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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 <vennw@nvidia.com> * remove duplicate places Signed-off-by: Yiheng Wang <vennw@nvidia.com> 4105 drops pt16 support (Project-MONAI#4106) * update sys req Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp test Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update code for torch>=1.7 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * autofix Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes import Signed-off-by: Wenqi Li <wenqil@nvidia.com> * clear cache Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove temp cmd Signed-off-by: Wenqi Li <wenqil@nvidia.com> Make `pixelshuffle` scriptable (Project-MONAI#4109) * Update the existing functionality to comply with the `torchscript.jit.script` function. Signed-off-by: Ramon Emiliani <ramon@afxmedical.com> meta tensor (Project-MONAI#4077) * meta tensor Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> 4084 Add kwargs for `Tensor.to()` in engines (Project-MONAI#4112) * [DLMED] add kwargs for to() API Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> fixes pytorch version tests (Project-MONAI#4127) Signed-off-by: Wenqi Li <wenqil@nvidia.com> update meta tensor api (Project-MONAI#4131) * update meta tensor api Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> runtests.sh isort (Project-MONAI#4134) Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> update citation (Project-MONAI#4133) Signed-off-by: Wenqi Li <wenqil@nvidia.com> `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 <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> [DLMED] fix file name in meta (Project-MONAI#4145) Signed-off-by: Nic Ma <nma@nvidia.com> 4116 Add support for advanced args of AMP (Project-MONAI#4132) * [DLMED] fix typo in bundle scripts Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add support for AMP args Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] fix flake8 Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> 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)
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‎.github/workflows/cron.yml‎

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runs-on: [self-hosted, linux, x64, common]
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strategy:
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matrix:
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pytorch-version: [1.6.0, 1.7.1, 1.8.1, 1.9.1, latest]
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pytorch-version: [1.7.1, 1.8.1, 1.9.1, 1.10.2, latest]
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steps:
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- uses: actions/checkout@v2
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- name: Install the dependencies
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python -m pip install --upgrade pip wheel
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python -m pip uninstall -y torch torchvision
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if [ ${{ matrix.pytorch-version }} == "latest" ]; then
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python -m pip install torch torchvision
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elif [ ${{ matrix.pytorch-version }} == "1.6.0" ]; then
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python -m pip install torch==1.6.0 torchvision==0.7.0
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python -m pip install torch torchvision --extra-index-url https://download.pytorch.org/whl/cu113
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elif [ ${{ matrix.pytorch-version }} == "1.7.1" ]; then
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python -m pip install torch==1.7.1 torchvision==0.8.2
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python -m pip install torch==1.7.1 torchvision==0.8.2 --extra-index-url https://download.pytorch.org/whl/cu113
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elif [ ${{ matrix.pytorch-version }} == "1.8.1" ]; then
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python -m pip install torch==1.8.1 torchvision==0.9.1
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python -m pip install torch==1.8.1 torchvision==0.9.1 --extra-index-url https://download.pytorch.org/whl/cu113
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elif [ ${{ matrix.pytorch-version }} == "1.9.1" ]; then
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python -m pip install torch==1.9.1 torchvision==0.10.1
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python -m pip install torch==1.9.1 torchvision==0.10.1 --extra-index-url https://download.pytorch.org/whl/cu113
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elif [ ${{ matrix.pytorch-version }} == "1.10.2" ]; then
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python -m pip install torch==1.10.2 torchvision==0.11.3 --extra-index-url https://download.pytorch.org/whl/cu113
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fi
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python -m pip install -r requirements-dev.txt
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python -m pip list

‎.github/workflows/pythonapp-gpu.yml‎

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pytorch: "-h"
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base: "nvcr.io/nvidia/pytorch:22.03-py3"
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- environment: PT110+CUDA102
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pytorch: "torch==1.10.1 torchvision==0.11.2"
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pytorch: "torch==1.10.2 torchvision==0.11.3"
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base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
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- environment: PT111+CUDA102
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pytorch: "torch==1.11.0 torchvision==0.12.0"

‎.github/workflows/pythonapp-min.yml‎

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strategy:
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fail-fast: false
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matrix:
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pytorch-version: [1.6.0, 1.7.1, 1.8.1, 1.9.1, 1.10.1, latest]
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pytorch-version: [1.7.1, 1.8.1, 1.9.1, 1.10.2, latest]
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timeout-minutes: 40
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steps:
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- uses: actions/checkout@v2
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# min. requirements
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if [ ${{ matrix.pytorch-version }} == "latest" ]; then
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python -m pip install torch
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elif [ ${{ matrix.pytorch-version }} == "1.6.0" ]; then
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python -m pip install torch==1.6.0
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elif [ ${{ matrix.pytorch-version }} == "1.7.1" ]; then
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python -m pip install torch==1.7.1
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elif [ ${{ matrix.pytorch-version }} == "1.8.1" ]; then
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python -m pip install torch==1.8.1
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elif [ ${{ matrix.pytorch-version }} == "1.9.1" ]; then
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python -m pip install torch==1.9.1
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elif [ ${{ matrix.pytorch-version }} == "1.10.1" ]; then
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python -m pip install torch==1.10.1
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elif [ ${{ matrix.pytorch-version }} == "1.10.2" ]; then
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python -m pip install torch==1.10.2
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fi
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python -m pip install -r requirements-min.txt
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python -m pip list

‎.github/workflows/pythonapp.yml‎

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# install the latest pytorch for testing
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# however, "pip install monai*.tar.gz" will build cpp/cuda with an isolated
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# fresh torch installation according to pyproject.toml
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python -m pip install torch>=1.6 torchvision
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python -m pip install torch>=1.7 torchvision
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- name: Check packages
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run: |
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pip uninstall monai

‎CITATION.cff‎

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abstract: "AI Toolkit for Healthcare Imaging"
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authors:
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- name: "MONAI Consortium"
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date-released: 2020-03-28
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version: "0.6.0"
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doi: "10.5281/zenodo.4323058"
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date-released: 2022-02-16
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version: "0.8.1"
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identifiers:
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- description: "This DOI represents all versions of MONAI, and will always resolve to the latest one."
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type: doi
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value: "10.5281/zenodo.4323058"
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license: "Apache-2.0"
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repository-code: "https://github.com/Project-MONAI/MONAI"
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cff-version: "1.1.0"
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url: "https://monai.io"
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cff-version: "1.2.0"
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message: "If you use this software, please cite it using these metadata."
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...

‎docs/source/data.rst‎

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.. autoclass:: PILReader
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:members:
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Whole slide image reader
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------------------------
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BaseWSIReader
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~~~~~~~~~~~~~
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.. autoclass:: BaseWSIReader
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:members:
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WSIReader
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~~~~~~~~~
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.. autoclass:: WSIReader
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:members:
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CuCIMWSIReader
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~~~~~~~~~~~~~~
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.. autoclass:: CuCIMWSIReader
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:members:
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Image writer
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------------
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TestTimeAugmentation
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~~~~~~~~~~~~~~~~~~~~
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.. autoclass:: monai.data.TestTimeAugmentation
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Meta Object
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-----------
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.. automodule:: monai.data.meta_obj
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:members:
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MetaTensor
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----------
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.. autoclass:: monai.data.MetaTensor
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:members:

‎docs/source/transforms.rst‎

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:members:
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:special-members: __call__
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MetaTensor
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^^^^^^^^^^
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`ToMetaTensord`
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"""""""""""""""
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.. autoclass:: ToMetaTensord
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:members:
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:special-members: __call__
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`FromMetaTensord`
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"""""""""""""""""
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.. autoclass:: FromMetaTensord
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:members:
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:special-members: __call__
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Transform Adaptors
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------------------
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.. automodule:: monai.transforms.adaptors

‎monai/bundle/scripts.py‎

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.. code-block:: bash
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python -m monai.bundle export network --filepath <export path> --ckpt_file <checkpoint path> ...
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python -m monai.bundle ckpt_export network --filepath <export path> --ckpt_file <checkpoint path> ...
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**override,
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_log_input_summary(tag="export", args=_args)
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_log_input_summary(tag="ckpt_export", args=_args)
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filepath_, ckpt_file_, config_file_, net_id_, meta_file_, key_in_ckpt_ = _pop_args(
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_args, "filepath", "ckpt_file", "config_file", net_id="", meta_file=None, key_in_ckpt=""
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)

‎monai/data/__init__.py‎

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from .folder_layout import FolderLayout
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from .grid_dataset import GridPatchDataset, PatchDataset, PatchIter, PatchIterd
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from .image_dataset import ImageDataset
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from .image_reader import ImageReader, ITKReader, NibabelReader, NumpyReader, PILReader, WSIReader
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from .image_reader import ImageReader, ITKReader, NibabelReader, NumpyReader, PILReader
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from .image_writer import (
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SUPPORTED_WRITERS,
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ImageWriter,
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resolve_writer,
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)
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from .iterable_dataset import CSVIterableDataset, IterableDataset, ShuffleBuffer
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from .meta_obj import MetaObj, get_track_meta, get_track_transforms, set_track_meta, set_track_transforms
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from .meta_tensor import MetaTensor
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from .nifti_saver import NiftiSaver
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from .nifti_writer import write_nifti
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from .png_saver import PNGSaver
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worker_init_fn,
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zoom_affine,
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)
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from .wsi_reader import BaseWSIReader, CuCIMWSIReader, WSIReader

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