Fix DeepMIL for TCGA CRCK dataset (#659)

While we updated DeepMIL for the Panda dataset to work with the latest changes, we did not update DeepMIL for the TCGA CRCK dataset.

This PR updates how the caching of the encoded tiles is done and how the checkpoints of the DeepMIL model is saved and loaded.

No additional tests are required since these are the same functions that we use for the Panda dataset. For all of them a test already exists.

Last, the PR updates the cudatoolkit version, Anton and I found that this is the root cause for all our problems with ddp

CHANGELOG.md

@@ -13,7 +13,6 @@ created.
 ## Upcoming
 
 ### Added
-- ([#649](https://github.com/microsoft/InnerEye-DeepLearning/pull/649)) Fix for the _convert_to_tensor_if_necessary method so that PIL.Image as well as np.array get converted to torch.Tensor.
 - ([#643](https://github.com/microsoft/InnerEye-DeepLearning/pull/643)) Test for recovery of SSL job. Tracks learning rate and train
 loss.
 - ([#594](https://github.com/microsoft/InnerEye-DeepLearning/pull/594)) When supplying a "--tag" argument, the AzureML jobs use that value as the display name, to more easily distinguish run.
@@ -51,6 +50,7 @@ jobs that run in AzureML.
 - ([#650](https://github.com/microsoft/InnerEye-DeepLearning/pull/650)) Enable fine-tuning in DeepMIL using PANDA as the classification task.
 
 ### Changed
+- ([#659](https://github.com/microsoft/InnerEye-DeepLearning/pull/659)) Update cudatoolkit version from 11.1 to 11.3.
 - ([#588](https://github.com/microsoft/InnerEye-DeepLearning/pull/588)) Replace SciPy with PIL.PngImagePlugin.PngImageFile to load png files.
 - ([#585](https://github.com/microsoft/InnerEye-DeepLearning/pull/585)) Switching to PyTorch 1.10.0 and torchvision 0.11.1
 - ([#576](https://github.com/microsoft/InnerEye-DeepLearning/pull/576)) The console output is no longer written to stdout.txt because AzureML handles that better now
@@ -87,6 +87,8 @@ gets uploaded to AzureML, by skipping all test folders.
 - ([#632](https://github.com/microsoft/InnerEye-DeepLearning/pull/632)) Nifti test data is no longer stored in Git LFS
 
 ### Fixed
+- ([#659](https://github.com/microsoft/InnerEye-DeepLearning/pull/659)) Fix caching and checkpointing for TCGA CRCk dataset.
+- ([#649](https://github.com/microsoft/InnerEye-DeepLearning/pull/649)) Fix for the _convert_to_tensor_if_necessary method so that PIL.Image as well as np.array get converted to torch.Tensor.
 - ([#606](https://github.com/microsoft/InnerEye-DeepLearning/pull/606)) Bug fix: registered models do not include the hi-ml submodule
 - ([#646](https://github.com/microsoft/InnerEye-DeepLearning/pull/646)) Workaround for bug in PL: CombinedLoader cannot be used for training data when using DDP
 - ([#593](https://github.com/microsoft/InnerEye-DeepLearning/pull/593)) Bug fix for hi-ml 0.1.11 issue (#130): empty mount point is turned into ".", which fails the AML job

InnerEye/ML/configs/histo_configs/classification/DeepSMILECrck.py

@@ -13,50 +13,51 @@
 - Schirris (2021). DeepSMILE: Self-supervised heterogeneity-aware multiple instance learning for DNA
 damage response defect classification directly from H&E whole-slide images. arXiv:2107.09405
 """
-from pathlib import Path
 from typing import Any, List
+from pathlib import Path
 import os
-
 from monai.transforms import Compose
 from pytorch_lightning.callbacks.model_checkpoint import ModelCheckpoint
 from pytorch_lightning.callbacks import Callback
 
-from health_ml.networks.layers.attention_layers import GatedAttentionLayer
-from health_azure.utils import get_workspace
 from health_azure.utils import CheckpointDownloader
+from health_azure.utils import get_workspace
+from health_ml.networks.layers.attention_layers import AttentionLayer
 from InnerEye.Common import fixed_paths
-from InnerEye.ML.configs.histo_configs.classification.BaseMIL import BaseMIL
+from InnerEye.ML.Histopathology.datamodules.base_module import CacheMode, CacheLocation
 from InnerEye.ML.Histopathology.datamodules.base_module import TilesDataModule
-from InnerEye.ML.Histopathology.datamodules.tcga_crck_module import (
- TcgaCrckTilesDataModule,
+from InnerEye.ML.Histopathology.datamodules.tcga_crck_module import TcgaCrckTilesDataModule
+from InnerEye.ML.common import get_best_checkpoint_path
+
+from InnerEye.ML.Histopathology.models.transforms import (
+ EncodeTilesBatchd,
+ LoadTilesBatchd,
 )
 from InnerEye.ML.Histopathology.models.encoders import (
  HistoSSLEncoder,
  ImageNetEncoder,
  ImageNetSimCLREncoder,
  InnerEyeSSLEncoder,
 )
-from InnerEye.ML.Histopathology.models.transforms import (
- EncodeTilesBatchd,
- LoadTilesBatchd,
-)
-from InnerEye.ML.Histopathology.datasets.tcga_crck_tiles_dataset import (
- TcgaCrck_TilesDataset,
-)
+from InnerEye.ML.configs.histo_configs.classification.BaseMIL import BaseMIL
+from InnerEye.ML.Histopathology.datasets.tcga_crck_tiles_dataset import TcgaCrck_TilesDataset
 
 
 class DeepSMILECrck(BaseMIL):
  def __init__(self, **kwargs: Any) -> None:
  # Define dictionary with default params that can be overriden from subclasses or CLI
  default_kwargs = dict(
  # declared in BaseMIL:
- pooling_type=GatedAttentionLayer.__name__,
+ pooling_type=AttentionLayer.__name__,
+ encoding_chunk_size=60,
+ cache_mode=CacheMode.MEMORY,
+ precache_location=CacheLocation.CPU,
  # declared in DatasetParams:
  local_dataset=Path("/tmp/datasets/TCGA-CRCk"),
  azure_dataset_id="TCGA-CRCk",
  # To mount the dataset instead of downloading in AML, pass --use_dataset_mount in the CLI
  # declared in TrainerParams:
- num_epochs=16,
+ num_epochs=50,
  # declared in WorkflowParams:
  number_of_cross_validation_splits=5,
  cross_validation_split_index=0,
@@ -120,7 +121,7 @@ def get_data_module(self) -> TilesDataModule:
  batch_size=self.batch_size,
  transform=transform,
  cache_mode=self.cache_mode,
- save_precache=self.save_precache,
+ precache_location=self.precache_location,
  cache_dir=self.cache_dir,
  number_of_cross_validation_splits=self.number_of_cross_validation_splits,
  cross_validation_split_index=self.cross_validation_split_index,
@@ -135,11 +136,23 @@ def get_path_to_best_checkpoint(self) -> Path:
  was applied there.
  """
  # absolute path is required for registering the model.
- return (
- fixed_paths.repository_root_directory()
- / self.checkpoint_folder_path
- / self.best_checkpoint_filename_with_suffix
- )
+ absolute_checkpoint_path = Path(fixed_paths.repository_root_directory(),
+ self.checkpoint_folder_path,
+ self.best_checkpoint_filename_with_suffix)
+ if absolute_checkpoint_path.is_file():
+ return absolute_checkpoint_path
+
+ absolute_checkpoint_path_parent = Path(fixed_paths.repository_parent_directory(),
+ self.checkpoint_folder_path,
+ self.best_checkpoint_filename_with_suffix)
+ if absolute_checkpoint_path_parent.is_file():
+ return absolute_checkpoint_path_parent
+
+ checkpoint_path = get_best_checkpoint_path(Path(self.checkpoint_folder_path))
+ if checkpoint_path.is_file():
+ return checkpoint_path
+
+ raise ValueError("Path to best checkpoint not found")
 
 
 class TcgaCrckImageNetMIL(DeepSMILECrck):

azure-pipelines/build-pr.yml

@@ -122,7 +122,7 @@ jobs:
  - name: tag
  value: 'TrainEnsemble'
  - name: more_switches
- value: '--pl_deterministic --log_level=DEBUG --regression_test_folder=RegressionTestResults/PR_TrainEnsemble'
+ value: '--pl_deterministic --log_level=DEBUG --regression_test_folder=RegressionTestResults/PR_TrainEnsemble --regression_test_csv_tolerance=1e-5'
  pool:
  vmImage: 'ubuntu-20.04'
  steps:

environment.yml

@@ -4,7 +4,7 @@ channels:
  - pytorch
  - conda-forge
 dependencies:
- - cudatoolkit=11.1
+ - cudatoolkit=11.3
  - pip=20.1.1
  - python=3.7.3
  - pytorch=1.10.0
@@ -28,6 +28,7 @@ dependencies:
  - gputil==1.4.0
  - h5py==2.10.0
  - ipython==7.31.1
+ - imageio==2.15.0
  - InnerEye-DICOM-RT==1.0.1
  - joblib==0.16.0
  - jupyter==1.0.0