merge master

.dockerignore

@@ -0,0 +1,12 @@
+# Ignore the following files/folders during docker build
+
+__pycache__/
+docs/
+
+.coverage
+.readthedocs.yml
+*.md
+*.toml
+
+!README.md
+

.github/workflows/cron.yml

@@ -56,11 +56,12 @@ jobs:
   cron-docker:
     if: github.repository == 'Project-MONAI/MONAI'
     container:
-      image: docker://projectmonai/monai:latest
+      image: localhost:5000/local_monai:dockerhub # use currently latest, locally available dockerhub image
       options: "--gpus all"
     runs-on: [self-hosted, linux, x64, common]
     steps:
     - name: Run tests report coverage
+      # The docker image process has done the compilation.  BUILD_MONAI=1 may not be necessary.
       run: |
         cd /opt/monai
         nvidia-smi

.github/workflows/setupapp.yml

@@ -149,11 +149,17 @@ jobs:
         ref: master
     - name: docker_build
       run: |
+        # build and run original docker image for local registry
         docker build -t localhost:5000/local_monai:latest -f Dockerfile .
         docker push localhost:5000/local_monai:latest
+        # build once more w/ tag "latest": remove flake package as it is not needed on hub.docker.com
         sed -i '/flake/d' requirements-dev.txt
         docker build -t projectmonai/monai:latest -f Dockerfile .
-        docker login -u projectmonai -p ${{ secrets.DOCKER_PW }}
+        # also push as tag "dockerhub" to local registry
+        docker image tag projectmonai/monai:latest localhost:5000/local_monai:dockerhub
+        docker push localhost:5000/local_monai:dockerhub
+        # distribute as always w/ tag "latest" to hub.docker.com
+        echo "${{ secrets.DOCKER_PW }}" | docker login -u projectmonai --password-stdin
         docker push projectmonai/monai:latest
         docker logout
 

CONTRIBUTING.md

@@ -32,6 +32,8 @@ _Pull request early_
 
 We encourage you to create pull requests early. It helps us track the contributions under development, whether they are ready to be merged or not. Change your pull request's title to begin with `[WIP]` until it is ready for formal review.
 
+Please note that, as per PyTorch, MONAI uses American English spelling. This means classes and variables should be: normali**z**e, visuali**z**e, colo~~u~~r, etc.
+
 ### Preparing pull requests
 To ensure the code quality, MONAI relies on several linting tools ([flake8 and its plugins](https://gitlab.com/pycqa/flake8), [black](https://github.com/psf/black), [isort](https://github.com/timothycrosley/isort)),
 static type analysis tools ([mypy](https://github.com/python/mypy), [pytype](https://github.com/google/pytype)), as well as a set of unit/integration tests.
@@ -58,7 +60,7 @@ pip install -U -r requirements-dev.txt  # install the latest tools
 
 License information: all source code files should start with this paragraph:
 ```
-# Copyright 2020 MONAI Consortium
+# Copyright 2020 - 2021 MONAI Consortium
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -71,6 +73,13 @@ License information: all source code files should start with this paragraph:
 
 ```
 
+##### Exporting modules
+
+If you intend for any variables/functions/classes to be available outside of the file with the edited functionality, then:
+
+- Create or append to the `__all__` variable (in the file in which functionality has been added), and
+- Add to the `__init__.py` file.
+
 #### Unit testing
 MONAI tests are located under `tests/`.
 

Dockerfile

@@ -1,4 +1,4 @@
-# Copyright 2020 MONAI Consortium
+# Copyright 2020 - 2021 MONAI Consortium
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -11,10 +11,11 @@
 
 ARG PYTORCH_IMAGE=nvcr.io/nvidia/pytorch:20.10-py3
 
-FROM ${PYTORCH_IMAGE} as base
+FROM ${PYTORCH_IMAGE}
+
+MAINTAINER MONAI Consortium <monai.miccai2019@gmail.com>
 
 WORKDIR /opt/monai
-ENV PATH=/opt/tools:$PATH
 
 # install full deps
 COPY requirements.txt requirements-min.txt requirements-dev.txt /tmp/
@@ -23,13 +24,24 @@ RUN cp /tmp/requirements.txt /tmp/req.bak \
   && python -m pip install --no-cache-dir --use-feature=2020-resolver -r /tmp/requirements-dev.txt
 
 # compile ext and remove temp files
-COPY . .
+# TODO: remark for issue [revise the dockerfile #1276](https://github.com/Project-MONAI/MONAI/issues/1276)
+# please specify exact files and folders to be copied -- else, basically always, the Docker build process cannot cache
+# this or anything below it and always will build from at most here; one file change leads to no caching from here on...
+
+COPY LICENSE setup.py setup.cfg versioneer.py runtests.sh .gitignore .gitattributes README.md MANIFEST.in ./
+COPY tests ./tests
+COPY monai ./monai
+COPY .git ./.git
 RUN BUILD_MONAI=1 FORCE_CUDA=1 python setup.py develop \
   && rm -rf build __pycache__
 
 # NGC Client
 WORKDIR /opt/tools
-RUN wget -q https://ngc.nvidia.com/downloads/ngccli_cat_linux.zip && \
+ARG NGC_CLI_URI="https://ngc.nvidia.com/downloads/ngccli_cat_linux.zip"
+RUN wget -q ${NGC_CLI_URI} && \
     unzip ngccli_cat_linux.zip && chmod u+x ngc && \
+    md5sum -c ngc.md5 && \
     rm -rf ngccli_cat_linux.zip ngc.md5
+# append /opt/tools to runtime path for NGC CLI to be accessible from all file system locations
+ENV PATH=${PATH}:/opt/tools
 WORKDIR /opt/monai

docs/source/conf.py

@@ -22,7 +22,7 @@
 
 # -- Project information -----------------------------------------------------
 project = "MONAI"
-copyright = "2020 MONAI Consortium"
+copyright = "2020 - 2021 MONAI Consortium"
 author = "MONAI Contributors"
 
 # The full version, including alpha/beta/rc tags

docs/source/losses.rst

@@ -43,6 +43,11 @@ Segmentation Losses
 .. autoclass:: generalized_wasserstein_dice
     :members:
 
+`DiceCELoss`
+~~~~~~~~~~~~
+.. autoclass:: DiceCELoss
+    :members:
+
 `FocalLoss`
 ~~~~~~~~~~~
 .. autoclass:: FocalLoss
@@ -52,3 +57,16 @@ Segmentation Losses
 ~~~~~~~~~~~~~
 .. autoclass:: TverskyLoss
     :members:
+
+Registration Losses
+-------------------
+
+`BendingEnergyLoss`
+~~~~~~~~~~~~~~~~~~~
+.. autoclass:: BendingEnergyLoss
+    :members:
+
+`LocalNormalizedCrossCorrelationLoss`
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. autoclass:: LocalNormalizedCrossCorrelationLoss
+    :members:

docs/source/metrics.rst

@@ -37,7 +37,3 @@ Metrics
 
 .. autoclass:: SurfaceDistanceMetric
     :members:
-
-`Occlusion sensitivity`
------------------------
-.. autofunction:: compute_occlusion_sensitivity

docs/source/networks.rst

@@ -183,6 +183,11 @@ Layers
 ~~~~~~~~~~~~~~~~
 .. autoclass:: GaussianFilter
     :members:
+
+`BilateralFilter`
+~~~~~~~~~~~~~~~~~
+.. autoclass:: BilateralFilter
+    :members:
 
 `HilbertTransform`
 ~~~~~~~~~~~~~~~~~~

docs/source/visualize.rst

@@ -17,4 +17,10 @@ Class activation map
 --------------------
 
 .. automodule:: monai.visualize.class_activation_maps
-  :members:
+  :members:
+
+Occlusion sensitivity
+---------------------
+
+.. automodule:: monai.visualize.occlusion_sensitivity
+  :members:

monai/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2020 MONAI Consortium
+# Copyright 2020 - 2021 MONAI Consortium
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -22,7 +22,7 @@
 __revision_id__ = version_dict.get("full-revisionid", None)
 del get_versions, version_dict
 
-__copyright__ = "(c) 2020 MONAI Consortium"
+__copyright__ = "(c) 2020 - 2021 MONAI Consortium"
 
 __basedir__ = os.path.dirname(__file__)
 

monai/apps/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2020 MONAI Consortium
+# Copyright 2020 - 2021 MONAI Consortium
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -9,5 +9,5 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from .datasets import *
-from .utils import *
+from .datasets import CrossValidation, DecathlonDataset, MedNISTDataset
+from .utils import check_hash, download_and_extract, download_url, extractall

monai/apps/datasets.py

@@ -1,4 +1,4 @@
-# Copyright 2020 MONAI Consortium
+# Copyright 2020 - 2021 MONAI Consortium
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at

monai/apps/utils.py

@@ -1,4 +1,4 @@
-# Copyright 2020 MONAI Consortium
+# Copyright 2020 - 2021 MONAI Consortium
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at

monai/config/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2020 MONAI Consortium
+# Copyright 2020 - 2021 MONAI Consortium
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -9,5 +9,13 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from .deviceconfig import *
-from .type_definitions import *
+from .deviceconfig import (
+    USE_COMPILED,
+    get_gpu_info,
+    get_system_info,
+    print_config,
+    print_debug_info,
+    print_gpu_info,
+    print_system_info,
+)
+from .type_definitions import IndexSelection, KeysCollection

monai/config/deviceconfig.py

@@ -1,4 +1,4 @@
-# Copyright 2020 MONAI Consortium
+# Copyright 2020 - 2021 MONAI Consortium
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -38,6 +38,16 @@
 psutil, has_psutil = optional_import("psutil")
 psutil_version = psutil.__version__ if has_psutil else "NOT INSTALLED or UNKNOWN VERSION."
 
+__all__ = [
+    "print_config",
+    "get_system_info",
+    "print_system_info",
+    "get_gpu_info",
+    "print_gpu_info",
+    "print_debug_info",
+    "USE_COMPILED",
+]
+
 
 def get_config_values():
     """

monai/config/type_definitions.py

@@ -1,4 +1,4 @@
-# Copyright 2020 MONAI Consortium
+# Copyright 2020 - 2021 MONAI Consortium
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -11,6 +11,8 @@
 
 from typing import Collection, Hashable, Iterable, Union
 
+__all__ = ["KeysCollection", "IndexSelection"]
+
 """Commonly used concepts
 This module provides naming and type specifications for commonly used concepts
 within the MONAI package. The intent is to explicitly identify information

monai/csrc/ext.cpp

@@ -1,5 +1,5 @@
 /*
-Copyright 2020 MONAI Consortium
+Copyright 2020 - 2021 MONAI Consortium
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
 You may obtain a copy of the License at
@@ -12,11 +12,16 @@ limitations under the License.
 */
 
 #include <torch/extension.h>
+
+#include "filtering/filtering.h"
 #include "lltm/lltm.h"
 #include "resample/pushpull.h"
 #include "utils/resample_utils.h"
 
 PYBIND11_MODULE(TORCH_EXTENSION_NAME, m) {
+  // filtering
+  m.def("bilateral_filter", &BilateralFilter, "Bilateral Filter");
+
   // lltm
   m.def("lltm_forward", &lltm_forward, "LLTM forward");
   m.def("lltm_backward", &lltm_backward, "LLTM backward");

monai/csrc/filtering/bilateral/bilateral.h

@@ -0,0 +1,42 @@
+/*
+Copyright 2020 - 2021 MONAI Consortium
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+    http://www.apache.org/licenses/LICENSE-2.0
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+*/
+
+#pragma once
+
+#include <torch/extension.h>
+#include "utils/common_utils.h"
+
+torch::Tensor BilateralFilterCpu(torch::Tensor input, float spatial_sigma, float color_sigma);
+torch::Tensor BilateralFilterPHLCpu(torch::Tensor input, float spatial_sigma, float color_sigma);
+
+#ifdef WITH_CUDA
+torch::Tensor BilateralFilterCuda(torch::Tensor input, float spatial_sigma, float color_sigma);
+torch::Tensor BilateralFilterPHLCuda(torch::Tensor input, float spatial_sigma, float color_sigma);
+#endif
+
+torch::Tensor BilateralFilter(torch::Tensor input, float spatial_sigma, float color_sigma, bool usePHL) {
+  torch::Tensor (*filterFunction)(torch::Tensor, float, float);
+
+#ifdef WITH_CUDA
+  if (torch::cuda::is_available() && input.is_cuda()) {
+    CHECK_CONTIGUOUS_CUDA(input);
+    filterFunction = usePHL ? &BilateralFilterPHLCuda : &BilateralFilterCuda;
+  } else {
+    filterFunction = usePHL ? &BilateralFilterPHLCpu : &BilateralFilterCpu;
+  }
+#else
+  filterFunction = usePHL ? &BilateralFilterPHLCpu : &BilateralFilterCpu;
+#endif
+
+  return filterFunction(input, spatial_sigma, color_sigma);
+}