Merge branch 'master' into patch-2

GANDLF/compute/loss_and_metric.py

@@ -25,26 +25,22 @@ def get_metric_output(metric_function, predicted, ground_truth, params):
 
 def get_loss_and_metrics(image, ground_truth, predicted, params):
     """
-    image: torch.Tensor
-        The input image stack according to requirements
-    ground_truth : torch.Tensor
-        The input ground truth for the corresponding image label
-    predicted : torch.Tensor
-        The input predicted label for the corresponding image label
-    params : dict
-        The parameters passed by the user yaml
-
-    Returns
-    -------
-    loss : torch.Tensor
-        The computed loss from the label and the output
-    metric_output : torch.Tensor
-        The computed metric from the label and the output
+    This function computes the loss and metrics for a given image, ground truth and predicted output.
+
+    Args:
+        image (torch.Tensor): The input image stack according to requirements.
+        ground_truth (torch.Tensor): The input ground truth for the corresponding image label.
+        predicted (torch.Tensor): The input predicted label for the corresponding image label.
+        params (dict): The parameters passed by the user yaml.
+
+    Returns:
+        torch.Tensor: The computed loss from the label and the prediction.
+        dict: The computed metric from the label and the prediction.
     """
     # this is currently only happening for mse_torch
     if isinstance(params["loss_function"], dict):
         # check for mse_torch
-        loss_function = global_losses_dict["mse"]
+        loss_function = global_losses_dict[list(params["loss_function"].keys())[0]]
     else:
         loss_str_lower = params["loss_function"].lower()
         if loss_str_lower in global_losses_dict:

GANDLF/losses/__init__.py

@@ -1,9 +1,15 @@
 """
 All the losses are to be called from here
 """
-from .segmentation import MCD_loss, MCD_log_loss, MCT_loss, KullbackLeiblerDivergence
+from .segmentation import (
+    MCD_loss,
+    MCD_log_loss,
+    MCT_loss,
+    KullbackLeiblerDivergence,
+    FocalLoss,
+)
 from .regression import CE, CEL, MSE_loss, L1_loss
-from .hybrid import DCCE, DCCE_Logits
+from .hybrid import DCCE, DCCE_Logits, DC_Focal
 
 
 # global defines for the losses
@@ -20,4 +26,6 @@
     "tversky": MCT_loss,
     "kld": KullbackLeiblerDivergence,
     "l1": L1_loss,
+    "focal": FocalLoss,
+    "dc_focal": DC_Focal,
 }

GANDLF/losses/hybrid.py

@@ -1,24 +1,20 @@
-from .segmentation import MCD_loss
+import torch
+
+from .segmentation import MCD_loss, FocalLoss
 from .regression import CCE_Generic, CE, CE_Logits
 
 
-def DCCE(predicted_mask, ground_truth, params):
+def DCCE(predicted_mask, ground_truth, params) -> torch.Tensor:
     """
     Calculates the Dice-Cross-Entropy loss.
 
-    Parameters
-    ----------
-    predicted_mask : torch.Tensor
-        Predicted mask
-    ground_truth : torch.Tensor
-        Ground truth mask
-    params : dict
-        Dictionary of parameters
-
-    Returns
-    -------
-    torch.Tensor
-        Calculated loss
+    Args:
+        predicted_mask (torch.Tensor): The predicted mask.
+        ground_truth (torch.Tensor): The ground truth mask.
+        params (dict): The parameters.
+
+    Returns:
+        torch.Tensor: The calculated loss.
     """
     dcce_loss = MCD_loss(predicted_mask, ground_truth, params) + CCE_Generic(
         predicted_mask, ground_truth, params, CE
@@ -30,21 +26,32 @@ def DCCE_Logits(predicted_mask, ground_truth, params):
     """
     Calculates the Dice-Cross-Entropy loss using logits.
 
-    Parameters
-    ----------
-    predicted_mask : torch.Tensor
-        Predicted mask logits
-    ground_truth : torch.Tensor
-        Ground truth mask
-    params : dict
-        Dictionary of parameters
-
-    Returns
-    -------
-    torch.Tensor
-        Calculated loss
+    Args:
+        predicted_mask (torch.Tensor): The predicted mask.
+        ground_truth (torch.Tensor): The ground truth mask.
+        params (dict): The parameters.
+
+    Returns:
+        torch.Tensor: The calculated loss.
     """
     dcce_loss = MCD_loss(predicted_mask, ground_truth, params) + CCE_Generic(
         predicted_mask, ground_truth, params, CE_Logits
     )
     return dcce_loss
+
+
+def DC_Focal(predicted_mask, ground_truth, params):
+    """
+    Calculates the Dice-Focal loss.
+
+    Args:
+        predicted_mask (torch.Tensor): The predicted mask.
+        ground_truth (torch.Tensor): The ground truth mask.
+        params (dict): The parameters.
+
+    Returns:
+        torch.Tensor: The calculated loss.
+    """
+    return MCD_loss(predicted_mask, ground_truth, params) + FocalLoss(
+        predicted_mask, ground_truth, params
+    )

GANDLF/losses/segmentation.py

@@ -3,22 +3,16 @@
 
 
 # Dice scores and dice losses
-def dice(predicted, target):
+def dice(predicted, target) -> torch.Tensor:
     """
-    This function computes a dice score between two tensors
+    This function computes a dice score between two tensors.
 
-    Parameters
-    ----------
-    predicted : Tensor
-        predicted value by the network
-    target : Tensor
-        Required target label to match the predicted with
-
-    Returns
-    -------
-    Tensor
-        Computed Dice Score
+    Args:
+        predicted (_type_): Predicted value by the network.
+        target (_type_): Required target label to match the predicted with
 
+    Returns:
+        torch.Tensor: The computed dice score.
     """
     predicted_flat = predicted.flatten()
     label_flat = target.flatten()
@@ -36,7 +30,7 @@ def MCD(predicted, target, num_class, weights=None, ignore_class=None, loss_type
     This function computes the mean class dice score between two tensors
 
     Args:
-        predicted (torch.Tensor): predicted generally by the network
+        predicted (torch.Tensor): Predicted generally by the network
         target (torch.Tensor): Required target label to match the predicted with
         num_class (int): Number of classes (including the background class)
         weights (list, optional): Dice weights for each class (excluding the background class), defaults to None
@@ -105,7 +99,7 @@ def tversky_loss(predicted, target, alpha=0.5, beta=0.5):
     This function calculates the Tversky loss between two tensors.
 
     Args:
-        predicted (torch.Tensor): predicted generally by the network
+        predicted (torch.Tensor): Predicted generally by the network
         target (torch.Tensor): Required target label to match the predicted with
         alpha (float, optional): Weight of false positives. Defaults to 0.5.
         beta (float, optional): Weight of false negatives. Defaults to 0.5.
@@ -138,7 +132,7 @@ def MCT_loss(predicted, target, params=None):
     This function calculates the Multi-Class Tversky loss between two tensors.
 
     Args:
-        predicted (torch.Tensor): predicted generally by the network
+        predicted (torch.Tensor): Predicted generally by the network
         target (torch.Tensor): Required target label to match the predicted with
         params (dict, optional): Additional parameters for computing loss function, including weights for each class
 
@@ -175,3 +169,57 @@ def KullbackLeiblerDivergence(mu, logvar, params=None):
     """
     loss = -0.5 * torch.sum(1 + logvar - mu.pow(2) - logvar.exp(), dim=-1)
     return loss.mean()
+
+
+def FocalLoss(predicted, target, params=None):
+    """
+    This function calculates the Focal loss between two tensors.
+
+    Args:
+        predicted (torch.Tensor): Predicted generally by the network
+        target (torch.Tensor): Required target label to match the predicted with
+        params (dict, optional): Additional parameters for computing loss function, including weights for each class
+
+    Returns:
+        torch.Tensor: Computed Focal Loss
+    """
+    gamma = 2.0
+    size_average = True
+    if isinstance(params["loss_function"], dict):
+        gamma = params["loss_function"].get("gamma", 2.0)
+        size_average = params["loss_function"].get("size_average", True)
+
+    def _focal_loss(preds, target, gamma, size_average=True):
+        """
+        Internal helper function to calcualte focal loss for a single class.
+
+        Args:
+            preds (torch.Tensor): predicted generally by the network
+            target (torch.Tensor): Required target label to match the predicted with
+            gamma (float): The gamma value for focal loss
+            size_average (bool, optional): Whether to average the loss across the batch. Defaults to True.
+
+        Returns:
+            torch.Tensor: Computed focal loss for a single class.
+        """
+        ce_loss = torch.nn.CrossEntropyLoss(reduce=False)
+        logpt = ce_loss(preds, target)
+        pt = torch.exp(-logpt)
+        loss = ((1 - pt) ** gamma) * logpt
+        return_loss = loss.sum()
+        if size_average:
+            return_loss = loss.mean()
+        return return_loss
+
+    acc_focal_loss = 0
+    num_classes = predicted.shape[1]
+
+    for i in range(num_classes):
+        curr_loss = _focal_loss(
+            predicted[:, i, ...], target[:, i, ...], gamma, size_average
+        )
+        if params is not None and params.get("weights") is not None:
+            curr_loss = curr_loss * params["weights"][i]
+        acc_focal_loss += curr_loss
+
+    return acc_focal_loss

GANDLF/parseConfig.py

@@ -41,7 +41,6 @@
     "optimizer": "adam",  # the optimizer
     "patch_sampler": "uniform",  # type of sampling strategy
     "scheduler": "triangle_modified",  # the default scheduler
-    "loss_function": "dc",  # default loss
     "clip_mode": None,  # default clip mode
 }
 
@@ -186,6 +185,11 @@ def parseConfig(config_file_path, version_check_flag=True):
                 params["loss_function"] = {}
                 params["loss_function"]["mse"] = {}
                 params["loss_function"]["mse"]["reduction"] = "mean"
+            elif params["loss_function"] == "focal":
+                params["loss_function"] = {}
+                params["loss_function"]["focal"] = {}
+                params["loss_function"]["focal"]["gamma"] = 2.0
+                params["loss_function"]["focal"]["size_average"] = True
 
     assert "metrics" in params, "'metrics' needs to be defined in the config file"
     if "metrics" in params:

docs/customize.md

@@ -39,7 +39,7 @@ This file contains mid-level information regarding various parameters that can b
 - Defined in the `loss_function` parameter of the model configuration.
 - By passing `weighted_loss: True`, the loss function will be weighted by the inverse of the class frequency.
 - This parameter controls the function which the model is trained. All options can be found [here](https://github.com/mlcommons/GaNDLF/blob/master/GANDLF/losses/__init__.py). Some examples are:
-    - Segmentation: dice (`dice` or `dc`), dice and cross entropy (`dcce`)
+    - Segmentation: dice (`dice` or `dc`), dice and cross entropy (`dcce`), focal loss (`focal`), dice and focal (`dc_focal`)
     - Classification/regression: mean squared error (`mse`)
     - And many more.
 

samples/config_all_options.yaml

@@ -112,6 +112,7 @@ scheduler:
 # Set which loss function you want to use - options : 'dc' - for dice only, 'dcce' - for sum of dice and CE and you can guess the next (only lower-case please)
 # options: dc (dice only), dc_log (-log of dice), ce (), dcce (sum of dice and ce), mse () ...
 # mse is the MSE defined by torch and can define a variable 'reduction'; see https://pytorch.org/docs/stable/generated/torch.nn.MSELoss.html#torch.nn.MSELoss
+# focal is the focal loss and can define 2 variables: gamma and size_average
 # use mse_torch for regression/classification problems and dice for segmentation
 loss_function: dc
 # this parameter weights the loss to handle imbalanced losses better
@@ -122,6 +123,12 @@ weighted_loss: True
 #      'reduction': 'mean' # see https://pytorch.org/docs/stable/generated/torch.nn.MSELoss.html#torch.nn.MSELoss for all options
 #    }
 #  }
+#loss_function:
+#  {
+#    'focal':{
+#      'gamma': 1.0
+#    }
+#  }
 # Which optimizer do you want to use - sgd, asgd, adam, adamw, adamax, sparseadam, rprop, adadelta, adagrad, rmsprop,
 # each has their own options and functionalities, which are initialized with defaults, see GANDLF.optimizers.wrap_torch for details
 optimizer: adam

testing/test_full.py

@@ -1213,30 +1213,45 @@ def test_train_metrics_regression_rad_2d(device):
 
 def test_train_losses_segmentation_rad_2d(device):
     print("23: Starting 2D Rad segmentation tests for losses")
-    # read and parse csv
-    parameters = parseConfig(
-        testingDir + "/config_segmentation.yaml", version_check_flag=False
-    )
-    training_data, parameters["headers"] = parseTrainingCSV(
-        inputDir + "/train_2d_rad_segmentation.csv"
-    )
-    parameters["modality"] = "rad"
-    parameters["patch_size"] = patch_size["2D"]
-    parameters["model"]["dimension"] = 2
-    parameters["model"]["class_list"] = [0, 255]
-    # disabling amp because some losses do not support Half, yet
-    parameters["model"]["amp"] = False
-    parameters["model"]["num_channels"] = 3
-    parameters["model"]["architecture"] = "resunet"
-    parameters["metrics"] = ["dice"]
-    parameters["model"]["onnx_export"] = False
-    parameters["model"]["print_summary"] = False
-    parameters = populate_header_in_parameters(parameters, parameters["headers"])
-    # loop through selected models and train for single epoch
-    for loss_type in ["dc", "dc_log", "dcce", "dcce_logits", "tversky"]:
+    # healper function to read and parse yaml and return parameters
+    def get_parameters_after_alteration(loss_type: str) -> dict:
+        parameters = parseConfig(
+            testingDir + "/config_segmentation.yaml", version_check_flag=False
+        )
         parameters["loss_function"] = loss_type
+        file_config_temp = get_temp_config_path()
+        with open(file_config_temp, "w") as file:
+            yaml.dump(parameters, file)
+        # read and parse csv
+        parameters = parseConfig(file_config_temp, version_check_flag=True)
         parameters["nested_training"]["testing"] = -5
         parameters["nested_training"]["validation"] = -5
+        training_data, parameters["headers"] = parseTrainingCSV(
+            inputDir + "/train_2d_rad_segmentation.csv"
+        )
+        parameters["modality"] = "rad"
+        parameters["patch_size"] = patch_size["2D"]
+        parameters["model"]["dimension"] = 2
+        parameters["model"]["class_list"] = [0, 255]
+        # disabling amp because some losses do not support Half, yet
+        parameters["model"]["amp"] = False
+        parameters["model"]["num_channels"] = 3
+        parameters["model"]["architecture"] = "resunet"
+        parameters["metrics"] = ["dice"]
+        parameters["model"]["onnx_export"] = False
+        parameters["model"]["print_summary"] = False
+        parameters = populate_header_in_parameters(parameters, parameters["headers"])
+        return parameters, training_data
+    # loop through selected models and train for single epoch
+    for loss_type in [
+        "dc", 
+        "dc_log", 
+        "dcce", 
+        "dcce_logits", 
+        "tversky",
+        "focal", 
+        "dc_focal"]:
+        parameters, training_data = get_parameters_after_alteration(loss_type)
         sanitize_outputDir()
         TrainingManager(
             dataframe=training_data,