- weizmann-sampl: remove the pipeline YAML embedded in the card. It had
drifted from the real pipeline.yaml (grid 300x400 vs 377x525, and missing
apply_window plus the lens-correction parameters), so the card now points
at that file as the single source of truth.
- politorino: visualize_tracking_on_image.py has been merged into
reconstruct.py, so describe that script's constants instead.
- concordia: visualize.py has been merged into reconstruct.py, so describe
the one combined figure rather than two separate outputs.
- Spell the library "zea" rather than "Zea" throughout.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
tue-cardiac/reconstruct.py was the only one of its kind left in the corpus.
The reconstruction scripts live in the OpenH-RF repo, next to the pipelines
they run; the corpus keeps the data cards and recipes.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Remove the Python helpers from twente-microbubblesim
The corpus ships data cards and pipeline recipes, not code, and these two were
the only helper modules in it. migrate_custom_names.py was a one-off patch that
has already run, and utils.py belongs next to the reconstruction script in the
OpenH-RF repo, where it still lives.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Fourteen files were stored with CRLF, so they showed up as wholly modified
against any LF copy and buried the real one-line changes underneath.
Adds a text=auto eol=lf rule, placed above the LFS rules because git applies
the last matching pattern and those set -text to keep binary payloads
untouched.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Ship the two configs the reconstruct scripts need
oslo/parameters.yaml drives the whole Oslo reconstruction: it maps each
acquisition to one of the pipeline_*.yaml files already here and gives the
display window. The pipelines shipped without it, so nothing said which one
an acquisition uses.
unc-openpros/pipeline.yaml was missing entirely, leaving that subset with no
recipe for its InversionNet inference chain.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Three changes. Nothing about the reconstructions changes except where noted.
**`num_patches` removed (25 files).** zea patches the beamforming grid itself now, at a fixed patch size. An explicit count did the same job worse: it fixes the number of patches, so each one grows with the grid, which is what zea warns about above 2048 pixels per patch.
**TUe-Cardiac pipelines written in block style (4 files).** They were the only ones using nested inline braces. Same operations and values, just readable.
**Three pipelines corrected:**
- `twente-cavitation` now names its beamformer. It was falling back to delay-and-sum while the submission reconstructs with minimum variance, so this one does change the image.
- `waterloo-largeartery` gains the `parameters: dynamic_range` block it was missing — the only pipeline without one.
- `tumunich` uses log compression instead of `power_compress`, which also drops a custom op zea cannot resolve.
Simplify root README and standardize institution credits (#4)
