From c2f9c80d4cf03b7093ed877d6d4e75cbc1203f5f Mon Sep 17 00:00:00 2001 From: fynnbe Date: Sat, 16 Mar 2024 00:22:20 +0100 Subject: [PATCH] fix for bioimageio packager --- .github/workflows/build.yml | 2 + weight_formats_spec.json | 196 ++++++++++++++++++++++++++++++++++++ 2 files changed, 198 insertions(+) create mode 100644 weight_formats_spec.json diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index ae9a765ae..3eb8fd78a 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -64,6 +64,8 @@ jobs: - name: Generate developer docs run: pdoc -o ./dist bioimageio.spec - run: cp README.md ./dist/README.md + - name: copy legacy file until BioImage.IO-packager is updated # TODO: remove if packager does not depend on it anymore + run: cp weight_formats_spec.json ./dist/weight_formats_spec.json - name: Get branch name to deploy to id: get_branch shell: bash diff --git a/weight_formats_spec.json b/weight_formats_spec.json new file mode 100644 index 000000000..9aebc1ec6 --- /dev/null +++ b/weight_formats_spec.json @@ -0,0 +1,196 @@ +{ + "consumers": { + "deepimagej": { + "background_image": "static/img/zoo-background.svg", + "config": { + "supported_weight_formats": [ + "torchscript", + "tensorflow_saved_model_bundle" + ] + }, + "explore_button_text": "Start Exploring", + "icon": "https://raw.githubusercontent.com/deepimagej/models/master/logos/icon.png", + "id": "deepimagej", + "logo": "https://raw.githubusercontent.com/deepimagej/models/master/logos/logo.png", + "name": "DeepImageJ", + "resource_types": [ + "model", + "notebook", + "application" + ], + "splash_feature_list": null, + "splash_subtitle": "A user-friendly plugin to run deep learning models in ImageJ", + "splash_title": "deepImageJ", + "tags": [ + "deepimagej" + ], + "url_root": "https://raw.githubusercontent.com/deepimagej/models/master" + }, + "fiji": { + "background_image": "static/img/zoo-background.svg", + "explore_button_text": "Start Exploring", + "icon": "https://fiji.sc/site/logo.png", + "id": "fiji", + "logo": "https://fiji.sc/site/logo.png", + "name": "Fiji", + "resource_types": [ + "model", + "notebook" + ], + "splash_feature_list": [], + "splash_subtitle": "Fiji is just ImageJ", + "splash_title": "Fiji", + "tags": [ + "fiji" + ], + "url_root": "https://raw.githubusercontent.com/oeway/ZeroCostDL4Mic/master" + }, + "hpa": { + "about_url": "https://www.proteinatlas.org/", + "background_image": "static/img/zoo-background.svg", + "default_type": "model", + "explore_button_text": "Start Exploring", + "icon": "https://raw.githubusercontent.com/bioimage-io/tfjs-bioimage-io/master/apps/hpa-logo.gif", + "id": "hpa", + "logo": "https://raw.githubusercontent.com/bioimage-io/tfjs-bioimage-io/master/apps/hpa-logo.gif", + "name": "HPA", + "resource_types": [ + "model", + "application" + ], + "splash_feature_list": [], + "splash_subtitle": null, + "splash_title": "The Human Protein Atlas", + "tags": [ + "hpa" + ] + }, + "ilastik": { + "background_image": "static/img/zoo-background.svg", + "config": { + "supported_weight_formats": [ + "torchscript", + "pytorch_state_dict", + "onnx" + ] + }, + "default_type": "model", + "explore_button_text": "Start Exploring", + "icon": "https://raw.githubusercontent.com/ilastik/bioimage-io-models/main/image/ilastik-fist-icon.png", + "id": "ilastik", + "logo": "https://raw.githubusercontent.com/ilastik/bioimage-io-models/main/image/ilastik-fist-icon.png", + "name": "ilastik", + "resource_types": [ + "model", + "application" + ], + "splash_feature_list": null, + "splash_subtitle": "the interactive learning and segmentation toolkit", + "splash_title": "ilastik", + "tags": [ + "ilastik" + ], + "url_root": "https://raw.githubusercontent.com/ilastik/bioimage-io-models/main" + }, + "imjoy": { + "background_image": "static/img/zoo-background.svg", + "config": { + "supported_weight_formats": [ + "onnx" + ] + }, + "default_type": "application", + "explore_button_text": "Start Exploring", + "icon": "https://imjoy.io/static/img/imjoy-icon.svg", + "id": "imjoy", + "logo": "https://imjoy.io/static/img/imjoy-icon.svg", + "name": "ImJoy", + "resource_types": [ + "notebook", + "application" + ], + "splash_feature_list": [ + "Minimal and flexible plugin powered web application", + "Server-less progressive web application with offline support", + "Rich and interactive user interface powered by web technologies" + ], + "splash_subtitle": "Deep Learning Made Easy!", + "splash_title": "ImJoy", + "tags": [ + "imjoy" + ], + "url_root": "https://raw.githubusercontent.com/imjoy-team/bioimage-io-models/master" + }, + "zero": { + "background_image": "static/img/zoo-background.svg", + "config": { + "supported_weight_formats": [ + "keras_hdf5" + ] + }, + "default_type": "application", + "explore_button_text": "Start Exploring", + "icon": "https://raw.githubusercontent.com/HenriquesLab/ZeroCostDL4Mic/master/Wiki_files/ZeroCostLogo.png", + "id": "zero", + "logo": "https://raw.githubusercontent.com/HenriquesLab/ZeroCostDL4Mic/master/Wiki_files/ZeroCostLogo.png", + "name": "ZeroCostDL4Mic", + "resource_types": [ + "model", + "application", + "dataset" + ], + "splash_feature_list": [], + "splash_subtitle": "A Google Colab based no-cost toolbox to explore Deep-Learning in Microscopy", + "splash_title": "ZeroCostDL4Mic", + "tags": [ + "ZeroCostDL4Mic" + ], + "url_root": "https://raw.githubusercontent.com/oeway/ZeroCostDL4Mic/master", + "version": "1.7.1" + } + }, + "weight_formats": { + "keras_hdf5": { + "consumers": [ + "zero" + ], + "description": "Keras HDF5 weights format", + "name": "Keras HDF5" + }, + "onnx": { + "consumers": [ + "ilastik", + "imjoy" + ], + "description": "ONNX weights format", + "name": "ONNX" + }, + "pytorch_state_dict": { + "consumers": [ + "ilastik" + ], + "description": "PyTorch state dictionary weights format", + "name": "Pytorch State Dict" + }, + "tensorflow_js": { + "consumers": [], + "description": "Tensorflow Javascript weights format", + "name": "Tensorflow.js" + }, + "tensorflow_saved_model_bundle": { + "consumers": [ + "deepimagej" + ], + "description": "Tensorflow Saved Model Bundle weights format", + "name": "Tensorflow Saved Model" + }, + "torchscript": { + "consumers": [ + "ilastik", + "deepimagej" + ], + "description": "Torchscript weights format", + "name": "Torchscript" + } + } +}