RyoMurakami commited on
Commit
d08355e
·
verified ·
1 Parent(s): e12656e

Sync data card: fix stale Data Validation section (zea API reconstruct.py), target description, rotation_angles_deg path

Browse files
Files changed (1) hide show
  1. README.md +15 -11
README.md CHANGED
@@ -23,7 +23,7 @@ size_categories:
23
  > + `../pipeline.yaml` for the reference reconstruction.
24
 
25
  ## Dataset Description
26
- Synthetic rotational 3D ultrasound acquisitions of point and cyst targets, captured
27
  with an **elevation-focused 1D linear array** that is rotated 180° about its axial
28
  axis (1° steps, 180 frames). Each acquisition stores the **raw per-element channel
29
  RF** for a single normal plane-wave transmit at every rotation angle — i.e. the data
@@ -122,7 +122,7 @@ reproducible from source and kept on lab storage.
122
  (`experiment__acq_exp_*.hdf5`), centre plane wave, ~182 measured rotation angles
123
  over ~180°.
124
  - **Frames per acquisition:** simulated 180 (one per 1° step); measured ~182 (the
125
- actual encoder angles are stored in `scan/rotation_angles_deg`, not necessarily
126
  uniform).
127
  - **Total size on disk:** simulated ~0.6–5 MB per case (zea gzip; point-target RF is
128
  sparse), measured ~80–92 MB per case (dense tissue RF); **~1.5 GB** for the full set
@@ -150,19 +150,23 @@ reproducible from source and kept on lab storage.
150
  N/A (synthetic phantom; no subjects/PHI).
151
 
152
  ## Data Validation
153
- `../reconstruct.py` (**runnable, verified** — numpy/h5py/scipy/matplotlib) loads a zea
154
- acquisition (`data/raw_data` + `scan/*`), runs in-plane plane-wave **DAS → envelope →
155
- log-compress** per rotation frame, and writes a B-mode PNG (representative angle +
156
- MAX-over-angle), auto-zoomed to the target depth band:
 
 
 
 
 
157
  ```
158
- python python/reconstruct.py data/<probe>__<target>.hdf5 --out out.png
159
  ```
160
- The equivalent native `zea.Pipeline` op chain (TOFCorrection DelayAndSum
161
- EnvelopeDetect → Normalize → LogCompress) is documented in `../pipeline.yaml`. The
162
- rotational **eSAF** across frames — the contribution of this dataset — is implemented in
163
  `../matlab/saf` (`recon_3d` → `safrot_backproj`); per-probe before/after eSAF reference
164
  images and a FWHM-vs-depth overview accompany the MATLAB `.mat` release
165
- (`../sim/dataset_overview.m`).
 
166
 
167
  ## Known Issues
168
  - **Paired SAF label — on-axis targets (r0 = 0) do not narrow, by design.** eSAF
 
23
  > + `../pipeline.yaml` for the reference reconstruction.
24
 
25
  ## Dataset Description
26
+ Synthetic rotational 3D ultrasound acquisitions of point, pair, and off-axis targets, captured
27
  with an **elevation-focused 1D linear array** that is rotated 180° about its axial
28
  axis (1° steps, 180 frames). Each acquisition stores the **raw per-element channel
29
  RF** for a single normal plane-wave transmit at every rotation angle — i.e. the data
 
122
  (`experiment__acq_exp_*.hdf5`), centre plane wave, ~182 measured rotation angles
123
  over ~180°.
124
  - **Frames per acquisition:** simulated 180 (one per 1° step); measured ~182 (the
125
+ actual encoder angles are stored in `custom/scan/rotation_angles_deg`, not necessarily
126
  uniform).
127
  - **Total size on disk:** simulated ~0.6–5 MB per case (zea gzip; point-target RF is
128
  sparse), measured ~80–92 MB per case (dense tissue RF); **~1.5 GB** for the full set
 
150
  N/A (synthetic phantom; no subjects/PHI).
151
 
152
  ## Data Validation
153
+ `../reconstruct.py` (**runnable, verified** — official `zea` API, no fallback code)
154
+ loads one zea acquisition, reads its acquisition parameters via
155
+ `zea.Config.from_path('../pipeline.yaml')` + `File.load_parameters`, beamforms the
156
+ rotation frame closest to 90° (the frame where an off-axis target lies in-plane) with
157
+ the native `zea.Pipeline` op chain **Cast → Demodulate → Beamform(delay_and_sum) →
158
+ EnvelopeDetect → Normalize → LogCompress** defined in `../pipeline.yaml`, and writes a
159
+ two-panel PNG: the B-mode image, and the per-frame probe **rotation angle**
160
+ (`custom/scan/rotation_angles_deg`) so downstream users know how to interpret the
161
+ frame axis — the special data this dataset adds, per reviewer feedback:
162
  ```
163
+ python ../reconstruct.py --input data/<probe>__<target>.hdf5 --output out.png
164
  ```
165
+ The rotational **eSAF** across frames the contribution of this dataset — is implemented in
 
 
166
  `../matlab/saf` (`recon_3d` → `safrot_backproj`); per-probe before/after eSAF reference
167
  images and a FWHM-vs-depth overview accompany the MATLAB `.mat` release
168
+ (`../sim/dataset_overview.m`), and the resulting paired `custom/labels/saf_bmode_volume`
169
+ is stored in every `.hdf5` (see Dataset Format above).
170
 
171
  ## Known Issues
172
  - **Paired SAF label — on-axis targets (r0 = 0) do not narrow, by design.** eSAF