Merge pull request #32 from Project-MONAI/master

merge master

Author: Nic-Ma

.github/workflows/cron.yml

@@ -53,6 +53,38 @@ jobs:
         fail_ci_if_error: false
         file: ./coverage.xml
 
+  cron-pt-image:
+    if: github.repository == 'Project-MONAI/MONAI'
+    container:
+      image: nvcr.io/nvidia/pytorch:20.12-py3  # testing with the latest pytorch base image
+      options: "--gpus all"
+    runs-on: [self-hosted, linux, x64, common]
+    steps:
+    - uses: actions/checkout@v2
+    - name: Install the dependencies
+      run: |
+        which python
+        python -m pip install --upgrade pip wheel
+        python -m pip install -r requirements-dev.txt
+        python -m pip list
+    - name: Run tests report coverage
+      run: |
+        export LAUNCH_DELAY=$[ $RANDOM % 16 * 60 ]
+        echo "Sleep $LAUNCH_DELAY"
+        sleep $LAUNCH_DELAY
+        nvidia-smi
+        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
+        echo $CUDA_VISIBLE_DEVICES
+        python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
+        python -c 'import torch; print(torch.rand(5,3, device=torch.device("cuda:0")))'
+        BUILD_MONAI=1 ./runtests.sh --coverage
+        coverage xml
+    - name: Upload coverage
+      uses: codecov/codecov-action@v1
+      with:
+        fail_ci_if_error: false
+        file: ./coverage.xml
+
   cron-docker:
     if: github.repository == 'Project-MONAI/MONAI'
     container:
@@ -61,7 +93,8 @@ jobs:
     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.
+      # The docker image process has done the compilation.
+      # BUILD_MONAI=1 is necessary for triggering the USE_COMPILED flag.
       run: |
         cd /opt/monai
         nvidia-smi

Dockerfile

@@ -9,7 +9,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-ARG PYTORCH_IMAGE=nvcr.io/nvidia/pytorch:20.10-py3
+ARG PYTORCH_IMAGE=nvcr.io/nvidia/pytorch:20.12-py3
 
 FROM ${PYTORCH_IMAGE}
 
@@ -21,7 +21,8 @@ WORKDIR /opt/monai
 COPY requirements.txt requirements-min.txt requirements-dev.txt /tmp/
 RUN cp /tmp/requirements.txt /tmp/req.bak \
   && awk '!/torch/' /tmp/requirements.txt > /tmp/tmp && mv /tmp/tmp /tmp/requirements.txt \
-  && python -m pip install --no-cache-dir --use-feature=2020-resolver -r /tmp/requirements-dev.txt
+  && python -m pip install --upgrade --no-cache-dir pip \
+  && python -m pip install --no-cache-dir -r /tmp/requirements-dev.txt
 
 # compile ext and remove temp files
 # TODO: remark for issue [revise the dockerfile #1276](https://github.com/Project-MONAI/MONAI/issues/1276)

docs/requirements.txt

@@ -2,7 +2,7 @@
 torch>=1.5
 pytorch-ignite==0.4.2
 numpy>=1.17
-itk
+itk>=5.0
 nibabel
 parameterized
 scikit-image>=0.14.2

docs/source/apps.rst

@@ -28,3 +28,27 @@ Applications
 .. autofunction:: extractall
 
 .. autofunction:: download_and_extract
+
+`Deepgrow`
+----------
+
+.. automodule:: monai.apps.deepgrow.dataset
+.. autofunction:: create_dataset
+
+.. automodule:: monai.apps.deepgrow.interaction
+.. autoclass:: Interaction
+    :members:
+
+.. automodule:: monai.apps.deepgrow.transforms
+.. autoclass:: AddInitialSeedPointd
+    :members:
+.. autoclass:: AddGuidanceSignald
+    :members:
+.. autoclass:: AddRandomGuidanced
+    :members:
+.. autoclass:: SpatialCropForegroundd
+    :members:
+.. autoclass:: FindDiscrepancyRegionsd
+    :members:
+.. autoclass:: FindAllValidSlicesd
+    :members:

docs/source/handlers.rst

@@ -85,6 +85,9 @@ Training stats handler
 
 Tensorboard handlers
 --------------------
+.. autoclass:: TensorBoardHandler
+    :members:
+
 .. autoclass:: TensorBoardStatsHandler
     :members:
 

docs/source/losses.rst

@@ -74,4 +74,12 @@ Registration Losses
 `GlobalMutualInformationLoss`
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 .. autoclass:: GlobalMutualInformationLoss
+    :members:
+
+Loss Wrappers
+--------------
+
+`MultiScaleLoss`
+~~~~~~~~~~~~~~~~~
+.. autoclass:: MultiScaleLoss
     :members:

docs/source/networks.rst

@@ -120,12 +120,12 @@ Blocks
 .. autoclass:: SubpixelUpSample
 
 `LocalNet DownSample Block`
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
 .. autoclass:: LocalNetDownSampleBlock
     :members:
 
 `LocalNet UpSample Block`
-~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~
 .. autoclass:: LocalNetUpSampleBlock
     :members:
 
@@ -135,10 +135,15 @@ Blocks
     :members:
 
 `Warp`
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~
 .. autoclass:: Warp
     :members:
 
+`DVF2DDF`
+~~~~~~~~~
+.. autoclass:: DVF2DDF
+    :members:
+
 Layers
 ------
 
@@ -201,7 +206,7 @@ Layers
 ~~~~~~~~~~~~~~~~
 .. autoclass:: GaussianFilter
     :members:
-    
+
 `BilateralFilter`
 ~~~~~~~~~~~~~~~~~
 .. autoclass:: BilateralFilter

docs/source/transforms.rst

@@ -237,6 +237,12 @@ IO
     :members:
     :special-members: __call__
 
+`SaveImage`
+"""""""""""
+.. autoclass:: SaveImage
+    :members:
+    :special-members: __call__
+
 Post-processing
 ^^^^^^^^^^^^^^^
 
@@ -702,6 +708,12 @@ IO (Dict)
     :members:
     :special-members: __call__
 
+`SaveImaged`
+""""""""""""
+.. autoclass:: SaveImaged
+    :members:
+    :special-members: __call__
+
 Post-processing (Dict)
 ^^^^^^^^^^^^^^^^^^^^^^
 
@@ -939,6 +951,12 @@ Utility (Dict)
     :members:
     :special-members: __call__
 
+`RandLambdad`
+"""""""""""""
+.. autoclass:: RandLambdad
+    :members:
+    :special-members: __call__
+
 `LabelToMaskd`
 """"""""""""""
 .. autoclass:: LabelToMaskd

monai/apps/datasets.py

@@ -94,7 +94,9 @@ def __init__(
         data = self._generate_data_list(dataset_dir)
         if transform == ():
             transform = LoadImaged("image")
-        super().__init__(data, transform, cache_num=cache_num, cache_rate=cache_rate, num_workers=num_workers)
+        CacheDataset.__init__(
+            self, data, transform, cache_num=cache_num, cache_rate=cache_rate, num_workers=num_workers
+        )
 
     def randomize(self, data: Optional[Any] = None) -> None:
         self.rann = self.R.random()
@@ -275,7 +277,9 @@ def __init__(
         self._properties = load_decathlon_properties(os.path.join(dataset_dir, "dataset.json"), property_keys)
         if transform == ():
             transform = LoadImaged(["image", "label"])
-        super().__init__(data, transform, cache_num=cache_num, cache_rate=cache_rate, num_workers=num_workers)
+        CacheDataset.__init__(
+            self, data, transform, cache_num=cache_num, cache_rate=cache_rate, num_workers=num_workers
+        )
 
     def get_indices(self) -> np.ndarray:
         """

monai/apps/deepgrow/__init__.py

@@ -0,0 +1,10 @@
+# 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.