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merge master #244

Merged
merged 95 commits into from
Oct 13, 2021
Merged

merge master #244

merged 95 commits into from
Oct 13, 2021

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Nic-Ma
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@Nic-Ma Nic-Ma commented Oct 13, 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>
Borda and others added 29 commits October 3, 2021 20:49
@Borda
remove redundant noqa (#3027)
8271d8e 
* apply yesqa

Signed-off-by: Jirka <jirka.borovec@seznam.cz>

* rev

Signed-off-by: Jirka <jirka.borovec@seznam.cz>

* expand

Signed-off-by: Jirka <jirka.borovec@seznam.cz>

* plugins

Signed-off-by: Jirka <jirka.borovec@seznam.cz>
@Nic-Ma
[DLMED] enhance label classes (#3061)
87e2ecd 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
[DLMED] enhance ScaleIntensity (#3062)
15c1f77 
Signed-off-by: Nic Ma <nma@nvidia.com>
@rijobro @ericspod
Extra transform examples (#3056)
a0aac6a 
* create images

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

* use brats

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

* update

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

* working

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

* rename file

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

* optional import matplotlib

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

* docstrings

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

* store images in https://github.com/Project-MONAI/DocImages

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

* extra transform example images

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

* most transforms

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

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

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

Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
@wyli
update backend (#3065)
26f20f4 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma
3063 Fix the complex Tensor issue in type conversion (#3064)
7ad0f6e 
* [DLMED] fix complex array issue

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

* [DLMED] fix test issue

Signed-off-by: Nic Ma <nma@nvidia.com>
@ericspod
Ae docs (#3067)
4618e85 
* Adding documentation for AutoEncoder and VarAutoEncoder

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@pre-commit-ci @wyli
[pre-commit.ci] pre-commit suggestions (#3069)
04060ff 
* [pre-commit.ci] pre-commit suggestions

updates:
- [github.com/asottile/pyupgrade: v2.27.0 → v2.29.0](asottile/pyupgrade@v2.27.0...v2.29.0)

* fixes #3071

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

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Wenqi Li <wenqil@nvidia.com>
@wyli
update workflow (#3073)
51b2380 
* update workflow

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

* fixes gpu tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@rijobro
correct panelled example images (#3068)
57a26a0 
* correct panelled example images

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@kate-sann5100
2755 Add b-spline kernel option (#2847)
1651f1b 
* 2755 Add b-spline kernel option

Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>
@wyli
daily tests for mmar loading (#3066)
6cf6a8d 
* adds integration tests

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

* temp tests

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

* cache pip

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

* fixes conc

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

* Revert "temp tests"

This reverts commit 5a931c6.

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

* print outcome

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>
@wyli
fixes mmar tests (#3077)
07c5f53 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
2231 enhances a few transform backends (#3075)
af88eeb 
* fixes RandGaussianSmooth

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

* minor fixes

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma
[DLMED] add more tests (#3080)
8d07aad 
Signed-off-by: Nic Ma <nma@nvidia.com>
@wyli
2357 Fixes unit test cases to run on GA100 (#3072)
6a2086d 
* relax atol for a100

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

* temp tests

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

* fixes #3071

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

* remove temp tests

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

* fixes tests

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

* update tests

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

* add tf32 tests

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

* fixes rtol wit tf32

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

* detect tf32

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

* update flag

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

* fixes testing util

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@yiheng-wang-nv
fix densenet264 error (#3081)
932abbe 
Signed-off-by: Yiheng Wang <vennw@nvidia.com>
@wyli
fixes figures (#3083)
6169c5d 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
fixes rst format issues (#3088)
54bd9db 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
oneof doc (#3090)
3b109f0 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@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 Nic-Ma merged commit b032f44 into Nic-Ma:3114-add-fast-integration-test Oct 13, 2021
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