merge master by Nic-Ma · Pull Request #90 · Nic-Ma/MONAI

Nic-Ma · 2021-04-27T00:58:43Z

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.

* update openmp flag Signed-off-by: Wenqi Li <[email protected]> * improves boundtype docs Signed-off-by: Wenqi Li <[email protected]> * update setup.py Signed-off-by: Wenqi Li <[email protected]> * input validation 1d Signed-off-by: Wenqi Li <[email protected]> * fixes typos Signed-off-by: Wenqi Li <[email protected]> * fixes typos Signed-off-by: Wenqi Li <[email protected]> * merge upstream changes Signed-off-by: Wenqi Li <[email protected]> * tests enums Signed-off-by: Wenqi Li <[email protected]> * init. test grid pull Signed-off-by: Wenqi Li <[email protected]> * update Signed-off-by: Wenqi Li <[email protected]> * test grid_pull Signed-off-by: Wenqi Li <[email protected]> * fixes min test Signed-off-by: Wenqi Li <[email protected]> * adds device tests Signed-off-by: Wenqi Li <[email protected]> * bwd tests Signed-off-by: Wenqi Li <[email protected]>

move transforms out of compose file. this is backwards compatible.

* pad_collation Signed-off-by: Richard Brown <[email protected]> * increase number of test cases to ensure required testing errors Signed-off-by: Richard Brown <[email protected]> * determinism in setUp Signed-off-by: Richard Brown <[email protected]> * pad collate for list of lists Signed-off-by: Richard Brown <[email protected]> * code format Signed-off-by: Richard Brown <[email protected]> * allow padding options Signed-off-by: Richard Brown <[email protected]>

decollate batch

enhance random range parameters If element `i` is iterable, then `uniform[-rotate_range[i][0], rotate_range[i][1])` will be used to generate the rotation parameter for the ith dimension. If not, `uniform[-rotate_range[i], rotate_range[i])` will be used. This can be altered on a per-dimension basis. E.g., `((0,3), 1, ...)`: for dim0, rotation will be in range `[0, 3]`, and for dim1 `[-1, 1]` will be used. Setting a single value will use `[-x, x]` for dim0 and nothing for the remaining dimensions. Backwards compatibility is ensured because the old behaviour used to do `uniform[-rotate_range[i], rotate_range[i])`, and this PR just adds the possibility to do `uniform[-rotate_range[i][0], rotate_range[i][1])`.

* Fixing issues preventing loss functions from being compatible with Torchscript Signed-off-by: Eric Kerfoot <[email protected]> * Updates Signed-off-by: Eric Kerfoot <[email protected]> * Updates Signed-off-by: Eric Kerfoot <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * Updates Signed-off-by: Eric Kerfoot <[email protected]> * Adding conditional skip to Torchscript tests Signed-off-by: Eric Kerfoot <[email protected]> Co-authored-by: monai-bot <[email protected]>

* [DLMED] fix length > 1024 issue in string list all gather Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue 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] add more test Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Yiheng Wang <[email protected]>

* DeleteChannel array, dictionary, tests Signed-off-by: Leo Tam <[email protected]> * formatting Signed-off-by: Leo Tam <[email protected]> * DeleteChannel array, dictionary, tests Signed-off-by: Leo Tam <[email protected]> * Register in transform init Signed-off-by: Leo Tam <[email protected]> * clean comment Signed-off-by: Leo Tam <[email protected]> * Dict init Signed-off-by: Leo Tam <[email protected]> * Register D and Dict Signed-off-by: Leo Tam <[email protected]> * Style fix Signed-off-by: Leo Tam <[email protected]> * Safety cast Signed-off-by: Leo Tam <[email protected]> * Changinging names from DeleteChannel to RemoveRepeatedChannel Signed-off-by: Leo Tam <[email protected]> * Lint fixes Signed-off-by: Leo Tam <[email protected]> * Test import fix, autofix again Signed-off-by: Leo Tam <[email protected]>

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

* update distcall Signed-off-by: Wenqi Li <[email protected]> * update final closing Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]>

* Add ToPIL transformation Signed-off-by: Behrooz <[email protected]> * Add ToPILd, ToPILD, ToPILDict Signed-off-by: Behrooz <[email protected]> * Remove has_pil Signed-off-by: Behrooz <[email protected]> * Include ToPIL, ToPILd, ToPILD, and ToPILDict Also include ToNumpyD, ToNumpyDict, TorchVisionD, and TorchVisionDict Signed-off-by: Behrooz <[email protected]> * Fix a typing issue Signed-off-by: Behrooz <[email protected]> * Fix PIL optional import Signed-off-by: Behrooz <[email protected]> * Add unittests for ToPIL and ToPILD Signed-off-by: Behrooz <[email protected]> * Fix formatting Signed-off-by: Behrooz <[email protected]> * Fix formatting Signed-off-by: Behrooz <[email protected]> * Add PILImage.Image as the input for ToNumpy and ToTensor Signed-off-by: Behrooz <[email protected]> * Fix type checking issue for PIL.Image.Image Signed-off-by: Behrooz <[email protected]> * Change PILImage_fromarray to lower case Signed-off-by: Behrooz <[email protected]>

add RandomizableTransform

* Add more tests to test_deepgrow_dataset Signed-off-by: YuanTingHsieh <[email protected]>

* Add inference transforms Signed-off-by: YuanTingHsieh <[email protected]> * Remove unused import Signed-off-by: YuanTingHsieh <[email protected]> * Fix review comments Signed-off-by: YuanTingHsieh <[email protected]> Co-authored-by: SACHIDANAND ALLE <[email protected]>

* [DLMED] add RandAxisFlip transforms Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix flake8 issues Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

fix big endianness problem for dictionary reading. Also allow dictionary image_only

* [DLMED] add AutoAdjustChannel transform Signed-off-by: Nic Ma <[email protected]> * [DLMED] add dict version transform Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix doc-build issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to Wenqi's comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update doc-strings 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]>

Allow missing keys

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

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

* Update load pretrain for densenet Signed-off-by: Yiheng Wang <[email protected]> * Fix isort issue Signed-off-by: Yiheng Wang <[email protected]>

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

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

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

* fixes #1285 Signed-off-by: Wenqi Li <[email protected]> * adds test Signed-off-by: Wenqi Li <[email protected]>

* fixes #1685 Signed-off-by: Wenqi Li <[email protected]> * add temp test Signed-off-by: Wenqi Li <[email protected]> * adds docstring Signed-off-by: Wenqi Li <[email protected]> * fixes dist sampler Signed-off-by: Wenqi Li <[email protected]> * remove temp tests Signed-off-by: Wenqi Li <[email protected]> * fixes type hint issue Signed-off-by: Wenqi Li <[email protected]>

* fixes data type in switching Signed-off-by: Wenqi Li <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]>

* Implement CuImageReader and OpenSlideReader Signed-off-by: Behrooz <[email protected]> * Add unittests for CuImageReader Signed-off-by: Behrooz <[email protected]> * Add unittests for OpenSlideReader Signed-off-by: Behrooz <[email protected]> * Sort imports Signed-off-by: Behrooz <[email protected]> * Add correct boundaries Signed-off-by: Behrooz <[email protected]> * Add test cases for reading patches on a grid for CuImage Signed-off-by: Behrooz <[email protected]> * Add patch whole slide imaging dataset for pathology Signed-off-by: Behrooz <[email protected]> * Add test case for read patches for OpenSlide Signed-off-by: Behrooz <[email protected]> * flake8 and few minor changes Signed-off-by: Behrooz <[email protected]> * black Signed-off-by: Behrooz <[email protected]> * flake8 Signed-off-by: Behrooz <[email protected]> * Add kwargs to CuImageReader and OpenSlideReader's read method Signed-off-by: Behrooz <[email protected]> * Change the type hint from np.dtype to DTypeLike Signed-off-by: Behrooz <[email protected]> * Fix a bug Signed-off-by: Behrooz <[email protected]> * Implement WSIReader and unittests Signed-off-by: Behrooz <[email protected]> * Minor updates Signed-off-by: Behrooz <[email protected]> * Fix few typing issues Signed-off-by: Behrooz <[email protected]> * Revert datasets Signed-off-by: Behrooz <[email protected]> * Add shape property to openslide image object Reverse size to be compatible with output size (hxw) Signed-off-by: Behrooz <[email protected]> * Add untittest for loading the whole image Reverse the size accroding to the WSIReader Signed-off-by: Behrooz <[email protected]> * Update the whole image size Signed-off-by: Behrooz <[email protected]> * Remove optional size Signed-off-by: Behrooz <[email protected]> * Remove optional dtype Signed-off-by: Behrooz <[email protected]> * Remove _get_spatial_shape return type Signed-off-by: Behrooz <[email protected]> * Reverse the orders of dimensions of `location` to be compatible with image shape Signed-off-by: Behrooz <[email protected]> * Change test cases to use smaller image and revese location's dimensions Signed-off-by: Behrooz <[email protected]> * Replace the test TIFF and some upgrades Signed-off-by: Behrooz <[email protected]> * Update dependencies for OpenSlide Signed-off-by: Behrooz <[email protected]> * Update unittests for OpenSlide and CuImage Signed-off-by: Behrooz <[email protected]> * Fix openslide dependency Signed-off-by: Behrooz <[email protected]> * Fix doc dependencies Signed-off-by: Behrooz <[email protected]> * Minor changes Signed-off-by: Behrooz <[email protected]> * Few variable name changes Signed-off-by: Behrooz <[email protected]> * Add EnsureChannelFirst Signed-off-by: Behrooz <[email protected]> * Add metadata to WSIReader Signed-off-by: Behrooz <[email protected]>

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]>

* [DLMED] save inverted meta dict Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * safe key get Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: monai-bot <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

@jhlegarreta

Based on the ITK welcome: https://github.com/InsightSoftwareConsortium/ITK/blob/master/CONTRIBUTING.md by @jhlegarreta

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

* [DLMED] add divisible K Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI tests Signed-off-by: Nic Ma <[email protected]>

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

* enhance persistent temp Signed-off-by: Wenqi Li <[email protected]> * fixes windows file rename issue Signed-off-by: Wenqi Li <[email protected]> * enhance multiprocess LMDB Signed-off-by: Wenqi Li <[email protected]> * remove usued vars Signed-off-by: Wenqi Li <[email protected]> * fixes LGTM errors Signed-off-by: Wenqi Li <[email protected]> * remove comparison-with-callable (W0143) Signed-off-by: Wenqi Li <[email protected]> * fixes pylint W0231 Signed-off-by: Wenqi Li <[email protected]> * fixes PYL-R1705 Signed-off-by: Wenqi Li <[email protected]> * fixes PYL-R1720 Signed-off-by: Wenqi Li <[email protected]> * fixes PTC-W0060 Signed-off-by: Wenqi Li <[email protected]> * fixes PYL-W0105 Signed-off-by: Wenqi Li <[email protected]> * fixes PTC-W0016 Signed-off-by: Wenqi Li <[email protected]>

* update box_start/end for deepgrow Signed-off-by: Richard Brown <[email protected]> * add test Signed-off-by: Richard Brown <[email protected]>

wyli and others added 30 commits February 24, 2021 15:02

move transforms out of compose file (#1623)

3a1c459

move transforms out of compose file. this is backwards compatible.

decollate batch (#1624)

69d9fcc

decollate batch

[DLMED] add progress arg (#1647)

c68d25e

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

1650-update distcall (#1652)

5875ae6

* update distcall Signed-off-by: Wenqi Li <[email protected]> * update final closing Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]>

Randomizable constructor (#1639)

1df6352

add RandomizableTransform

Add more tests to test_deepgrow_dataset (#1654)

4b8819a

* Add more tests to test_deepgrow_dataset Signed-off-by: YuanTingHsieh <[email protected]>

allow dictionary image only and test endianness (#1669)

20e17b2

fix big endianness problem for dictionary reading. Also allow dictionary image_only

[1662] Allow missing keys (#1676)

421c0a9

Allow missing keys

nifti saver squeeze dims (#1680)

27543c8

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

improve gradcam doc (#1682)

b533afd

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

fixes integration tests (#1683)

7cfb529

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

Update load pretrain for densenet (#1684)

4bd9cf3

* Update load pretrain for densenet Signed-off-by: Yiheng Wang <[email protected]> * Fix isort issue Signed-off-by: Yiheng Wang <[email protected]>

revise the dtype according to the discussion (#1671)

8cc200f

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

Fix senet pretrained weights issue (#1689)

ac9f953

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

1680 Add squeeze SegmentationSaver handler (#1686)

380f042

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

1285 adds module list (#1690)

114faf0

* fixes #1285 Signed-off-by: Wenqi Li <[email protected]> * adds test Signed-off-by: Wenqi Li <[email protected]>

fixes data type in switching (#1694)

75b5772

* fixes data type in switching Signed-off-by: Wenqi Li <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]>

[DLMED] add WSIReader to LoadImage (#1695)

232e8a5

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

wyli and others added 29 commits April 14, 2021 12:59

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]>

Add pointers to issues for community contributors (#2071)

7379ab8

Start with a welcoming statement in the contributing docs (#2072)

e0035b1

Based on the ITK welcome: https://github.com/InsightSoftwareConsortium/ITK/blob/master/CONTRIBUTING.md by @jhlegarreta

Remove transpose from the tissue masks (#2074)

fea9307

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

RandTorchVisionD update (#2076)

f45108b

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

update box_start/end for deepgrow (#2088)

dde1100

* update box_start/end for deepgrow Signed-off-by: Richard Brown <[email protected]> * add test Signed-off-by: Richard Brown <[email protected]>

Nic-Ma merged commit ac21fe9 into Nic-Ma:2092-enhance-nifti-log Apr 27, 2021

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merge master#90

merge master#90
Nic-Ma merged 209 commits intoNic-Ma:2092-enhance-nifti-logfrom
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Nic-Ma commented Apr 27, 2021

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Nic-Ma commented Apr 27, 2021

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