Replacement Apply and Resample #5436

atbenmurray · 2022-10-30T11:15:51Z

Signed-off-by: Ben Murray ben.murray@gmail.com

Description

This is part of the work towards #4855. It adds:

a lazy apply method
A transform-like wrapper for apply called Apply
~~- MetaMatrix and related functionality to represent abstracted grid and matrix transforms with metadata~~
A universal resample function that can be used to apply grid / matrix transforms
~~- Functional spatial and croppad implementations that define but don't apply transforms~~

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.

monai/transforms/lazy/functional.py

wyli · 2022-11-01T16:01:28Z

/black
thanks, I think this PR introduces quite a few APIs at a time and some of them (MatrixFactory/MetaMatrix) need more discussions... is it possible to make it smaller, for example, only including croppad, apply, and an example of SpatialCrop transform, so that we can create a working example of lazy cropping, then finalise the functional and apply API? cc @ericspod @rijobro @Nic-Ma

atbenmurray · 2022-11-01T16:26:38Z

thanks, I think this PR introduces quite a few APIs at a time and some of them (MatrixFactory/MetaMatrix) need more discussions... is it possible to make it smaller, for example, only including croppad, apply, and an example of SpatialCrop transform, so that we can create a working example of lazy cropping, then finalise the functional and apply API? cc @ericspod @rijobro @Nic-Ma

The problem is that MatrixFactory/MetaMatrix are the classes by which a lot of the internal stuff for lazy resampling is done. They could certainly change before the PR goes in, but that would necessitate some plumbing to happen and I don't know if I'll have time before I am on holiday. The key thing here at the moment is that this PR doesn't change any existing behaviour so if we want to refactor we certainly can.

What they do:

MatrixFactory is an attempt to wrap up the various affine operations in a way that it can be simply constructed by either defining dimensions, device etc or by passing a tensor so that is determined automatically, and used in an OO way.
MetaTensor is the transformation + metadata that accompanies it. It contains either a Matrix or a Grid object, depending

In theory, one or both could go, but it might make everything somewhat verbose. Neither are supposed to be user-facing

Might be a good topic for tomorrow, but I am trying to get the PRs as populated as possible for tonight.

…nd dictionary transforms to operate while waiting for PR #5436 Signed-off-by: Ben Murray <ben.murray@gmail.com>

…al, array and dictionary transforms to operate while waiting for PR #5436 Signed-off-by: Ben Murray <ben.murray@gmail.com>

…5436 Signed-off-by: Ben Murray <ben.murray@gmail.com>

monai/transforms/meta_matrix.py

…with rabasing and automatic signatures Signed-off-by: Ben Murray <ben.murray@gmail.com>

Signed-off-by: Ben Murray <ben.murray@gmail.com>

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

Signed-off-by: Ben Murray <ben.murray@gmail.com>

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

Signed-off-by: Ben Murray <ben.murray@gmail.com>

Signed-off-by: monai-bot <monai.miccai2019@gmail.com>

- `_pending_operations` defaults to `MetaObj.get_default_applied_operations()` - removes the unused `Apply` class - fixes unit tests, style checks - torch.pi doesn't exist before torch 1.10 Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

monai/transforms/lazy/utils.py

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

wyli

@atbenmurray please make more changes if needed and let me know when you think it's ready.. cc @Nic-Ma this mainly introduces necessary APIs monai.transforms.lazy.*

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

wyli · 2022-11-24T21:52:11Z

/build

atbenmurray mentioned this pull request Oct 30, 2022

Apply and Resample #5420

Closed

7 tasks

atbenmurray requested review from Nic-Ma, rijobro, ericspod and wyli October 30, 2022 11:18

atbenmurray mentioned this pull request Oct 30, 2022

Lazy Resampling #4855

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33 tasks

wyli reviewed Nov 1, 2022

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atbenmurray self-assigned this Nov 2, 2022

atbenmurray added a commit that referenced this pull request Nov 2, 2022

Adding in placeholders and functions required for functional, array a…

c0c5558

…nd dictionary transforms to operate while waiting for PR #5436 Signed-off-by: Ben Murray <ben.murray@gmail.com>

atbenmurray added a commit that referenced this pull request Nov 2, 2022

Adding in additional placeholders and functions required for function…

7a41b3f

…al, array and dictionary transforms to operate while waiting for PR #5436 Signed-off-by: Ben Murray <ben.murray@gmail.com>

atbenmurray added a commit that referenced this pull request Nov 2, 2022

Adding in additional placeholders and functions required for function…

57c66e4

…al, array and dictionary transforms to operate while waiting for PR #5436 Signed-off-by: Ben Murray <ben.murray@gmail.com>

atbenmurray added a commit that referenced this pull request Nov 2, 2022

Putting comments on utils methods that have been duplicated from PR #…

ae486d1

…5436 Signed-off-by: Ben Murray <ben.murray@gmail.com>

wyli reviewed Nov 4, 2022

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wyli added this to the Lazy resampling (+ cache-based dataset refactoring) [P1 v1.1] milestone Nov 4, 2022

wyli force-pushed the lr_apply_2 branch 3 times, most recently from 95ed4a1 to 87c4356 Compare November 12, 2022 23:03

wyli force-pushed the lr_apply_2 branch from 5e2aaa3 to fc8b226 Compare November 22, 2022 17:24

atbenmurray and others added 10 commits November 23, 2022 09:51

Commit of functionality on replacement lr_apply branch due to issues …

d557549

…with rabasing and automatic signatures Signed-off-by: Ben Murray <ben.murray@gmail.com>

adding functional tests for flip, resize and spacing

49e7ed6

Signed-off-by: Ben Murray <ben.murray@gmail.com>

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

61dbe11

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

Adding additional spatial functional unit tests

9c11d4d

Signed-off-by: Ben Murray <ben.murray@gmail.com>

Work on apply and matmul tests

77d7c31

Signed-off-by: Ben Murray <ben.murray@gmail.com>

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

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Adding tests for matmul and matrix_matrix

23a05fa

Signed-off-by: Ben Murray <ben.murray@gmail.com>

Removing spatial functional transforms from this PR

a67ef17

Signed-off-by: Ben Murray <ben.murray@gmail.com>

Removing croppad functional transforms from this PR

b25a6cb

Signed-off-by: Ben Murray <ben.murray@gmail.com>

Removing spatial functional tests as they are no longer part of this PR

42f33a2

Signed-off-by: Ben Murray <ben.murray@gmail.com>

monai-bot and others added 5 commits November 23, 2022 09:51

[MONAI] code formatting

1177263

Signed-off-by: monai-bot <monai.miccai2019@gmail.com>

minor updates

1492f40

- `_pending_operations` defaults to `MetaObj.get_default_applied_operations()` - removes the unused `Apply` class - fixes unit tests, style checks - torch.pi doesn't exist before torch 1.10 Signed-off-by: Wenqi Li <wenqil@nvidia.com>

apply/matmul/resample MVP

2d4122b

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

rearrange modules, adds back matrix/grid types

6c4db35

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

matmul -> combine_transforms

9eb5279

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

wyli force-pushed the lr_apply_2 branch from fc8b226 to 9eb5279 Compare November 23, 2022 11:00

wyli added 3 commits November 23, 2022 11:10

remove unused

17574cb

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

adds docstrings

e067b6e

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

adds testing

c5aa26c

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

wyli marked this pull request as ready for review November 23, 2022 13:10

wyli reviewed Nov 23, 2022

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monai/transforms/lazy/utils.py Outdated Show resolved Hide resolved

DDF -> DisplacementField

3c2d1ec

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

wyli approved these changes Nov 23, 2022

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wyli mentioned this pull request Nov 23, 2022

Compose deformation vector fields (DVFs) #4604

Open

wyli and others added 2 commits November 24, 2022 12:20

Merge remote-tracking branch 'upstream/dev' into lr_apply_2

3f7e679

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Merge branch 'dev' into lr_apply_2

1a124ba

wyli merged commit 2c7ba9e into dev Nov 25, 2022

wyli deleted the lr_apply_2 branch November 25, 2022 11:00

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Replacement Apply and Resample #5436

Replacement Apply and Resample #5436

atbenmurray commented Oct 30, 2022 •

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wyli commented Nov 24, 2022

Replacement Apply and Resample #5436

Replacement Apply and Resample #5436

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