merge master by Nic-Ma · Pull Request #161 · Nic-Ma/MONAI

Nic-Ma · 2021-07-06T07:54:07Z

Fixes # .

Description

A few sentences describing the changes proposed in this pull request.

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 --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.

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

* handling error Signed-off-by: Wenqi Li <[email protected]> * temp test Signed-off-by: Wenqi Li <[email protected]> * fixes tests Signed-off-by: Wenqi Li <[email protected]> * Revert "temp test" This reverts commit 60661ae. Signed-off-by: Wenqi Li <[email protected]>

* update dev version Signed-off-by: Wenqi Li <[email protected]> * typo fix Signed-off-by: Wenqi Li <[email protected]>

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

TTA progress bar, use torch for mode, add label meta_data

* follow up of #1992 Signed-off-by: Wenqi Li <[email protected]> * update spacing inverse Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] update TransformInverter Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix deepcopy 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: Wenqi Li <[email protected]>

* [DLMED] add more tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] add nearest test cases Signed-off-by: Nic Ma <[email protected]>

* adds a what's new page Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] add SaliencyInferer Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance CAM logic Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Co-authored-by: Richard Brown <[email protected]> Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Richard Brown <[email protected]>

* [DLMED] enhance unit tests 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]>

* [DLMED] add warning 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]>

* Jupyter and other additions Signed-off-by: Eric Kerfoot <[email protected]>

* allow slicing with SpatialCrop(d) Signed-off-by: Richard Brown <[email protected]>

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

* fixes docstring Signed-off-by: Wenqi Li <[email protected]> * update example Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] add alias Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] add unit tests 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: Nic Ma <[email protected]>

* [DLMED] add more alias 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]>

* Implement RandTorchVisionD Signed-off-by: Behrooz <[email protected]> * Add unittest for RandTorchVisiond Signed-off-by: Behrooz <[email protected]> * Update docs Signed-off-by: Behrooz <[email protected]> * Formatting Signed-off-by: Behrooz <[email protected]>

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

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

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

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

* [DLMED] check the label data for Tensor Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>

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

* [DLMED] add `device` and `to_tensor` args Signed-off-by: Nic Ma <[email protected]> * [DLMED] add support for non-tensor output Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove detach.cpu Signed-off-by: Nic Ma <[email protected]>

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

* fix duplication of key_transforms in RandSpatialCropSamplesd Signed-off-by: Richard Brown <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] only deep copy unmodified Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]> Co-authored-by: Nic Ma <[email protected]>

Signed-off-by: Yiheng Wang <[email protected]>

* [DLMED] enhance ToTensor Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>

#2455) * add clara_train_covid19_3d_ct_classification and clara_train_covid19_annotation_ct_lung_1 point to pt version of covid19 lung annotation model Signed-off-by: Holger Roth <[email protected]>

* [DLMED] add pad options Signed-off-by: Nic Ma <[email protected]> * [DLMED] add to dict transforms Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

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

* [DLMED] update ignite to 0.4.5 Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add dynamic data list in CacheDataset Signed-off-by: Nic Ma <[email protected]> * [DLMED] add support to PersistentDataset Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance dataset Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update_data -> set_data Signed-off-by: Nic Ma <[email protected]>

Signed-off-by: Holger Roth <[email protected]>

…grow (#2442) Signed-off-by: vnath <[email protected]>

…2315) * [WIP] 2220 Decollate batch into list of tensors after model forward (#2244) * [DLMED] add support for Activation transform Signed-off-by: Nic Ma <[email protected]> * [DLMED] change all the array level post transforms to channel-first Signed-off-by: Nic Ma <[email protected]> * [DLMED] update all the IO, utility, post transforms Signed-off-by: Nic Ma <[email protected]> * [DLMED] update engines for list of dict Signed-off-by: Nic Ma <[email protected]> * [DLMED] update all the event handlers Signed-off-by: Nic Ma <[email protected]> * [DLMED] support non-batch data Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update based on the latest APIs Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix all the unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issues Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove unused import Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix integration test Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix integration tests Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix integration tests Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] add support to copy scalar Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix wrong unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix doc issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix broken tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix unit tests Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] simplify CSV saver Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] add copy_scalar_to_batch util Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] change to preprocessing and postprocessing Signed-off-by: Nic Ma <[email protected]> * [DLMED] change file name to postprocessing Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo in doc-string Signed-off-by: Nic Ma <[email protected]> * [DLMED] add Decollated back Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update to use ignite v0.4.5 metrics API Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix conflicts Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * fixes #2452 Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: monai-bot <[email protected]>

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

* enhance version compare Signed-off-by: Wenqi Li <[email protected]> * update Signed-off-by: Wenqi Li <[email protected]> * remove unused Signed-off-by: Wenqi Li <[email protected]> * remove unused vars Signed-off-by: Wenqi Li <[email protected]> * update debug info Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * non integer comparison Signed-off-by: Wenqi Li <[email protected]> * adds tests Signed-off-by: Wenqi Li <[email protected]> * no temp tests Signed-off-by: Wenqi Li <[email protected]> * update test Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Nic Ma <[email protected]>

* [DLMED] add deprecated decorator Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance doc-string Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

Signed-off-by: Jeff VanOss <[email protected]>

* [DLMED] add support to compare metrics Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>

* add UNETR, ViT Signed-off-by: ahatamizadeh <[email protected]> * add UNETR, ViT Signed-off-by: ahatamizadeh <[email protected]> * add UNETR, ViT Signed-off-by: ahatamizadeh <[email protected]> * add UNETR, ViT Signed-off-by: ahatamizadeh <[email protected]> * add UNETR, ViT Signed-off-by: ahatamizadeh <[email protected]> * add UNETR, ViT Signed-off-by: ahatamizadeh <[email protected]> * add UNETR, ViT Signed-off-by: ahatamizadeh <[email protected]>

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

* [DLMED] fix PatchEmbeddingBlock Signed-off-by: Nic Ma <[email protected]> * [DLMED] correct typehint Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix pos_embed and Rearrange types Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix nn.module Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix vit Signed-off-by: Nic Ma <[email protected]> * [DLMED] update docs Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix UNetr Signed-off-by: Nic Ma <[email protected]>

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

* 21.04->21.06 Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * temp test Signed-off-by: Wenqi Li <[email protected]> * Revert "temp test" This reverts commit f5385c2. Signed-off-by: Wenqi Li <[email protected]> * Revert "temp tests" This reverts commit 4468dcc. Signed-off-by: Wenqi Li <[email protected]> * update version number Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] add ignite dist support Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] change key_metric_score_sign to a bool flag Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

* [DLMED] add decollate logic Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix plot Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] update classification integration test Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] restore decollate logic Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

* [DLMED] fix strict_shape Signed-off-by: Nic Ma <[email protected]> * [DLMED] add warning message Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] add links Signed-off-by: Nic Ma <[email protected]> * [DLMED] Enhance doc-strings Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance CI tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 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]>

* [DLMED] make get_model_spec API Signed-off-by: Nic Ma <[email protected]> * [DLMED] unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]>

…2518) * [DLMED] update lr_scheduler links Signed-off-by: Nic Ma <[email protected]> * [DLMED] update all the other links Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]>

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

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

wyli and others added 30 commits April 11, 2021 11:07

add timeout (#1989)

f5d5737

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

1889 update preview version number (#1991)

b4d8780

* update dev version Signed-off-by: Wenqi Li <[email protected]> * typo fix Signed-off-by: Wenqi Li <[email protected]>

fix comprehension error (#1995)

d1f4e6f

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

TTA progress bar, use torch for mode, add label meta_data (#1992)

b3eb73a

TTA progress bar, use torch for mode, add label meta_data

include meta when inverting (#1997)

d72f61e

* follow up of #1992 Signed-off-by: Wenqi Li <[email protected]> * update spacing inverse Signed-off-by: Wenqi Li <[email protected]>

update (#2000)

2707407

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

Add more test for nearest interpolation in TransformInverter (#2001)

583e35b

* [DLMED] add more tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] add nearest test cases Signed-off-by: Nic Ma <[email protected]>

2003 - adds a what's new page (#2005)

2c6d688

* adds a what's new page Signed-off-by: Wenqi Li <[email protected]>

2007 Enhance the unit tests of MapLabelValue transform (#2008)

5f47407

* [DLMED] enhance unit tests 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]>

2011 Add warning for resample in SegnmentationSaver (#2013)

88806e1

* [DLMED] add warning 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]>

Plot engine fix (#2015)

357e6d4

* Jupyter and other additions Signed-off-by: Eric Kerfoot <[email protected]>

allow slicing with SpatialCrop(d) (#1954)

9f4da6a

* allow slicing with SpatialCrop(d) Signed-off-by: Richard Brown <[email protected]>

raising error tolerance to prevent rare failure (#2025)

abcca9b

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

fixes tutorial issue 183 (#2031)

9f409c1

* fixes docstring Signed-off-by: Wenqi Li <[email protected]> * update example Signed-off-by: Wenqi Li <[email protected]>

[DLMED] enhance error message (#2038)

a7a9430

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

2032 Add more alias for other networks (#2040)

170fc91

* [DLMED] add more alias 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]>

[DLMED] add post_func arg (#2049)

fc1546a

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

update docstring example (#2055)

de677ca

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

fixes tutorial issue 184 (#2053)

14976b5

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

Update cucim to 0.19.0 (#2057)

8057ae8

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

2044 Add check for label data type (#2060)

13bf996

* [DLMED] check the label data for Tensor Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>

[DLMED] enhance metrics (#2061)

51ecc48

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

fixes tutorial 190 (#2063)

5cbcaf6

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

yiheng-wang-nv and others added 29 commits June 26, 2021 06:00

Fix docstring error (#2461)

eb29e99

Signed-off-by: Yiheng Wang <[email protected]>

2453 Enhance ToTensor transform to support data with no dim (#2454)

9f9b63a

* [DLMED] enhance ToTensor Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>

add clara_train_covid19_3d_ct_classification and clara_train_covid19_… (

1a707f0

#2455) * add clara_train_covid19_3d_ct_classification and clara_train_covid19_annotation_ct_lung_1 point to pt version of covid19 lung annotation model Signed-off-by: Holger Roth <[email protected]>

update_model_desc_prostate_spleen (#2466)

7b08d40

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

2399 update ignite to v0.4.5 (#2451)

91ea1b6

* [DLMED] update ignite to 0.4.5 Signed-off-by: Nic Ma <[email protected]>

update clara_pt_covid19_3d_ct_classification model description (#2472)

cdf05b0

Signed-off-by: Holger Roth <[email protected]>

Model Description in apps/mmars updated with NGC description for Deep…

0aa936f

…grow (#2442) Signed-off-by: vnath <[email protected]>

2273 update model items (#2473)

f831c7f

Update blossom-ci.yml (#2484)

50d8391

match keys in doc code examples (#2469)

11af59a

Signed-off-by: Jeff VanOss <[email protected]>

update google drive links (#2491)

f4894bb

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

fixes pillow version (#2503)

ce45640

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

2512 Make get_model_spec API (#2515)

f3d436a

* [DLMED] make get_model_spec API Signed-off-by: Nic Ma <[email protected]> * [DLMED] unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]>

enhance one-hot documentation (#2521)

cfcce58

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

[DLMED] add first to from_engine (#2524)

025dee7

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

Nic-Ma merged commit 65096cc into Nic-Ma:2525-decollate-deepgrow Jul 6, 2021

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merge master#161

merge master#161
Nic-Ma merged 421 commits intoNic-Ma:2525-decollate-deepgrowfrom
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Nic-Ma commented Jul 6, 2021

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Nic-Ma commented Jul 6, 2021

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