tristan-deep commited on
Commit
57c638b
·
verified ·
1 Parent(s): fa053c5

dartmouth-uct: sync data card, pipeline and figures with GitHub

Browse files

Syncs the dartmouth-uct card, pipeline and figures on the Hub with the reviewed state on GitHub (open-h/OpenH-RF).

`pipeline.yaml` now calls `usct_reflectivity_das` bare. `compounding: coherent` is that operation's default, so the explicit parameter was redundant.

Adds the figure the card leads with, `assets/phantom_179604449_z200.png`: a 2D-sim breast cross-section reconstructed by `reconstruct.py` beside the ground-truth sound-speed and attenuation maps stored in the same file. `assets/main.png` is the release image and is not embedded in the card.

The card's links are fixed for the Hub: `reconstruct.py` now points at the script on GitHub rather than a path that only resolves in a checkout, the data file points at its blob here, and the references to `convert_2d_to_zea.py` / `convert_3d_to_zea.py` are dropped since neither is published. The run instructions match the script as it stands: set `ZEA_FILE` at the top and run it, with `SOS_MAP = True` swapping constant-sound-speed delays for a straight-ray integral through the ground-truth map.

Files changed: 4.

```
+ dartmouth-uct/assets/main.png
+ dartmouth-uct/assets/phantom_179604449_z200.png
~ dartmouth-uct/README.md
~ dartmouth-uct/pipeline.yaml
```

dartmouth-uct/README.md CHANGED
@@ -1,5 +1,12 @@
1
  # OpenH-RF Sub-Dataset: 2D Ring-Array USCT Waveforms from 2D- and 3D-k-Wave Simulations
2
 
 
 
 
 
 
 
 
3
  ## Dataset Description
4
 
5
  This sub-dataset provides **pre-beamformed channel-domain radio-frequency
@@ -102,10 +109,7 @@ plane**, y = elevation), and the voxel-level ground truth as native zea map fiel
102
  per-pixel `coordinates`). Tissue class is stored in `metadata/annotations`
103
  (`anatomy`, `label`); only fields with no standard spec home (z-plane indices,
104
  element focus) are zea `CustomElement`s under the top-level `custom/` group. Files
105
- are laid out by simulation type: `data/2d/` (2D-sim) and `data/3d/` (3D-sim),
106
- produced by
107
- [`convert_2d_to_zea.py`](convert_2d_to_zea.py) and
108
- [`convert_3d_to_zea.py`](convert_3d_to_zea.py) respectively.
109
 
110
  **Pre-processing applied before packaging:**
111
  - 2D-sim: temporal decimation by 3× (20 MHz → 6.67 MHz native simulation rate).
@@ -197,7 +201,7 @@ Not applicable — all data are synthetic. Aggregate phantom statistics:
197
 
198
  ## Data Validation
199
 
200
- A single reference reconstruction, [`reconstruct.py`](reconstruct.py), serves
201
  **both** sub-datasets. It builds a `zea.Pipeline` whose beamforming stage is
202
  zea's dedicated `zea.ops.USCTReflectivityDAS` — a round-trip time-of-flight
203
  Delay-And-Sum that, for every pixel, coherently sums over all transmit/receive
@@ -214,10 +218,10 @@ drive the reconstruction directly. A resulting image whose bright skin boundary
214
  traces the ground-truth contour confirms the geometry, timing, and transmit
215
  parameters were recorded correctly.
216
 
217
- ```
218
- python reconstruct.py --input data/2d/phantom_xxx.hdf5
219
- python reconstruct.py --input data/3d/phantom_xxx.hdf5
220
- ```
221
 
222
  ## Known Issues
223
 
 
1
  # OpenH-RF Sub-Dataset: 2D Ring-Array USCT Waveforms from 2D- and 3D-k-Wave Simulations
2
 
3
+ ![Ring-array USCT reflectivity reconstruction of a digital breast phantom, next to its ground-truth sound-speed and attenuation maps](assets/phantom_179604449_z200.png)
4
+
5
+ A 2D-sim breast cross-section,
6
+ [`data/2d/phantom_179604449_z200.hdf5`](https://huggingface.co/datasets/nvidia/OpenH-RF/blob/main/dartmouth-uct/data/2d/phantom_179604449_z200.hdf5),
7
+ reconstructed by [`reconstruct.py`](https://github.com/open-h/OpenH-RF/blob/main/datasets/dartmouth-uct/reconstruct.py) beside the ground-truth sound-speed
8
+ and attenuation maps stored in the file.
9
+
10
  ## Dataset Description
11
 
12
  This sub-dataset provides **pre-beamformed channel-domain radio-frequency
 
109
  per-pixel `coordinates`). Tissue class is stored in `metadata/annotations`
110
  (`anatomy`, `label`); only fields with no standard spec home (z-plane indices,
111
  element focus) are zea `CustomElement`s under the top-level `custom/` group. Files
112
+ are laid out by simulation type: `data/2d/` (2D-sim) and `data/3d/` (3D-sim).
 
 
 
113
 
114
  **Pre-processing applied before packaging:**
115
  - 2D-sim: temporal decimation by 3× (20 MHz → 6.67 MHz native simulation rate).
 
201
 
202
  ## Data Validation
203
 
204
+ A single reference reconstruction, [`reconstruct.py`](https://github.com/open-h/OpenH-RF/blob/main/datasets/dartmouth-uct/reconstruct.py), serves
205
  **both** sub-datasets. It builds a `zea.Pipeline` whose beamforming stage is
206
  zea's dedicated `zea.ops.USCTReflectivityDAS` — a round-trip time-of-flight
207
  Delay-And-Sum that, for every pixel, coherently sums over all transmit/receive
 
218
  traces the ground-truth contour confirms the geometry, timing, and transmit
219
  parameters were recorded correctly.
220
 
221
+ Set `ZEA_FILE` at the top of the script and run `python reconstruct.py`; the
222
+ figure at the top of this card is its output. `SOS_MAP = True` swaps the
223
+ constant-sound-speed delays for a straight-ray integral through the
224
+ ground-truth map.
225
 
226
  ## Known Issues
227
 
dartmouth-uct/assets/main.png ADDED

Git LFS Details

  • SHA256: 671a70fa24a37d4c4acf97398612d152a3c383f0b6734c1be57a672d44565fa2
  • Pointer size: 131 Bytes
  • Size of remote file: 684 kB
dartmouth-uct/assets/phantom_179604449_z200.png ADDED

Git LFS Details

  • SHA256: 9f4e587601d5d27e14d102e203b8057c26d1003ea9858ea79c95712aa277c1a9
  • Pointer size: 131 Bytes
  • Size of remote file: 209 kB
dartmouth-uct/pipeline.yaml CHANGED
@@ -5,9 +5,7 @@ pipeline:
5
  dtype: float32
6
  - name: patched_grid
7
  operations:
8
- - name: usct_reflectivity_das
9
- params:
10
- compounding: coherent
11
  params:
12
  with_batch_dim: false
13
  jit_options: null
 
5
  dtype: float32
6
  - name: patched_grid
7
  operations:
8
+ - usct_reflectivity_das
 
 
9
  params:
10
  with_batch_dim: false
11
  jit_options: null