📝 Start ML/SSL API. Fix some formatting issues

microsoft · peterhessey · Aug 16, 2022 · Aug 5, 2022 · Aug 5, 2022 · Aug 8, 2022
commit 6a1273f2a7abb60a97a5bc6964a505e997a9e4ce
diff --git a/InnerEye/ML/SSL/datamodules_and_datasets/transforms_utils.py b/InnerEye/ML/SSL/datamodules_and_datasets/transforms_utils.py
@@ -33,11 +33,11 @@ def get_ssl_transforms_from_config(config: CfgNode,
     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)
+        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.
+        will be added to the transformation passed through the config. This is needed for single channel images as CXR.
     """
     train_transforms = create_transforms_from_config(config, apply_augmentations=True,
                                                      expand_channels=expand_channels)

diff --git a/InnerEye/ML/models/architectures/base_model.py b/InnerEye/ML/models/architectures/base_model.py
@@ -186,8 +186,7 @@ def generate_model_summary(self, crop_size: Optional[TupleInt3] = None,
         When called again with the same crop_size, the summary is not created again.
 
         :param crop_size: The crop size for which the summary should be created. If not provided,
-        the minimum allowed crop size is used.
-
+            the minimum allowed crop size is used.
         :param log_summaries_to_files: whether to write the summary to a file
         """
         if crop_size is None:

diff --git a/InnerEye/ML/models/architectures/unet_3d.py b/InnerEye/ML/models/architectures/unet_3d.py
@@ -43,7 +43,8 @@ class UNetDecodeBlock(torch.nn.Module):
 
         :param channels: A tuple containing the number of input and output channels
         :param upsample_kernel_size: Spatial support of upsampling kernels. If an integer is provided, the same value
-        will be repeated for all three dimensions. For non-cubic kernels please pass a list or tuple with three elements
+            will be repeated for all three dimensions. For non-cubic kernels please pass a list or tuple with three
+            elements.
 
         :param upsampling_stride: Upsamling factor used in deconvolutional layer. Similar to the `upsample_kernel_size`
         parameter, if an integer is passed, the same upsampling factor will be used for all three dimensions.

diff --git a/InnerEye/ML/pipelines/inference.py b/InnerEye/ML/pipelines/inference.py
@@ -202,12 +202,12 @@ def create_from_checkpoint(path_to_checkpoint: Path,
         If there is no checkpoint file for the given epoch, return None.
 
         :param path_to_checkpoint: The path to the checkpoint that we want to load
-        model_config.checkpoint_folder
-
+            model_config.checkpoint_folder
         :param model_config: Model related configurations.
         :param pipeline_id: Numeric identifier for the pipeline (useful for logging when ensembling)
-        :return InferencePipeline: an instantiated inference pipeline instance, or None if there was no checkpoint
-        file for this epoch.
+
+        :returns InferencePipeline: an instantiated inference pipeline instance, or None if there was no checkpoint
+            file for this epoch.
         """
         if not path_to_checkpoint.is_file():
             # not raising a value error here: This is used to create individual pipelines for ensembles,

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -61,7 +61,7 @@
 
 # -- Options for HTML output -------------------------------------------------
 
-# The theme to use for HTML and HTML Help pages.  See the documentation for
+# The theme to use for HTML and HTML Help pages.  See the documentation fora
 # a list of builtin themes.
 #
 html_theme = 'furo'

diff --git a/docs/source/rst/api/ML/SSL/datamodules_and_datasets/index.rst b/docs/source/rst/api/ML/SSL/datamodules_and_datasets/index.rst
@@ -0,0 +1,26 @@
+SSL Datamodules and Datasets
+============================
+
+Datasets
+----------
+
+.. automodule:: InnerEye.ML.SSL.datamodules_and_datasets.cifar_datasets
+
+.. automodule:: InnerEye.ML.SSL.datamodules_and_datasets.cxr_datasets
+
+
+Dataset Class Utils
+--------------------
+
+.. automodule:: InnerEye.ML.SSL.datamodules_and_datasets.dataset_cls_utils
+
+Datamodules
+-----------
+
+.. automodule:: InnerEye.ML.SSL.datamodules_and_datasets.datamodules
+
+
+Transformation Utils
+--------------------
+
+.. automodule:: InnerEye.ML.SSL.datamodules_and_datasets.transforms_utils
diff --git a/docs/source/rst/api/ML/SSL/index.rst b/docs/source/rst/api/ML/SSL/index.rst
@@ -1,2 +1,8 @@
-SSL
-===
+Self-Supervised Learning (SSL)
+==============================
+
+.. toctree::
+    lightning_containers/index
+    lightning_modules/index
+    datamodules_and_datasets/index
+    utils/index
diff --git a/docs/source/rst/api/ML/SSL/lightning_containers/index.rst b/docs/source/rst/api/ML/SSL/lightning_containers/index.rst
@@ -0,0 +1,2 @@
+SSL Lightning Containers
+========================
diff --git a/docs/source/rst/api/ML/SSL/lightning_modules/index.rst b/docs/source/rst/api/ML/SSL/lightning_modules/index.rst
@@ -0,0 +1,2 @@
+SSL Lightning Modules
+=====================
diff --git a/docs/source/rst/api/ML/SSL/utils/index.rst b/docs/source/rst/api/ML/SSL/utils/index.rst
@@ -0,0 +1,2 @@
+SSL Utils
+==========
diff --git a/docs/source/rst/api/ML/configs.rst b/docs/source/rst/api/ML/configs.rst
diff --git a/docs/source/rst/api/ML/index.rst b/docs/source/rst/api/ML/index.rst
@@ -7,6 +7,8 @@ Machine learning
    models/index
    dataset/index
    augmentations/index
+   pipelines/index
+   SSL/index
+   utils/index
    runner
    photometric_normalization
-   pipelines
diff --git a/docs/source/rst/api/ML/pipelines.rst b/docs/source/rst/api/ML/pipelines.rst
diff --git a/docs/source/rst/api/ML/pipelines/index.rst b/docs/source/rst/api/ML/pipelines/index.rst
@@ -1,2 +1,13 @@
 Pipelines
 =========
+
+Inference
+---------
+
+.. automodule:: InnerEye.ML.pipelines.inference
+
+.. automodule:: InnerEye.ML.pipelines.scalar_inference
+
+Enesemble
+---------
+.. automodule:: InnerEye.ML.pipelines.ensemble