imaging-metadata-converter

Convert custom (vendor-specific) imaging acquisition metadata to common metadata.

The target is the imaging model, a LinkML model built from LiMi and extended with electron-microscopy and other imaging metadata; depending on linkml-runtime.

The model, and the metaseed profile made from it, are maintained here (see Maintaining the model); they were developed in imaging-metadata-consolidator, which this repository replaces.

Documentation, with a browser for the whole model and a map of what the converter produces: https://nl-bioimaging.github.io/imaging-metadata-converter/

Installation

pip install .

Or, for development (editable install plus the tests):

pip install -e .
python -m pytest tests

Quick start

1. Convert a metadata dict

from imaging_metadata_converter import convert_metadata

custom = {
    'Make': 'Acme',
    'Model': 'Widget-1000',
    'Scan': {'ResolutionX': 1024, 'ResolutionY': 768},
}

common = convert_metadata(custom)
# {'Instrument': {'Manufacturer': 'Acme', 'Model': 'Widget-1000'},
#  'Pixels': {'SizeX': 1024, 'SizeY': 768},
#  'SourceMap': {'Instrument.Manufacturer': 'Make', 'Instrument.Model': 'Model',
#                'Pixels.SizeX': 'Scan.ResolutionX', 'Pixels.SizeY': 'Scan.ResolutionY'}}

SourceMap records the source path of every output field, so renamed and collapsed keys stay recoverable from the output alone.

A value the model spells otherwise, listed as an alias of one of its enumeration values, is written in the model's spelling: Leica's immersion "OIL" as Oil, BigDataViewer's unit "micron" as µm. Its SourceMap entry then records the source's spelling too: {"Source": "...Immersion", "SourceValue": "OIL"}.

The input is whatever metadata dict you already extracted from your file or acquisition software; the output is the same information placed on the common model. Nested dicts and lists of dicts are walked recursively.

2. Reuse the mapper for many files

The model and mappings are parsed once per mapper instance, so create one mapper and convert repeatedly rather than calling convert_metadata in a tight loop:

import json
from pathlib import Path

from imaging_metadata_converter import AcquisitionMetadataMapper

mapper = AcquisitionMetadataMapper()

for path in Path('examples').glob('*.json'):
    custom = json.loads(path.read_text(encoding='utf-8'))
    common = mapper.convert_metadata(custom)
    print(path.name, sorted(common))

3. Use your own model or mappings

mapper = AcquisitionMetadataMapper(
    schema_file='my_model.yaml', mappings_file='my_mappings.json',
    combinations_file='my_combinations.json')

Each argument accepts a file path; omitting one uses the packaged file. The model is a LinkML model like models/imaging.yaml.

Examples

examples/ holds real acquisition metadata from a range of instruments, used by tests/test_examples.py and handy as input while extending the mappings:

Example	Source
Cikteq SEM4000x Automap.json	Cikteq SEM4000x (Automap)
Cikteq SEM4000x Normal.json	Cikteq SEM4000x (Normal)
Delmic FAST-EM.json	Delmic FAST-EM
EMSIS Xarosa.json	EMSIS Xarosa
TFS Phenom Pharos.json	Thermo Fisher Phenom Pharos
TFS TALOSF.json, TFS TALOSF 2.json	Thermo Fisher Talos F
Zeiss Supra55 Fibics ATLAS.json	Zeiss Supra55 (Fibics ATLAS)
ome-tiff.json	OME-TIFF derived metadata
dicom.json	DICOM (dummy patient data)
lif_metadata.json, lif_tilescan_metadata.json	Leica LIF (LAS X)
lif_sp5_metadata.json	Leica LIF (LAS AF, a TCS SP5)
lif_lmd7_metadata.json	Leica LIF (LMD7 laser microdissection)
platy_tomography.json	BigDataViewer (SpimData) tomography
svs_metadata.json	Aperio SVS

output/ holds what the converter makes of each, as YAML, written by scripts/convert_examples.py.

How mapping works

Each source value is placed by a rule in mappings/mappings.json, else where its path's end names a model path (an OME-derived source's Pixels.SizeX); mappings/combinations.json builds values from several (a date from its date, time and zone), and a few vendor steps join what a source spreads over its structure (Leica's sequential channels, a detector's settings for the image). A value is never written over another: where its target is taken, it stays at its source path, as does every value no rule or model path names, and the output's SourceMap names the source of every value, so nothing is lost and every value can be traced.

"Beam.WD": "Image.ElectronBeamSettings.WorkingDistance.Value",
"PixelSpacing[0]": {"target": "Pixels.PhysicalSizeY", "unit": "mm"},
"Vacuum.*": "Instrument.Vacuum"

How the mapping works (docs/mapping.md) describes it in full, with examples: model paths, every form of rule, matching by name, vendor wrappers, combinations, the vendor steps and the SourceMap.

The model

models/imaging.yaml is LiMi as a LinkML model, importing imaging_extension.yaml (metadata beyond LiMi, mostly electron microscopy), imaging_provenance.yaml (Property, SourceFile, SourceMapping) and imaging_units.yaml (the unit enumerations). ModelPaths reads it into the dotted paths the mapper uses:

from imaging_metadata_converter import ModelPaths

tree = ModelPaths().tree()
tree['Pixels']['PhysicalSizeX']
# 'PositiveFloat'

Every leaf's value is its range: a type (string, float, datetime, ...), an enumeration (UnitsLength, ...) or, for a reference, the class it refers to. The ranges are descriptive, not enforced: the mapper matches on paths only, never validates a value against its range and never coerces one, so whatever the source held is written through unchanged (combinations aside).

The model page of the documentation browses every path, flags the ones the extensions add and the ones a mapping rule targets, and describes where the model comes from; how the mapping works describes, with examples, how a source's values reach them.

Data files

• src/imaging_metadata_converter/models/imaging.yaml and its imports - the imaging model (see The model).
• src/imaging_metadata_converter/mappings/mappings.json - source field to model field mappings.
• src/imaging_metadata_converter/mappings/combinations.json - values built from others (see Combinations).

Maintaining the model

Outside the package, scripts/ holds the tools the model is maintained with; Maintaining the model in the documentation describes them in full.

• scripts/linkml_converter.py - converted the LiMi XSD (reference/) into the model, once; the model is edited by hand since, so it refuses to overwrite it without --force. Kept for comparing a future LiMi XSD.
• scripts/metaseed_generator.py - generates the metaseed profile profile/imaging.metaseed.yaml (imaging 2.0; 1.1 is published on the metaseed Hub) from the model; rerun it after a change to the model.
• scripts/dataset_exporter.py - exports each example as a metaseed dataset of the profile into export/, with every value the model has no field for kept as a Property record.
• scripts/model_fit.py - how well each example can be expressed in the model, from its dataset in export/: whether the output keeps and traces every input value (100% each), the source keys covered by a rule or automatically, and the ones not covered, with why. analyse() returns these statistics for any conversion, analyse_metadata() for a source dict (also the docs' Model fit page).

The tests check that profile/ and export/ are up to date and lose no data; the tests of the XSD conversion need linkml and those validating export/ with metaseed need metaseed, and are skipped without them.

Documentation

The documentation site is built with MkDocs from docs/ and published to GitHub Pages on every push to main. To build it locally:

pip install -e ".[docs]"
mkdocs serve

Nothing on the model pages is stored in the repository. The MkDocs hook scripts/docs_data.py reads the packaged model and mappings as the site is built: it writes the JSON the model browser fetches (data/model.json, added.json, mappings.json, details.json) into the site, fills in the model's counts on model.md, and the examples' fit on model-fit.md. A new version of the model files or an edited mappings.json shows up on the next build, with nothing to regenerate.

Use of AI

Generative AI coding assistants were used in developing this software, including tests and documentation. All changes are directed and approved by a maintainer, and checked by automated tests where applicable.

License

MIT