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Update legacy ID to BMZ nickname id #344

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Update legacy ID to BMZ nickname id #344

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2c94214
update legacy bmz id to nickname id
mariana-gferreira Feb 28, 2025
8a6f305
add Diffusion model for SMLM notebook to manifest
mariana-gferreira Feb 28, 2025
e21ede6
update legacy id with bmz nickname
mariana-gferreira Mar 5, 2025
77329c7
Merge branch 'master' into bioimageio_manifest_id_update
mariana-gferreira Mar 5, 2025
b7de817
export_bmz_notebook revert
mariana-gferreira Mar 5, 2025
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2 changes: 1 addition & 1 deletion .github/workflows/export_notebook.yml
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Expand Up @@ -40,6 +40,6 @@ jobs:
- name: Output artifact URL
run: echo "Artifact URL is https://nightly.link/HenriquesLab/ZeroCostDL4Mic/actions/runs/${{ github. run_id }}/${{ inputs.notebook_name }}.zip"
- name: Stage the ZIP file into BioImage.IO
run: python3 Tools/stage_bmz_notebook.py --id "zero/${{ inputs.notebook_name }}" --url "https://nightly.link/HenriquesLab/ZeroCostDL4Mic/actions/runs/${{ github. run_id }}/${{ inputs.notebook_name }}.zip" # --token "${{ secrets.GITHUB_TOKEN }}"
run: python3 Tools/stage_bmz_notebook.py --id "${{ inputs.notebook_name }}" --url "https://nightly.link/HenriquesLab/ZeroCostDL4Mic/actions/runs/${{ github. run_id }}/${{ inputs.notebook_name }}.zip" # --token "${{ secrets.GITHUB_TOKEN }}"
env:
PAT_GITHUB: ${{ secrets.PAT_GITHUB }}
120 changes: 61 additions & 59 deletions Tools/parser_dicts_variables.py
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@@ -1,65 +1,67 @@
dict_manifest_to_version = {
'Notebook_Augmentor_ZeroCostDL4Mic': 'Augmentor' ,
'Notebook_CARE_2D_ZeroCostDL4Mic': 'CARE (2D)' ,
'Notebook_CARE_3D_ZeroCostDL4Mic': 'CARE (3D)' ,
'Notebook_Cellpose_2D_ZeroCostDL4Mic': 'Cellpose' ,
'Notebook_CycleGAN_2D_ZeroCostDL4Mic': 'CycleGAN' ,
'Notebook_DFCAN_ZeroCostDL4Mic': 'DFCAN 2D' ,
'Notebook_DRMIME_ZeroCostDL4Mic': 'DRMIME' ,
'Notebook_DecoNoising_2D_ZeroCostDL4Mic': 'DecoNoising' ,
'Notebook_Deep-STORM_2D_ZeroCostDL4Mic': 'Deep-STORM' ,
'Notebook_Deep-STORM_2D_ZeroCostDL4Mic_DeepImageJ': 'Deep-STORM BioimageIO' ,
'Notebook_DenoiSeg_2D_ZeroCostDL4Mic': 'DenoiSeg' ,
'Notebook_Detectron2_ZeroCostDL4Mic': 'Detectron 2D' ,
'Notebook_EmbedSeg_2D_ZeroCostDL4Mic': 'EmbedSeg 2D' ,
'Notebook_Interactive_Segmentation_Kaibu_2D_ZeroCostDL4Mic': 'Kaibu' ,
'Notebook_MaskRCNN_ZeroCostDL4Mic': 'MaskRCNN' ,
'Notebook_Noise2Void_2D_ZeroCostDL4Mic': 'Noise2Void (2D)' ,
'Notebook_Noise2Void_3D_ZeroCostDL4Mic': 'Noise2Void (3D)' ,
'Notebook_Quality_Control_ZeroCostDL4Mic': 'Quality_control' ,
'Notebook_RCAN_3D_ZeroCostDL4Mic': '3D RCAN' ,
'Notebook_RetinaNet_ZeroCostDL4Mic': 'RetinaNet' ,
'Notebook_SplineDist_2D_ZeroCostDL4Mic': 'SplineDist (2D)' ,
'Notebook_StarDist_2D_ZeroCostDL4Mic': 'StarDist 2D' ,
'Notebook_StarDist_3D_ZeroCostDL4Mic': 'StarDist 3D' ,
'Notebook_U-Net_2D_ZeroCostDL4Mic': 'U-Net (2D)',
'Notebook_U-Net_2D_multilabel_ZeroCostDL4Mic': 'U-Net (2D) multilabel',
'Notebook_U-Net_3D_ZeroCostDL4Mic': 'U-Net (3D)' ,
'Notebook_YOLOv2_ZeroCostDL4Mic': 'YOLOv2' ,
'Notebook_fnet_2D_ZeroCostDL4Mic': 'fnet (2D)' ,
'Notebook_fnet_3D_ZeroCostDL4Mic': 'fnet (3D)' ,
'Notebook_pix2pix_2D_ZeroCostDL4Mic': 'pix2pix' ,
'WGAN_ZeroCostDL4Mic.ipynb': 'WGAN 2D',
}
'light-swimsuit': 'Augmentor',
'fun-high-heels': 'CARE (2D)',
'opalescent-ribbon': 'CARE (3D)',
'polished-t-shirt': 'Cellpose',
'flattering-bikini': 'CycleGAN',
'mesmerizing-shoe': 'DFCAN 2D',
'playful-scarf': 'Diffusion model for SMLM',
'irresistible-swimsuit': 'DRMIME',
'flexible-helmet': 'DecoNoising',
'inspiring-sandal': 'Deep-STORM',
'silky-shorts': 'Deep-STORM BioimageIO',
'smooth-safety-vest': 'DenoiSeg',
'convenient-t-shirt': 'Detectron 2D',
'smooth-graduation-hat': 'EmbedSeg 2D',
'timeless-running-shirt': 'Kaibu',
'regal-ribbon': 'MaskRCNN',
'brisk-scarf': 'Noise2Void (2D)',
'cozy-hiking-boot': 'Noise2Void (3D)',
'lively-t-shirt': 'Quality_control',
'striking-necktie': '3D RCAN',
'convenient-purse': 'RetinaNet',
'uplifting-backpack': 'SplineDist (2D)',
'exciting-backpack': 'StarDist 2D',
'cheerful-cap': 'StarDist 3D',
'resplendent-ribbon': 'U-Net (2D)',
'whimsical-helmet': 'U-Net (2D) multilabel',
'joyful-top-hat': 'U-Net (3D)',
'bold-shorts': 'YOLOv2',
'limited-edition-crown': 'fnet (2D)',
'authoritative-ballet-shoes': 'fnet (3D)',
'fluid-glasses': 'pix2pix',
'slinky-bikini': 'WGAN 2D'
}

dict_dl4miceverywhere_to_manifest = {
'CARE_2D_DL4Mic': 'Notebook_CARE_2D_ZeroCostDL4Mic',
'CARE_3D_DL4Mic': 'Notebook_CARE_3D_ZeroCostDL4Mic',
'Cellpose_2D_DL4Mic': 'Notebook_Cellpose_2D_ZeroCostDL4Mic',
'CycleGAN_DL4Mic': 'Notebook_CycleGAN_2D_ZeroCostDL4Mic',
'DFCAN_DL4Mic': 'Notebook_DFCAN_ZeroCostDL4Mic',
'DRMIME_2D_DL4Mic': 'Notebook_DRMIME_ZeroCostDL4Mic',
'DecoNoising_2D_DL4Mic': 'Notebook_DecoNoising_2D_ZeroCostDL4Mic',
'Deep-STORM_2D_DL4Mic': 'Notebook_Deep-STORM_2D_ZeroCostDL4Mic',
'DenoiSeg_DL4Mic': 'Notebook_DenoiSeg_2D_ZeroCostDL4Mic',
'Detectron2_2D_DL4Mic': 'Notebook_Detectron2_ZeroCostDL4Mic',
'Embedseg_DL4Mic': 'Notebook_EmbedSeg_2D_ZeroCostDL4Mic',
'MaskRCNN_DL4Mic': 'Notebook_MaskRCNN_ZeroCostDL4Mic',
'Noise2Void_2D_DL4Mic': 'Notebook_Noise2Void_2D_ZeroCostDL4Mic',
'Noise2Void_3D_DL4Mic': 'Notebook_Noise2Void_3D_ZeroCostDL4Mic',
'3D-RCAN_DL4Mic': 'Notebook_RCAN_3D_ZeroCostDL4Mic',
'RetinaNet_DL4Mic': 'Notebook_RetinaNet_ZeroCostDL4Mic',
'SplineDist_2D_DL4Mic': 'Notebook_SplineDist_2D_ZeroCostDL4Mic',
'StarDist_2D_DL4Mic': 'Notebook_StarDist_2D_ZeroCostDL4Mic',
'StarDist_3D_DL4Mic': 'Notebook_StarDist_3D_ZeroCostDL4Mic',
'U-Net_2D_DL4Mic': 'Notebook_U-Net_2D_ZeroCostDL4Mic',
'U-Net_2D_Multilabel_DL4Mic': 'Notebook_U-Net_2D_multilabel_ZeroCostDL4Mic',
'U-Net_3D_DL4Mic': 'Notebook_U-Net_3D_ZeroCostDL4Mic',
'YOLOv2_DL4Mic': 'Notebook_YOLOv2_ZeroCostDL4Mic',
'fnet_2D_DL4Mic': 'Notebook_fnet_2D_ZeroCostDL4Mic',
'fnet_3D_DL4Mic': 'Notebook_fnet_3D_ZeroCostDL4Mic',
'pix2pix_DL4Mic': 'Notebook_pix2pix_2D_ZeroCostDL4Mic',
'WGAN_DL4Mic': 'WGAN_ZeroCostDL4Mic.ipynb',
'CARE_2D_DL4Mic': 'fun-high-heels',
'CARE_3D_DL4Mic': 'opalescent-ribbon',
'Cellpose_2D_DL4Mic': 'polished-t-shirt',
'CycleGAN_DL4Mic': 'flattering-bikini',
'DFCAN_DL4Mic': 'mesmerizing-shoe',
'Diffusion_SMLM_DL4Mic': 'playful-scarf',
'DRMIME_2D_DL4Mic': 'irresistible-swimsuit',
'DecoNoising_2D_DL4Mic': 'flexible-helmet',
'Deep-STORM_2D_DL4Mic': 'inspiring-sandal',
'DenoiSeg_DL4Mic': 'smooth-safety-vest',
'Detectron2_2D_DL4Mic': 'convenient-t-shirt',
'Embedseg_DL4Mic': 'smooth-graduation-hat',
'MaskRCNN_DL4Mic': 'regal-ribbon',
'Noise2Void_2D_DL4Mic': 'brisk-scarf',
'Noise2Void_3D_DL4Mic': 'cozy-hiking-boot',
'3D-RCAN_DL4Mic': 'striking-necktie',
'RetinaNet_DL4Mic': 'convenient-purse',
'SplineDist_2D_DL4Mic': 'uplifting-backpack',
'StarDist_2D_DL4Mic': 'exciting-backpack',
'StarDist_3D_DL4Mic': 'cheerful-cap',
'U-Net_2D_DL4Mic': 'resplendent-ribbon',
'U-Net_2D_Multilabel_DL4Mic': 'whimsical-helmet',
'U-Net_3D_DL4Mic': 'joyful-top-hat',
'YOLOv2_DL4Mic': 'bold-shorts',
'fnet_2D_DL4Mic': 'limited-edition-crown',
'fnet_3D_DL4Mic': 'authoritative-ballet-shoes',
'pix2pix_DL4Mic': 'fluid-glasses',
'WGAN_DL4Mic': 'slinky-bikini'
}

dict_dl4miceverywhere_to_version = {dl4mic_name: dict_manifest_to_version[dict_dl4miceverywhere_to_manifest[dl4mic_name]] for dl4mic_name in dict_dl4miceverywhere_to_manifest.keys()}
140 changes: 140 additions & 0 deletions Tools/update_manifest_legacy_id.ipynb
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@@ -0,0 +1,140 @@
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# ZeroCost manifest update\n",
"replace legacy id with bmz id\n",
"\n",
"add license to datasets"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Add License to datasets"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"from ruyaml import YAML\n",
"from pathlib import Path\n",
"from bioimageio.core import load_description\n",
"\n",
"# Load the YAML file\n",
"manifest_path = Path('../manifest.bioimage.io.yaml')\n",
"\n",
"with open(manifest_path, 'r', encoding='utf8') as f:\n",
" yaml = YAML()\n",
" yaml.preserve_quotes = True\n",
" manifest = yaml.load(f)\n",
"\n",
"# Update the manifest file with the correct bioimage.io id and add license to datasets\n",
"for element in manifest['collection']:\n",
" \n",
" # Add license to datasets\n",
" if element['type'] == 'dataset':\n",
" try:\n",
" element['license']\n",
" except:\n",
" element['license'] = 'CC-BY-4.0'\n",
"\n",
"\n",
"# Save the modified YAML data back to the file\n",
"with open(manifest_path, 'w', encoding='utf8') as f:\n",
" yaml = YAML()\n",
" yaml.preserve_quotes = True\n",
" yaml.default_flow_style = False\n",
" yaml.indent(mapping=2, sequence=4, offset=2)\n",
" yaml.width = 10e10\n",
" yaml.dump(manifest, f)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Convert legacy ID to new bioimage model zoo ID"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"from ruyaml import YAML\n",
"from pathlib import Path\n",
"from bioimageio.core import load_description\n",
"\n",
"# Load the YAML file\n",
"manifest_path = Path('../manifest.bioimage.io.yaml')\n",
"\n",
"with open(manifest_path, 'r', encoding='utf8') as f:\n",
" yaml = YAML()\n",
" yaml.preserve_quotes = True\n",
" manifest = yaml.load(f)\n",
"\n",
"\n",
"# Update the manifest file with the correct bioimage.io id and add license to datasets\n",
"for element in manifest['collection']:\n",
" \n",
" # Get the bioimage.io id from the app RDF file and update the manifest file\n",
" try:\n",
" app_rdf = load_description('zero/' + element['id'])\n",
" app_bmz_id = app_rdf.config['bioimageio']['nickname']\n",
" element['id'] = app_bmz_id\n",
" except:\n",
" pass\n",
"\n",
" # Update the links in the manifest file\n",
" if 'links' in element:\n",
" links=[]\n",
" for link in element['links']:\n",
" if link == 'Notebook Preview':\n",
" continue\n",
" link_rdf = load_description( 'zero/' + link )\n",
" link_bmz_id = link_rdf.config['bioimageio']['nickname']\n",
" links.append(link_bmz_id)\n",
" element['links'] = links\n",
"\n",
"\n",
"# Save the modified YAML data back to the file\n",
"with open(manifest_path, 'w', encoding='utf8') as f:\n",
" yaml = YAML()\n",
" yaml.preserve_quotes = True\n",
" yaml.default_flow_style = False\n",
" yaml.indent(mapping=2, sequence=4, offset=2)\n",
" yaml.width = 10e10\n",
" yaml.dump(manifest, f)"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "zc_manifest_update",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.13.2"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
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