sras-viewer/scan_format.md

SRAS Scan Binary Format — Version 6

Each .sras file contains one complete scan: all GR rotation angles and all Y rows. Files are named {prefix}.sras.

Starting in v6, each angle only scans the bounding box of the nominal ROI rotated by that specific angle — not the worst case across all angles — so x_start, x_delta (and therefore n_frames, the points/row count) and n_rows all vary per angle. A 0°/180° scan of a wide, short ROI needs far fewer rows than a 45° scan of the same ROI, and the file format reflects that instead of forcing every angle to the largest bounding box.

---

File Layout

[Global Header           — 49 bytes]
[Angle Table             — n_angles × 4 bytes  (float32 per angle, degrees)]
[Per-Angle Geometry Table— n_angles × 14 bytes (x_start f32, x_delta f32, n_frames u32, n_rows u16)]
[Row Table (ragged)      — sum(n_rows) × 4 bytes (float32 per row, angle-major)]
[Preamble Blocks         — n_channels × (uint16 length + UTF-8 WFMOutpre string)]
[Background Block        — uint32 n_bg_samples + n_bg_samples × int8 bytes]
[Waveform Data (ragged)  — per angle: n_rows[a] × n_channels × n_frames[a] × samples_per_frame × bps bytes]

All multi-byte integers and floats use big-endian byte order (> in Python's struct module).

---

Global Header (49 bytes)

Offset	Size	Type	Field	Description
0	4	4s	magic	Always SRAS (0x53 0x52 0x41 0x53)
4	1	uint8	version	Format version — 6
5	2	uint16	n_angles	Number of GR rotation angles
7	4	float32	x_start_nominal	Nominal (pre-rotation) X scan start, mm
11	4	float32	y_start_nominal	Nominal (pre-rotation) Y scan start, mm
15	4	float32	x_delta_nominal	Nominal (pre-rotation) X scan width, mm
19	4	float32	y_delta_nominal	Nominal (pre-rotation) Y scan height, mm
23	4	float32	row_spacing_mm	Y spacing between rows, mm
27	4	float32	velocity_mm_s	Stage scan velocity in mm/s
31	4	float32	laser_freq_hz	Laser repetition rate in Hz
35	4	uint32	samples_per_frame	Time samples per waveform
39	8	float64	sample_rate_hz	Oscilloscope sample rate in Hz (e.g. 6.25e9)
47	1	uint8	bytes_per_sample	Bytes per ADC sample: 1 = int8, 2 = int16
48	1	uint8	n_channels	Number of channels recorded (currently 3)

Total header size: 49 bytes — verified: struct.calcsize(">4sBHfffffffIdBB") == 49.

The *_nominal fields describe the ROI as originally entered on the New Scan page (XS/YS/XD/YD), before per-angle bounding-box expansion. They are for reference/reconstruction only — the actual per-angle scan geometry used for acquisition is in the Per-Angle Geometry Table below.

---

Angle Table

Immediately after the header: n_angles big-endian float32 values, one per GR angle (degrees, 0–180).

angle[0], angle[1], …, angle[n_angles - 1]

---

Per-Angle Geometry Table

Immediately after the angle table: n_angles fixed-size records, one per angle (same order as the angle table), each 14 bytes:

Size	Type	Field	Description
4	float32	x_start	X scan start for this angle's bounding box, mm
4	float32	x_delta	X scan width for this angle's bounding box, mm
4	uint32	n_frames	A-scans per row for this angle (FastFrame count)
2	uint16	n_rows	Number of Y rows scanned for this angle

Format string per record: ">ffIH".

---

Row Table (ragged)

Immediately after the per-angle geometry table: for each angle in order, that angle's n_rows big-endian float32 Y positions (mm), concatenated with no padding between angles.

# angle 0's rows, then angle 1's rows, …
y_mm[0][0], …, y_mm[0][n_rows[0]-1], y_mm[1][0], …, y_mm[n_angles-1][n_rows[-1]-1]

Row-table boundaries for angle a are derived from the per-angle geometry table: sum(n_rows[0:a]) gives the starting index into the flattened array.

---

Preamble Blocks

Immediately after the row table: n_channels length-prefixed UTF-8 strings, one per channel in SCAN_CHANNELS order (CH1, CH3, CH4). Each block is:

uint16  length   — byte length of the following UTF-8 string
bytes   preamble — WFMOutpre response string from the oscilloscope

The preamble captures per-channel scaling constants (YMULT, YOFF, YZERO) needed to convert raw ADC values to volts.

---

Background Block

Immediately after the preamble blocks: a single CH1 waveform captured with the Helios (generation) laser enabled and the Genesis (detection) laser disabled. This provides a noise/background reference for subtraction during post-processing.

uint32  n_bg_samples   — number of samples in the background waveform
int8[]  bg_data        — raw ADC samples (same encoding as waveform data)

n_bg_samples equals samples_per_frame under normal acquisition settings.

---

Waveform Data (ragged)

Immediately after the background block. Data is stored in angle-major, row-minor order, but unlike earlier versions each angle contributes a different number of rows (n_rows[a]) and a different number of frames per row (n_frames[a]), both taken from that angle's Per-Angle Geometry Table entry. Within each row, channels are interleaved in ascending channel-index order, with each channel's FastFrame data written in frame order.

for angle a in 0 … n_angles-1:
  for row in 0 … n_rows[a]-1:
    for channel in [CH1, CH3, CH4]:          # 3 channels, fixed order
      for frame in 0 … n_frames[a]-1:
        samples[0 … samples_per_frame-1]     # bps bytes each

Each sample is a raw signed ADC value. With bytes_per_sample = 1 this is int8 (−128 … +127). With bytes_per_sample = 2 this is big-endian int16.

Total data size:

sum over angles a of: n_rows[a] × 3 × n_frames[a] × samples_per_frame × bytes_per_sample

Incomplete files: If a scan is aborted the file is closed immediately and the data block will be shorter than the expected size. Readers should reconstruct the expected per-angle byte offsets from the Per-Angle Geometry Table and check file_size against the running total before reshaping — a fixed (n_angles, n_rows, ...) reshape (as in pre-v6 readers) will not work since row/frame counts are no longer uniform across angles.

---

Spatial Mapping

The k-th waveform (frame) in a row corresponds to the k-th laser pulse that hit the sample. For a row belonging to angle a, the physical X position of that pulse is:

x_k = x_start[a] + k * (velocity_mm_s / laser_freq_hz)

using that angle's x_start from the Per-Angle Geometry Table (not x_start_nominal).

---

Acquisition Settings (fixed by sc3_aui_app.py)

Parameter	Value
Oscilloscope trigger	CH2, rising edge, 1.24 V
Trigger offset	0 % (trigger at left edge)
Sample rate	6.25 GS/s (160 ps/sample)
Channels recorded	CH1, CH3, CH4
Stage X velocity	100 mm/s
Stage X acceleration	1500 mm/s²
Stage X trigger out	Logic-high at max velocity
Acquisition mode	FastFrame, Normal trigger

---

Version History

Version	Change
1	One file per row; header included angle_idx, row_idx, angle_deg, y_mm.
2	One file per scan; global header with n_angles/n_rows; separate angle and row tables; three channels (CH1, CH3, CH4) per row.
3	Added preamble blocks (WFMOutpre strings) after the row table, one length-prefixed UTF-8 block per channel.
4	Added background waveform block (CH1, Helios ON / Genesis OFF) after the preamble blocks; stored as uint32 sample count followed by raw int8 ADC bytes.
5	(skipped)
6	Each angle now scans only the bounding box of the nominal ROI rotated by that angle instead of the AABB-expanded worst case across all angles. Header no longer carries a single global x_start/x_delta/n_rows — replaced with *_nominal reference fields plus a new Per-Angle Geometry Table (x_start, x_delta, n_frames, n_rows per angle) and a ragged Row Table / Waveform Data block sized per angle. Not compatible with pre-v6 readers that assume uniform geometry. sras_viewer.py reads v6 natively (per-angle n_rows/n_frames/x_start); the "Pre-process and Save as v5" fast-path export is not offered for v6 files since the flat v5 layout cannot represent per-angle geometry.