[WIP] Support Deepgrow 2D/3D Training by SachidanandAlle · Pull Request #1329 · Project-MONAI/MONAI

SachidanandAlle · 2020-12-08T02:35:46Z

Fixes # .

Description

Support Deegrow 2D/3D training (training example will be added into Tutorials)

Status

Work in progress

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 --codeformat --coverage.
Quick tests passed locally by running ./runtests.sh --quick.
In-line docstrings updated.
Documentation updated, tested make html command in the docs/ folder.

wyli · 2020-12-08T10:00:33Z

thanks! i put a few todos here for discussion:

the transforms should inherit monai.transforms.Transform so that the dataset caching could work properly https://github.com/Project-MONAI/MONAI/blob/master/monai/transforms/compose.py#L26
ideally the core functionality should only rely on numpy and torch, the other packages should be imported with the optional_import method

MONAI/monai/utils/module.py

Line 114 in 4907f39

def optional_import(
make_grid_with_titles looks nice, it could be in the visualize folder (is it possible to avoid cv2, and add support for https://pytorch.org/docs/stable/tensorboard.html#torch.utils.tensorboard.writer.SummaryWriter.add_image)
scipy.ndimage.filters.gaussian_filter could be replaced by

MONAI/monai/networks/layers/simplelayers.py

Line 133 in 4907f39

class GaussianFilter(nn.Module):

example:

MONAI/monai/data/utils.py

Line 522 in 4f2df00

pt_gaussian = GaussianFilter(len(patch_size), sigmas).to(device=device, dtype=torch.float)
some normalisation could be replaced by monai.transforms.ScaleIntensityRange

MONAI/monai/transforms/intensity/array.py

Line 282 in 4907f39

class ScaleIntensityRange(Transform):
DeepgrowStatsHandler implements quite a few features might need another iteration to split it into smaller/specific event handlers.
some overview docs/links about how deepgrow works

I feel it's important to set up some regression tests before any of these refactorings it'll also be very helpful for other people that continue maintaining this module

cc @Nic-Ma

tvercaut · 2020-12-08T20:28:23Z

Interesting. I couldn't see a paper reference within the code. Is this a re-implementation of https://arxiv.org/abs/1903.08205?

Having some documentation, and maybe even an exemplar tutorial / example use case would be great.

Signed-off-by: Sachidanand Alle <[email protected]>

* adds a bounding box transform Signed-off-by: Wenqi Li <[email protected]> * fixes integration Signed-off-by: Wenqi Li <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

… build (#1327) flake8-executable is GPL'ed Signed-off-by: Isaac Yang <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

* adds test init_reader Signed-off-by: Wenqi Li <[email protected]> * fixes loadimage Signed-off-by: Wenqi Li <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

* [DLMED] refine generate_spatial_bounding_box Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] add check for margin value Signed-off-by: Nic Ma <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

* Working on DynUNet Torchscript compatibility Signed-off-by: Eric Kerfoot <[email protected]> * Working on DynUNet Torchscript compatibility Signed-off-by: Eric Kerfoot <[email protected]> * Working on DynUNet Torchscript compatibility Signed-off-by: Eric Kerfoot <[email protected]> * Working on DynUNet Torchscript compatibility Signed-off-by: Eric Kerfoot <[email protected]> * Working on DynUNet Torchscript compatibility Signed-off-by: Eric Kerfoot <[email protected]> Co-authored-by: Yiheng Wang <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

* fixes params groups Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

* [DLMED] enhance save_final in CheckpointSaver Signed-off-by: Nic Ma <[email protected]> * [DLMED] add log message Signed-off-by: Nic Ma <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

* adding simple profiling tools Signed-off-by: charliebudd <[email protected]> * removing old timing decorator Signed-off-by: charliebudd <[email protected]> * auto-reformatting Signed-off-by: charliebudd <[email protected]> * removing unnecessary list comprehension in sum() Signed-off-by: charliebudd <[email protected]> * adding imports to __init__.py Signed-off-by: charliebudd <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

…ed. #1210. Requires torch.fft module and PyTorch 1.7.0+. (#1287) Signed-off-by: Christian Baker <[email protected]> * New tests/utils.py unittest decorators added: SkipIfModule(), SkipIfBeforePyTorchVersion() and SkipIfAtLeastPyTorchVersion Signed-off-by: Christian Baker <[email protected]> * New unit tests added test_hilbert_transform.py and test_detect_envelope.py Signed-off-by: Christian Baker <[email protected]> * New exception InvalidPyTorchVersionError implemented in monai/utils/module.py Signed-off-by: Christian Baker <[email protected]> * New class HilbertTransform implemented in monai/networks/layers/simplelayers.py Signed-off-by: Christian Baker <[email protected]> * New class DetectEnvelope implemented in monai/transforms/intensity/array.py, uses HilbertTransform Signed-off-by: Christian Baker <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

* ci/cd with 1.7.1 Signed-off-by: Wenqi Li <[email protected]> * revise various tests, fixes docs Signed-off-by: Wenqi Li <[email protected]> * temp full tests Signed-off-by: Wenqi Li <[email protected]> * remove temp. tests Signed-off-by: Wenqi Li <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

* [DLMED] add astype in NormalizeIntensity transform Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

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

* add striding for occlusion sensitivity Signed-off-by: Richard Brown <[email protected]> * autofix changes Signed-off-by: Richard Brown <[email protected]> * baseline - sensitivity Signed-off-by: Rich <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

Signed-off-by: Sachidanand Alle <[email protected]>

* [DLMED] update highlights page Signed-off-by: Nic Ma <[email protected]> * [DLMED] update arch module chart Signed-off-by: Nic Ma <[email protected]> * [DLMED] update GradCam, LoadImage, TorchScript, Layer wise LR, Occlusion sensitivity Signed-off-by: Nic Ma <[email protected]> * [DLMED] add partition dataset and cross validation Signed-off-by: Nic Ma <[email protected]> * adds CAM vis. Signed-off-by: Wenqi Li <[email protected]> * adds a cam link Signed-off-by: Wenqi Li <[email protected]> * patchdataset desc. Signed-off-by: Wenqi Li <[email protected]> * update fig Signed-off-by: Wenqi Li <[email protected]> * adds tutorial links Signed-off-by: Wenqi Li <[email protected]> * update tutorial link Signed-off-by: Wenqi Li <[email protected]> * fixes typos Signed-off-by: Wenqi Li <[email protected]> * [DLMED] remove DeepGrow from arch chart Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

…et label (#1347) Signed-off-by: Isaac Yang <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

* Add AddExtremePointsChannel transform Signed-off-by: Mohammad Adil <[email protected]> * permutation -> perturbation Signed-off-by: Wenqi Li <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: YuanTingHsieh <[email protected]> Co-authored-by: Wenqi Li <[email protected]> Co-authored-by: monai-bot <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

Signed-off-by: Sachidanand Alle <[email protected]>

* Update hausdorff metric Signed-off-by: yiheng-wang-nv <[email protected]> * Update surface distance Signed-off-by: yiheng-wang-nv <[email protected]> * fix reduction type error Signed-off-by: yiheng-wang-nv <[email protected]> * Add handlers for new metrics Signed-off-by: yiheng-wang-nv <[email protected]> * Simplify distance code Signed-off-by: yiheng-wang-nv <[email protected]> * autofixes and typo fixes Signed-off-by: Wenqi Li <[email protected]> * fixes lgtm typos Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

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

* Fix randomness in dictionary transform Signed-off-by: YuanTingHsieh <[email protected]> * Fix optional Signed-off-by: YuanTingHsieh <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

* Update docs for GitHub Discussion tab Signed-off-by: Richard Brown <[email protected]> * discussion -> discussions Signed-off-by: Richard Brown <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

* fixes #1346 Signed-off-by: Wenqi Li <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

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

Signed-off-by: charliebudd <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

* AE: check lens of stride and channel match Signed-off-by: Richard Brown <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

…cs (#1374) Signed-off-by: charliebudd <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

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

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

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

* Initial cpu implementation Signed-off-by: charliebudd <[email protected]> * hue speed increase moving away from torch tensors Signed-off-by: charliebudd <[email protected]> * allowing generic channel dimension size Signed-off-by: charliebudd <[email protected]> * allowing generic dimensionality Signed-off-by: charliebudd <[email protected]> * manual testing script for bilateral filter Signed-off-by: charliebudd <[email protected]> * Initial commit of CRF using permutohedral lattice to optimise message passing, implementation from https://github.com/SamuelJoutard/Permutohedral_attention_module Signed-off-by: charliebudd <[email protected]> * temporary example scripts demonstrating the usage of crf and phl, and some data to process Signed-off-by: charliebudd <[email protected]> * alternate phl implementation using a more efficient cuda hashtable, code currently untested due to windows build issues, implementation from https://github.com/SamuelJoutard/Permutohedral_attention_module Signed-off-by: charliebudd <[email protected]> * c++ cpu permutohedral lattice implementation Signed-off-by: charliebudd <[email protected]> * comparison script Signed-off-by: charliebudd <[email protected]> * cleaning Signed-off-by: charliebudd <[email protected]> * backwards pass Signed-off-by: charliebudd <[email protected]> * initial cuda brute force kernel Signed-off-by: charliebudd <[email protected]> * reverting setup.py Signed-off-by: charliebudd <[email protected]> * working cuda kernel for brute force 2d kernel Signed-off-by: charliebudd <[email protected]> * fixing unresolved symbols when compiling without cuda Signed-off-by: charliebudd <[email protected]> * removing macros file Signed-off-by: charliebudd <[email protected]> * placeholder cuda phl implementation Signed-off-by: charliebudd <[email protected]> * changing test case color sigma Signed-off-by: charliebudd <[email protected]> * Initial import of reference cuda phl implementation Signed-off-by: charliebudd <[email protected]> * fixing cuda kernel color weight error Signed-off-by: charliebudd <[email protected]> * initial edits to cuda phl code Signed-off-by: charliebudd <[email protected]> * fixing errors in cuda phl implementation Signed-off-by: charliebudd <[email protected]> * removing logging from cuda phl Signed-off-by: charliebudd <[email protected]> * using template data_ptr function Signed-off-by: charliebudd <[email protected]> * fixed cpu phl implementation Signed-off-by: charliebudd <[email protected]> * updating cpu phl to run on arbitrary input dimensions and channles Signed-off-by: charliebudd <[email protected]> * 2d and 3d testing scripts Signed-off-by: charliebudd <[email protected]> * Generalising permutohedral implementation to remove independance on width and height Signed-off-by: charliebudd <[email protected]> * removing width and height from permutohedral filter function and implementing templated feature creation Signed-off-by: charliebudd <[email protected]> * fixed typo Signed-off-by: charliebudd <[email protected]> * exteneding 3d testing script Signed-off-by: charliebudd <[email protected]> * generalising bruteforce cuda implementation Signed-off-by: charliebudd <[email protected]> * updating testing scripts Signed-off-by: charliebudd <[email protected]> * file organisiation Signed-off-by: charliebudd <[email protected]> * fixing weight error in cpu bruteforce implementation, also inlineing functions Signed-off-by: charliebudd <[email protected]> * some refactoring and introducing proper batch handling Signed-off-by: charliebudd <[email protected]> * fixing indexing error at border Signed-off-by: charliebudd <[email protected]> * fixing some artifacts in cuda phl for high color sigmas Signed-off-by: charliebudd <[email protected]> * fixing gaussian kernel function for cpu and cuda bruteforce Signed-off-by: charliebudd <[email protected]> * ensuring kernel is an odd numbered size Signed-off-by: charliebudd <[email protected]> * adding tests for precised implementation Signed-off-by: charliebudd <[email protected]> * adding approximate imlpementation test Signed-off-by: charliebudd <[email protected]> * templating implementations based on scalar_type Signed-off-by: charliebudd <[email protected]> * cleaning up Signed-off-by: charliebudd <[email protected]> * code formatting Signed-off-by: charliebudd <[email protected]> * removing half precision implementation for permutohedral due to errors caused on windows Signed-off-by: charliebudd <[email protected]> * skipping cuda tests if cuda missing Signed-off-by: charliebudd <[email protected]> * reformating Signed-off-by: charliebudd <[email protected]> * adding unit test skip based on cpp extention availablility Signed-off-by: charliebudd <[email protected]> * removing unused import Signed-off-by: charliebudd <[email protected]> * changing to use of THCatomic add Signed-off-by: charliebudd <[email protected]> * adding missing licenses Signed-off-by: charliebudd <[email protected]> * clang reformat Signed-off-by: charliebudd <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

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

…inference Signed-off-by: Sachidanand Alle <[email protected]>

Signed-off-by: Sachidanand Alle <[email protected]>

SachidanandAlle · 2020-12-23T20:43:16Z

Refer: #1395

tvercaut mentioned this pull request Dec 8, 2020

Versatile distance transforms (Euclidean and Geodesic) #1332

Open

SachidanandAlle mentioned this pull request Dec 14, 2020

Tutorial to run train/evaluation/inference for a 2D/3D Deepgrow Model Project-MONAI/tutorials#88

Merged

SachidanandAlle and others added 26 commits December 23, 2020 12:26

[WIP] Support Deepgrow 2D/3D Training

0bec313

Signed-off-by: Sachidanand Alle <[email protected]>

Remove sample train scripts from PR

4feb450

Signed-off-by: Sachidanand Alle <[email protected]>

Adds an image to bounding box transform (#1326)

67851f5

* adds a bounding box transform Signed-off-by: Wenqi Li <[email protected]> * fixes integration Signed-off-by: Wenqi Li <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

Remove flake8 from requirements-dev.txt during public container image…

dce81d5

… build (#1327) flake8-executable is GPL'ed Signed-off-by: Isaac Yang <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

fixes tutorial #82 (#1331)

85e7abe

* adds test init_reader Signed-off-by: Wenqi Li <[email protected]> * fixes loadimage Signed-off-by: Wenqi Li <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

fixes params groups (#1339)

7aeb01e

* fixes params groups Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

1338 Enhance save_final in CheckpointSaver handler (#1341)

ee5d509

* [DLMED] enhance save_final in CheckpointSaver Signed-off-by: Nic Ma <[email protected]> * [DLMED] add log message Signed-off-by: Nic Ma <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

fixes #1353 (#1354)

22ef301

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

support both 2D and 3D transform for deepgrow

2a652fe

Signed-off-by: Sachidanand Alle <[email protected]>

Add ConvertToMultiChannelBasedOnBratsClassesd to handle BraTS18 datas…

bff4d3a

…et label (#1347) Signed-off-by: Isaac Yang <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

Clean up not required items

e83a69f

Signed-off-by: Sachidanand Alle <[email protected]>

remove not-used args for dataset creation

0bbf956

Signed-off-by: Sachidanand Alle <[email protected]>

Update changelog for 0.4.0 (#1355)

c0a7ec1

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

Fix randomness in AddExtremePointsChanneld transform (#1363)

10508a2

* Fix randomness in dictionary transform Signed-off-by: YuanTingHsieh <[email protected]> * Fix optional Signed-off-by: YuanTingHsieh <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

Update docs for GitHub Discussion tab (#1364)

3c13dae

* Update docs for GitHub Discussion tab Signed-off-by: Richard Brown <[email protected]> * discussion -> discussions Signed-off-by: Richard Brown <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

1346-enhance-highresnet-acti-norm (#1365)

ea6d4e3

* fixes #1346 Signed-off-by: Wenqi Li <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

wyli and others added 14 commits December 23, 2020 12:26

update weekly preview (#1366)

8458cd5

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

adding .venv directory to ignores for flake8 and isort (#1371)

00db833

Signed-off-by: charliebudd <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

adding modules to requirments-dev.txt that are needed to build the do…

7414dd3

…cs (#1374) Signed-off-by: charliebudd <[email protected]> Signed-off-by: Sachidanand Alle <[email protected]>

[DLMED] add missing import (#1376)

e7f491a

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

adds jpeg (#1379)

4ae9521

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

[DLMED] add missing arg in GANTrainer (#1383)

27d4885

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

update contributing and normalis* -> normaliz* (#1388)

80a3641

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

Support deepgrow stats handler for detailed metrics + transforms for …

99d5262

…inference Signed-off-by: Sachidanand Alle <[email protected]>

Fix build

e0b32b5

Signed-off-by: Sachidanand Alle <[email protected]>

Fix coverage

bda97fd

Signed-off-by: Sachidanand Alle <[email protected]>

Fix optional import

cf66ac7

Signed-off-by: Sachidanand Alle <[email protected]>

Fix optional import

8a5049a

Signed-off-by: Sachidanand Alle <[email protected]>

SachidanandAlle closed this Dec 23, 2020

SachidanandAlle mentioned this pull request Dec 23, 2020

[WIP] Support to train/run Deepgrow 2D/3D models #1395

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[WIP] Support Deepgrow 2D/3D Training#1329

[WIP] Support Deepgrow 2D/3D Training#1329
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