merge master by Nic-Ma · Pull Request #108 · Nic-Ma/MONAI

Nic-Ma · 2021-05-19T01:46:10Z

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.

* 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]>

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

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

* [DLMED] add Affined transform 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]>

* update for torch 1.8.0 Signed-off-by: Wenqi Li <[email protected]> * mute codecov upload error Signed-off-by: Wenqi Li <[email protected]>

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

with allow_missing_keys_mode

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

* fixes #1500 update grid dataset to support patch level transforms Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] update type of arg in workflows 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] fix flake8 issue 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]>

* 1651 implement RegUNet Signed-off-by: kate-sann5100 <[email protected]>

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

* Update MONAI Docker with OpenSlide dependencies Signed-off-by: Behrooz <[email protected]> * Update cron job to install apt dependencies Signed-off-by: Behrooz <[email protected]>

* use eval for getting class_idx for gradcam

* skip RandAffine if possible Signed-off-by: Richard Brown <[email protected]> * add randaffined Signed-off-by: Richard Brown <[email protected]> * mypy fix Signed-off-by: Richard Brown <[email protected]> * check consistency Signed-off-by: Richard Brown <[email protected]>

* [DLMED] use shutil.move instead 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]> Co-authored-by: Wenqi Li <[email protected]>

This reverts commit 9c62769. Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] add notnans to summary Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix bug in the dist test Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance the percent Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] update tests 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]>

fix cachedataset w persistent workers problem by deep copying first non-deterministic transform

* adding proposal implementation for reg. metrics Signed-off-by: masadcv <[email protected]> * add ignite wrappers regression metrics, needs test Signed-off-by: masadcv <[email protected]> * refactoring and adding docstrings with equations Signed-off-by: masadcv <[email protected]>

* [DLMED] enhance unit test of UNet Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance tests Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add Invertd transform Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix doc build Signed-off-by: Nic Ma <[email protected]> * [DLMED] skip min test Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix CI test Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance docs Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance doc-string 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]>

Signed-off-by: Richard Brown <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]>

* [DLMED] enhance Invertd and SaveImage Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more test Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove unwanted files 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] enhance doc-string 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]>

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

* Add reference for surface distance metric Signed-off-by: Yiheng Wang <[email protected]> * Add reference for hausdorff distance Signed-off-by: Yiheng Wang <[email protected]>

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

fix set visible devices

* better way of managing Cache Signed-off-by: Coen <[email protected]> * Update test_smartcachedataset.py Signed-off-by: Coen <[email protected]>

* fixes docstring Signed-off-by: Wenqi Li <[email protected]> * 2099 docstring updates Signed-off-by: Wenqi Li <[email protected]>

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

test network consistency

* enhance norm and act layers Signed-off-by: Yiheng Wang <[email protected]> * write generic norm and act layers Signed-off-by: Yiheng Wang <[email protected]> * Fix flake8 errors Signed-off-by: Yiheng Wang <[email protected]>

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

gibbs transform

* enhance get layers Signed-off-by: Wenqi Li <[email protected]> * codeformat/typo fixes Signed-off-by: Wenqi Li <[email protected]> * fixes type errors Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] add RandScaleCrop Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update for corner case Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo 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]>

* Add array and dictionary based CoordConv transforms Signed-off-by: Mark <[email protected]> * Add comments and input checks Signed-off-by: Mark Graham <[email protected]> * Add docs for CoordConv Signed-off-by: Mark Graham <[email protected]> * Add tests for CoordConv Signed-off-by: Mark Graham <[email protected]> * Renames to AddCoordinateChannels and simplifies transform code Signed-off-by: Mark Graham <[email protected]> * Test input channel is unchanged and shorten code more Signed-off-by: Mark Graham <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: Richard Brown <[email protected]> Co-authored-by: monai-bot <[email protected]>

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

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

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

* [DLMED] enhance CSVSaver Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix test errors 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]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] update accoring to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

YuanTingHsieh and others added 30 commits March 1, 2021 16:07

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]>

Raise import error for openslide and cuimage (#1699)

66811fe

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

1604 Revise docstring cam (#1705)

b25b3d3

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

1704 Add Affined transform (#1709)

ce6628a

* [DLMED] add Affined transform 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]>

1693 update for pytorch 1.8 (#1700)

133f42a

* update for torch 1.8.0 Signed-off-by: Wenqi Li <[email protected]> * mute codecov upload error Signed-off-by: Wenqi Li <[email protected]>

[DLMED] update datasets (#1712)

634b32d

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

with allow_missing_keys_mode (#1714)

08af0cc

with allow_missing_keys_mode

update links (#1717)

f4560a1

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

1500-update grid dataset to support patch level transforms (#1679)

cbddce9

* fixes #1500 update grid dataset to support patch level transforms Signed-off-by: Wenqi Li <[email protected]>

1651 implement RegUNet (#1658)

78ec66f

* 1651 implement RegUNet Signed-off-by: kate-sann5100 <[email protected]>

remove print msg (#1730)

ea1d04b

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

Fix MONAI docker dependency (#1731)

a462714

* Update MONAI Docker with OpenSlide dependencies Signed-off-by: Behrooz <[email protected]> * Update cron job to install apt dependencies Signed-off-by: Behrooz <[email protected]>

[1710] Gradcam eval (#1734)

d4c201e

* use eval for getting class_idx for gradcam

rijobro and others added 29 commits May 6, 2021 21:31

Revert "Pytype fix (#2153)" (#2157)

2a4c9e5

This reverts commit 9c62769. Signed-off-by: Wenqi Li <[email protected]>

fix cachedataset w persistent workers problem by deep copying (#2121)

4259151

fix cachedataset w persistent workers problem by deep copying first non-deterministic transform

2155 Enhance tests of UNet for user's case (#2160)

68e2d78

* [DLMED] enhance unit test of UNet Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance tests Signed-off-by: Nic Ma <[email protected]>

delete set_visible_devices (#2168)

eca3f19

Signed-off-by: Richard Brown <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]>

fix typo (#2176)

3045ade

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

Add reference for surface distance metric (#2182)

6b0df49

* Add reference for surface distance metric Signed-off-by: Yiheng Wang <[email protected]> * Add reference for hausdorff distance Signed-off-by: Yiheng Wang <[email protected]>

fix set visible devices (#2174)

6c0d8d7

fix set visible devices

More efficient SmartCacheLoader (#2181)

4ef7d22

* better way of managing Cache Signed-off-by: Coen <[email protected]> * Update test_smartcachedataset.py Signed-off-by: Coen <[email protected]>

2099 - enhances dataloader/randomizable docstrings (#2188)

a5cf253

* fixes docstring Signed-off-by: Wenqi Li <[email protected]> * 2099 docstring updates Signed-off-by: Wenqi Li <[email protected]>

tested (#2192)

b94fe25

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

initial network consistency test (#2171)

e68af74

test network consistency

enhance norm and act layers (#2166)

29a0373

* enhance norm and act layers Signed-off-by: Yiheng Wang <[email protected]> * write generic norm and act layers Signed-off-by: Yiheng Wang <[email protected]> * Fix flake8 errors Signed-off-by: Yiheng Wang <[email protected]>

update msg (#2197)

05e1ec2

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

Added Gibbs transform (#2163)

0e6f945

gibbs transform

enhance get layers API (#2199)

95726b0

* enhance get layers Signed-off-by: Wenqi Li <[email protected]> * codeformat/typo fixes Signed-off-by: Wenqi Li <[email protected]> * fixes type errors Signed-off-by: Wenqi Li <[email protected]>

fixes logo link (#2202)

bbca50d

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

Add warnings for inf/nan surface distance (#2205)

ca0bda1

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

allow sequence for network consistency (#2209)

fed0136

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

Nic-Ma merged commit 35679ff into Nic-Ma:2208-add-meta-key May 19, 2021

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merge master#108

merge master#108
Nic-Ma merged 263 commits intoNic-Ma:2208-add-meta-keyfrom
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Nic-Ma commented May 19, 2021

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