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merge master#269

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Nic-Ma:3212-add-datalist-checkfrom
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Nov 2, 2021
Merged

merge master#269
Nic-Ma merged 148 commits into
Nic-Ma:3212-add-datalist-checkfrom
Project-MONAI:dev

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@Nic-Ma Nic-Ma commented Nov 2, 2021

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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
* 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: 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

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Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
* Update with cupy.ndarray

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* 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 29 commits October 22, 2021 03:52
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* update to torch 1.10

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

* temp tests

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

* fixes for torch 1.10

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

* fixes coverage tests

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

* fixes tests

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

* type fixes

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

* Revert "temp tests"

This reverts commit cb3e0c7.

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

* fixes tests

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

* fixes for windows

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

* fixes integration

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

* fixes #3171

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

* temp fix windows

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
…3158)

* [DLMED] add example in doc-string

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

* [DLMED] add example about copy_cache

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

* [DLMED] update according to comments

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* [MONAI] python code formatting

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* [DLMED] fix flake8

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

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* revise docstrings

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

* update based on comments

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* fixes windows tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
* adds util logger

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* update based on comments

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* update based on comments

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* [DLMED] add scale_datalist

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

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* [DLMED] add utitlity

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* [DLMED] update according to comments

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* [DLMED] update according to comments

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* [DLMED] fix CI for old PyTorch

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* [DLMED] update according to comments

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* [DLMED] fix flake8

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)

* Torch `BoundingRect`, `FillHoles`, VoteEnsemble`

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* fix

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* fix

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* fix

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* skip test_fill_holesd

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* merge fix

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* fixes

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* np->np/pt->pt

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* no type check

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* return ndarrayortensor

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* MeanEnsemble

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* [DLMED] add preparebatch

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* [DLMED] fix min tests

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* [DLMED] fix min tests

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* [DLMED] add backend

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* [DLMED] add backend

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* [DLMED] fix PyTorch 1.5.1 test

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

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* squeeze non-spatial dims in nib-reader

Signed-off-by: Bryn Lloyd <lloyd@itis.swiss>

* fix: add squeeze_non_spatial_dims=False option

Signed-off-by: Bryn Lloyd <lloyd@itis.swiss>

* fix: add docstring for arg

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* fix: add docstring for arg

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* fix: typos

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remove flooring
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* Fixes focal loss when reduction=none

Signed-off-by: joncrall <jon.crall@kitware.com>

* Added doctest example, fixed mypy errors

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* Linting and test fixes

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* Change dice loss to return broadcastable reductions

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* Fixed backwards compatibility issues

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* Fix masked loss test

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* [DLMED] enhance document

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* fix test_probnmsd

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* fix for older pt

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* [DLMED] add metrics check

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…#3224)

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* adds plot util

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* [DLMED] fix 2 CSVIterableDataset issues

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* [DLMED] fix 2 CSVIterableDataset issues

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@Nic-Ma Nic-Ma merged commit b24b0de into Nic-Ma:3212-add-datalist-check Nov 2, 2021
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