bioimageio.spec 0.4.9

Parser and validator library for BioImage.IO specifications

Specifications for BioImage.IO

This repository contains specifications defined by the BioImage.IO community. These specifications are used for defining fields in YAML files which we called Resource Description Files or RDF. The RDFs can be downloaded or uploaded to the bioimage.io website, produced or consumed by BioImage.IO-compatible consumers(e.g. image analysis software or other website). Currently we defined two types of RDFs: a dedicated RDF specification for AI models (i.e. model RDF) and a general RDF specification. The model RDF is a RDF with additional fields that specifically designed for describing AI models.

All the BioImage.IO-compatible RDF must fulfill the following rules:

• Must be a YAML file encoded as UTF-8; If yaml syntax version is not specified to be 1.1 in the first line by % YAML 1.1 it must be equivalent in yaml 1.1 and yaml 1.2. For differences see https://yaml.readthedocs.io/en/latest/pyyaml.html#differences-with-pyyaml.
• The RDF file extension must be .yaml (not .yml)
• The RDF file can be saved in a folder (or virtual folder) or in a zip package, the following additional rules must apply:
  1. When stored in a local file system folder, github repo, zenodo deposition, blob storage virtual folder or similar kind, the RDF file name should match the pattern of *.rdf.yaml, for example my-model.rdf.yaml.
  2. When the RDF file and other files are zipped into a RDF package, it must be named as rdf.yaml.

As a general guideline, please follow the model RDF spec to describe AI models and use the general RDF spec for other resource types including dataset, application. You will find more details about these two specifications in the following sections. Please also note that the best way to check whether your RDF file is BioImage.IO-compliant is to run the BioImage.IO Validator against it.

Resource Description File Specification

A BioImage.IO-compatible Resource Description File (RDF) is a YAML file with a set of specifically defined fields.

You can find detailed field definitions here:

• general RDF spec (latest)
• general RDF spec (0.2.x)

The specifications are also available as json schemas:

• general RDF spec (0.2.x, json schema)

Here you can find some examples for using RDF to describe applications, notebooks, datasets etc.

Model Resource Description File Specification

Besides the general RDF spec, the Model Resource Description File Specification(model RDF) defines a file format for representing pretrained AI models in YAML format. This format is used to describe models hosted on the BioImage.IO model repository site.

You can find the latest model RDF here:

• model RDF spec (latest)

Here is a list of model RDF Examples:

• Model RDF Examples.

Collection Resource Description File Specification

The Collection Resource Description File Specification(collection RDF) defines a file format for representing collections of resources for the BioImage.IO website.

You can find the latest collection RDF here:

• collection RDF spec (latest)

Linking resource items

You can create links to connect resource items by adding another resource item id to the links field. For example, if you want to associate an applicaiton with a model, you can set the links field of the models like the following:

application:
  - id: HPA-Classification
    source: https://raw.githubusercontent.com/bioimage-io/tfjs-bioimage-io/master/apps/HPA-Classification.imjoy.html

model:
  - id: HPAShuffleNetV2
    source: https://raw.githubusercontent.com/bioimage-io/tfjs-bioimage-io/master/models/HPAShuffleNetV2/HPAShuffleNetV2.model.yaml
    links:
      - HPA-Classification

Hosting RDFs

You can host the resource description file on one of the public git repository website, including Zenodo Github, Gitlab, Bitbucket, or Gist. In order to make it available in https://bioimage.io, you can submit the RDF package via the uploader.

Recommendations

• For AI models, consider using the model-specific spec (i.e. model RDF) instead of the general RDF. Only fallback to the general RDF if writing model specific RDF is not possible for some reason.
• The RDF or package file name should not contain spaces or special characters, it should be concise, descriptive, in kebab case or camel case.
• Due to the limitations of storage services such as Zenodo, which does not support subfolders, it is recommended to place other files in the same directory level of the RDF file and try to avoid using subdirectories.
• Use the bioimage.io spec validator to verify your YAML file
• Store the yaml file in a version controlled Git repository (e.g. Github or Gitlab)
• Use or upgrade to the latest format version

bioimageio command-line interface (CLI)

The BioImage.IO command line tool makes it easy to work with BioImage.IO RDFs. A basic version of it, documented here, is provided by the bioimageio.spec package, which is extended by the bioimageio.core package.

validate

It is recommended to use this validator to verify your models when you write it manually or develop tools for generating RDF files.

Use the validate command to check for formatting errors like missing or invalid values:

bioimageio validate <MY-MODEL-SOURCE>

<MY-MODEL-SOURCE> may be a local RDF yaml "<MY-MODEL>/rdf.yaml" or a DOI / URL to a zenodo record, or a URL to an rdf.yaml file.

To see if your model is compatible to the latest bioimage.io model format use the spec validator with the --update-format flag:

bioimageio validate --update-format `<MY-MODEL-SOURCE>`

The output of the validate command will indicate missing or invalid fields in the model file. For example, if the field timestamp was missing it would print the following:

{'timestamp': ['Missing data for required field.']}

or if the field test_inputs does not contain a list, it would print:

{'test_inputs': ['Not a valid list.']}.

update-format

Similar to the validate command with --update-format flag the update-format command attempts to convert an RDF to the latest applicable format version, but saves the result in a file for further manual editing:

bioimageio update-format <MY-MODEL-SOURCE> <OUTPUT-PATH>

bioimageio.spec Python package

The bioimageio.spec package allows to work with BioImage.IO RDFs within Python. The commands on which the bioimageio CLI is based can be used as functions. Additionally, IO functions are provided to work with BioImage.IO RDFs as 'raw nodes' Python objects, e.g. the raw representation of a model RDF 0.4 at bioimageio.spec.model.v0_4.raw_nodes. The bioimageio.core package extends this 'raw' representation for more convenience.

installation

bioimageio.spec can be installed with either pip or conda:

# pip
pip install -U bioimageio.spec

# conda
conda install -c conda-forge bioimageio.spec

As a dependency it is included in bioimageio.core library, which extends bioimageio.spec with more powerful commands like 'predict'.

Environment variables

Name	Default	Description
BIOIMAGEIO_USE_CACHE	"true"	Enables simple URL to file cache. possible, case-insensitive, positive values are: "true", "yes", "1". Any other value is interpreted as "false"
BIOIMAGEIO_CACHE_PATH	generated tmp folder	File path for simple URL to file cache; changes of URL source are not detected.
BIOIMAGEIO_CACHE_WARNINGS_LIMIT	"3"	Maximum number of warnings generated for simple cache hits.

Changelog

bioimageio.spec 0.4.9

• small bugixes
• better type hints
• improved tests

bioimageio.spec 0.4.8post1

• add axes and eps to scale_mean_var

bioimageio.spec 0.4.7post1

• add simple forward compatibility by treating future format versions as latest known (for the respective resource type)

bioimageio.spec 0.4.6post3

• Make CLI output more readable
• find redirected URLs when checking for URL availability

bioimageio.spec 0.4.6post2

• Improve error message for non-existing RDF file path given as string
• Improve documentation for model RDF's documentation field

bioimageio.spec 0.4.6post1

• fix enrich_partial_rdf_with_imjoy_plugin (see https://github.com/bioimage-io/spec-bioimage-io/pull/452)

bioimageio.spec 0.4.5post16

• fix rdf_update of entries in resolve_collection_entries()

bioimageio.spec 0.4.5post15

• pass root to enrich_partial_rdf arg of resolve_collection_entries()

bioimageio.spec 0.4.5post14

• keep ResourceDescrption.root_path as URI for remote resources. This fixes the collection RDF as the collection entries are resolved after the collection RDF has been loaded.

bioimageio.spec 0.4.5post13

• new bioimageio.spec.partner module adding validate-partner-collection command if optional 'lxml' dependency is available

bioimageio.spec 0.4.5post12

• new env var BIOIMAGEIO_CACHE_WARNINGS_LIMIT (default: 3) to avoid spam from cache hit warnings
• more robust conversion of ImportableSourceFile for absolute paths to relative paths (don't fail on non-path source file)

bioimageio.spec 0.4.5post11

• resolve symlinks when transforming absolute to relative paths during serialization; see #438

bioimageio.spec 0.4.5post10

• fix loading of collection RDF with id (id used to be ignored)

bioimageio.spec 0.4.5post9

• support loading bioimageio resources by their animal nickname (currently only models have nicknames).

bioimageio.spec 0.4.5post8

• any field previously expecting a local relative path is now also accepting an absolute path
• load_raw_resource_description returns a raw resource description which has no relative paths (any relative paths are converted to absolute paths).

bioimageio.spec 0.4.4post7

• add command commands.update_rdf()/update-rdf(cli)

bioimageio.spec 0.4.4post2

• fix unresolved ImportableSourceFile

bioimageio.spec 0.4.4post1

• fix collection RDF conversion for type field

bioimageio.spec 0.4.3post1

• fix to shape validation for model RDF 0.4: output shape now needs to be bigger than halo
• moved objects from bioimageio.spec.shared.utils to bioimageio.spec.shared[.node_transformer]
• additional keys to validation summary: bioimageio_spec_version, status

bioimageio.spec 0.4.2post4

• fixes to general RDF:
  • ignore value of field root_path if present in yaml. This field is used internally and always present in RDF nodes.

bioimageio.spec 0.4.1.post5

• fixes to collection RDF:
  • RDFs specified directly in collection RDF are validated correctly even if their source field does not point to an RDF.
  • nesting of collection RDF allowed

bioimageio.spec 0.4.1.post4

• fixed missing field icon in general RDF's raw node
• fixes to collection RDF:
  • RDFs specified directly in collection RDF are validated correctly
  • no nesting of collection RDF allowed for now
  • links is no longer an explicit collection entry field ("moved" to unknown)

bioimageio.spec 0.4.1.post0

• new model spec 0.3.5 and 0.4.1

bioimageio.spec 0.4.0.post3

• load_raw_resource_description no longer accepts update_to_current_format kwarg (use update_to_format instead)

bioimageio.spec 0.4.0.post2

• load_raw_resource_description accepts update_to_format kwarg

RDF Format Versions

bioimageio.spec 0.4.9

• Non-breaking changes
  • make pre-/postprocessing kwargs mode and axes always optional for model RDF 0.3 and 0.4

model RDF 0.4.8

• Non-breaking changes
  • cite field is now optional

RDF 0.2.2 and model RDF 0.4.7

• Breaking changes that are fully auto-convertible
  • name field may not include '/' or '' (conversion removes these)

model RDF 0.4.6

• Non-breaking changes
  • Implicit output shape can be expanded by inserting null into shape:scale and indicating length of new dimension D in the offset field. Keep in mind that D=2*'offset'.

model RDF 0.4.5

• Breaking changes that are fully auto-convertible
  • parent field changed to hold a string that is a BioImage.IO ID, a URL or a local relative path (and not subfields uri and sha256)

model RDF 0.4.4

• Non-breaking changes
  • new optional field training_data

dataset RDF 0.2.2

• Non-breaking changes
  • explicitly define and document dataset RDF (for now, clone of general RDF with type="dataset")

model RDF 0.4.3

• Non-breaking changes
  • add optional field download_url
  • add optional field dependencies to all weight formats (not only pytorch_state_dict)
  • add optional pytorch_version to the pytorch_state_dict and torchscript weight formats

model RDF 0.4.2

• Bug fixes:
  • in a pytorch_state_dict weight entry architecture is no longer optional.

collection RDF 0.2.2

• Non-breaking changes
  • make authors, cite, documentation and tags optional
• Breaking changes that are fully auto-convertible
  • Simplifies collection RDF 0.2.1 by merging resource type fields together to a collection field, holindg a list of all resources in the specified collection.

(general) RDF 0.2.2 / model RDF 0.3.6 / model RDF 0.4.2

• Non-breaking changes
  • rdf_source new optional field
  • id new optional field

collection RDF 0.2.1

• First official release, extends general RDF with fields application, model, dataset, notebook and (nested) collection, which hold lists linking to respective resources.

(general) RDF 0.2.1

• Non-breaking changes
  • add optional email and github_user fields to entries in authors
  • add optional maintainers field (entries like in authors but github_user is required (and name is not))

model RDF 0.4.1

• Breaking changes that are fully auto-convertible
  • moved field dependencies to weights:pytorch_state_dict:dependencies
• Non-breaking changes
  • documentation field accepts URLs as well

model RDF 0.3.5

• Non-breaking changes
  • documentation field accepts URLs as well

model RDF 0.4.0

• Breaking changes
  • model inputs and outputs may not use duplicated names.
  • model field sha256 is required if pytorch_state_dict weights are defined. and is now moved to the pytroch_state_dict entry as architecture_sha256.
• Breaking changes that are fully auto-convertible
  • model fields language and framework are removed.
  • model field source is renamed architecture and is moved together with kwargs to the pytorch_state_dict weights entry (if it exists, otherwise they are removed).
  • the weight format pytorch_script was renamed to torchscript.
• Other changes
  • model inputs (like outputs) may be defined by scaleing and offseting a reference_tensor
  • a maintainers field was added to the model RDF.
  • the entries in the authors field may now additionally contain email or github_user.
  • the summary returned by the validate command now also contains a list of warnings.
  • an update_format command was added to aid with updating older RDFs by applying auto-conversion.

model RDF 0.3.4

• Non-breaking changes
  • Add optional parameter eps to scale_range postprocessing.

model RDF 0.3.3

• Breaking changes that are fully auto-convertible
  • reference_input for implicit output tensor shape was renamed to reference_tensor

model RDF 0.3.2

• Breaking changes
  • The RDF file name in a package should be rdf.yaml for all the RDF (not model.yaml);
  • Change authors and packaged_by fields from List[str] to List[Author] with Author consisting of a dictionary {name: '<Full name>', affiliation: '<Affiliation>', orcid: 'optional orcid id'};
  • Add a mandatory type field to comply with the general RDF. Only valid value is 'model' for model RDF;
  • Only allow license identifier from the SPDX license list;
• Other changes
  • Add optional version field (default 0.1.0) to keep track of model changes;
  • Allow the values in the attachments list to be any values besides URI;