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OpenH-RF

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Syncs the weizmann-sampl card and figures on the Hub with the reviewed state on GitHub (open-h/OpenH-RF).

One correction to the field table: raw_data's axial dimension is 2176, not 4096 — and 2048 in one of the 30 acquisitions. The table now states both.

Adds the three figures. assets/30_1.gif is the cine loop the card now leads with, reconstructed from data/30_1.hdf5 with the pipeline.yaml in this folder. assets/three_patients_grid.png is the validation figure — three frames from each of three subjects — which the card embedded from the folder root, where it was never uploaded, so it was broken here; its caption now describes the figure instead of a reconstruct.py invocation that no longer matches the script. assets/30_1.png is a single frame from the loop and is not embedded in the card.

GitHub PR:

• tristan-deep/OpenH-RF#7 — update quantitative values in READMEs (checked with data on HF)

Files changed: 4.

+ weizmann-sampl/assets/30_1.gif
+ weizmann-sampl/assets/30_1.png
+ weizmann-sampl/assets/three_patients_grid.png
~ weizmann-sampl/README.md

Update — common card layout. The card now follows the layout shared by every OpenH-RF dataset: frontmatter with a name, a stand-alone title, the hero image with an italic caption linking the sample it shows, Description, Contributor(s), Creation Date and the standard CC BY 4.0 text, then a new Processing the Dataset section (the zea process command where the pipeline carries the whole reconstruction, and the reconstruct.py link) followed by Dataset Format, which opens with the zea version. Hard line breaks are gone so the Hub wraps paragraphs itself; the longer sections keep their content.

GitHub PRs:

• tristan-deep/OpenH-RF#28 — Restructure all data cards to the common README layout

Files changed: 1.

~ weizmann-sampl/README.md

Update — main image. Adds assets/main.png: a bare B-mode (no axes, no text) of frame 20 of data/30_1.hdf5, rendered with zea process from the pipeline.yaml in this folder. It is the release image and is not embedded in the card.

GitHub: 0ec64e2 on main

Files changed: 1.

+ weizmann-sampl/assets/main.png

Thanks @tristan-deep . Looks good to me but the gif looks a little fast. Should we get the submitters to sign off as well?

Thanks @tristan-deep . Looks good to me but the gif looks a little fast. Should we get the submitters to sign off as well?

Submitters should still sign off, but I confirmed that the gif plays back at the right speed as defined in the time to next transmits stored in the file. I agree it looks a bit fast, but not unreasonable I think.

Some analysis:

Every one of the 30 files stores scan/time_to_next_transmit with a fixed frame period: 127 transmits × 101 µs plus a 50 ms pause after the last transmit, 62.8 ms per frame. That's 15.9 fps, identical in every frame of every file. How the gif uses it: zea process reads time_to_next_transmit (via parameters.frames_per_second) and sets the gif fps from it: 15.9 → 16 fps → 62 ms per frame. The GIF format stores delays in hundredths of a second, so that became 60 ms, which plays about 5% fast. It takes consecutive frames from the start of the file without skipping any, so the gif's 18 frames are the first 18 of 30_1.hdf5.
Why it could still look fast: the stored timing is the Verasonics sequence as programmed, not a measurement. The card's own Known Issues say transfer bottlenecks can cause dropped frames. If frames were dropped during acquisition, the real frame rate was below 15.9 fps, and nothing in the file lets us check that. The contributors would need to confirm the rate they actually got, for example from the acquisition time tags if they kept them.

Seems the best we can do with the info we have!

Now Weizmann confirmed as well!

Thanks @tristan-deep !