rebase dev and add box utils#3586
Merged
Can-Zhao merged 59 commits intoProject-MONAI:feature/1741-detectionfrom Jan 5, 2022
Merged
rebase dev and add box utils#3586Can-Zhao merged 59 commits intoProject-MONAI:feature/1741-detectionfrom
Can-Zhao merged 59 commits intoProject-MONAI:feature/1741-detectionfrom
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* 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]>
…ct-MONAI#3431) * [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]>
…3427) * 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]>
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]>
…3494) * [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 Project-MONAI#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]>
Signed-off-by: Wenqi Li <[email protected]>
…#3499) * [DLMED] correct kwargs Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix grammar Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] add SavitzkyGolaySmoothd 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]>
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* Adding Torchscript utility functions 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 * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * Adding Torchscript utility functions Signed-off-by: Eric Kerfoot <[email protected]> * Added test for extra files 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 * Update Signed-off-by: Eric Kerfoot <[email protected]> * Update 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 * Update Signed-off-by: Eric Kerfoot <[email protected]> * Update Signed-off-by: Eric Kerfoot <[email protected]> * Updates 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 * Updates Signed-off-by: Eric Kerfoot <[email protected]> * Updates 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: monai-bot <[email protected]> Co-authored-by: Nic Ma <[email protected]>
* [DLMED] change to utility transforms Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance args Signed-off-by: Nic Ma <[email protected]>
* adds missing item Signed-off-by: Wenqi Li <[email protected]> * update the contributing guide Signed-off-by: Wenqi Li <[email protected]> * update copyright headers Signed-off-by: Wenqi Li <[email protected]>
* util to check the licence info Signed-off-by: Wenqi Li <[email protected]> * update flags Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>
… APIs (Project-MONAI#3526) * [DLMED] clarify old APIs Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>
* [DLMED] update to 21.12 Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] add PyTorch 1.9 test Signed-off-by: Nic Ma <[email protected]>
* [DLMED] add missing args Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] update progress arg Signed-off-by: Nic Ma <[email protected]>
* [DLMED] fix oneof Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] update index Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * Revert "[DLMED] update according to comments" This reverts commit c6c3a35. Signed-off-by: Nic Ma <[email protected]> * Revert "[DLMED] update index" This reverts commit 649a7c5. Signed-off-by: Nic Ma <[email protected]>
* drop py36 support Signed-off-by: Wenqi Li <[email protected]> * drop 20.09 test because of python min version 3.6 Signed-off-by: Wenqi Li <[email protected]> * update tests Signed-off-by: Wenqi Li <[email protected]> * error->warning, revise copyright Signed-off-by: Wenqi Li <[email protected]>
* has cupy check Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>
* adds min. memory testing utils Signed-off-by: Wenqi Li <[email protected]> * include valueerror for robust outcome Signed-off-by: Wenqi Li <[email protected]> * ensure float Signed-off-by: Wenqi Li <[email protected]> * msg improvements Signed-off-by: Wenqi Li <[email protected]> * update threshold Signed-off-by: Wenqi Li <[email protected]> * remove ref Signed-off-by: Wenqi Li <[email protected]> * separate disttests Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] remove warning Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]>
Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
* Adding smooth deform transform Signed-off-by: Eric Kerfoot <[email protected]> * Update Signed-off-by: Eric Kerfoot <[email protected]> * Updates Signed-off-by: Eric Kerfoot <[email protected]> * Docs update Signed-off-by: Eric Kerfoot <[email protected]> * Type fixing 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 * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * Fix Signed-off-by: Eric Kerfoot <[email protected]> * Fix 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 * Fix for moveaxis Signed-off-by: Eric Kerfoot <[email protected]> * Fix for moveaxis Signed-off-by: Eric Kerfoot <[email protected]> * Adding example images, random field sized reduced to (10,10,10) Signed-off-by: Eric Kerfoot <[email protected]> * Changed backend Signed-off-by: Eric Kerfoot <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * Tweak 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: monai-bot <[email protected]>
* runtest.sh defaults to no build/install Signed-off-by: Wenqi Li <[email protected]> * following test case conventions for multiprocessing - adding `_dist` to multiprocessing test cases - decouple multiprocessing LMDB tests from `test_lmdbdataset` Signed-off-by: Wenqi Li <[email protected]> * exclude lmdbdataset tests in min_tests Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: Eric Kerfoot <[email protected]>
Signed-off-by: Eric Kerfoot <[email protected]>
…Project-MONAI#3558) Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Nic Ma <[email protected]>
* [DLMED] update dataset summary Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance data type Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix pickle issue Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
updates: - [github.com/pre-commit/pre-commit-hooks: v4.0.1 → v4.1.0](pre-commit/pre-commit-hooks@v4.0.1...v4.1.0) - [github.com/asottile/pyupgrade: v2.29.0 → v2.31.0](asottile/pyupgrade@v2.29.0...v2.31.0) - [github.com/asottile/yesqa: v1.2.3 → v1.3.0](asottile/yesqa@v1.2.3...v1.3.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* adds metadata when loading dicom series Signed-off-by: Wenqi Li <[email protected]> * fixes timed tests Signed-off-by: Wenqi Li <[email protected]> * update based on comments Signed-off-by: Wenqi Li <[email protected]>
* Create codeql-analysis.yml Signed-off-by: Wenqi Li <[email protected]> * build cpp Signed-off-by: Wenqi Li <[email protected]> * fixes Multiplication result converted to larger type Signed-off-by: Wenqi Li <[email protected]> * fixes url parsing Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] add log handler Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI test Signed-off-by: Nic Ma <[email protected]> * [DLMED] test CI Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix logging Signed-off-by: Nic Ma <[email protected]> * [DLMED] temp test Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix wrong unit test Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix wrong test cases Signed-off-by: Nic Ma <[email protected]>
Can-Zhao
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Fixes # .
Description
rebase dev
add box utils
Status
Work in progress
Types of changes
./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests --disttests.make htmlcommand in thedocs/folder.