merge master by Nic-Ma · Pull Request #50 · Nic-Ma/MONAI

Nic-Ma · 2021-03-23T12:08:15Z

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>

* [DLMED] update ignite to 0.4.4 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix ignite compatible issues 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>

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

* [DLMED] fix docs 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>

lossless inverse transforms (non-croppad)

) * [DLMED] add greater_or_equal 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> Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>

* [DLMED] enhance CheckpointLoader Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more unit tests 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> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com>

* Update WSIReader with cuCIM Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update unittests for cuCIM Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

* Add to_onehot_y and include_background Signed-off-by: Yiheng Wang <vennw@nvidia.com> * Add parameters to test seg loss Signed-off-by: Yiheng Wang <vennw@nvidia.com> * modify log softmax Signed-off-by: Yiheng Wang <vennw@nvidia.com> * Modify weight format Signed-off-by: Yiheng Wang <vennw@nvidia.com>

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

Zoomd and RandZoomd

Inverse Rotated and RandRotated

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

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

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

* Implement FROC metric Signed-off-by: yiheng-wang-nv <vennw@nvidia.com> * Fix doc error Signed-off-by: yiheng-wang-nv <vennw@nvidia.com> * Change param lowercase Signed-off-by: yiheng-wang-nv <vennw@nvidia.com> * Update calculate functions Signed-off-by: yiheng-wang-nv <vennw@nvidia.com> * fix mypy error Signed-off-by: yiheng-wang-nv <vennw@nvidia.com> * Update parameter names Signed-off-by: Yiheng Wang <vennw@nvidia.com>

* fix RandZoomd collation Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * dont check class ID on windows Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * if elif change Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * code review Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * remove extra import Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * win32 change Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * changes Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * update RandAxisFlipd Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * help message more general Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * more changes Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * use torch Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * wyli changes Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * more changes Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * skip test if win32 Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * get default mp Signed-off-by: Wenqi Li <wenqil@nvidia.com> * dedicated fail test Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * requires reason Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> Co-authored-by: Wenqi Li <wenqil@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>

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>

Nic-Ma and others added 29 commits March 15, 2021 19:40

update contrib guide to include some recent changes in dev tools (#1763)

3ea9ed4

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

1768 Update docs based on feedback (#1774)

13a2c59

* [DLMED] fix docs 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>

lossless inverse (#1767)

3406398

lossless inverse transforms (non-croppad)

Update WSIReader with cuCIM (#1773)

bcbd685

* Update WSIReader with cuCIM Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com> * Update unittests for cuCIM Signed-off-by: Behrooz <3968947+behxyz@users.noreply.github.com>

Inverse Spacingd (#1779)

5588528

Inverse Resized (#1780)

46154ec

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

Inverse Zoomd and RandZoomd (#1778)

cf3bd1a

Zoomd and RandZoomd

Inverse Rotated (#1782)

592806a

Inverse Rotated and RandRotated

Inverse Affined and RandAffined (#1781)

7f0e789

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

Fix type error (#1792)

053d0c8

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

Update cucim to remove warning message (#1799)

f063a47

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

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>

Nic-Ma merged commit e37ab69 into Nic-Ma:1814-enhance-apply-trans Mar 23, 2021

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merge master#50

merge master#50
Nic-Ma merged 86 commits into
Nic-Ma:1814-enhance-apply-transfrom
Project-MONAI:master

Nic-Ma commented Mar 23, 2021

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Nic-Ma commented Mar 23, 2021

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