Merge branch 'main' into vsalva/precommit-hooks

Author: vale-salvatelli

CHANGELOG.md

@@ -26,6 +26,7 @@ jobs that run in AzureML.
 
 ### Changed
 - ([#531](https://github.com/microsoft/InnerEye-DeepLearning/pull/531)) Updated PL to 1.3.8, torchmetrics and pl-bolts and changed relevant metrics and SSL code API.
+- ([#555](https://github.com/microsoft/InnerEye-DeepLearning/pull/555)) Make the SSLContainer compatible with new datasets
 - ([#533](https://github.com/microsoft/InnerEye-DeepLearning/pull/533)) Better defaults for inference on ensemble children.
 - ([#536](https://github.com/microsoft/InnerEye-DeepLearning/pull/536)) Inference will not run on the validation set by default, this can be turned on
 via the `--inference_on_val_set` flag.

InnerEye/ML/SSL/datamodules_and_datasets/datamodules.py

@@ -29,6 +29,7 @@ def __init__(self,
                  num_workers: int = 6,
                  batch_size: int = 32,
                  seed: int = 42,
+                 drop_last: bool = True,
                  *args: Any, **kwargs: Any) -> None:
         """
         Wrapper around VisionDatamodule to load torchvision dataset into a pytorch-lightning module.
@@ -42,16 +43,17 @@ def __init__(self,
         :param val_transforms: transforms to use at validation time
         :param data_dir: data directory where to find the data
         :param val_split: proportion of training dataset to use for validation
-        :param num_workers: number of processes for dataloaders.
-        :param batch_size: batch size for training & validation.
+        :param num_workers: number of processes for dataloaders
+        :param batch_size: batch size for training & validation
         :param seed: random seed for dataset splitting
+        :param drop_last: bool, if true it drops the last incomplete batch
         """
         data_dir = data_dir if data_dir is not None else os.getcwd()
         super().__init__(data_dir=data_dir,
                          val_split=val_split,
                          num_workers=num_workers,
                          batch_size=batch_size,
-                         drop_last=True,
+                         drop_last=drop_last,
                          train_transforms=train_transforms,
                          val_transforms=val_transforms,
                          seed=seed,

InnerEye/ML/SSL/datamodules_and_datasets/transforms_utils.py

@@ -10,16 +10,17 @@
 from pl_bolts.models.self_supervised.simclr import SimCLRTrainDataTransform
 from yacs.config import CfgNode
 
-from InnerEye.ML.augmentations.transform_pipeline import create_cxr_transforms_from_config
+from InnerEye.ML.augmentations.transform_pipeline import create_transforms_from_config
 
 
-def get_cxr_ssl_transforms(config: CfgNode,
-                           return_two_views_per_sample: bool,
-                           use_training_augmentations_for_validation: bool = False) -> Tuple[Any, Any]:
+def get_ssl_transforms_from_config(config: CfgNode,
+                                   return_two_views_per_sample: bool,
+                                   use_training_augmentations_for_validation: bool = False,
+                                   expand_channels: bool = True) -> Tuple[Any, Any]:
     """
     Returns training and validation transforms for CXR.
     Transformations are constructed in the following way:
-    1. Construct the pipeline of augmentations in create_chest_xray_transform (e.g. resize, flip, affine) as defined
+    1. Construct the pipeline of augmentations in create_transform_from_config (e.g. resize, flip, affine) as defined
     by the config.
     2. If we just want to construct the transformation pipeline for a classification model or for the linear evaluator
     of the SSL module, return this pipeline.
@@ -29,14 +30,18 @@ def get_cxr_ssl_transforms(config: CfgNode,
 
     :param config: configuration defining which augmentations to apply as well as their intensities.
     :param return_two_views_per_sample: if True the resulting transforms will return two versions of each sample they
-    are called on. If False, simply return one transformed version of the sample.
+    are called on. If False, simply return one transformed version of the sample centered and cropped.
     :param use_training_augmentations_for_validation: If True, use augmentation at validation time too.
     This is required for SSL validation loss to be meaningful. If False, only apply basic processing step
     (no augmentations)
+    :param expand_channels: if True the expand channel transformation from InnerEye.ML.augmentations.image_transforms
+    will be added to the transformation passed through the config. This is needed for single channel images as CXR.
     """
-    train_transforms = create_cxr_transforms_from_config(config, apply_augmentations=True)
-    val_transforms = create_cxr_transforms_from_config(config,
-                                                       apply_augmentations=use_training_augmentations_for_validation)
+    train_transforms = create_transforms_from_config(config, apply_augmentations=True,
+                                                     expand_channels=expand_channels)
+    val_transforms = create_transforms_from_config(config,
+                                                   apply_augmentations=use_training_augmentations_for_validation,
+                                                   expand_channels=expand_channels)
     if return_two_views_per_sample:
         train_transforms = DualViewTransformWrapper(train_transforms)  # type: ignore
         val_transforms = DualViewTransformWrapper(val_transforms)  # type: ignore

InnerEye/ML/SSL/lightning_containers/ssl_container.py

@@ -17,7 +17,7 @@
 from InnerEye.ML.SSL.datamodules_and_datasets.datamodules import CombinedDataModule, InnerEyeVisionDataModule
 from InnerEye.ML.SSL.datamodules_and_datasets.transforms_utils import InnerEyeCIFARLinearHeadTransform, \
     InnerEyeCIFARTrainTransform, \
-    get_cxr_ssl_transforms
+    get_ssl_transforms_from_config
 from InnerEye.ML.SSL.encoders import get_encoder_output_dim
 from InnerEye.ML.SSL.lightning_modules.byol.byol_module import BYOLInnerEye
 from InnerEye.ML.SSL.lightning_modules.simclr_module import SimCLRInnerEye
@@ -96,6 +96,7 @@ class SSLContainer(LightningContainer):
     learning_rate_linear_head_during_ssl_training = param.Number(default=1e-4,
                                                                  doc="Learning rate for linear head training during "
                                                                      "SSL training.")
+    drop_last = param.Boolean(default=True, doc="If True drops the last incomplete batch")
 
     def setup(self) -> None:
         from InnerEye.ML.SSL.lightning_containers.ssl_image_classifier import SSLClassifierContainer
@@ -166,8 +167,8 @@ def create_model(self) -> LightningModule:
                 f"Found {self.ssl_training_type.value}")
         model.hparams.update({'ssl_type': self.ssl_training_type.value,
                               "num_classes": self.data_module.num_classes})
-        self.encoder_output_dim = get_encoder_output_dim(model, self.data_module)
 
+        self.encoder_output_dim = get_encoder_output_dim(model, self.data_module)
         return model
 
     def get_data_module(self) -> InnerEyeDataModuleTypes:
@@ -186,7 +187,7 @@ def _create_ssl_data_modules(self, is_ssl_encoder_module: bool) -> InnerEyeVisio
         """
         Returns torch lightning data module for encoder or linear head
 
-        :param is_ssl_encoder_module: whether to return the data module for SSL training or for linear heard. If true,
+        :param is_ssl_encoder_module: whether to return the data module for SSL training or for linear head. If true,
         :return transforms with two views per sample (batch like (img_v1, img_v2, label)). If False, return only one
         view per sample but also return the index of the sample in the dataset (to make sure we don't use twice the same
         batch in one training epoch (batch like (index, img_v1, label), as classifier dataloader expected to be shorter
@@ -209,7 +210,8 @@ def _create_ssl_data_modules(self, is_ssl_encoder_module: bool) -> InnerEyeVisio
                                       data_dir=str(datamodule_args.dataset_path),
                                       batch_size=batch_size_per_gpu,
                                       num_workers=self.num_workers,
-                                      seed=self.random_seed)
+                                      seed=self.random_seed,
+                                      drop_last=self.drop_last)
         dm.prepare_data()
         dm.setup()
         return dm
@@ -223,25 +225,39 @@ def _get_transforms(self, augmentation_config: Optional[CfgNode],
         examples.
         :param dataset_name: name of the dataset, value has to be in SSLDatasetName, determines which transformation
         pipeline to return.
-        :param is_ssl_encoder_module: if True the transformation pipeline will yield two version of the image it is
-        applied on. If False, return only one transformation.
+        :param is_ssl_encoder_module: if True the transformation pipeline will yield two versions of the image it is
+        applied on and it applies the training transformations also at validation time. Note that if your transformation 
+        does not contain any randomness, the pipeline will return two identical copies. If False, it will return only one 
+        transformation.
         :return: training transformation pipeline and validation transformation pipeline.
         """
         if dataset_name in [SSLDatasetName.RSNAKaggleCXR.value,
                             SSLDatasetName.NIHCXR.value,
                             SSLDatasetName.CheXpert.value,
                             SSLDatasetName.Covid.value]:
             assert augmentation_config is not None
-            train_transforms, val_transforms = get_cxr_ssl_transforms(augmentation_config,
-                                                                      return_two_views_per_sample=is_ssl_encoder_module,
-                                                                      use_training_augmentations_for_validation=is_ssl_encoder_module)
+            train_transforms, val_transforms = get_ssl_transforms_from_config(
+                augmentation_config,
+                return_two_views_per_sample=is_ssl_encoder_module,
+                use_training_augmentations_for_validation=is_ssl_encoder_module
+            )
         elif dataset_name in [SSLDatasetName.CIFAR10.value, SSLDatasetName.CIFAR100.value]:
             train_transforms = \
                 InnerEyeCIFARTrainTransform(32) if is_ssl_encoder_module else InnerEyeCIFARLinearHeadTransform(32)
             val_transforms = \
                 InnerEyeCIFARTrainTransform(32) if is_ssl_encoder_module else InnerEyeCIFARLinearHeadTransform(32)
+        elif augmentation_config:
+            train_transforms, val_transforms = get_ssl_transforms_from_config(
+                augmentation_config,
+                return_two_views_per_sample=is_ssl_encoder_module,
+                use_training_augmentations_for_validation=is_ssl_encoder_module,
+                expand_channels=False,
+            )
+            logging.warning(f"Dataset {dataset_name} unknown. The config will be consumed by "
+                            f"get_ssl_transforms() to create the augmentation pipeline, make sure "
+                            f"the transformations in your configs are compatible. ")
         else:
-            raise ValueError(f"Dataset {dataset_name} unknown.")
+            raise ValueError(f"Dataset {dataset_name} unknown and no config has been passed.")
 
         return train_transforms, val_transforms
 

InnerEye/ML/augmentations/transform_pipeline.py

@@ -86,16 +86,22 @@ def __call__(self, data: ImageData) -> torch.Tensor:
         return self.transform_image(data)
 
 
-def create_cxr_transforms_from_config(config: CfgNode,
-                                      apply_augmentations: bool) -> ImageTransformationPipeline:
+def create_transforms_from_config(config: CfgNode,
+                                  apply_augmentations: bool,
+                                  expand_channels: bool = True) -> ImageTransformationPipeline:
     """
-    Defines the image transformations pipeline used in Chest-Xray datasets. Can be used for other types of
-    images data, type of augmentations to use and strength are expected to be defined in the config.
+    Defines the image transformations pipeline from a config file. It has been designed for Chest X-Ray
+    images but it can be used for other types of images data, type of augmentations to use and strength are
+    expected to be defined in the config. The channel expansion is needed for gray images.
     :param config: config yaml file fixing strength and type of augmentation to apply
     :param apply_augmentations: if True return transformation pipeline with augmentations. Else,
     disable augmentations i.e. only resize and center crop the image.
+    :param expand_channels: if True the expand channel transformation from InnerEye.ML.augmentations.image_transforms
+    will be added to the transformation passed through the config. This is needed for single channel images as CXR.
     """
-    transforms: List[Any] = [ExpandChannels()]
+    transforms: List[Any] = []
+    if expand_channels:
+        transforms.append(ExpandChannels())
     if apply_augmentations:
         if config.augmentation.use_random_affine:
             transforms.append(RandomAffine(

InnerEye/ML/configs/classification/CovidModel.py

@@ -23,7 +23,8 @@
 from InnerEye.ML.SSL.lightning_containers.ssl_container import EncoderName
 from InnerEye.ML.SSL.lightning_modules.ssl_classifier_module import SSLClassifier
 from InnerEye.ML.SSL.utils import create_ssl_image_classifier, load_yaml_augmentation_config
-from InnerEye.ML.augmentations.transform_pipeline import create_cxr_transforms_from_config
+from InnerEye.ML.augmentations.transform_pipeline import create_transforms_from_config
+
 from InnerEye.ML.common import ModelExecutionMode
 
 from InnerEye.ML.configs.ssl.CXR_SSL_configs import path_linear_head_augmentation_cxr
@@ -137,9 +138,9 @@ def get_model_train_test_dataset_splits(self, dataset_df: pd.DataFrame) -> Datas
     def get_image_transform(self) -> ModelTransformsPerExecutionMode:
         config = load_yaml_augmentation_config(path_linear_head_augmentation_cxr)
         train_transforms = Compose(
-            [DicomPreparation(), create_cxr_transforms_from_config(config, apply_augmentations=True)])
+            [DicomPreparation(), create_transforms_from_config(config, apply_augmentations=True)])
         val_transforms = Compose(
-            [DicomPreparation(), create_cxr_transforms_from_config(config, apply_augmentations=False)])
+            [DicomPreparation(), create_transforms_from_config(config, apply_augmentations=False)])
 
         return ModelTransformsPerExecutionMode(train=train_transforms,
                                                val=val_transforms,

Tests/ML/augmentations/test_transform_pipeline.py

@@ -7,6 +7,7 @@
 import PIL
 import pytest
 import torch
+
 from torchvision.transforms import (
     CenterCrop,
     ColorJitter,
@@ -46,7 +47,6 @@
 test_4d_scan_as_tensor = torch.ones([5, 4, *image_size]) * 255.0
 test_4d_scan_as_tensor[..., 10:15, 10:20] = 1
 
-
 @pytest.mark.parametrize("use_different_transformation_per_channel", [True, False])
 def test_torchvision_on_various_input(
     use_different_transformation_per_channel: bool,
@@ -136,17 +136,19 @@ def test_custom_tf_on_various_input(
     )
 
 
-def test_create_transform_pipeline_from_config() -> None:
+@pytest.mark.parametrize("expand_channels", [True, False])
+def test_create_transform_pipeline_from_config(expand_channels: bool) -> None:
     """
     Tests that the pipeline returned by create_transform_pipeline_from_config returns the expected transformation.
     """
+
     transformation_pipeline = create_cxr_transforms_from_config(
-        cxr_augmentation_config, apply_augmentations=True
+        cxr_augmentation_config, apply_augmentations=True,
+        expand_channels=expand_channels
     )
     fake_cxr_as_array = np.ones([256, 256]) * 255.0
     fake_cxr_as_array[100:150, 100:200] = 1
-    fake_cxr_image = PIL.Image.fromarray(fake_cxr_as_array).convert("L")
-
+    
     all_transforms = [
         ExpandChannels(),
         RandomAffine(degrees=180, translate=(0, 0), shear=40),
@@ -160,23 +162,28 @@ def test_create_transform_pipeline_from_config() -> None:
         AddGaussianNoise(std=0.05, p_apply=0.5),
     ]
 
+    if expand_channels:
+        all_transforms.insert(0, ExpandChannels())
+        # expand channels is used for single-channel input images
+        fake_image = PIL.Image.fromarray(fake_cxr_as_array).convert("L")
+        # In the pipeline the image is converted to tensor before applying the transformations. Do the same here.
+        image = ToTensor()(fake_image).reshape([1, 1, 256, 256])
+    else:
+        fake_3d_array = np.dstack([fake_cxr_as_array, fake_cxr_as_array, fake_cxr_as_array])
+        fake_image = PIL.Image.fromarray(fake_3d_array.astype(np.uint8)).convert("RGB")
+        # In the pipeline the image is converted to tensor before applying the transformations. Do the same here.
+        image = ToTensor()(fake_image).reshape([1, 3, 256, 256])
+
     np.random.seed(3)
     torch.manual_seed(3)
     random.seed(3)
-
-    transformed_image = transformation_pipeline(fake_cxr_image)
+    transformed_image = transformation_pipeline(fake_image)
     assert isinstance(transformed_image, torch.Tensor)
-    # Expected pipeline
-    image = np.ones([256, 256]) * 255.0
-    image[100:150, 100:200] = 1
-    image = PIL.Image.fromarray(image).convert("L")
-    # In the pipeline the image is converted to tensor before applying the transformations. Do the same here.
-    image = ToTensor()(image).reshape([1, 1, 256, 256])
 
+    # Expected pipeline
     np.random.seed(3)
     torch.manual_seed(3)
     random.seed(3)
-
     expected_transformed = image
     for t in all_transforms:
         expected_transformed = t(expected_transformed)
@@ -187,11 +194,15 @@ def test_create_transform_pipeline_from_config() -> None:
 
     # Test the evaluation pipeline
     transformation_pipeline = create_cxr_transforms_from_config(
-        cxr_augmentation_config, apply_augmentations=False
+        cxr_augmentation_config, apply_augmentations=False,  
+        expand_channels=expand_channels,
     )
     transformed_image = transformation_pipeline(image)
     assert isinstance(transformed_image, torch.Tensor)
-    all_transforms = [ExpandChannels(), Resize(size=256), CenterCrop(size=224)]
+    all_transforms = [Resize(size=256), CenterCrop(size=224)]
+    if expand_channels:
+        all_transforms.insert(0, ExpandChannels())
+
     expected_transformed = image
     for t in all_transforms:
         expected_transformed = t(expected_transformed)