merge master #227

Nic-Ma · 2021-09-24T01:24:13Z

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>

* fixes tutorial issue 352 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * simplified Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] enhance tensor transforms Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix mypy Signed-off-by: Nic Ma <nma@nvidia.com>

…abelClasses`, `RandCropByLabelClassesd` (#2967) Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* enhance affinegrid to use torch backend Signed-off-by: Wenqi Li <wenqil@nvidia.com> * style fixes Signed-off-by: Wenqi Li <wenqil@nvidia.com> * codeformat fixes Signed-off-by: Wenqi Li <wenqil@nvidia.com> * backend affien grid Signed-off-by: Wenqi Li <wenqil@nvidia.com> * device support Signed-off-by: Wenqi Li <wenqil@nvidia.com> * less lookup Signed-off-by: Wenqi Li <wenqil@nvidia.com> * create grid with torch backend Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * default to torch create grid Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes unit test Signed-off-by: Wenqi Li <wenqil@nvidia.com> * randaffine with create grid Signed-off-by: Wenqi Li <wenqil@nvidia.com> * create_grid backend change for spatial transforms Signed-off-by: Wenqi Li <wenqil@nvidia.com> * create control grid tensor Signed-off-by: Wenqi Li <wenqil@nvidia.com> * enhance spatial, and crop xforms - Update test_rand_deform_grid.py - center_scale_crop - center_spatial_crop - rand_scale_crop - rand_spatial_crop - rand_spatial_crop_samples Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes invert Signed-off-by: Wenqi Li <wenqil@nvidia.com> * tensor resize, unit test fixes Signed-off-by: Wenqi Li <wenqil@nvidia.com>

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

* update multimodal doc and model names (Transchex) Signed-off-by: ahatamizadeh <ahatamizadeh@nvidia.com>

* remove deprecated Signed-off-by: Wenqi Li <wenqil@nvidia.com> * min-test list Signed-off-by: Wenqi Li <wenqil@nvidia.com> * preserves tests from tests/test_handler_transform_inverter.py Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* enhance nightly test Signed-off-by: Wenqi Li <wenqil@nvidia.com> * print after the test for information Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* dimension check for pretrained model weights This PR implements a dimension check, before trying to load pre-trained model weights. Signed-off-by: neuronflow <zournyque@gmail.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Signed-off-by: neuronflow <zournyque@gmail.com> * multi line split error Signed-off-by: neuronflow <zournyque@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

…tatement (#2996) * Refactor unnecessary `else` / `elif` when `if` block has a `return` statement * Remove unnecessary lambda expression (#2997) Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> * type fixes Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove repeated init Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes import, unused vars Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] add copy option Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance test Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* 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>

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 18 commits September 17, 2021 15:37

fixes tutorial issue 352 (#2968)

dc3e263

* fixes tutorial issue 352 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * simplified Signed-off-by: Wenqi Li <wenqil@nvidia.com>

2231 Enhance tensor transforms (#2966)

ecbb03b

* [DLMED] enhance tensor transforms Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix mypy Signed-off-by: Nic Ma <nma@nvidia.com>

Torch RandCropByPosNegLabel, RandCropByPosNegLabeld, `RandCropByL…

e2e2d08

…abelClasses`, `RandCropByLabelClassesd` (#2967) Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

Add make the name of wsi reader lowercase (#2973)

e2e5e31

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

update multimodal doc and model names (Transchex) (#2979)

731bad8

* update multimodal doc and model names (Transchex) Signed-off-by: ahatamizadeh <ahatamizadeh@nvidia.com>

2914 remove the deprecated API for v0.7 (#2981)

f786957

* remove deprecated Signed-off-by: Wenqi Li <wenqil@nvidia.com> * min-test list Signed-off-by: Wenqi Li <wenqil@nvidia.com> * preserves tests from tests/test_handler_transform_inverter.py Signed-off-by: Wenqi Li <wenqil@nvidia.com>

2985 - enhance nightly test (#2986)

b791ed2

* enhance nightly test Signed-off-by: Wenqi Li <wenqil@nvidia.com> * print after the test for information Signed-off-by: Wenqi Li <wenqil@nvidia.com>

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>

Nic-Ma merged commit 0ccfc62 into Nic-Ma:enhance-0.7-doc Sep 24, 2021

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merge master #227

merge master #227

Nic-Ma commented Sep 24, 2021

merge master #227

merge master #227

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Nic-Ma commented Sep 24, 2021

Description

Status

Types of changes