merge master#389
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Nic-Ma merged 472 commits intoNic-Ma:3969-update-installation-docfrom Mar 21, 2022
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* fixes crop types Signed-off-by: Wenqi Li <[email protected]> * fixes dtypes Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] enhance doc Signed-off-by: Nic Ma <[email protected]> * [DLMED] update based on Yiheng's comments Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] add channel dim Signed-off-by: Nic Ma <[email protected]> * [DLMED] add RGB support Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>
* [DLMED] add support for other pickle Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] test flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] test flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>
* fixes pickle mod Signed-off-by: Wenqi Li <[email protected]> * update pickle Signed-off-by: Wenqi Li <[email protected]> * docstring Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* [DLMED] enhance not-nan reduction Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>
…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 <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update Signed-off-by: Wenqi Li <[email protected]> * [DLMED] add args and update default (#3418) Signed-off-by: Nic Ma <[email protected]> Signed-off-by: Wenqi Li <[email protected]> * update docstrings Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Patricio Astudillo <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Wenqi Li <[email protected]> Co-authored-by: Nic Ma <[email protected]>
* update vitautoenc Signed-off-by: Wenqi Li <[email protected]> * update based on the comments; compatibility with the previous model weights Signed-off-by: Wenqi Li <[email protected]>
* Update WSIReader level/location/size calculation Signed-off-by: Behrooz <[email protected]> * Update location downsampling Signed-off-by: Behrooz <[email protected]> * Update tests and add a new test case Signed-off-by: Behrooz <[email protected]> * Update few names and logics Signed-off-by: Behrooz <[email protected]> * Fix the dependency issue Signed-off-by: Behrooz <[email protected]> * Check for imagecodecs + tifffile Signed-off-by: Behrooz <[email protected]> * Remove new test case that uses too much memory Signed-off-by: Behrooz <[email protected]> * Add new case and ignore level=0 for TiffFile Signed-off-by: Behrooz <[email protected]> * Address comments Signed-off-by: Behrooz <[email protected]> Co-authored-by: Nic Ma <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* Update TiffFile backend to read only the entire image Signed-off-by: Behrooz <[email protected]>
* [DLMED] extract write logic 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] update according to comments Signed-off-by: Nic Ma <[email protected]>
* [DLMED] add dataframe Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance CSV iterable dataset Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typehints Signed-off-by: Nic Ma <[email protected]> * [DLMED] add comment 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] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix file close issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix doc Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]>
* [DLMED] add BaseWorkflow Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] add *args, **kwargs Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>
* [DLMED] fix deprecated arg Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]>
* enhance dynunet Signed-off-by: Yiheng Wang <[email protected]> * fix black issue Signed-off-by: Yiheng Wang <[email protected]> * use strict=False Signed-off-by: Yiheng Wang <[email protected]> * fix black 21.12 error Signed-off-by: Yiheng Wang <[email protected]> * enhance code and update docstring Signed-off-by: Yiheng Wang <[email protected]>
* fixes deprecated args Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>
improve error message if reader nott available
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] add dataset generator Signed-off-by: Nic Ma <[email protected]> * [DLMED] add DatasetGenerator Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] fix wrong test Signed-off-by: Nic Ma <[email protected]> * [DLMED] simplify according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove return Signed-off-by: Nic Ma <[email protected]> * [DLMED] update rtol for CI Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>
* [DLMED] add missing docs Signed-off-by: Nic Ma <[email protected]> * [DLMED] add missing components Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix test Signed-off-by: Nic Ma <[email protected]>
* [DLMED] add channel-wise Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] skip test if before 1.7 Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> Co-authored-by: monai-bot <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* [DLMED] add Iteration base class 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]>
Signed-off-by: Yiheng Wang <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* Remove dead link from highlights.md Signed-off-by: Ioannis Valasakis <[email protected]>
* fix non intensity error Signed-off-by: Yiheng Wang <[email protected]> * remove useless torch mod Signed-off-by: Yiheng Wang <[email protected]> * convert type before return Signed-off-by: Yiheng Wang <[email protected]> * update convert Signed-off-by: Yiheng Wang <[email protected]>
* Add SliceInferer for slice-by-slice infer Signed-off-by: Suraj Pai <[email protected]>
Signed-off-by: Yiheng Wang <[email protected]>
* 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 <[email protected]> * ignore Signed-off-by: Richard Brown <[email protected]>
* fix unittest error Signed-off-by: Yiheng Wang <[email protected]> * unify version Signed-off-by: Yiheng Wang <[email protected]>
* Revert "inverse ResampleToMatchd (#3856)" This reverts commit 82ec2fe. Signed-off-by: Wenqi Li <[email protected]> * Revert "Revert "inverse ResampleToMatchd (#3856)"" This reverts commit 6698ef5. Signed-off-by: Wenqi Li <[email protected]> * support of writer names Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>
* add shape info when raising errors Signed-off-by: Yiheng Wang <[email protected]>
* update Transchex model Signed-off-by: ahatamizadeh <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] add config parser Signed-off-by: Nic Ma <[email protected]> * [DLMED] simplify parse logic Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more function tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix torchvision tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] add standard run API Signed-off-by: Nic Ma <[email protected]> * [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 <[email protected]> * [DLMED] update API Signed-off-by: Nic Ma <[email protected]> * [DLMED] simplify API Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance doc and unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] clear API Signed-off-by: Nic Ma <[email protected]> * [DLMED] simplify usage APIs Signed-off-by: Nic Ma <[email protected]> * [DLMED] support root config Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix update reference typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] update usage API Signed-off-by: Nic Ma <[email protected]> * revise APIs and docstrings Signed-off-by: Wenqi Li <[email protected]> * remove->discard Signed-off-by: Wenqi Li <[email protected]> * [DLMED] minor change Signed-off-by: Nic Ma <[email protected]> * [DLMED] update code Signed-off-by: Nic Ma <[email protected]> * update usage Signed-off-by: Wenqi Li <[email protected]> * [DLMED] update doc Signed-off-by: Nic Ma <[email protected]> * [DLMED] add end-to-end test Signed-off-by: Nic Ma <[email protected]> * [DLMED] update doc Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix optional import Signed-off-by: Nic Ma <[email protected]> * [DLMED] refine APIs Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] add support to only use part of the file to override Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] update to latest Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update `fire` supported dict arg Signed-off-by: Nic Ma <[email protected]> * [DLMED] add examples to doc-string Signed-off-by: Nic Ma <[email protected]> * [DLMED] skip windows test for paths Signed-off-by: Nic Ma <[email protected]> * [DLMED] skip windows Signed-off-by: Nic Ma <[email protected]> * [DLMED] update windows Signed-off-by: Nic Ma <[email protected]> * [DLMED] update command Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix windows test Signed-off-by: Nic Ma <[email protected]> * [DLMED] construct class Signed-off-by: Nic Ma <[email protected]> * [DLMED] restore design Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix args override Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] test windows Signed-off-by: Nic Ma <[email protected]> * [DLMED] test windows Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] refactor config reading logic Signed-off-by: Nic Ma <[email protected]> * [DLMED] add doc-string Signed-off-by: Nic Ma <[email protected]> * [DLMED] add export and test Signed-off-by: Nic Ma <[email protected]> * [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 <[email protected]> * fixes doc tests Signed-off-by: Wenqi Li <[email protected]> * [DLMED] enhance test Signed-off-by: Nic Ma <[email protected]> * rel import Signed-off-by: Wenqi Li <[email protected]> * [DLMED] refine macro Signed-off-by: Nic Ma <[email protected]> * fixes flake8 f401 Signed-off-by: Wenqi Li <[email protected]> * mv to monai.bundle Signed-off-by: Wenqi Li <[email protected]> * fixes split_path_id, update docstrings Signed-off-by: Wenqi Li <[email protected]> * fixes mypy Signed-off-by: Wenqi Li <[email protected]> * update cli, update according to the comments Signed-off-by: Wenqi Li <[email protected]> * [DLMED] fix typo in doc-string Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to discussion Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix path_id match Signed-off-by: Nic Ma <[email protected]> * revise according to the comments Signed-off-by: Wenqi Li <[email protected]> * [DLMED] update config item Signed-off-by: Nic Ma <[email protected]> * [DLMED] update patterns Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance disabled Signed-off-by: Nic Ma <[email protected]> * special chars to utils Signed-off-by: Wenqi Li <[email protected]> * remove circular import Signed-off-by: Wenqi Li <[email protected]> * configreader -> configparser following cpython/configparser Signed-off-by: Wenqi Li <[email protected]> * printing Signed-off-by: Wenqi Li <[email protected]> * fixes typing Signed-off-by: Wenqi Li <[email protected]> * [DLMED] unify "_name_" and "_path_" Signed-off-by: Nic Ma <[email protected]> * [DLMED] update to "_target_" Signed-off-by: Nic Ma <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Wenqi Li <[email protected]>
Signed-off-by: Yiheng Wang <[email protected]>
* Adding archive specification document Signed-off-by: Eric Kerfoot <[email protected]> * Adding archive specification document Signed-off-by: Eric Kerfoot <[email protected]> * Adding archive specification document Signed-off-by: Eric Kerfoot <[email protected]> * [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 <[email protected]> * Adding archive specification document Signed-off-by: Eric Kerfoot <[email protected]> * Adding archive specification document Signed-off-by: Eric Kerfoot <[email protected]> * Updated specification Signed-off-by: Eric Kerfoot <[email protected]> * [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 <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: GreySeaWolf <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
* fixes #3921 Signed-off-by: Wenqi Li <[email protected]> * fixes Signed-off-by: Wenqi Li <[email protected]> * fixes mypy Signed-off-by: Wenqi Li <[email protected]> * remove temp tests Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] add ignore_data API Signed-off-by: Nic Ma <[email protected]> * [DLMED] optimize the API Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix mypy Signed-off-by: Nic Ma <[email protected]>
* [DLMED] complete temp test schema Signed-off-by: Nic Ma <[email protected]> * [DLMED] add cmd line API Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] add optional import Signed-off-by: Nic Ma <[email protected]> * [DLMED] test with download link Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance doc-string Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix mypy Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove DS_Store 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 tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] change "target_id" to "runner_id" Signed-off-by: Nic Ma <[email protected]> * [DLMED] simplify command line Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix print summary logic Signed-off-by: Nic Ma <[email protected]> * [DLMED] update log print to logging Signed-off-by: Nic Ma <[email protected]> * [DLMED] compact commands Signed-off-by: Nic Ma <[email protected]> * [DLMED] unify args update Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] skip windows Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] optimize error log Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update accoding to comments Signed-off-by: Nic Ma <[email protected]>
* optional lps to ras Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * fixes #3934 Signed-off-by: Wenqi Li <[email protected]> * update env Signed-off-by: Wenqi Li <[email protected]>
fix docstring typo Signed-off-by: victolee0 <[email protected]>
* enhance 1st conv layer of ResNet Signed-off-by: Yiheng Wang <[email protected]> * [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 <[email protected]> * use ensure_tuple_rep Signed-off-by: Yiheng Wang <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* [DLMED] enhance reader Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix docs Signed-off-by: Nic Ma <[email protected]>
* fixes #3934 Signed-off-by: Wenqi Li <[email protected]> * min_test update Signed-off-by: Wenqi Li <[email protected]> * cu115 tests Signed-off-by: Wenqi Li <[email protected]> * update tests Signed-off-by: Wenqi Li <[email protected]>
* use enum for dicece reduction Signed-off-by: Yiheng Wang <[email protected]> * use look up option Signed-off-by: Yiheng Wang <[email protected]>
* [DLMED] update to 21.10 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo in integration test config Signed-off-by: Nic Ma <[email protected]>
* attention unet Signed-off-by: Juan Pablo de la Cruz Gutiérrez <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * fixed issues and added suggested improvements Signed-off-by: Juan Pablo de la Cruz Gutierrez <[email protected]> * fixed flake issues * smaller tests Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: monai-bot <[email protected]>
* [DLMED] add verify script Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests and doc Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] skip min tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove doc-string Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] update device names Signed-off-by: Nic Ma <[email protected]> * [DLMED] update doc-string examples Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance error message Signed-off-by: Nic Ma <[email protected]> * [DLMED] cpu:0 to cpu Signed-off-by: Nic Ma <[email protected]> * [DLMED] adjust "dataset_dir" Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Yiheng Wang <[email protected]>
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Fixes # .
Description
A few sentences describing the changes proposed in this pull request.
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Ready/Work in progress/Hold
Types of changes
./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests.make htmlcommand in thedocs/folder.