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Merged
Nic-Ma merged 115 commits into from
Oct 20, 2021
Merged

merge master #250

Nic-Ma merged 115 commits into from
Oct 20, 2021

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@Nic-Ma Nic-Ma commented Oct 20, 2021

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 -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.

wyli and others added 30 commits September 8, 2021 12:38
@wyli
2901 ndim -> spatial_dims (#2903)
7cfc8ea 
* ndim -> spatial_dims

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* dimensions -> spatial_dims

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* deprecated arg with auto replacement

Signed-off-by: Wenqi Li
@Nic-Ma
2898 Merge LocalPatchShuffle with RandCoarseDropout (#2907)
7f3050a 
* [DLMED] merge LocalPatchShuffle

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] enhance doc-string

Signed-off-by: Nic Ma <nma@nvidia.com>
@rijobro
Torch Zoom (#2916)
e52a0fe 
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@rijobro
Torch RandRotate90 (#2915)
281c17e 
Torch RandRotate
@bhashemian
CuPy to Tensor (#2919)
ef09811 
* Add cupy to tensor

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Add unittest for cupy>tensor

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@Nic-Ma @wyli
[DLMED] add dict version shuffle (#2918)
e2965db 
Signed-off-by: Nic Ma <nma@nvidia.com>

Co-authored-by: Wenqi Li <wenqil@nvidia.com>
@bhashemian
Add device to ToTensor (#2926)
448cdca
@Nic-Ma
2920 Enhance padding mode for Tensor data (#2921)
c50235c 
* [DLMED] enhance the pad mode

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update all the tensor pad related

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix error tests

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix GPU tests

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>
@wyli
fixes #2939 (#2940)
1c2608f 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
enhance docstring (#2938)
76dc5c2 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma
[DLMED] enhance scale intensity transforms (#2941)
8651b62 
Signed-off-by: Nic Ma <nma@nvidia.com>
@wyli
2715 enhance resnet downsampling block (#2937)
132aa37 
* con1_padding -> conv1_padding

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* simpler init.

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes 2715

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* adds 3d tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes flake8 error

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@rijobro
ThresholdIntensity, ThresholdIntensityd (#2944)
8765fc7 
* ThresholdIntensity, ThresholdIntensityd

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@diazandr3s
Add dropout arg in DynUNet init (#2947)
01feacb 
* Add dropout arg in DynUNet init

Signed-off-by: Andres <diazandr3s@gmail.com>
@Nic-Ma @wyli
2925 Add device option to EnsureType (#2942)
7ab0711 
* [DLMED] add device option

Signed-off-by: Nic Ma <nma@nvidia.com>

* look up options for types

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* adds unit tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Co-authored-by: Wenqi Li <wenqil@nvidia.com>
@rijobro
ScaleIntensityRange, ScaleIntensityRanged, ScaleIntensityRangePercent…
f26a712 
…iles, ScaleIntensityRangePercentilesd (#2943)

ScaleIntensityRange, ScaleIntensityRanged, ScaleIntensityRangePercentiles, ScaleIntensityRangePercentilesd
@rijobro
Rotate, Rotated, RandRotate, RandRotated (#2945)
f77a799 
Rotate, Rotated, RandRotate, RandRotated
@rijobro
AffineGrid, RandAffineGrid, Resample, Affine, RandAffine, Affined, Ra…
a14ed1b 
…ndAffined, Rand2dElastic, Rand3dElastic, Rand2dElasticd, Rand3dElasticd (#2922)

* AffineGrid, RandAffineGrid, Resample

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* Affine, RandAffine, Affined, RandAffined

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* deprecate as_tensor_output

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* fixes

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* remove plotting

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* Rand2dElastic, Rand3dElastic, Rand2dElasticd, Rand3dElasticd

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* CropForeground

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* fix Invertd

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@rijobro
All transforms support torch and numpy (#2949)
7c45d01 
* transforms convert to the necessary type

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@bhashemian
Add dtype to ToCupy (#2950)
ff9c80f 
* Add dtype to ToCuPy

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Add unittests to include dtype

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Implement convert_to_cupy

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Addressed all comments

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Addressed all comments

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Add dtype for Sequence

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@Nic-Ma
2948 Enhance the transform to delete items (#2952)
c624ffc 
* [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] remove unnecessary arg

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix style issue

Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
2951 Optimize type_conversion logic (#2955)
2f4b582 
* [DLMED] enhance type conversion

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix CI test

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] add more unit tests

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix flake8

Signed-off-by: Nic Ma <nma@nvidia.com>
@wyli
2231 Fixes tutorial 353 (#2954)
0f17aa9 
* fixes tutorial 353

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* adding type tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* improves type checks

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes flake8

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes as channel first

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* type test option

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* ndarray suuport

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes unit tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

 update

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* bash option for windows test

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes unit tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* enhance norm intensity tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes merge tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma
[DLMED] fix float64 bug (#2961)
fb2c2e9 
Signed-off-by: Nic Ma <nma@nvidia.com>
@ahatamiz
add multi-modal (vision + language) transformers (#2962)
3b6f479 
* add multimodal transformers

Signed-off-by: ahatamizadeh <ahatamizadeh@nvidia.com>
@rijobro
Torch: map_binary_to_indices, map_classes_to_indices, `correct_cr…
71ebd91 
…op_centers`, `generate_pos_neg_label_crop_centers`, `generate_label_classes_crop_centers` (#2958)

torch map_binary_to_indices, map_classes_to_indices, correct_crop_centers, generate_pos_neg_label_crop_centers, generate_label_classes_crop_centers
@bhashemian
cuCIM Transform (#2932)
38403ed 
* Implement CuCIM wrapper transfrom

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@rijobro
torch SpatialCrop, SpatialCropd (#2963)
0c39281 
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@bhashemian
Update with cupy.ndarray (#2965)
43a4342 
* Update with cupy.ndarray

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Change to use has_cp

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Change the format

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* Fix a bug

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@ericspod
Fix for Jupyter plotting (#2964)
46e594f 
* Fix for Jupyter plotting

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

* Fix for Jupyter plotting

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

* Fix for Jupyter plotting

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
Nic-Ma and others added 29 commits October 8, 2021 18:50
@Nic-Ma @wyli
3082 Enhance heavy random computation of transforms (#3086)
484bb5c 
* [DLMED] enhance random computation

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>

Co-authored-by: Wenqi Li <wenqil@nvidia.com>
@rijobro @wyli
Torch CropForeground, HistogramNormalize, RandHistogramShift (#…
dc970c7 
…3079)

* Torch `CropForeground`, `HistogramNormalize`, `RandHistogramShift`

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* fix

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

Co-authored-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma
[DLMED] fix wrong doc-string (#3096)
ce38a93 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
2998 Add MLFlowHandler (#3099)
31f9c1e 
* [DLMED] add MLFlowHandler

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] add optional import

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix doc format

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix CI test

Signed-off-by: Nic Ma <nma@nvidia.com>
@rijobro
KeepLargestConnectedComponent(d) example transforms (#3108)
7b1b772 
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@rijobro
Torch AddCoordinateChannels, ExtremePointsChannel, `RandWeightedC…
c346956 
…rop` (#3078)

Torch `AddCoordinateChannels`, `ExtremePointsChannel`, `RandWeightedCrop`
@Nic-Ma
Fix wrong doc-strings in several handlers (#3109)
712d90b 
* [DLMED] fix wrong doc

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>
@wyli
3097 - deprecated_arg replacing name (#3107)
3c8cc78 
* fixes 33097

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes typo

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update based on comments

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma
3087 enhance usage of intensity RandomizableTransform (#3094)
e0f84f2 
* [DLMED] update intensity transforms

Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
3087 Enhance other RandomizableTransform transforms (#3113)
ce76ec7 
* [DLMED] update all the other transforms

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix CI tests

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix CPU test

Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma @wyli
[DLMED] fix 1.5.1 cron test (#3121)
9b9516c 
Signed-off-by: Nic Ma <nma@nvidia.com>

Co-authored-by: Wenqi Li <wenqil@nvidia.com>
@wyli
3122 pytorch versions tests (#3123)
c4dd43f 
* adds new tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* temp tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes the tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* split yml

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes typo

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@BenTenmann
feat: refactor seg-net for easier use (#3057)
ed9cd41 
* feat: refactor seg-net for easier use

Signed-off-by: BenTenmann <benji.tenmann@me.com>
@wyli @monai-bot
3127 fixes autopep8 error (#3128)
e29a6ea 
* ignores E402 Module level import not at top of file

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* exlcude

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* ignore

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [MONAI] python code formatting

Signed-off-by: monai-bot <monai.miccai2019@gmail.com>

Co-authored-by: monai-bot <monai.miccai2019@gmail.com>
@Nic-Ma @ericspod @wyli
[DLMED] add state attr (#3125)
356af91 
Signed-off-by: Nic Ma <nma@nvidia.com>

Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Co-authored-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma
3124 3126 Fix integration tests (#3130)
cd6e90c 
* [DLMED] add state attr

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix integration test

Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma @wyli
3114 Add fast training integration test (#3120)
6dc65db 
* [DLMED] add integration test

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] add more random test

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>

Co-authored-by: Wenqi Li <wenqil@nvidia.com>
@rijobro
allow ROIs bigger than im for RandCropByLabelClasses, RandCropByPosNe…
6155724 
…gLabel (#3129)

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@wyli
skip tests for torch 1.5 (#3131)
ff08334 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
senet tests with testing data (#3136)
1259042 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
3134 fixes module alias (#3135)
0a9d8aa 
* add alias tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* monai.losses.dice

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* monai.utils.deprecated

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* monai.networks.nets.senet

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* monai.networks.nets.dynunet

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* monai.networks.nets.unet

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* monai.networks.nets.densenet

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* monai.networks.nets.ahnet

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* only check for the existing modules

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes docs

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
3133 pytorch image 2109 (#3137)
3573079 
* upgrade torch image to 2109

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* temp tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* more time for fast training

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* Revert "temp tests"

This reverts commit a5b4447.

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@yiheng-wang-nv @pre-commit-ci
2186 add Grid Distortion transform (#3117)
d538aa5 
* add griddistortion

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

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

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

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

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

* fix pre-commit ci black error

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* add unittest

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@Nic-Ma
400 Add example in the doc-string of Metric (#3139)
467138f 
* [DLMED] add metric example

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>
@wyli
update rand grid distortions (#3144)
071879e 
* update rand grid distortion

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update docs

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update based on comments

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes formatting and errors

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma
Add Tensor support to CropForegroundd transform (#3140)
6938313 
* [DLMED] add Tensor to CropForegroundd transform

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] enhance data conversion

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] add more tests and fix convert tensor issue

Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
[DLMED] fix data type issue (#3143)
2920dd3 
Signed-off-by: Nic Ma <nma@nvidia.com>
@deepsource-autofix @monai-bot
Refactor unnecessary else / elif when if block has a return s…
c4fe607 
…tatement (#3147)

* Refactor unnecessary `else` / `elif` when `if` block has a `return` statement

* black --skip-magic-trailing-comma

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [MONAI] python code formatting

Signed-off-by: monai-bot <monai.miccai2019@gmail.com>

Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>
Co-authored-by: monai-bot <monai.miccai2019@gmail.com>
@wyli
2824 deprecate self-hosted docker tests (#3145)
dfcfa9a 
* update versioning

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* build docker

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* install docker

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* remove selfhosted

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update docs

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* ubuntu cpu tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* full tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* test docker options

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* full tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* full tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* exclude open slide tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* temp tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* full tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* temp checkout

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* full tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* full tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes flake8 error

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* skip weights downloading when http error out

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma Nic-Ma merged commit 87c9dbf into Nic-Ma:add-handler-example-link Oct 20, 2021
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