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Add GDSdataset #6778

Merged
merged 19 commits into from
Jul 27, 2023
Merged

Add GDSdataset #6778

merged 19 commits into from
Jul 27, 2023

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KumoLiu
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@KumoLiu KumoLiu commented Jul 26, 2023 •
edited by wyli
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Description

part of #6231
Add GDSDataset.
After loading with GDS, data lost shape and dtype, so in this PR, add this information manually.

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.

KumoLiu and others added 13 commits July 19, 2023 11:24
@KumoLiu
add GDSDataset
77eecff 
Signed-off-by: KumoLiu <[email protected]>
@KumoLiu
Merge remote-tracking branch 'origin/dev' into gdsdataset
232b6e7
@KumoLiu
add unittest
98aa1b6 
Signed-off-by: KumoLiu <[email protected]>
@KumoLiu
Merge remote-tracking branch 'origin/dev' into gdsdataset
dd5dd8c
@KumoLiu
update unittests
0ccac95 
Signed-off-by: KumoLiu <[email protected]>
@KumoLiu
Merge branch 'dev' of https://github.com/Project-MONAI/MONAI into gds…
6229ccc 
…dataset
@KumoLiu
minor fix
e6837f9 
Signed-off-by: KumoLiu <[email protected]>
@KumoLiu
add docstring
203f4f8 
Signed-off-by: KumoLiu <[email protected]>
@KumoLiu
fix flake8
fa50f5c 
Signed-off-by: KumoLiu <[email protected]>
@KumoLiu
fix mypy
96758c0 
Signed-off-by: KumoLiu <[email protected]>
@KumoLiu
update unittest
0961453 
Signed-off-by: KumoLiu <[email protected]>
@KumoLiu
Merge branch 'dev' into gdsdataset
fffa512
@KumoLiu
fix flake8
2209709 
Signed-off-by: KumoLiu <[email protected]>
@KumoLiu KumoLiu marked this pull request as draft July 26, 2023 08:50
@KumoLiu
add skip test
98a62c6 
Signed-off-by: KumoLiu <[email protected]>
@KumoLiu KumoLiu requested review from wyli, atbenmurray, ericspod and Nic-Ma and removed request for atbenmurray July 26, 2023 13:02
@KumoLiu KumoLiu marked this pull request as ready for review July 26, 2023 13:03
wyli
wyli reviewed Jul 26, 2023
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thanks, I have a few minor comments inline:

monai/data/dataset.py Outdated Show resolved Hide resolved
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KumoLiu and others added 3 commits July 27, 2023 11:20
@KumoLiu @wyli
Update docstring
d0058c8 
Co-authored-by: Wenqi Li <[email protected]>
Signed-off-by: YunLiu <[email protected]>
@KumoLiu
update docstring
304efee 
Signed-off-by: KumoLiu <[email protected]>
@KumoLiu
cache meta in self._meta_cache
d3c240e 
Signed-off-by: KumoLiu <[email protected]>
wyli
wyli approved these changes Jul 27, 2023
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Thanks, it looks good to me.

@wyli
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wyli commented Jul 27, 2023

/build

@wyli wyli enabled auto-merge (squash) July 27, 2023 07:07
@wyli wyli merged commit b02c37c into Project-MONAI:dev Jul 27, 2023
25 of 30 checks passed
@KumoLiu KumoLiu deleted the gdsdataset branch July 27, 2023 08:04
@KumoLiu KumoLiu mentioned this pull request Jul 27, 2023
Merged
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wyli pushed a commit to Project-MONAI/tutorials that referenced this pull request Jul 28, 2023
@KumoLiu
remove the draft version of the GDSDataset (#1473)
ddf61ab 
### Description
- After Project-MONAI/MONAI#6778, `GDSDataset`
has been added in core, remove the draft version in the tutorial.
- Update the result based on the new version

### 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.
- [ ] For security purposes, please check the contents and remove any
sensitive info such as user names and private key.
- [ ] 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
- [ ] Notebook runs automatically `./runner.sh -t <path to .ipynb file>`

Signed-off-by: KumoLiu <[email protected]>
boneseva pushed a commit to boneseva/MONAI-tutorials that referenced this pull request Apr 21, 2024
@KumoLiu
remove the draft version of the GDSDataset (Project-MONAI#1473)
e91c3ce 
### Description
- After Project-MONAI/MONAI#6778, `GDSDataset`
has been added in core, remove the draft version in the tutorial.
- Update the result based on the new version

### 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.
- [ ] For security purposes, please check the contents and remove any
sensitive info such as user names and private key.
- [ ] 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
- [ ] Notebook runs automatically `./runner.sh -t <path to .ipynb file>`

Signed-off-by: KumoLiu <[email protected]>
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Reviewers

@wyli wyli wyli approved these changes

@ericspod ericspod Awaiting requested review from ericspod

@Nic-Ma Nic-Ma Awaiting requested review from Nic-Ma

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@KumoLiu @wyli