Phase 3: viewer reads v6 via mmap; extract analysis core
The viewer could only parse v2-v4 headers while the app has been writing v6 for some time — it could not open ANY file the current app produces. It now uses core.sras_format directly (v6 only, per user decision). New core/sras_analysis.py (Qt-free): ChannelCalibration, image reducers, and SawPipeline. sras_viewer.py keeps only Qt. Memory (measured, 92 MB synthetic scan, separate processes): old eager path +305 MB read()+slice-copy+astype+float32 mean new mmap path + 31 MB zero-copy view + mean(dtype=) -> identical DC image; old scaled at ~3.3x file size, new at image size - load_angle() returns a read-only mmap view instead of reading the whole data block, then copying it twice - SAW sweeps keep one scalar per pixel (process_shot_metrics) instead of retaining 5 full arrays x pixel count in a results list - CH1 float32 materializes only for pixels passing the DC mask - matched filter caches the template FFT instead of recomputing per pixel - opening a new file drops every reference to the old one (compute/ template/diagnostic workers used to pin the previous multi-GB mapping) Responsiveness: - 250 ms debounce coalesces spinbox storms into one recompute - grating change is a display-time scalar multiply, not a full FFT rerun - colormap/clim reuse the AxesImage (set_data/set_clim) instead of clf() + rebuilding the colorbar; draw_idle() throughout - SAW diagnostics (21 pipeline runs) and CSV export moved off the GUI thread Also: ragged per-angle geometry is respected (v6 angles differ in rows/ frames), truncated scans show only rows present on disk, dead decimation path and v2 fallback branch removed, scipy added to viewer requirements. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
This commit is contained in:
Thomas Ales
@@ -0,0 +1,296 @@
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"""SRAS analysis: scope calibration, image reducers, and the SAW
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matched-filter pipeline. Qt-free; operates on the per-angle arrays
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returned by core.sras_format.SrasFile.load_angle().
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Channel semantics (fixed by the acquisition app):
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CH1 — RF Acoustic Packet: FFT → peak frequency
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CH3 — Bias A (DC): waveform mean
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CH4 — Bias B (DC): waveform mean — also the RF valid-pixel mask source
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"""
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from __future__ import annotations
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import os
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import re
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from concurrent.futures import ThreadPoolExecutor
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from dataclasses import dataclass
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import numpy as np
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from scipy.signal import butter, hilbert, sosfiltfilt
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# Channel indices into the on-disk channel axis (order fixed by SCAN_CHANNELS)
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CH1_IDX, CH3_IDX, CH4_IDX = 0, 1, 2
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# Fallback scope calibration for preambles missing YMULT/YOFF/YZERO:
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# 50 mV/div, 8 div full-scale, int8 ADC, position = -2.72 div
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FALLBACK_YMULT_MV = 1.5625 # mV per ADC count
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FALLBACK_YOFF_ADC = -87.04 # ADC count that represents 0 V
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def parse_preamble(preamble: str) -> dict[str, float]:
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"""Extract YMULT, YOFF, YZERO from a Tektronix WFMOutpre string."""
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result = {}
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for key in ("YMULT", "YOFF", "YZERO"):
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m = re.search(rf'\b{key}\s+([-+]?\d*\.?\d+(?:[Ee][+-]?\d+)?)', preamble)
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if m:
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result[key] = float(m.group(1))
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return result
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@dataclass
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class ChannelCalibration:
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"""Per-channel ADC↔mV conversion, parsed from the file's preambles."""
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ymult_mv: list[float]
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yoff_adc: list[float]
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yzero_mv: list[float]
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@classmethod
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def from_preambles(cls, preambles: list[str]) -> "ChannelCalibration":
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cal = cls([], [], [])
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for p in preambles:
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vals = parse_preamble(p)
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# YMULT/YZERO from the scope are in V; stored here in mV
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cal.ymult_mv.append(vals.get("YMULT", FALLBACK_YMULT_MV / 1000) * 1000)
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cal.yoff_adc.append(vals.get("YOFF", FALLBACK_YOFF_ADC))
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cal.yzero_mv.append(vals.get("YZERO", 0.0) * 1000)
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return cal
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def adc_to_mv(self, adc, ch: int):
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return (adc - self.yoff_adc[ch]) * self.ymult_mv[ch] + self.yzero_mv[ch]
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def mv_to_adc(self, mv, ch: int):
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return (mv - self.yzero_mv[ch]) / self.ymult_mv[ch] + self.yoff_adc[ch]
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def power_spectrum(waveform: np.ndarray) -> np.ndarray:
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"""FFT power with the DC bin suppressed."""
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power = np.abs(np.fft.rfft(waveform)) ** 2
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power[..., 0] = 0.0
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return power
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# ---------------------------------------------------------------------------
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# Image reducers — all take the (n_rows, n_ch, n_frames, spf) angle view
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# ---------------------------------------------------------------------------
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def compute_dc_image(angle_view: np.ndarray, ch_idx: int) -> np.ndarray:
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"""Mean of each waveform → (n_rows, n_frames) float32.
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Computed directly on the int8 view — no float32 copy of the block.
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"""
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return angle_view[:, ch_idx].mean(axis=-1, dtype=np.float32)
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def _valid_ch1_waveforms(angle_view: np.ndarray, calib: ChannelCalibration,
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dc_threshold_mv: float,
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background: np.ndarray | None,
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) -> tuple[np.ndarray, np.ndarray]:
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"""CH4-DC mask + float32 CH1 waveforms for only the pixels that pass.
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Materializes float32 for the valid pixels alone (fancy-index on the int8
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view first), so a mostly-masked angle costs almost nothing.
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"""
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dc4_mv = calib.adc_to_mv(compute_dc_image(angle_view, CH4_IDX), CH4_IDX)
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valid = dc4_mv >= dc_threshold_mv
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if not valid.any():
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return valid, np.empty((0, angle_view.shape[-1]), dtype=np.float32)
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waves = angle_view[:, CH1_IDX][valid].astype(np.float32) # (n_valid, spf)
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if background is not None:
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waves -= background
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return valid, waves
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def compute_rf_image(angle_view: np.ndarray, calib: ChannelCalibration,
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freq_axis_mhz: np.ndarray,
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dc_threshold_mv: float,
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background: np.ndarray | None = None,
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gate_start_ns: float | None = None,
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gate_end_ns: float | None = None,
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time_axis_ns: np.ndarray | None = None) -> np.ndarray:
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"""FFT of each CH1 waveform; pixel = peak frequency in MHz.
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Pixels whose CH4 DC mean (in mV) is below dc_threshold_mv are 0 and the
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FFT is skipped for them. Optional time gate zeroes samples outside
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[gate_start_ns, gate_end_ns] before the FFT.
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"""
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valid, waves = _valid_ch1_waveforms(angle_view, calib, dc_threshold_mv, background)
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img = np.zeros(valid.shape, dtype=np.float32)
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if len(waves):
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if (gate_start_ns is not None or gate_end_ns is not None) and time_axis_ns is not None:
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keep = np.ones(len(time_axis_ns), dtype=bool)
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if gate_start_ns is not None:
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keep &= time_axis_ns >= gate_start_ns
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if gate_end_ns is not None:
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keep &= time_axis_ns <= gate_end_ns
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waves[:, ~keep] = 0.0
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peak_bins = np.argmax(power_spectrum(waves), axis=-1)
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img[valid] = freq_axis_mhz[peak_bins]
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return img
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def compute_saw_image(angle_view: np.ndarray, calib: ChannelCalibration,
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dc_threshold_mv: float,
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pipeline: "SawPipeline", mode: str,
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background: np.ndarray | None = None) -> np.ndarray:
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"""Matched-filter pipeline over every valid pixel.
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mode : "amplitude" → MF envelope peak in the SAW window
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"tof" → arrival time (ns) of that peak
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Only the requested scalar is kept per pixel — the per-shot intermediate
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arrays are dropped inside the worker instead of being accumulated.
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"""
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valid, waves = _valid_ch1_waveforms(angle_view, calib, dc_threshold_mv, background)
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img = np.zeros(valid.shape, dtype=np.float32)
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if len(waves):
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key = "peak_amplitude" if mode == "amplitude" else "peak_time_ns"
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def _scalar(w):
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return pipeline.process_shot_metrics(w)[key]
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n_workers = min(os.cpu_count() or 4, len(waves))
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with ThreadPoolExecutor(max_workers=n_workers) as executor:
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img[valid] = np.fromiter(executor.map(_scalar, waves),
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dtype=np.float32, count=len(waves))
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return img
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# ---------------------------------------------------------------------------
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# SAW signal processing pipeline
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# ---------------------------------------------------------------------------
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class SawPipeline:
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"""EMI-cleaning and SAW extraction pipeline.
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Stages (each independently bypassable):
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1. EMI gate — cosine-taper the first `emi_gate_ns` ns to suppress the
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laser-firing burst at t≈0; leaves the SAW packet alone.
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2. Bandpass — 6th-order Butterworth zero-phase (sosfiltfilt).
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3. Matched filter — FFT cross-correlation with a Hann-windowed template
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built from the average of N clean shots.
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4. Analytic — Hilbert transform of MF output → amplitude envelope.
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"""
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def __init__(self, sample_rate_hz: float,
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emi_gate_ns: float = 50.0,
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bp_lo_mhz: float = 85.0,
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bp_hi_mhz: float = 200.0,
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saw_window_ns: tuple[float, float] = (80.0, 350.0)):
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self.sample_rate_hz = float(sample_rate_hz)
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self.emi_gate_ns = float(emi_gate_ns)
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self.bp_lo_mhz = float(bp_lo_mhz)
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self.bp_hi_mhz = float(bp_hi_mhz)
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self.saw_window_ns = (float(saw_window_ns[0]), float(saw_window_ns[1]))
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self.template: np.ndarray | None = None
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self._template_fft: dict[int, np.ndarray] = {} # nfft → rfft(template)
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self._emi_gate_samples = max(1, int(round(
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self.emi_gate_ns * 1e-9 * self.sample_rate_hz)))
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nyq = self.sample_rate_hz / 2.0
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lo = np.clip(self.bp_lo_mhz * 1e6 / nyq, 1e-6, 0.999)
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hi = np.clip(self.bp_hi_mhz * 1e6 / nyq, lo + 1e-6, 0.9999)
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# 6th-order Butterworth → 12th-order bandpass; ~120 dB/decade rolloff
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self._sos = butter(6, [lo, hi], btype='bandpass', output='sos')
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def gate_emi(self, signal: np.ndarray) -> np.ndarray:
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"""Cosine-taper (raised cosine 0→1) the first emi_gate samples.
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The taper rolls up smoothly from zero so the abrupt EMI burst is
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suppressed without introducing a step discontinuity at the gate edge.
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"""
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n = min(self._emi_gate_samples, len(signal))
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out = signal.copy()
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out[:n] *= 0.5 * (1.0 - np.cos(np.pi * np.arange(n) / n))
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return out
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def bandpass(self, signal: np.ndarray) -> np.ndarray:
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"""Zero-phase IIR Butterworth bandpass (sosfiltfilt), float32 in/out."""
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return sosfiltfilt(self._sos, signal).astype(np.float32, copy=False)
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def build_template(self, waveforms: np.ndarray) -> None:
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"""Average N shots (EMI-gated + bandpassed), Hann-windowed to the
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declared SAW window, to form the matched-filter template."""
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processed = np.stack([
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self.bandpass(self.gate_emi(np.asarray(w, dtype=np.float32)))
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for w in waveforms
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])
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avg = processed.mean(axis=0)
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n = len(avg)
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t_ns = np.arange(n) / self.sample_rate_hz * 1e9
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i0 = max(0, int(np.searchsorted(t_ns, self.saw_window_ns[0])))
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i1 = min(n, int(np.searchsorted(t_ns, self.saw_window_ns[1])))
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windowed = np.zeros(n, dtype=np.float32)
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if i1 > i0:
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windowed[i0:i1] = avg[i0:i1] * np.hanning(i1 - i0)
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self.template = windowed
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self._template_fft.clear()
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def matched_filter(self, signal: np.ndarray) -> tuple[np.ndarray, np.ndarray]:
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"""FFT cross-correlation with the template → (mf_output, envelope)."""
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if self.template is None:
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raise RuntimeError("No template — call build_template() first")
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n = len(signal)
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nfft = 1 << (n + len(self.template) - 1).bit_length()
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T = self._template_fft.get(nfft)
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if T is None:
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T = np.conj(np.fft.rfft(self.template, nfft))
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self._template_fft[nfft] = T
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S = np.fft.rfft(signal, nfft)
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mf = np.fft.irfft(S * T, nfft)[:n]
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env = np.abs(hilbert(mf))
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return mf.astype(np.float32, copy=False), env.astype(np.float32, copy=False)
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def process_shot(self, signal: np.ndarray) -> dict:
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"""EMI gate → bandpass → matched filter on one shot; returns every
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stage plus metrics (for diagnostics displays)."""
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raw = np.asarray(signal, dtype=np.float32)
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gated = self.gate_emi(raw)
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filtered = self.bandpass(gated)
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if self.template is not None:
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mf_out, env = self.matched_filter(filtered)
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else:
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mf_out = filtered.copy()
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env = np.abs(hilbert(filtered)).astype(np.float32)
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metrics = self._envelope_metrics(env, filtered)
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return {
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"raw": raw,
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"gated": gated,
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"filtered": filtered,
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"mf_output": mf_out,
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"envelope": env,
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"sample_rate_hz": self.sample_rate_hz,
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**metrics,
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}
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def process_shot_metrics(self, signal: np.ndarray) -> dict:
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"""Like process_shot but returns only the scalar metrics — used for
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whole-image sweeps where retaining per-shot arrays would multiply
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memory by the pixel count."""
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filtered = self.bandpass(self.gate_emi(np.asarray(signal, dtype=np.float32)))
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if self.template is not None:
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_, env = self.matched_filter(filtered)
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else:
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env = np.abs(hilbert(filtered))
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return self._envelope_metrics(env, filtered)
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def _envelope_metrics(self, env: np.ndarray, filtered: np.ndarray) -> dict:
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sr = self.sample_rate_hz
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t_ns = np.arange(len(env)) / sr * 1e9
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s0, s1 = self.saw_window_ns
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roi = (t_ns >= s0) & (t_ns <= s1)
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if roi.any():
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peak_sample = int(np.where(roi)[0][np.argmax(env[roi])])
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else:
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peak_sample = int(np.argmax(env))
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peak_amplitude = float(env[peak_sample])
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peak_time_ns = float(peak_sample / sr * 1e9)
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# SNR: peak / RMS of the noise floor inside the gated EMI region
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noise_seg = filtered[:self._emi_gate_samples]
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noise_rms = float(np.sqrt(np.mean(noise_seg ** 2))) if len(noise_seg) else 1.0
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return {
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"peak_amplitude": peak_amplitude,
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"peak_sample": peak_sample,
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"peak_time_ns": peak_time_ns,
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"snr": peak_amplitude / noise_rms if noise_rms > 0 else 0.0,
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}
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+513
-938
File diff suppressed because it is too large
Load Diff
@@ -1,3 +1,4 @@
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PyQt6==6.10.2
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numpy==2.4.1
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matplotlib==3.10.8
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scipy==1.16.3
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@@ -0,0 +1,142 @@
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"""core.sras_analysis + the viewer's LoadedScan/compute path, run headlessly
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over the golden fixtures."""
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from pathlib import Path
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import numpy as np
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import pytest
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from core.sras_analysis import (
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CH1_IDX, CH4_IDX, ChannelCalibration, FALLBACK_YMULT_MV,
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SawPipeline, compute_dc_image, compute_rf_image, power_spectrum,
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)
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GOLDEN = Path(__file__).parent / "golden"
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def _loaded_scan(name="complete.sras"):
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# Imported lazily: sras_viewer pulls in PyQt6/matplotlib.
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from sras_viewer import LoadedScan
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return LoadedScan(str(GOLDEN / name))
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def test_loaded_scan_basics():
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scan = _loaded_scan()
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assert scan.rows_available == [3, 3]
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assert scan.background is not None and len(scan.background) == 8
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assert len(scan.calib.ymult_mv) == 3
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view = scan.angle_view(0)
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assert view.shape == (3, 3, 4, 8)
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scan.close()
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def test_loaded_scan_truncated_rows():
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scan = _loaded_scan("trunc_rowboundary_a1.sras")
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assert scan.rows_available == [3, 2]
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assert scan.angle_view(1).shape[0] == 2
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scan = _loaded_scan("header_only.sras")
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assert scan.rows_available == [0, 0]
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assert scan.angle_view(0).shape[0] == 0
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def test_compute_dc_image_matches_manual():
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scan = _loaded_scan()
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view = scan.angle_view(0)
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img = compute_dc_image(view, CH4_IDX)
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manual = view[:, CH4_IDX].astype(np.float64).mean(axis=-1)
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assert img.shape == (3, 4)
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assert img.dtype == np.float32
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np.testing.assert_allclose(img, manual, rtol=1e-6)
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def test_compute_rf_image_mask_and_values():
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scan = _loaded_scan()
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view = scan.angle_view(0)
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sras = scan.sras
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f_mhz = sras.freq_axis_mhz(sras.header.samples_per_frame)
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# Threshold below everything: all pixels valid, values from the freq axis
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img_all = compute_rf_image(view, scan.calib, f_mhz, dc_threshold_mv=-1e9)
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assert img_all.shape == (3, 4)
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assert set(np.unique(img_all)).issubset(set(f_mhz))
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# Threshold above everything: fully masked, zero image, no FFT work
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img_none = compute_rf_image(view, scan.calib, f_mhz, dc_threshold_mv=1e9)
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assert not img_none.any()
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def test_compute_rf_image_gate_zeroes_samples():
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scan = _loaded_scan()
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view = scan.angle_view(0)
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sras = scan.sras
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f_mhz = sras.freq_axis_mhz(sras.header.samples_per_frame)
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t_ns = sras.time_axis_ns()
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||||
img = compute_rf_image(view, scan.calib, f_mhz, dc_threshold_mv=-1e9,
|
||||
gate_start_ns=float(t_ns[2]), gate_end_ns=float(t_ns[5]),
|
||||
time_axis_ns=t_ns)
|
||||
assert img.shape == (3, 4)
|
||||
|
||||
|
||||
def test_calibration_roundtrip_and_fallback():
|
||||
cal = ChannelCalibration.from_preambles(["", "", ""])
|
||||
assert cal.ymult_mv == [FALLBACK_YMULT_MV] * 3
|
||||
assert cal.mv_to_adc(cal.adc_to_mv(42.0, 0), 0) == pytest.approx(42.0)
|
||||
|
||||
cal2 = ChannelCalibration.from_preambles(
|
||||
["YMULT 1.0E-3;YOFF -10.0;YZERO 2.0E-3"])
|
||||
assert cal2.ymult_mv[0] == pytest.approx(1.0)
|
||||
assert cal2.yoff_adc[0] == pytest.approx(-10.0)
|
||||
assert cal2.yzero_mv[0] == pytest.approx(2.0)
|
||||
|
||||
|
||||
def test_power_spectrum_dc_suppressed():
|
||||
x = np.ones(64, dtype=np.float32) * 5.0
|
||||
p = power_spectrum(x)
|
||||
assert p[0] == 0.0
|
||||
assert not p[1:].any()
|
||||
|
||||
|
||||
def test_saw_pipeline_finds_injected_packet():
|
||||
sr = 6.25e9
|
||||
n = 1250
|
||||
t = np.arange(n) / sr
|
||||
rng = np.random.default_rng(42)
|
||||
|
||||
def make_shot(delay_ns=200.0):
|
||||
sig = rng.normal(0, 0.05, n).astype(np.float32)
|
||||
packet = np.exp(-((t * 1e9 - delay_ns) / 25.0) ** 2) \
|
||||
* np.sin(2 * np.pi * 140e6 * t)
|
||||
return sig + 3.0 * packet.astype(np.float32)
|
||||
|
||||
pipe = SawPipeline(sr, emi_gate_ns=50.0, bp_lo_mhz=85.0, bp_hi_mhz=200.0,
|
||||
saw_window_ns=(80.0, 350.0))
|
||||
pipe.build_template(np.stack([make_shot() for _ in range(10)]))
|
||||
assert pipe.template is not None
|
||||
|
||||
metrics = pipe.process_shot_metrics(make_shot())
|
||||
assert metrics["peak_time_ns"] == pytest.approx(200.0, abs=15.0)
|
||||
assert metrics["snr"] > 3.0
|
||||
|
||||
# process_shot returns the same metrics plus the stage arrays
|
||||
full = pipe.process_shot(make_shot())
|
||||
for key in ("raw", "gated", "filtered", "mf_output", "envelope"):
|
||||
assert isinstance(full[key], np.ndarray)
|
||||
|
||||
|
||||
def test_compute_saw_image_scalars_only():
|
||||
# Synthetic angle view: golden frames (8 samples) are too short for the
|
||||
# 6th-order zero-phase bandpass; real records are >1000 samples.
|
||||
from core.sras_analysis import compute_saw_image
|
||||
rng = np.random.default_rng(1)
|
||||
view = rng.integers(-40, 40, size=(3, 3, 4, 512), dtype=np.int8)
|
||||
view[:, CH4_IDX] = 100 # every pixel passes the DC mask
|
||||
calib = ChannelCalibration.from_preambles(["", "", ""])
|
||||
|
||||
pipe = SawPipeline(6.25e9, saw_window_ns=(10.0, 70.0))
|
||||
pipe.build_template(view[0, CH1_IDX, :4].astype(np.float32))
|
||||
img = compute_saw_image(view, calib, -1e9, pipe, "amplitude")
|
||||
assert img.shape == (3, 4)
|
||||
assert img.dtype == np.float32
|
||||
assert (img > 0).all()
|
||||
|
||||
tof = compute_saw_image(view, calib, -1e9, pipe, "tof")
|
||||
assert tof.shape == (3, 4)
|
||||
Reference in New Issue
Block a user