[don't merge] this PR is for dev code comparisons/discussions #4536

wyli · 2022-06-20T08:18:44Z

for the convenience of comparing dev vs feature/MetaTensor

Status

Ready/Work in progress/Hold

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.

* collate , decollate, dataset, dataloader, out= Signed-off-by: Richard Brown <[email protected]> * mypy Signed-off-by: Richard Brown <[email protected]> * skip decollation for pytorch 1.7 Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * add batch index testing Signed-off-by: Richard Brown <[email protected]> * fixes Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * load image meta tensor Signed-off-by: Richard Brown <[email protected]> * splitdims fix Signed-off-by: Richard Brown <[email protected]> * flake8 Signed-off-by: Richard Brown <[email protected]> * fix test_nifti_rw Signed-off-by: Richard Brown <[email protected]> * test_smartcachedataset Signed-off-by: Richard Brown <[email protected]> * test fixes Signed-off-by: Richard Brown <[email protected]> * test fixes Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * fixes Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * fixes Signed-off-by: Richard Brown <[email protected]> * fix wsi test Signed-off-by: Richard Brown <[email protected]> * changes after code review Signed-off-by: Richard Brown <[email protected]> Signed-off-by: Wenqi Li <[email protected]>

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

* temp tests Signed-off-by: Wenqi Li <[email protected]> * fixes fast training Signed-off-by: Wenqi Li <[email protected]> * seg 3d Signed-off-by: Wenqi Li <[email protected]> * revert temp tests Signed-off-by: Wenqi Li <[email protected]>

* MetaTensor channel transforms Signed-off-by: Richard Brown <[email protected]> * fixes Signed-off-by: Richard Brown <[email protected]> * typo Signed-off-by: Richard Brown <[email protected]> * fixes Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * remove deepcopy Signed-off-by: Richard Brown <[email protected]> * fixes Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * Merge remote-tracking branch 'MONAI/dev' into MetaTensor_channel Signed-off-by: Richard Brown <[email protected]> * metatensor convert helper Signed-off-by: Richard Brown <[email protected]> * autofix Signed-off-by: Richard Brown <[email protected]> * Merge branch 'feature/MetaTensor' into MetaTensor_channel Signed-off-by: Richard Brown <[email protected]> * Revert "Merge remote-tracking branch 'MONAI/dev' into MetaTensor_channel" This reverts commit 6a5f888. Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * FIXME Signed-off-by: Richard Brown <[email protected]> * update_meta docstring Signed-off-by: Richard Brown <[email protected]> * fix test Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * fix str Signed-off-by: Richard Brown <[email protected]> * format, update str Signed-off-by: Wenqi Li <[email protected]> * fixes comp. torch.solve for metatensor Signed-off-by: Wenqi Li <[email protected]> * fixes inverse collation Signed-off-by: Wenqi Li <[email protected]> * fixes resample to match Signed-off-by: Wenqi Li <[email protected]> * fixes resample to matchd Signed-off-by: Wenqi Li <[email protected]> * fixes integration bundle run Signed-off-by: Wenqi Li <[email protected]> * fixes image dataset test Signed-off-by: Wenqi Li <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * fixes integration Signed-off-by: Wenqi Li <[email protected]> * fixes mypy Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]> Co-authored-by: monai-bot <[email protected]>

* temp tests Signed-off-by: Wenqi Li <[email protected]> * temp test Signed-off-by: Wenqi Li <[email protected]> * fixes rotated test Signed-off-by: Wenqi Li <[email protected]> * mednist dataset fix Signed-off-by: Wenqi Li <[email protected]> * fixes Signed-off-by: Wenqi Li <[email protected]> * remove temp tests Signed-off-by: Wenqi Li <[email protected]>

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

* meta_tensor orientation Signed-off-by: Richard Brown <[email protected]> * extra doc Signed-off-by: Richard Brown <[email protected]> * code review Signed-off-by: Richard Brown <[email protected]> * updates Signed-off-by: Richard Brown <[email protected]> * flake8 fix Signed-off-by: Richard Brown <[email protected]>

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

…4296) * `remove_extra_metadata` etc `transforms/utils.py` -> `data/utils.py` Signed-off-by: Richard Brown <[email protected]> * [MONAI] code formatting Signed-off-by: monai-bot <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * fixes Signed-off-by: Richard Brown <[email protected]> * bug fixes Signed-off-by: Richard Brown <[email protected]> * fixes Signed-off-by: Richard Brown <[email protected]> * fixes to test_inverse Signed-off-by: Richard Brown <[email protected]> * fixes Signed-off-by: Richard Brown <[email protected]> * fixxx Signed-off-by: Richard Brown <[email protected]> Co-authored-by: monai-bot <[email protected]>

Signed-off-by: Richard Brown <[email protected]>

* inverse `Orientation` Signed-off-by: Richard Brown <[email protected]> * fixes Signed-off-by: Richard Brown <[email protected]>

* Spacing MetaTensor Signed-off-by: Richard Brown <[email protected]>

Signed-off-by: Richard Brown <[email protected]>

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

Signed-off-by: Richard Brown <[email protected]>

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

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

Signed-off-by: monai-bot <[email protected]>

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

* at least scale one Signed-off-by: Wenqi Li <[email protected]> * add more tests Signed-off-by: Wenqi Li <[email protected]> * dict-based tests Signed-off-by: Wenqi Li <[email protected]> * reviewed intensity transforms Signed-off-by: Wenqi Li <[email protected]> * review post Signed-off-by: Wenqi Li <[email protected]> * review utils Signed-off-by: Wenqi Li <[email protected]> * integration tests Signed-off-by: Wenqi Li <[email protected]> * adds pixdim property, fixes typos Signed-off-by: Wenqi Li <[email protected]>

* metatensor Lambda/RandLambda/splitdim Signed-off-by: Wenqi Li <[email protected]> * fixes unit test Signed-off-by: Wenqi Li <[email protected]>

* compatible data type conversion Signed-off-by: Wenqi Li <[email protected]> * fixes mypy Signed-off-by: Wenqi Li <[email protected]>

Nic-Ma · 2022-06-20T08:42:38Z

Minor comments:

Is it better to use torch.empty() here?
https://github.com/Project-MONAI/MONAI/blob/feature/MetaTensor/monai/utils/type_conversion.py#L54
I see the convert_to_tensor() and convert_to_tensor() are very similar, maybe we can combine them or at least simplify them?

Thanks.

wyli · 2022-06-20T10:06:18Z

some design decisions we had today:

each transform and the inverse will only change the most recent element in applied_operations
each transform's input can be numpy/torch/metatensor
each transform's output depends on get_track_meta, flag on: output metatensor with default meta if needed, flag off: output torch tensor cc @Project-MONAI/core-reviewers

monai/data/meta_tensor.py

monai/transforms/croppad/dictionary.py

monai/data/meta_tensor.py

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

* whats new/migration guide

fixes #4530 Signed-off-by: Wenqi Li <[email protected]>

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

tests/test_crop_base.py

* fix lamdba metadtensor Signed-off-by: Richard Brown <[email protected]>

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

wyli · 2022-07-19T13:19:48Z

all features are now on the dev branch

wyli and others added 30 commits May 11, 2022 23:54

enable cron tests

d6d01b1

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

fixes tests (#4229)

cdec93d

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

4246 integration meta (#4248)

ca64702

* temp tests Signed-off-by: Wenqi Li <[email protected]> * fixes fast training Signed-off-by: Wenqi Li <[email protected]> * seg 3d Signed-off-by: Wenqi Li <[email protected]> * revert temp tests Signed-off-by: Wenqi Li <[email protected]>

Merge branch 'dev' into feature/MetaTensor

509ac73

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

Merge remote-tracking branch 'upstream/dev' into feature/MetaTensor

8d53447

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

Merge remote-tracking branch 'MONAI/dev' into feature/MetaTensor

d648b6f

Signed-off-by: Richard Brown <[email protected]>

inverse Orientation (#4305)

d4f88b8

* inverse `Orientation` Signed-off-by: Richard Brown <[email protected]> * fixes Signed-off-by: Richard Brown <[email protected]>

sync dev into feature branch (#4326)

5301766

Spacing MetaTensor (#4319)

361cac3

* Spacing MetaTensor Signed-off-by: Richard Brown <[email protected]>

Merge remote-tracking branch 'MONAI/dev' into feature/MetaTensor

49c69e0

Signed-off-by: Richard Brown <[email protected]>

fix

9d738fa

Signed-off-by: Richard Brown <[email protected]>

Merge branch 'dev' into feature/MetaTensor

fc5c340

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

Meta tensor spatial resample (#4332)

86863ac

Signed-off-by: Richard Brown <[email protected]>

Merge branch 'dev' into feature/MetaTensor

e2b1e6b

Merge remote-tracking branch 'upstream/dev' into feature/MetaTensor

e199c67

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

SaveImage to use MetaTensor (#4370)

9320f7e

Metatensor integration tests OK (#4407)

7bdf1c6

Merge branch 'dev' into feature/MetaTensor

1bd9f97

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

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

96af4a8

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

[MONAI] code formatting

5933464

Signed-off-by: monai-bot <[email protected]>

resolve conflicts

72cc2b0

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

Merge branch 'metatensor-merging' into feature/MetaTensor

8ed38fd

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

Merge branch 'dev' into metatensor-merging

a6f09fb

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

fixes solve

b568fd8

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

resolve conflicts

c417b0f

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

wyli added 3 commits June 17, 2022 07:25

some util transforms to support MetaTensor (#4527)

6bcbde8

* metatensor Lambda/RandLambda/splitdim Signed-off-by: Wenqi Li <[email protected]> * fixes unit test Signed-off-by: Wenqi Li <[email protected]>

Compatibility metatensor data convert (#4532)

d56c8d9

* compatible data type conversion Signed-off-by: Wenqi Li <[email protected]> * fixes mypy Signed-off-by: Wenqi Li <[email protected]>

wyli commented Jun 20, 2022

View reviewed changes

monai/data/meta_tensor.py Outdated Show resolved Hide resolved

wyli commented Jun 20, 2022

View reviewed changes

monai/transforms/croppad/dictionary.py Show resolved Hide resolved

wyli commented Jun 20, 2022

View reviewed changes

monai/data/meta_tensor.py Outdated Show resolved Hide resolved

wyli mentioned this pull request Jun 20, 2022

MetaTensor non-breaking changes #4539

Merged

1 task

Rand affine fix (#4528)

db9e49b

wyli commented Jun 20, 2022

View reviewed changes

monai/data/meta_tensor.py Outdated Show resolved Hide resolved

Merge remote-tracking branch 'upstream/dev' into sync-metatensor

8b9a27b

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

Nic-Ma mentioned this pull request Jun 21, 2022

Move metatensor support into dev branch (crop/pad) #4548

Merged

7 tasks

rijobro and others added 3 commits June 21, 2022 11:14

MetaTensor -- whats new/migration guide (#4543)

2338404

* whats new/migration guide

4530 optional SummaryWriter (#4546)

b9452b2

fixes #4530 Signed-off-by: Wenqi Li <[email protected]>

Merge remote-tracking branch 'upstream/dev' into feature/MetaTensor

cb94233

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

wyli commented Jun 21, 2022

View reviewed changes

tests/test_crop_base.py Show resolved Hide resolved

rijobro and others added 10 commits June 21, 2022 19:02

Lambda fix metatensor (#4541)

ac56784

* fix lamdba metadtensor Signed-off-by: Richard Brown <[email protected]>

Merge branch 'dev' into merging-dev-into-metatensor

b81693c

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

merging dev into metatensor

995cab9

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

Merge branch 'dev' into merging-dev-into-metatensor

17043d2

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

fixes test

b36c7b9

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

Merge branch 'dev' into merging-dev-into-metatensor

d659e05

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

Merge branch 'dev' into merging-dev-into-metatensor

bfdd3bd

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

Merge remote-tracking branch 'upstream/dev' into feature/MetaTensor

79fbd34

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

fixes mypy

2e15a91

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

Merge branch 'dev' into merging-dev-into-metatensor

9414800

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

wyli closed this Jul 19, 2022

wyli deleted the feature/MetaTensor branch July 25, 2022 10:10

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[don't merge] this PR is for dev code comparisons/discussions #4536

[don't merge] this PR is for dev code comparisons/discussions #4536

wyli commented Jun 20, 2022

Nic-Ma commented Jun 20, 2022

wyli commented Jun 20, 2022

wyli commented Jul 19, 2022

[don't merge] this PR is for dev code comparisons/discussions #4536

[don't merge] this PR is for dev code comparisons/discussions #4536

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wyli commented Jun 20, 2022

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Nic-Ma commented Jun 20, 2022

wyli commented Jun 20, 2022

wyli commented Jul 19, 2022