merge master by Nic-Ma · Pull Request #95 · Nic-Ma/MONAI

Nic-Ma · 2021-04-28T05:31:32Z

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>

* allow slicing with SpatialCrop(d) Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk>

* fixes docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update example Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* [DLMED] add alias Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] add unit tests 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>

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

* [DLMED] add more alias 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>

* Implement RandTorchVisionD Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Add unittest for RandTorchVisiond Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update docs Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Formatting Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

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

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

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

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

* [DLMED] check the label data for Tensor Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

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

* [DLMED] add `device` and `to_tensor` args Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add support for non-tensor output Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] remove detach.cpu Signed-off-by: Nic Ma <nma@nvidia.com>

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

* fix duplication of key_transforms in RandSpatialCropSamplesd Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * [DLMED] only deep copy unmodified 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>

* [DLMED] save inverted meta dict Signed-off-by: Nic Ma <nma@nvidia.com> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com> * safe key get 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>

@jhlegarreta

Based on the ITK welcome: https://github.com/InsightSoftwareConsortium/ITK/blob/master/CONTRIBUTING.md by @jhlegarreta

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

* [DLMED] add divisible K Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 issue Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix CI tests Signed-off-by: Nic Ma <nma@nvidia.com>

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

* enhance persistent temp Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes windows file rename issue Signed-off-by: Wenqi Li <wenqil@nvidia.com> * enhance multiprocess LMDB Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove usued vars Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes LGTM errors Signed-off-by: Wenqi Li <wenqil@nvidia.com> * remove comparison-with-callable (W0143) Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes pylint W0231 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes PYL-R1705 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes PYL-R1720 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes PTC-W0060 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes PYL-W0105 Signed-off-by: Wenqi Li <wenqil@nvidia.com> * fixes PTC-W0016 Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update box_start/end for deepgrow Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * add test Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

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

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

* [DLMED] fix classification issue Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] add detach for Tensor Signed-off-by: Nic Ma <nma@nvidia.com> * fixes test Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* adding error messaging for unsupported tensor shapes Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> * [MONAI] python code formatting Signed-off-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>

rijobro and others added 29 commits April 16, 2021 13:01

allow slicing with SpatialCrop(d) (#1954)

9f4da6a

* allow slicing with SpatialCrop(d) Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

raising error tolerance to prevent rare failure (#2025)

abcca9b

Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk>

fixes tutorial issue 183 (#2031)

9f409c1

* fixes docstring Signed-off-by: Wenqi Li <wenqil@nvidia.com> * update example Signed-off-by: Wenqi Li <wenqil@nvidia.com>

[DLMED] enhance error message (#2038)

a7a9430

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

2032 Add more alias for other networks (#2040)

170fc91

* [DLMED] add more alias 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>

[DLMED] add post_func arg (#2049)

fc1546a

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

update docstring example (#2055)

de677ca

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

fixes tutorial issue 184 (#2053)

14976b5

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

Update cucim to 0.19.0 (#2057)

8057ae8

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

2044 Add check for label data type (#2060)

13bf996

* [DLMED] check the label data for Tensor Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

[DLMED] enhance metrics (#2061)

51ecc48

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

fixes tutorial 190 (#2063)

5cbcaf6

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

Add pointers to issues for community contributors (#2071)

7379ab8

Start with a welcoming statement in the contributing docs (#2072)

e0035b1

Based on the ITK welcome: https://github.com/InsightSoftwareConsortium/ITK/blob/master/CONTRIBUTING.md by @jhlegarreta

Remove transpose from the tissue masks (#2074)

fea9307

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

RandTorchVisionD update (#2076)

f45108b

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

update box_start/end for deepgrow (#2088)

dde1100

* update box_start/end for deepgrow Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * add test Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

2092 Enhance NIfTI writer logging (#2093)

8f2856d

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

[DLMED] add flag (#2094)

5eb9198

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

2095 fix multi-gpu issue in ClassificationSaver (#2096)

9e1a7d4

* [DLMED] fix classification issue Signed-off-by: Nic Ma <nma@nvidia.com>

Add detach to the tensors in handlers (#2100)

feb3a33

* [DLMED] add detach for Tensor Signed-off-by: Nic Ma <nma@nvidia.com> * fixes test Signed-off-by: Wenqi Li <wenqil@nvidia.com> Co-authored-by: Wenqi Li <wenqil@nvidia.com>

Adding error messaging for unsupported tensor shapes (#2089)

1f2247e

* adding error messaging for unsupported tensor shapes Signed-off-by: chaliebudd <charles.budd@kcl.ac.uk> * [MONAI] python code formatting Signed-off-by: monai-bot <monai.miccai2019@gmail.com>

Nic-Ma merged commit bfd0738 into Nic-Ma:enhance-smartcache-doc Apr 28, 2021

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merge master#95

merge master#95
Nic-Ma merged 214 commits intoNic-Ma:enhance-smartcache-docfrom
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Nic-Ma commented Apr 28, 2021

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