monai.inferers import sliding_window_inference
+from octopi import stopping_criteria
+from monai.transforms import AsDiscrete
+from monai.data import decollate_batch
+import torch, os, mlflow, re
+import torch_ema as ema
+from tqdm import tqdm 
+import numpy as np
+
+# Not Ideal, but Necessary if Class is Missing From Dataset
+import warnings
+warnings.filterwarnings("ignore", category=UserWarning)
+
+class ModelTrainer:
+
+    def __init__(self, 
+                 model, 
+                 device,
+                 loss_function, 
+                 metrics_function, 
+                 optimizer, 
+                 use_ema: bool = True):
+
+        self.model = model
+        self.device = device
+        self.loss_function = loss_function
+        self.metrics_function = metrics_function
+        self.optimizer = optimizer
+
+        self.parallel_mlflow = False
+        self.client = None
+        self.trial_run_id = None  
+
+        # Default F-Beta Value
+        self.beta = 2
+
+        # Initialize EMAHandler for the model
+        self.ema_experiment = use_ema
+        if self.ema_experiment:
+            self.ema_handler = ema.ExponentialMovingAverage(self.model.parameters(), decay=0.99)
+
+        # Initialize Figure and Axes for Plotting
+        self.fig = None; self.axs = None
+
+    def set_parallel_mlflow(self, 
+                            client,
+                            trial_run_id):
+        
+        self.parallel_mlflow = True
+        self.client = client
+        self.trial_run_id = trial_run_id
+    
+    def train_update(self):
+
+        step = 0
+        epoch_loss = 0
+        self.model.train()
+        for batch_data in self.train_loader:
+            step += 1
+            inputs = batch_data["image"].to(self.device)  # Shape: [B, C, H, W, D]
+            labels = batch_data["label"].to(self.device)  # Shape: [B, C, H, W, D]
+            self.optimizer.zero_grad()
+            outputs = self.model(inputs)    # Output shape: [B, num_classes, H, W, D] 
+            loss = self.loss_function(outputs, labels)
+            loss.backward()
+            self.optimizer.step()
+
+            # Update EMA weights
+            if self.ema_experiment:
+                self.ema_handler.update()
+
+            # Update running epoch loss
+            epoch_loss += loss.item()
+        
+        # Compute and log average epoch loss
+        epoch_loss /= step
+        return epoch_loss
+
+    def validate_update(self):
+        """
+        Perform validation and compute metrics, including validation loss.
+        """        
+
+        # Set model to evaluation mode
+        self.model.eval()
+        val_loss = 0
+        with torch.no_grad():
+            for val_data in self.val_loader:
+                val_inputs = val_data["image"].to(self.device)
+                val_labels = val_data["label"].to(self.device)
+                
+                # Apply sliding window inference
+                # roi_size=self.input_dim, # try setting a set size of 128, 144 or 160? 
+                val_outputs = sliding_window_inference(
+                    inputs=val_inputs, 
+                    roi_size=(144,144,144),
+                    sw_batch_size=4,
+                    predictor=self.model, 
+                    overlap=0.5,
+                    device=self.device
+                )
+
+                # Compute the loss for this batch
+                loss = self.loss_function(val_outputs, val_labels)  # Assuming self.loss_function is defined
+                val_loss += loss.item()  # Accumulate the loss                
+
+                # Apply post-processing
+                metric_val_outputs = [self.post_pred(i) for i in decollate_batch(val_outputs)]
+                metric_val_labels = [self.post_label(i) for i in decollate_batch(val_labels)]                             
+                
+                # Compute metrics
+                self.metrics_function(y_pred=metric_val_outputs, y=metric_val_labels)             
+
+        # # Contains recall, precision, and f1 for each class
+        metric_values = self.metrics_function.aggregate(reduction='mean_batch')
+
+        # Compute average validation loss and add to metrics dictionary
+        val_loss /= len(self.val_loader)
+        metric_values.append(val_loss)
+
+        return metric_values
+
+    def train(
+        self,
+        data_load_gen,
+        model_save_path: str = 'results',
+        my_num_samples: int = 15,
+        crop_size: int = 96,
+        max_epochs: int = 100,
+        val_interval: int = 15,
+        lr_scheduler_type: str = 'cosine', 
+        best_metric: str = 'avg_f1',
+        use_mlflow: bool = False,
+        verbose: bool = False
+    ):
+
+        # best lr scheduler options are cosine or reduce
+        self.warmup_epochs = 5
+        self.warmup_lr_factor = 0.1
+        self.min_lr = 1e-6
+
+        self.max_epochs = max_epochs
+        self.crop_size = crop_size
+        self.num_samples = my_num_samples
+        self.val_interval = val_interval
+        self.use_mlflow = use_mlflow
+
+        # Create Save Folder if It Doesn't Exist
+        if model_save_path is not None:
+            os.makedirs(model_save_path, exist_ok=True)  
+
+        Nclass = data_load_gen.Nclasses
+        self.create_results_dictionary(Nclass)  
+
+        # Resolve the best metric
+        best_metric = self.resolve_best_metric(best_metric)
+
+        # Stopping Criteria
+        self.stopping_criteria = stopping_criteria.EarlyStoppingChecker(monitor_metric=best_metric, val_interval=val_interval)            
+
+        self.post_pred = AsDiscrete(argmax=True, to_onehot=Nclass)
+        self.post_label = AsDiscrete(to_onehot=Nclass)                             
+
+        # Produce Dataloaders for the First Training Iteration
+        self.train_loader, self.val_loader = data_load_gen.create_train_dataloaders(crop_size=crop_size, num_samples=my_num_samples)
+        self.input_dim = data_load_gen.input_dim
+
+        # Save the original learning rate
+        original_lr = self.optimizer.param_groups[0]['lr']
+        self.load_learning_rate_scheduler(lr_scheduler_type)
+
+        # Initialize tqdm around the epoch loop
+        for epoch in tqdm(range(max_epochs), desc="Training Progress", unit="epoch"):
+
+            # Reload dataloaders periodically
+            if data_load_gen.reload_frequency > 0 and (epoch + 1) % data_load_gen.reload_frequency == 0:
+                self.train_loader, self.val_loader = data_load_gen.create_train_dataloaders(num_samples=my_num_samples)
+                # Lower the learning rate for the warm-up period
+                for param_group in self.optimizer.param_groups:
+                    param_group['lr'] = original_lr * self.warmup_lr_factor
+
+            # Compute and log average epoch loss           
+            epoch_loss = self.train_update()
+
+            # Check for NaN in the loss
+            if self.stopping_criteria.should_stop_training(epoch_loss):
+                tqdm.write(f"Training stopped early due to {self.stopping_criteria.get_stopped_reason()}")
+                break
+
+            current_lr = self.optimizer.param_groups[0]['lr']
+            self.my_log_metrics( metrics_dict={"loss": epoch_loss}, curr_step=epoch + 1 )
+            self.my_log_metrics( metrics_dict={"learning_rate": current_lr}, curr_step=epoch + 1 )                        
+
+            # Validation and metric logging
+            if (epoch + 1) % val_interval == 0 or (epoch + 1) == max_epochs:
+                if verbose:
+                    tqdm.write(f"Epoch {epoch + 1}/{max_epochs}, avg_train_loss: {epoch_loss:.4f}")
+
+                # Validate the Model with or without EMA
+                if self.ema_experiment:
+                    with self.ema_handler.average_parameters():
+                        metric_values = self.validate_update()
+                else:
+                    metric_values = self.validate_update()
+
+                # Log all metrics
+                self.my_log_metrics( metrics_dict=metric_values, curr_step=epoch + 1 )
+
+                # Update tqdm description        
+                if verbose:
+                    (avg_f1, avg_recall, avg_precision) = (self.results['avg_f1'][-1][1], 
+                                                           self.results['avg_recall'][-1][1], 
+                                                           self.results['avg_precision'][-1][1])
+                    tqdm.write(f"Epoch {epoch + 1}/{max_epochs}, avg_f1_score: {avg_f1:.4f}, avg_recall: {avg_recall:.4f}, avg_precision: {avg_precision:.4f}")
+
+                # Reset metrics function
+                self.metrics_function.reset()
+
+                # Save the best model
+                if self.results[best_metric][-1][1] > self.results["best_metric"]:
+                    self.results["best_metric"] = self.results[best_metric][-1][1]
+                    self.results["best_metric_epoch"] = epoch + 1
+
+                    # Read Model Weights and Save
+                    if self.ema_experiment:
+                        with self.ema_handler.average_parameters():
+                            self.save_model(model_save_path)
+                    else:
+                        self.save_model(model_save_path)
+
+                # Save plot if Local Training Call
+                if not self.use_mlflow:
+                    self.fig, self.axs = viz.plot_training_results(
+                        self.results, 
+                        save_plot=os.path.join(model_save_path, "net_train_history.png"), 
+                        fig=self.fig, 
+                        axs=self.axs)
+
+                # After Validation Metrics are Logged, Check for Early Stopping
+                if self.stopping_criteria.should_stop_training(epoch_loss, results=self.results, check_metrics=True):
+                    tqdm.write(f"Training stopped early due to {self.stopping_criteria.get_stopped_reason()}")
+                    break
+
+            # Run the learning rate scheduler
+            early_stop = self.run_scheduler(data_load_gen, original_lr, epoch, val_interval, lr_scheduler_type)
+            if early_stop:
+                break
+
+        return self.results
+
+    def load_learning_rate_scheduler(self, type: str = 'cosine'):
+        """
+        Initialize and return the learning rate scheduler based on the given type.
+        """
+        # Configure learning rate scheduler based on the type
+        if type == "cosine":
+            self.lr_scheduler = torch.optim.lr_scheduler.CosineAnnealingLR(
+                self.optimizer, T_max=self.max_epochs, eta_min=self.min_lr )
+        elif type == "onecyle":
+            max_lr = 1e-3
+            steps_per_epoch = len(self.train_loader)
+            self.lr_scheduler = torch.optim.lr_scheduler.OneCycleLR(
+                self.optimizer, max_lr=max_lr, epochs=self.max_epochs, steps_per_epoch=steps_per_epoch )
+        elif type == "reduce":
+            mode = "min"
+            patience = 3
+            factor = 0.5
+            self.lr_scheduler = torch.optim.lr_scheduler.ReduceLROnPlateau(
+                self.optimizer, mode=mode, patience=patience, factor=factor )
+        elif type == 'exponential':
+            gamma = 0.9
+            self.lr_scheduler = torch.optim.lr_scheduler.ExponentialLR(
+                self.optimizer, gamma=gamma)
+        else:
+            raise ValueError(f"Unsupported scheduler type: {type}")
+
+    def run_scheduler(
+        self, 
+        data_load_gen, 
+        original_lr: float,
+        epoch: int,
+        val_interval: int,
+        type: str
+        ):
+        """
+        Manage the learning rate scheduler, including warm-up and normal scheduling.
+        """
+        # Apply warm-up logic
+        if (epoch + 1) <= self.warmup_epochs:
+            for param_group in self.optimizer.param_groups:
+                param_group['lr'] = original_lr * self.warmup_lr_factor
+            return False  # Continue training
+
+        # Step the scheduler
+        if isinstance(self.lr_scheduler, torch.optim.lr_scheduler.CosineAnnealingLR):
+            self.lr_scheduler.step()
+        elif isinstance(self.lr_scheduler, torch.optim.lr_scheduler.ReduceLROnPlateau) and (epoch + 1) % val_interval == 0:
+            metric_value = self.results['val_loss'][-1][1]
+            self.lr_scheduler.step(metric_value)
+        else:
+            self.lr_scheduler.step()  # Step for other schedulers
+
+        # Check learning rate for early stopping
+        current_lr = self.optimizer.param_groups[0]['lr']
+        if current_lr < self.min_lr and type != 'onecycle':
+            print(f"Early stopping triggered at epoch {epoch + 1} as learning rate fell below {self.min_lr}.")
+            return True  # Indicate early stopping
+
+        return False  # Continue training
+        
+    def save_model(self, model_save_path: str):
+
+        # Store Model Weights as Member Variable
+        self.model_weights = self.model.state_dict()
+
+        # Save Model Weights to *.pth file
+        if model_save_path is not None:
+            torch.save(self.model_weights, os.path.join(model_save_path, "best_model.pth"))
+
+    def create_results_dictionary(self, Nclass: int):
+
+        self.results = {
+            'loss': [],
+            'val_loss': [],
+            'avg_f1': [],
+            'avg_recall': [],
+            'avg_precision': [],
+            'avg_fbeta': [],
+            'best_metric': -1,  # Initialize as None or a default value
+            'best_metric_epoch': -1
+        }
+
+        for i in range(Nclass-1):
+            self.results[f'fbeta_class{i+1}'] = []
+            self.results[f'f1_class{i+1}'] = []
+            self.results[f'recall_class{i+1}'] = []
+            self.results[f'precision_class{i+1}'] = []
+
+        self.metric_names = self.results.keys()
+
+    def my_log_metrics(
+        self,
+        metrics_dict: dict,
+        curr_step: int,
+        ):
+
+        # If metrics_dict contains multiple elements (e.g., recall, precision, f1), process them
+        if len(metrics_dict) > 1:
+
+            # Extract individual metrics 
+            # (assume metrics_dict contains recall, precision, f1, val_loss in sequence)
+            recall, precision, f1s, val_loss = metrics_dict[0], metrics_dict[1], metrics_dict[2], metrics_dict[3]
+
+            # Log per-class metrics
+            metrics_to_log = {}
+            for i, (rec, prec, f1) in enumerate(zip(recall, precision, f1s)):
+                metrics_to_log[f"recall_class{i+1}"] = rec.item()
+                metrics_to_log[f"precision_class{i+1}"] = prec.item()
+                metrics_to_log[f"f1_class{i+1}"] = f1.item()
+                metrics_to_log[f"fbeta_class{i+1}"] = self.fbeta(prec, rec).item()
+
+            # Prepare average metrics
+            metrics_to_log["avg_recall"] = recall.mean().cpu().item()
+            metrics_to_log["avg_precision"] = precision.mean().cpu().item()
+            metrics_to_log["avg_f1"] = f1s.mean().cpu().item()
+            metrics_to_log["avg_fbeta"] = self.fbeta(precision, recall).mean().cpu().item()
+            metrics_to_log['val_loss'] = val_loss
+
+            # Update metrics_dict for further logging
+            metrics_dict = metrics_to_log
+
+        # Log all metrics (per-class and average metrics)
+        for metric_name, value in metrics_dict.items():
+            if metric_name not in self.results:
+                self.results[metric_name] = []
+            self.results[metric_name].append((curr_step, value))
+
+        # Log to MLflow or client
+        if self.client is not None and self.trial_run_id is not None:
+            for metric_name, value in metrics_dict.items():
+                self.client.log_metric(
+                    run_id=self.trial_run_id,
+                    key=metric_name,
+                    value=value,
+                    step=curr_step,
+                )
+        elif self.use_mlflow:
+            for metric_name, value in metrics_dict.items():
+                mlflow.log_metric(metric_name, value, step=curr_step)
+
+    def fbeta(self, precision, recall):
+
+        # Handle division by zero
+        numerator = (1 + self.beta**2) * (precision * recall)
+        denominator = (self.beta**2 * precision) + recall
+        
+        # Use torch.where to handle zero cases
+        result = torch.where(
+            denominator > 0,
+            numerator / denominator,
+            torch.zeros_like(precision)
+        )
+        return result
+
+    def my_log_params(
+        self,
+        params_dict: dict, 
+        ):
+
+        if self.client is not None and self.trial_run_id is not None:
+            for key, value in params_dict.items():
+                self.client.log_param(run_id=self.trial_run_id, key=key, value=value)
+        else:
+            mlflow.log_params(params_dict)  
+
+    # Example input: best_metric = 'fBeta2_class3' or 'fBeta1' or 'f1_class2'
+    def resolve_best_metric(self, best_metric):
+        fbeta_pattern = r"^fBeta(\d+)(?:_class(\d+))?$"  # Matches fBetaX or fBetaX_classY
+        match = re.match(fbeta_pattern, best_metric)
+
+        if match:
+            self.beta = int(match.group(1))  # Extract beta value
+            class_part = match.group(2)
+            if class_part:
+                best_metric = f'fbeta_class{class_part}'  # fBeta2_class3 → fbeta_class3
+            else:
+                best_metric = 'avg_fbeta'  # fBeta2 → avg_fbeta
+
+        elif best_metric in self.metric_names:
+            pass  # It's already a valid metric in the results dict
+
+        else:
+            print(f"'{best_metric}' is not a valid metric. Defaulting to 'avg_f1'.\n")
+            best_metric = 'avg_f1'
+
+        return best_metric
+