450 update AsDiscrete #451
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Signed-off-by: Yiheng Wang <vennw@nvidia.com>
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Signed-off-by: Yiheng Wang <vennw@nvidia.com>
Signed-off-by: Yiheng Wang <vennw@nvidia.com>
Signed-off-by: Yiheng Wang <vennw@nvidia.com>
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Most of the tutorials have been tested without errors.
Wish authors of these tutorials can help to test them after this PR is merged. I found two bugs when testing:
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wyli
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Nov 26, 2021
wyli
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Dec 1, 2021
* initialize dints tutorials Signed-off-by: dongy <dongy@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <dongy@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * Update README.md * Update README.md * update scripts Signed-off-by: dongy <dongy@nvidia.com> * Change Dints interface * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Modify scripts for new Dints interface * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * Test push * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update readme Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * Add readme * Update readme * Change lr in search * update readme Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * Enable single GPU * update readme Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * Add visualization tutorial transform image (#448) * [DLMED] add visualization tutorial Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add image Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update notebook Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update notebook Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add reference image Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix PEP error Signed-off-by: Nic Ma <nma@nvidia.com> * Update spleen_segmentation_3d.ipynb (#455) The `pip install` statement is missing pytorch-ignite. Changing: `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm]"` to `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm, ignite]"` * Figures added, pretrained weights link added, minor fixes (#456) * Figures added, pretrained weights link added, minor fixes Signed-off-by: vnath <vnath@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: vnath <vnath@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add itkwidgets example in notebook (#454) * [DLMED] add itkwidgets Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add reference screenshot Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update to PLS orientation Signed-off-by: Nic Ma <nma@nvidia.com> * MIL example (#431) * MIL example Signed-off-by: myron <amyronenko@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <amyronenko@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <amyronenko@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * small updates Signed-off-by: myron <amyronenko@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated images Signed-off-by: myron <amyronenko@nvidia.com> * gdown for json Signed-off-by: myron <amyronenko@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update README Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Fix formatting and typos Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * small fixes Signed-off-by: myron <amyronenko@nvidia.com> * stats Signed-off-by: myron <amyronenko@nvidia.com> * pip install Signed-off-by: myron <amyronenko@nvidia.com> * README fixes Signed-off-by: myron <amyronenko@nvidia.com> Co-authored-by: am <am> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Behrooz <3968947+drbeh@users.noreply.github.com> Co-authored-by: Nic Ma <nma@nvidia.com> * 450 update AsDiscrete (#451) * update asdiscrete Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update postprocessing figures Signed-off-by: Yiheng Wang <vennw@nvidia.com> * fix version error of mutual info Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update to use include in torchin Signed-off-by: Yiheng Wang <vennw@nvidia.com> * 459 update nvidia flare 2.0 example (#460) * update nvidia flare 2.0 example Signed-off-by: Yiheng Wang <vennw@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * enhance code format Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update folder and readme Signed-off-by: Yiheng Wang <vennw@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Weights Link Updated (#465) Signed-off-by: vnath <vnath@nvidia.com> Co-authored-by: vnath <vnath@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixes readme typos Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update readmes Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update readme Signed-off-by: Wenqi Li <wenqil@nvidia.com> * qa commit Signed-off-by: Wenqi Li <wenqil@nvidia.com> * link Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: dongy <dongy@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: heyufan1995 <heyufan1995@gmail.com> Co-authored-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> Co-authored-by: Nic Ma <nma@nvidia.com> Co-authored-by: nvahmadi <85887144+nvahmadi@users.noreply.github.com> Co-authored-by: Vishwesh <vishwesh.nath@gmail.com> Co-authored-by: vnath <vnath@nvidia.com> Co-authored-by: myron <myron@users.noreply.github.com> Co-authored-by: Behrooz <3968947+drbeh@users.noreply.github.com> Co-authored-by: Yiheng Wang <68361391+yiheng-wang-nv@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>
wyli
pushed a commit
that referenced
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Dec 7, 2021
* initialize dints tutorials Signed-off-by: dongy <dongy@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <dongy@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * Update README.md * Update README.md * update scripts Signed-off-by: dongy <dongy@nvidia.com> * Change Dints interface * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Modify scripts for new Dints interface * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * Test push * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update readme Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * Add readme * Update readme * Change lr in search * update readme Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * Enable single GPU * update readme Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * Add visualization tutorial transform image (#448) * [DLMED] add visualization tutorial Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add image Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update notebook Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update notebook Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add reference image Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix PEP error Signed-off-by: Nic Ma <nma@nvidia.com> * Update spleen_segmentation_3d.ipynb (#455) The `pip install` statement is missing pytorch-ignite. Changing: `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm]"` to `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm, ignite]"` * Figures added, pretrained weights link added, minor fixes (#456) * Figures added, pretrained weights link added, minor fixes Signed-off-by: vnath <vnath@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: vnath <vnath@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add itkwidgets example in notebook (#454) * [DLMED] add itkwidgets Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add reference screenshot Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update to PLS orientation Signed-off-by: Nic Ma <nma@nvidia.com> * MIL example (#431) * MIL example Signed-off-by: myron <amyronenko@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <amyronenko@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <amyronenko@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * small updates Signed-off-by: myron <amyronenko@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated images Signed-off-by: myron <amyronenko@nvidia.com> * gdown for json Signed-off-by: myron <amyronenko@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update README Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Fix formatting and typos Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * small fixes Signed-off-by: myron <amyronenko@nvidia.com> * stats Signed-off-by: myron <amyronenko@nvidia.com> * pip install Signed-off-by: myron <amyronenko@nvidia.com> * README fixes Signed-off-by: myron <amyronenko@nvidia.com> Co-authored-by: am <am> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Behrooz <3968947+drbeh@users.noreply.github.com> Co-authored-by: Nic Ma <nma@nvidia.com> * 450 update AsDiscrete (#451) * update asdiscrete Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update postprocessing figures Signed-off-by: Yiheng Wang <vennw@nvidia.com> * fix version error of mutual info Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update to use include in torchin Signed-off-by: Yiheng Wang <vennw@nvidia.com> * 459 update nvidia flare 2.0 example (#460) * update nvidia flare 2.0 example Signed-off-by: Yiheng Wang <vennw@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * enhance code format Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update folder and readme Signed-off-by: Yiheng Wang <vennw@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Weights Link Updated (#465) Signed-off-by: vnath <vnath@nvidia.com> Co-authored-by: vnath <vnath@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixes readme typos Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update readmes Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update readme Signed-off-by: Wenqi Li <wenqil@nvidia.com> * qa commit Signed-off-by: Wenqi Li <wenqil@nvidia.com> * link Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Add plot arch_code utils * Fix bugs in search and update readme * Fix combination weights bug * Small typo update * Fix minor bug in train_dints * update scripts Signed-off-by: dongy <dongy@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * update scripts Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * Update Readme * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: dongy <dongy@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: heyufan1995 <heyufan1995@gmail.com>
wyli
pushed a commit
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Dec 7, 2021
* initialize dints tutorials Signed-off-by: dongy <dongy@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <dongy@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * Update README.md * Update README.md * update scripts Signed-off-by: dongy <dongy@nvidia.com> * Change Dints interface * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Modify scripts for new Dints interface * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * Test push * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update readme Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * Add readme * Update readme * Change lr in search * update readme Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * Enable single GPU * update readme Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * Add visualization tutorial transform image (#448) * [DLMED] add visualization tutorial Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add image Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update notebook Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update notebook Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add reference image Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix PEP error Signed-off-by: Nic Ma <nma@nvidia.com> * Update spleen_segmentation_3d.ipynb (#455) The `pip install` statement is missing pytorch-ignite. Changing: `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm]"` to `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm, ignite]"` * Figures added, pretrained weights link added, minor fixes (#456) * Figures added, pretrained weights link added, minor fixes Signed-off-by: vnath <vnath@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: vnath <vnath@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add itkwidgets example in notebook (#454) * [DLMED] add itkwidgets Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add reference screenshot Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update to PLS orientation Signed-off-by: Nic Ma <nma@nvidia.com> * MIL example (#431) * MIL example Signed-off-by: myron <amyronenko@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <amyronenko@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <amyronenko@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * small updates Signed-off-by: myron <amyronenko@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated images Signed-off-by: myron <amyronenko@nvidia.com> * gdown for json Signed-off-by: myron <amyronenko@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update README Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Fix formatting and typos Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * small fixes Signed-off-by: myron <amyronenko@nvidia.com> * stats Signed-off-by: myron <amyronenko@nvidia.com> * pip install Signed-off-by: myron <amyronenko@nvidia.com> * README fixes Signed-off-by: myron <amyronenko@nvidia.com> Co-authored-by: am <am> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Behrooz <3968947+drbeh@users.noreply.github.com> Co-authored-by: Nic Ma <nma@nvidia.com> * 450 update AsDiscrete (#451) * update asdiscrete Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update postprocessing figures Signed-off-by: Yiheng Wang <vennw@nvidia.com> * fix version error of mutual info Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update to use include in torchin Signed-off-by: Yiheng Wang <vennw@nvidia.com> * 459 update nvidia flare 2.0 example (#460) * update nvidia flare 2.0 example Signed-off-by: Yiheng Wang <vennw@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * enhance code format Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update folder and readme Signed-off-by: Yiheng Wang <vennw@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Weights Link Updated (#465) Signed-off-by: vnath <vnath@nvidia.com> Co-authored-by: vnath <vnath@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixes readme typos Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update readmes Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update readme Signed-off-by: Wenqi Li <wenqil@nvidia.com> * qa commit Signed-off-by: Wenqi Li <wenqil@nvidia.com> * link Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Add plot arch_code utils * Fix bugs in search and update readme * Fix combination weights bug * Small typo update * Fix minor bug in train_dints * update scripts Signed-off-by: dongy <dongy@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * update scripts Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * Update Readme * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Change arch code keys * update scripts Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * update scripts Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> Co-authored-by: dongy <dongy@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: heyufan1995 <heyufan1995@gmail.com>
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* update asdiscrete Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update postprocessing figures Signed-off-by: Yiheng Wang <vennw@nvidia.com> * fix version error of mutual info Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update to use include in torchin Signed-off-by: Yiheng Wang <vennw@nvidia.com>
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Apr 21, 2024
* initialize dints tutorials Signed-off-by: dongy <dongy@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <dongy@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * Update README.md * Update README.md * update scripts Signed-off-by: dongy <dongy@nvidia.com> * Change Dints interface * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Modify scripts for new Dints interface * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * Test push * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update readme Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * Add readme * Update readme * Change lr in search * update readme Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * Enable single GPU * update readme Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * Add visualization tutorial transform image (Project-MONAI#448) * [DLMED] add visualization tutorial Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add image Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update notebook Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update notebook Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add reference image Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix PEP error Signed-off-by: Nic Ma <nma@nvidia.com> * Update spleen_segmentation_3d.ipynb (Project-MONAI#455) The `pip install` statement is missing pytorch-ignite. Changing: `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm]"` to `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm, ignite]"` * Figures added, pretrained weights link added, minor fixes (Project-MONAI#456) * Figures added, pretrained weights link added, minor fixes Signed-off-by: vnath <vnath@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: vnath <vnath@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add itkwidgets example in notebook (Project-MONAI#454) * [DLMED] add itkwidgets Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add reference screenshot Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update to PLS orientation Signed-off-by: Nic Ma <nma@nvidia.com> * MIL example (Project-MONAI#431) * MIL example Signed-off-by: myron <amyronenko@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <amyronenko@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <amyronenko@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * small updates Signed-off-by: myron <amyronenko@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated images Signed-off-by: myron <amyronenko@nvidia.com> * gdown for json Signed-off-by: myron <amyronenko@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update README Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Fix formatting and typos Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * small fixes Signed-off-by: myron <amyronenko@nvidia.com> * stats Signed-off-by: myron <amyronenko@nvidia.com> * pip install Signed-off-by: myron <amyronenko@nvidia.com> * README fixes Signed-off-by: myron <amyronenko@nvidia.com> Co-authored-by: am <am> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Behrooz <3968947+drbeh@users.noreply.github.com> Co-authored-by: Nic Ma <nma@nvidia.com> * 450 update AsDiscrete (Project-MONAI#451) * update asdiscrete Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update postprocessing figures Signed-off-by: Yiheng Wang <vennw@nvidia.com> * fix version error of mutual info Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update to use include in torchin Signed-off-by: Yiheng Wang <vennw@nvidia.com> * 459 update nvidia flare 2.0 example (Project-MONAI#460) * update nvidia flare 2.0 example Signed-off-by: Yiheng Wang <vennw@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * enhance code format Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update folder and readme Signed-off-by: Yiheng Wang <vennw@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Weights Link Updated (Project-MONAI#465) Signed-off-by: vnath <vnath@nvidia.com> Co-authored-by: vnath <vnath@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixes readme typos Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update readmes Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update readme Signed-off-by: Wenqi Li <wenqil@nvidia.com> * qa commit Signed-off-by: Wenqi Li <wenqil@nvidia.com> * link Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: dongy <dongy@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: heyufan1995 <heyufan1995@gmail.com> Co-authored-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> Co-authored-by: Nic Ma <nma@nvidia.com> Co-authored-by: nvahmadi <85887144+nvahmadi@users.noreply.github.com> Co-authored-by: Vishwesh <vishwesh.nath@gmail.com> Co-authored-by: vnath <vnath@nvidia.com> Co-authored-by: myron <myron@users.noreply.github.com> Co-authored-by: Behrooz <3968947+drbeh@users.noreply.github.com> Co-authored-by: Yiheng Wang <68361391+yiheng-wang-nv@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>
boneseva
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Apr 21, 2024
* initialize dints tutorials Signed-off-by: dongy <dongy@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <dongy@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * Update README.md * Update README.md * update scripts Signed-off-by: dongy <dongy@nvidia.com> * Change Dints interface * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Modify scripts for new Dints interface * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * Test push * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update readme Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * Add readme * Update readme * Change lr in search * update readme Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * Enable single GPU * update readme Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * Add visualization tutorial transform image (Project-MONAI#448) * [DLMED] add visualization tutorial Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add image Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update notebook Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update notebook Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add reference image Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix PEP error Signed-off-by: Nic Ma <nma@nvidia.com> * Update spleen_segmentation_3d.ipynb (Project-MONAI#455) The `pip install` statement is missing pytorch-ignite. Changing: `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm]"` to `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm, ignite]"` * Figures added, pretrained weights link added, minor fixes (Project-MONAI#456) * Figures added, pretrained weights link added, minor fixes Signed-off-by: vnath <vnath@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: vnath <vnath@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add itkwidgets example in notebook (Project-MONAI#454) * [DLMED] add itkwidgets Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add reference screenshot Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update to PLS orientation Signed-off-by: Nic Ma <nma@nvidia.com> * MIL example (Project-MONAI#431) * MIL example Signed-off-by: myron <amyronenko@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <amyronenko@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <amyronenko@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * small updates Signed-off-by: myron <amyronenko@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated images Signed-off-by: myron <amyronenko@nvidia.com> * gdown for json Signed-off-by: myron <amyronenko@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update README Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Fix formatting and typos Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * small fixes Signed-off-by: myron <amyronenko@nvidia.com> * stats Signed-off-by: myron <amyronenko@nvidia.com> * pip install Signed-off-by: myron <amyronenko@nvidia.com> * README fixes Signed-off-by: myron <amyronenko@nvidia.com> Co-authored-by: am <am> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Behrooz <3968947+drbeh@users.noreply.github.com> Co-authored-by: Nic Ma <nma@nvidia.com> * 450 update AsDiscrete (Project-MONAI#451) * update asdiscrete Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update postprocessing figures Signed-off-by: Yiheng Wang <vennw@nvidia.com> * fix version error of mutual info Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update to use include in torchin Signed-off-by: Yiheng Wang <vennw@nvidia.com> * 459 update nvidia flare 2.0 example (Project-MONAI#460) * update nvidia flare 2.0 example Signed-off-by: Yiheng Wang <vennw@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * enhance code format Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update folder and readme Signed-off-by: Yiheng Wang <vennw@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Weights Link Updated (Project-MONAI#465) Signed-off-by: vnath <vnath@nvidia.com> Co-authored-by: vnath <vnath@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixes readme typos Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update readmes Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update readme Signed-off-by: Wenqi Li <wenqil@nvidia.com> * qa commit Signed-off-by: Wenqi Li <wenqil@nvidia.com> * link Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Add plot arch_code utils * Fix bugs in search and update readme * Fix combination weights bug * Small typo update * Fix minor bug in train_dints * update scripts Signed-off-by: dongy <dongy@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * update scripts Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * Update Readme * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: dongy <dongy@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: heyufan1995 <heyufan1995@gmail.com>
boneseva
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Apr 21, 2024
* initialize dints tutorials Signed-off-by: dongy <dongy@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <dongy@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * Update README.md * Update README.md * update scripts Signed-off-by: dongy <dongy@nvidia.com> * Change Dints interface * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Modify scripts for new Dints interface * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * Test push * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update readme Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * Add readme * Update readme * Change lr in search * update readme Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * Enable single GPU * update readme Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * Add visualization tutorial transform image (Project-MONAI#448) * [DLMED] add visualization tutorial Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add image Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update notebook Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update notebook Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add reference image Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix PEP error Signed-off-by: Nic Ma <nma@nvidia.com> * Update spleen_segmentation_3d.ipynb (Project-MONAI#455) The `pip install` statement is missing pytorch-ignite. Changing: `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm]"` to `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm, ignite]"` * Figures added, pretrained weights link added, minor fixes (Project-MONAI#456) * Figures added, pretrained weights link added, minor fixes Signed-off-by: vnath <vnath@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: vnath <vnath@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add itkwidgets example in notebook (Project-MONAI#454) * [DLMED] add itkwidgets Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add reference screenshot Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update to PLS orientation Signed-off-by: Nic Ma <nma@nvidia.com> * MIL example (Project-MONAI#431) * MIL example Signed-off-by: myron <amyronenko@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <amyronenko@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <amyronenko@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * small updates Signed-off-by: myron <amyronenko@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated images Signed-off-by: myron <amyronenko@nvidia.com> * gdown for json Signed-off-by: myron <amyronenko@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update README Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Fix formatting and typos Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * small fixes Signed-off-by: myron <amyronenko@nvidia.com> * stats Signed-off-by: myron <amyronenko@nvidia.com> * pip install Signed-off-by: myron <amyronenko@nvidia.com> * README fixes Signed-off-by: myron <amyronenko@nvidia.com> Co-authored-by: am <am> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Behrooz <3968947+drbeh@users.noreply.github.com> Co-authored-by: Nic Ma <nma@nvidia.com> * 450 update AsDiscrete (Project-MONAI#451) * update asdiscrete Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update postprocessing figures Signed-off-by: Yiheng Wang <vennw@nvidia.com> * fix version error of mutual info Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update to use include in torchin Signed-off-by: Yiheng Wang <vennw@nvidia.com> * 459 update nvidia flare 2.0 example (Project-MONAI#460) * update nvidia flare 2.0 example Signed-off-by: Yiheng Wang <vennw@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * enhance code format Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update folder and readme Signed-off-by: Yiheng Wang <vennw@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Weights Link Updated (Project-MONAI#465) Signed-off-by: vnath <vnath@nvidia.com> Co-authored-by: vnath <vnath@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixes readme typos Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update readmes Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update readme Signed-off-by: Wenqi Li <wenqil@nvidia.com> * qa commit Signed-off-by: Wenqi Li <wenqil@nvidia.com> * link Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Add plot arch_code utils * Fix bugs in search and update readme * Fix combination weights bug * Small typo update * Fix minor bug in train_dints * update scripts Signed-off-by: dongy <dongy@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * update scripts Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * Update Readme * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Change arch code keys * update scripts Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> * update scripts Signed-off-by: Dong Yang <dongy@dongy-mlt.client.nvidia.com> Co-authored-by: dongy <dongy@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: heyufan1995 <heyufan1995@gmail.com>
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Signed-off-by: Yiheng Wang vennw@nvidia.com
Fixes #450 .
Most of the tutorials are updated to use the latest API of
AsDiscrete.Some of them are not covered:
deployment/, it requires to use MONAI 0.6federated_learning/substra, it requires to use MONAI 0.3federated_learning/nvflare, I'm working on a huge change of it in order to match up with the upcoming new release of nvflare, thus a separate PR will be submitted for it.Status
Ready
Checks
./runner [-p <regex_pattern>]