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Zarr Merger #6633

Merged
merged 24 commits into from
Jun 28, 2023
Merged

Zarr Merger #6633

merged 24 commits into from
Jun 28, 2023

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drbeh
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@drbeh drbeh commented Jun 20, 2023 •
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Fixes #6006

Description

This PR implements ZarrAvgMerger which can be used for patch inference. Also a use case is demonstrated here.

Types of changes

  • Non-breaking change (fix or new feature that would not break existing functionality).
  • 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.

@drbeh drbeh changed the title Zarr mergers Zarr Merger Jun 20, 2023
@drbeh drbeh mentioned this pull request Jun 20, 2023
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@drbeh drbeh requested a review from JHancox June 21, 2023 00:54
@ericspod
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We do also need tests to cover this code. Zarr does look interesting, I wonder if it would have other application MONAI, eg. data handling in transforms.

JHancox
JHancox reviewed Jun 22, 2023
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monai/inferers/merger.py Outdated Show resolved Hide resolved
@drbeh drbeh enabled auto-merge (squash) June 22, 2023 17:02
@drbeh drbeh disabled auto-merge June 22, 2023 17:02
dzenanz
dzenanz reviewed Jun 26, 2023
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drbeh and others added 13 commits June 26, 2023 11:02
@drbeh
add zarr dependency
b3c4ad4 
Signed-off-by: Behrooz <[email protected]>
@drbeh
Implement ZarrAvgMerger
5b7ea1d 
Signed-off-by: Behrooz <[email protected]>
@pre-commit-ci @drbeh
[pre-commit.ci] auto fixes from pre-commit.com hooks
571498c 
for more information, see https://pre-commit.ci
@drbeh
update docs
fe1cbc8 
Signed-off-by: Behrooz <[email protected]>
@drbeh
update docs
0a1aa3d 
Signed-off-by: Behrooz <[email protected]>
@drbeh
update docstring
8e8594e 
Signed-off-by: Behrooz <[email protected]>
@drbeh
add info about Zarr in docstring
1a9d0f8 
Signed-off-by: Behrooz <[email protected]>
@pre-commit-ci @drbeh
[pre-commit.ci] auto fixes from pre-commit.com hooks
5c51200 
for more information, see https://pre-commit.ci
@drbeh
add unit tests
fdb3969 
Signed-off-by: Behrooz <[email protected]>
@drbeh
exclude zarr tests from min tests
70bf188 
Signed-off-by: Behrooz <[email protected]>
@drbeh
add thread locks
e74658b 
Signed-off-by: Behrooz <[email protected]>
@drbeh
remove compression for temp zarr arrays
bf33fb5 
Signed-off-by: Behrooz <[email protected]>
@drbeh
add flexibility to define compressors for all zarr arrays
5bc1f94 
Signed-off-by: Behrooz <[email protected]>
@drbeh
change to skip unless
9bd6ce1 
Signed-off-by: Behrooz <[email protected]>
@drbeh drbeh requested review from ericspod and JHancox June 26, 2023 15:07
@drbeh
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drbeh commented Jun 26, 2023

Hi @ericspod, please take another look and let me know if you have any other comments. Thanks

@drbeh drbeh enabled auto-merge (squash) June 27, 2023 19:45
wyli
wyli reviewed Jun 28, 2023
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@drbeh drbeh requested review from wyli and JHancox June 28, 2023 13:47
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wyli commented Jun 28, 2023

/build

@drbeh drbeh disabled auto-merge June 28, 2023 13:59
@drbeh drbeh enabled auto-merge (squash) June 28, 2023 13:59
wyli
wyli approved these changes Jun 28, 2023
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looks good to me, @ericspod please feel free to follow up if anything missing

ericspod
ericspod approved these changes Jun 28, 2023
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Looks good, I had just very minor changes to docs.

monai/inferers/merger.py Outdated Show resolved Hide resolved
monai/inferers/merger.py Outdated Show resolved Hide resolved
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drbeh and others added 4 commits June 28, 2023 13:11
@drbeh @ericspod
Update monai/inferers/merger.py
8145c08 
Co-authored-by: Eric Kerfoot <[email protected]>
Signed-off-by: Dr. Behrooz Hashemian <[email protected]>
@drbeh @ericspod
Update monai/inferers/merger.py
3b84aee 
Co-authored-by: Eric Kerfoot <[email protected]>
Signed-off-by: Dr. Behrooz Hashemian <[email protected]>
@drbeh @ericspod
Update monai/inferers/merger.py
a7f4f93 
Co-authored-by: Eric Kerfoot <[email protected]>
Signed-off-by: Dr. Behrooz Hashemian <[email protected]>
@drbeh
Merge branch 'dev' into zarr-mergers
52d8898
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wyli commented Jun 28, 2023

/build

@drbeh drbeh merged commit ae95bf9 into Project-MONAI:dev Jun 28, 2023
@drbeh drbeh deleted the zarr-mergers branch June 28, 2023 18:16
drbeh added a commit to Project-MONAI/tutorials that referenced this pull request Jul 4, 2023
@drbeh
Add zarr merger notebook section (#1433)
5884947 
This PR add an example for `ZarrAvgMerger` to be plugged into
`PatchInferer` along with `WSISlidingWindowSplitter`.

Note: Project-MONAI/MONAI#6633 in MONAI core
should be merged before this one.

### Checks
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Avoid including large-size files in the PR.
- [x] Clean up long text outputs from code cells in the notebook.
- [x] For security purposes, please check the contents and remove any
sensitive info such as user names and private key.
- [x] Ensure (1) hyperlinks and markdown anchors are working (2) use
relative paths for tutorial repo files (3) put figure and graphs in the
`./figure` folder
- [x] Notebook runs automatically `./runner.sh -t <path to .ipynb file>`

---------

Signed-off-by: Behrooz <[email protected]>
boneseva pushed a commit to boneseva/MONAI-tutorials that referenced this pull request Apr 21, 2024
@drbeh
Add zarr merger notebook section (Project-MONAI#1433)
7d835e3 
This PR add an example for `ZarrAvgMerger` to be plugged into
`PatchInferer` along with `WSISlidingWindowSplitter`.

Note: Project-MONAI/MONAI#6633 in MONAI core
should be merged before this one.

### Checks
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Avoid including large-size files in the PR.
- [x] Clean up long text outputs from code cells in the notebook.
- [x] For security purposes, please check the contents and remove any
sensitive info such as user names and private key.
- [x] Ensure (1) hyperlinks and markdown anchors are working (2) use
relative paths for tutorial repo files (3) put figure and graphs in the
`./figure` folder
- [x] Notebook runs automatically `./runner.sh -t <path to .ipynb file>`

---------

Signed-off-by: Behrooz <[email protected]>
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@KumoLiu KumoLiu KumoLiu left review comments

@dzenanz dzenanz dzenanz left review comments

@JHancox JHancox JHancox approved these changes

@ericspod ericspod ericspod approved these changes

@wyli wyli wyli approved these changes

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Implement Zarr Merger
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@drbeh @ericspod @wyli @dzenanz @JHancox @KumoLiu