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Update large_files.yml for bundles #642

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yiheng-wang-nv opened this issue Sep 9, 2024 · 2 comments · Fixed by #646
Closed

Update large_files.yml for bundles #642

yiheng-wang-nv opened this issue Sep 9, 2024 · 2 comments · Fixed by #646

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@yiheng-wang-nv
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some bundles use google drive to save large files, and the data are hosted in another place, thus we can update them

cc @KumoLiu @Nic-Ma
@ericspod
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ericspod commented Sep 9, 2024

These bundles reference gdrive in their large_files.yml URLs:

  • brats_mri_axial_slices_generative_diffusion
  • brats_mri_generative_diffusion
  • brats_mri_segmentation
  • breast_density_classification
  • classification_template
  • endoscopic_inbody_classification
  • endoscopic_tool_segmentation
  • lung_nodule_ct_detection
  • maisi_ct_generative
  • mednist_reg
  • multi_organ_segmentation
  • pancreas_ct_dints_segmentation
  • pathology_nuclei_classification
  • pathology_nuclei_segmentation_classification
  • pathology_nuclick_annotation
  • pathology_tumor_detection
  • renalStructures_CECT_segmentation
  • renalStructures_UNEST_segmentation
  • spleen_ct_segmentation
  • spleen_deepedit_annotation
  • swin_unetr_btcv_segmentation
  • ventricular_short_axis_3label
  • vista3d
  • wholeBody_ct_segmentation
  • wholeBrainSeg_Large_UNEST_segmentation

We are also storing some model weights and data in the releases for this repo, so we should be consistent about where we choose to store such things. Unless Github objects the storage in releases would work for everything I'd have thought.

@yiheng-wang-nv
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Since we do some changes for the following bundles in: #620 I updated for them in a commit:

brats_mri_axial_slices_generative_diffusion
brats_mri_generative_diffusion
vista3d
pathology_nuclei_classification
pathology_nuclei_segmentation_classification
swin_unetr_btcv_segmentation

For other bundles, I will submit a PR to address that

@yiheng-wang-nv yiheng-wang-nv mentioned this issue Sep 10, 2024
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yiheng-wang-nv added a commit that referenced this issue Sep 11, 2024
@yiheng-wang-nv @ericspod
642 (part 1) update large files for bundles [skip ci] (#646)
ebdbeb6 
Fixes #642 .

### Description
A few sentences describing the changes proposed in this pull request.

### Status
**Ready/Work in progress/Hold**

### 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"`).

---------

Signed-off-by: Yiheng Wang <[email protected]>
Signed-off-by: Yiheng Wang <[email protected]>
Co-authored-by: Eric Kerfoot <[email protected]>
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642 (part 1) update large files for bundles [skip ci] yiheng-wang-nv/model-zoo
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@ericspod @yiheng-wang-nv