Thomas Ales
f745efe7e0
Previously the FFT was always run unmasked (dc_threshold_mv=-1e9) so the result could be cached independent of the threshold, with masking applied afterward as a display-time step. That meant every pixel's CH1 waveform was read and FFT'd even when most of the scan is background — wasted work now that the DC map (and its threshold mask) is already known ahead of time via the DC precompute cache. compute_rf_image now takes the real threshold and an optional precomputed dc4_mv array (reused from the DC cache, avoiding a redundant CH4 read), and skips the FFT for masked-out pixels entirely, same as before this threshold-caching detour was introduced. The masked-out CH1 samples are also never read from disk: the boolean valid-pixel mask is applied to the raw memmap slice before any dtype conversion, so numpy only pages in the bytes for pixels that pass the threshold. Threshold is therefore back to being part of the FFT cache key (changing it now decides which pixels get computed at all, so it can't be satisfied from a cache built for a different threshold) — but the recompute it triggers reuses the cached DC4 image and skips both the FFT and the I/O for masked pixels, so it's much cheaper than the original full-image compute. Grating and colormap remain pure post-processing with no recompute. Verified bit-identical output against the un-optimized reference path on synthetic data (including scattered, non-row-aligned masking), and timed on the real 532 GB / 17-angle file: angle 0's FFT (75.2% of pixels above the default 50 mV threshold) went from ~121s (fully unmasked) to 114s (FFT skipped, I/O not skipped) to 90.2s with this change (both skipped). Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
2620 lines
107 KiB
Python
2620 lines
107 KiB
Python
#!/usr/bin/env python3
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"""
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SRAS Scan File Viewer
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PyQt6 application for visualizing channel data from .sras binary scan files.
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Channel semantics (fixed by sc3_aui_app.py acquisition settings):
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CH1 — RF Acoustic Packet (AC-coupled, 100 mV/div): FFT → peak frequency
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CH3 — Bias A (DC-coupled, 50 mV/div): waveform mean
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CH4 — Bias B (DC-coupled, 50 mV/div): waveform mean
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RF images are masked: pixels where CH4_dc < dc_threshold show 0.
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Frame-count correction: the scanner writes the *configured* frame count in the
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header before acquisition, but the scope may acquire fewer frames. The actual
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count is computed from the file size and used for the reshape so channels are
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correctly aligned.
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Scan geometry: v6 files scan a different bounding box per angle (x_start,
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x_delta, n_frames, n_rows all vary by angle), so geometry is exposed per-angle
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via SrasFile.n_rows / n_frames / x_start_mm arrays and the x_axis_mm() /
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y_positions_mm() methods. v2–v5 files have uniform geometry across angles, so
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those arrays simply repeat the same value n_angles times.
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"""
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import re
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import sys
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import struct
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import faulthandler
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import numpy as np
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from pathlib import Path
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import os
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faulthandler.enable() # print a native stack trace on SIGSEGV/SIGABRT/etc.
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from PyQt6.QtWidgets import (
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QApplication, QMainWindow, QWidget, QVBoxLayout, QHBoxLayout,
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QGroupBox, QLabel, QPushButton, QComboBox, QSpinBox, QDoubleSpinBox,
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QFileDialog, QSizePolicy, QSplitter, QCheckBox, QFrame, QProgressDialog,
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QDialog, QDialogButtonBox, QRadioButton, QButtonGroup,
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)
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from PyQt6.QtGui import QAction
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from PyQt6.QtCore import Qt, QThread, pyqtSignal, QObject
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from matplotlib.backends.backend_qtagg import FigureCanvasQTAgg, NavigationToolbar2QT
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from matplotlib.figure import Figure
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from matplotlib.patches import Polygon
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from matplotlib.lines import Line2D
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from matplotlib.path import Path as MplPath
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# ---------------------------------------------------------------------------
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# FFT backend
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# ---------------------------------------------------------------------------
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_pyfftw_available = False
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try:
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import pyfftw
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pyfftw.interfaces.cache.enable()
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_pyfftw_available = True
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except ImportError:
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pass
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import scipy.fft as scipy_fft
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# Runtime-mutable settings changed via FftOptionsDialog
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_fft_backend = "numpy" # "numpy" or "pyfftw"
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def _do_rfft(x: np.ndarray, n: int | None = None, axis: int = -1,
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workers: int = 1) -> np.ndarray:
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"""Dispatch rfft to the selected backend with optional multithreading."""
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if _fft_backend == "pyfftw" and _pyfftw_available:
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return pyfftw.interfaces.numpy_fft.rfft(x, n=n, axis=axis, threads=workers)
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return scipy_fft.rfft(x, n=n, axis=axis, workers=workers)
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# ---------------------------------------------------------------------------
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# SRAS format
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# ---------------------------------------------------------------------------
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# v2–v5: fixed header, uniform geometry across angles (43 bytes)
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HDR_FMT = ">4sBHHffffIIdBB"
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HDR_SIZE = struct.calcsize(HDR_FMT) # 43 bytes
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# v6: fixed header, per-angle geometry in a separate table (49 bytes)
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HDR_FMT_V6 = ">4sBHfffffffIdBB"
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HDR_SIZE_V6 = struct.calcsize(HDR_FMT_V6) # 49 bytes
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# v6: per-angle geometry table record (x_start, x_delta, n_frames, n_rows)
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GEO_FMT_V6 = ">ffIH"
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GEO_SIZE_V6 = struct.calcsize(GEO_FMT_V6) # 14 bytes
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# Fixed-order channels in the file: index 0=CH1, 1=CH3, 2=CH4
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# Fixed channel indices into the .sras data array (CH1=RF, CH3/CH4=Bias DC)
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CH1_IDX, CH3_IDX, CH4_IDX = 0, 1, 2
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CH_LABELS = [
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"CH1 — RF (FFT peak freq)",
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"CH3 — Bias A (DC mean)",
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"CH4 — Bias B (DC mean)",
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"CH1 — Velocity (SRAS)",
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]
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CH_NAMES = ["CH1", "CH3", "CH4", "VEL"]
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# Combo index for the derived velocity mode (uses CH1_IDX data)
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VELOCITY_MODE_IDX = 3
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# All modes that operate on CH1 waveforms
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CH1_DERIVED_MODES = (CH1_IDX, VELOCITY_MODE_IDX)
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# Fallback scope calibration used only when reading v2 files without embedded
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# preambles. v3+ files carry the WFMOutpre string so these are not used.
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# 50 mV/div, 8 div full-scale, int8 ADC, position = -2.72 div
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# ymult = 50 mV × 8 / 256 = 1.5625 mV/count
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# yoff = position × (256/8) = -2.72 × 32 = -87.04 (ADC count for 0 V)
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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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CMAPS = ["gray", "viridis", "plasma", "inferno", "hot", "jet", "RdBu_r", "seismic"]
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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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Returns a dict with float values for whichever keys are present.
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YMULT is left in V/count as the scope reports it.
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"""
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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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def mv_to_adc(mv: float, ymult_mv: float = _FALLBACK_YMULT_MV,
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yoff_adc: float = _FALLBACK_YOFF_ADC,
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yzero_mv: float = 0.0) -> float:
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return (mv - yzero_mv) / ymult_mv + yoff_adc
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def adc_to_mv(adc: float, ymult_mv: float = _FALLBACK_YMULT_MV,
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yoff_adc: float = _FALLBACK_YOFF_ADC,
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yzero_mv: float = 0.0) -> float:
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return (adc - yoff_adc) * ymult_mv + yzero_mv
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# ---------------------------------------------------------------------------
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# File parser
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# ---------------------------------------------------------------------------
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class SrasFile:
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"""Parsed in-memory representation of a v2–v6 .sras file.
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Scan geometry (rows, frames, x_start) is exposed per-angle via the
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``n_rows`` / ``n_frames`` / ``x_start_mm`` arrays and the ``x_axis_mm()``
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/ ``y_positions_mm()`` methods, since v6 files scan a different bounding
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box per angle. v2–v5 files have uniform geometry, so these arrays just
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repeat the same value ``n_angles`` times. Waveform data is likewise
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exposed as ``data[angle_idx]``, an array of shape
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``(n_rows[a], n_channels, n_frames[a], samples_per_frame)``.
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"""
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def __init__(self, path: str):
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self.path = Path(path)
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self._parse()
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def _parse(self):
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with open(self.path, "rb") as f:
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magic = f.read(4)
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if magic != b"SRAS":
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raise ValueError(f"Bad magic bytes: {magic!r}")
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(version,) = struct.unpack(">B", f.read(1))
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self.version = version
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if version in (2, 3, 4, 5):
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self._parse_legacy()
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elif version == 6:
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self._parse_v6()
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else:
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raise ValueError(f"Unsupported version: {version}")
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# ------------------------------------------------------------------
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# v2–v5 parsing (uniform geometry, flat waveform block)
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# ------------------------------------------------------------------
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def _parse_legacy(self):
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with open(self.path, "rb") as f:
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fields = struct.unpack(HDR_FMT, f.read(HDR_SIZE))
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(magic, ver, n_angles, n_rows, x_start, x_delta, vel, freq,
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n_frames_hdr, spf, sr, bps, n_ch) = fields
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self.n_angles = n_angles
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self.velocity_mm_s = float(vel)
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self.laser_freq_hz = float(freq)
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self.n_frames_header = n_frames_hdr # configured count (may be wrong)
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self.samples_per_frame = spf
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self.sample_rate_hz = float(sr)
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self.bytes_per_sample = bps
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self.n_channels = n_ch
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# Precomputed-image cache (populated when reading a v5 file).
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# These are (n_angles, n_rows, n_frames) float32 arrays or None.
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self.precomputed_freq_mhz: np.ndarray | None = None
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self.precomputed_dc4_mv: np.ndarray | None = None
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self.precomputed_dc3_mv: np.ndarray | None = None
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self.precomputed_bg_sub: bool = False
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self.scan_aborted = False
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self.n_angles_declared = n_angles
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with open(self.path, "rb") as f:
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f.seek(HDR_SIZE)
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angles = np.frombuffer(f.read(n_angles * 4), dtype=">f4").astype(np.float32)
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y_pos = np.frombuffer(f.read(n_rows * 4), dtype=">f4").astype(np.float32)
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if ver >= 3:
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preambles = []
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for _ in range(n_ch):
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(length,) = struct.unpack(">H", f.read(2))
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preambles.append(f.read(length).decode("utf-8"))
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self.preambles = preambles
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self.ch_ymult_mv = []
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self.ch_yoff_adc = []
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self.ch_yzero_mv = []
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for p in preambles:
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cal = _parse_preamble(p)
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# YMULT from scope is V/count; store as mV/count
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self.ch_ymult_mv.append(cal.get("YMULT", _FALLBACK_YMULT_MV / 1000) * 1000)
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self.ch_yoff_adc.append(cal.get("YOFF", _FALLBACK_YOFF_ADC))
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# YZERO from scope is in V; store as mV
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self.ch_yzero_mv.append(cal.get("YZERO", 0.0) * 1000)
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else:
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self.preambles = None
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self.ch_ymult_mv = [_FALLBACK_YMULT_MV] * n_ch
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self.ch_yoff_adc = [_FALLBACK_YOFF_ADC] * n_ch
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self.ch_yzero_mv = [0.0] * n_ch
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if ver >= 4:
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(n_bg,) = struct.unpack(">I", f.read(4))
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self.background = np.frombuffer(f.read(n_bg), dtype=np.int8).astype(np.float32)
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else:
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self.background = None
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# Record the byte offset where raw waveform data begins.
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# np.memmap will use this to map only the waveform section.
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data_offset = f.tell()
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# ---- Determine actual frame count from file size ---------------
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# For v4 and earlier the header n_frames may be the *configured*
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# count before acquisition; the actual count is derived from the
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# bytes on disk. For v5 files a PREC tail follows the waveform
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# data, so we must not include those extra bytes in the frame count.
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file_size = self.path.stat().st_size
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samples_per_row_per_ch = n_ch * spf
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# Upper bound: bytes from data_offset to end of file
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available_bytes = file_size - data_offset
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if ver == 5:
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actual_n_frames = n_frames_hdr
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remainder = 0
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else:
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total_samples = available_bytes // bps
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actual_n_frames = total_samples // (n_angles * n_rows * samples_per_row_per_ch)
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remainder = total_samples % (n_angles * n_rows * samples_per_row_per_ch)
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self.frame_count_mismatch = (actual_n_frames != n_frames_hdr)
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self.n_frames_remainder = remainder
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# ---- Memory-map the waveform data (zero RAM cost) --------------
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# Instead of f.read() → astype() (which peaks at 2× file size),
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# memmap lets the OS page only the bytes that are actually touched.
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waveform_dtype = np.int8 if bps == 1 else ">i2"
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waveform_shape = (n_angles, n_rows, n_ch, actual_n_frames, spf)
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data5d = np.memmap(
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str(self.path),
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dtype=waveform_dtype,
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mode="r",
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offset=data_offset,
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shape=waveform_shape,
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)
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# Expose as a list of per-angle views so downstream code shares one
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# indexing convention with v6: sras.data[a][row, ch, frame, sample]
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self.data = [data5d[a] for a in range(n_angles)]
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# Uniform per-angle geometry, repeated so callers don't need to
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# special-case legacy vs. v6 files.
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self.n_rows = np.full(n_angles, n_rows, dtype=np.int64)
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self.n_frames = np.full(n_angles, actual_n_frames, dtype=np.int64)
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self.x_start_mm = np.full(n_angles, float(x_start), dtype=np.float64)
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self._y_pos_per_angle = [y_pos] * n_angles
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self.angles_deg = angles
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# ---- Read v5 precomputed section if present --------------------
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if ver >= 5:
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waveform_bytes = actual_n_frames * n_angles * n_rows * n_ch * spf * bps
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prec_offset = data_offset + waveform_bytes
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if file_size > prec_offset:
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self._parse_prec_section(prec_offset, n_angles, n_rows, actual_n_frames)
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def _parse_prec_section(self, offset: int,
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n_angles: int, n_rows: int, n_frames: int):
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"""Parse the v5 PREC tail that holds precomputed images."""
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_PREC_MAGIC = b"PREC"
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px = n_rows * n_frames # pixels per angle image
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img_bytes = px * 4 # float32
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with open(self.path, "rb") as f:
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f.seek(offset)
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header_raw = f.read(6) # magic(4) + fmt_ver(1) + flags(1)
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if len(header_raw) < 6 or header_raw[:4] != _PREC_MAGIC:
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return
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flags = header_raw[5]
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self.precomputed_bg_sub = bool(flags & 0x01)
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(n_stored,) = struct.unpack(">H", f.read(2))
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if n_stored == 0:
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return
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freq_buf = np.zeros((n_angles, n_rows, n_frames), dtype=np.float32)
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dc4_buf = np.zeros((n_angles, n_rows, n_frames), dtype=np.float32)
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dc3_buf = np.zeros((n_angles, n_rows, n_frames), dtype=np.float32)
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for _ in range(n_stored):
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(aidx,) = struct.unpack(">H", f.read(2))
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if aidx >= n_angles:
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break
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freq_buf[aidx] = np.frombuffer(
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f.read(img_bytes), dtype=">f4").reshape(n_rows, n_frames)
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dc4_buf[aidx] = np.frombuffer(
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f.read(img_bytes), dtype=">f4").reshape(n_rows, n_frames)
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dc3_buf[aidx] = np.frombuffer(
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f.read(img_bytes), dtype=">f4").reshape(n_rows, n_frames)
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self.precomputed_freq_mhz = freq_buf
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self.precomputed_dc4_mv = dc4_buf
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self.precomputed_dc3_mv = dc3_buf
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# ------------------------------------------------------------------
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# v6 parsing (per-angle geometry, ragged waveform blocks)
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# ------------------------------------------------------------------
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def _parse_v6(self):
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with open(self.path, "rb") as f:
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fields = struct.unpack(HDR_FMT_V6, f.read(HDR_SIZE_V6))
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(magic, ver, n_angles, x_start_nom, y_start_nom, x_delta_nom,
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y_delta_nom, row_spacing, vel, freq, spf, sr, bps, n_ch) = fields
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n_angles_declared = n_angles
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self.velocity_mm_s = float(vel)
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self.laser_freq_hz = float(freq)
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self.samples_per_frame = spf
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self.sample_rate_hz = float(sr)
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self.bytes_per_sample = bps
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self.n_channels = n_ch
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# Reference-only fields: the ROI as entered before per-angle
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# bounding-box expansion. Actual per-angle geometry used for
|
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# rendering comes from the Per-Angle Geometry Table below.
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self.x_start_nominal_mm = float(x_start_nom)
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self.y_start_nominal_mm = float(y_start_nom)
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self.x_delta_nominal_mm = float(x_delta_nom)
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self.y_delta_nominal_mm = float(y_delta_nom)
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self.row_spacing_mm = float(row_spacing)
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self.n_frames_header = None
|
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self.frame_count_mismatch = False
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self.n_frames_remainder = 0
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|
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self.precomputed_freq_mhz: np.ndarray | None = None
|
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self.precomputed_dc4_mv: np.ndarray | None = None
|
||
self.precomputed_dc3_mv: np.ndarray | None = None
|
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self.precomputed_bg_sub: bool = False
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angles = np.frombuffer(f.read(n_angles * 4), dtype=">f4").astype(np.float32)
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x_start = np.empty(n_angles, dtype=np.float64)
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n_frames = np.empty(n_angles, dtype=np.int64)
|
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n_rows = np.empty(n_angles, dtype=np.int64)
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for a in range(n_angles):
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xs, xd, nf, nr = struct.unpack(GEO_FMT_V6, f.read(GEO_SIZE_V6))
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||
x_start[a] = xs
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||
n_frames[a] = nf
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n_rows[a] = nr
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||
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y_pos_per_angle = []
|
||
for a in range(n_angles):
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nr = int(n_rows[a])
|
||
y_pos_per_angle.append(
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np.frombuffer(f.read(nr * 4), dtype=">f4").astype(np.float32))
|
||
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preambles = []
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||
for _ in range(n_ch):
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(length,) = struct.unpack(">H", f.read(2))
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preambles.append(f.read(length).decode("utf-8"))
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||
self.preambles = preambles
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||
self.ch_ymult_mv = []
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||
self.ch_yoff_adc = []
|
||
self.ch_yzero_mv = []
|
||
for p in preambles:
|
||
cal = _parse_preamble(p)
|
||
self.ch_ymult_mv.append(cal.get("YMULT", _FALLBACK_YMULT_MV / 1000) * 1000)
|
||
self.ch_yoff_adc.append(cal.get("YOFF", _FALLBACK_YOFF_ADC))
|
||
self.ch_yzero_mv.append(cal.get("YZERO", 0.0) * 1000)
|
||
|
||
(n_bg,) = struct.unpack(">I", f.read(4))
|
||
self.background = np.frombuffer(f.read(n_bg), dtype=np.int8).astype(np.float32)
|
||
|
||
data_offset = f.tell()
|
||
|
||
# ---- Memory-map each angle's ragged waveform block -------------
|
||
# v6 gives each angle its own row/frame count, so waveform data is
|
||
# no longer one uniform (n_angles, n_rows, ...) block — each angle's
|
||
# block sits at a different offset with its own shape. An aborted
|
||
# scan truncates the file mid-angle; per the format spec we keep
|
||
# whatever complete angles are present rather than refusing to open
|
||
# the file.
|
||
file_size = self.path.stat().st_size
|
||
waveform_dtype = np.int8 if bps == 1 else ">i2"
|
||
|
||
data = []
|
||
offset = data_offset
|
||
n_complete = 0
|
||
for a in range(n_angles):
|
||
nr = int(n_rows[a])
|
||
nf = int(n_frames[a])
|
||
nbytes = nr * n_ch * nf * spf * bps
|
||
if offset + nbytes > file_size:
|
||
break
|
||
data.append(np.memmap(
|
||
str(self.path), dtype=waveform_dtype, mode="r",
|
||
offset=offset, shape=(nr, n_ch, nf, spf),
|
||
))
|
||
offset += nbytes
|
||
n_complete += 1
|
||
|
||
if n_complete == 0:
|
||
raise ValueError(
|
||
"v6 file has no complete angle blocks — scan was aborted "
|
||
"before the first angle finished.")
|
||
|
||
self.data = data
|
||
self.n_angles = n_complete
|
||
self.n_angles_declared = n_angles_declared
|
||
self.scan_aborted = n_complete < n_angles_declared
|
||
self.angles_deg = angles[:n_complete]
|
||
self.x_start_mm = x_start[:n_complete]
|
||
self.n_frames = n_frames[:n_complete]
|
||
self.n_rows = n_rows[:n_complete]
|
||
self._y_pos_per_angle = y_pos_per_angle[:n_complete]
|
||
|
||
# ------------------------------------------------------------------
|
||
# v5 writer
|
||
# ------------------------------------------------------------------
|
||
|
||
def write_v5(self, dest_path: str,
|
||
freq_images: np.ndarray,
|
||
dc4_images: np.ndarray,
|
||
dc3_images: np.ndarray,
|
||
bg_sub_applied: bool,
|
||
progress_cb=None):
|
||
"""Write a v5 .sras file to *dest_path*.
|
||
|
||
Copies the raw waveform bytes verbatim from the current file,
|
||
bumps the version byte to 5, patches n_frames_hdr to the actual
|
||
frame count, then appends the PREC section.
|
||
|
||
*freq_images* / *dc4_images* / *dc3_images*:
|
||
shape (n_angles, n_rows, n_frames) float32.
|
||
|
||
*progress_cb*: optional callable(fraction: float) for UI updates.
|
||
|
||
Only valid for v2–v5 source files, which have uniform per-angle
|
||
geometry. v6 files scan a different bounding box per angle and
|
||
cannot be losslessly represented in the flat v5 layout.
|
||
"""
|
||
if self.version == 6:
|
||
raise NotImplementedError(
|
||
"Pre-process to v5 is not supported for v6 source files "
|
||
"(per-angle geometry does not fit the flat v5 layout).")
|
||
|
||
import shutil
|
||
|
||
dest = Path(dest_path)
|
||
src = self.path
|
||
n_rows0 = int(self.n_rows[0])
|
||
n_frames0 = int(self.n_frames[0])
|
||
|
||
# --- Copy the source file verbatim, then patch the header -------
|
||
shutil.copy2(str(src), str(dest))
|
||
|
||
waveform_bytes = (self.n_angles * n_rows0 * self.n_channels
|
||
* n_frames0 * self.samples_per_frame
|
||
* self.bytes_per_sample)
|
||
|
||
with open(str(dest), "r+b") as f:
|
||
# Patch version byte (offset 4 in the header struct)
|
||
f.seek(4)
|
||
f.write(struct.pack("B", 5))
|
||
|
||
# Patch n_frames_hdr (uint32, big-endian) with the actual count.
|
||
# Locate its offset: magic(4) + ver(1) + n_angles(2) + n_rows(2) = 9
|
||
# then x_start(4)+x_delta(4)+vel(4)+freq(4) = 16, total = 25
|
||
# then n_frames_hdr is at offset 25 as ">I" (4 bytes)
|
||
f.seek(25)
|
||
f.write(struct.pack(">I", n_frames0))
|
||
|
||
# Truncate anything after the waveform data (e.g. old PREC tail)
|
||
# and seek to the append position.
|
||
waveform_end = self._data_offset_for_write()
|
||
f.seek(waveform_end + waveform_bytes)
|
||
f.truncate()
|
||
|
||
# --- Write PREC section -------------------------------------
|
||
n_stored = self.n_angles
|
||
flags = 0x01 if bg_sub_applied else 0x00
|
||
f.write(b"PREC")
|
||
f.write(struct.pack("BB", 1, flags))
|
||
f.write(struct.pack(">H", n_stored))
|
||
|
||
for aidx in range(n_stored):
|
||
if progress_cb is not None:
|
||
progress_cb(aidx / n_stored)
|
||
f.write(struct.pack(">H", aidx))
|
||
f.write(freq_images[aidx].astype(">f4").tobytes())
|
||
f.write(dc4_images[aidx].astype(">f4").tobytes())
|
||
f.write(dc3_images[aidx].astype(">f4").tobytes())
|
||
|
||
if progress_cb is not None:
|
||
progress_cb(1.0)
|
||
|
||
def _data_offset_for_write(self) -> int:
|
||
"""Return the file offset where waveform data starts (used by write_v5)."""
|
||
# Re-derive the offset by walking the header fields, since we do not
|
||
# persist data_offset as an attribute from _parse.
|
||
with open(self.path, "rb") as f:
|
||
fields = struct.unpack(HDR_FMT, f.read(HDR_SIZE))
|
||
ver = fields[1]
|
||
n_ch = fields[12]
|
||
n_rows0 = int(self.n_rows[0])
|
||
|
||
with open(self.path, "rb") as f:
|
||
f.seek(HDR_SIZE)
|
||
f.read(self.n_angles * 4) # angles
|
||
f.read(n_rows0 * 4) # y_pos
|
||
if ver >= 3:
|
||
for _ in range(n_ch):
|
||
(length,) = struct.unpack(">H", f.read(2))
|
||
f.read(length)
|
||
if ver >= 4:
|
||
(n_bg,) = struct.unpack(">I", f.read(4))
|
||
f.read(n_bg)
|
||
return f.tell()
|
||
|
||
# ------------------------------------------------------------------
|
||
# Axes helpers
|
||
# ------------------------------------------------------------------
|
||
|
||
@property
|
||
def pixel_x_mm(self) -> float:
|
||
return self.velocity_mm_s / self.laser_freq_hz
|
||
|
||
def x_axis_mm(self, angle_idx: int) -> np.ndarray:
|
||
n = int(self.n_frames[angle_idx])
|
||
return self.x_start_mm[angle_idx] + np.arange(n) * self.pixel_x_mm
|
||
|
||
def y_positions_mm(self, angle_idx: int) -> np.ndarray:
|
||
return self._y_pos_per_angle[angle_idx]
|
||
|
||
def time_axis_ns(self) -> np.ndarray:
|
||
return np.arange(self.samples_per_frame) / self.sample_rate_hz * 1e9
|
||
|
||
def freq_axis_mhz(self, n_fft: int | None = None) -> np.ndarray:
|
||
n = n_fft if n_fft is not None else self.samples_per_frame
|
||
return np.fft.rfftfreq(n, d=1.0 / self.sample_rate_hz) / 1e6
|
||
|
||
|
||
# ---------------------------------------------------------------------------
|
||
# Image computation (vectorised)
|
||
# ---------------------------------------------------------------------------
|
||
|
||
|
||
# Rows are batched so the float32 working buffer for one channel's chunk
|
||
# (chunk_rows × n_frames × spf × 4 bytes) stays under this budget. A fixed
|
||
# row count (the original design) works fine for small legacy scans but is
|
||
# catastrophic for a v6 scan with a large per-angle frame/sample count —
|
||
# e.g. a 7500-frame × 2500-sample angle needs ~2.4 GB for a single 32-row
|
||
# chunk, times several such buffers alive at once for the FFT step, which
|
||
# can exceed physical RAM entirely on its own. Sizing the chunk to the
|
||
# actual dimensions keeps peak RAM bounded regardless of scan size.
|
||
_CHUNK_BYTES_BUDGET = 128 * 1024 * 1024 # ~128 MB per channel-buffer chunk
|
||
_CHUNK_ROWS_MAX = 32 # cap for small scans (old behavior)
|
||
|
||
|
||
def _chunk_rows_for(n_frames: int, samples_per_frame: int) -> int:
|
||
bytes_per_row = max(1, n_frames * samples_per_frame * 4) # float32
|
||
rows = _CHUNK_BYTES_BUDGET // bytes_per_row
|
||
return int(max(1, min(_CHUNK_ROWS_MAX, rows)))
|
||
|
||
|
||
def compute_dc_image(sras: SrasFile, angle_idx: int, ch_idx: int) -> np.ndarray:
|
||
"""Mean of each waveform → (n_rows, n_frames) float32.
|
||
|
||
Processes in row chunks sized to a fixed memory budget (see
|
||
``_chunk_rows_for``) so the float32 working buffer stays bounded
|
||
regardless of scan size.
|
||
"""
|
||
n_rows = int(sras.n_rows[angle_idx])
|
||
n_frames = int(sras.n_frames[angle_idx])
|
||
data = sras.data[angle_idx]
|
||
chunk_rows = _chunk_rows_for(n_frames, sras.samples_per_frame)
|
||
img = np.empty((n_rows, n_frames), dtype=np.float32)
|
||
for r0 in range(0, n_rows, chunk_rows):
|
||
r1 = min(r0 + chunk_rows, n_rows)
|
||
img[r0:r1] = (
|
||
data[r0:r1, ch_idx, :, :]
|
||
.astype(np.float32)
|
||
.mean(axis=-1)
|
||
)
|
||
return img
|
||
|
||
|
||
def compute_rf_image(sras: SrasFile, angle_idx: int,
|
||
dc_threshold_mv: float,
|
||
apply_bg_sub: bool = True,
|
||
n_fft: int | None = None,
|
||
dc4_mv: np.ndarray | None = None) -> np.ndarray:
|
||
"""FFT of each CH1 waveform; pixel = peak frequency in MHz.
|
||
|
||
Pixels where CH4_dc < dc_threshold_mv are set to 0 — and the FFT is
|
||
never run for them, since that's the expensive part. The masked-out
|
||
CH1 samples are also never *read*: the boolean mask is applied to the
|
||
raw memmap slice before any dtype conversion, so numpy only pages in
|
||
the bytes for pixels that pass the threshold (an untouched memmap
|
||
page is never read from disk). If the DC4 image for this angle is
|
||
already known (e.g. from the DC-channel precompute cache), pass it as
|
||
*dc4_mv* (mV, shape (n_rows, n_frames)) to reuse it directly instead
|
||
of re-reading/re-averaging the CH4 channel here; otherwise it's
|
||
computed chunk-by-chunk internally (which does need every pixel's
|
||
CH4 data, since that's what determines validity in the first place).
|
||
|
||
Fast path: if the file contains v5 precomputed peak-frequency images,
|
||
and zero-padding is not active, and the bg-sub flag matches, the stored
|
||
images are used directly — no FFT is run.
|
||
|
||
Otherwise, data is processed in row chunks sized to a fixed memory
|
||
budget (see ``_chunk_rows_for``) to bound peak RAM regardless of scan
|
||
size.
|
||
"""
|
||
n_rows = int(sras.n_rows[angle_idx])
|
||
n_frames = int(sras.n_frames[angle_idx])
|
||
data = sras.data[angle_idx]
|
||
|
||
# ---- Fast path: v5 precomputed images ----------------------------------
|
||
can_use_precomputed = (
|
||
sras.precomputed_freq_mhz is not None
|
||
and n_fft is None # no custom zero-padding
|
||
and sras.precomputed_bg_sub == (apply_bg_sub and sras.background is not None)
|
||
)
|
||
if can_use_precomputed:
|
||
freq_img = sras.precomputed_freq_mhz[angle_idx].copy()
|
||
dc4_img = sras.precomputed_dc4_mv[angle_idx]
|
||
freq_img[dc4_img < dc_threshold_mv] = 0.0
|
||
return freq_img
|
||
|
||
# ---- Chunked FFT path --------------------------------------------------
|
||
freq_axis = sras.freq_axis_mhz(n_fft)
|
||
img = np.zeros((n_rows, n_frames), dtype=np.float32)
|
||
_n_workers = os.cpu_count() or 4
|
||
n_fft_bins = n_fft if n_fft is not None else sras.samples_per_frame
|
||
chunk_rows = _chunk_rows_for(n_frames, max(sras.samples_per_frame, n_fft_bins))
|
||
|
||
for r0 in range(0, n_rows, chunk_rows):
|
||
r1 = min(r0 + chunk_rows, n_rows)
|
||
|
||
# DC mask for this chunk (float32 expansion is only chunk-sized)
|
||
if dc4_mv is not None:
|
||
dc4_chunk = dc4_mv[r0:r1]
|
||
else:
|
||
dc4_raw = data[r0:r1, CH4_IDX, :, :].astype(np.float32)
|
||
dc4_chunk = adc_to_mv(dc4_raw.mean(axis=-1),
|
||
sras.ch_ymult_mv[CH4_IDX],
|
||
sras.ch_yoff_adc[CH4_IDX],
|
||
sras.ch_yzero_mv[CH4_IDX])
|
||
del dc4_raw
|
||
valid = dc4_chunk >= dc_threshold_mv # True = above threshold = run FFT
|
||
|
||
if not valid.any():
|
||
continue
|
||
|
||
# Index the raw memmap slice with the boolean mask *before*
|
||
# converting dtype — this is a lazy view until touched, so only
|
||
# the (n_valid, spf) selected elements are actually read from
|
||
# disk; masked-out pixels' pages are never paged in at all.
|
||
valid_waves = data[r0:r1, CH1_IDX, :, :][valid].astype(np.float32)
|
||
|
||
if apply_bg_sub and sras.background is not None:
|
||
valid_waves -= sras.background # background is 1-D (spf,)
|
||
|
||
fft_pow = np.abs(_do_rfft(valid_waves, n=n_fft, axis=-1, workers=_n_workers)) ** 2
|
||
del valid_waves
|
||
fft_pow[:, 0] = 0.0 # suppress DC bin
|
||
peak_bins = np.argmax(fft_pow, axis=-1)
|
||
del fft_pow
|
||
|
||
img[r0:r1][valid] = freq_axis[peak_bins]
|
||
|
||
return img
|
||
|
||
|
||
# ---------------------------------------------------------------------------
|
||
# Background workers
|
||
# ---------------------------------------------------------------------------
|
||
|
||
class LoadWorker(QObject):
|
||
finished = pyqtSignal(object) # SrasFile | None
|
||
error = pyqtSignal(str)
|
||
|
||
def __init__(self, path: str):
|
||
super().__init__()
|
||
self._path = path
|
||
|
||
def run(self):
|
||
try:
|
||
self.finished.emit(SrasFile(self._path))
|
||
except Exception as exc:
|
||
self.error.emit(str(exc))
|
||
self.finished.emit(None)
|
||
|
||
|
||
class ComputeWorker(QObject):
|
||
"""Computes one displayable image for (angle, channel).
|
||
|
||
For CH1/Velocity (FFT-derived) channels, the FFT is only run for
|
||
pixels whose DC4 (Bias B) mean is at or above dc_threshold_mv — masked
|
||
pixels are left at 0 MHz without ever being FFT'd, since that's the
|
||
expensive part of a scan. If the DC4 image for this angle is already
|
||
known (e.g. from the DC-channel precompute cache), pass it in as
|
||
*dc4_mv* to skip re-reading the CH4 channel from disk entirely.
|
||
|
||
Emits a plain ``np.ndarray`` (already in display units, masked for
|
||
CH1/Velocity) for both DC and FFT-derived channels.
|
||
"""
|
||
finished = pyqtSignal(object)
|
||
error = pyqtSignal(str)
|
||
|
||
def __init__(self, sras: SrasFile, angle_idx: int,
|
||
ch_idx: int,
|
||
apply_bg_sub: bool = True,
|
||
n_fft: int | None = None,
|
||
dc_threshold_mv: float = 0.0,
|
||
dc4_mv: np.ndarray | None = None):
|
||
super().__init__()
|
||
self._sras = sras
|
||
self._angle = angle_idx
|
||
self._ch = ch_idx
|
||
self._apply_bg_sub = apply_bg_sub
|
||
self._n_fft = n_fft
|
||
self._dc_threshold = dc_threshold_mv
|
||
self._dc4_mv = dc4_mv
|
||
|
||
def run(self):
|
||
try:
|
||
if self._ch in (CH1_IDX, VELOCITY_MODE_IDX):
|
||
img = compute_rf_image(
|
||
self._sras, self._angle, dc_threshold_mv=self._dc_threshold,
|
||
apply_bg_sub=self._apply_bg_sub, n_fft=self._n_fft,
|
||
dc4_mv=self._dc4_mv)
|
||
self.finished.emit(img)
|
||
else:
|
||
# DC channels: convert ADC counts → mV
|
||
adc_img = compute_dc_image(self._sras, self._angle, self._ch)
|
||
img = adc_to_mv(adc_img,
|
||
self._sras.ch_ymult_mv[self._ch],
|
||
self._sras.ch_yoff_adc[self._ch],
|
||
self._sras.ch_yzero_mv[self._ch])
|
||
self.finished.emit(img)
|
||
except Exception as exc:
|
||
self.error.emit(str(exc))
|
||
|
||
|
||
class DcPrecomputeWorker(QObject):
|
||
"""Computes CH3/CH4 DC images for every angle in the background.
|
||
|
||
DC images are cheap (a per-waveform mean, no FFT) compared to the
|
||
CH1/Velocity FFT, so precomputing them for the whole file right after
|
||
load makes switching angles instant while on a DC channel, and also
|
||
means the FFT masking step (which needs a DC4 image) rarely has to
|
||
wait on anything. Emits one ``angle_done`` signal per angle as it
|
||
completes rather than waiting for the whole file, so the cache fills
|
||
in progressively.
|
||
"""
|
||
angle_done = pyqtSignal(int, np.ndarray, np.ndarray) # angle_idx, dc3_mv, dc4_mv
|
||
finished = pyqtSignal()
|
||
error = pyqtSignal(str)
|
||
|
||
def __init__(self, sras: SrasFile):
|
||
super().__init__()
|
||
self._sras = sras
|
||
self._stop = False
|
||
|
||
def stop(self):
|
||
self._stop = True
|
||
|
||
def run(self):
|
||
try:
|
||
for a in range(self._sras.n_angles):
|
||
if self._stop:
|
||
break
|
||
dc3_mv = adc_to_mv(
|
||
compute_dc_image(self._sras, a, CH3_IDX),
|
||
self._sras.ch_ymult_mv[CH3_IDX],
|
||
self._sras.ch_yoff_adc[CH3_IDX],
|
||
self._sras.ch_yzero_mv[CH3_IDX])
|
||
dc4_mv = adc_to_mv(
|
||
compute_dc_image(self._sras, a, CH4_IDX),
|
||
self._sras.ch_ymult_mv[CH4_IDX],
|
||
self._sras.ch_yoff_adc[CH4_IDX],
|
||
self._sras.ch_yzero_mv[CH4_IDX])
|
||
self.angle_done.emit(a, dc3_mv, dc4_mv)
|
||
self.finished.emit()
|
||
except Exception as exc:
|
||
self.error.emit(str(exc))
|
||
|
||
|
||
class PreprocessWorker(QObject):
|
||
"""Compute all-angle FFT and DC images and write a v5 file.
|
||
|
||
Emits ``progress(int)`` (0–100) as each angle completes and
|
||
``finished(str)`` with an empty string on success or an error message
|
||
on failure. Only used for v2–v5 source files (uniform geometry).
|
||
"""
|
||
progress = pyqtSignal(int) # 0–100
|
||
finished = pyqtSignal(str) # empty = success, else error message
|
||
|
||
def __init__(self, sras: SrasFile, dest_path: str, apply_bg_sub: bool):
|
||
super().__init__()
|
||
self._sras = sras
|
||
self._dest_path = dest_path
|
||
self._apply_bg_sub = apply_bg_sub
|
||
|
||
def run(self):
|
||
try:
|
||
sras = self._sras
|
||
n = sras.n_angles
|
||
n_rows0 = int(sras.n_rows[0])
|
||
n_frames0 = int(sras.n_frames[0])
|
||
freq_images = np.empty((n, n_rows0, n_frames0), dtype=np.float32)
|
||
dc4_images = np.empty_like(freq_images)
|
||
dc3_images = np.empty_like(freq_images)
|
||
|
||
for aidx in range(n):
|
||
# Compute raw peak-frequency (no DC-threshold masking yet)
|
||
freq_images[aidx] = compute_rf_image(
|
||
sras, aidx, dc_threshold_mv=-1e9, # mask nothing
|
||
apply_bg_sub=self._apply_bg_sub)
|
||
|
||
# DC images (ADC counts → mV)
|
||
dc4_images[aidx] = adc_to_mv(
|
||
compute_dc_image(sras, aidx, CH4_IDX),
|
||
sras.ch_ymult_mv[CH4_IDX],
|
||
sras.ch_yoff_adc[CH4_IDX],
|
||
sras.ch_yzero_mv[CH4_IDX])
|
||
dc3_images[aidx] = adc_to_mv(
|
||
compute_dc_image(sras, aidx, CH3_IDX),
|
||
sras.ch_ymult_mv[CH3_IDX],
|
||
sras.ch_yoff_adc[CH3_IDX],
|
||
sras.ch_yzero_mv[CH3_IDX])
|
||
|
||
self.progress.emit(int((aidx + 1) / n * 90))
|
||
|
||
bg_sub_flag = self._apply_bg_sub and sras.background is not None
|
||
sras.write_v5(
|
||
self._dest_path,
|
||
freq_images, dc4_images, dc3_images,
|
||
bg_sub_applied=bg_sub_flag,
|
||
progress_cb=lambda frac: self.progress.emit(90 + int(frac * 10)),
|
||
)
|
||
self.finished.emit("")
|
||
except Exception as exc:
|
||
self.finished.emit(str(exc))
|
||
|
||
|
||
# ---------------------------------------------------------------------------
|
||
# ROI (free quadrilateral in data coordinates)
|
||
# ---------------------------------------------------------------------------
|
||
|
||
class RoiQuad:
|
||
"""Free quadrilateral defined in data coordinates (mm).
|
||
|
||
Stored as 4 corner points (shape (4, 2)) in CCW order: BL, BR, TR, TL.
|
||
Each corner can be positioned independently, allowing skewed /
|
||
non-orthogonal regions of interest. Because it lives in scan/data
|
||
coords it persists unchanged when the displayed channel/mode switches.
|
||
"""
|
||
|
||
def __init__(self, pts: np.ndarray):
|
||
"""pts : array-like, shape (4, 2)."""
|
||
self._pts = np.asarray(pts, dtype=np.float64).reshape(4, 2).copy()
|
||
|
||
@classmethod
|
||
def from_bbox(cls, x0: float, y0: float,
|
||
x1: float, y1: float) -> "RoiQuad":
|
||
"""Create an axis-aligned rectangle from two opposite corners."""
|
||
lx, rx = min(x0, x1), max(x0, x1)
|
||
by, ty = min(y0, y1), max(y0, y1)
|
||
pts = np.array([[lx, by], [rx, by], [rx, ty], [lx, ty]])
|
||
return cls(pts)
|
||
|
||
def copy(self) -> "RoiQuad":
|
||
return RoiQuad(self._pts.copy())
|
||
|
||
def corners(self) -> np.ndarray:
|
||
"""World-coord corners, shape (4, 2), CCW: BL, BR, TR, TL."""
|
||
return self._pts.copy()
|
||
|
||
def centroid(self) -> np.ndarray:
|
||
"""Mean of the four corners."""
|
||
return self._pts.mean(axis=0)
|
||
|
||
def bbox_size(self) -> np.ndarray:
|
||
"""Width and height of the axis-aligned bounding box, shape (2,)."""
|
||
return self._pts.max(axis=0) - self._pts.min(axis=0)
|
||
|
||
def contains(self, x: float, y: float) -> bool:
|
||
return bool(MplPath(self._pts).contains_point((x, y)))
|
||
|
||
def mask_for_grid(self, x_axis: np.ndarray,
|
||
y_axis: np.ndarray) -> np.ndarray:
|
||
"""Boolean mask (n_rows, n_frames) of pixels whose centres lie
|
||
inside the quadrilateral.
|
||
"""
|
||
X, Y = np.meshgrid(np.asarray(x_axis, dtype=np.float64),
|
||
np.asarray(y_axis, dtype=np.float64))
|
||
points = np.column_stack([X.ravel(), Y.ravel()])
|
||
inside = MplPath(self._pts).contains_points(points)
|
||
return inside.reshape(X.shape)
|
||
|
||
|
||
# ---------------------------------------------------------------------------
|
||
# Matplotlib canvases
|
||
# ---------------------------------------------------------------------------
|
||
|
||
class ImageCanvas(FigureCanvasQTAgg):
|
||
pixel_clicked = pyqtSignal(int, int) # row_idx, frame_idx
|
||
roi_changed = pyqtSignal() # emitted when ROI is created / edited / cleared
|
||
draw_mode_changed = pyqtSignal(bool) # emitted when "draw new ROI" arm toggles
|
||
|
||
# Interaction state values
|
||
_IDLE = "idle"
|
||
_DRAW_NEW = "draw_new"
|
||
_MOVE = "move"
|
||
_DRAG_CORNER = "drag_corner"
|
||
|
||
# Hit tolerance (display pixels) for handles.
|
||
_HANDLE_PX = 12
|
||
_CLICK_THRESH_PX = 4 # releases within this of press count as a click
|
||
|
||
def __init__(self, parent=None):
|
||
fig = Figure(figsize=(7, 5), tight_layout=True)
|
||
self.ax = fig.add_subplot(111)
|
||
super().__init__(fig)
|
||
self.setParent(parent)
|
||
self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding)
|
||
self._extent = None
|
||
self._img_shape = None
|
||
|
||
# ROI state
|
||
self._roi: RoiQuad | None = None
|
||
self._roi_artists: list = []
|
||
self._state = self._IDLE
|
||
self._draw_mode = False
|
||
|
||
# Per-interaction snapshots / anchors
|
||
self._press_xy : tuple[float, float] | None = None
|
||
self._press_pixel : tuple[float, float] | None = None
|
||
self._press_button = None
|
||
self._snapshot : RoiQuad | None = None
|
||
self._drag_corner_idx: int = -1
|
||
self._move_anchor = None # press-point in world coords
|
||
self._draw_previous : RoiQuad | None = None
|
||
|
||
self.mpl_connect("button_press_event", self._on_press)
|
||
self.mpl_connect("motion_notify_event", self._on_motion)
|
||
self.mpl_connect("button_release_event", self._on_release)
|
||
|
||
# ------------------------------------------------------------------
|
||
# Public API
|
||
# ------------------------------------------------------------------
|
||
|
||
def show_image(self, img: np.ndarray, extent: list[float], cmap: str,
|
||
vmin: float, vmax: float, xlabel: str, ylabel: str, title: str,
|
||
colorbar_label: str = ""):
|
||
self.figure.clf()
|
||
self.ax = self.figure.add_subplot(111)
|
||
# Patches and lines are destroyed by figure.clf(); drop stale refs.
|
||
self._roi_artists = []
|
||
|
||
self._extent = extent
|
||
self._img_shape = img.shape
|
||
|
||
im = self.ax.imshow(
|
||
img, aspect="auto", origin="upper",
|
||
extent=extent, cmap=cmap, vmin=vmin, vmax=vmax,
|
||
interpolation="nearest",
|
||
)
|
||
cb = self.figure.colorbar(im, ax=self.ax, fraction=0.046, pad=0.04)
|
||
if colorbar_label:
|
||
cb.set_label(colorbar_label)
|
||
|
||
self.ax.set_xlabel(xlabel)
|
||
self.ax.set_ylabel(ylabel)
|
||
self.ax.set_title(title)
|
||
|
||
# Re-draw the ROI (if any) on top of the fresh image so it persists
|
||
# unchanged across mode / angle / channel switches.
|
||
self._draw_roi()
|
||
self.draw()
|
||
|
||
def get_roi(self) -> RoiQuad | None:
|
||
return self._roi
|
||
|
||
def set_roi(self, roi: RoiQuad | None):
|
||
self._roi = roi.copy() if roi is not None else None
|
||
self._draw_roi()
|
||
self.draw_idle()
|
||
self.roi_changed.emit()
|
||
|
||
def clear_roi(self):
|
||
self._roi = None
|
||
self._remove_roi_artists()
|
||
self.draw_idle()
|
||
self.roi_changed.emit()
|
||
|
||
def start_drawing(self):
|
||
"""Arm the next click+drag on the image to create a new ROI,
|
||
replacing any existing one."""
|
||
self._draw_mode = True
|
||
self.setCursor(Qt.CursorShape.CrossCursor)
|
||
self.draw_mode_changed.emit(True)
|
||
|
||
def cancel_drawing(self):
|
||
if self._draw_mode:
|
||
self._draw_mode = False
|
||
self.setCursor(Qt.CursorShape.ArrowCursor)
|
||
self.draw_mode_changed.emit(False)
|
||
|
||
# ------------------------------------------------------------------
|
||
# Rendering
|
||
# ------------------------------------------------------------------
|
||
|
||
def _remove_roi_artists(self):
|
||
for a in self._roi_artists:
|
||
try:
|
||
a.remove()
|
||
except (ValueError, AttributeError, NotImplementedError):
|
||
pass
|
||
self._roi_artists = []
|
||
|
||
def _draw_roi(self):
|
||
self._remove_roi_artists()
|
||
if self._roi is None or self.ax is None:
|
||
return
|
||
corners = self._roi.corners()
|
||
|
||
# Filled quad outline
|
||
poly = Polygon(corners, closed=True, fill=True,
|
||
facecolor="#ffd93a", edgecolor="#e53935",
|
||
alpha=0.22, linewidth=2.0, zorder=10)
|
||
self.ax.add_patch(poly)
|
||
self._roi_artists.append(poly)
|
||
|
||
# Sharp edge (no fill) for better visibility over bright images
|
||
edge = Polygon(corners, closed=True, fill=False,
|
||
edgecolor="#e53935", linewidth=1.8, zorder=11)
|
||
self.ax.add_patch(edge)
|
||
self._roi_artists.append(edge)
|
||
|
||
# Corner handles (white fill, red edge) — drag each independently
|
||
handles = self.ax.scatter(corners[:, 0], corners[:, 1],
|
||
s=60, c="white", edgecolors="#e53935",
|
||
linewidths=1.6, zorder=13)
|
||
self._roi_artists.append(handles)
|
||
|
||
# ------------------------------------------------------------------
|
||
# Hit testing (uses display pixels for handles, data coords for "inside")
|
||
# ------------------------------------------------------------------
|
||
|
||
def _hit_test(self, event) -> tuple[str, int | None] | None:
|
||
if self._roi is None or self.ax is None:
|
||
return None
|
||
if event.x is None or event.y is None:
|
||
return None
|
||
corners = self._roi.corners()
|
||
corners_disp = self.ax.transData.transform(corners)
|
||
click = np.array([event.x, event.y])
|
||
|
||
for i in range(4):
|
||
if np.hypot(*(corners_disp[i] - click)) <= self._HANDLE_PX:
|
||
return ("corner", i)
|
||
|
||
if event.xdata is not None and event.ydata is not None:
|
||
if self._roi.contains(event.xdata, event.ydata):
|
||
return ("inside", None)
|
||
return None
|
||
|
||
# ------------------------------------------------------------------
|
||
# Mouse event handlers
|
||
# ------------------------------------------------------------------
|
||
|
||
def _on_press(self, event):
|
||
if event.inaxes is not self.ax or self._extent is None:
|
||
return
|
||
if event.button != 1: # only left mouse button
|
||
return
|
||
# If the matplotlib toolbar is in pan / zoom mode, let it handle
|
||
# the interaction instead of starting a ROI manipulation.
|
||
tb = getattr(self, "toolbar", None)
|
||
if tb is not None and getattr(tb, "mode", ""):
|
||
return
|
||
|
||
self._press_xy = (event.xdata, event.ydata)
|
||
self._press_pixel = (event.x, event.y)
|
||
self._press_button = event.button
|
||
|
||
if self._draw_mode:
|
||
self._draw_previous = self._roi.copy() if self._roi else None
|
||
self._roi = RoiQuad.from_bbox(event.xdata, event.ydata,
|
||
event.xdata, event.ydata)
|
||
self._state = self._DRAW_NEW
|
||
self._draw_roi()
|
||
self.draw_idle()
|
||
return
|
||
|
||
hit = self._hit_test(event)
|
||
if hit is None:
|
||
self._state = self._IDLE
|
||
return
|
||
|
||
kind, idx = hit
|
||
self._snapshot = self._roi.copy()
|
||
|
||
if kind == "corner":
|
||
self._state = self._DRAG_CORNER
|
||
self._drag_corner_idx = idx
|
||
elif kind == "inside":
|
||
self._state = self._MOVE
|
||
self._move_anchor = (event.xdata, event.ydata)
|
||
|
||
def _on_motion(self, event):
|
||
if self._state == self._IDLE:
|
||
return
|
||
if event.xdata is None or event.ydata is None:
|
||
return
|
||
if event.inaxes is not self.ax:
|
||
return
|
||
|
||
if self._state == self._DRAW_NEW:
|
||
x0, y0 = self._press_xy
|
||
x1, y1 = event.xdata, event.ydata
|
||
self._roi = RoiQuad.from_bbox(x0, y0, x1, y1)
|
||
|
||
elif self._state == self._MOVE:
|
||
dx = event.xdata - self._move_anchor[0]
|
||
dy = event.ydata - self._move_anchor[1]
|
||
self._roi._pts = self._snapshot.corners() + np.array([dx, dy])
|
||
|
||
elif self._state == self._DRAG_CORNER:
|
||
self._roi._pts[self._drag_corner_idx] = [event.xdata, event.ydata]
|
||
|
||
self._draw_roi()
|
||
self.draw_idle()
|
||
|
||
def _on_release(self, event):
|
||
if event.button != 1 and self._press_button != 1:
|
||
return
|
||
prev_state = self._state
|
||
self._state = self._IDLE
|
||
|
||
if prev_state == self._DRAW_NEW:
|
||
# Reject zero-area or vanishingly-small quads
|
||
if self._extent is not None:
|
||
x0, x1, y_bot, y_top = self._extent
|
||
# Minimum: 1% of each axis range
|
||
min_w = abs(x1 - x0) * 0.01
|
||
min_h = abs(y_bot - y_top) * 0.01
|
||
else:
|
||
min_w = min_h = 1e-6
|
||
if self._roi is not None:
|
||
bbox = self._roi.bbox_size()
|
||
too_small = bbox[0] < min_w or bbox[1] < min_h
|
||
else:
|
||
too_small = True
|
||
if too_small:
|
||
self._roi = self._draw_previous
|
||
self._draw_previous = None
|
||
self.cancel_drawing()
|
||
self._draw_roi()
|
||
self.draw_idle()
|
||
self.roi_changed.emit()
|
||
self._press_xy = self._press_pixel = None
|
||
self._press_button = None
|
||
return
|
||
|
||
if prev_state in (self._MOVE, self._DRAG_CORNER):
|
||
self._draw_roi()
|
||
self.draw_idle()
|
||
self.roi_changed.emit()
|
||
self._press_xy = self._press_pixel = None
|
||
self._press_button = None
|
||
return
|
||
|
||
# IDLE → treat as pixel click if release is close to press
|
||
if (self._press_pixel is not None and event.x is not None and
|
||
event.y is not None and self._extent is not None):
|
||
dx_px = event.x - self._press_pixel[0]
|
||
dy_px = event.y - self._press_pixel[1]
|
||
if (dx_px * dx_px + dy_px * dy_px
|
||
<= self._CLICK_THRESH_PX * self._CLICK_THRESH_PX
|
||
and event.inaxes is self.ax
|
||
and event.xdata is not None):
|
||
x0, x1, y_bot, y_top = self._extent
|
||
n_rows, n_frames = self._img_shape
|
||
col = int((event.xdata - x0) / (x1 - x0) * n_frames)
|
||
row = int((event.ydata - y_top) / (y_bot - y_top) * n_rows)
|
||
col = max(0, min(col, n_frames - 1))
|
||
row = max(0, min(row, n_rows - 1))
|
||
self.pixel_clicked.emit(row, col)
|
||
|
||
self._press_xy = self._press_pixel = None
|
||
self._press_button = None
|
||
|
||
|
||
class WaveformCanvas(FigureCanvasQTAgg):
|
||
def __init__(self, parent=None):
|
||
fig = Figure(figsize=(8, 3), tight_layout=True)
|
||
self.ax_wave = fig.add_subplot(121)
|
||
self.ax_right = fig.add_subplot(122)
|
||
super().__init__(fig)
|
||
self.setParent(parent)
|
||
self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding)
|
||
|
||
def show_rf_waveform(self, sras: SrasFile, angle_idx: int,
|
||
row_idx: int, frame_idx: int,
|
||
apply_bg_sub: bool = True):
|
||
"""CH1 RF: time-domain + FFT spectrum.
|
||
|
||
If apply_bg_sub is True and sras.background is not None, the background
|
||
waveform is overlaid on the time-domain plot and the FFT is computed
|
||
on the subtracted signal. The unsubtracted FFT is also shown faintly
|
||
for comparison.
|
||
"""
|
||
data = sras.data[angle_idx]
|
||
waveform = data[row_idx, CH1_IDX, frame_idx, :].astype(np.float32)
|
||
t_ns = sras.time_axis_ns()
|
||
f_mhz = sras.freq_axis_mhz()
|
||
dc3_val = data[row_idx, CH3_IDX, frame_idx, :].astype(np.float32).mean()
|
||
dc4_val = data[row_idx, CH4_IDX, frame_idx, :].astype(np.float32).mean()
|
||
|
||
bg = sras.background if (apply_bg_sub and sras.background is not None) else None
|
||
waveform_plot = waveform - bg if bg is not None else waveform
|
||
|
||
self.ax_wave.cla()
|
||
self.ax_right.cla()
|
||
|
||
if bg is not None:
|
||
self.ax_wave.plot(t_ns, waveform, linewidth=0.5, color="#aaaaaa",
|
||
label="raw", zorder=1)
|
||
self.ax_wave.plot(t_ns, bg, linewidth=0.5, color="#e07030",
|
||
linestyle="--", label="background", zorder=2)
|
||
self.ax_wave.plot(t_ns, waveform_plot, linewidth=0.7, color="#4488cc",
|
||
label="subtracted", zorder=3)
|
||
self.ax_wave.legend(fontsize=7, loc="upper right")
|
||
else:
|
||
self.ax_wave.plot(t_ns, waveform, linewidth=0.7, color="#4488cc")
|
||
|
||
self.ax_wave.set_xlabel("Time (ns)")
|
||
self.ax_wave.set_ylabel("ADC counts")
|
||
bg_tag = " [bg sub]" if bg is not None else ""
|
||
self.ax_wave.set_title(
|
||
f"CH1 RF row={row_idx} frame={frame_idx}{bg_tag}\n"
|
||
f"CH3={dc3_val:.1f} CH4={dc4_val:.1f} "
|
||
f"({adc_to_mv(dc3_val, sras.ch_ymult_mv[CH3_IDX], sras.ch_yoff_adc[CH3_IDX], sras.ch_yzero_mv[CH3_IDX]):.2f} / "
|
||
f"{adc_to_mv(dc4_val, sras.ch_ymult_mv[CH4_IDX], sras.ch_yoff_adc[CH4_IDX], sras.ch_yzero_mv[CH4_IDX]):.2f} mV)",
|
||
fontsize=8,
|
||
)
|
||
|
||
# FFT of the (possibly subtracted) waveform
|
||
power_sub = np.abs(np.fft.rfft(waveform_plot)) ** 2
|
||
power_sub[0] = 0.0
|
||
peak_idx = int(np.argmax(power_sub))
|
||
peak_mhz = f_mhz[peak_idx]
|
||
|
||
if bg is not None:
|
||
# Also show the unsubtracted FFT for reference
|
||
power_raw = np.abs(np.fft.rfft(waveform)) ** 2
|
||
power_raw[0] = 0.0
|
||
self.ax_right.plot(f_mhz, power_raw, linewidth=0.5, color="#aaaaaa",
|
||
label="raw FFT", zorder=1)
|
||
|
||
self.ax_right.plot(f_mhz, power_sub, linewidth=0.7, color="#4488cc",
|
||
label="subtracted FFT" if bg is not None else None, zorder=2)
|
||
self.ax_right.axvline(peak_mhz, color="tomato", linestyle="--",
|
||
linewidth=1.2, label=f"peak = {peak_mhz:.1f} MHz")
|
||
self.ax_right.set_xlabel("Frequency (MHz)")
|
||
self.ax_right.set_ylabel("Power (arb.)")
|
||
self.ax_right.set_title("FFT Power Spectrum")
|
||
self.ax_right.set_xlim(0, 500)
|
||
self.ax_right.legend(fontsize=8)
|
||
|
||
self.draw()
|
||
|
||
def show_dc_waveform(self, sras: SrasFile, angle_idx: int, ch_idx: int,
|
||
row_idx: int, frame_idx: int):
|
||
"""CH3 or CH4 DC: time-domain + mean annotation."""
|
||
waveform = sras.data[angle_idx][row_idx, ch_idx, frame_idx, :].astype(np.float32)
|
||
t_ns = sras.time_axis_ns()
|
||
mean_val = float(waveform.mean())
|
||
mean_mv = adc_to_mv(mean_val, sras.ch_ymult_mv[ch_idx], sras.ch_yoff_adc[ch_idx],
|
||
sras.ch_yzero_mv[ch_idx])
|
||
|
||
self.ax_wave.cla()
|
||
self.ax_right.cla()
|
||
|
||
self.ax_wave.plot(t_ns, waveform, linewidth=0.7, color="#4488cc")
|
||
self.ax_wave.axhline(mean_val, color="tomato", linestyle="--",
|
||
linewidth=1.2, label=f"mean = {mean_val:.2f} ADC")
|
||
self.ax_wave.set_xlabel("Time (ns)")
|
||
self.ax_wave.set_ylabel("ADC counts")
|
||
self.ax_wave.set_title(
|
||
f"{CH_NAMES[ch_idx]} DC row={row_idx} frame={frame_idx}"
|
||
)
|
||
self.ax_wave.legend(fontsize=8)
|
||
|
||
self.ax_right.text(
|
||
0.5, 0.5,
|
||
f"DC mode\n\n"
|
||
f"mean = {mean_val:.3f} ADC\n"
|
||
f" = {mean_mv:.3f} mV",
|
||
ha="center", va="center",
|
||
transform=self.ax_right.transAxes, fontsize=11,
|
||
)
|
||
self.ax_right.set_axis_off()
|
||
|
||
self.draw()
|
||
|
||
|
||
# ---------------------------------------------------------------------------
|
||
# FFT Options dialog
|
||
# ---------------------------------------------------------------------------
|
||
|
||
class FftOptionsDialog(QDialog):
|
||
"""Configure FFT backend and zero-padding.
|
||
|
||
Changes take effect only when the user clicks Apply. Cancel discards
|
||
all pending edits. The live 'frequency resolution' label updates as
|
||
the user adjusts the pad factor so they can see the trade-off before
|
||
committing.
|
||
"""
|
||
|
||
def __init__(self, parent=None, *,
|
||
current_backend: str,
|
||
current_pad_factor: int,
|
||
samples_per_frame: int | None,
|
||
sample_rate_hz: float | None,
|
||
grating_um: float):
|
||
super().__init__(parent)
|
||
self.setWindowTitle("FFT Options")
|
||
self.setModal(True)
|
||
self.setMinimumWidth(380)
|
||
|
||
self._samples_per_frame = samples_per_frame
|
||
self._sample_rate_hz = sample_rate_hz
|
||
self._grating_um = grating_um
|
||
|
||
layout = QVBoxLayout(self)
|
||
|
||
# ---- Backend ---------------------------------------------------
|
||
grp_backend = QGroupBox("FFT Backend")
|
||
bl = QVBoxLayout(grp_backend)
|
||
|
||
self._btn_numpy = QRadioButton(
|
||
"NumPy FFT (always available)")
|
||
self._btn_pyfftw = QRadioButton(
|
||
"pyFFTW (faster for large arrays)" if _pyfftw_available
|
||
else "pyFFTW (not installed — run: pip install pyfftw)")
|
||
self._btn_pyfftw.setEnabled(_pyfftw_available)
|
||
|
||
self._backend_group = QButtonGroup(self)
|
||
self._backend_group.addButton(self._btn_numpy, id=0)
|
||
self._backend_group.addButton(self._btn_pyfftw, id=1)
|
||
|
||
if current_backend == "pyfftw" and _pyfftw_available:
|
||
self._btn_pyfftw.setChecked(True)
|
||
else:
|
||
self._btn_numpy.setChecked(True)
|
||
|
||
bl.addWidget(self._btn_numpy)
|
||
bl.addWidget(self._btn_pyfftw)
|
||
layout.addWidget(grp_backend)
|
||
|
||
# ---- Zero-padding ----------------------------------------------
|
||
grp_zp = QGroupBox("Zero-Padding")
|
||
zl = QVBoxLayout(grp_zp)
|
||
|
||
pad_row = QHBoxLayout()
|
||
pad_row.addWidget(QLabel("Pad factor:"))
|
||
self._spin_pad = QSpinBox()
|
||
self._spin_pad.setRange(1, 256)
|
||
self._spin_pad.setValue(max(1, current_pad_factor))
|
||
self._spin_pad.setToolTip(
|
||
"Multiply the waveform length by this factor via zero-padding\n"
|
||
"before computing the FFT.\n"
|
||
"1 = no padding (natural length).\n"
|
||
"Powers of 2 (2, 4, 8 …) give the best performance."
|
||
)
|
||
self._spin_pad.valueChanged.connect(self._update_info)
|
||
pad_row.addWidget(self._spin_pad)
|
||
zl.addLayout(pad_row)
|
||
|
||
self._lbl_nfft = QLabel()
|
||
self._lbl_freq_res = QLabel()
|
||
self._lbl_vel_res = QLabel()
|
||
for lbl in (self._lbl_nfft, self._lbl_freq_res, self._lbl_vel_res):
|
||
lbl.setStyleSheet("font-size: 11px; color: #aaa;")
|
||
zl.addWidget(lbl)
|
||
|
||
layout.addWidget(grp_zp)
|
||
|
||
# ---- Buttons ---------------------------------------------------
|
||
buttons = QDialogButtonBox()
|
||
self._apply_btn = buttons.addButton(
|
||
"Apply", QDialogButtonBox.ButtonRole.AcceptRole)
|
||
self._cancel_btn = buttons.addButton(
|
||
"Cancel", QDialogButtonBox.ButtonRole.RejectRole)
|
||
self._apply_btn.clicked.connect(self.accept)
|
||
self._cancel_btn.clicked.connect(self.reject)
|
||
layout.addWidget(buttons)
|
||
|
||
self._update_info()
|
||
|
||
# ------------------------------------------------------------------
|
||
|
||
def _update_info(self):
|
||
spf = self._samples_per_frame
|
||
sr = self._sample_rate_hz
|
||
pad = self._spin_pad.value()
|
||
|
||
if spf is None or sr is None:
|
||
self._lbl_nfft.setText("Load a file to preview FFT parameters.")
|
||
self._lbl_freq_res.setText("")
|
||
self._lbl_vel_res.setText("")
|
||
return
|
||
|
||
n_fft = spf * pad
|
||
freq_res_hz = sr / n_fft
|
||
freq_res_mhz = freq_res_hz / 1e6
|
||
# v (m/s) = freq (MHz) × grating (µm)
|
||
vel_res_ms = freq_res_mhz * self._grating_um
|
||
|
||
self._lbl_nfft.setText(
|
||
f"FFT points: {spf} × {pad} = {n_fft:,}")
|
||
self._lbl_freq_res.setText(
|
||
f"Frequency bin: {freq_res_mhz:.4f} MHz ({freq_res_hz / 1e3:.2f} kHz)")
|
||
self._lbl_vel_res.setText(
|
||
f"Velocity bin: {vel_res_ms:.3f} m/s "
|
||
f"(at grating = {self._grating_um:.2f} µm)")
|
||
|
||
def get_backend(self) -> str:
|
||
return "pyfftw" if self._btn_pyfftw.isChecked() and _pyfftw_available else "numpy"
|
||
|
||
def get_pad_factor(self) -> int:
|
||
return max(1, self._spin_pad.value())
|
||
|
||
|
||
# ---------------------------------------------------------------------------
|
||
# Main window
|
||
# ---------------------------------------------------------------------------
|
||
|
||
class SrasViewerWindow(QMainWindow):
|
||
def __init__(self, initial_path: str | None = None):
|
||
super().__init__()
|
||
self.setWindowTitle("SRAS Scan Viewer")
|
||
self.resize(1560, 840)
|
||
self.setAcceptDrops(True)
|
||
|
||
self._sras: SrasFile | None = None
|
||
self._current_image: np.ndarray | None = None
|
||
self._current_angle: int = 0
|
||
self._current_ch: int = 0
|
||
self._load_thread: QThread | None = None
|
||
self._compute_thread: QThread | None = None
|
||
self._pending_angle: int = 0
|
||
self._pending_ch: int = 0
|
||
self._pending_bg_sub: bool = True
|
||
self._pending_threshold: float = 50.0 # mV
|
||
self._progress_dlg: QProgressDialog | None = None
|
||
|
||
# FFT settings (configured via FFT Options dialog)
|
||
self._fft_pad_factor: int = 1 # 1 = no padding
|
||
self._pending_fft_pad_factor: int = 1
|
||
|
||
self._preprocess_thread: QThread | None = None
|
||
|
||
# Display-only settings (colormap, grating) never trigger a
|
||
# recompute — they're applied to cached data on redraw. DC images
|
||
# (CH3/CH4) are cheap and precomputed for every angle in the
|
||
# background right after load. CH1/Velocity FFT images are
|
||
# computed lazily (with a progress popup) the first time an
|
||
# angle/threshold combination is viewed — using the cached DC4
|
||
# image to skip the FFT entirely for masked-out pixels — and
|
||
# cached per (angle, bg_sub, n_fft, threshold) so revisiting the
|
||
# same combination is free.
|
||
self._dc_cache: dict[tuple[int, int], np.ndarray] = {}
|
||
self._fft_cache: dict[tuple[int, bool, int | None, float], np.ndarray] = {}
|
||
self._dc_precompute_thread: QThread | None = None
|
||
self._dc_precompute_worker: DcPrecomputeWorker | None = None
|
||
self._dc_generation: int = 0
|
||
|
||
self._build_ui()
|
||
|
||
if initial_path:
|
||
self._load_file(initial_path)
|
||
|
||
# ------------------------------------------------------------------
|
||
# UI construction
|
||
# ------------------------------------------------------------------
|
||
|
||
def _build_ui(self):
|
||
central = QWidget()
|
||
self.setCentralWidget(central)
|
||
root = QHBoxLayout(central)
|
||
root.setContentsMargins(8, 8, 8, 8)
|
||
root.setSpacing(8)
|
||
|
||
# ---- Left control panel ----------------------------------------
|
||
panel = QWidget()
|
||
panel.setFixedWidth(260)
|
||
panel_layout = QVBoxLayout(panel)
|
||
panel_layout.setContentsMargins(0, 0, 0, 0)
|
||
panel_layout.setSpacing(6)
|
||
root.addWidget(panel)
|
||
|
||
# File
|
||
grp_file = QGroupBox("File")
|
||
fl = QVBoxLayout(grp_file)
|
||
self.btn_open = QPushButton("Open .sras…")
|
||
self.btn_open.clicked.connect(self._on_open)
|
||
self.lbl_filename = QLabel("No file loaded")
|
||
self.lbl_filename.setWordWrap(True)
|
||
self.lbl_filename.setStyleSheet("color: #888; font-size: 11px;")
|
||
fl.addWidget(self.btn_open)
|
||
fl.addWidget(self.lbl_filename)
|
||
panel_layout.addWidget(grp_file)
|
||
|
||
# Scan info
|
||
grp_info = QGroupBox("Scan Info")
|
||
il = QVBoxLayout(grp_info)
|
||
self._info = {}
|
||
for key in ("Angles", "Rows", "Frames / row", "Samples / frame",
|
||
"Sample rate", "X start", "Pixel Δx", "Laser freq"):
|
||
lbl = QLabel(f"{key}: —")
|
||
lbl.setWordWrap(True)
|
||
lbl.setStyleSheet("font-size: 11px;")
|
||
il.addWidget(lbl)
|
||
self._info[key] = lbl
|
||
# Frame count warning (hidden until needed)
|
||
self.lbl_frame_warn = QLabel("")
|
||
self.lbl_frame_warn.setWordWrap(True)
|
||
self.lbl_frame_warn.setStyleSheet("color: #e07000; font-size: 11px;")
|
||
il.addWidget(self.lbl_frame_warn)
|
||
# Background DC-precompute progress (hidden until a file is loaded)
|
||
self.lbl_dc_precompute = QLabel("")
|
||
self.lbl_dc_precompute.setWordWrap(True)
|
||
self.lbl_dc_precompute.setStyleSheet("color: #4a90d9; font-size: 11px;")
|
||
il.addWidget(self.lbl_dc_precompute)
|
||
panel_layout.addWidget(grp_info)
|
||
|
||
# View settings
|
||
grp_view = QGroupBox("View Settings")
|
||
vl = QVBoxLayout(grp_view)
|
||
|
||
# Angle
|
||
ar = QHBoxLayout()
|
||
ar.addWidget(QLabel("Angle:"))
|
||
self.spin_angle = QSpinBox()
|
||
self.spin_angle.setRange(0, 0)
|
||
self.spin_angle.setEnabled(False)
|
||
self.spin_angle.editingFinished.connect(self._on_view_changed)
|
||
self.lbl_angle_deg = QLabel("—")
|
||
ar.addWidget(self.spin_angle)
|
||
ar.addWidget(self.lbl_angle_deg)
|
||
vl.addLayout(ar)
|
||
|
||
# Channel
|
||
cr = QHBoxLayout()
|
||
cr.addWidget(QLabel("Channel:"))
|
||
self.combo_channel = QComboBox()
|
||
self.combo_channel.addItems(CH_LABELS)
|
||
self.combo_channel.setEnabled(False)
|
||
self.combo_channel.currentIndexChanged.connect(self._on_channel_changed)
|
||
cr.addWidget(self.combo_channel)
|
||
vl.addLayout(cr)
|
||
|
||
# DC threshold (for RF / CH1 masking)
|
||
sep = QFrame()
|
||
sep.setFrameShape(QFrame.Shape.HLine)
|
||
sep.setStyleSheet("color: #555;")
|
||
vl.addWidget(sep)
|
||
|
||
self.grp_threshold = QGroupBox("RF Mask Threshold (CH1 only)")
|
||
tl = QVBoxLayout(self.grp_threshold)
|
||
thr_row = QHBoxLayout()
|
||
thr_row.addWidget(QLabel("DC threshold:"))
|
||
self.spin_threshold_mv = QDoubleSpinBox()
|
||
self.spin_threshold_mv.setRange(-500.0, 500.0)
|
||
self.spin_threshold_mv.setDecimals(3)
|
||
self.spin_threshold_mv.setSingleStep(0.025)
|
||
self.spin_threshold_mv.setSuffix(" mV")
|
||
self.spin_threshold_mv.setValue(50.0)
|
||
self.spin_threshold_mv.setEnabled(False)
|
||
self.spin_threshold_mv.editingFinished.connect(self._on_threshold_changed)
|
||
thr_row.addWidget(self.spin_threshold_mv)
|
||
tl.addLayout(thr_row)
|
||
self.lbl_threshold_adc = QLabel(f"≈ {mv_to_adc(50.0):.1f} ADC counts") # updated on file load
|
||
self.lbl_threshold_adc.setStyleSheet("font-size: 11px; color: #888;")
|
||
tl.addWidget(self.lbl_threshold_adc)
|
||
vl.addWidget(self.grp_threshold)
|
||
|
||
# Background subtraction (v4+ files only)
|
||
self.chk_bg_sub = QCheckBox("Background subtraction (CH1 only)")
|
||
self.chk_bg_sub.setChecked(True)
|
||
self.chk_bg_sub.setEnabled(False)
|
||
self.chk_bg_sub.setToolTip(
|
||
"Subtract the stored background waveform from each CH1 frame\n"
|
||
"before computing the FFT (v4+ files only)."
|
||
)
|
||
self.chk_bg_sub.toggled.connect(self._on_bg_sub_toggled)
|
||
vl.addWidget(self.chk_bg_sub)
|
||
|
||
# Velocity settings (visible only in velocity mode)
|
||
self.grp_velocity = QGroupBox("Velocity Settings (CH1 only)")
|
||
vel_l = QVBoxLayout(self.grp_velocity)
|
||
grat_row = QHBoxLayout()
|
||
grat_row.addWidget(QLabel("Grating size:"))
|
||
self.spin_grating_um = QDoubleSpinBox()
|
||
self.spin_grating_um.setRange(0.1, 1000.0)
|
||
self.spin_grating_um.setDecimals(2)
|
||
self.spin_grating_um.setSingleStep(0.5)
|
||
self.spin_grating_um.setSuffix(" µm")
|
||
self.spin_grating_um.setValue(25)
|
||
self.spin_grating_um.setEnabled(False)
|
||
self.spin_grating_um.editingFinished.connect(self._on_grating_changed)
|
||
grat_row.addWidget(self.spin_grating_um)
|
||
vel_l.addLayout(grat_row)
|
||
self.lbl_velocity_formula = QLabel("v (m/s) = freq (MHz) × grating (µm)")
|
||
self.lbl_velocity_formula.setStyleSheet("font-size: 10px; color: #888;")
|
||
vel_l.addWidget(self.lbl_velocity_formula)
|
||
self.grp_velocity.setVisible(False)
|
||
# (grp_velocity will be added to the right panel below)
|
||
|
||
# Export
|
||
self.btn_export_csv = QPushButton("Export Image as CSV…")
|
||
self.btn_export_csv.setEnabled(False)
|
||
self.btn_export_csv.setToolTip(
|
||
"Save the current CH1 image (one scan row per CSV line)."
|
||
)
|
||
self.btn_export_csv.clicked.connect(self._on_export_csv)
|
||
vl.addWidget(self.btn_export_csv)
|
||
|
||
panel_layout.addWidget(grp_view)
|
||
|
||
# ---- ROI (Region of Interest) ---------------------------------
|
||
grp_roi = QGroupBox("ROI (Region of Interest)")
|
||
rl = QVBoxLayout(grp_roi)
|
||
|
||
self.btn_draw_roi = QPushButton("Draw ROI")
|
||
self.btn_draw_roi.setCheckable(True)
|
||
self.btn_draw_roi.setEnabled(False)
|
||
self.btn_draw_roi.setToolTip(
|
||
"Arm next click+drag on the image to draw a new ROI\n"
|
||
"(replaces any existing one). Click again to cancel.\n"
|
||
"After drawing, drag inside to move, grab corners to resize,\n"
|
||
"or use the handle above the top edge to rotate.\n"
|
||
"The ROI is persistent across channels / modes / angles."
|
||
)
|
||
self.btn_draw_roi.toggled.connect(self._on_draw_roi_toggled)
|
||
rl.addWidget(self.btn_draw_roi)
|
||
|
||
self.btn_clear_roi = QPushButton("Clear ROI")
|
||
self.btn_clear_roi.setEnabled(False)
|
||
self.btn_clear_roi.clicked.connect(self._on_clear_roi)
|
||
rl.addWidget(self.btn_clear_roi)
|
||
|
||
self.btn_export_roi = QPushButton("Export ROI as CSV…")
|
||
self.btn_export_roi.setEnabled(False)
|
||
self.btn_export_roi.setToolTip(
|
||
"Save every pixel whose centre lies inside the ROI as CSV.\n"
|
||
"Columns: row, frame, x_mm, y_mm, value.\n"
|
||
"Corner coordinates of the quad are written in the file header."
|
||
)
|
||
self.btn_export_roi.clicked.connect(self._on_export_roi_csv)
|
||
rl.addWidget(self.btn_export_roi)
|
||
|
||
self.lbl_roi_center = QLabel("centroid: —")
|
||
self.lbl_roi_size = QLabel("bbox: —")
|
||
self.lbl_roi_npix = QLabel("pixels inside: —")
|
||
for lbl in (self.lbl_roi_center, self.lbl_roi_size, self.lbl_roi_npix):
|
||
lbl.setStyleSheet("font-size: 11px; color: #aaa;")
|
||
rl.addWidget(lbl)
|
||
|
||
panel_layout.addWidget(grp_roi)
|
||
panel_layout.addStretch()
|
||
|
||
# ---- Display Options group (added to right panel below) ------------
|
||
grp_display = QGroupBox("Display Options")
|
||
dl = QVBoxLayout(grp_display)
|
||
|
||
cmr = QHBoxLayout()
|
||
cmr.addWidget(QLabel("Colormap:"))
|
||
self.combo_cmap = QComboBox()
|
||
self.combo_cmap.addItems(CMAPS)
|
||
self.combo_cmap.setCurrentText("gray")
|
||
self.combo_cmap.setEnabled(False)
|
||
self.combo_cmap.currentIndexChanged.connect(self._on_cmap_changed)
|
||
cmr.addWidget(self.combo_cmap)
|
||
dl.addLayout(cmr)
|
||
|
||
self.chk_auto = QCheckBox("Auto-scale colormap")
|
||
self.chk_auto.setChecked(True)
|
||
self.chk_auto.toggled.connect(self._on_autoscale_toggled)
|
||
dl.addWidget(self.chk_auto)
|
||
|
||
for label, attr in (("min:", "spin_vmin"), ("max:", "spin_vmax")):
|
||
row = QHBoxLayout()
|
||
row.addWidget(QLabel(label))
|
||
spin = QDoubleSpinBox()
|
||
spin.setRange(-1e9, 1e9)
|
||
spin.setDecimals(4)
|
||
spin.setEnabled(False)
|
||
spin.editingFinished.connect(self._on_manual_range_changed)
|
||
setattr(self, attr, spin)
|
||
row.addWidget(spin)
|
||
dl.addLayout(row)
|
||
|
||
# ---- Right: image + waveform splitter --------------------------
|
||
splitter = QSplitter(Qt.Orientation.Vertical)
|
||
root.addWidget(splitter, stretch=1)
|
||
|
||
# Image canvas
|
||
img_widget = QWidget()
|
||
img_vl = QVBoxLayout(img_widget)
|
||
img_vl.setContentsMargins(0, 0, 0, 0)
|
||
self.image_canvas = ImageCanvas()
|
||
self.image_canvas.pixel_clicked.connect(self._on_pixel_clicked)
|
||
self.image_canvas.roi_changed.connect(self._on_roi_changed)
|
||
self.image_canvas.draw_mode_changed.connect(self._on_draw_mode_changed)
|
||
toolbar = NavigationToolbar2QT(self.image_canvas, img_widget)
|
||
img_vl.addWidget(toolbar)
|
||
img_vl.addWidget(self.image_canvas)
|
||
splitter.addWidget(img_widget)
|
||
|
||
# Waveform inspector
|
||
wave_widget = QWidget()
|
||
wave_vl = QVBoxLayout(wave_widget)
|
||
wave_vl.setContentsMargins(0, 0, 0, 0)
|
||
self.lbl_wave_hint = QLabel(
|
||
"Click a pixel in the image above to inspect its waveform."
|
||
)
|
||
self.lbl_wave_hint.setAlignment(Qt.AlignmentFlag.AlignCenter)
|
||
self.lbl_wave_hint.setStyleSheet("color: #888; font-size: 11px;")
|
||
self.wave_canvas = WaveformCanvas()
|
||
wave_vl.addWidget(self.lbl_wave_hint)
|
||
wave_vl.addWidget(self.wave_canvas)
|
||
splitter.addWidget(wave_widget)
|
||
|
||
splitter.setSizes([580, 250])
|
||
|
||
# ---- Right control panel -------------------------------------------
|
||
right_panel = QWidget()
|
||
right_panel.setFixedWidth(270)
|
||
right_panel_layout = QVBoxLayout(right_panel)
|
||
right_panel_layout.setContentsMargins(0, 0, 0, 0)
|
||
right_panel_layout.setSpacing(6)
|
||
right_panel_layout.addWidget(self.grp_velocity)
|
||
right_panel_layout.addWidget(grp_display)
|
||
right_panel_layout.addStretch()
|
||
root.addWidget(right_panel)
|
||
|
||
self.statusBar().showMessage("Open an .sras file to begin.")
|
||
|
||
# ---- Menu bar ----------------------------------------------------------
|
||
menubar = self.menuBar()
|
||
fft_menu = menubar.addMenu("&FFT")
|
||
fft_act = QAction("FFT &Options…", self)
|
||
fft_act.setStatusTip("Configure FFT backend and zero-padding")
|
||
fft_act.triggered.connect(self._on_fft_options)
|
||
fft_menu.addAction(fft_act)
|
||
|
||
fft_menu.addSeparator()
|
||
self._preprocess_act = QAction("&Pre-process and Save as v5…", self)
|
||
self._preprocess_act.setStatusTip(
|
||
"Compute FFT and DC images for all angles and save to a v5 file "
|
||
"for instant re-opening (no FFT on load). Not available for v6 files.")
|
||
self._preprocess_act.setEnabled(False)
|
||
self._preprocess_act.triggered.connect(self._on_preprocess)
|
||
fft_menu.addAction(self._preprocess_act)
|
||
|
||
# ------------------------------------------------------------------
|
||
# Drag-and-drop
|
||
# ------------------------------------------------------------------
|
||
|
||
def dragEnterEvent(self, event):
|
||
urls = event.mimeData().urls()
|
||
if urls and urls[0].toLocalFile().lower().endswith(".sras"):
|
||
event.acceptProposedAction()
|
||
|
||
def dropEvent(self, event):
|
||
self._load_file(event.mimeData().urls()[0].toLocalFile())
|
||
|
||
# ------------------------------------------------------------------
|
||
# File loading
|
||
# ------------------------------------------------------------------
|
||
|
||
def _on_open(self):
|
||
path, _ = QFileDialog.getOpenFileName(
|
||
self, "Open SRAS File", "", "SRAS Files (*.sras);;All Files (*)"
|
||
)
|
||
if path:
|
||
self._load_file(path)
|
||
|
||
def _load_file(self, path: str):
|
||
if self._load_thread is not None:
|
||
return
|
||
# Claim self._load_thread before any call below that can pump the
|
||
# Qt event loop — see the comment in _start_compute for why.
|
||
self._load_worker = LoadWorker(path)
|
||
self._load_thread = QThread()
|
||
self._load_worker.moveToThread(self._load_thread)
|
||
self._load_thread.started.connect(self._load_worker.run)
|
||
self._load_worker.finished.connect(self._on_load_done)
|
||
self._load_worker.error.connect(
|
||
lambda msg: self.statusBar().showMessage(f"Error: {msg}")
|
||
)
|
||
self._load_worker.finished.connect(self._load_thread.quit)
|
||
self._load_thread.finished.connect(self._on_load_thread_finished)
|
||
|
||
self.btn_open.setEnabled(False)
|
||
self.statusBar().showMessage(f"Loading {Path(path).name}…")
|
||
self._show_progress(f"Loading {Path(path).name}…")
|
||
|
||
self._load_thread.start()
|
||
|
||
def _on_load_thread_finished(self):
|
||
# See the comment in _on_compute_thread_finished: wait() before
|
||
# releasing our reference to avoid destroying a QThread whose OS
|
||
# thread hasn't fully joined yet.
|
||
if self._load_thread is not None:
|
||
self._load_thread.wait()
|
||
self._load_thread = None
|
||
|
||
def _on_load_done(self, sras):
|
||
self._close_progress()
|
||
self.btn_open.setEnabled(True)
|
||
if sras is None:
|
||
return
|
||
self._sras = sras
|
||
self._current_image = None
|
||
|
||
# Caches (and any in-flight DC precompute) belong to the previous
|
||
# file's geometry — discard and start fresh.
|
||
self._dc_cache = {}
|
||
self._fft_cache = {}
|
||
self.lbl_dc_precompute.setText("")
|
||
|
||
# A ROI from the previous file no longer matches the new scan's
|
||
# geometry, so discard it on every load.
|
||
self.image_canvas.clear_roi()
|
||
|
||
self.lbl_filename.setText(sras.path.name)
|
||
|
||
self.spin_angle.blockSignals(True)
|
||
self.spin_angle.setRange(0, max(0, sras.n_angles - 1))
|
||
self.spin_angle.setValue(0)
|
||
self.spin_angle.blockSignals(False)
|
||
|
||
# DC channels are cheap and give an instant, fluid overview of a
|
||
# scan; CH1/Velocity require an FFT per pixel that can take minutes
|
||
# on a large scan, so don't default to it.
|
||
self.combo_channel.blockSignals(True)
|
||
self.combo_channel.setCurrentIndex(CH4_IDX)
|
||
self.combo_channel.blockSignals(False)
|
||
|
||
self._update_controls_enabled(True)
|
||
# Refresh the ADC-count label now that we have file calibration
|
||
self._on_threshold_changed()
|
||
self._on_view_changed()
|
||
|
||
# Precompute DC images for every angle in the background so
|
||
# switching angles while viewing a DC channel is instant, and the
|
||
# FFT masking step rarely has to wait on a DC4 image either.
|
||
self._start_dc_precompute()
|
||
|
||
# ------------------------------------------------------------------
|
||
# Scan info panel
|
||
# ------------------------------------------------------------------
|
||
|
||
def _update_scan_info_labels(self):
|
||
s = self._sras
|
||
if s is None:
|
||
return
|
||
angle_idx = self.spin_angle.value()
|
||
self._info["Angles"].setText(f"Angles: {s.n_angles}")
|
||
self._info["Rows"].setText(f"Rows: {s.n_rows[angle_idx]}")
|
||
self._info["Frames / row"].setText(f"Frames / row: {s.n_frames[angle_idx]}")
|
||
self._info["Samples / frame"].setText(f"Samples / frame: {s.samples_per_frame}")
|
||
self._info["Sample rate"].setText(f"Sample rate: {s.sample_rate_hz/1e9:.4g} GS/s")
|
||
self._info["X start"].setText(f"X start: {s.x_start_mm[angle_idx]:.4g} mm")
|
||
self._info["Pixel Δx"].setText(f"Pixel Δx: {s.pixel_x_mm*1e3:.3g} µm")
|
||
self._info["Laser freq"].setText(f"Laser freq: {s.laser_freq_hz/1e3:.4g} kHz")
|
||
|
||
notes = []
|
||
if s.frame_count_mismatch:
|
||
notes.append(
|
||
f"! Header n_frames={s.n_frames_header}, "
|
||
f"actual={s.n_frames[angle_idx]} (scanner bug — corrected)"
|
||
)
|
||
if s.scan_aborted:
|
||
notes.append(
|
||
f"! Scan aborted: {s.n_angles}/{s.n_angles_declared} angles complete"
|
||
)
|
||
if s.background is not None:
|
||
notes.append(f"Background waveform: {len(s.background)} samples")
|
||
if s.precomputed_freq_mhz is not None:
|
||
bg_note = " (bg-sub)" if s.precomputed_bg_sub else " (no bg-sub)"
|
||
notes.append(f"v5: precomputed images present{bg_note} — display is instant")
|
||
if s.version == 6:
|
||
notes.append("v6 format: rows / frames / x_start are per-angle")
|
||
self.lbl_frame_warn.setText("\n".join(notes))
|
||
|
||
# ------------------------------------------------------------------
|
||
# Controls
|
||
# ------------------------------------------------------------------
|
||
|
||
def _update_controls_enabled(self, enabled: bool):
|
||
s = self._sras
|
||
self.spin_angle.setEnabled(enabled and s is not None and s.n_angles > 1)
|
||
self.combo_channel.setEnabled(enabled)
|
||
self.combo_cmap.setEnabled(enabled)
|
||
self.chk_auto.setEnabled(enabled)
|
||
manual = enabled and not self.chk_auto.isChecked()
|
||
self.spin_vmin.setEnabled(manual)
|
||
self.spin_vmax.setEnabled(manual)
|
||
ch_idx = self.combo_channel.currentIndex()
|
||
is_ch1 = enabled and ch_idx in CH1_DERIVED_MODES
|
||
# Threshold and bg-sub apply to all CH1 modes
|
||
self.spin_threshold_mv.setEnabled(is_ch1)
|
||
has_bg = enabled and s is not None and s.background is not None
|
||
self.chk_bg_sub.setEnabled(has_bg and is_ch1)
|
||
# Velocity grating spinbox
|
||
is_vel = enabled and ch_idx == VELOCITY_MODE_IDX
|
||
self.spin_grating_um.setEnabled(is_vel)
|
||
self.grp_velocity.setVisible(is_vel)
|
||
# CSV export: enabled when a CH1-derived image is displayed
|
||
self.btn_export_csv.setEnabled(is_ch1 and self._current_image is not None)
|
||
# ROI: always usable once a file is loaded (independent of channel)
|
||
self.btn_draw_roi.setEnabled(enabled and s is not None)
|
||
# Pre-process: available for v2–v5 files when loaded and not already running
|
||
can_preprocess = (enabled and s is not None and s.version != 6
|
||
and self._preprocess_thread is None)
|
||
self._preprocess_act.setEnabled(can_preprocess)
|
||
self._update_roi_ui()
|
||
|
||
def _on_channel_changed(self):
|
||
ch_idx = self.combo_channel.currentIndex()
|
||
has_file = self._sras is not None
|
||
is_ch1 = ch_idx in CH1_DERIVED_MODES
|
||
self.spin_threshold_mv.setEnabled(is_ch1 and has_file)
|
||
has_bg = has_file and self._sras.background is not None
|
||
self.chk_bg_sub.setEnabled(has_bg and is_ch1)
|
||
is_vel = ch_idx == VELOCITY_MODE_IDX
|
||
self.spin_grating_um.setEnabled(is_vel and has_file)
|
||
self.grp_velocity.setVisible(is_vel)
|
||
self.btn_export_csv.setEnabled(is_ch1 and has_file and self._current_image is not None)
|
||
self._on_view_changed()
|
||
|
||
def _on_bg_sub_toggled(self):
|
||
# Background subtraction changes the FFT input, so it genuinely
|
||
# invalidates the cached raw FFT (the cache key includes it) —
|
||
# _refresh_display() will recompute only if there's no cache hit
|
||
# for the new bg-sub state.
|
||
if self._sras is not None:
|
||
if self.combo_channel.currentIndex() in CH1_DERIVED_MODES:
|
||
self._refresh_display()
|
||
|
||
def _on_grating_changed(self):
|
||
# Grating is a pure post-multiply on the cached frequency image —
|
||
# never needs a recompute.
|
||
if self._sras is not None and self.combo_channel.currentIndex() == VELOCITY_MODE_IDX:
|
||
self._refresh_display()
|
||
|
||
def _on_export_csv(self):
|
||
if self._current_image is None or self._sras is None:
|
||
return
|
||
ch_idx = self._current_ch
|
||
angle = self._current_angle
|
||
ch_name = CH_NAMES[ch_idx]
|
||
default_name = (
|
||
f"{self._sras.path.stem}_angle{angle}_{ch_name}.csv"
|
||
)
|
||
path, _ = QFileDialog.getSaveFileName(
|
||
self, "Export Image as CSV",
|
||
str(self._sras.path.parent / default_name),
|
||
"CSV files (*.csv);;All files (*)",
|
||
)
|
||
if not path:
|
||
return
|
||
np.savetxt(path, self._current_image, delimiter=",", fmt="%.6g")
|
||
self.statusBar().showMessage(f"Exported {Path(path).name}")
|
||
|
||
# ------------------------------------------------------------------
|
||
# ROI (rectangle on the image)
|
||
# ------------------------------------------------------------------
|
||
|
||
def _on_draw_roi_toggled(self, checked: bool):
|
||
if checked:
|
||
self.image_canvas.start_drawing()
|
||
self.statusBar().showMessage(
|
||
"Click and drag on the image to draw a new rectangle.")
|
||
else:
|
||
self.image_canvas.cancel_drawing()
|
||
|
||
def _on_draw_mode_changed(self, active: bool):
|
||
# Keep the toggle button's visual state in sync with the canvas.
|
||
self.btn_draw_roi.blockSignals(True)
|
||
self.btn_draw_roi.setChecked(active)
|
||
self.btn_draw_roi.blockSignals(False)
|
||
|
||
def _on_roi_changed(self):
|
||
self._update_roi_ui()
|
||
|
||
def _update_roi_ui(self):
|
||
roi = self.image_canvas.get_roi()
|
||
if roi is None:
|
||
self.lbl_roi_center.setText("centroid: —")
|
||
self.lbl_roi_size.setText("bbox: —")
|
||
self.lbl_roi_npix.setText("pixels inside: —")
|
||
self.btn_clear_roi.setEnabled(False)
|
||
self.btn_export_roi.setEnabled(False)
|
||
return
|
||
cen = roi.centroid()
|
||
bbox = roi.bbox_size()
|
||
self.lbl_roi_center.setText(
|
||
f"centroid: ({cen[0]:.3f}, {cen[1]:.3f}) mm")
|
||
self.lbl_roi_size.setText(
|
||
f"bbox: {bbox[0]:.3f} × {bbox[1]:.3f} mm")
|
||
npix = 0
|
||
if self._sras is not None:
|
||
try:
|
||
mask = roi.mask_for_grid(self._sras.x_axis_mm(self._current_angle),
|
||
self._sras.y_positions_mm(self._current_angle))
|
||
npix = int(mask.sum())
|
||
except Exception:
|
||
npix = 0
|
||
self.lbl_roi_npix.setText(f"pixels inside: {npix}")
|
||
self.btn_clear_roi.setEnabled(True)
|
||
self.btn_export_roi.setEnabled(
|
||
self._current_image is not None and npix > 0)
|
||
|
||
def _on_clear_roi(self):
|
||
self.image_canvas.clear_roi()
|
||
self.statusBar().showMessage("ROI cleared")
|
||
|
||
def _on_roi_angle_edited(self):
|
||
pass # rotation control removed — corners are dragged individually
|
||
|
||
def _on_export_roi_csv(self):
|
||
if self._current_image is None or self._sras is None:
|
||
return
|
||
roi = self.image_canvas.get_roi()
|
||
if roi is None:
|
||
self.statusBar().showMessage("No ROI — draw one first")
|
||
return
|
||
s = self._sras
|
||
x_axis = s.x_axis_mm(self._current_angle)
|
||
y_axis = s.y_positions_mm(self._current_angle)
|
||
X, Y = np.meshgrid(np.asarray(x_axis, dtype=np.float64),
|
||
np.asarray(y_axis, dtype=np.float64))
|
||
mask = roi.mask_for_grid(x_axis, y_axis)
|
||
if not mask.any():
|
||
self.statusBar().showMessage("ROI does not overlap any pixel")
|
||
return
|
||
img = self._current_image
|
||
if img.shape != mask.shape:
|
||
self.statusBar().showMessage(
|
||
f"ROI shape {mask.shape} does not match image {img.shape}")
|
||
return
|
||
|
||
rows_idx, frames_idx = np.where(mask)
|
||
xs = X[mask]
|
||
ys = Y[mask]
|
||
vals = img[mask]
|
||
|
||
ch_idx = self._current_ch
|
||
ch_name = CH_NAMES[ch_idx]
|
||
angle = self._current_angle
|
||
default_name = (f"{s.path.stem}_angle{angle}_{ch_name}_ROI.csv")
|
||
path, _ = QFileDialog.getSaveFileName(
|
||
self, "Export ROI as CSV",
|
||
str(s.path.parent / default_name),
|
||
"CSV files (*.csv);;All files (*)",
|
||
)
|
||
if not path:
|
||
return
|
||
|
||
pts = roi.corners()
|
||
corners_str = " ".join(f"({p[0]:.6g},{p[1]:.6g})" for p in pts)
|
||
header = (
|
||
f"# ROI quad corners (BL BR TR TL) mm: {corners_str}\n"
|
||
f"# source: {s.path.name}, channel={ch_name}, "
|
||
f"angle_idx={angle}, angle_deg={s.angles_deg[angle]:.4g}\n"
|
||
f"# n_pixels={int(mask.sum())}\n"
|
||
"row,frame,x_mm,y_mm,value"
|
||
)
|
||
data = np.column_stack([
|
||
rows_idx.astype(np.int64),
|
||
frames_idx.astype(np.int64),
|
||
xs, ys, vals.astype(np.float64),
|
||
])
|
||
# integer columns first, floats after — use a per-column format list
|
||
np.savetxt(path, data, delimiter=",",
|
||
fmt=["%d", "%d", "%.6g", "%.6g", "%.6g"],
|
||
header=header, comments="")
|
||
self.statusBar().showMessage(
|
||
f"Exported ROI ({int(mask.sum())} pixels) to {Path(path).name}")
|
||
|
||
def _on_threshold_changed(self):
|
||
mv = self.spin_threshold_mv.value()
|
||
if self._sras is not None:
|
||
ymult = self._sras.ch_ymult_mv[CH4_IDX]
|
||
yoff = self._sras.ch_yoff_adc[CH4_IDX]
|
||
yzero = self._sras.ch_yzero_mv[CH4_IDX]
|
||
else:
|
||
ymult, yoff, yzero = _FALLBACK_YMULT_MV, _FALLBACK_YOFF_ADC, 0.0
|
||
self.lbl_threshold_adc.setText(f"≈ {mv_to_adc(mv, ymult, yoff, yzero):.1f} ADC counts")
|
||
# Threshold decides which pixels get an FFT at all (see
|
||
# ComputeWorker), so changing it is a genuine cache key change —
|
||
# _refresh_display() recomputes only on a miss, and that recompute
|
||
# reuses the cached DC4 image to skip masked-out pixels.
|
||
if self._sras is not None and self.combo_channel.currentIndex() in CH1_DERIVED_MODES:
|
||
self._refresh_display()
|
||
|
||
def _on_autoscale_toggled(self, checked: bool):
|
||
manual = not checked
|
||
self.spin_vmin.setEnabled(manual and self._sras is not None)
|
||
self.spin_vmax.setEnabled(manual and self._sras is not None)
|
||
if self._sras is not None and self._current_image is not None:
|
||
self._redraw_image(self._current_image)
|
||
|
||
def _on_manual_range_changed(self):
|
||
if not self.chk_auto.isChecked() and self._current_image is not None:
|
||
self._redraw_image(self._current_image)
|
||
|
||
def _on_cmap_changed(self):
|
||
# Colormap is purely how the existing image is rendered — never
|
||
# needs a recompute.
|
||
if self._current_image is not None:
|
||
self._redraw_image(self._current_image)
|
||
|
||
def _on_view_changed(self):
|
||
if self._sras is None:
|
||
return
|
||
idx = self.spin_angle.value()
|
||
self.lbl_angle_deg.setText(f"({self._sras.angles_deg[idx]:.1f}°)")
|
||
self._update_scan_info_labels()
|
||
self._refresh_display()
|
||
|
||
# ------------------------------------------------------------------
|
||
# Computation
|
||
# ------------------------------------------------------------------
|
||
|
||
def _current_n_fft(self) -> int | None:
|
||
pad_factor = self._fft_pad_factor
|
||
if pad_factor <= 1 or self._sras is None:
|
||
return None
|
||
return self._sras.samples_per_frame * pad_factor
|
||
|
||
def _scale_for_display(self, freq_mhz: np.ndarray, ch_idx: int) -> np.ndarray:
|
||
"""Velocity is a pure post-multiply of the (already DC-masked)
|
||
cached frequency image — never worth a recompute on its own."""
|
||
if ch_idx == VELOCITY_MODE_IDX:
|
||
return freq_mhz * self.spin_grating_um.value()
|
||
return freq_mhz
|
||
|
||
def _refresh_display(self):
|
||
"""Show the image for the current angle/channel/threshold, using
|
||
cached data whenever possible and only falling back to a
|
||
background compute (with progress popup) when genuinely nothing
|
||
is cached yet for these settings."""
|
||
if self._sras is None:
|
||
return
|
||
angle_idx = self.spin_angle.value()
|
||
ch_idx = self.combo_channel.currentIndex()
|
||
|
||
if ch_idx in (CH3_IDX, CH4_IDX):
|
||
cached = self._dc_cache.get((angle_idx, ch_idx))
|
||
if cached is not None:
|
||
self._show_image_now(cached, angle_idx, ch_idx)
|
||
return
|
||
elif ch_idx in (CH1_IDX, VELOCITY_MODE_IDX):
|
||
apply_bg_sub = self.chk_bg_sub.isChecked()
|
||
threshold_mv = self.spin_threshold_mv.value()
|
||
key = (angle_idx, apply_bg_sub, self._current_n_fft(), threshold_mv)
|
||
raw = self._fft_cache.get(key)
|
||
if raw is not None:
|
||
img = self._scale_for_display(raw, ch_idx)
|
||
self._show_image_now(img, angle_idx, ch_idx)
|
||
return
|
||
|
||
# Nothing cached for these settings — need a real compute. Changing
|
||
# the DC threshold changes *which* pixels get an FFT at all, so it
|
||
# can't be satisfied from the cache — but with the DC map already
|
||
# known, the recompute skips the FFT for masked-out pixels and is
|
||
# much cheaper than a full-image compute would be.
|
||
self._start_compute()
|
||
|
||
def _show_image_now(self, img: np.ndarray, angle_idx: int, ch_idx: int):
|
||
"""Display an already-available image with no compute involved."""
|
||
self._current_image = img
|
||
self._current_angle = angle_idx
|
||
self._current_ch = ch_idx
|
||
self.btn_export_csv.setEnabled(ch_idx in CH1_DERIVED_MODES)
|
||
self._redraw_image(img)
|
||
self._update_roi_ui()
|
||
|
||
# ------------------------------------------------------------------
|
||
# Background compute (only reached on a genuine cache miss)
|
||
# ------------------------------------------------------------------
|
||
|
||
def _start_compute(self):
|
||
if self._sras is None:
|
||
return
|
||
if self._compute_thread is not None:
|
||
return # re-check in _on_compute_thread_finished
|
||
|
||
angle_idx = self.spin_angle.value()
|
||
ch_idx = self.combo_channel.currentIndex()
|
||
apply_bg_sub = self.chk_bg_sub.isChecked()
|
||
threshold_mv = self.spin_threshold_mv.value()
|
||
pad_factor = self._fft_pad_factor
|
||
n_fft = self._current_n_fft()
|
||
# Reuse the cached DC4 image (if the precompute has reached this
|
||
# angle) so the FFT compute skips masked-out pixels entirely and
|
||
# doesn't need to re-read the CH4 channel from disk.
|
||
dc4_mv = self._dc_cache.get((angle_idx, CH4_IDX))
|
||
|
||
self._pending_angle = angle_idx
|
||
self._pending_ch = ch_idx
|
||
self._pending_bg_sub = apply_bg_sub
|
||
self._pending_threshold = threshold_mv
|
||
self._pending_fft_pad_factor = pad_factor
|
||
|
||
# Claim self._compute_thread *before* anything below that can pump
|
||
# the Qt event loop (e.g. QProgressDialog.show() on first display).
|
||
# If that happened first, a re-entrant editingFinished/signal could
|
||
# slip past the guard above, start a second thread, and then have
|
||
# this call's own assignment clobber (and destroy while still
|
||
# running) that second thread's QThread object — which aborts the
|
||
# process. Assigning immediately closes that window.
|
||
self._compute_worker = ComputeWorker(
|
||
self._sras, angle_idx, ch_idx, apply_bg_sub, n_fft=n_fft,
|
||
dc_threshold_mv=threshold_mv, dc4_mv=dc4_mv,
|
||
)
|
||
self._compute_thread = QThread()
|
||
self._compute_worker.moveToThread(self._compute_thread)
|
||
self._compute_thread.started.connect(self._compute_worker.run)
|
||
self._compute_worker.finished.connect(self._on_compute_done)
|
||
self._compute_worker.error.connect(
|
||
lambda msg: self.statusBar().showMessage(f"Compute error: {msg}")
|
||
)
|
||
self._compute_worker.finished.connect(self._compute_thread.quit)
|
||
self._compute_thread.finished.connect(self._on_compute_thread_finished)
|
||
|
||
if ch_idx in (CH1_IDX, VELOCITY_MODE_IDX):
|
||
self.statusBar().showMessage("Computing FFT…")
|
||
self._show_progress(
|
||
f"Computing FFT for angle {angle_idx}…\n"
|
||
"This can take a while on a large scan — result is cached "
|
||
"so revisiting this angle/mode/threshold will be instant."
|
||
)
|
||
else:
|
||
self.statusBar().showMessage("Computing DC image…")
|
||
self._show_progress(f"Computing DC image for angle {angle_idx}…")
|
||
|
||
self._compute_thread.start()
|
||
|
||
def _on_compute_thread_finished(self):
|
||
# Block until the OS thread has actually joined before dropping our
|
||
# last reference — deallocating a QThread whose thread hasn't fully
|
||
# terminated yet logs "QThread: Destroyed while thread is still
|
||
# running" and aborts the process. The finished() signal fires as
|
||
# the thread is winding down but does not guarantee it has joined.
|
||
if self._compute_thread is not None:
|
||
self._compute_thread.wait()
|
||
self._compute_thread = None
|
||
angle_idx = self.spin_angle.value()
|
||
ch_idx = self.combo_channel.currentIndex()
|
||
apply_bg_sub = self.chk_bg_sub.isChecked()
|
||
threshold_mv = self.spin_threshold_mv.value()
|
||
if (angle_idx, ch_idx, apply_bg_sub, threshold_mv, self._fft_pad_factor) != (
|
||
self._pending_angle, self._pending_ch, self._pending_bg_sub,
|
||
self._pending_threshold, self._pending_fft_pad_factor):
|
||
# Settings changed while this compute was running — re-dispatch
|
||
# through the cache-aware path in case that now-current
|
||
# combination happens to already be cached.
|
||
self._refresh_display()
|
||
|
||
def _on_compute_done(self, result):
|
||
self._close_progress()
|
||
angle_idx = self._pending_angle
|
||
ch_idx = self._pending_ch
|
||
|
||
if ch_idx in (CH1_IDX, VELOCITY_MODE_IDX):
|
||
masked_freq_mhz = result
|
||
key = (angle_idx, self._pending_bg_sub, self._current_n_fft(),
|
||
self._pending_threshold)
|
||
self._fft_cache[key] = masked_freq_mhz
|
||
img = self._scale_for_display(masked_freq_mhz, ch_idx)
|
||
else:
|
||
img = result
|
||
self._dc_cache[(angle_idx, ch_idx)] = img
|
||
|
||
self._show_image_now(img, angle_idx, ch_idx)
|
||
|
||
# ------------------------------------------------------------------
|
||
# Background DC precompute (all angles, so switching is fluid)
|
||
# ------------------------------------------------------------------
|
||
|
||
def _start_dc_precompute(self):
|
||
if self._sras is None:
|
||
return
|
||
self._dc_generation += 1
|
||
generation = self._dc_generation
|
||
n_angles = self._sras.n_angles
|
||
|
||
worker = DcPrecomputeWorker(self._sras)
|
||
thread = QThread()
|
||
worker.moveToThread(thread)
|
||
thread.started.connect(worker.run)
|
||
worker.angle_done.connect(
|
||
lambda a, dc3, dc4, g=generation: self._on_dc_precompute_angle_done(
|
||
g, a, dc3, dc4, n_angles)
|
||
)
|
||
worker.error.connect(
|
||
lambda msg: self.statusBar().showMessage(f"DC precompute error: {msg}", 5000)
|
||
)
|
||
worker.finished.connect(thread.quit)
|
||
worker.error.connect(thread.quit)
|
||
thread.finished.connect(lambda: self._on_dc_precompute_thread_finished(thread))
|
||
|
||
# See _start_compute for why the thread/worker are claimed on self
|
||
# before .start() rather than after.
|
||
self._dc_precompute_worker = worker
|
||
self._dc_precompute_thread = thread
|
||
thread.start()
|
||
|
||
def _on_dc_precompute_angle_done(self, generation: int, angle_idx: int,
|
||
dc3_mv: np.ndarray, dc4_mv: np.ndarray,
|
||
n_angles: int):
|
||
if generation != self._dc_generation:
|
||
return # stale result from a previously-loaded file — discard
|
||
self._dc_cache[(angle_idx, CH3_IDX)] = dc3_mv
|
||
self._dc_cache[(angle_idx, CH4_IDX)] = dc4_mv
|
||
done = sum(1 for a in range(n_angles) if (a, CH4_IDX) in self._dc_cache)
|
||
if done < n_angles:
|
||
self.lbl_dc_precompute.setText(
|
||
f"Precomputing DC images: {done}/{n_angles} angles ready…")
|
||
else:
|
||
self.lbl_dc_precompute.setText("DC images ready for all angles.")
|
||
# If we just finished the angle/channel the user is currently
|
||
# looking at and it wasn't shown yet (e.g. they switched here
|
||
# before precompute caught up and are still waiting), show it now.
|
||
if (self._sras is not None and angle_idx == self.spin_angle.value()
|
||
and self._compute_thread is None
|
||
and self.combo_channel.currentIndex() in (CH3_IDX, CH4_IDX)
|
||
and (self._current_angle != angle_idx
|
||
or self._current_ch != self.combo_channel.currentIndex())):
|
||
self._refresh_display()
|
||
|
||
def _on_dc_precompute_thread_finished(self, thread: QThread):
|
||
# See the comment in _on_compute_thread_finished: wait() before
|
||
# releasing the reference to avoid destroying a QThread whose OS
|
||
# thread hasn't fully joined yet.
|
||
thread.wait()
|
||
if self._dc_precompute_thread is thread:
|
||
self._dc_precompute_thread = None
|
||
self._dc_precompute_worker = None
|
||
|
||
def _redraw_image(self, img: np.ndarray):
|
||
s = self._sras
|
||
angle_idx = self._current_angle
|
||
x_axis = s.x_axis_mm(angle_idx)
|
||
y_axis = s.y_positions_mm(angle_idx)
|
||
dx = x_axis[1] - x_axis[0] if len(x_axis) > 1 else s.pixel_x_mm
|
||
dy = float(y_axis[1] - y_axis[0]) if len(y_axis) > 1 else 1.0
|
||
|
||
extent = [
|
||
x_axis[0] - dx / 2,
|
||
x_axis[-1] + dx / 2,
|
||
y_axis[-1] + dy / 2,
|
||
y_axis[0] - dy / 2,
|
||
]
|
||
|
||
if self.chk_auto.isChecked():
|
||
vmin, vmax = float(img.min()), float(img.max())
|
||
for spin, val in ((self.spin_vmin, vmin), (self.spin_vmax, vmax)):
|
||
spin.blockSignals(True)
|
||
spin.setValue(val)
|
||
spin.blockSignals(False)
|
||
else:
|
||
vmin = self.spin_vmin.value()
|
||
vmax = self.spin_vmax.value()
|
||
|
||
ch_idx = self._current_ch
|
||
angle_deg = s.angles_deg[self._current_angle]
|
||
ch_label = CH_LABELS[ch_idx]
|
||
|
||
if ch_idx == CH1_IDX:
|
||
mode_str = "RF"
|
||
unit = "Peak frequency (MHz)"
|
||
colorbar_label = "MHz"
|
||
elif ch_idx == VELOCITY_MODE_IDX:
|
||
grating = self.spin_grating_um.value()
|
||
mode_str = "Velocity"
|
||
unit = "Velocity (m/s)"
|
||
colorbar_label = "m/s"
|
||
ch_label = f"Velocity [grating={grating:.2f} µm]"
|
||
else:
|
||
mode_str = "DC"
|
||
unit = "DC mean (mV)"
|
||
colorbar_label = "mV"
|
||
|
||
title = f"{CH_NAMES[ch_idx]} | {mode_str} | {angle_deg:.1f}°"
|
||
|
||
self.image_canvas.show_image(
|
||
img, extent,
|
||
cmap=self.combo_cmap.currentText(),
|
||
vmin=vmin, vmax=vmax,
|
||
xlabel="X (mm)", ylabel="Y (mm)",
|
||
title=title,
|
||
colorbar_label=colorbar_label,
|
||
)
|
||
self.statusBar().showMessage(
|
||
f"{s.path.name} | {ch_label} @ {angle_deg:.1f}° "
|
||
f"| {img.shape[1]} × {img.shape[0]} px | {unit}"
|
||
)
|
||
|
||
# ------------------------------------------------------------------
|
||
# Pixel inspector
|
||
# ------------------------------------------------------------------
|
||
|
||
def _on_pixel_clicked(self, row_idx: int, frame_idx: int):
|
||
if self._sras is None or self._current_image is None:
|
||
return
|
||
self.lbl_wave_hint.hide()
|
||
ch_idx = self._current_ch
|
||
if ch_idx in CH1_DERIVED_MODES:
|
||
self.wave_canvas.show_rf_waveform(
|
||
self._sras, self._current_angle, row_idx, frame_idx,
|
||
apply_bg_sub=self.chk_bg_sub.isChecked(),
|
||
)
|
||
else:
|
||
self.wave_canvas.show_dc_waveform(
|
||
self._sras, self._current_angle, ch_idx, row_idx, frame_idx
|
||
)
|
||
|
||
# ------------------------------------------------------------------
|
||
# Progress dialog helpers
|
||
# ------------------------------------------------------------------
|
||
|
||
def _show_progress(self, message: str):
|
||
if self._progress_dlg is not None:
|
||
self._progress_dlg.setLabelText(message)
|
||
return
|
||
dlg = QProgressDialog(message, "", 0, 0, self)
|
||
dlg.setWindowTitle("Please wait…")
|
||
dlg.setCancelButton(None)
|
||
dlg.setWindowModality(Qt.WindowModality.WindowModal)
|
||
dlg.setMinimumDuration(300) # only appears if operation takes > 300 ms
|
||
dlg.show()
|
||
self._progress_dlg = dlg
|
||
|
||
def _close_progress(self):
|
||
if self._progress_dlg is not None:
|
||
self._progress_dlg.close()
|
||
self._progress_dlg = None
|
||
|
||
# ------------------------------------------------------------------
|
||
# Pre-process → save v5
|
||
# ------------------------------------------------------------------
|
||
|
||
def _on_preprocess(self):
|
||
if self._sras is None:
|
||
return
|
||
if self._preprocess_thread is not None:
|
||
return
|
||
s = self._sras
|
||
if s.version == 6:
|
||
self.statusBar().showMessage(
|
||
"Pre-process to v5 is not supported for v6 files (per-angle geometry).")
|
||
return
|
||
default_name = s.path.stem + "_v5" + s.path.suffix
|
||
dest, _ = QFileDialog.getSaveFileName(
|
||
self, "Save Pre-processed v5 File",
|
||
str(s.path.parent / default_name),
|
||
"SRAS files (*.sras);;All files (*)",
|
||
)
|
||
if not dest:
|
||
return
|
||
if self._preprocess_thread is not None:
|
||
return # a second trigger snuck in while the save dialog was open
|
||
|
||
apply_bg = self.chk_bg_sub.isChecked() and s.background is not None
|
||
|
||
n_total = s.n_angles
|
||
n_px = int(s.n_rows[0]) * int(s.n_frames[0])
|
||
approx_mb = n_total * n_px * 3 * 4 / 1e6
|
||
|
||
# Claim self._preprocess_thread before any call below that can pump
|
||
# the Qt event loop — see the comment in _start_compute for why.
|
||
self._preprocess_worker = PreprocessWorker(s, dest, apply_bg)
|
||
self._preprocess_thread = QThread()
|
||
self._preprocess_worker.moveToThread(self._preprocess_thread)
|
||
self._preprocess_thread.started.connect(self._preprocess_worker.run)
|
||
self._preprocess_worker.progress.connect(self._on_preprocess_progress)
|
||
self._preprocess_worker.finished.connect(self._on_preprocess_done)
|
||
self._preprocess_worker.finished.connect(self._preprocess_thread.quit)
|
||
self._preprocess_thread.finished.connect(self._on_preprocess_thread_finished)
|
||
|
||
self._preprocess_act.setEnabled(False)
|
||
self._show_progress(
|
||
f"Pre-processing {n_total} angle(s) "
|
||
f"({int(s.n_rows[0])}×{int(s.n_frames[0])} px each, ~{approx_mb:.0f} MB output)…"
|
||
)
|
||
|
||
self._preprocess_thread.start()
|
||
|
||
def _on_preprocess_progress(self, pct: int):
|
||
if self._progress_dlg is not None:
|
||
self._progress_dlg.setValue(pct)
|
||
|
||
def _on_preprocess_done(self, error_msg: str):
|
||
self._close_progress()
|
||
if error_msg:
|
||
self.statusBar().showMessage(f"Pre-process failed: {error_msg}")
|
||
else:
|
||
self.statusBar().showMessage("v5 file written — re-open it for instant display.")
|
||
|
||
def _on_preprocess_thread_finished(self):
|
||
# See the comment in _on_compute_thread_finished: wait() before
|
||
# releasing our reference to avoid destroying a QThread whose OS
|
||
# thread hasn't fully joined yet.
|
||
if self._preprocess_thread is not None:
|
||
self._preprocess_thread.wait()
|
||
self._preprocess_thread = None
|
||
self._preprocess_act.setEnabled(
|
||
self._sras is not None and self._sras.version != 6)
|
||
|
||
# ------------------------------------------------------------------
|
||
# FFT Options
|
||
# ------------------------------------------------------------------
|
||
|
||
def _on_fft_options(self):
|
||
global _fft_backend
|
||
spf = self._sras.samples_per_frame if self._sras is not None else None
|
||
sr = self._sras.sample_rate_hz if self._sras is not None else None
|
||
dlg = FftOptionsDialog(
|
||
self,
|
||
current_backend=_fft_backend,
|
||
current_pad_factor=self._fft_pad_factor,
|
||
samples_per_frame=spf,
|
||
sample_rate_hz=sr,
|
||
grating_um=self.spin_grating_um.value(),
|
||
)
|
||
if dlg.exec() == QDialog.DialogCode.Accepted:
|
||
_fft_backend = dlg.get_backend()
|
||
self._fft_pad_factor = dlg.get_pad_factor()
|
||
# Pad factor changes the FFT bin count, so it genuinely
|
||
# invalidates the cached raw FFT (part of the cache key) —
|
||
# _refresh_display() will recompute only on a cache miss.
|
||
if self._sras is not None and self.combo_channel.currentIndex() in (
|
||
CH1_IDX, VELOCITY_MODE_IDX):
|
||
self._refresh_display()
|
||
|
||
# ------------------------------------------------------------------
|
||
|
||
def closeEvent(self, event):
|
||
if self._dc_precompute_worker is not None:
|
||
self._dc_precompute_worker.stop()
|
||
for attr in ("_load_thread", "_compute_thread", "_preprocess_thread",
|
||
"_dc_precompute_thread"):
|
||
t = getattr(self, attr, None)
|
||
if t is not None:
|
||
t.quit()
|
||
t.wait(2000)
|
||
super().closeEvent(event)
|
||
|
||
|
||
# ---------------------------------------------------------------------------
|
||
|
||
def main():
|
||
app = QApplication(sys.argv)
|
||
initial = sys.argv[1] if len(sys.argv) > 1 else None
|
||
window = SrasViewerWindow(initial_path=initial)
|
||
window.show()
|
||
sys.exit(app.exec())
|
||
|
||
|
||
if __name__ == "__main__":
|
||
main()
|