Integrate half precision in sklearn based task

CHANGELOG.md

@@ -2,6 +2,13 @@
 # Changelog
 All notable changes to this project will be documented in this file.
 
+### [1.5.6]
+
+#### Added
+
+- Add support for half precision training and inference for sklearn based tasks
+- Add gradcam export for sklearn training
+
 ### [1.5.5]
 
 #### Fixed 

docs/tutorials/examples/sklearn_classification.md

@@ -147,6 +147,8 @@ datamodule:
 
 task:
   device: cuda:0
+  half_precision: false
+  gradcam: false
   automatic_batch_size:
     starting_batch_size: 1024
     disable: true
@@ -160,6 +162,7 @@ task:
 
 This will train a logistic regression classifier using a resnet18 backbone, resizing the images to 224x224 and using a 5-fold cross validation. The `class_to_idx` parameter is used to map the class names to indexes, the indexes will be used to train the classifier. The `output` parameter is used to specify the output folder and the type of output to save. The `export.types` parameter can be used to export the model in different formats, at the moment `torchscript`, `onnx` and `pytorch` are supported.
 The backbone (in torchscript and pytorch format) will be saved along with the classifier. `test_full_data` is used to specify if a final test should be performed on all the data (after training on the training and validation datasets).
+It's possible to enable half precision training by setting `half_precision` to `true` and export gradcam results by setting `gradcam` to `true`.
 
 Optionally it's possible to enable the automatic batch size finder by setting `automatic_batch_size.disable` to `false`. This will try to find the maximum batch size that can be used on the given device without running out of memory. The `starting_batch_size` parameter is used to specify the starting batch size to use for the search, the algorithm will start from this value and will try to divide it by two until it doesn't run out of memory.
 Finally, the `save_model_summary` parameter can be used to save the backbone information in a text file called `model_summary.txt` located in the root of the output folder.

docs/tutorials/examples/sklearn_patch_classification.md

@@ -223,6 +223,7 @@ datamodule:
 
 task:
   device: cuda:2
+  half_precision: false
   automatic_batch_size:
     starting_batch_size: 1024
     disable: true
@@ -235,6 +236,7 @@ task:
 
 This will train a resnet18 model on the given dataset, using 256 as batch size and skipping the background class during training.
 The experiment results will be saved under the `classification_patch_experiment` folder. The deployment model will be generated but only the classifier will be saved (in joblib format), to reconstruct patches for evaluation the `major_voting` method will be used.
+It is possible to extract features in half precision by setting `half_precision` to true. The `automatic_batch_size` parameter can be used to automatically adjust the batch size to fit the memory of the device. The `starting_batch_size` parameter is used to specify the starting batch size, the algorithm will try to decrease the batch size until it can fit the batch into memory. The `disable` parameter can be used to disable the automatic batch size adjustment.
 
 ### Run
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "quadra"
-version = "1.5.5"
+version = "1.5.6"
 description = "Deep Learning experiment orchestration library"
 authors = [
   "Federico Belotti <federico.belotti@orobix.com>",

quadra/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "1.5.5"
+__version__ = "1.5.6"
 
 
 def get_version():

quadra/configs/task/sklearn_classification.yaml

@@ -1,5 +1,7 @@
 _target_: quadra.tasks.SklearnClassification
 device: cuda:0
+half_precision: false
+gradcam: false
 automatic_batch_size:
   starting_batch_size: 1024
   disable: true

quadra/configs/task/sklearn_classification_patch.yaml

@@ -1,5 +1,6 @@
 _target_: quadra.tasks.PatchSklearnClassification
 device: cuda:0
+half_precision: false
 automatic_batch_size:
   starting_batch_size: 1024
   disable: true

quadra/tasks/classification.py

@@ -332,6 +332,11 @@ def generate_report(self) -> None:
         if not self.run_test or self.config.trainer.get("fast_dev_run"):
             self.datamodule.setup(stage="test")
 
+        if "16" in self.trainer.precision:
+            log.warning("Gradcam is currently not supported with half precision, it will be disabled")
+            self.module.gradcam = False
+            self.gradcam = False
+
         predictions_outputs = self.trainer.predict(
             model=self.module, datamodule=self.datamodule, ckpt_path=self.best_model_path
         )
@@ -473,6 +478,8 @@ class SklearnClassification(Generic[SklearnClassificationDataModuleT], Task[Skle
         output: Dictionary defining which kind of outputs to generate. Defaults to None.
         automatic_batch_size: Whether to automatically find the largest batch size that fits in memory.
         save_model_summary: Whether to save a model_summary.txt file containing the model summary.
+        half_precision: Whether to use half precision during training.
+        gradcam: Whether to compute gradcams for test results.
     """
 
     def __init__(
@@ -482,6 +489,8 @@ def __init__(
         device: str,
         automatic_batch_size: DictConfig,
         save_model_summary: bool = False,
+        half_precision: bool = False,
+        gradcam: bool = False,
     ):
         super().__init__(config=config)
 
@@ -495,13 +504,16 @@ def __init__(
             "test_accuracy": [],
             "test_results": [],
             "test_labels": [],
+            "cams": [],
         }
         self.export_folder = "deployment_model"
         self.deploy_info_file = "model.json"
         self.train_dataloader_list: List[torch.utils.data.DataLoader] = []
         self.test_dataloader_list: List[torch.utils.data.DataLoader] = []
         self.automatic_batch_size = automatic_batch_size
         self.save_model_summary = save_model_summary
+        self.half_precision = half_precision
+        self.gradcam = gradcam
 
     @property
     def device(self) -> str:
@@ -558,6 +570,14 @@ def backbone(self, backbone_config):
 
         self._backbone = ModelSignatureWrapper(self._backbone)
         self._backbone.eval()
+        if self.half_precision:
+            if self.device == "cpu":
+                raise ValueError("Half precision is not supported on CPU")
+            self._backbone.half()
+
+            if self.gradcam:
+                log.warning("Gradcam is currently not supported with half precision, it will be disabled")
+                self.gradcam = False
         self._backbone.to(self.device)
 
     @property
@@ -622,21 +642,23 @@ def train(self) -> None:
                     train_features=all_features_sorted[0:train_len], train_labels=all_labels_sorted[0:train_len]
                 )
 
-                _, pd_cm, accuracy, res, _ = self.trainer.test(
+                _, pd_cm, accuracy, res, cams = self.trainer.test(
                     test_dataloader=test_dataloader,
                     test_features=all_features_sorted[train_len:],
                     test_labels=all_labels_sorted[train_len:],
                     class_to_keep=class_to_keep,
                     idx_to_class=train_dataloader.dataset.idx_to_class,
                     predict_proba=True,
+                    gradcam=self.gradcam,
                 )
             else:
                 self.trainer.fit(train_dataloader=train_dataloader)
-                _, pd_cm, accuracy, res, _ = self.trainer.test(
+                _, pd_cm, accuracy, res, cams = self.trainer.test(
                     test_dataloader=test_dataloader,
                     class_to_keep=class_to_keep,
                     idx_to_class=train_dataloader.dataset.idx_to_class,
                     predict_proba=True,
+                    gradcam=self.gradcam,
                 )
 
             # save results
@@ -649,6 +671,7 @@ def train(self) -> None:
                     for i in res["real_label"].unique().tolist()
                 ]
             )
+            self.metadata["cams"].append(cams)
 
     def extract_model_summary(
         self, feature_extractor: torch.nn.Module | BaseEvaluationModel, dl: torch.utils.data.DataLoader
@@ -670,7 +693,8 @@ def extract_model_summary(
 
             if hasattr(feature_extractor, "parameters"):
                 # Move input to the correct device
-                x1 = x1.to(next(feature_extractor.parameters()).device)
+                parameter = next(feature_extractor.parameters())
+                x1 = x1.to(parameter.device).to(parameter.dtype)
                 x1 = x1[0].unsqueeze(0)  # Remove batch dimension
 
                 model_info = None
@@ -725,8 +749,8 @@ def test_full_data(self) -> None:
 
         # Put backbone on the correct device as it may be moved after export
         self.backbone.to(self.device)
-        _, pd_cm, accuracy, res, _ = self.trainer.test(
-            test_dataloader=test_dataloader, idx_to_class=idx_to_class, predict_proba=True
+        _, pd_cm, accuracy, res, cams = self.trainer.test(
+            test_dataloader=test_dataloader, idx_to_class=idx_to_class, predict_proba=True, gradcam=self.gradcam
         )
 
         output_folder_test = "test"
@@ -741,6 +765,7 @@ def test_full_data(self) -> None:
             test_dataloader=test_dataloader,
             config=self.config,
             output=self.output,
+            grayscale_cams=cams,
         )
 
     def export(self) -> None:
@@ -757,7 +782,7 @@ def export(self) -> None:
             config=self.config,
             model=self.backbone,
             export_folder=self.export_folder,
-            half_precision=False,
+            half_precision=self.half_precision,
             input_shapes=input_shapes,
             idx_to_class=idx_to_class,
             pytorch_model_type="backbone",
@@ -789,6 +814,7 @@ def generate_report(self) -> None:
                 test_dataloader=self.test_dataloader_list[count],
                 config=self.config,
                 output=self.output,
+                grayscale_cams=self.metadata["cams"][count],
             )
         final_confusion_matrix = sum(cm_list)
 
@@ -1104,7 +1130,11 @@ def prepare_gradcam(self) -> None:
             return
 
         if isinstance(self.deployment_model.model.features_extractor, timm.models.resnet.ResNet):
-            target_layers = [cast(BaseNetworkBuilder, self.deployment_model.model).features_extractor.layer4[-1]]
+            target_layers = [
+                cast(BaseNetworkBuilder, self.deployment_model.model).features_extractor.layer4[
+                    -1
+                ]  # type: ignore[index]
+            ]
             self.cam = GradCAM(
                 model=self.deployment_model.model,
                 target_layers=target_layers,

quadra/tasks/patch.py

@@ -33,6 +33,7 @@ class PatchSklearnClassification(Task[PatchSklearnClassificationDataModule]):
         device: The device to use
         output: Dictionary defining which kind of outputs to generate. Defaults to None.
         automatic_batch_size: Whether to automatically find the largest batch size that fits in memory.
+        half_precision: Whether to use half precision.
     """
 
     def __init__(
@@ -41,6 +42,7 @@ def __init__(
         output: DictConfig,
         device: str,
         automatic_batch_size: DictConfig,
+        half_precision: bool = False,
     ):
         super().__init__(config=config)
         self.device: str = device
@@ -58,6 +60,7 @@ def __init__(
         }
         self.export_folder: str = "deployment_model"
         self.automatic_batch_size = automatic_batch_size
+        self.half_precision = half_precision
 
     @property
     def model(self) -> ClassifierMixin:
@@ -87,6 +90,10 @@ def backbone(self, backbone_config):
 
         self._backbone = ModelSignatureWrapper(self._backbone)
         self._backbone.eval()
+        if self.half_precision:
+            if self.device == "cpu":
+                raise ValueError("Half precision is not supported on CPU")
+            self._backbone.half()
         self._backbone = self._backbone.to(self.device)
 
     def prepare(self) -> None:
@@ -222,7 +229,7 @@ def export(self) -> None:
             config=self.config,
             model=self.backbone,
             export_folder=self.export_folder,
-            half_precision=False,
+            half_precision=self.half_precision,
             input_shapes=input_shapes,
             idx_to_class=idx_to_class,
             pytorch_model_type="backbone",

quadra/utils/models.py

@@ -14,7 +14,12 @@
 from timm.models.vision_transformer import Mlp
 from torch import nn
 
-from quadra.models.evaluation import BaseEvaluationModel, TorchEvaluationModel, TorchscriptEvaluationModel
+from quadra.models.evaluation import (
+    BaseEvaluationModel,
+    ONNXEvaluationModel,
+    TorchEvaluationModel,
+    TorchscriptEvaluationModel,
+)
 from quadra.utils import utils
 from quadra.utils.vit_explainability import VitAttentionGradRollout
 
@@ -109,7 +114,7 @@ def get_feature(
     if isinstance(feature_extractor, (TorchEvaluationModel, TorchscriptEvaluationModel)):
         # If we are working with torch based evaluation models we need to extract the model
         feature_extractor = feature_extractor.model
-    else:
+    elif isinstance(feature_extractor, ONNXEvaluationModel):
         gradcam = False
 
     feature_extractor.eval()
@@ -146,8 +151,11 @@ def get_feature(
             x1, y1 = b
 
             if hasattr(feature_extractor, "parameters"):
-                # Move input to the correct device
-                x1 = x1.to(next(feature_extractor.parameters()).device)
+                # Move input to the correct device and dtype
+                parameter = next(feature_extractor.parameters())
+                x1 = x1.to(parameter.device).to(parameter.dtype)
+            elif isinstance(feature_extractor, BaseEvaluationModel):
+                x1 = x1.to(feature_extractor.device).to(feature_extractor.model_dtype)
 
             if gradcam:
                 y_hat = cast(