merge master by Nic-Ma · Pull Request #223 · Nic-Ma/MONAI

Nic-Ma · 2021-09-17T03:25:00Z

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>

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>

Nic-Ma merged commit e3d8e68 into Nic-Ma:2231-enhance-tensor-transforms Sep 17, 2021

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merge master#223

merge master#223
Nic-Ma merged 30 commits intoNic-Ma:2231-enhance-tensor-transformsfrom
Project-MONAI:dev

Nic-Ma commented Sep 17, 2021

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Nic-Ma commented Sep 17, 2021

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