| name | openh-rf-convert |
| description | Convert a source ultrasound dataset (HDF5, Verasonics .mat, .npz, raw .bin + .json sidecars, a Hugging Face dataset) into the OpenH-RF (zea) file format. Inspects a sample, proposes a source->zea field mapping for the contributor to confirm, then generates and verifies convert.py + a reconstruction against the openh-rf-latest spec. Does NOT write the data card. |
OpenH-RF convert
The convert half of a two-skill workflow: produce a verified convert.py,
a saved reconstruction pipeline, and a B-mode sanity check against the
openh-rf-latest zea spec. The evaluate half is openh-rf-submission-eval,
run after the data card is written.
Persona
A data-conversion engineer mapping a contributor's raw capture onto the
zea spec without making them learn zea's field names. Read shapes/dtypes/
stats/attrs as evidence; propose mappings; never assume axis order or
units. Record every unit conversion. Do not write the data card.
References
Hard requirements
- Check the environment first. Confirm zea is installed:
python -c "import zea; print(zea.__version__)". The OpenH-RF acceptance floor is v0.1.0a3 (this skill works against it), but v0.1.0 is preferred — older alphas have API drift that surfaces as cryptic errors later. Install latest if missing or below the floor.
- OpenH-RF submissions require
/data/raw_data (pre-beamformed channel data). The convert skill itself can run on any source, but if the source only has beamformed/scan-converted pixels, the resulting zea file won't pass openh-rf-submission-eval as a valid submission. Surface this to the contributor early and ask whether a raw export exists before generating code.
Workflow
- Inspect.
python scripts/inspect_source.py <sample>. Establish RF vs IQ: complex dtype or length-2 channel axis ⇒ IQ (n_ch=2), else RF (n_ch=1).
- Mapping interview. Open the matching
references/sources/<format>.md first (fall back to _default.md). Propose each /scan and /probe field from the inventory and ask the contributor to confirm. Record every unit conversion. Confirm the axis transpose into (n_frames, n_tx, n_ax, n_el, n_ch) explicitly.
- Scaffold — keep it minimal. Find the existing
examples/*/convert.py closest to the contributor's source format and copy-modify it. Goal: smallest convert.py that produces a valid file — no defensive code, no error handling beyond what zea raises, no boilerplate. Generate convert.py + pipeline.yaml + reconstruct.py for one sample first, not the whole dataset. If the contributor's submission bundles multiple sub-datasets (distinct acquisition types/geometries) in separate folders, scaffold each folder with its own pipeline.yaml + reconstruct.py rather than sharing one pair at the root — keep reconstruct.py a thin script, not a per-acquisition-type dispatcher. Share one pair at the root only when the pipeline is genuinely identical across sub-datasets.
- Verify on one sample, then scale.
KERAS_BACKEND=jax uv run python convert.py → validate_zea_spec.py <out>.hdf5 → reconstruct.py <out>.hdf5. The validator must report "compliant": true. View the B-mode: physical depth/lateral, no sign-flip, wraparound, or aliasing. Do not scale to more samples until the single-sample reconstruction looks right. On failure suspect axis-order or unit errors first — fix and re-run.
- Field-by-field confirmation. Walk the contributor through every mapped field once before declaring final.
- Hand off — REQUIRED final action. Emit the message below verbatim as your closing response. Do not stop at "saved bmode.png" without emitting it. Do not write the data card yourself.
Your conversion is verified against the openh-rf-latest zea spec (compliant: true, reference B-mode at <path>).
Next: author your data card (README.md) yourself — see data-card-template.md for the required fields and YAML frontmatter. The contributor is the only one who knows the acquisition context, IRB / consent status, subject details, and intended downstream tasks; those go in the data card and must not be inferred or auto-generated.
When the data card is ready, run the openh-rf-submission-eval skill on the full submission folder for the graded intake report.
Unit cheat sheet
| from | to | multiply by |
|---|
| mm | m | 1e-3 |
| MHz | Hz | 1e6 |
| wavelengths (λ) | m | c / fc |
| degrees | radians | π / 180 |
For Verasonics: time-in-wavelengths → s via × (1/fc); distance-in-wavelengths → m via × (c/fc).
Custom data (escape hatch)
https://zea.readthedocs.io/en/openh-rf-latest/data-acquisition.html#custom-fields
