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sync metatensor branch with dev #4184

Merged
merged 9 commits into from
Apr 26, 2022
Merged

sync metatensor branch with dev #4184

merged 9 commits into from
Apr 26, 2022

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wyli
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@wyli wyli commented Apr 26, 2022

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 -f -u --net --coverage.
  • Quick tests passed locally by running ./runtests.sh --quick --unittests --disttests.
  • In-line docstrings updated.
  • Documentation updated, tested make html command in the docs/ folder.

yiheng-wang-nv and others added 9 commits April 22, 2022 17:03
@yiheng-wang-nv @pre-commit-ci @Nic-Ma
4095 Add bundle download (#4114)
e0e2e65 
* draft download

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

* update bundle download

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

* add url and load

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

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* rename args and remove a few places

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

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fix flake8 issue

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

* enhance with reviews

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

* add instantiate for load

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

* fix black error

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

* add unittest

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

* add load to docs

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

* add skip

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

* add schemaerror

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

* fix partial places

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

* download zip bundle

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

* [DLMED] restore Exception for test

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

* update ts features

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

* add config_files test case

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

* enhance docstring example for args_file

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

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
Disable pylint error and fix CI tests of new tifffile (#4162)
710781b 
* workaround

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

* [DLMED] fix tifffile issue

Signed-off-by: Nic Ma <nma@nvidia.com>
@dongyang0122
Fixed an error in DiNTS model implementation and enabled act and norm…
d69c5ee 
… layer options (#4157)

* fixed a bug

Signed-off-by: dongy <dongy@nvidia.com>

* autofix

Signed-off-by: dongy <dongy@nvidia.com>

* update test case

Signed-off-by: dongy <dongy@nvidia.com>

Co-authored-by: dongy <dongy@nvidia.com>
@drbeh
Split transform (#4153)
0cdec83 
* Redesign whole slide image reading (#4107)

* Redesign BaseWSIReader,  WSIReader, CuCIMWSIReader

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

* Add unittests for WSIReader

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

* Add image mode for output validation

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

* Update docs

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

* Update references to new WSIReader

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

* Remove legacy WSIReader

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

* Update unittests

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

* Update docs

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

* sort imports

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

* Clean up imports

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

* Update docstrings

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

* Update docs and docstrings

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

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Fix a typo

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

* Remove redundant checking

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

* Update read and other methods

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

* Update wsireader to support multi image and update docstrings

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

* Make workaround for CuImage objects

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

* Add unittests for multi image reading

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

* Update a note about cucim

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

* Update type hints and docstrings

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

* Implement Split transform

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

* Add unittests

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

* Update formatting

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

* Implement SplitDict

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

* Add unittests for SplitDict

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

* Add docs

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

* Remove images from docs

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

* Address all comments

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

* Add example and size check

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

* Update docs

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

* Revert references to new wsireader

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

* Add missing comma

Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>
@yiheng-wang-nv
fix bundle download test issue (#4169)
8f5c992 
Signed-off-by: Yiheng Wang <vennw@nvidia.com>
@Nic-Ma
4094 Enhance ckpt_export to save config files (#4159)
e688989 
* [DLMED] enhance checkpoint export

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

* [DLMED] update according to comments

Signed-off-by: Nic Ma <nma@nvidia.com>
@drbeh @Nic-Ma
Move RGB/RGBA checks to base class (#4171)
d63f490 
Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com>

Co-authored-by: Nic Ma <nma@nvidia.com>
@pxLi @wyli
[CICD] To support temp dgx runner (#4175)
10cbeff 
* Support new temp dgx runner

Signed-off-by: Peixin Li <pxli@nyu.edu>

* atol 1e-5

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

Co-authored-by: Wenqi Li <wenqil@nvidia.com>
@ericspod
Test fix for AMP kwargs (#4178)
6393927 
Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>
@wyli wyli merged commit 724f73f into MetaTensor Apr 26, 2022
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7 participants
@wyli @yiheng-wang-nv @Nic-Ma @dongyang0122 @drbeh @pxLi @ericspod