ome-zarr-transformations-conformance 0.1.0

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ome-zarr-transformations-conformance

Test fixtures for RFC-5 transformations for OME-Zarr.

Structure

Each directory in ./cases/ represents a test case. It is an OME-Zarr Scene; it contains a zarr.json whose attributes contains an ome object which itself contains a scene object as described by the OME-Zarr v0.6+ specification. This scene contains a transform graph.

The dingus

Implementations of OME-Zarr transformations should provide a "dingus" CLI whose last 4 positional arguments MUST be:

• PATH: a path to an OME-Zarr hierarchy on the file system
• SOURCE: the name of the source coordinate system
• TARGET: the name of the target coordinate system
• COORDINATES: a JSON-serialised array of D-length arrays of numbers, where D is the dimensionality of a single coordinates

The dingus MUST then

1. open the OME-Zarr hierarchy at PATH and parse the $.ome.scene from the attributes
2. calculate a transformation from the coordinate system with name specified by SOURCE to the coordinate system with name specified by TARGET (this may require inverting one or more transforms)
3. apply this transformation to the COORDINATES array
4. print to STDOUT a JSON-serialised Response object
5. exit with status code 0

If any of the above steps are not supported by the implementation, the dingus MUST exit with a status code other than 0. It MAY print to STDOUT a JSON-serialised Error object.

Object: Response

field	necessity	type	description
coordinates	MUST	array of array of number	The resulting coordinates from transforming the input.
message	MAY	string	Free-text details.

Object: Error

field	necessity	type	description
message	MAY	string	Free-text description of error.

Test procedure

Each OME-Zarr hierarchy additionally includes a conformance.toml, which describes the test case. The implementation's dingus CLI does not need to parse this.

The transform_conformance.py script:

• iterates through all test cases
• parses the conformance.toml
• calls the provided dingus CLI, supplying the test case path, the source and target coordinate system names, and the source coordinates
• reads the output of the dingus CLI
  • if the return code is 0
    • if should_error = false, parse the response and check the output coordinates against those defined in target.coordinates, using the defined tolerances
    • if should_error = true, fail the test
  • if the return code is non-zero
    • if should_error = true, pass the test
    • if should_error = false, fail the test
• builds a table of test successes and failures, potentially including any messages returned by the dingus CLI

It is called like:

./transformation_conformance.py ./cases -- myDingus --some-arg anotherArg

This in turn calls the dingus repeatedly, seeing arguments like

myDingus --some-arg anotherArg './cases/translation.ome.zarr' 'input' 'output' '[[1, 2]]'

Configs

For convenience, simple test cases can be configured by a single TOML file representing the OME-Zarr scene and Conformance objects; see ./cases_config/ directory and the ./write_cases.py script.

Where invert = true, also create a test which switches the source and target objects.

More complicated test cases cannot be configured this way.