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180 Update bundles to support monai 1.0.1#179

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yiheng-wang-nv merged 2 commits intodevfrom
178-update-brats-bundle
Nov 7, 2022
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180 Update bundles to support monai 1.0.1#179
yiheng-wang-nv merged 2 commits intodevfrom
178-update-brats-bundle

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@yiheng-wang-nv yiheng-wang-nv commented Nov 4, 2022

Fixes #180 .

Description

This PR is used to update brats_mri_segmentation and spleen_ct_segmentation bundles to support monai 1.0.1 and pytorch 1.13.0

Status

Ready

Please ensure all the checkboxes:

  • Codeformat tests passed locally by running ./runtests.sh --codeformat.
  • In-line docstrings updated.
  • Update version and changelog in metadata.json if changing an existing bundle.
  • Please ensure the naming rules in config files meet our requirements (please refer to: CONTRIBUTING.md).
  • Ensure versions of packages such as monai, pytorch and numpy are correct in metadata.json.
  • Descriptions should be consistent with the content, such as eval_metrics of the provided weights and TorchScript modules.
  • Files larger than 25MB are excluded and replaced by providing download links in large_file.yml.
  • Avoid using path that contains personal information within config files (such as use /home/your_name/ for "bundle_root").

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/build

@yiheng-wang-nv yiheng-wang-nv changed the title 178 Update brats bundle to support monai 1.0.1 180 Update bundles to support monai 1.0.1 Nov 4, 2022
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/build

@yiheng-wang-nv yiheng-wang-nv enabled auto-merge (squash) November 7, 2022 05:50
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/build

@yiheng-wang-nv yiheng-wang-nv merged commit ee2b802 into dev Nov 7, 2022
@yiheng-wang-nv yiheng-wang-nv deleted the 178-update-brats-bundle branch November 7, 2022 06:16
yiheng-wang-nv added a commit that referenced this pull request Nov 8, 2022
Fixes #180 and #186 

### Description
This PR follows #179 and #182 to update some of the remanent bundles
into monai 1.0.1 version:
`endoscopic_inbody_classification` and `endoscopic_tool_segmentation`
are verified by @binliunls ,
`spleen_deepedit_annotation`, `pancreas_ct_dints_segmentation` are
verified by myself.

`lung_nodule_ct_detection` is updated without detailed check due to the
size of the dataset.

For `pathology_tumor_detection`, as mentioned in:
Project-MONAI/MONAI#5485 in order to match
monai 1.0.1, this bundle is adjusted to not support torchscript.


### Status
**Ready**

### Please ensure all the checkboxes:
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Codeformat tests passed locally by running `./runtests.sh
--codeformat`.
- [ ] In-line docstrings updated.
- [ ] Update `version` and `changelog` in `metadata.json` if changing an
existing bundle.
- [ ] Please ensure the naming rules in config files meet our
requirements (please refer to: `CONTRIBUTING.md`).
- [ ] Ensure versions of packages such as `monai`, `pytorch` and `numpy`
are correct in `metadata.json`.
- [ ] Descriptions should be consistent with the content, such as
`eval_metrics` of the provided weights and TorchScript modules.
- [ ] Files larger than 25MB are excluded and replaced by providing
download links in `large_file.yml`.
- [ ] Avoid using path that contains personal information within config
files (such as use `/home/your_name/` for `"bundle_root"`).

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
yiheng-wang-nv added a commit to yiheng-wang-nv/model-zoo that referenced this pull request Jul 29, 2024
Fixes Project-MONAI#180  .

### Description
This PR is used to update `brats_mri_segmentation` and
`spleen_ct_segmentation` bundles to support monai 1.0.1 and pytorch
1.13.0

### Status
**Ready**

### Please ensure all the checkboxes:
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Codeformat tests passed locally by running `./runtests.sh
--codeformat`.
- [ ] In-line docstrings updated.
- [ ] Update `version` and `changelog` in `metadata.json` if changing an
existing bundle.
- [ ] Please ensure the naming rules in config files meet our
requirements (please refer to: `CONTRIBUTING.md`).
- [ ] Ensure versions of packages such as `monai`, `pytorch` and `numpy`
are correct in `metadata.json`.
- [ ] Descriptions should be consistent with the content, such as
`eval_metrics` of the provided weights and TorchScript modules.
- [ ] Files larger than 25MB are excluded and replaced by providing
download links in `large_file.yml`.
- [ ] Avoid using path that contains personal information within config
files (such as use `/home/your_name/` for `"bundle_root"`).
yiheng-wang-nv added a commit to yiheng-wang-nv/model-zoo that referenced this pull request Jul 29, 2024
Fixes Project-MONAI#180 and Project-MONAI#186 

### Description
This PR follows Project-MONAI#179 and Project-MONAI#182 to update some of the remanent bundles
into monai 1.0.1 version:
`endoscopic_inbody_classification` and `endoscopic_tool_segmentation`
are verified by @binliunls ,
`spleen_deepedit_annotation`, `pancreas_ct_dints_segmentation` are
verified by myself.

`lung_nodule_ct_detection` is updated without detailed check due to the
size of the dataset.

For `pathology_tumor_detection`, as mentioned in:
Project-MONAI/MONAI#5485 in order to match
monai 1.0.1, this bundle is adjusted to not support torchscript.


### Status
**Ready**

### Please ensure all the checkboxes:
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Codeformat tests passed locally by running `./runtests.sh
--codeformat`.
- [ ] In-line docstrings updated.
- [ ] Update `version` and `changelog` in `metadata.json` if changing an
existing bundle.
- [ ] Please ensure the naming rules in config files meet our
requirements (please refer to: `CONTRIBUTING.md`).
- [ ] Ensure versions of packages such as `monai`, `pytorch` and `numpy`
are correct in `metadata.json`.
- [ ] Descriptions should be consistent with the content, such as
`eval_metrics` of the provided weights and TorchScript modules.
- [ ] Files larger than 25MB are excluded and replaced by providing
download links in `large_file.yml`.
- [ ] Avoid using path that contains personal information within config
files (such as use `/home/your_name/` for `"bundle_root"`).

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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Update Bundles to use MONAI 1.0.1 and pytorch 1.13.0

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