merge master by Nic-Ma · Pull Request #267 · Nic-Ma/MONAI

Nic-Ma · 2021-10-31T15:04:42Z

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 <[email protected]> * dimensions -> spatial_dims Signed-off-by: Wenqi Li <[email protected]> * deprecated arg with auto replacement Signed-off-by: Wenqi Li

* [DLMED] merge LocalPatchShuffle Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance doc-string Signed-off-by: Nic Ma <[email protected]>

Signed-off-by: Richard Brown <[email protected]>

Torch RandRotate

* Add cupy to tensor Signed-off-by: Behrooz <[email protected]> * Add unittest for cupy>tensor Signed-off-by: Behrooz <[email protected]>

Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* [DLMED] enhance the pad mode Signed-off-by: Nic Ma <[email protected]> * [DLMED] update all the tensor pad related Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix error tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix GPU tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: Nic Ma <[email protected]>

* con1_padding -> conv1_padding Signed-off-by: Wenqi Li <[email protected]> * simpler init. Signed-off-by: Wenqi Li <[email protected]> * fixes 2715 Signed-off-by: Wenqi Li <[email protected]> * adds 3d tests Signed-off-by: Wenqi Li <[email protected]> * fixes flake8 error Signed-off-by: Wenqi Li <[email protected]>

* ThresholdIntensity, ThresholdIntensityd Signed-off-by: Richard Brown <[email protected]>

* Add dropout arg in DynUNet init Signed-off-by: Andres <[email protected]>

* [DLMED] add device option Signed-off-by: Nic Ma <[email protected]> * look up options for types Signed-off-by: Wenqi Li <[email protected]> * adds unit tests Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

…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 <[email protected]> * Affine, RandAffine, Affined, RandAffined Signed-off-by: Richard Brown <[email protected]> * deprecate as_tensor_output Signed-off-by: Richard Brown <[email protected]> * fixes Signed-off-by: Richard Brown <[email protected]> * remove plotting Signed-off-by: Richard Brown <[email protected]> * Rand2dElastic, Rand3dElastic, Rand2dElasticd, Rand3dElasticd Signed-off-by: Richard Brown <[email protected]> * CropForeground Signed-off-by: Richard Brown <[email protected]> * fix Invertd Signed-off-by: Richard Brown <[email protected]>

* transforms convert to the necessary type Signed-off-by: Richard Brown <[email protected]>

* Add dtype to ToCuPy Signed-off-by: Behrooz <[email protected]> * Add unittests to include dtype Signed-off-by: Behrooz <[email protected]> * Implement convert_to_cupy Signed-off-by: Behrooz <[email protected]> * Addressed all comments Signed-off-by: Behrooz <[email protected]> * Addressed all comments Signed-off-by: Behrooz <[email protected]> * Add dtype for Sequence Signed-off-by: Behrooz <[email protected]>

* [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove unnecessary arg Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix style issue Signed-off-by: Nic Ma <[email protected]>

* [DLMED] enhance type conversion Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI test Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]>

* fixes tutorial 353 Signed-off-by: Wenqi Li <[email protected]> * adding type tests Signed-off-by: Wenqi Li <[email protected]> * improves type checks Signed-off-by: Wenqi Li <[email protected]> * fixes flake8 Signed-off-by: Wenqi Li <[email protected]> * fixes as channel first Signed-off-by: Wenqi Li <[email protected]> * type test option Signed-off-by: Wenqi Li <[email protected]> * ndarray suuport Signed-off-by: Wenqi Li <[email protected]> * fixes unit tests Signed-off-by: Wenqi Li <[email protected]> update Signed-off-by: Wenqi Li <[email protected]> * bash option for windows test Signed-off-by: Wenqi Li <[email protected]> * fixes unit tests Signed-off-by: Wenqi Li <[email protected]> * enhance norm intensity tests Signed-off-by: Wenqi Li <[email protected]> * fixes merge tests Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: Nic Ma <[email protected]>

* add multimodal transformers Signed-off-by: ahatamizadeh <[email protected]>

…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 <[email protected]>

Signed-off-by: Richard Brown <[email protected]>

* Update with cupy.ndarray Signed-off-by: Behrooz <[email protected]> * Change to use has_cp Signed-off-by: Behrooz <[email protected]> * Change the format Signed-off-by: Behrooz <[email protected]> * Fix a bug Signed-off-by: Behrooz <[email protected]>

* Fix for Jupyter plotting Signed-off-by: Eric Kerfoot <[email protected]> * Fix for Jupyter plotting Signed-off-by: Eric Kerfoot <[email protected]> * Fix for Jupyter plotting Signed-off-by: Eric Kerfoot <[email protected]>

* update versioning Signed-off-by: Wenqi Li <[email protected]> * build docker Signed-off-by: Wenqi Li <[email protected]> * install docker Signed-off-by: Wenqi Li <[email protected]> * remove selfhosted Signed-off-by: Wenqi Li <[email protected]> * update docs Signed-off-by: Wenqi Li <[email protected]> * ubuntu cpu tests Signed-off-by: Wenqi Li <[email protected]> * full tests Signed-off-by: Wenqi Li <[email protected]> * test docker options Signed-off-by: Wenqi Li <[email protected]> * full tests Signed-off-by: Wenqi Li <[email protected]> * full tests Signed-off-by: Wenqi Li <[email protected]> * exclude open slide tests Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * full tests Signed-off-by: Wenqi Li <[email protected]> * temp checkout Signed-off-by: Wenqi Li <[email protected]> * full tests Signed-off-by: Wenqi Li <[email protected]> * full tests Signed-off-by: Wenqi Li <[email protected]> * fixes flake8 error Signed-off-by: Wenqi Li <[email protected]> * skip weights downloading when http error out Signed-off-by: Wenqi Li <[email protected]>

* temp tests Signed-off-by: Wenqi Li <[email protected]> * adds doker Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * update Signed-off-by: Wenqi Li <[email protected]> * update Signed-off-by: Wenqi Li <[email protected]> * check branches Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * fixes cmp Signed-off-by: Wenqi Li <[email protected]> * remove temp tests Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] add tutorial link Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] update spacing and orientation transforms Signed-off-by: Nic Ma <[email protected]> * [DLMED] update others Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix test Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

* update to torch 1.10 Signed-off-by: Wenqi Li <[email protected]> * temp tests Signed-off-by: Wenqi Li <[email protected]> * fixes for torch 1.10 Signed-off-by: Wenqi Li <[email protected]> * fixes coverage tests Signed-off-by: Wenqi Li <[email protected]> * fixes tests Signed-off-by: Wenqi Li <[email protected]> * type fixes Signed-off-by: Wenqi Li <[email protected]> * Revert "temp tests" This reverts commit cb3e0c7. Signed-off-by: Wenqi Li <[email protected]> * fixes tests Signed-off-by: Wenqi Li <[email protected]> * fixes for windows Signed-off-by: Wenqi Li <[email protected]> * fixes integration Signed-off-by: Wenqi Li <[email protected]> * fixes #3171 Signed-off-by: Wenqi Li <[email protected]> * temp fix windows Signed-off-by: Wenqi Li <[email protected]>

…3158) * [DLMED] add example in doc-string Signed-off-by: Nic Ma <[email protected]> * [DLMED] add example about copy_cache Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>

* revise docstrings Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * fixes windows tests Signed-off-by: Wenqi Li <[email protected]>

* adds util logger Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add scale_datalist Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* [DLMED] add utitlity Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI for old PyTorch Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI issue Signed-off-by: Nic Ma <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

) * Torch `BoundingRect`, `FillHoles`, VoteEnsemble` Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * fix Signed-off-by: Richard Brown <[email protected]> * skip test_fill_holesd Signed-off-by: Richard Brown <[email protected]> * merge fix Signed-off-by: Richard Brown <[email protected]> * fixes Signed-off-by: Richard Brown <[email protected]> * np->np/pt->pt Signed-off-by: Richard Brown <[email protected]> * no type check Signed-off-by: Richard Brown <[email protected]> * return ndarrayortensor Signed-off-by: Richard Brown <[email protected]> * MeanEnsemble Signed-off-by: Richard Brown <[email protected]>

* [DLMED] add preparebatch Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix min tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix min tests Signed-off-by: Nic Ma <[email protected]>

* [DLMED] add backend Signed-off-by: Nic Ma <[email protected]> * [DLMED] add backend Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix PyTorch 1.5.1 test Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more tests Signed-off-by: Nic Ma <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: monai-bot <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* squeeze non-spatial dims in nib-reader Signed-off-by: Bryn Lloyd <[email protected]> * fix: add squeeze_non_spatial_dims=False option Signed-off-by: Bryn Lloyd <[email protected]> * fix: add docstring for arg Signed-off-by: Bryn Lloyd <[email protected]> * fix: add docstring for arg Signed-off-by: Bryn Lloyd <[email protected]> * fix: typos Signed-off-by: Bryn Lloyd <[email protected]> Co-authored-by: Bryn Lloyd <[email protected]>

Signed-off-by: Nic Ma <[email protected]>

remove flooring

Signed-off-by: Nic Ma <[email protected]>

* Fixes focal loss when reduction=none Signed-off-by: joncrall <[email protected]> * Added doctest example, fixed mypy errors Signed-off-by: joncrall <[email protected]> * Linting and test fixes Signed-off-by: joncrall <[email protected]> * Change dice loss to return broadcastable reductions Signed-off-by: joncrall <[email protected]> * Fixed backwards compatibility issues Signed-off-by: joncrall <[email protected]> * Fix masked loss test Signed-off-by: joncrall <[email protected]>

* [DLMED] enhance document Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

* Torch `ProbNMS`, `LabelFilter` Signed-off-by: Richard Brown <[email protected]> * fix test_probnmsd Signed-off-by: Richard Brown <[email protected]> * fix for older pt Signed-off-by: Richard Brown <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

* [DLMED] enhance the doc-string Signed-off-by: Nic Ma <[email protected]> * [DLMED] add shuffle Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] change to ShuffleBuffer Signed-off-by: Nic Ma <[email protected]> * update according to discussions Signed-off-by: Wenqi Li <[email protected]> * [DLMED] add multi-workers support Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix docs Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] improve perf Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* [DLMED] add metrics check Signed-off-by: Nic Ma <[email protected]> * [DLMED] update workflow Signed-off-by: Nic Ma <[email protected]> * [DLMED] add reduction Signed-off-by: Nic Ma <[email protected]> * [DLMED] add reduction to metric handlers Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>

Signed-off-by: Wenqi Li <[email protected]>

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 <[email protected]> * dimensions -> spatial_dims Signed-off-by: Wenqi Li <[email protected]> * 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 <[email protected]> * [DLMED] enhance doc-string Signed-off-by: Nic Ma <[email protected]>

Torch Zoom (#2916)

e52a0fe

Signed-off-by: Richard Brown <[email protected]>

Torch RandRotate90 (#2915)

281c17e

Torch RandRotate

CuPy to Tensor (#2919)

ef09811

* Add cupy to tensor Signed-off-by: Behrooz <[email protected]> * Add unittest for cupy>tensor Signed-off-by: Behrooz <[email protected]>

[DLMED] add dict version shuffle (#2918)

e2965db

Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

Add device to ToTensor (#2926)

448cdca

fixes #2939 (#2940)

1c2608f

Signed-off-by: Wenqi Li <[email protected]>

enhance docstring (#2938)

76dc5c2

Signed-off-by: Wenqi Li <[email protected]>

[DLMED] enhance scale intensity transforms (#2941)

8651b62

Signed-off-by: Nic Ma <[email protected]>

ThresholdIntensity, ThresholdIntensityd (#2944)

8765fc7

* ThresholdIntensity, ThresholdIntensityd Signed-off-by: Richard Brown <[email protected]>

Add dropout arg in DynUNet init (#2947)

01feacb

* Add dropout arg in DynUNet init Signed-off-by: Andres <[email protected]>

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 <[email protected]>

2948 Enhance the transform to delete items (#2952)

c624ffc

* [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove unnecessary arg Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix style issue Signed-off-by: Nic Ma <[email protected]>

[DLMED] fix float64 bug (#2961)

fb2c2e9

Signed-off-by: Nic Ma <[email protected]>

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

3b6f479

* add multimodal transformers Signed-off-by: ahatamizadeh <[email protected]>

cuCIM Transform (#2932)

38403ed

* Implement CuCIM wrapper transfrom Signed-off-by: Behrooz <[email protected]>

torch SpatialCrop, SpatialCropd (#2963)

0c39281

Signed-off-by: Richard Brown <[email protected]>

Update with cupy.ndarray (#2965)

43a4342

* Update with cupy.ndarray Signed-off-by: Behrooz <[email protected]> * Change to use has_cp Signed-off-by: Behrooz <[email protected]> * Change the format Signed-off-by: Behrooz <[email protected]> * Fix a bug Signed-off-by: Behrooz <[email protected]>

Fix for Jupyter plotting (#2964)

46e594f

* Fix for Jupyter plotting Signed-off-by: Eric Kerfoot <[email protected]> * Fix for Jupyter plotting Signed-off-by: Eric Kerfoot <[email protected]> * Fix for Jupyter plotting Signed-off-by: Eric Kerfoot <[email protected]>

wyli and others added 29 commits October 19, 2021 20:03

Add tutorial link to doc-string of handlers (#3150)

4785ede

* [DLMED] add tutorial link Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]>

update based on comments (#3156)

e641722

Signed-off-by: Wenqi Li <[email protected]>

fixes #3165 (#3166)

536e056

Signed-off-by: Wenqi Li <[email protected]>

2929 revise docstrings (#3170)

ee8b981

* revise docstrings Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * fixes windows tests Signed-off-by: Wenqi Li <[email protected]>

3159 adds a default util logger (#3160)

7964d45

* adds util logger Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>

[DLMED] add link and update chart (#3179)

299367e

Signed-off-by: Nic Ma <[email protected]>

3174 Add support to scale datalist (#3175)

a2027ec

* [DLMED] add scale_datalist Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

fixes url (#3183)

53b98ac

Signed-off-by: Wenqi Li <[email protected]>

[DLMED] fix iteration bug (#3202)

c877001

Signed-off-by: Nic Ma <[email protected]>

2755 fix bug (#3196)

95ed167

remove flooring

[DLMED] add param at runtime (#3205)

11ff52a

Signed-off-by: Nic Ma <[email protected]>

3210 Fix misleading document in the Torchvision netadapter (#3211)

d932c5a

* [DLMED] enhance document Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]>

minor typo fixes (#3209)

a7bc776

Signed-off-by: Wenqi Li <[email protected]>

Torch ProbNMS, LabelFilter (#3203)

1c1c50f

* Torch `ProbNMS`, `LabelFilter` Signed-off-by: Richard Brown <[email protected]> * fix test_probnmsd Signed-off-by: Richard Brown <[email protected]> * fix for older pt Signed-off-by: Richard Brown <[email protected]>

remove used param (#3206)

f43a927

Signed-off-by: Wenqi Li <[email protected]>

fixes iterable tests (#3221)

ec479d5

Signed-off-by: Wenqi Li <[email protected]>

Nic-Ma merged commit 9a74e4f into Nic-Ma:fix-csviterabledataset Oct 31, 2021

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merge master#267

merge master#267
Nic-Ma merged 143 commits intoNic-Ma:fix-csviterabledatasetfrom
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Nic-Ma commented Oct 31, 2021

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