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* [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]>
* [DLMED] support string dtype Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance dtype in ToCupy 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]>
* [DLMED] support string dtype Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance dtype in ToCupy Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* Update to not include number for the name of the first range Signed-off-by: Behrooz <[email protected]> * Update CuCIM and TorchVision wrappers to include name Signed-off-by: Behrooz <[email protected]> * Update nvtx range to append undelying class for wrapper tranforms Signed-off-by: Behrooz <[email protected]> * Add new test cases to cover changes Signed-off-by: Behrooz <[email protected]> * Update cucim and torchvision check Signed-off-by: Behrooz <[email protected]>
* [DLMED] add missing images Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix 3471 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix AsDiscrete Signed-off-by: Nic Ma <[email protected]>
* make bending energy loss invariant to resolution fixes #3485 Signed-off-by: Ebrahim Ebrahim <[email protected]> * 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 <[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]>
Signed-off-by: Nic Ma <[email protected]>
* fixes #3942 Signed-off-by: Wenqi Li <[email protected]> * adds import statement Signed-off-by: Wenqi Li <[email protected]> * more tests Signed-off-by: Wenqi Li <[email protected]> * update to resolve import statement Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]> * update Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Yiheng Wang <[email protected]>
* Minor change to UNet to permit greater modifiability Signed-off-by: Eric Kerfoot <[email protected]> * Type fix Signed-off-by: Eric Kerfoot <[email protected]> * Reverting minor change Signed-off-by: Eric Kerfoot <[email protected]>
* Check images dimensions and color channels Signed-off-by: Behrooz <[email protected]>
* fixes multiprocessing memory issue Signed-off-by: Wenqi Li <[email protected]> * Revert "Workaround OOM issue in classification 2D integration tests (#3949)" This reverts commit 6ea9742. Signed-off-by: Wenqi Li <[email protected]> * update tests Signed-off-by: Wenqi Li <[email protected]> * [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 <[email protected]> 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 <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo in test Signed-off-by: Nic Ma <[email protected]> * [DLMED] add description Signed-off-by: Nic Ma <[email protected]> * [DLMED] optimize the logic Signed-off-by: Nic Ma <[email protected]>
* fixes docstrings Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>
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Fixes # .
Description
A few sentences describing the changes proposed in this pull request.
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Types of changes
./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests.make htmlcommand in thedocs/folder.