merge master #392

Nic-Ma · 2022-03-24T01:11:24Z

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.

* [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>

* enhance dynunet Signed-off-by: Yiheng Wang <vennw@nvidia.com> * fix black issue Signed-off-by: Yiheng Wang <vennw@nvidia.com> * use strict=False Signed-off-by: Yiheng Wang <vennw@nvidia.com> * fix black 21.12 error Signed-off-by: Yiheng Wang <vennw@nvidia.com> * enhance code and update docstring Signed-off-by: Yiheng Wang <vennw@nvidia.com>

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

improve error message if reader nott available

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

* [DLMED] add dataset generator Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add DatasetGenerator Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] fix wrong test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] simplify according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] remove return Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update rtol for CI Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* [DLMED] add missing docs Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add missing components Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix test Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] add channel-wise Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] skip test if before 1.7 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: Nic Ma <nma@nvidia.com>

* [DLMED] add Iteration base class 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>

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

* [DLMED] support string dtype Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance dtype in ToCupy Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] add Iteration base class 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>

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

* [DLMED] support string dtype Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance dtype in ToCupy Signed-off-by: Nic Ma <nma@nvidia.com>

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

* Update to not include number for the name of the first range Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update CuCIM and TorchVision wrappers to include name Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update nvtx range to append undelying class for wrapper tranforms Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Add new test cases to cover changes Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> * Update cucim and torchvision check Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* [DLMED] add missing images Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix 3471 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix AsDiscrete Signed-off-by: Nic Ma <nma@nvidia.com>

* make bending energy loss invariant to resolution fixes #3485 Signed-off-by: Ebrahim Ebrahim <ebrahim.ebrahim@kitware.com> * set BendingEnergyLoss default normalize to False Maybe it's more important that the default behavior match usage of the term "bending energy" elsewhere, rather than that it be the most convenient behavior. Signed-off-by: Ebrahim Ebrahim <ebrahim.ebrahim@kitware.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>

* [DLMED] complete temp test schema Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add cmd line API 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> * [DLMED] add optional import Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] test with download link Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance doc-string Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix mypy Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] remove DS_Store 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 more tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] change "target_id" to "runner_id" Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] simplify command line Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix print summary logic Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update log print to logging Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] compact commands Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] unify args update Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] skip windows Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] optimize error log Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update accoding to comments Signed-off-by: Nic Ma <nma@nvidia.com>

* optional lps to ras Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes #3934 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update env Signed-off-by: Wenqi Li <wenqil@nvidia.com>

fix docstring typo Signed-off-by: victolee0 <39608452+victolee0@users.noreply.github.com>

* enhance 1st conv layer of ResNet Signed-off-by: Yiheng Wang <vennw@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * modify net adapeter unittest Signed-off-by: Yiheng Wang <vennw@nvidia.com> * use ensure_tuple_rep Signed-off-by: Yiheng Wang <vennw@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [DLMED] enhance reader Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix docs Signed-off-by: Nic Ma <nma@nvidia.com>

* fixes #3934 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * min_test update Signed-off-by: Wenqi Li <wenqil@nvidia.com> * cu115 tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update tests Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* use enum for dicece reduction Signed-off-by: Yiheng Wang <vennw@nvidia.com> * use look up option Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* [DLMED] update to 21.10 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo in integration test config Signed-off-by: Nic Ma <nma@nvidia.com>

* attention unet Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * fixed issues and added suggested improvements Signed-off-by: Juan Pablo de la Cruz Gutierrez <juampatronics@gmail.com> * fixed flake issues * smaller tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* [DLMED] add verify script 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> * [DLMED] add unit tests and doc Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] skip min tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] remove doc-string Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update device names Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update doc-string examples Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance error message Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] cpu:0 to cpu Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] adjust "dataset_dir" Signed-off-by: Nic Ma <nma@nvidia.com>

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

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

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

* fixes #3942 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds import statement Signed-off-by: Wenqi Li <wenqil@nvidia.com> * more tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update to resolve import statement Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com>

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

* Minor change to UNet to permit greater modifiability Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Type fix Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Reverting minor change Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

* Check images dimensions and color channels Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

* fixes multiprocessing memory issue Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "Workaround OOM issue in classification 2D integration tests (#3949)" This reverts commit 6ea9742. Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update tests 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 * fixes typo Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [DLMED] support relative ids Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo in test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add description Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] optimize the logic Signed-off-by: Nic Ma <nma@nvidia.com>

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

Nic-Ma and others added 30 commits December 1, 2021 11:29

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>

471- fixes deprecated args (#3447)

29e9ab3

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

improve error message if reader nott available (#3457)

a7bc4a3

improve error message if reader nott available

adds the missing imports (#3462)

d2543ad

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

revise MILModel docstring (#3459)

82576e7

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

deprecate reduction (#3464)

4b5ad0b

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

Add missing components to API doc (#3468)

89f0bd4

* [DLMED] add missing docs Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add missing components Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix test Signed-off-by: Nic Ma <nma@nvidia.com>

[DLMED] remove cls (#3475)

a4c1300

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

Add Iteration base class (#3472)

360c52f

* [DLMED] add Iteration base class 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>

fix link error (#3488)

cb70e13

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

3465 Support string as dtype (#3478)

9ef0070

* [DLMED] support string dtype Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance dtype in ToCupy Signed-off-by: Nic Ma <nma@nvidia.com>

Add Iteration base class (#3472)

2cbb54c

* [DLMED] add Iteration base class 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>

fix link error (#3488)

45af170

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

3465 Support string as dtype (#3478)

9ccc5ee

* [DLMED] support string dtype Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance dtype in ToCupy Signed-off-by: Nic Ma <nma@nvidia.com>

[DLMED] update to 0.4.7 (#3483)

7a66f18

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

3471 3491 Add example images for intensity transforms (#3494)

9927691

* [DLMED] add missing images Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix 3471 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix AsDiscrete Signed-off-by: Nic Ma <nma@nvidia.com>

wyli and others added 29 commits March 7, 2022 10:51

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>

3914 optional lps to ras (#3929)

d8121d2

* optional lps to ras Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes #3934 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update env Signed-off-by: Wenqi Li <wenqil@nvidia.com>

fix vnet typo (#3935)

f22067f

fix docstring typo Signed-off-by: victolee0 <39608452+victolee0@users.noreply.github.com>

3943 Enhance LoadImage transform for customized readers (#3944)

3b771bb

* [DLMED] enhance reader Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix docs Signed-off-by: Nic Ma <nma@nvidia.com>

3919 Use enums for reduction in DiceCELoss (#3953)

6ff8535

* use enum for dicece reduction Signed-off-by: Yiheng Wang <vennw@nvidia.com> * use look up option Signed-off-by: Yiheng Wang <vennw@nvidia.com>

Workaround OOM issue in classification 2D integration tests (#3949)

6ea9742

* [DLMED] update to 21.10 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo in integration test config Signed-off-by: Nic Ma <nma@nvidia.com>

optional meta_file (#3952)

55e6018

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

update cachedataset num workers (#3963)

7ee3488

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

[DLMED] update installation doc (#3970)

be25a72

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

fix fstring bugs (#3972)

459b188

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

Contain WSIReader to colored 2D images (#3979)

bdeb662

* Check images dimensions and color channels Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

3987 - fixes docstrings and adds checks (#3988)

7d8bb9b

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

Nic-Ma merged commit 25b443b into Nic-Ma:3990-fix-flake8 Mar 24, 2022

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

merge master #392

merge master #392

Nic-Ma commented Mar 24, 2022

merge master #392

merge master #392

Conversation

Nic-Ma commented Mar 24, 2022

Description

Status

Types of changes