Skip to content

Ae docs#3067

Merged
wyli merged 52 commits intoProject-MONAI:devfrom
ericspod:ae_docs
Oct 4, 2021
Merged

Ae docs#3067
wyli merged 52 commits intoProject-MONAI:devfrom
ericspod:ae_docs

Conversation

@ericspod
Copy link
Copy Markdown
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 <[email protected]>
@ericspod
Docs Update
d303886 
Signed-off-by: Eric Kerfoot <[email protected]>
@bhashemian @ericspod
cuCIM Transform (#2932)
4170f3b 
* Implement CuCIM wrapper transfrom

Signed-off-by: Behrooz <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@rijobro @ericspod
torch SpatialCrop, SpatialCropd (#2963)
6ff564a 
Signed-off-by: Richard Brown <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@bhashemian @ericspod
Update with cupy.ndarray (#2965)
32589cc 
* Update with cupy.ndarray

Signed-off-by: Behrooz <[email protected]>

* Change to use has_cp

Signed-off-by: Behrooz <[email protected]>

* Change the format

Signed-off-by: Behrooz <[email protected]>

* Fix a bug

Signed-off-by: Behrooz <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@ericspod
Fix for Jupyter plotting (#2964)
3aa24ea 
* Fix for Jupyter plotting

Signed-off-by: Eric Kerfoot <[email protected]>

* Fix for Jupyter plotting

Signed-off-by: Eric Kerfoot <[email protected]>

* Fix for Jupyter plotting

Signed-off-by: Eric Kerfoot <[email protected]>
@wyli @ericspod
fixes tutorial issue 352 (#2968)
c240f82 
* fixes tutorial issue 352

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

* simplified

Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@Nic-Ma @ericspod
2231 Enhance tensor transforms (#2966)
efc52e9 
* [DLMED] enhance tensor transforms

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix tests

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix mypy

Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@rijobro @ericspod
Torch RandCropByPosNegLabel, RandCropByPosNegLabeld, `RandCropByL…
e47f3b6 
…abelClasses`, `RandCropByLabelClassesd` (#2967)

Signed-off-by: Richard Brown <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@wyli @ericspod
enhance affinegrid to use torch backend (#2969)
061300a 
* enhance affinegrid to use torch backend

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

* style fixes

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

* codeformat fixes

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

* backend affien grid

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

* device support

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

* less lookup

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

* create grid with torch backend

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

* fixes tests

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

* default to torch create grid

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

* fixes unit test

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

* randaffine with create grid

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

* create_grid backend change for spatial transforms

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

* create control grid tensor

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

* 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 <[email protected]>

* fixes invert

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

* tensor resize, unit test fixes

Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@bhashemian @ericspod
Add make the name of wsi reader lowercase (#2973)
692be31 
Signed-off-by: Behrooz <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@ahatamiz @ericspod
update multimodal doc and model names (Transchex) (#2979)
0d7c487 
* update multimodal doc and model names (Transchex)

Signed-off-by: ahatamizadeh <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@wyli @ericspod
2914 remove the deprecated API for v0.7 (#2981)
08d8b7a 
* remove deprecated

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

* min-test list

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

* preserves tests from tests/test_handler_transform_inverter.py

Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@wyli @ericspod
2985 - enhance nightly test (#2986)
9f0fa08 
* enhance nightly test

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

* print after the test for information

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

* [MONAI] python code formatting

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

* multi line split error

Signed-off-by: neuronflow <[email protected]>

Co-authored-by: monai-bot <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@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 <[email protected]>

* remove repeated init

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

* fixes import, unused vars

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

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

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] enhance test

Signed-off-by: Nic Ma <[email protected]>

* [MONAI] python code formatting

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

Co-authored-by: monai-bot <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@wyli @ericspod
3002 - compatibility with torch 1.9.1 (#3003)
89c5b16 
* test 1.9.1

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

* temp tests

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

* Revert "temp tests"

This reverts commit 1f27a63.

Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@wyli @ericspod
Fix cucim dep compatibility (#3006)
ced1cbe 
* fixes cucim compatibility

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

* simplified import

Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@wyli @ericspod
update cucim dep (#3007)
b9eac8a 
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@Nic-Ma @ericspod
[DLMED] fix CI test (#3008)
5b2a195 
Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@Nic-Ma @ericspod
3009 Update highlights web page (#3013)
2938412 
* [DLMED] update highlights

Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@wyli @ericspod
2914 release note, and what's new for v0.7 (#2992)
579c61a 
* release note v0.7

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

* adds whatsnew 07

Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@wyli @ericspod
delaying the removal (#3015)
5036654 
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@wyli @ericspod
update preview version tag (#3016)
4b06838 
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@Nic-Ma @ericspod
Enhance 0.7 README doc (#3017)
167cbd2 
* [DLMED] update README

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] update what's new

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] use whatsnew link

Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@Nic-Ma @ericspod
3020 Enhance what's new for transfomer networks (#3019)
624a3d6 
* [DLMED] add more doc

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] edit change log

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add command to get transform backend

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] enhance the doc

Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@rijobro @ericspod
Torch GaussianSmooth, RandGaussianSmooth, GaussianSharpen, `Ran…
defb2bc 
…dGaussianSharpen` (#2971)

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

Signed-off-by: Eric Kerfoot <[email protected]>
@Borda @ericspod
apply pyupgrade (#3026)
655a16b 
* apply pyupgrade

Signed-off-by: Jirka <[email protected]>

* exclude monai/_version.py

Signed-off-by: Jirka <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@wyli @Nic-Ma @ericspod
3018 enhance version string check (#3022)
087ed84 
* enhance the release version string check

Signed-off-by: GitHub <[email protected]>

* update the releasing steps

Signed-off-by: GitHub <[email protected]>

Co-authored-by: Nic Ma <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
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 <[email protected]>

* [DLMED] fix flake8 issues

Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@wyli @ericspod
enhance DataStats to include dtype (#3043)
613bed6 
* print dtype along with type

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

* update tests

Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@wyli @ericspod
enhance error handling (#3042)
f27cc4e 
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@rijobro @ericspod
2792 - Torch GibbsNoise, RandGibbsNoise, KSpaceSpikeNoise, RandKSpace…
27bb163 
…SpikeNoise (#2974)

GibbsNoise, RandGibbsNoise, KSpaceSpikeNoise, RandKSpaceSpikeNoise

Signed-off-by: Eric Kerfoot <[email protected]>
@rijobro @ericspod
AdjustContrast, AdjustContrastd, RandAdjustContrast, RandAdjustContra…
a4ca5fc 
…std (#3044)

Signed-off-by: Richard Brown <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@wyli @ericspod
remove false positive tests (#3046)
6fb63ac 
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@rijobro @ericspod
Torch Spacing, Spacingd (#3045)
ef79653 
Torch `Spacing`, `Spacingd`

Signed-off-by: Eric Kerfoot <[email protected]>
@wyli @Nic-Ma @ericspod
2975 torch fgbgtoindices (#3038)
c048809 
* torch fgbgtoindices

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

* unravel indices

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

* simplified

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

Co-authored-by: Nic Ma <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@Nic-Ma @ericspod
3051 Fix dtype issue in Spacing transform (#3052)
5b2f8b1 
* [DLMED] fix spacing dtype

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix dtype

Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@ericspod
Documentation update
af6ffa6 
Signed-off-by: Eric Kerfoot <[email protected]>
@ericspod
Adding documentation
dc8de2a 
Signed-off-by: Eric Kerfoot <[email protected]>
@rijobro @ericspod
Create transform images (#3039)
99b185a 
create example transform images

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

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix CI test

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] use default to avoid overflow

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix CI error

Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@Nic-Ma @ericspod
[DLMED] fix broken link (#3059)
8938881 
Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@Borda @ericspod
remove redundant noqa (#3027)
0d0d6f8 
* apply yesqa

Signed-off-by: Jirka <[email protected]>

* rev

Signed-off-by: Jirka <[email protected]>

* expand

Signed-off-by: Jirka <[email protected]>

* plugins

Signed-off-by: Jirka <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@Nic-Ma @ericspod
[DLMED] enhance label classes (#3061)
7bbfde7 
Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@Nic-Ma @ericspod
[DLMED] enhance ScaleIntensity (#3062)
e88b170 
Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@rijobro @ericspod
Extra transform examples (#3056)
c3d72ec 
* create images

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

* use brats

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

* update

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

* working

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

* rename file

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

* optional import matplotlib

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

* docstrings

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

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

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

* extra transform example images

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

* most transforms

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

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

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

Co-authored-by: Eric Kerfoot <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@wyli @ericspod
update backend (#3065)
e66cea0 
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@Nic-Ma @ericspod
3063 Fix the complex Tensor issue in type conversion (#3064)
61999c0 
* [DLMED] fix complex array issue

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] fix test issue

Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
@ericspod
Formatting
56e93bb 
Signed-off-by: Eric Kerfoot <[email protected]>
@ericspod
Merge branch 'dev' into ae_docs
fb92e92
wyli
wyli approved these changes Oct 4, 2021
View reviewed changes
Copy link
Copy Markdown
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