Add 195 zea acquisitions (190 sim + 5 measured) with paired SAF labels

.gitattributes

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data/LICENSE

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+Creative Commons Attribution 4.0 International (CC BY 4.0)
+
+This sub-dataset (simulated rotational 3D ultrasound raw channel data for
+elevational Synthetic Aperture Focusing) is licensed under the Creative Commons
+Attribution 4.0 International License.
+
+You are free to:
+  - Share — copy and redistribute the material in any medium or format
+  - Adapt — remix, transform, and build upon the material for any purpose,
+    even commercially
+
+Under the following terms:
+  - Attribution — You must give appropriate credit, provide a link to the
+    license, and indicate if changes were made.
+
+Full license text: https://creativecommons.org/licenses/by/4.0/legalcode
+Summary:           https://creativecommons.org/licenses/by/4.0/
+
+When using this dataset, please cite:
+  R. Murakami et al., "Elevational Synthetic Aperture Focusing for Rotated
+  Array-Based Three-Dimensional Ultrasound Imaging," IEEE Access, 2025.

data/README.md

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+---
+pretty_name: "OpenH-RF — eSAF Rotational 3D US Raw Channel Data (Medical FUSION Lab, WPI)"
+license: cc-by-4.0
+task_categories:
+  - image-to-image
+tags:
+  - ultrasound
+  - rf
+  - openh-rf
+  - 3d
+  - beamforming
+  - elevational-saf
+language:
+  - en
+size_categories:
+  - n<1K
+---
+
+# OpenH-RF Sub-Dataset — Rotational 3D US Raw Channel Data for Elevational SAF (Simulated + Measured Phantom)
+
+> One `.hdf5` per acquisition, zea file format. Raw **per-element channel data**
+> (pre-beamforming). See `manifest.json` for the full list and `../reconstruct.py`
+> + `../pipeline.yaml` for the reference reconstruction.
+
+## Dataset Description
+Synthetic rotational 3D ultrasound acquisitions of point and cyst targets, captured
+with an **elevation-focused 1D linear array** that is rotated 180° about its axial
+axis (1° steps, 180 frames). Each acquisition stores the **raw per-element channel
+RF** for a single normal plane-wave transmit at every rotation angle — i.e. the data
+*before* in-plane beamforming — which is what enables flexible offline beamforming and
+the **elevational Synthetic Aperture Focusing (eSAF)** method. The targets span a wide
+depth range to capture the depth-dependent elevational beam thickness (the artifact
+eSAF corrects). The release is **mostly simulated (Field II)**, complemented by a
+small set of **real measured phantom** rotational scans acquired with the physical
+Japan Probe 68-element array (same geometry as the simulation) over a shallow-to-focal
+depth series (10–45 mm). **Simulated + measured phantom** data (no in-vivo / subjects).
+
+## Dataset Contributor(s)
+Medical FUSION Laboratory, Worcester Polytechnic Institute. Contact: Ryo Murakami.
+
+## Dataset Creation Date
+06/15/2026.
+
+## License / Terms of Use
+CC BY 4.0 (see `LICENSE`). Simulated data — no IP/consent constraints.
+
+## Intended Usage
+Advanced beamforming and **elevational resolution recovery** for rotational 3D US
+(eSAF), elevation-PSF / aperture-growth studies, and as a reproducible raw-channel-data
+benchmark for rotational synthetic-aperture reconstruction.
+
+## Dataset Characterization
+- **Data Collection Method:** synthetic, generated with **Field II** (Jensen) run in
+  **MATLAB**. The main release is a **probe × target grid** produced by
+  `../sim/batch_sim_probe_target.m` (with `../sim/sim_probe_catalog.m` /
+  `../sim/sim_target_catalog.m`): for each (probe type, target) it uses `xdc_focused_array`
+  + `calc_scat_multi` to produce the raw per-element channel RF at every rotation angle
+  (scatterer rotated about the axial axis, transducer fixed), then `../sim/sim_dataset_to_zea.py`
+  repackages every case into the zea format here. **10 probe types** span lateral aperture
+  (`n_el` 32/68/128, pitch 0.1/0.2/0.3 mm), elevation height `H` (4/8/12 mm), and elevation
+  focal depth `R` (25/45/90 mm + unfocused) — see the probe table in `manifest.json`.
+  (The earlier 18-acquisition set generated by `../sim/batch_generate_fieldii.m` +
+  `../sim/mat_to_zea.py`, and a pure-Python analytic forward model `../sim/forward_sim.py`,
+  remain available as compatible alternatives with the identical schema.)
+  **Measured phantom acquisitions (5):** real rotational scans of the physical Japan
+  Probe 68-element array on a wire/point phantom, acquired with CPWC channel-RF capture
+  (`../experiment/Ryo_SetUp_JP68_PWCompound_3D_ChannelRF.m`) and a Galil-controlled 180°
+  rotation. Each scan is time-tag-synced (frames → motor angles) and reduced to the
+  **single centre (normal) plane wave per angle** by `../experiment/sync_channel_rf.m`
+  (so the schema matches the simulation, n_tx = 1), then converted with the same
+  `../sim/sim_dataset_to_zea.py`. They span a shallow-to-focal depth series (10, 20, 30,
+  40, 45 mm nominal target depth).
+- **Labeling Method:** synthetic ground truth (exact target positions known; in
+  `manifest.json`).
+- **Acquisition system (simulated):** Japan Probe JP_Linear_68 — 68-element linear
+  array, pitch 0.2 mm, element width 0.15 mm, element height 8 mm, **elevational lens
+  focus 45 mm** (Field II `xdc_focused_array` with 500 elevation math sub-elements);
+  center frequency 10 MHz; sampling 40 MHz (NS200BW, 4 samples/wavelength); speed of
+  sound 1490 m/s; single normal plane-wave transmit per rotation angle; 180° rotation,
+  1° step (180 frames). Parameters match the paper simulation (`makeslices_field2.m`).
+
+## Dataset Format
+zea file format (HDF5), one file per acquisition. Pre-processing — *simulated:* none
+beyond the forward model (raw RF, not demodulated/decimated); *measured:* time-tag
+frame→angle synchronisation, per-angle dwell averaging, and centre-plane-wave selection
+(still raw per-element RF, not demodulated/decimated). Rotation angle per frame is
+stored as a zea **custom** element at `custom/scan/rotation_angles_deg`. Every file is
+written with `zea.File.create()` (`../sim/sim_dataset_to_zea.py`) and carries a
+`zea_version` stamp, so zea loads it natively (not as a legacy file).
+
+**Paired pre-/post-SAF labels (the dataset's target output).** Each file also carries
+the **elevational-SAF reconstructed 3D B-mode volume** at
+`custom/labels/saf_bmode_volume` (with `custom/labels/saf_{x,y,z}_mm` axes). This is
+the *post*-SAF **output/label** paired with the *pre*-beamformed **input** (`data/raw_data`):
+the raw channel RF is back-projected through the published eSAF algorithm
+(`../matlab/saf/safrot_backproj.m`: in-plane DAS → `recon_3d` → `safrot_backproj`,
+elevational focus 45 mm, f-number 45/8) into a 3D volume `B_SAF(x,y,z)`, generated by
+`../sim/make_saf_all.m` → `../experiment/run_esaf_synced.m` and written into the zea
+file by `../sim/pack_saf_labels.py`. The stored volume is the normalized envelope over
+a thin depth window (±2 mm) about the target; per-case arc-FWHM before/after and gain
+are in `manifest.json` and on the dataset (`arc_fwhm_before_after_mm` attribute).
+
+A **MATLAB `.mat` version** of the same raw channel data + metadata, plus a
+**reference eSAF-beamformed** result and a `_ref.png` figure, is provided **per
+acquisition** alongside the source grid as `sim_dataset_out/<probe>/<target>.mat`
+and `..._ref.png` (each `.mat` holds the raw RF, the in-plane DAS, the metadata and
+the eSAF output produced with the published algorithm `../matlab/saf/safrot_backproj.m`:
+in-plane DAS → `recon_3d` → `safrot_backproj`, f-number 45/8). A FWHM-vs-depth
+overview across probes is `sim_dataset_out/dataset_overview_r4.png`
+(`../sim/dataset_overview.m`). (`.mat`/`.hdf5` are git-ignored; the zea `.hdf5` set
+plus these `.mat`/`_ref.png` are delivered via Drive/S3.)
+
+## Dataset Quantification
+- **Acquisitions:** **195** = **190 simulated** + **5 measured phantom**.
+  - *Simulated (190):* **10 probe types × 19 targets** (16 single points over depth
+    {20,45,80,130} mm × radial offset from the rotation centre {0,2,4,6} mm, plus 3
+    pair/oblique cases). The probe and target axes are listed in `manifest.json`. (The
+    earlier compatible set has 18 acquisitions.)
+  - *Measured (5):* real rotational phantom scans at nominal depths {10,20,30,40,45} mm
+    (`experiment__acq_exp_*.hdf5`), centre plane wave, ~182 measured rotation angles
+    over ~180°.
+- **Frames per acquisition:** simulated 180 (one per 1° step); measured ~182 (the
+  actual encoder angles are stored in `scan/rotation_angles_deg`, not necessarily
+  uniform).
+- **Total size on disk:** simulated ~0.6–5 MB per case (zea gzip; point-target RF is
+  sparse), measured ~80–92 MB per case (dense tissue RF); **~1.5 GB** for the full set
+  (including the paired `saf_bmode_volume` labels).
+- **Train/val/test split:** N/A (benchmark / characterization set; the probe × depth ×
+  radius axes are the intended study dimensions).
+
+### Per-sample feature table
+| field (HDF5 path)                 | shape                          | dtype   | units | description |
+|-----------------------------------|--------------------------------|---------|-------|-------------|
+| `data/raw_data`                   | (180, 1, n_ax, 68, 1)          | float32 | a.u.  | raw per-element channel RF; dims = (frame=rotation, tx, axial, element, ch) |
+| `scan/probe_geometry`             | (68, 3)                        | float32 | m     | element positions (lateral x, 0, 0) |
+| `scan/sampling_frequency`         | scalar                         | float32 | Hz    | 4.0e7 |
+| `scan/center_frequency`           | scalar                         | float32 | Hz    | 1.0e7 |
+| `scan/sound_speed`                | scalar                         | float32 | m/s   | 1490 |
+| `scan/initial_times`              | (1,)                           | float32 | s     | t0 (first-sample time) |
+| `scan/t0_delays`                  | (1, 68)                        | float32 | s     | transmit delays (0; normal plane wave) |
+| `scan/polar_angles`               | (1,)                           | float32 | rad   | transmit steering (0) |
+| `custom/scan/rotation_angles_deg` | (180,)                         | float32 | deg   | probe rotation angle per frame (zea custom element) |
+| `custom/labels/saf_bmode_volume`  | (n_el, n_el, n_z)              | float32 | a.u.  | **paired label**: elevational-SAF reconstructed 3D B-mode volume `B_SAF(x,y,z)` (normalized envelope) |
+| `custom/labels/saf_x_mm` / `saf_y_mm` | (n_el,)                    | float32 | mm    | lateral / elevation axes of `saf_bmode_volume` |
+| `custom/labels/saf_z_mm`          | (n_z,)                         | float32 | mm    | depth axis of `saf_bmode_volume` (target ± ~2 mm) |
+
+## Subject Metadata
+N/A (synthetic phantom; no subjects/PHI).
+
+## Data Validation
+`../reconstruct.py` (**runnable, verified** — numpy/h5py/scipy/matplotlib) loads a zea
+acquisition (`data/raw_data` + `scan/*`), runs in-plane plane-wave **DAS → envelope →
+log-compress** per rotation frame, and writes a B-mode PNG (representative angle +
+MAX-over-angle), auto-zoomed to the target depth band:
+```
+python python/reconstruct.py data/<probe>__<target>.hdf5 --out out.png
+```
+The equivalent native `zea.Pipeline` op chain (TOFCorrection → DelayAndSum →
+EnvelopeDetect → Normalize → LogCompress) is documented in `../pipeline.yaml`. The
+rotational **eSAF** across frames — the contribution of this dataset — is implemented in
+`../matlab/saf` (`recon_3d` → `safrot_backproj`); per-probe before/after eSAF reference
+images and a FWHM-vs-depth overview accompany the MATLAB `.mat` release
+(`../sim/dataset_overview.m`).
+
+## Known Issues
+- **Paired SAF label — on-axis targets (r0 = 0) do not narrow, by design.** eSAF
+  refocuses the *rotational elevation smear*; a target sitting on the rotation axis has
+  essentially no smear, so its `saf_bmode_volume` is not sharper than the input (arc-FWHM
+  gain < 1). This is expected physics, not a defect — the 40 on-axis cases (median gain
+  ~0.5×) are included so the pair covers the degenerate no-smear case. Off-axis targets
+  away from the 45 mm focus improve most (median ~1.35×; up to ~5–9×); targets at the
+  focal depth (~45 mm) and weak-elevation-focus probes (`efocus_deep_90`, `elev_unfocused`)
+  have little smear to recover. The eSAF back-projection uses a fixed elevational focus
+  of 45 mm; per-depth focus tuning (see `../docs/eSAF_focus_depth_study_JP.md`) can further
+  sharpen deep off-axis cases but was not applied here (single as-designed focus).
+- **Simulated** data (Field II spatial-impulse-response model): realistic transducer
+  field, but no tissue attenuation, aberration, multiple scattering, or electronic
+  noise. Not a substitute for measured data.
+- Speed of sound is 1490 m/s, matching the paper Table 1 and the experiment.
+- A single normal plane-wave transmit per rotation angle is simulated (the dataset
+  stores n_tx = 1); multi-angle compounding is left to downstream users.
+- **Measured scans:** acquired as 7-angle CPWC; only the **centre (0°) plane wave** is
+  kept here to match the n_tx = 1 schema. The dwell frames per angle are averaged before
+  storage (noise reduction). Real reflectors are not ideal point scatterers — expect
+  reverberation/clutter near the surface and specular layering; rotation angles are the
+  measured encoder values (slightly non-uniform, full span ≈ 180°, sign per encoder
+  direction). The elevational lens focus is the nominal 45 mm, but the effective
+  back-projection focus for eSAF is depth-dependent on real data (see
+  `../docs/eSAF_focus_depth_study_JP.md`).
+
+## Ethical Considerations
+None. The data is either fully synthetic (Field II) or measured on an **inanimate
+phantom** — no human or animal subjects, no PHI, no consent/IRB constraints.

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