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Add padding to filter to ensure same size after anti-aliasing Use replicate padding insteadof zero padding to avoid artifacts for non-zero boundary Reuse GaussianSmooth 4073 Enhance DynUNet doc-strings (Project-MONAI#4102) * Fix doc strings error Signed-off-by: Yiheng Wang <[email protected]> * remove duplicate places Signed-off-by: Yiheng Wang <[email protected]> 4105 drops pt16 support (Project-MONAI#4106) * update sys req Signed-off-by: Wenqi Li <[email protected]> * temp test Signed-off-by: Wenqi Li <[email protected]> * update code for torch>=1.7 Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * fixes tests Signed-off-by: Wenqi Li <[email protected]> * autofix Signed-off-by: Wenqi Li <[email protected]> * fixes import Signed-off-by: Wenqi Li <[email protected]> * clear cache Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * remove temp cmd Signed-off-by: Wenqi Li <[email protected]> Make `pixelshuffle` scriptable (Project-MONAI#4109) * Update the existing functionality to comply with the `torchscript.jit.script` function. Signed-off-by: Ramon Emiliani <[email protected]> meta tensor (Project-MONAI#4077) * meta tensor Signed-off-by: Richard Brown <[email protected]> 4084 Add kwargs for `Tensor.to()` in engines (Project-MONAI#4112) * [DLMED] add kwargs for to() API Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]> fixes pytorch version tests (Project-MONAI#4127) Signed-off-by: Wenqi Li <[email protected]> update meta tensor api (Project-MONAI#4131) * update meta tensor api Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> runtests.sh isort (Project-MONAI#4134) Signed-off-by: Richard Brown <[email protected]> update citation (Project-MONAI#4133) Signed-off-by: Wenqi Li <[email protected]> `ToMetaTensor` and `FromMetaTensor` transforms (Project-MONAI#4115) to and from meta no skip if before pytorch 1.7 (Project-MONAI#4139) * no skip if before pytorch 1.7 Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> [DLMED] fix file name in meta (Project-MONAI#4145) Signed-off-by: Nic Ma <[email protected]> 4116 Add support for advanced args of AMP (Project-MONAI#4132) * [DLMED] fix typo in bundle scripts Signed-off-by: Nic Ma <[email protected]> * [DLMED] add support for AMP args Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]> New wsireader (Project-MONAI#4147) `MetaTensor`: collate; decollate; dataset; dataloader; out=; indexing and iterating across batches (Project-MONAI#4137) `MetaTensor`: collate; decollate; dataset; dataloader; out=; indexing and iterating across batches (Project-MONAI#4137)
Can-Zhao · May 10, 2022 · 4379e90 · 4379e90
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diff --git a/.github/workflows/cron.yml b/.github/workflows/cron.yml
@@ -15,7 +15,7 @@ jobs:
     runs-on: [self-hosted, linux, x64, common]
     strategy:
       matrix:
-        pytorch-version: [1.6.0, 1.7.1, 1.8.1, 1.9.1, latest]
+        pytorch-version: [1.7.1, 1.8.1, 1.9.1, 1.10.2, latest]
     steps:
     - uses: actions/checkout@v2
     - name: Install the dependencies
@@ -24,15 +24,15 @@ jobs:
         python -m pip install --upgrade pip wheel
         python -m pip uninstall -y torch torchvision
         if [ ${{ matrix.pytorch-version }} == "latest" ]; then
-          python -m pip install torch torchvision
-        elif [ ${{ matrix.pytorch-version }} == "1.6.0" ]; then
-          python -m pip install torch==1.6.0 torchvision==0.7.0
+          python -m pip install torch torchvision --extra-index-url https://download.pytorch.org/whl/cu113
         elif [ ${{ matrix.pytorch-version }} == "1.7.1" ]; then
-          python -m pip install torch==1.7.1 torchvision==0.8.2
+          python -m pip install torch==1.7.1 torchvision==0.8.2 --extra-index-url https://download.pytorch.org/whl/cu113
         elif [ ${{ matrix.pytorch-version }} == "1.8.1" ]; then
-          python -m pip install torch==1.8.1 torchvision==0.9.1
+          python -m pip install torch==1.8.1 torchvision==0.9.1 --extra-index-url https://download.pytorch.org/whl/cu113
         elif [ ${{ matrix.pytorch-version }} == "1.9.1" ]; then
-          python -m pip install torch==1.9.1 torchvision==0.10.1
+          python -m pip install torch==1.9.1 torchvision==0.10.1 --extra-index-url https://download.pytorch.org/whl/cu113
+        elif [ ${{ matrix.pytorch-version }} == "1.10.2" ]; then
+          python -m pip install torch==1.10.2 torchvision==0.11.3 --extra-index-url https://download.pytorch.org/whl/cu113
         fi
         python -m pip install -r requirements-dev.txt
         python -m pip list

diff --git a/.github/workflows/pythonapp-gpu.yml b/.github/workflows/pythonapp-gpu.yml
@@ -50,7 +50,7 @@ jobs:
             pytorch: "-h"
             base: "nvcr.io/nvidia/pytorch:22.03-py3"
           - environment: PT110+CUDA102
-            pytorch: "torch==1.10.1 torchvision==0.11.2"
+            pytorch: "torch==1.10.2 torchvision==0.11.3"
             base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
           - environment: PT111+CUDA102
             pytorch: "torch==1.11.0 torchvision==0.12.0"

diff --git a/.github/workflows/pythonapp-min.yml b/.github/workflows/pythonapp-min.yml
@@ -119,7 +119,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        pytorch-version: [1.6.0, 1.7.1, 1.8.1, 1.9.1, 1.10.1, latest]
+        pytorch-version: [1.7.1, 1.8.1, 1.9.1, 1.10.2, latest]
     timeout-minutes: 40
     steps:
     - uses: actions/checkout@v2
@@ -148,16 +148,14 @@ jobs:
         # min. requirements
         if [ ${{ matrix.pytorch-version }} == "latest" ]; then
           python -m pip install torch
-        elif [ ${{ matrix.pytorch-version }} == "1.6.0" ]; then
-          python -m pip install torch==1.6.0
         elif [ ${{ matrix.pytorch-version }} == "1.7.1" ]; then
           python -m pip install torch==1.7.1
         elif [ ${{ matrix.pytorch-version }} == "1.8.1" ]; then
           python -m pip install torch==1.8.1
         elif [ ${{ matrix.pytorch-version }} == "1.9.1" ]; then
           python -m pip install torch==1.9.1
-        elif [ ${{ matrix.pytorch-version }} == "1.10.1" ]; then
-          python -m pip install torch==1.10.1
+        elif [ ${{ matrix.pytorch-version }} == "1.10.2" ]; then
+          python -m pip install torch==1.10.2
         fi
         python -m pip install -r requirements-min.txt
         python -m pip list

diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml
@@ -137,7 +137,7 @@ jobs:
         # install the latest pytorch for testing
         # however, "pip install monai*.tar.gz" will build cpp/cuda with an isolated
         # fresh torch installation according to pyproject.toml
-        python -m pip install torch>=1.6 torchvision
+        python -m pip install torch>=1.7 torchvision
     - name: Check packages
       run: |
         pip uninstall monai

diff --git a/CITATION.cff b/CITATION.cff
@@ -6,11 +6,15 @@ title: "MONAI: Medical Open Network for AI"
 abstract: "AI Toolkit for Healthcare Imaging"
 authors:
   - name: "MONAI Consortium"
-date-released: 2020-03-28
-version: "0.6.0"
-doi: "10.5281/zenodo.4323058"
+date-released: 2022-02-16
+version: "0.8.1"
+identifiers:
+  - description: "This DOI represents all versions of MONAI, and will always resolve to the latest one."
+    type: doi
+    value: "10.5281/zenodo.4323058"
 license: "Apache-2.0"
 repository-code: "https://github.com/Project-MONAI/MONAI"
-cff-version: "1.1.0"
+url: "https://monai.io"
+cff-version: "1.2.0"
 message: "If you use this software, please cite it using these metadata."
 ...
diff --git a/docs/source/data.rst b/docs/source/data.rst
@@ -152,11 +152,24 @@ PILReader
 .. autoclass:: PILReader
   :members:
 
+Whole slide image reader
+------------------------
+
+BaseWSIReader
+~~~~~~~~~~~~~
+.. autoclass:: BaseWSIReader
+  :members:
+
 WSIReader
 ~~~~~~~~~
 .. autoclass:: WSIReader
   :members:
 
+CuCIMWSIReader
+~~~~~~~~~~~~~~
+.. autoclass:: CuCIMWSIReader
+  :members:
+
 Image writer
 ------------
 
@@ -271,3 +284,14 @@ ThreadDataLoader
 TestTimeAugmentation
 ~~~~~~~~~~~~~~~~~~~~
 .. autoclass:: monai.data.TestTimeAugmentation
+
+
+Meta Object
+-----------
+.. automodule:: monai.data.meta_obj
+    :members:
+
+MetaTensor
+----------
+.. autoclass:: monai.data.MetaTensor
+   :members:
diff --git a/docs/source/transforms.rst b/docs/source/transforms.rst
@@ -1842,6 +1842,21 @@ Utility (Dict)
     :members:
     :special-members: __call__
 
+MetaTensor
+^^^^^^^^^^
+
+`ToMetaTensord`
+"""""""""""""""
+.. autoclass:: ToMetaTensord
+    :members:
+    :special-members: __call__
+
+`FromMetaTensord`
+"""""""""""""""""
+.. autoclass:: FromMetaTensord
+    :members:
+    :special-members: __call__
+
 Transform Adaptors
 ------------------
 .. automodule:: monai.transforms.adaptors

diff --git a/monai/bundle/scripts.py b/monai/bundle/scripts.py
@@ -363,7 +363,7 @@ def ckpt_export(
 
     .. code-block:: bash
 
-        python -m monai.bundle export network --filepath <export path> --ckpt_file <checkpoint path> ...
+        python -m monai.bundle ckpt_export network --filepath <export path> --ckpt_file <checkpoint path> ...
 
     Args:
         net_id: ID name of the network component in the config, it must be `torch.nn.Module`.
@@ -390,7 +390,7 @@ def ckpt_export(
         key_in_ckpt=key_in_ckpt,
         **override,
     )
-    _log_input_summary(tag="export", args=_args)
+    _log_input_summary(tag="ckpt_export", args=_args)
     filepath_, ckpt_file_, config_file_, net_id_, meta_file_, key_in_ckpt_ = _pop_args(
         _args, "filepath", "ckpt_file", "config_file", net_id="", meta_file=None, key_in_ckpt=""
     )

diff --git a/monai/data/__init__.py b/monai/data/__init__.py
@@ -34,7 +34,7 @@
 from .folder_layout import FolderLayout
 from .grid_dataset import GridPatchDataset, PatchDataset, PatchIter, PatchIterd
 from .image_dataset import ImageDataset
-from .image_reader import ImageReader, ITKReader, NibabelReader, NumpyReader, PILReader, WSIReader
+from .image_reader import ImageReader, ITKReader, NibabelReader, NumpyReader, PILReader
 from .image_writer import (
     SUPPORTED_WRITERS,
     ImageWriter,
@@ -46,6 +46,8 @@
     resolve_writer,
 )
 from .iterable_dataset import CSVIterableDataset, IterableDataset, ShuffleBuffer
+from .meta_obj import MetaObj, get_track_meta, get_track_transforms, set_track_meta, set_track_transforms
+from .meta_tensor import MetaTensor
 from .nifti_saver import NiftiSaver
 from .nifti_writer import write_nifti
 from .png_saver import PNGSaver
@@ -85,3 +87,4 @@
     worker_init_fn,
     zoom_affine,
 )
+from .wsi_reader import BaseWSIReader, CuCIMWSIReader, WSIReader