Merge branch 'version_update_for_release' of https://github.com/sarthakpati/GaNDLF into imagenet_acs

Author: sarthakpati

GANDLF/compute/forward_pass.py

@@ -15,7 +15,9 @@
     get_unique_timestamp,
     resample_image,
     reverse_one_hot,
+    get_ground_truths_and_predictions_tensor,
 )
+from GANDLF.metrics import overall_stats
 from tqdm import tqdm
 
 
@@ -99,6 +101,13 @@ def validate_network(
                     "output_predictions_" + get_unique_timestamp() + ".csv",
                 )
 
+    # get ground truths for classification problem, validation set
+    if is_classification and mode == "validation":
+        (
+            ground_truth_array,
+            predictions_array,
+        ) = get_ground_truths_and_predictions_tensor(params, "validation_data")
+
     for batch_idx, (subject) in enumerate(
         tqdm(valid_dataloader, desc="Looping over " + mode + " data")
     ):
@@ -192,6 +201,11 @@ def validate_network(
             final_loss, final_metric = get_loss_and_metrics(
                 image, valuesToPredict, pred_output, params
             )
+
+            if is_classification and mode == "validation":
+                predictions_array[batch_idx] = (
+                    torch.argmax(pred_output[0], 0).cpu().item()
+                )
             # # Non network validation related
             total_epoch_valid_loss += final_loss.detach().cpu().item()
             for metric in final_metric.keys():
@@ -283,7 +297,7 @@ def validate_network(
                         attention_map, patches_batch[torchio.LOCATION]
                     )
                 else:
-                    _, _, output = result
+                    _, _, output, _ = result
 
                 if params["problem_type"] == "segmentation":
                     aggregator.add_batch(
@@ -359,6 +373,10 @@ def validate_network(
             else:
                 # final regression output
                 output_prediction = output_prediction / len(patch_loader)
+                if is_classification and mode == "validation":
+                    predictions_array[batch_idx] = (
+                        torch.argmax(output_prediction[0], 0).cpu().item()
+                    )
                 if params["save_output"]:
                     outputToWrite += (
                         str(epoch)
@@ -453,6 +471,11 @@ def validate_network(
     if label_ground_truth is not None:
         average_epoch_valid_loss = total_epoch_valid_loss / len(valid_dataloader)
         print("     Epoch Final   " + mode + " loss : ", average_epoch_valid_loss)
+        # get overall stats for classification
+        if is_classification and mode == "validation":
+            average_epoch_valid_metric = overall_stats(
+                predictions_array, ground_truth_array, params
+            )
         for metric in params["metrics"]:
             if isinstance(total_epoch_valid_metric[metric], np.ndarray):
                 to_print = (
@@ -461,6 +484,7 @@ def validate_network(
             else:
                 to_print = total_epoch_valid_metric[metric] / len(valid_dataloader)
             average_epoch_valid_metric[metric] = to_print
+        for metric in average_epoch_valid_metric.keys():
             print(
                 "     Epoch Final   " + mode + " " + metric + " : ",
                 average_epoch_valid_metric[metric],

GANDLF/compute/step.py

@@ -80,6 +80,7 @@ def step(model, image, label, params, train=True):
         else:
             output = model(image)
 
+    attention_map = None
     if "medcam_enabled" in params and params["medcam_enabled"]:
         output, attention_map = output
 
@@ -97,7 +98,4 @@ def step(model, image, label, params, train=True):
         if "medcam_enabled" in params and params["medcam_enabled"]:
             attention_map = torch.unsqueeze(attention_map, -1)
 
-    if not ("medcam_enabled" in params and params["medcam_enabled"]):
-        return loss, metric_output, output
-    else:
-        return loss, metric_output, output, attention_map
+    return loss, metric_output, output, attention_map

GANDLF/compute/training_loop.py

@@ -16,7 +16,9 @@
     version_check,
     write_training_patches,
     print_model_summary,
+    get_ground_truths_and_predictions_tensor,
 )
+from GANDLF.metrics import overall_stats
 from GANDLF.logger import Logger
 from .step import step
 from .forward_pass import validate_network
@@ -69,6 +71,12 @@ def train_network(model, train_dataloader, optimizer, params):
         if params["verbose"]:
             print("Using Automatic mixed precision", flush=True)
 
+    # get ground truths
+    if params["problem_type"] == "classification":
+        (
+            ground_truth_array,
+            predictions_array,
+        ) = get_ground_truths_and_predictions_tensor(params, "training_data")
     # Set the model to train
     model.train()
     for batch_idx, (subject) in enumerate(
@@ -104,7 +112,15 @@ def train_network(model, train_dataloader, optimizer, params):
             params["subject_spacing"] = subject["spacing"]
         else:
             params["subject_spacing"] = None
-        loss, calculated_metrics, _ = step(model, image, label, params)
+        loss, calculated_metrics, output, _ = step(model, image, label, params)
+        # store predictions for classification
+        if params["problem_type"] == "classification":
+            predictions_array[
+                batch_idx
+                * params["batch_size"] : (batch_idx + 1)
+                * params["batch_size"]
+            ] = (torch.argmax(output[0], 0).cpu().item())
+
         nan_loss = torch.isnan(loss)
         second_order = (
             hasattr(optimizer, "is_second_order") and optimizer.is_second_order
@@ -175,6 +191,12 @@ def train_network(model, train_dataloader, optimizer, params):
 
     average_epoch_train_loss = total_epoch_train_loss / len(train_dataloader)
     print("     Epoch Final   train loss : ", average_epoch_train_loss)
+
+    # get overall stats for classification
+    if params["problem_type"] == "classification":
+        average_epoch_train_metric = overall_stats(
+            predictions_array, ground_truth_array, params
+        )
     for metric in params["metrics"]:
         if isinstance(total_epoch_train_metric[metric], np.ndarray):
             to_print = (
@@ -183,6 +205,7 @@ def train_network(model, train_dataloader, optimizer, params):
         else:
             to_print = total_epoch_train_metric[metric] / len(train_dataloader)
         average_epoch_train_metric[metric] = to_print
+    for metric in average_epoch_train_metric.keys():
         print(
             "     Epoch Final   train " + metric + " : ",
             average_epoch_train_metric[metric],

GANDLF/metrics/__init__.py

@@ -12,6 +12,7 @@
 )
 from .regression import classification_accuracy, balanced_acc_score, per_label_accuracy
 from .generic import recall_score, precision_score, iou_score, f1_score, accuracy
+from .classification import overall_stats
 
 
 # global defines for the metrics
@@ -35,5 +36,5 @@
     "recall": recall_score,
     "iou": iou_score,
     "balanced_accuracy": balanced_acc_score,
-    "per_label_accuracy": per_label_accuracy,
+    "per_label_one_hot_accuracy": per_label_accuracy,
 }

GANDLF/metrics/classification.py

@@ -0,0 +1,86 @@
+import torchmetrics as tm
+
+
+def get_output_from_calculator(predictions, ground_truth, calculator):
+    """
+    Helper function to get the output from a calculator.
+
+    Args:
+        predictions (torch.Tensor): The output of the model.
+        ground_truth (torch.Tensor): The ground truth labels.
+        calculator (torchmetrics.Metric): The calculator to use.
+
+    Returns:
+        float: The output from the calculator.
+    """
+    temp_output = calculator(predictions, ground_truth)
+    if temp_output.dim() > 0:
+        temp_output = temp_output.cpu().tolist()
+    else:
+        temp_output = temp_output.cpu().item()
+    return temp_output
+
+
+def overall_stats(predictions, ground_truth, params):
+    """
+    Generates a dictionary of metrics calculated on the overall predictions and ground truths.
+
+    Args:
+        predictions (torch.Tensor): The output of the model.
+        ground_truth (torch.Tensor): The ground truth labels.
+        params (dict): The parameter dictionary containing training and data information.
+
+    Returns:
+        dict: A dictionary of metrics.
+    """
+    assert (
+        params["problem_type"] == "classification"
+    ), "Only classification is supported for overall stats"
+    assert len(predictions) == len(
+        ground_truth
+    ), "Predictions and ground truth must be of same length"
+
+    output_metrics = {}
+
+    average_types_keys = {
+        "global": "micro",
+        "per_class": "none",
+        "per_class_average": "macro",
+        "per_class_weighted": "weighted",
+    }
+    # metrics that need the "average" parameter
+    for average_type, average_type_key in average_types_keys.items():
+        calculators = {
+            "accuracy": tm.Accuracy(
+                num_classes=params["model"]["num_classes"], average=average_type_key
+            ),
+            "precision": tm.Precision(
+                num_classes=params["model"]["num_classes"], average=average_type_key
+            ),
+            "recall": tm.Recall(
+                num_classes=params["model"]["num_classes"], average=average_type_key
+            ),
+            "f1": tm.F1(
+                num_classes=params["model"]["num_classes"], average=average_type_key
+            ),
+            ## weird error for multi-class problem, where pos_label is not getting set
+            # "aucroc": tm.AUROC(
+            #     num_classes=params["model"]["num_classes"], average=average_type_key
+            # ),
+        }
+        for metric_name, calculator in calculators.items():
+            output_metrics[
+                f"{metric_name}_{average_type}"
+            ] = get_output_from_calculator(predictions, ground_truth, calculator)
+    # metrics that do not have any "average" parameter
+    calculators = {
+        "auc": tm.AUC(reorder=True),
+        ## weird error for multi-class problem, where pos_label is not getting set
+        # "roc": tm.ROC(num_classes=params["model"]["num_classes"]),
+    }
+    for metric_name, calculator in calculators.items():
+        output_metrics[metric_name] = get_output_from_calculator(
+            predictions, ground_truth, calculator
+        )
+
+    return output_metrics

GANDLF/utils/__init__.py

@@ -19,6 +19,7 @@
     get_class_imbalance_weights_classification,
     get_linear_interpolation_mode,
     print_model_summary,
+    get_ground_truths_and_predictions_tensor,
 )
 
 from .write_parse import (

GANDLF/utils/tensor.py

@@ -419,3 +419,26 @@ def print_model_summary(
     )
     temp_output = stats.to_readable(stats.total_mult_adds)
     print("\tTotal # of operations:", temp_output[1], temp_output[0])
+
+
+def get_ground_truths_and_predictions_tensor(params, loader_type):
+    """
+    This function is used to get the ground truths and predictions for a given loader type.
+
+    Args:
+        params (dict): The parameters passed by the user yaml.
+        loader_type (str): The loader type for which the ground truths and predictions are to be returned.
+
+    Returns:
+        torch.Tensor, torch.Tensor: The ground truths and base predictions for the given loader type.
+    """
+    ground_truth_array = torch.from_numpy(
+        params[loader_type][
+            params[loader_type].columns[params["headers"]["predictionHeaders"]]
+        ]
+        .to_numpy()
+        .ravel()
+    ).type(torch.int)
+    predictions_array = torch.zeros_like(ground_truth_array)
+
+    return ground_truth_array, predictions_array

GANDLF/version.py

@@ -1,3 +1,3 @@
 #!/usr/bin/env python3
 # -*- coding: UTF-8 -*-
-__version__ = "0.0.15-dev"
+__version__ = "0.0.16-dev"

HISTORY.md

@@ -1,3 +1,7 @@
+## 0.0.16- 
+- ImageNet pre-trained models for UNet with variable encoders is now available
+- ACS/Soft conversion is available for ImageNet-pretrained UNet
+
 ## 0.0.15
 - Updated `setup.py` for `python>=3.8`
 - `stride_size` is now handled internally for histology data
@@ -9,8 +13,7 @@
 - Per class accuracy has been added as a metric
 - Dedicated rescaling preprocessing function added for increased flexibility
 - Largest Connected Component Analysis is now added
-- ImageNet pre-trained models for UNet with variable encoders is now available
-- ACS/Soft conversion is available for ImageNet-pretrained UNet
+- Included metrics using overall predictions and ground truths
 
 ## 0.0.14
 

samples/config_all_options.yaml

@@ -1,8 +1,8 @@
 # affix version
 version:
   {
-    minimum: 0.0.15,
-    maximum: 0.0.15 # this should NOT be made a variable, but should be tested after every tag is created
+    minimum: 0.0.16,
+    maximum: 0.0.16 # this should NOT be made a variable, but should be tested after every tag is created
   }
 ## Choose the model parameters here
 model:

samples/config_classification.yaml

@@ -1,8 +1,8 @@
 # affix version
 version:
   {
-    minimum: 0.0.15,
-    maximum: 0.0.15 # this should NOT be made a variable, but should be tested after every tag is created
+    minimum: 0.0.16,
+    maximum: 0.0.16 # this should NOT be made a variable, but should be tested after every tag is created
   }
 # Choose the model parameters here
 model:

samples/config_regression.yaml

@@ -1,8 +1,8 @@
 # affix version
 version:
   {
-    minimum: 0.0.15,
-    maximum: 0.0.15 # this should NOT be made a variable, but should be tested after every tag is created
+    minimum: 0.0.16,
+    maximum: 0.0.16 # this should NOT be made a variable, but should be tested after every tag is created
   }
 # Choose the model parameters here
 model:

samples/config_segmentation_brats.yaml

@@ -1,8 +1,8 @@
 # affix version
 version:
   {
-    minimum: 0.0.15,
-    maximum: 0.0.15 # this should NOT be made a variable, but should be tested after every tag is created
+    minimum: 0.0.16,
+    maximum: 0.0.16 # this should NOT be made a variable, but should be tested after every tag is created
   }
 # Choose the model parameters here
 model:

samples/config_segmentation_histology.yaml

@@ -1,8 +1,8 @@
 # affix version
 version:
   {
-    minimum: 0.0.15,
-    maximum: 0.0.15 # this should NOT be made a variable, but should be tested after every tag is created
+    minimum: 0.0.16,
+    maximum: 0.0.16 # this should NOT be made a variable, but should be tested after every tag is created
   }
 # Choose the model parameters here
 model:

testing/config_classification.yaml

@@ -14,7 +14,7 @@ metrics:
     }
   - accuracy
   - balanced_accuracy
-  - per_label_accuracy
+  - per_label_one_hot_accuracy
   - precision: {
       average: weighted,
     }
@@ -53,7 +53,7 @@ save_output: false
 scaling_factor: 1
 scheduler: triangle
 version:
-  maximum: 0.0.15
+  maximum: 0.0.16
   minimum: 0.0.14
 weighted_loss: True
 which_model: resunet

testing/config_regression.yaml

@@ -37,7 +37,7 @@ save_output: false
 scaling_factor: 1
 scheduler: triangle
 version:
-  maximum: 0.0.15
+  maximum: 0.0.16
   minimum: 0.0.14
 weighted_loss: false
 which_model: resunet