245 Update tutorials with new API (part 1) by yiheng-wang-nv · Pull Request #246 · Project-MONAI/tutorials

yiheng-wang-nv · 2021-07-01T10:09:46Z

Signed-off-by: Yiheng Wang [email protected]

Partially fixes #245 .

Description

This PR updates all files (except the files that do not need to be changed with new APIs) in:

2d_classification
2d_segmentation
3d_classification
3d_segmentation
acceleration
modules/dynunet_pipeline
modules/engines

All of the changed files in the above folders have been tested locally.

The following folders are not updated due to version limitations:

deployment requires to use MONAI 0.5.2
federated_learning/nvflare requires to use nvflare==1.0.0 which requires to use MONAI 0.5.2
federated_learning/substra requires to use MONAI 0.3.0

For other folders:

deepgrow has some compatibility issue ( see Deepgrow Interaction is not compatiable with decollate_batch for v 0.6.0 (8/July) MONAI#2525), I will submit another PR for it after the issue is solved
Update: the issue has been solved in MONAI, and the updated version is submitted, see 245 Update deepgrow example with new API (part 3) #254 .
~~Other files in modules/ will be started soon, and I will also submit another PR for them~~
Update: the updated version is submitted, see 245 Update tutorials with new API (part 2) #253 .

Status

Ready

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review-notebook-app · 2021-07-01T10:54:21Z

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This commit is used to remove irrelevant changes such as image changes. Signed-off-by: Yiheng Wang <[email protected]>

…-api Signed-off-by: Yiheng Wang <[email protected]>

Signed-off-by: Yiheng Wang <[email protected]>

2d_classification/mednist_tutorial.ipynb

2d_segmentation/torch/unet_evaluation_array.py

2d_segmentation/torch/unet_evaluation_dict.py

3d_classification/ignite/densenet_evaluation_array.py

3d_classification/ignite/densenet_evaluation_dict.py

3d_segmentation/torch/unet_evaluation_array.py

3d_segmentation/spleen_segmentation_3d_lightning.ipynb

3d_segmentation/torch/unet_evaluation_dict.py

3d_segmentation/torch/unet_inference_dict.py

modules/dynunet_pipeline/evaluator.py

Signed-off-by: Yiheng Wang <[email protected]>

Nic-Ma · 2021-07-09T10:22:19Z

Hi @wyli ,

I already reviewed this PR with comments, as it's a big PR, could you please help also take a look if you are available in case I missed some important thing?

Thanks in advance.

Signed-off-by: Yiheng Wang <[email protected]>

…torials into 245-update-with-new-api

Nic-Ma

Thanks for the quick update.
Looks good to me now.
@wyli could you please help double confirm it?

Thanks in advance.

wyli

Looks good to me, I'll rerun the nightly tests after this pr

Nic-Ma · 2021-07-12T11:16:22Z

Looks good to me, I'll rerun the nightly tests after this pr

Hi @wyli ,

Should we tag 0.6.0 for this repo when all the tests passed?

Thanks in advance.

wyli · 2021-07-12T12:47:46Z

sure I tagged 0.6.0

Nic-Ma · 2021-07-14T01:54:39Z

sure I tagged 0.6.0

Hi @wyli ,

Could you please help also tag 0.5.3? Otherwise, the users using the old version can't find suitable tutorials now.

Thanks.

wyli · 2021-07-14T11:44:54Z

sure I tagged 0.6.0

Hi @wyli ,

Could you please help also tag 0.5.3? Otherwise, the users using the old version can't find suitable tutorials now.

Thanks.

I couldn't find a good version for v0.5.3, do you have any idea?

Nic-Ma · 2021-07-14T12:30:06Z

sure I tagged 0.6.0

Hi @wyli ,
Could you please help also tag 0.5.3? Otherwise, the users using the old version can't find suitable tutorials now.
Thanks.

I couldn't find a good version for v0.5.3, do you have any idea?

Hi @wyli ,

I think maybe we can tag at this commit for v0.5.3?
9261e7d

Thanks.

* Re-modify ipynb tutorials This commit is used to remove irrelevant changes such as image changes. Signed-off-by: Yiheng Wang <[email protected]> * Remove useless log changes Signed-off-by: Yiheng Wang <[email protected]> * Run lightning cells Signed-off-by: Yiheng Wang <[email protected]> * update 3d reg Signed-off-by: Yiheng Wang <[email protected]> * restore paired_lung_ct.ipynb Signed-off-by: Yiheng Wang <[email protected]> * Add totensor Signed-off-by: Yiheng Wang <[email protected]> * update acceleration Signed-off-by: Yiheng Wang <[email protected]> * update acceletation and use from engine Signed-off-by: Yiheng Wang <[email protected]> * fix pep8 errors Signed-off-by: Yiheng Wang <[email protected]> * update based on review Signed-off-by: Yiheng Wang <[email protected]> * update to use SaveImage Signed-off-by: Yiheng Wang <[email protected]> Co-authored-by: Nic Ma <[email protected]>

Nic-Ma mentioned this pull request Jul 2, 2021

ValueError while training the model for Brain Tumor Segmentation #78

Closed

Re-modify ipynb tutorials

53b1b64

This commit is used to remove irrelevant changes such as image changes. Signed-off-by: Yiheng Wang <[email protected]>

yiheng-wang-nv force-pushed the 245-update-with-new-api branch from b9c3cf3 to 53b1b64 Compare July 2, 2021 15:32

yiheng-wang-nv added 8 commits July 2, 2021 23:47

Merge remote-tracking branch 'origin/master' into 245-update-with-new…

84cf0c6

…-api Signed-off-by: Yiheng Wang <[email protected]>

Remove useless log changes

1ca6f93

Signed-off-by: Yiheng Wang <[email protected]>

Run lightning cells

9e7aaa5

Signed-off-by: Yiheng Wang <[email protected]>

update 3d reg

3c0f995

Signed-off-by: Yiheng Wang <[email protected]>

restore paired_lung_ct.ipynb

c1f99a9

Signed-off-by: Yiheng Wang <[email protected]>

Add totensor

f71dfec

Signed-off-by: Yiheng Wang <[email protected]>

Merge branch 'master' into 245-update-with-new-api

f66d9f6

update acceleration

17a37de

Signed-off-by: Yiheng Wang <[email protected]>

wyli mentioned this pull request Jul 5, 2021

2478 Update highlight features page for v0.6 Project-MONAI/MONAI#2490

Merged

7 tasks

yiheng-wang-nv added 2 commits July 6, 2021 15:54

update acceletation and use from engine

f7233b4

Signed-off-by: Yiheng Wang <[email protected]>

fix pep8 errors

0070543

Signed-off-by: Yiheng Wang <[email protected]>

yiheng-wang-nv changed the title ~~[WIP] 245 Update a part of tutorials~~ 245 Update tutorials with new API (part 1) Jul 6, 2021

yiheng-wang-nv marked this pull request as ready for review July 6, 2021 08:37

yiheng-wang-nv mentioned this pull request Jul 6, 2021

Update all the examples & notebooks to use new APIs #245

Closed

yiheng-wang-nv requested review from Nic-Ma, rijobro and wyli July 6, 2021 08:38

deepib assigned yiheng-wang-nv Jul 6, 2021

yiheng-wang-nv mentioned this pull request Jul 7, 2021

245 Update tutorials with new API (part 2) #253

Merged

1 task

yiheng-wang-nv added 3 commits July 8, 2021 08:58

Merge branch 'master' into 245-update-with-new-api

353ea84

Merge branch 'master' into 245-update-with-new-api

340595e

Merge branch 'master' into 245-update-with-new-api

fd6cd2b

Nic-Ma reviewed Jul 9, 2021

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wyli mentioned this pull request Jul 9, 2021

v0.5 to v0.6 migration guide? Project-MONAI/MONAI#2563

Closed

yiheng-wang-nv and others added 2 commits July 9, 2021 16:53

update based on review

5b50c63

Signed-off-by: Yiheng Wang <[email protected]>

Merge branch 'master' into 245-update-with-new-api

a1dc425

yiheng-wang-nv and others added 3 commits July 10, 2021 00:27

update to use SaveImage

f682c0c

Signed-off-by: Yiheng Wang <[email protected]>

Merge branch 'master' into 245-update-with-new-api

d5d00ef

Merge branch '245-update-with-new-api' of github.com:Project-MONAI/tu…

6e156e4

…torials into 245-update-with-new-api

Nic-Ma approved these changes Jul 12, 2021

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wyli approved these changes Jul 12, 2021

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Nic-Ma merged commit 28630e7 into master Jul 12, 2021

wyli deleted the 245-update-with-new-api branch July 12, 2021 12:47

wyli mentioned this pull request Jul 12, 2021

Update all the examples & notebooks to use new APIs (14/July) Project-MONAI/MONAI#2402

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