initial dints tutorials by dongyang0122 · Pull Request #449 · Project-MONAI/tutorials

dongyang0122 · 2021-11-19T06:40:21Z

Signed-off-by: dongy [email protected]

Fixes # .

Description

Neural architecture search examples with DiNTS, including both architecture search and model re-training.

Status

Ready/Work in progress/Hold

Checks

Notebook runs automatically ./runner [-p <regex_pattern>]

Signed-off-by: dongy <[email protected]>

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Signed-off-by: dongy <[email protected]>

for more information, see https://pre-commit.ci

Signed-off-by: dongy <[email protected]>

for more information, see https://pre-commit.ci

Signed-off-by: dongy <[email protected]>

Signed-off-by: Dong Yang <[email protected]>

* [DLMED] add visualization tutorial Signed-off-by: Nic Ma <[email protected]> * [DLMED] add image Signed-off-by: Nic Ma <[email protected]> * [DLMED] update notebook Signed-off-by: Nic Ma <[email protected]> * [DLMED] update notebook Signed-off-by: Nic Ma <[email protected]> * [DLMED] add reference image Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix PEP error Signed-off-by: Nic Ma <[email protected]>

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 Signed-off-by: vnath <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: vnath <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [DLMED] add itkwidgets Signed-off-by: Nic Ma <[email protected]> * [DLMED] add reference screenshot Signed-off-by: Nic Ma <[email protected]> * [DLMED] update to PLS orientation Signed-off-by: Nic Ma <[email protected]>

* MIL example Signed-off-by: myron <[email protected]> * [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 <[email protected]> * [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 <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * small updates Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated images Signed-off-by: myron <[email protected]> * gdown for json Signed-off-by: myron <[email protected]> * [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 <[email protected]> * Fix formatting and typos Signed-off-by: Behrooz <[email protected]> * small fixes Signed-off-by: myron <[email protected]> * stats Signed-off-by: myron <[email protected]> * pip install Signed-off-by: myron <[email protected]> * README fixes Signed-off-by: myron <[email protected]> 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 <[email protected]> Co-authored-by: Nic Ma <[email protected]>

* update asdiscrete Signed-off-by: Yiheng Wang <[email protected]> * update postprocessing figures Signed-off-by: Yiheng Wang <[email protected]> * fix version error of mutual info Signed-off-by: Yiheng Wang <[email protected]> * update to use include in torchin Signed-off-by: Yiheng Wang <[email protected]>

* update nvidia flare 2.0 example Signed-off-by: Yiheng Wang <[email protected]> * [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 <[email protected]> * update folder and readme Signed-off-by: Yiheng Wang <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Signed-off-by: vnath <[email protected]> Co-authored-by: vnath <[email protected]>

review-notebook-app · 2021-12-01T18:03:40Z

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Signed-off-by: Wenqi Li <[email protected]>

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Signed-off-by: Wenqi Li <[email protected]>

wyli

initial version with major implementation details

Signed-off-by: Wenqi Li <[email protected]>

* initialize dints tutorials Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Update README.md * Update README.md * update scripts Signed-off-by: dongy <[email protected]> * 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 <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Test push * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update readme Signed-off-by: Dong Yang <[email protected]> * Add readme * Update readme * Change lr in search * update readme Signed-off-by: Dong Yang <[email protected]> * Enable single GPU * update readme Signed-off-by: Dong Yang <[email protected]> * Add visualization tutorial transform image (Project-MONAI#448) * [DLMED] add visualization tutorial Signed-off-by: Nic Ma <[email protected]> * [DLMED] add image Signed-off-by: Nic Ma <[email protected]> * [DLMED] update notebook Signed-off-by: Nic Ma <[email protected]> * [DLMED] update notebook Signed-off-by: Nic Ma <[email protected]> * [DLMED] add reference image Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix PEP error Signed-off-by: Nic Ma <[email protected]> * 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 <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: vnath <[email protected]> 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 <[email protected]> * [DLMED] add reference screenshot Signed-off-by: Nic Ma <[email protected]> * [DLMED] update to PLS orientation Signed-off-by: Nic Ma <[email protected]> * MIL example (Project-MONAI#431) * MIL example Signed-off-by: myron <[email protected]> * [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 <[email protected]> * [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 <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * small updates Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated images Signed-off-by: myron <[email protected]> * gdown for json Signed-off-by: myron <[email protected]> * [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 <[email protected]> * Fix formatting and typos Signed-off-by: Behrooz <[email protected]> * small fixes Signed-off-by: myron <[email protected]> * stats Signed-off-by: myron <[email protected]> * pip install Signed-off-by: myron <[email protected]> * README fixes Signed-off-by: myron <[email protected]> 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 <[email protected]> Co-authored-by: Nic Ma <[email protected]> * 450 update AsDiscrete (Project-MONAI#451) * update asdiscrete Signed-off-by: Yiheng Wang <[email protected]> * update postprocessing figures Signed-off-by: Yiheng Wang <[email protected]> * fix version error of mutual info Signed-off-by: Yiheng Wang <[email protected]> * update to use include in torchin Signed-off-by: Yiheng Wang <[email protected]> * 459 update nvidia flare 2.0 example (Project-MONAI#460) * update nvidia flare 2.0 example Signed-off-by: Yiheng Wang <[email protected]> * [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 <[email protected]> * update folder and readme Signed-off-by: Yiheng Wang <[email protected]> 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 <[email protected]> Co-authored-by: vnath <[email protected]> * [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 <[email protected]> * update readmes Signed-off-by: Wenqi Li <[email protected]> * update readme Signed-off-by: Wenqi Li <[email protected]> * qa commit Signed-off-by: Wenqi Li <[email protected]> * link Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: dongy <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: heyufan1995 <[email protected]> Co-authored-by: Dong Yang <[email protected]> Co-authored-by: Nic Ma <[email protected]> Co-authored-by: nvahmadi <[email protected]> Co-authored-by: Vishwesh <[email protected]> Co-authored-by: vnath <[email protected]> Co-authored-by: myron <[email protected]> Co-authored-by: Behrooz <[email protected]> Co-authored-by: Yiheng Wang <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

initialize dints tutorials

163a008

Signed-off-by: dongy <[email protected]>

dongyang0122 requested a review from wyli November 19, 2021 06:40

[pre-commit.ci] auto fixes from pre-commit.com hooks

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dongyang0122 requested a review from Nic-Ma November 19, 2021 06:40

dongyang0122 self-assigned this Nov 19, 2021

dongyang0122 changed the title ~~initialize dints tutorials~~ [WIP] initialize dints tutorials Nov 19, 2021

dongy and others added 24 commits November 22, 2021 06:56

update scripts

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update scripts

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Merge branch 'master' of https://github.com/dongyang0122/tutorials

85ee1a0

update scripts

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Signed-off-by: dongy <[email protected]>

Update README.md

981b303

Update README.md

d98ca94

update scripts

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Signed-off-by: dongy <[email protected]>

Merge branch 'master' of https://github.com/dongyang0122/tutorials

dcd4e10

Change Dints interface

0d3c8e7

[pre-commit.ci] auto fixes from pre-commit.com hooks

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Merge branch 'master' of github.com:dongyang0122/tutorials

1981544

Modify scripts for new Dints interface

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Merge branch 'master' of github.com:dongyang0122/tutorials

fc2f277

update scripts

698a9a0

Signed-off-by: dongy <[email protected]>

update scripts

4a44993

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update scripts

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update scripts

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Test push

396c1ae

update scripts

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update scripts

0a1cc78

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update scripts

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update readme

3122caf

Signed-off-by: Dong Yang <[email protected]>

Add readme

6ccdd50

heyufan1995 and others added 14 commits November 30, 2021 17:29

Merge branch 'master' of github.com:dongyang0122/tutorials

51f3127

Update readme

79c9aab

Change lr in search

d29f086

update readme

bdc759e

Signed-off-by: Dong Yang <[email protected]>

Enable single GPU

b2b1170

update readme

1c72524

Signed-off-by: Dong Yang <[email protected]>

Update spleen_segmentation_3d.ipynb (#455)

03990f9

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]"`

Add itkwidgets example in notebook (#454)

f573bec

* [DLMED] add itkwidgets Signed-off-by: Nic Ma <[email protected]> * [DLMED] add reference screenshot Signed-off-by: Nic Ma <[email protected]> * [DLMED] update to PLS orientation Signed-off-by: Nic Ma <[email protected]>

Weights Link Updated (#465)

cfbd3d2

Signed-off-by: vnath <[email protected]> Co-authored-by: vnath <[email protected]>

wyli and others added 6 commits December 1, 2021 18:07

Merge remote-tracking branch 'upstream/master'

f3ea3c9

Signed-off-by: Wenqi Li <[email protected]>

[pre-commit.ci] auto fixes from pre-commit.com hooks

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fixes readme typos

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Signed-off-by: Wenqi Li <[email protected]>

Merge remote-tracking branch 'dong/master'

cf5594e

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update readmes

6fb6b3e

Signed-off-by: Wenqi Li <[email protected]>

update readme

76120b6

Signed-off-by: Wenqi Li <[email protected]>

wyli changed the title ~~[WIP] initialize dints tutorials~~ initial dints tutorials Dec 1, 2021

qa commit

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Signed-off-by: Wenqi Li <[email protected]>

wyli approved these changes Dec 1, 2021

View reviewed changes

link

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Signed-off-by: Wenqi Li <[email protected]>

wyli merged commit 99e16a7 into Project-MONAI:master Dec 1, 2021

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initial dints tutorials#449

initial dints tutorials#449
wyli merged 48 commits intoProject-MONAI:masterfrom
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dongyang0122 commented Nov 19, 2021

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dongyang0122 commented Nov 19, 2021

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