Add vista3d inferers #8021

heyufan1995 · 2024-08-15T15:20:55Z

Fixes # .

Description

A few sentences describing the changes proposed in this pull request.

Types of changes

Non-breaking change (fix or new feature that would not break existing functionality).
Breaking change (fix or new feature that would cause existing functionality to change).
New tests added to cover the changes.
Integration tests passed locally by running ./runtests.sh -f -u --net --coverage.
Quick tests passed locally by running ./runtests.sh --quick --unittests --disttests.
In-line docstrings updated.
Documentation updated, tested make html command in the docs/ folder.

Signed-off-by: heyufan1995 <heyufan1995@gmail.com>

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

monai/inferers/utils.py

monai/networks/nets/vista3d.py

monai/apps/vista3d/inferer.py

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

monai/apps/vista3d/inferer.py

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

tests/test_point_based_window_inferer.py

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

monai/apps/vista3d/transforms.py

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

Signed-off-by: heyufan1995 <heyufan1995@gmail.com>

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

Signed-off-by: heyufan1995 <heyufan1995@gmail.com>

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

Signed-off-by: heyufan1995 <heyufan1995@gmail.com>

monai/apps/vista3d/__init__.py

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

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

monai/apps/vista3d/inferer.py

monai/apps/vista3d/transforms.py

monai/inferers/utils.py

monai/apps/vista3d/inferer.py

Signed-off-by: heyufan1995 <heyufan1995@gmail.com>

…I into add-vista3d-other-utils

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

Signed-off-by: heyufan1995 <heyufan1995@gmail.com>

…I into add-vista3d-other-utils

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

mingxin-zheng

Thanks for fixing the docstrings! I don't have other suggestions on this PR.

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

KumoLiu · 2024-08-21T03:36:14Z

/build

Signed-off-by: heyufan1995 <heyufan1995@gmail.com>

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

monai/apps/vista3d/workflow.py

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

monai/apps/vista3d/sampler.py

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

Signed-off-by: heyufan1995 <heyufan1995@gmail.com>

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

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

KumoLiu · 2024-08-23T05:29:17Z

/build

KumoLiu · 2024-08-23T06:39:00Z

/build

KumoLiu · 2024-08-23T08:02:23Z

[2024-08-23T07:19:14.039Z] ======================================================================
[2024-08-23T07:19:14.039Z] ERROR: test_result_0 (tests.test_vista3d_transforms.TestVistaPostTransformd)
[2024-08-23T07:19:14.039Z] ----------------------------------------------------------------------
[2024-08-23T07:19:14.039Z] Traceback (most recent call last):
[2024-08-23T07:19:14.039Z]   File "/usr/local/lib/python3.9/dist-packages/parameterized/parameterized.py", line 620, in standalone_func
[2024-08-23T07:19:14.039Z]     return func(*(a + p.args), **p.kwargs, **kw)
[2024-08-23T07:19:14.039Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/test_vista3d_transforms.py", line 89, in test_result
[2024-08-23T07:19:14.039Z]     result = transform(input_data)
[2024-08-23T07:19:14.039Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/monai/apps/vista3d/transforms.py", line 170, in __call__
[2024-08-23T07:19:14.039Z]     pred[pred == frac] = data["label_prompt"][i - 1].to(pred.dtype)
[2024-08-23T07:19:14.039Z] RuntimeError: Expected all tensors to be on the same device, but found at least two devices, cuda:0 and cpu!
[2024-08-23T07:19:14.039Z] 
[2024-08-23T07:19:14.039Z] ----------------------------------------------------------------------
[2024-08-23T07:19:14.039Z] Ran 15586 tests in 1326.707s

mingxin-zheng

The PR looks good to me, and only had a minor comment below. Thanks!

monai/apps/vista3d/inferer.py

KumoLiu · 2024-08-26T02:56:40Z

Hi @heyufan1995 and @yiheng-wang-nv, could you please help take a look at this ci error and also address @mingxin-zheng's comments, then I can trigger more tests and merge the PR. Thanks.

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

KumoLiu · 2024-08-26T03:31:24Z

/build

Add vista3d inferers

cae979a

Signed-off-by: heyufan1995 <heyufan1995@gmail.com>

heyufan1995 requested review from KumoLiu and yiheng-wang-nv August 15, 2024 15:20

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yiheng-wang-nv reviewed Aug 16, 2024

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yiheng-wang-nv reviewed Aug 16, 2024

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fix format issues

ee3ceaa

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yiheng-wang-nv reviewed Aug 16, 2024

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add tests

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yiheng-wang-nv reviewed Aug 16, 2024

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add vista3d transforms

519154e

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

yiheng-wang-nv reviewed Aug 16, 2024

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yiheng-wang-nv and others added 6 commits August 16, 2024 20:47

update inputs doc string

4b579e1

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

Add transforms

42d29be

Signed-off-by: heyufan1995 <heyufan1995@gmail.com>

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

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Add test

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Signed-off-by: heyufan1995 <heyufan1995@gmail.com>

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Add more test

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Signed-off-by: heyufan1995 <heyufan1995@gmail.com>

KumoLiu reviewed Aug 19, 2024

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KumoLiu added this to the VISTA 3D [P0 v1.4] milestone Aug 19, 2024

yiheng-wang-nv and others added 2 commits August 19, 2024 15:26

fix issues

f44e9df

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

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KumoLiu requested review from Nic-Ma, ericspod and mingxin-zheng August 19, 2024 08:33

KumoLiu reviewed Aug 19, 2024

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heyufan1995 and others added 6 commits August 20, 2024 11:09

Update docstring

cb7446b

Signed-off-by: heyufan1995 <heyufan1995@gmail.com>

Merge branch 'add-vista3d-other-utils' of github.com:heyufan1995/MONA…

6c8bba5

…I into add-vista3d-other-utils

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

144b753

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Update docstring

7127c10

Signed-off-by: heyufan1995 <heyufan1995@gmail.com>

Merge branch 'add-vista3d-other-utils' of github.com:heyufan1995/MONA…

d4bb986

…I into add-vista3d-other-utils

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

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mingxin-zheng approved these changes Aug 20, 2024

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fix doc issue

c0e20b5

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

KumoLiu approved these changes Aug 21, 2024

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heyufan1995 and others added 2 commits August 21, 2024 17:00

Add generate_prompt_pairs

c8e1e44

Signed-off-by: heyufan1995 <heyufan1995@gmail.com>

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KumoLiu reviewed Aug 22, 2024

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KumoLiu requested review from mingxin-zheng and yiheng-wang-nv August 22, 2024 03:23

fix issues

f1686bc

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

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yiheng-wang-nv and others added 5 commits August 22, 2024 16:40

update kwargs

8c1d7b6

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

Fix bug in convert point to disc and add more doc

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Signed-off-by: heyufan1995 <heyufan1995@gmail.com>

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autofix

7b5f5f6

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

Merge branch 'dev' into add-vista3d-other-utils

6ee3629

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resolve issues

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Signed-off-by: Yiheng Wang <vennw@nvidia.com>

KumoLiu merged commit 872585d into Project-MONAI:dev Aug 26, 2024

Add vista3d inferers #8021

Add vista3d inferers #8021

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heyufan1995 commented Aug 15, 2024

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