merge master by Nic-Ma · Pull Request #236 · Nic-Ma/MONAI

Nic-Ma · 2021-10-04T09:56:03Z

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.

* 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

* [DLMED] merge LocalPatchShuffle Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance doc-string Signed-off-by: Nic Ma <nma@nvidia.com>

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

Torch RandRotate

* 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>

Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* [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>

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

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

* 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>

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

* Add dropout arg in DynUNet init Signed-off-by: Andres <diazandr3s@gmail.com>

* [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>

…iles, ScaleIntensityRangePercentilesd (#2943) ScaleIntensityRange, ScaleIntensityRanged, ScaleIntensityRangePercentiles, ScaleIntensityRangePercentilesd

Rotate, Rotated, RandRotate, RandRotated

…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>

* transforms convert to the necessary type Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* 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>

* [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>

* [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>

* 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>

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

* add multimodal transformers Signed-off-by: ahatamizadeh <ahatamizadeh@nvidia.com>

…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

* Implement CuCIM wrapper transfrom Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

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

* 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>

* 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>

* test 1.9.1 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "temp tests" This reverts commit 1f27a63. Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes cucim compatibility Signed-off-by: Wenqi Li <wenqil@nvidia.com> * simplified import Signed-off-by: Wenqi Li <wenqil@nvidia.com>

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

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

* [DLMED] update highlights Signed-off-by: Nic Ma <nma@nvidia.com>

* release note v0.7 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds whatsnew 07 Signed-off-by: Wenqi Li <wenqil@nvidia.com>

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

* [DLMED] update README Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update what's new Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] use whatsnew link Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] add more doc Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] edit change log Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add command to get transform backend Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance the doc Signed-off-by: Nic Ma <nma@nvidia.com>

…dGaussianSharpen` (#2971) Torch `GaussianSmooth`, `RandGaussianSmooth`, `GaussianSharpen`, `RandGaussianSharpen`

* apply pyupgrade Signed-off-by: Jirka <jirka.borovec@seznam.cz> * exclude monai/_version.py Signed-off-by: Jirka <jirka.borovec@seznam.cz>

* enhance the release version string check Signed-off-by: GitHub <noreply@github.com> * update the releasing steps Signed-off-by: GitHub <noreply@github.com> Co-authored-by: Nic Ma <nma@nvidia.com>

* [DLMED] update ignite 0.4.6 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issues Signed-off-by: Nic Ma <nma@nvidia.com>

* print dtype along with type Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update tests Signed-off-by: Wenqi Li <wenqil@nvidia.com>

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

…SpikeNoise (#2974) GibbsNoise, RandGibbsNoise, KSpaceSpikeNoise, RandKSpaceSpikeNoise

…std (#3044) Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

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

Torch `Spacing`, `Spacingd`

* torch fgbgtoindices Signed-off-by: Wenqi Li <wenqil@nvidia.com> * unravel indices Signed-off-by: Wenqi Li <wenqil@nvidia.com> * simplified Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix spacing dtype Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix dtype Signed-off-by: Nic Ma <nma@nvidia.com>

create example transform images

* [DLMED] fix crop performance issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix CI test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] use default to avoid overflow Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix CI error Signed-off-by: Nic Ma <nma@nvidia.com>

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

* 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>

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

* 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 and others added 30 commits September 8, 2021 12:38

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

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>

Torch Zoom (#2916)

e52a0fe

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

Torch RandRotate90 (#2915)

281c17e

Torch RandRotate

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>

[DLMED] add dict version shuffle (#2918)

e2965db

Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

Add device to ToTensor (#2926)

448cdca

fixes #2939 (#2940)

1c2608f

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

enhance docstring (#2938)

76dc5c2

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

[DLMED] enhance scale intensity transforms (#2941)

8651b62

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

ThresholdIntensity, ThresholdIntensityd (#2944)

8765fc7

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

Add dropout arg in DynUNet init (#2947)

01feacb

* Add dropout arg in DynUNet init Signed-off-by: Andres <diazandr3s@gmail.com>

ScaleIntensityRange, ScaleIntensityRanged, ScaleIntensityRangePercent…

f26a712

…iles, ScaleIntensityRangePercentilesd (#2943) ScaleIntensityRange, ScaleIntensityRanged, ScaleIntensityRangePercentiles, ScaleIntensityRangePercentilesd

Rotate, Rotated, RandRotate, RandRotated (#2945)

f77a799

Rotate, Rotated, RandRotate, RandRotated

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>

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>

[DLMED] fix float64 bug (#2961)

fb2c2e9

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

add multi-modal (vision + language) transformers (#2962)

3b6f479

* add multimodal transformers Signed-off-by: ahatamizadeh <ahatamizadeh@nvidia.com>

cuCIM Transform (#2932)

38403ed

* Implement CuCIM wrapper transfrom Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

torch SpatialCrop, SpatialCropd (#2963)

0c39281

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

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>

wyli and others added 29 commits September 22, 2021 15:35

3002 - compatibility with torch 1.9.1 (#3003)

ed2d12c

* test 1.9.1 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "temp tests" This reverts commit 1f27a63. Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Fix cucim dep compatibility (#3006)

dfe8528

* fixes cucim compatibility Signed-off-by: Wenqi Li <wenqil@nvidia.com> * simplified import Signed-off-by: Wenqi Li <wenqil@nvidia.com>

update cucim dep (#3007)

b3406ae

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

[DLMED] fix CI test (#3008)

eed14df

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

3009 Update highlights web page (#3013)

46bf30d

* [DLMED] update highlights Signed-off-by: Nic Ma <nma@nvidia.com>

2914 release note, and what's new for v0.7 (#2992)

64fa255

* release note v0.7 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds whatsnew 07 Signed-off-by: Wenqi Li <wenqil@nvidia.com>

delaying the removal (#3015)

bfa054b

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

update preview version tag (#3016)

f06de43

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

Enhance 0.7 README doc (#3017)

aa4eb5d

* [DLMED] update README Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update what's new Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] use whatsnew link Signed-off-by: Nic Ma <nma@nvidia.com>

Torch GaussianSmooth, RandGaussianSmooth, GaussianSharpen, `Ran…

453a9c0

…dGaussianSharpen` (#2971) Torch `GaussianSmooth`, `RandGaussianSmooth`, `GaussianSharpen`, `RandGaussianSharpen`

apply pyupgrade (#3026)

a477905

* apply pyupgrade Signed-off-by: Jirka <jirka.borovec@seznam.cz> * exclude monai/_version.py Signed-off-by: Jirka <jirka.borovec@seznam.cz>

3018 enhance version string check (#3022)

a0130d1

* enhance the release version string check Signed-off-by: GitHub <noreply@github.com> * update the releasing steps Signed-off-by: GitHub <noreply@github.com> Co-authored-by: Nic Ma <nma@nvidia.com>

3028 update ignite CI tests to 0.4.6 (#3029)

fe93596

* [DLMED] update ignite 0.4.6 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issues Signed-off-by: Nic Ma <nma@nvidia.com>

enhance DataStats to include dtype (#3043)

28fb7d6

* print dtype along with type Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update tests Signed-off-by: Wenqi Li <wenqil@nvidia.com>

enhance error handling (#3042)

e4dd504

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

2792 - Torch GibbsNoise, RandGibbsNoise, KSpaceSpikeNoise, RandKSpace…

fc478b0

…SpikeNoise (#2974) GibbsNoise, RandGibbsNoise, KSpaceSpikeNoise, RandKSpaceSpikeNoise

AdjustContrast, AdjustContrastd, RandAdjustContrast, RandAdjustContra…

0c03376

…std (#3044) Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

remove false positive tests (#3046)

f85ad48

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

Torch Spacing, Spacingd (#3045)

bf561bb

Torch `Spacing`, `Spacingd`

2975 torch fgbgtoindices (#3038)

f909a6b

* torch fgbgtoindices Signed-off-by: Wenqi Li <wenqil@nvidia.com> * unravel indices Signed-off-by: Wenqi Li <wenqil@nvidia.com> * simplified Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Nic Ma <nma@nvidia.com>

3051 Fix dtype issue in Spacing transform (#3052)

d15cedd

* [DLMED] fix spacing dtype Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix dtype Signed-off-by: Nic Ma <nma@nvidia.com>

Create transform images (#3039)

a589c82

create example transform images

[DLMED] fix broken link (#3059)

3b5af50

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

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>

[DLMED] enhance label classes (#3061)

87e2ecd

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

[DLMED] enhance ScaleIntensity (#3062)

15c1f77

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

Nic-Ma merged commit 81ef4a8 into Nic-Ma:3063-fix-np-convert Oct 4, 2021

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merge master#236

merge master#236
Nic-Ma merged 70 commits intoNic-Ma:3063-fix-np-convertfrom
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Nic-Ma commented Oct 4, 2021

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