merge master by Nic-Ma · Pull Request #55 · Nic-Ma/MONAI

Nic-Ma · 2021-03-26T11:28:29Z

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 --codeformat --coverage.
Quick tests passed locally by running ./runtests.sh --quick.
In-line docstrings updated.
Documentation updated, tested make html command in the docs/ folder.

* update openmp flag Signed-off-by: Wenqi Li <wenqil@nvidia.com> * improves boundtype docs Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update setup.py Signed-off-by: Wenqi Li <wenqil@nvidia.com> * input validation 1d Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typos Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes typos Signed-off-by: Wenqi Li <wenqil@nvidia.com> * merge upstream changes Signed-off-by: Wenqi Li <wenqil@nvidia.com> * tests enums Signed-off-by: Wenqi Li <wenqil@nvidia.com> * init. test grid pull Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update Signed-off-by: Wenqi Li <wenqil@nvidia.com> * test grid_pull Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes min test Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds device tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * bwd tests Signed-off-by: Wenqi Li <wenqil@nvidia.com>

move transforms out of compose file. this is backwards compatible.

* pad_collation Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * increase number of test cases to ensure required testing errors Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * determinism in setUp Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * pad collate for list of lists Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * code format Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * allow padding options Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

decollate batch

enhance random range parameters If element `i` is iterable, then `uniform[-rotate_range[i][0], rotate_range[i][1])` will be used to generate the rotation parameter for the ith dimension. If not, `uniform[-rotate_range[i], rotate_range[i])` will be used. This can be altered on a per-dimension basis. E.g., `((0,3), 1, ...)`: for dim0, rotation will be in range `[0, 3]`, and for dim1 `[-1, 1]` will be used. Setting a single value will use `[-x, x]` for dim0 and nothing for the remaining dimensions. Backwards compatibility is ensured because the old behaviour used to do `uniform[-rotate_range[i], rotate_range[i])`, and this PR just adds the possibility to do `uniform[-rotate_range[i][0], rotate_range[i][1])`.

* Fixing issues preventing loss functions from being compatible with Torchscript Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Updates Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Updates Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * Updates Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Adding conditional skip to Torchscript tests Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* [DLMED] fix length > 1024 issue in string list all gather Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue 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 test Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Yiheng Wang <68361391+yiheng-wang-nv@users.noreply.github.com>

* DeleteChannel array, dictionary, tests Signed-off-by: Leo Tam <leot@nvidia.com> * formatting Signed-off-by: Leo Tam <leot@nvidia.com> * DeleteChannel array, dictionary, tests Signed-off-by: Leo Tam <leot@nvidia.com> * Register in transform init Signed-off-by: Leo Tam <leot@nvidia.com> * clean comment Signed-off-by: Leo Tam <leot@nvidia.com> * Dict init Signed-off-by: Leo Tam <leot@nvidia.com> * Register D and Dict Signed-off-by: Leo Tam <leot@nvidia.com> * Style fix Signed-off-by: Leo Tam <leot@nvidia.com> * Safety cast Signed-off-by: Leo Tam <leot@nvidia.com> * Changinging names from DeleteChannel to RemoveRepeatedChannel Signed-off-by: Leo Tam <leot@nvidia.com> * Lint fixes Signed-off-by: Leo Tam <leot@nvidia.com> * Test import fix, autofix again Signed-off-by: Leo Tam <leot@nvidia.com>

Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>

* update distcall Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update final closing Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>

* Add ToPIL transformation Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add ToPILd, ToPILD, ToPILDict Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Remove has_pil Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Include ToPIL, ToPILd, ToPILD, and ToPILDict Also include ToNumpyD, ToNumpyDict, TorchVisionD, and TorchVisionDict Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Fix a typing issue Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Fix PIL optional import Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add unittests for ToPIL and ToPILD Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Fix formatting Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Fix formatting Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add PILImage.Image as the input for ToNumpy and ToTensor Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Fix type checking issue for PIL.Image.Image Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Change PILImage_fromarray to lower case Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

add RandomizableTransform

* Add more tests to test_deepgrow_dataset Signed-off-by: YuanTingHsieh <yuantinghsieh@gmail.com>

* Add inference transforms Signed-off-by: YuanTingHsieh <yuantinghsieh@gmail.com> * Remove unused import Signed-off-by: YuanTingHsieh <yuantinghsieh@gmail.com> * Fix review comments Signed-off-by: YuanTingHsieh <yuantinghsieh@gmail.com> Co-authored-by: SACHIDANAND ALLE <sachidanand.alle@gmail.com>

* [DLMED] add RandAxisFlip transforms Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] fix flake8 issues Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

fix big endianness problem for dictionary reading. Also allow dictionary image_only

* [DLMED] add AutoAdjustChannel transform Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add dict version transform Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] fix doc-build issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to Wenqi's comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update doc-strings 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>

Allow missing keys

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

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

* Update load pretrain for densenet Signed-off-by: Yiheng Wang <vennw@nvidia.com> * Fix isort issue Signed-off-by: Yiheng Wang <vennw@nvidia.com>

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

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

* [DLMED] add suqeeze to handler Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

* fixes #1285 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds test Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes #1685 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * add temp test Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes dist sampler Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove temp tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes type hint issue Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes data type in switching Signed-off-by: Wenqi Li <wenqil@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* Implement CuImageReader and OpenSlideReader Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add unittests for CuImageReader Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add unittests for OpenSlideReader Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Sort imports Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add correct boundaries Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add test cases for reading patches on a grid for CuImage Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add patch whole slide imaging dataset for pathology Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add test case for read patches for OpenSlide Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * flake8 and few minor changes Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * black Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * flake8 Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add kwargs to CuImageReader and OpenSlideReader's read method Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Change the type hint from np.dtype to DTypeLike Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Fix a bug Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Implement WSIReader and unittests Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Minor updates Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Fix few typing issues Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Revert datasets Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add shape property to openslide image object Reverse size to be compatible with output size (hxw) Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add untittest for loading the whole image Reverse the size accroding to the WSIReader Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update the whole image size Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Remove optional size Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Remove optional dtype Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Remove _get_spatial_shape return type Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Reverse the orders of dimensions of `location` to be compatible with image shape Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Change test cases to use smaller image and revese location's dimensions Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Replace the test TIFF and some upgrades Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update dependencies for OpenSlide Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update unittests for OpenSlide and CuImage Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Fix openslide dependency Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Fix doc dependencies Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Minor changes Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Few variable name changes Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add EnsureChannelFirst Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add metadata to WSIReader Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

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

* Remove WSIReader from LoadImage Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Remove WSIReader from LoadImaged Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

* add pretrain options Signed-off-by: Yiheng Wang <vennw@nvidia.com>

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* Jupyter and other additions Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Jupyter utilities update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Jupyter utilities update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Jupyter utilities update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Jupyter utilities update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Jupyter utilities update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Jupyter utilities update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Jupyter utilities update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Jupyter utilities update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Jupyter utilities update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> Co-authored-by: Nic Ma <nma@nvidia.com> Co-authored-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

batch inverse

* add pretrain options Signed-off-by: Yiheng Wang <vennw@nvidia.com> * rewrite error message add test cases Signed-off-by: Yiheng Wang <vennw@nvidia.com>

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* cron tutorial notebooks Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* allow None for switch endianness Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * add PIL testing Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* Jupyter and other additions Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Jupyter utilities update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

* [DLMED] update ROCAUC Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] fix CI tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

test time augmentations

* fixes tutorial issue 150 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * revise based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* [DLMED] enhance transform logging Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] ignore type warning Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* [DLMED] add eval mode in Evaluators Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>

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

Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>

* 1837--collating Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes transform device Signed-off-by: Wenqi Li <wenqil@nvidia.com> * reverting self.affine Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* conditional random field implementation Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

* [DLMED] fix affine error and thread-safe issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update CI tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update typehints Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.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] make cachedataset to be thread-safe Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] remove inverse ID check Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] restore CacheDataset and inverse transform Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* Implement PatchWSIDataset and SmartCachePathWSIDataset Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Remove label preprocessing and adopt new type of inputs Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update type hints Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add init file Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Change grid_size to grid_shape Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add a unittest for PatchWSIDataset Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add more unittests Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update docstrings and make minor changes Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Convert labels to numpy to match the change in dataset Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update location from center to corner Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update unittests locations from center to corner Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update docs for pathology datasets Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update type hint and doc Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update docstrings Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Format docstring Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update length of the smartcache dataset Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add unittest for SmartCachePatchWSIDataset Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Minor changes and fixes Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add unnittest for OpenSlide option Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add new line Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Remove SmartCachePatchWSIDataset test to fix it Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * move init docstring to class docstring Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

* Implement fully convolutional version of torchvision models Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update networks init with TorchVisionFullyConvModel Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add unittests for TorchVisionFullyConvModel Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add another test case Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Upate docs for TorchVisionFullyConvModel Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Make torchvision import optional Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Skip the tests if torchvision not available Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Improve the model based on comments Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update and add test cases Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

* Add label dimensions to be compatible with changes in model output Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update test case outputs and add new test case Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

* fixes init affinehead Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes unit tests Signed-off-by: Wenqi Li <wenqil@nvidia.com>

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

* fixes #1857, SpatialCrop is compatible with tensors Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update val comparisons Signed-off-by: Wenqi Li <wenqil@nvidia.com>

wyli and others added 30 commits February 24, 2021 15:02

move transforms out of compose file (#1623)

3a1c459

move transforms out of compose file. this is backwards compatible.

decollate batch (#1624)

69d9fcc

decollate batch

[DLMED] add progress arg (#1647)

c68d25e

Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>

1650-update distcall (#1652)

5875ae6

* update distcall Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update final closing Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>

Randomizable constructor (#1639)

1df6352

add RandomizableTransform

Add more tests to test_deepgrow_dataset (#1654)

4b8819a

* Add more tests to test_deepgrow_dataset Signed-off-by: YuanTingHsieh <yuantinghsieh@gmail.com>

allow dictionary image only and test endianness (#1669)

20e17b2

fix big endianness problem for dictionary reading. Also allow dictionary image_only

[1662] Allow missing keys (#1676)

421c0a9

Allow missing keys

nifti saver squeeze dims (#1680)

27543c8

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

improve gradcam doc (#1682)

b533afd

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

fixes integration tests (#1683)

7cfb529

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

Update load pretrain for densenet (#1684)

4bd9cf3

* Update load pretrain for densenet Signed-off-by: Yiheng Wang <vennw@nvidia.com> * Fix isort issue Signed-off-by: Yiheng Wang <vennw@nvidia.com>

revise the dtype according to the discussion (#1671)

8cc200f

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

Fix senet pretrained weights issue (#1689)

ac9f953

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

1680 Add squeeze SegmentationSaver handler (#1686)

380f042

* [DLMED] add suqeeze to handler Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

1285 adds module list (#1690)

114faf0

* fixes #1285 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds test Signed-off-by: Wenqi Li <wenqil@nvidia.com>

fixes data type in switching (#1694)

75b5772

* fixes data type in switching Signed-off-by: Wenqi Li <wenqil@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 WSIReader to LoadImage (#1695)

232e8a5

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

bhashemian and others added 29 commits March 18, 2021 22:18

Remove WSIReader from LoadImage (#1796)

4411758

* Remove WSIReader from LoadImage Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Remove WSIReader from LoadImaged Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

1804 add pretrain options (#1805)

7d25743

* add pretrain options Signed-off-by: Yiheng Wang <vennw@nvidia.com>

1809 add std shift intensity transform (#1810)

70388fa

* add pretrain options Signed-off-by: Yiheng Wang <vennw@nvidia.com>

PadListDataCollate transform (#1813)

3e313d2

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

Batch inverse (#1795)

a2aeb40

batch inverse

1804 add pretrain for densenet senet by using subclass (#1812)

b6f213e

* add pretrain options Signed-off-by: Yiheng Wang <vennw@nvidia.com> * rewrite error message add test cases Signed-off-by: Yiheng Wang <vennw@nvidia.com>

remove .value from InverseKeys enum (#1817)

5151b15

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

cron tutorial notebooks (#1783)

06e1e99

* cron tutorial notebooks Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

refactor CommonKeys (#1825)

a8f83e1

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

Jupyter followup (#1826)

c4bb4cb

* Jupyter and other additions Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk> * Jupyter utilities update Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

Test time augmentations (#1794)

83855b9

test time augmentations

fixes tutorial issue 150 (#1830)

8ddd09f

* fixes tutorial issue 150 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * revise based on comments Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

1807 Enhance SmartCacheDataset with shuffle and exception (#1832)

e8e2f3e

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

fix device bug (#1841)

f8c3901

Signed-off-by: kate-sann5100 <yiwen.li@st-annes.ox.ac.uk>

truncate plot title string (#1843)

c3f1e02

Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

Conditional Random Field (#1806)

b6d1cea

* conditional random field implementation Signed-off-by: charliebudd <charles.budd@kcl.ac.uk>

identity init. for global net (#1849)

126768f

* fixes init affinehead Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes unit tests Signed-off-by: Wenqi Li <wenqil@nvidia.com>

[DLMED] fix SmartCache warning (#1855)

e0feb53

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

1857 - SpatialCrop supports with tensors (#1858)

149216e

* fixes #1857, SpatialCrop is compatible with tensors Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update val comparisons Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Nic-Ma merged commit fa07c62 into Nic-Ma:1862-fix-checkpoint-permission Mar 26, 2021

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merge master#55

merge master#55
Nic-Ma merged 103 commits into
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Nic-Ma commented Mar 26, 2021

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