merge master #72

Nic-Ma · 2021-04-08T14:29:43Z

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>

* update to use pytorch2103 Signed-off-by: Wenqi Li <wenqil@nvidia.com>

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

* [DLMED] SaveImage supports patch data 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] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

This reverts commit 4bd26f9. Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Nic Ma <nma@nvidia.com>

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

* [DLMED] add EarlyStop handler Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] enhance validation handler Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add set_trainer support Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more check 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] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] change to save patch_index in meta_dict Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] remove error import 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> Co-authored-by: monai-bot <monai.miccai2019@gmail.com>

* Enabled partial checkpoint loading Allowing partial loading of a model via strict=False. Signed-off-by: Petru-Daniel Tudosiu <petru.daniel@tudosiu.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] simplify strict arg Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Nic Ma <nma@nvidia.com>

* less warning msg; remove PILImage types Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove engine type Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * add quick py36 37 tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp tests Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "temp tests" This reverts commit deaed40. Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "temp tests" This reverts commit 3e8d8f4. Signed-off-by: Wenqi Li <wenqil@nvidia.com> * min test exclude senet test Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update Signed-off-by: Wenqi Li <wenqil@nvidia.com> * temp test Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "temp test" This reverts commit 31f40a0. Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update get gpu id Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update docsstrings Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* Add ProbNMS to transforts/post/array Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Implement ProbNMSDict Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update the usage and add unittests Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update docs Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Correct docs Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Correct test case Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

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

* Implement garbage collector handler Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Make trigger_event lower case Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add unittest for garbage collector Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update docs Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Exclude from min test Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Fix a typo Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Fix a bug Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

* [DLMED] add strict_shape option Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * update test case Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes test config Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] enhance decathlon datalist Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add unit test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Behrooz <3968947+behxyz@users.noreply.github.com>

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

* adds docker tag action Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds tag info Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update versioneer Signed-off-by: Wenqi Li <wenqil@nvidia.com>

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

* refactor docker building Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update docs deps. Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes https://github.com/Project-MONAI/MONAI/runs/2283148095\?check_suite_focus\=true\#step:7:8972 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * Revert "fixes https://github.com/Project-MONAI/MONAI/runs/2283148095\?check_suite_focus\=true\#step:7:8972" This reverts commit 1407400. Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* Update garbage collection assertion to a more reliable one Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Remove print Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

* Working ParameterScheduler Added a new ParameterScheduler handler and the required tests. Signed-off-by: Petru-Daniel Tudosiu <petru.daniel@tudosiu.com>

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

* [DLMED] add support for addtional events Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add unit tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typehints Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * fixes typos Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: monai-bot <monai.miccai2019@gmail.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* fixes #1965 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] enhance 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>

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>

wyli and others added 29 commits April 2, 2021 12:12

1919 - test pt 2103 (#1920)

4bd26f9

* update to use pytorch2103 Signed-off-by: Wenqi Li <wenqil@nvidia.com>

fixes typos (#1924)

d9e68c8

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

Revert "1919 - test pt 2103 (#1920)" (#1925)

e7d3d66

This reverts commit 4bd26f9. Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Nic Ma <nma@nvidia.com>

skip warp tests before torch 18 (#1927)

e871ee3

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

update docstrings (#1931)

e80cc4a

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

update get_package_version (#1930)

30523c0

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

enhance min/exact version check (#1937)

23f98f3

fixes ThreadDataLoader (#1945)

baf1bec

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

fixes itk dep. version (#1944)

a6b8f2a

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

Add progress bar to LesionFROC (#1951)

fbce3c2

Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

pipeline for releasing the docker images (#1953)

501026b

* adds docker tag action Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds tag info Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update versioneer Signed-off-by: Wenqi Li <wenqil@nvidia.com>

remove unused RandomizableTransform (#1952)

81cfbf0

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

1956 - docker image building pipelines (#1957)

5c411d1

* refactor docker building Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Update garbage collection assertion (#1959)

d6ed956

* Update garbage collection assertion to a more reliable one Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Remove print Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

Working ParameterScheduler (#1949)

7581255

* Working ParameterScheduler Added a new ParameterScheduler handler and the required tests. Signed-off-by: Petru-Daniel Tudosiu <petru.daniel@tudosiu.com>

[DLMED] remove warning (#1962)

baca6e0

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

1965 - register_backward_hook (#1966)

8cbd59a

* fixes #1965 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * adds docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com>

1968 Enhance meta data doc-string in SegmentationSaver (#1969)

d56c002

* [DLMED] enhance 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>

Nic-Ma merged commit 808c8b6 into Nic-Ma:1977-inverse-interpolation-mode Apr 8, 2021

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Nic-Ma commented Apr 8, 2021

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merge master #72

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Nic-Ma commented Apr 8, 2021

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