Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Ae docs #3067

Merged
merged 52 commits into from
Oct 4, 2021
Merged

Ae docs #3067

merged 52 commits into from
Oct 4, 2021

Conversation

ericspod
Copy link
Member

@ericspod ericspod commented Oct 4, 2021

Description

Some documentation added to networks based on feedback from the bootcamp.

Status

Ready

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.
  • In-line docstrings updated.
  • Documentation updated, tested make html command in the docs/ folder.

ericspod and others added 30 commits October 4, 2021 17:27
@ericspod
Adding documentation for AutoEncoder and VarAutoEncoder
8c35fb0 
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@ericspod
Docs Update
d303886 
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@bhashemian @ericspod
cuCIM Transform (#2932)
4170f3b 
* Implement CuCIM wrapper transfrom

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@rijobro @ericspod
torch SpatialCrop, SpatialCropd (#2963)
6ff564a 
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@bhashemian @ericspod
Update with cupy.ndarray (#2965)
32589cc 
* Update with cupy.ndarray

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Change to use has_cp

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Change the format

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Fix a bug

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@ericspod
Fix for Jupyter plotting (#2964)
3aa24ea 
* Fix for Jupyter plotting

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

* Fix for Jupyter plotting

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

* Fix for Jupyter plotting

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@wyli @ericspod
fixes tutorial issue 352 (#2968)
c240f82 
* fixes tutorial issue 352

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

* simplified

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@Nic-Ma @ericspod
2231 Enhance tensor transforms (#2966)
efc52e9 
* [DLMED] enhance tensor transforms

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix tests

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix mypy

Signed-off-by: Nic Ma <nma@nvidia.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@rijobro @ericspod
Torch RandCropByPosNegLabel, RandCropByPosNegLabeld, `RandCropByL…
e47f3b6 
…abelClasses`, `RandCropByLabelClassesd` (#2967)

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@wyli @ericspod
enhance affinegrid to use torch backend (#2969)
061300a 
* enhance affinegrid to use torch backend

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

* style fixes

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

* codeformat fixes

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

* backend affien grid

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

* device support

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

* less lookup

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

* create grid with torch backend

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

* fixes tests

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

* default to torch create grid

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

* fixes unit test

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

* randaffine with create grid

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

* create_grid backend change for spatial transforms

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

* create control grid tensor

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

* enhance spatial, and crop xforms

  - Update test_rand_deform_grid.py
  - center_scale_crop
  - center_spatial_crop
  - rand_scale_crop
  - rand_spatial_crop
  - rand_spatial_crop_samples

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

* fixes invert

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

* tensor resize, unit test fixes

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@bhashemian @ericspod
Add make the name of wsi reader lowercase (#2973)
692be31 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@ahatamiz @ericspod
update multimodal doc and model names (Transchex) (#2979)
0d7c487 
* update multimodal doc and model names (Transchex)

Signed-off-by: ahatamizadeh <ahatamizadeh@nvidia.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@wyli @ericspod
2914 remove the deprecated API for v0.7 (#2981)
08d8b7a 
* remove deprecated

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

* min-test list

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

* preserves tests from tests/test_handler_transform_inverter.py

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@wyli @ericspod
2985 - enhance nightly test (#2986)
9f0fa08 
* enhance nightly test

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

* print after the test for information

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@neuronflow @monai-bot @ericspod
dimension check for pretrained model weights (#2984)
c662a7f 
* dimension check for pretrained model weights

This PR implements a dimension check, before trying to load pre-trained model weights.

Signed-off-by: neuronflow <zournyque@gmail.com>

* [MONAI] python code formatting

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

* multi line split error

Signed-off-by: neuronflow <zournyque@gmail.com>

Co-authored-by: monai-bot <monai.miccai2019@gmail.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@deepsource-autofix @wyli @ericspod
Refactor unnecessary else / elif when if block has a return s…
fa4034c 
…tatement (#2996)

* Refactor unnecessary `else` / `elif` when `if` block has a `return` statement

* Remove unnecessary lambda expression (#2997)

Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>

* type fixes

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

* remove repeated init

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

* fixes import, unused vars

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

Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Co-authored-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@Nic-Ma @monai-bot @ericspod
3000 Support not copy in CacheDataset (#3001)
5601868 
* [DLMED] add copy option

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] enhance test

Signed-off-by: Nic Ma <nma@nvidia.com>

* [MONAI] python code formatting

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

Co-authored-by: monai-bot <monai.miccai2019@gmail.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@wyli @ericspod
3002 - compatibility with torch 1.9.1 (#3003)
89c5b16 
* test 1.9.1

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

* temp tests

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

* Revert "temp tests"

This reverts commit 1f27a63.

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@wyli @ericspod
Fix cucim dep compatibility (#3006)
ced1cbe 
* fixes cucim compatibility

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

* simplified import

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@wyli @ericspod
update cucim dep (#3007)
b9eac8a 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@Nic-Ma @ericspod
[DLMED] fix CI test (#3008)
5b2a195 
Signed-off-by: Nic Ma <nma@nvidia.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@Nic-Ma @ericspod
3009 Update highlights web page (#3013)
2938412 
* [DLMED] update highlights

Signed-off-by: Nic Ma <nma@nvidia.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@wyli @ericspod
2914 release note, and what's new for v0.7 (#2992)
579c61a 
* release note v0.7

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

* adds whatsnew 07

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@wyli @ericspod
delaying the removal (#3015)
5036654 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@wyli @ericspod
update preview version tag (#3016)
4b06838 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@Nic-Ma @ericspod
Enhance 0.7 README doc (#3017)
167cbd2 
* [DLMED] update README

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update what's new

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] use whatsnew link

Signed-off-by: Nic Ma <nma@nvidia.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@Nic-Ma @ericspod
3020 Enhance what's new for transfomer networks (#3019)
624a3d6 
* [DLMED] add more doc

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] edit change log

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] add command to get transform backend

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] enhance the doc

Signed-off-by: Nic Ma <nma@nvidia.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@rijobro @ericspod
Torch GaussianSmooth, RandGaussianSmooth, GaussianSharpen, `Ran…
defb2bc 
…dGaussianSharpen` (#2971)

Torch `GaussianSmooth`, `RandGaussianSmooth`, `GaussianSharpen`, `RandGaussianSharpen`

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@Borda @ericspod
apply pyupgrade (#3026)
655a16b 
* apply pyupgrade

Signed-off-by: Jirka <jirka.borovec@seznam.cz>

* exclude monai/_version.py

Signed-off-by: Jirka <jirka.borovec@seznam.cz>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@wyli @Nic-Ma @ericspod
3018 enhance version string check (#3022)
087ed84 
* enhance the release version string check

Signed-off-by: GitHub <noreply@github.com>

* update the releasing steps

Signed-off-by: GitHub <noreply@github.com>

Co-authored-by: Nic Ma <nma@nvidia.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
Nic-Ma and others added 22 commits October 4, 2021 17:27
@Nic-Ma @ericspod
3028 update ignite CI tests to 0.4.6 (#3029)
2748e07 
* [DLMED] update ignite 0.4.6

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix flake8 issues

Signed-off-by: Nic Ma <nma@nvidia.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@wyli @ericspod
enhance DataStats to include dtype (#3043)
613bed6 
* print dtype along with type

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

* update tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@wyli @ericspod
enhance error handling (#3042)
f27cc4e 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@rijobro @ericspod
2792 - Torch GibbsNoise, RandGibbsNoise, KSpaceSpikeNoise, RandKSpace…
27bb163 
…SpikeNoise (#2974)

GibbsNoise, RandGibbsNoise, KSpaceSpikeNoise, RandKSpaceSpikeNoise

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@rijobro @ericspod
AdjustContrast, AdjustContrastd, RandAdjustContrast, RandAdjustContra…
a4ca5fc 
…std (#3044)

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@wyli @ericspod
remove false positive tests (#3046)
6fb63ac 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@rijobro @ericspod
Torch Spacing, Spacingd (#3045)
ef79653 
Torch `Spacing`, `Spacingd`

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@wyli @Nic-Ma @ericspod
2975 torch fgbgtoindices (#3038)
c048809 
* torch fgbgtoindices

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

* unravel indices

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

* simplified

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

Co-authored-by: Nic Ma <nma@nvidia.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@Nic-Ma @ericspod
3051 Fix dtype issue in Spacing transform (#3052)
5b2f8b1 
* [DLMED] fix spacing dtype

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix dtype

Signed-off-by: Nic Ma <nma@nvidia.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@ericspod
Documentation update
af6ffa6 
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@ericspod
Adding documentation
dc8de2a 
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@rijobro @ericspod
Create transform images (#3039)
99b185a 
create example transform images

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@Nic-Ma @ericspod
2975 Fix the perf issue of RandCropByPosNegLabel (#3050)
8279055 
* [DLMED] fix crop performance issue

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix CI test

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] use default to avoid overflow

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix CI error

Signed-off-by: Nic Ma <nma@nvidia.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@Nic-Ma @ericspod
[DLMED] fix broken link (#3059)
8938881 
Signed-off-by: Nic Ma <nma@nvidia.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@Borda @ericspod
remove redundant noqa (#3027)
0d0d6f8 
* apply yesqa

Signed-off-by: Jirka <jirka.borovec@seznam.cz>

* rev

Signed-off-by: Jirka <jirka.borovec@seznam.cz>

* expand

Signed-off-by: Jirka <jirka.borovec@seznam.cz>

* plugins

Signed-off-by: Jirka <jirka.borovec@seznam.cz>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@Nic-Ma @ericspod
[DLMED] enhance label classes (#3061)
7bbfde7 
Signed-off-by: Nic Ma <nma@nvidia.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@Nic-Ma @ericspod
[DLMED] enhance ScaleIntensity (#3062)
e88b170 
Signed-off-by: Nic Ma <nma@nvidia.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@rijobro @ericspod
Extra transform examples (#3056)
c3d72ec 
* create images

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* use brats

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* update

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* working

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* rename file

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* optional import matplotlib

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* docstrings

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* store images in https://github.com/Project-MONAI/DocImages

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* extra transform example images

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* most transforms

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

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

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

Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@wyli @ericspod
update backend (#3065)
e66cea0 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@Nic-Ma @ericspod
3063 Fix the complex Tensor issue in type conversion (#3064)
61999c0 
* [DLMED] fix complex array issue

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix test issue

Signed-off-by: Nic Ma <nma@nvidia.com>
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@ericspod
Formatting
56e93bb 
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@ericspod
Merge branch 'dev' into ae_docs
fb92e92
wyli
wyli approved these changes Oct 4, 2021
View reviewed changes
Copy link
Contributor

@wyli wyli left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks, it looks good to me.

@wyli wyli enabled auto-merge (squash) October 4, 2021 16:34
@wyli wyli merged commit 4618e85 into Project-MONAI:dev Oct 4, 2021
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@wyli wyli wyli approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
8 participants
@ericspod @wyli @bhashemian @rijobro @Nic-Ma @ahatamiz @neuronflow @Borda