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merge master#35

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Nic-Ma merged 13 commits intoNic-Ma:1668-add-rand-axis-flipfrom
Project-MONAI:master
Mar 1, 2021
Merged

merge master#35
Nic-Ma merged 13 commits intoNic-Ma:1668-add-rand-axis-flipfrom
Project-MONAI:master

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@Nic-Ma Nic-Ma commented Mar 1, 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 --codeformat --coverage.
  • Quick tests passed locally by running ./runtests.sh --quick.
  • In-line docstrings updated.
  • Documentation updated, tested make html command in the docs/ folder.

wyli and others added 13 commits February 24, 2021 15:02
* update openmp flag

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

* improves boundtype docs

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

* update setup.py

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

* input validation 1d

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

* fixes typos

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

* fixes typos

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

* merge upstream changes

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

* tests enums

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

* init. test grid pull

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

* update

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

* test grid_pull

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

* fixes min test

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

* adds device tests

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

* bwd tests

Signed-off-by: Wenqi Li <[email protected]>
move transforms out of compose file. this is backwards compatible.
* pad_collation

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

* increase number of test cases to ensure required testing errors

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

* determinism in setUp

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

* pad collate for list of lists

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

* code format

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

* allow padding options

Signed-off-by: Richard Brown <[email protected]>
decollate batch
enhance random range parameters

If element `i` is iterable, then `uniform[-rotate_range[i][0], rotate_range[i][1])` will be used to generate the rotation parameter for the ith dimension. If not, `uniform[-rotate_range[i], rotate_range[i])` will be used. This can be altered on a per-dimension basis. E.g., `((0,3), 1, ...)`: for dim0, rotation will be in range `[0, 3]`, and for dim1 `[-1, 1]` will be used. Setting a single value will use `[-x, x]` for dim0 and nothing for the remaining dimensions.

Backwards compatibility is ensured because the old behaviour used to do `uniform[-rotate_range[i], rotate_range[i])`, and this PR just adds the possibility to do `uniform[-rotate_range[i][0], rotate_range[i][1])`.
* Fixing issues preventing loss functions from being compatible with Torchscript

Signed-off-by: Eric Kerfoot <[email protected]>

* Updates

Signed-off-by: Eric Kerfoot <[email protected]>

* Updates

Signed-off-by: Eric Kerfoot <[email protected]>

* [MONAI] python code formatting

Signed-off-by: monai-bot <[email protected]>

* Updates

Signed-off-by: Eric Kerfoot <[email protected]>

* Adding conditional skip to Torchscript tests

Signed-off-by: Eric Kerfoot <[email protected]>

Co-authored-by: monai-bot <[email protected]>
* [DLMED] fix length > 1024 issue in string list all gather

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

* [DLMED] fix flake8 issue

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] add more test

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

Co-authored-by: Yiheng Wang <[email protected]>
* DeleteChannel array, dictionary, tests

Signed-off-by: Leo Tam <[email protected]>

* formatting

Signed-off-by: Leo Tam <[email protected]>

* DeleteChannel array, dictionary, tests

Signed-off-by: Leo Tam <[email protected]>

* Register in transform init

Signed-off-by: Leo Tam <[email protected]>

* clean comment

Signed-off-by: Leo Tam <[email protected]>

* Dict init

Signed-off-by: Leo Tam <[email protected]>

* Register D and Dict

Signed-off-by: Leo Tam <[email protected]>

* Style fix

Signed-off-by: Leo Tam <[email protected]>

* Safety cast

Signed-off-by: Leo Tam <[email protected]>

* Changinging names from DeleteChannel to RemoveRepeatedChannel

Signed-off-by: Leo Tam <[email protected]>

* Lint fixes

Signed-off-by: Leo Tam <[email protected]>

* Test import fix, autofix again

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

Co-authored-by: Eric Kerfoot <[email protected]>
* update distcall

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

* update final closing

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

Co-authored-by: Eric Kerfoot <[email protected]>
* Add ToPIL transformation

Signed-off-by: Behrooz <[email protected]>

* Add ToPILd, ToPILD, ToPILDict

Signed-off-by: Behrooz <[email protected]>

* Remove has_pil

Signed-off-by: Behrooz <[email protected]>

* Include ToPIL, ToPILd, ToPILD, and ToPILDict

Also include ToNumpyD, ToNumpyDict, TorchVisionD, and TorchVisionDict

Signed-off-by: Behrooz <[email protected]>

* Fix a typing issue

Signed-off-by: Behrooz <[email protected]>

* Fix PIL optional import

Signed-off-by: Behrooz <[email protected]>

* Add unittests for ToPIL and ToPILD

Signed-off-by: Behrooz <[email protected]>

* Fix formatting

Signed-off-by: Behrooz <[email protected]>

* Fix formatting

Signed-off-by: Behrooz <[email protected]>

* Add PILImage.Image as the input for ToNumpy and ToTensor

Signed-off-by: Behrooz <[email protected]>

* Fix type checking issue for PIL.Image.Image

Signed-off-by: Behrooz <[email protected]>

* Change PILImage_fromarray to lower case

Signed-off-by: Behrooz <[email protected]>
add RandomizableTransform
* Add more tests to test_deepgrow_dataset

Signed-off-by: YuanTingHsieh <[email protected]>
@Nic-Ma Nic-Ma merged commit 2bc2450 into Nic-Ma:1668-add-rand-axis-flip Mar 1, 2021
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7 participants