merge master #386

Nic-Ma · 2022-03-14T09:42:55Z

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.

* 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>

* [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>

* 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>

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

* [DLMED] fix None value Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add unit tests Signed-off-by: Nic Ma <nma@nvidia.com>

* add dints model Signed-off-by: dongy <dongy@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * rename scripts Signed-off-by: dongy <dongy@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * rename scripts Signed-off-by: dongy <dongy@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <dongy@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <dongy@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * Move stem out of dints * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add test dints cell, mixop and dints bug fix * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Change dints.stem * update scripts Signed-off-by: dongy <dongy@nvidia.com> * adds doc; update test_factorized_reduce.py Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstring of mixops Signed-off-by: Wenqi Li <wenqil@nvidia.com> * ReLU -> Acti Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update mixops cell Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove forward() Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * Add dints comments * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add device to dints and fix unit test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixes typos Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fix docstrings Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fix docstrings Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update mixop and cell Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * Add dints comments * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Remove arch_codes in forward * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add Dints weight parameter function * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <dongy@nvidia.com> * Fix 2D Dints bugs, unit testing, and commenting * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * dints/dints_blocks updates Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update ram cost Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <dongy@nvidia.com> * [DLMED] add TorchScript Signed-off-by: Nic Ma <nma@nvidia.com> * Fix dints bug, add comments, torchscript support * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update scripts Signed-off-by: dongy <dongy@nvidia.com> * update docstrings; remoted `is_search` Signed-off-by: Wenqi Li <wenqil@nvidia.com> * torchscript dints inference Signed-off-by: Wenqi Li <wenqil@nvidia.com> * test fixes Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes gpu tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes dints cell tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * skip for previous torch versions Signed-off-by: Wenqi Li <wenqil@nvidia.com> * inplace grads Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove warning msg Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: dongy <dongy@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Yufan He <heyufan1995@gmail.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Nic Ma <nma@nvidia.com>

* [DLMED] add frame_dim Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix CI test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] remove doc-string of args "currently not used" Signed-off-by: Nic Ma <nma@nvidia.com>

* whats new in 0.8 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * updated based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Nic Ma <nma@nvidia.com>

* update changelog for v0.8.0 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Nic Ma <nma@nvidia.com>

* [DLMED] update highlights for v0.8 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add tutorial link Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add MLFlow related Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update description and charts Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update chart name Signed-off-by: Nic Ma <nma@nvidia.com> * update docs Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update dints link Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update highlights Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

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

* fixes typos Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typos Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes crop types Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes dtypes Signed-off-by: Wenqi Li <wenqil@nvidia.com>

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

* [DLMED] enhance doc Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update based on Yiheng's comments Signed-off-by: Nic Ma <nma@nvidia.com>

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

* [DLMED] add channel dim Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add RGB support Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] add support for other pickle Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] fix flake8 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] test flake8 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] test flake8 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> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* fixes pickle mod Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update pickle Signed-off-by: Wenqi Li <wenqil@nvidia.com> * docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com>

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

* [DLMED] enhance not-nan reduction Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

…ks (#3419) * Update segresnet_block.py making the activation function a parameter to the class of the ResBlock * Update segresnet.py * passing activation to the residual blocks * little change * signed Signed-off-by: Patricio Astudillo <patricio.astudillo@robovision.ai> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [DLMED] add args and update default (#3418) Signed-off-by: Nic Ma <nma@nvidia.com> Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docstrings Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Patricio Astudillo <patricio.astudillo@robovision.ai> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Nic Ma <nma@nvidia.com>

* update vitautoenc Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on the comments; compatibility with the previous model weights Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* Update WSIReader level/location/size calculation Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update location downsampling Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update tests and add a new test case Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update few names and logics Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Fix the dependency issue Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Check for imagecodecs + tifffile Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Remove new test case that uses too much memory Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add new case and ignore level=0 for TiffFile Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Address comments Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> Co-authored-by: Nic Ma <nma@nvidia.com>

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

* Update TiffFile backend to read only the entire image Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* [DLMED] extract write logic 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] add dataframe Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance CSV iterable dataset Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typehints Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add comment 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] fix file close issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix doc Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* [DLMED] add BaseWorkflow Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] add *args, **kwargs Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* [DLMED] fix deprecated arg Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

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

* ResampleToMatch Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * mypy Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * safe get, fixes min test Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* update contrib guide Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update testing data Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typos Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Signed-off-by: Yiheng Wang <vennw@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* intensity augmentation transforms Signed-off-by: yc7620 <yaniel.cabrera20@imperial.ac.uk> * [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 <monai.miccai2019@gmail.com> * mapping via bitbucket operation Signed-off-by: yc7620 <yaniel.cabrera20@imperial.ac.uk> * [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 <monai.miccai2019@gmail.com> Co-authored-by: yc7620 <yaniel.cabrera20@imperial.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> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] fix margin region in crop Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add to other transforms Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update arg name Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* Add failing test Signed-off-by: Sven Koitka <sven.koitka@uk-essen.de> * Fix reshape after ViT Signed-off-by: Sven Koitka <sven.koitka@uk-essen.de> * Remove unused import Signed-off-by: Sven Koitka <sven.koitka@uk-essen.de>

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* [DLMED] add config parser Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] simplify parse logic Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more function tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix torchvision tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance update_config to support multiple items Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance doc and unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] clear API Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] simplify usage APIs Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] support root config Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix update reference typo Signed-off-by: Nic Ma <nma@nvidia.com> * revise APIs and docstrings Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove->discard Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [DLMED] minor change Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* enhance to use spatial_size Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes unit test Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds unit tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * check that metadata matches Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * add checks to test Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> Co-authored-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

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

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

* Remove dead link from highlights.md Signed-off-by: Ioannis Valasakis <code@wizofe.uk>

* fix non intensity error Signed-off-by: Yiheng Wang <vennw@nvidia.com> * remove useless torch mod Signed-off-by: Yiheng Wang <vennw@nvidia.com> * convert type before return Signed-off-by: Yiheng Wang <vennw@nvidia.com> * update convert Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* Add SliceInferer for slice-by-slice infer Signed-off-by: Suraj Pai <b.pai@maastrichtuniversity.nl>

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* Update CSVDataset in dataset.py `kwargs` argument currently addresses merge operation. There is no way to change `kwargs` for `read_csv ()` call (e.g. to change delimiter from standard `,` to `\t`. Suggestion: Have `kwargs_read_csv` and `kwargs_merge` arguments to allow separate and finer user-control over both loading & merging mechanism.

* inverse ResampleToMatchd Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * ignore Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* fix unittest error Signed-off-by: Yiheng Wang <vennw@nvidia.com> * unify version Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* Revert "inverse ResampleToMatchd (#3856)" This reverts commit 82ec2fe. Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "Revert "inverse ResampleToMatchd (#3856)"" This reverts commit 6698ef5. Signed-off-by: Wenqi Li <wenqil@nvidia.com> * support of writer names Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* add shape info when raising errors Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* update Transchex model Signed-off-by: ahatamizadeh <ahatamizadeh@nvidia.com>

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

* [DLMED] add config parser Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] simplify parse logic Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more function tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix torchvision tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add standard run API Signed-off-by: Nic Ma <nma@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [DLMED] enhance update_config to support multiple items Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update API Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] simplify API Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance doc and unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] clear API Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] simplify usage APIs Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] support root config Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix update reference typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update usage API Signed-off-by: Nic Ma <nma@nvidia.com> * revise APIs and docstrings Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove->discard Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [DLMED] minor change Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update code Signed-off-by: Nic Ma <nma@nvidia.com> * update usage Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [DLMED] update doc Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add end-to-end test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update doc Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix optional import Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] refine APIs Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add support to only use part of the file to override Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update to latest Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments 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 `fire` supported dict arg Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add examples to doc-string Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] skip windows test for paths Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] skip windows Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update windows Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update command Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix windows test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] construct class Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] restore design Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix args override Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] test windows Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] test windows Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] refactor config reading logic Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add doc-string Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add export and test Signed-off-by: Nic Ma <nma@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * python -m monai.bundle Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes doc tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [DLMED] enhance test Signed-off-by: Nic Ma <nma@nvidia.com> * rel import Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [DLMED] refine macro Signed-off-by: Nic Ma <nma@nvidia.com> * fixes flake8 f401 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * mv to monai.bundle Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes split_path_id, update docstrings Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes mypy Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update cli, update according to the comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [DLMED] fix typo in doc-string Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to discussion Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix path_id match Signed-off-by: Nic Ma <nma@nvidia.com> * revise according to the comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [DLMED] update config item Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update patterns Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance disabled Signed-off-by: Nic Ma <nma@nvidia.com> * special chars to utils Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove circular import Signed-off-by: Wenqi Li <wenqil@nvidia.com> * configreader -> configparser following cpython/configparser Signed-off-by: Wenqi Li <wenqil@nvidia.com> * printing Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typing Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [DLMED] unify "_name_" and "_path_" Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update to "_target_" Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* Adding archive specification document Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Adding archive specification document Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Adding archive specification document 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 archive specification document Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Adding archive specification document Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Adding archive specification document Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Updated specification 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 * Updated specification 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: GreySeaWolf <GreySeaWolf@users.noreply.github.com> Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com>

* fixes #3921 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes mypy Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove temp tests Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] add ignore_data API Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] optimize the API Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix mypy Signed-off-by: Nic Ma <nma@nvidia.com>

bhashemian and others added 30 commits November 23, 2021 15:47

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>

fixes readme links (#3380)

839f7ef

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

3387 Fix 0.0 or None value in AsDiscrete (#3393)

721f6f7

* [DLMED] fix None value Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add unit tests Signed-off-by: Nic Ma <nma@nvidia.com>

3368 add frame_dim to TensorBoard plot utility (#3385)

a640dde

* [DLMED] add frame_dim Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix CI test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] remove doc-string of args "currently not used" Signed-off-by: Nic Ma <nma@nvidia.com>

update changelog for v0.8.0 (#3382)

d4c1bbe

* update changelog for v0.8.0 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Nic Ma <nma@nvidia.com>

[DLMED] postpone remove version (#3399)

dca8b1c

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

fixes typos/style in dints.py (#3395)

d625b61

* fixes typos Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typos Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

3404 fixes crop types (#3403)

714d00d

* fixes crop types Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes dtypes Signed-off-by: Wenqi Li <wenqil@nvidia.com>

update weekly build prefix (#3406)

1763381

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

3405 Enhance doc-string of MIL model for data shape (#3407)

4a3db69

* [DLMED] enhance doc Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update based on Yiheng's comments Signed-off-by: Nic Ma <nma@nvidia.com>

fixes docstring ref. (#3408)

7d4386f

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

3398 Support 3D RGB image in matshow3d (#3400)

8a1454a

* [DLMED] add channel dim Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add RGB support Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

fixes pickle mod (#3416)

071264d

* fixes pickle mod Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update pickle Signed-off-by: Wenqi Li <wenqil@nvidia.com> * docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com>

[DLMED] add args and update default (#3418)

ff9bbfa

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

3392 enhance reduction doc-string for Nan values (#3424)

fc9abb9

* [DLMED] enhance not-nan reduction Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

3194 update vitautoenc for 2d (#3420)

f94e768

* update vitautoenc Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on the comments; compatibility with the previous model weights Signed-off-by: Wenqi Li <wenqil@nvidia.com>

update create_file_basename (#3436)

035f91c

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

Update TiffFile backend in WSIReader (#3438)

f6a0c87

* Update TiffFile backend to read only the entire image Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

Enhance deprecated arg for kwargs in CSV datasets (#3446)

a17813b

* [DLMED] fix deprecated arg Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

wyli and others added 29 commits February 21, 2022 11:02

fixes #3788 according to the suggestions (#3824)

b0f70e2

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

3708 update testing data contrib (#3835)

2770092

* update contrib guide Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update testing data Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typos Signed-off-by: Wenqi Li <wenqil@nvidia.com>

update link in MedNISTDataset (#3840)

fd63af4

Signed-off-by: Yiheng Wang <vennw@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

Fix reshape in ViTAutoEnc (#3841)

2cfb896

* Add failing test Signed-off-by: Sven Koitka <sven.koitka@uk-essen.de> * Fix reshape after ViT Signed-off-by: Sven Koitka <sven.koitka@uk-essen.de> * Remove unused import Signed-off-by: Sven Koitka <sven.koitka@uk-essen.de>

KeepLargest... by default use all labels (#3776)

3af9d73

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

add status check (#3846)

d6327a7

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

[DLMED] update to 22.02 (#3869)

da5807d

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

clarify the usage of set determinism (#3855)

84ee799

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

Remove dead link from highlights.md (#3870)

c35485c

* Remove dead link from highlights.md Signed-off-by: Ioannis Valasakis <code@wizofe.uk>

SliceInferer for slice-by-slice infererence (#3602)

4ffe6be

* Add SliceInferer for slice-by-slice infer Signed-off-by: Suraj Pai <b.pai@maastrichtuniversity.nl>

enhance contrastive loss (#3873)

e45dfad

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

inverse ResampleToMatchd (#3856)

82ec2fe

* inverse ResampleToMatchd Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * ignore Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

3879 Fix TestKeepLargestConnectedComponent issue (#3895)

2ffad76

* fix unittest error Signed-off-by: Yiheng Wang <vennw@nvidia.com> * unify version Signed-off-by: Yiheng Wang <vennw@nvidia.com>

3883 Add addition shape info when raise related errors (#3896)

16ea7d6

* add shape info when raising errors Signed-off-by: Yiheng Wang <vennw@nvidia.com>

update Transchex model (#3897)

26bc1a9

* update Transchex model Signed-off-by: ahatamizadeh <ahatamizadeh@nvidia.com>

sw inferer progress (#3899)

4b66746

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

Make unetr support torchscript (#3923)

38b6437

Signed-off-by: Yiheng Wang <vennw@nvidia.com>

3921 - test with torch 1.11 (#3926)

4c2899a

* fixes #3921 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes mypy Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove temp tests Signed-off-by: Wenqi Li <wenqil@nvidia.com>

3904 improve output_transform of handlers (#3913)

7587e71

* [DLMED] add ignore_data API Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] optimize the API Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix mypy Signed-off-by: Nic Ma <nma@nvidia.com>

Nic-Ma merged commit d8eb04a into Nic-Ma:enhance_reader_locate Mar 14, 2022

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merge master #386

merge master #386

Nic-Ma commented Mar 14, 2022

merge master #386

merge master #386

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Nic-Ma commented Mar 14, 2022

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