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Merged
Nic-Ma merged 214 commits into from
Nov 24, 2021
Merged

merge master #298

Nic-Ma merged 214 commits into from
Nov 24, 2021

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@Nic-Ma Nic-Ma commented Nov 24, 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>
Nic-Ma and others added 29 commits November 15, 2021 15:26
@Nic-Ma
[DLMED] enhance metrics in workflow (#3341)
4d83fc0 
Signed-off-by: Nic Ma <nma@nvidia.com>
@myron @bhashemian
MIL component to extract patches (#3237)
9ec1d14 
* MIL component to extract patches

Signed-off-by: myron <amyronenko@nvidia.com>

* MIL component to extract patches

Signed-off-by: myron <amyronenko@nvidia.com>

* random flag, minor fixes

Signed-off-by: myron <amyronenko@nvidia.com>

* minor fixes for padding

Signed-off-by: myron <amyronenko@nvidia.com>

* improve tests

Signed-off-by: myron <amyronenko@nvidia.com>

Co-authored-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@myron @Nic-Ma @bhashemian
MIL Component - MILModel (#3236)
45d4a61 
* 3251 Add dependency check in WSIReader (#3312)

* [DLMED] add dep check

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

* [DLMED] fix typo

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

* [DLMED] update according to comments

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

* [DLMED] MILmodel  PR

Signed-off-by: myron <amyronenko@nvidia.com>

* small updates

Signed-off-by: myron <amyronenko@nvidia.com>

* fix jit issues

Signed-off-by: myron <amyronenko@nvidia.com>

* jit fix attempt

Signed-off-by: myron <amyronenko@nvidia.com>

* removing Enum

Signed-off-by: myron <amyronenko@nvidia.com>

Co-authored-by: Nic Ma <nma@nvidia.com>
Co-authored-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@wyli
3329 compatibility with pathlike obj (#3332)
4c2c1dc 
* update pathlike obj

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

* support of pathlike obj

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

* review path obj

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

* update tests

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

* autofix

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

* fixes unit test

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

* update based on comments

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

* fixes dep issue

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma
3292 Add support for no keys in all the transforms when allow_missing…
b7daf80 
…_keys is True (#3325)

* [DLMED] enhance no keys for allow_missing_keys

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

* [DLMED] update according to comments

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

* [DLMED] update according to comments

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

* [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
[DLMED] refine doc (#3349)
0a7a4f1 
Signed-off-by: Nic Ma <nma@nvidia.com>
@wyli
fixes mednist dataset (#3348)
b86d751 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
close file (#3342)
33b6d61 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
3350 drops pytorch 1.5.x support (#3353)
2e83cd2 
* drop pytorch 1.5.x

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

* update premerge gpu

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

* update based on comments

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma
3322 Optimize performance of the astype usage in arrays (#3338)
bf55246 
* [DLMED] optimize astype

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

* [DLMED] improve astype

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

* [DLMED] fix flake8

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

* [DLMED] update according to comments

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

* [DLMED] update according to comments

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

* [DLMED] update according to comments

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

* [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
3346 Simplify AsDiscrete transform (#3352)
6a20052 
* [DLMED] simiplify AsDiscrete transform

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

* [DLMED] update tests

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

* [DLMED] update according to comments

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

* [DLMED] update according to comments

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

* [DLMED] add examples

Signed-off-by: Nic Ma <nma@nvidia.com>
@bhashemian
Fix casting for tile step (#3355)
c3fd5a9 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@wyli
remove dynunetv1 blocks (#3360)
f7e4cc3 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma
3357 Add wrap_sequence to several transforms (#3358)
79bca25 
* [DLMED] add wrap_sequence

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

* [DLMED] update default value

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

* [DLMED] fix tests

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

* [DLMED] fix typo

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

* [DLMED] add more tests

Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
[DLMED] enhance doc-string (#3363)
d89807f 
Signed-off-by: Nic Ma <nma@nvidia.com>
@bhashemian @wyli
Update setup.cfg with tifffile and imagecodes (#3362)
a4e7ba0 
* Add tiffile and imagecodes to build option dependencies

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

* update optional dep

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

Co-authored-by: Wenqi Li <wenqil@nvidia.com>
@myron
unit tests for step (#3361)
9048166 
Signed-off-by: myron <amyronenko@nvidia.com>
@wyli
backward compatible as discrete (#3367)
e36fbd3 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@ericspod @pre-commit-ci @wyli
Smooth field (#3252)
b01c63e 
* Adding smooth field transforms

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

* Adding smooth field transforms

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

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

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

* Adding smooth field transforms

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

* Adding smooth field transforms

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

* Updates to smooth field transforms

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

* Updates to smooth field transforms

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

* Updates to smooth field transforms

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

* Updates to smooth field transforms

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Wenqi Li <wenqil@nvidia.com>
@dongyang0122
adds dints blocks (#3372)
73d9afa 
Co-authored-by: dongy <dongy@nvidia.com>
@wyli
Fixes typos in documentation (#3364)
5e54d3e 
* fixes typos in docstring

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

* fixes type errors

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

* fixes the docstrings

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

* fixes typo

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma @wyli
[DLMED] add frame_dim (#3369)
d0e72fb 
Signed-off-by: Nic Ma <nma@nvidia.com>

Co-authored-by: Wenqi Li <wenqil@nvidia.com>
@wyli
3370 option of zip_longest to decollate (#3373)
37930a9 
* option to zip_longest

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

* adds a pad option

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

* fixes batch size

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

* update based on comments

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@bhashemian
Numpy Implementation of SplitOnGrid (#3378)
5adf30b
@bhashemian
TileOnGrid support for Tensor input (#3384)
5d87b23
@bhashemian
Fix SplitOnGrid issue (#3386)
0cfecbb 
* Refactor some variable names

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

* Fix SplitOnGrid issue with numpy backend

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

* Add unittest to cover the fixed issue

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

* Rename c_image to n_channels

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@Nic-Ma
3387 fix threshold value issue in AsDiscrete (#3388)
9cc339d 
* [DLMED] fix threshold issue

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

* [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>
@ericspod @pre-commit-ci @monai-bot
Adding repeats option to ThreadDataLoader (#3389)
5f68a22 
* Adding repeats option to ThreadDataLoader

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

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

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

* Adding repeats option to ThreadDataLoader

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

* [MONAI] python code formatting

Signed-off-by: monai-bot <monai.miccai2019@gmail.com>

* Update thread_buffer.py

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

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

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: monai-bot <monai.miccai2019@gmail.com>
@wyli
fixes readme links (#3380)
839f7ef 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@Nic-Ma Nic-Ma merged commit bda5044 into Nic-Ma:3387-fix-threshold-none Nov 24, 2021
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