merge master #190
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merge master #190
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Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] enhance TTA Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]>
* [DLMED] enhance doc-string for spatial shape Signed-off-by: Nic Ma <[email protected]> * [DLMED] add ill test case Signed-off-by: Nic Ma <[email protected]> * [DLMED] update test error Signed-off-by: Nic Ma <[email protected]> * update docstring and add more test cases Signed-off-by: Yiheng Wang <[email protected]> * [DLMED] add link to doc-string Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance doc-string Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Yiheng Wang <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] enhance doc-string Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance the sanity check Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]>
* [DLMED] add RandCoarseDropout Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] add dict version transform Signed-off-by: Nic Ma <[email protected]> * [DLMED] updated according to comments Signed-off-by: Nic Ma <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
* [DLMED] init the transform Signed-off-by: Nic Ma <[email protected]> * [DLMED] update doc-string Signed-off-by: Nic Ma <[email protected]> * [DLMED] complete array transform Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] add dict transform and inverse tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix mypy type Signed-off-by: Nic Ma <[email protected]> * [DLMED] change to enhance Resize transform Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix CI tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix TTA Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix mypy error Signed-off-by: Nic Ma <[email protected]>
* added stain norm and tests Signed-off-by: Neha Srivathsa <[email protected]> * import changes Signed-off-by: Neha Srivathsa <[email protected]> * changed stain extraction tests Signed-off-by: Neha Srivathsa <[email protected]> * edited stain norm tests Signed-off-by: Neha Srivathsa <[email protected]> * convert floats to float32 Signed-off-by: Neha Srivathsa <[email protected]> * added uint8 assumption to docstring Signed-off-by: Neha Srivathsa <[email protected]> * add error case Signed-off-by: Neha Srivathsa <[email protected]> * formatting change Signed-off-by: Neha Srivathsa <[email protected]> * modify tests wrt cupy import Signed-off-by: Neha Srivathsa <[email protected]> * minor change to pass lint test Signed-off-by: Neha Srivathsa <[email protected]> * import changes Signed-off-by: Neha Srivathsa <[email protected]> * refactored classes Signed-off-by: Neha Srivathsa <[email protected]> * Restructure and rename transforms Signed-off-by: Behrooz <[email protected]> * added dict transform Signed-off-by: Neha Srivathsa <[email protected]> * Move stain_extractor to init Signed-off-by: Behrooz <[email protected]> * Exclude pathology transform tests from mini tests Signed-off-by: Behrooz <[email protected]> * Fix type checking for cupy ndarray Signed-off-by: Behrooz <[email protected]> * Include pathology transform tests Signed-off-by: Behrooz <[email protected]> * Update to cupy 9.0.0 Signed-off-by: Behrooz <[email protected]> * Remove exact version for cupy Signed-off-by: Behrooz <[email protected]> * add to docs Signed-off-by: Neha Srivathsa <[email protected]> * Organize into stain dir Signed-off-by: Behrooz <[email protected]> * Add/update init files Signed-off-by: Behrooz <[email protected]> * Transit all from cupy to numpy Signed-off-by: Behrooz <[email protected]> * Update imports Signed-off-by: Behrooz <[email protected]> * Update test cases for numpy Signed-off-by: Behrooz <[email protected]> * Rename to NormalizeHEStains and NormalizeHEStainsD Signed-off-by: Behrooz <[email protected]> * Add dictionary variant names Signed-off-by: Behrooz <[email protected]> * Fix typing and formatting Signed-off-by: Behrooz <[email protected]> * Fix docs Signed-off-by: Behrooz <[email protected]> * Update test cases Signed-off-by: Behrooz <[email protected]> * Fix clip max Signed-off-by: Behrooz <[email protected]> * Fix var typing Signed-off-by: Behrooz <[email protected]> * Fix a typing issue Signed-off-by: Behrooz <[email protected]> * Update default values, and change D to d Signed-off-by: Behrooz <[email protected]> * Update docs Signed-off-by: Behrooz <[email protected]> * Add image value check Signed-off-by: Behrooz <[email protected]> * Add test cases for negative and invalid values Signed-off-by: Behrooz <[email protected]> Co-authored-by: Neha Srivathsa <[email protected]> Co-authored-by: nsrivathsa <[email protected]>
* Add DatasetCalculator Signed-off-by: Yiheng Wang <[email protected]> * update docstring Signed-off-by: Yiheng Wang <[email protected]> * use multiprocessing Signed-off-by: Yiheng Wang <[email protected]> * update to use dataset and other places Signed-off-by: Yiheng Wang <[email protected]> * update to support array return Signed-off-by: Yiheng Wang <[email protected]> * update with new testcases and change name Signed-off-by: Yiheng Wang <[email protected]> * update min test Signed-off-by: Yiheng Wang <[email protected]> * update unittest Signed-off-by: Yiheng Wang <[email protected]> * fix vstack error Signed-off-by: Yiheng Wang <[email protected]>
…m part of dataset (#2667) * [DLMED] add RandCompose Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] change to enhance RandLambda Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove RandCompose Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix format Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance doc Signed-off-by: Nic Ma <[email protected]> * [DLMED] add inverse operation Signed-off-by: Nic Ma <[email protected]> * [DLMED] add more tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix subprogress issue Signed-off-by: Nic Ma <[email protected]>
* Restructure transforms into a directory Signed-off-by: Behrooz <[email protected]> * Fix a typo Signed-off-by: Behrooz <[email protected]> Co-authored-by: Behrooz <[email protected]>
* Moved fourier functions to their own class. Modified RandKSpaceSpikeNoised. 1. Allow RandKSpaceSpikeNoised to work with arbitrary keys. 2. Introduced Fourier transform to keep the forward/backward fourier mappings. Signed-off-by: Yaniel Cabrera <[email protected]> * removed old code Signed-off-by: Yaniel Cabrera <[email protected]> * Ignore torch.fft tests if not present Ignore tests with versions of Pytorch which lack the module fft. Signed-off-by: Yaniel Cabrera <[email protected]> * update Signed-off-by: Yaniel Cabrera <[email protected]> * typing update Signed-off-by: Yaniel Cabrera <[email protected]> * added unit test for Fourier Signed-off-by: Yaniel Cabrera <[email protected]> * added unit test for Fourier Signed-off-by: Yaniel Cabrera <[email protected]> * fixing black Signed-off-by: Yaniel Cabrera <[email protected]>
This is to address an issue in the bibtex conversion. Signed-off-by: Tom Vercauteren <[email protected]>
… meta data (#2685) * [DLMED] add IntensityStats transform Signed-off-by: Nic Ma <[email protected]> * [DLMED] add unit tests Signed-off-by: Nic Ma <[email protected]> * [DLMED] add dict version transform Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance ShiftIntensity transform Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] change to utility Signed-off-by: Nic Ma <[email protected]> * [DLMED] adjust to look_up_option Signed-off-by: Nic Ma <[email protected]> * [DLMED] add multi-processing test Signed-off-by: Nic Ma <[email protected]> * [DLMED] add mask option Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix flake8 Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix typo Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix pickle issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] enhance error message Signed-off-by: Nic Ma <[email protected]> * [DLMED] add pickle test Signed-off-by: Nic Ma <[email protected]> * [MONAI] python code formatting Signed-off-by: monai-bot <[email protected]> * [DLMED] enhance pickle test Signed-off-by: Nic Ma <[email protected]> Co-authored-by: monai-bot <[email protected]>
* [DLMED] update doc-strings of Affine transforms Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix format issue Signed-off-by: Nic Ma <[email protected]> * [DLMED] update according to comments Signed-off-by: Nic Ma <[email protected]> * [DLMED] remove coord link Signed-off-by: Nic Ma <[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.