#!/usr/bin/env python3 """ SRAS Scan File Viewer PyQt6 application for visualizing channel data from .sras binary scan files. Channel semantics (fixed by sc3_aui_app.py acquisition settings): CH1 — RF Acoustic Packet (AC-coupled, 100 mV/div): FFT → peak frequency CH3 — Bias A (DC-coupled, 50 mV/div): waveform mean CH4 — Bias B (DC-coupled, 50 mV/div): waveform mean RF images are masked: pixels where CH4_dc < dc_threshold show 0. Frame-count correction: the scanner writes the *configured* frame count in the header before acquisition, but the scope may acquire fewer frames. The actual count is computed from the file size and used for the reshape so channels are correctly aligned. Scan geometry: v6/v7 files scan a different bounding box per angle (x_start, x_delta, n_frames, n_rows all vary by angle), so geometry is exposed per-angle via SrasFile.n_rows / n_frames / x_start_mm arrays and the x_axis_mm() / y_positions_mm() methods. v2–v5 files have uniform geometry across angles, so those arrays simply repeat the same value n_angles times. v7 files are v6 files with an optional trailing cache section holding precomputed per-angle DC and/or FFT images (see scan_format.md), so display never has to recompute them after the "Convert" menu's batch actions have stored them once. """ import re import sys import struct import faulthandler import numpy as np from pathlib import Path from dataclasses import dataclass import os faulthandler.enable() # print a native stack trace on SIGSEGV/SIGABRT/etc. from PyQt6.QtWidgets import ( QApplication, QMainWindow, QWidget, QVBoxLayout, QHBoxLayout, QGroupBox, QLabel, QPushButton, QComboBox, QSpinBox, QDoubleSpinBox, QFileDialog, QSizePolicy, QSplitter, QCheckBox, QFrame, QProgressDialog, QDialog, QDialogButtonBox, QRadioButton, QButtonGroup, ) from PyQt6.QtGui import QAction from PyQt6.QtCore import Qt, QThread, pyqtSignal, QObject from matplotlib.backends.backend_qtagg import FigureCanvasQTAgg, NavigationToolbar2QT from matplotlib.figure import Figure from matplotlib.patches import Polygon from matplotlib.lines import Line2D from matplotlib.path import Path as MplPath # --------------------------------------------------------------------------- # FFT backend # --------------------------------------------------------------------------- _pyfftw_available = False try: import pyfftw pyfftw.interfaces.cache.enable() _pyfftw_available = True except ImportError: pass import scipy.fft as scipy_fft import scipy.ndimage as scipy_ndimage # Runtime-mutable settings changed via FftOptionsDialog _fft_backend = "numpy" # "numpy" or "pyfftw" def _do_rfft(x: np.ndarray, n: int | None = None, axis: int = -1, workers: int = 1) -> np.ndarray: """Dispatch rfft to the selected backend with optional multithreading.""" if _fft_backend == "pyfftw" and _pyfftw_available: return pyfftw.interfaces.numpy_fft.rfft(x, n=n, axis=axis, threads=workers) return scipy_fft.rfft(x, n=n, axis=axis, workers=workers) # --------------------------------------------------------------------------- # SRAS format # --------------------------------------------------------------------------- # v2–v5: fixed header, uniform geometry across angles (43 bytes) HDR_FMT = ">4sBHHffffIIdBB" HDR_SIZE = struct.calcsize(HDR_FMT) # 43 bytes # v6: fixed header, per-angle geometry in a separate table (49 bytes) HDR_FMT_V6 = ">4sBHfffffffIdBB" HDR_SIZE_V6 = struct.calcsize(HDR_FMT_V6) # 49 bytes # v6: per-angle geometry table record (x_start, x_delta, n_frames, n_rows) GEO_FMT_V6 = ">ffIH" GEO_SIZE_V6 = struct.calcsize(GEO_FMT_V6) # 14 bytes # v7: identical to v6 (same header/geometry/waveform layout, version byte # is the only header difference) plus an optional trailing cache section # ("CACH") holding precomputed per-angle DC and/or FFT images so a v7 file # never needs to recompute them on open. See scan_format.md for the full # spec. Sub-block sizes are per-angle (n_rows[a] * n_frames[a]), taken from # the Per-Angle Geometry Table already parsed for v6 — no new geometry # fields are needed. CACH_MAGIC = b"CACH" CACH_HDR_FMT = ">4sBB" # magic, cach_version, block_flags CACH_HDR_SIZE = struct.calcsize(CACH_HDR_FMT) # 6 bytes CACH_VERSION = 1 CACH_FLAG_DC = 0x01 CACH_FLAG_FFT = 0x02 SDCB_MAGIC = b"SDCB" SDCB_HDR_FMT = ">4sBH" # magic, reserved, n_stored SDCB_HDR_SIZE = struct.calcsize(SDCB_HDR_FMT) # 7 bytes SFFT_MAGIC = b"SFFT" SFFT_HDR_FMT = ">4sBH" # magic, flags, n_stored SFFT_HDR_SIZE = struct.calcsize(SFFT_HDR_FMT) # 7 bytes SFFT_FLAG_BG_SUB = 0x01 # Fixed-order channels in the file: index 0=CH1, 1=CH3, 2=CH4 # Fixed channel indices into the .sras data array (CH1=RF, CH3/CH4=Bias DC) CH1_IDX, CH3_IDX, CH4_IDX = 0, 1, 2 CH_LABELS = [ "CH1 — RF (FFT peak freq)", "CH3 — Bias A (DC mean)", "CH4 — Bias B (DC mean)", "CH1 — Velocity (SRAS)", ] CH_NAMES = ["CH1", "CH3", "CH4", "VEL"] # Combo index for the derived velocity mode (uses CH1_IDX data) VELOCITY_MODE_IDX = 3 # All modes that operate on CH1 waveforms CH1_DERIVED_MODES = (CH1_IDX, VELOCITY_MODE_IDX) # Fallback scope calibration used only when reading v2 files without embedded # preambles. v3+ files carry the WFMOutpre string so these are not used. # 50 mV/div, 8 div full-scale, int8 ADC, position = -2.72 div # ymult = 50 mV × 8 / 256 = 1.5625 mV/count # yoff = position × (256/8) = -2.72 × 32 = -87.04 (ADC count for 0 V) _FALLBACK_YMULT_MV = 1.5625 # mV per ADC count _FALLBACK_YOFF_ADC = -87.04 # ADC count that represents 0 V CMAPS = ["gray", "viridis", "plasma", "inferno", "hot", "jet", "RdBu_r", "seismic"] def _parse_preamble(preamble: str) -> dict[str, float]: """Extract YMULT, YOFF, YZERO from a Tektronix WFMOutpre string. Returns a dict with float values for whichever keys are present. YMULT is left in V/count as the scope reports it. """ result = {} for key in ("YMULT", "YOFF", "YZERO"): m = re.search(rf'\b{key}\s+([-+]?\d*\.?\d+(?:[Ee][+-]?\d+)?)', preamble) if m: result[key] = float(m.group(1)) return result def mv_to_adc(mv: float, ymult_mv: float = _FALLBACK_YMULT_MV, yoff_adc: float = _FALLBACK_YOFF_ADC, yzero_mv: float = 0.0) -> float: return (mv - yzero_mv) / ymult_mv + yoff_adc def adc_to_mv(adc: float, ymult_mv: float = _FALLBACK_YMULT_MV, yoff_adc: float = _FALLBACK_YOFF_ADC, yzero_mv: float = 0.0) -> float: return (adc - yoff_adc) * ymult_mv + yzero_mv # --------------------------------------------------------------------------- # File parser # --------------------------------------------------------------------------- class SrasFile: """Parsed in-memory representation of a v2–v7 .sras file. Scan geometry (rows, frames, x_start) is exposed per-angle via the ``n_rows`` / ``n_frames`` / ``x_start_mm`` arrays and the ``x_axis_mm()`` / ``y_positions_mm()`` methods, since v6/v7 files scan a different bounding box per angle. v2–v5 files have uniform geometry, so these arrays just repeat the same value ``n_angles`` times. Waveform data is likewise exposed as ``data[angle_idx]``, an array of shape ``(n_rows[a], n_channels, n_frames[a], samples_per_frame)``. v7 files (v6 plus an optional trailing cache section) expose any stored precomputed images as ``precomputed_dc3_mv`` / ``precomputed_dc4_mv`` / ``precomputed_freq_mhz`` — for v6/v7 these are ragged per-angle lists (``list[np.ndarray | None]``, one entry per angle); for v5 they are dense ``(n_angles, n_rows, n_frames)`` arrays, since v5 geometry is uniform. """ def __init__(self, path: str): self.path = Path(path) self._parse() def _parse(self): with open(self.path, "rb") as f: magic = f.read(4) if magic != b"SRAS": raise ValueError(f"Bad magic bytes: {magic!r}") (version,) = struct.unpack(">B", f.read(1)) self.version = version if version in (2, 3, 4, 5): self._parse_legacy() elif version in (6, 7): self._parse_v6() else: raise ValueError(f"Unsupported version: {version}") # ------------------------------------------------------------------ # v2–v5 parsing (uniform geometry, flat waveform block) # ------------------------------------------------------------------ def _parse_legacy(self): with open(self.path, "rb") as f: fields = struct.unpack(HDR_FMT, f.read(HDR_SIZE)) (magic, ver, n_angles, n_rows, x_start, x_delta, vel, freq, n_frames_hdr, spf, sr, bps, n_ch) = fields self.n_angles = n_angles self.velocity_mm_s = float(vel) self.laser_freq_hz = float(freq) self.n_frames_header = n_frames_hdr # configured count (may be wrong) self.samples_per_frame = spf self.sample_rate_hz = float(sr) self.bytes_per_sample = bps self.n_channels = n_ch # Precomputed-image cache (populated when reading a v5 file). # These are (n_angles, n_rows, n_frames) float32 arrays or None. self.precomputed_freq_mhz: np.ndarray | None = None self.precomputed_dc4_mv: np.ndarray | None = None self.precomputed_dc3_mv: np.ndarray | None = None self.precomputed_bg_sub: bool = False self.scan_aborted = False self.n_angles_declared = n_angles with open(self.path, "rb") as f: f.seek(HDR_SIZE) angles = np.frombuffer(f.read(n_angles * 4), dtype=">f4").astype(np.float32) y_pos = np.frombuffer(f.read(n_rows * 4), dtype=">f4").astype(np.float32) if ver >= 3: preambles = [] for _ in range(n_ch): (length,) = struct.unpack(">H", f.read(2)) preambles.append(f.read(length).decode("utf-8")) self.preambles = preambles self.ch_ymult_mv = [] self.ch_yoff_adc = [] self.ch_yzero_mv = [] for p in preambles: cal = _parse_preamble(p) # YMULT from scope is V/count; store as mV/count self.ch_ymult_mv.append(cal.get("YMULT", _FALLBACK_YMULT_MV / 1000) * 1000) self.ch_yoff_adc.append(cal.get("YOFF", _FALLBACK_YOFF_ADC)) # YZERO from scope is in V; store as mV self.ch_yzero_mv.append(cal.get("YZERO", 0.0) * 1000) else: self.preambles = None self.ch_ymult_mv = [_FALLBACK_YMULT_MV] * n_ch self.ch_yoff_adc = [_FALLBACK_YOFF_ADC] * n_ch self.ch_yzero_mv = [0.0] * n_ch if ver >= 4: (n_bg,) = struct.unpack(">I", f.read(4)) self.background = np.frombuffer(f.read(n_bg), dtype=np.int8).astype(np.float32) else: self.background = None # Record the byte offset where raw waveform data begins. # np.memmap will use this to map only the waveform section. data_offset = f.tell() # ---- Determine actual frame count from file size --------------- # For v4 and earlier the header n_frames may be the *configured* # count before acquisition; the actual count is derived from the # bytes on disk. For v5 files a PREC tail follows the waveform # data, so we must not include those extra bytes in the frame count. file_size = self.path.stat().st_size samples_per_row_per_ch = n_ch * spf # Upper bound: bytes from data_offset to end of file available_bytes = file_size - data_offset if ver == 5: actual_n_frames = n_frames_hdr remainder = 0 else: total_samples = available_bytes // bps actual_n_frames = total_samples // (n_angles * n_rows * samples_per_row_per_ch) remainder = total_samples % (n_angles * n_rows * samples_per_row_per_ch) self.frame_count_mismatch = (actual_n_frames != n_frames_hdr) self.n_frames_remainder = remainder # ---- Memory-map the waveform data (zero RAM cost) -------------- # Instead of f.read() → astype() (which peaks at 2× file size), # memmap lets the OS page only the bytes that are actually touched. waveform_dtype = np.int8 if bps == 1 else ">i2" waveform_shape = (n_angles, n_rows, n_ch, actual_n_frames, spf) data5d = np.memmap( str(self.path), dtype=waveform_dtype, mode="r", offset=data_offset, shape=waveform_shape, ) # Expose as a list of per-angle views so downstream code shares one # indexing convention with v6: sras.data[a][row, ch, frame, sample] self.data = [data5d[a] for a in range(n_angles)] # Uniform per-angle geometry, repeated so callers don't need to # special-case legacy vs. v6 files. self.n_rows = np.full(n_angles, n_rows, dtype=np.int64) self.n_frames = np.full(n_angles, actual_n_frames, dtype=np.int64) self.x_start_mm = np.full(n_angles, float(x_start), dtype=np.float64) self._y_pos_per_angle = [y_pos] * n_angles self.angles_deg = angles # ---- Read v5 precomputed section if present -------------------- if ver >= 5: waveform_bytes = actual_n_frames * n_angles * n_rows * n_ch * spf * bps prec_offset = data_offset + waveform_bytes if file_size > prec_offset: self._parse_prec_section(prec_offset, n_angles, n_rows, actual_n_frames) def _parse_prec_section(self, offset: int, n_angles: int, n_rows: int, n_frames: int): """Parse the v5 PREC tail that holds precomputed images.""" _PREC_MAGIC = b"PREC" px = n_rows * n_frames # pixels per angle image img_bytes = px * 4 # float32 with open(self.path, "rb") as f: f.seek(offset) header_raw = f.read(6) # magic(4) + fmt_ver(1) + flags(1) if len(header_raw) < 6 or header_raw[:4] != _PREC_MAGIC: return flags = header_raw[5] self.precomputed_bg_sub = bool(flags & 0x01) (n_stored,) = struct.unpack(">H", f.read(2)) if n_stored == 0: return freq_buf = np.zeros((n_angles, n_rows, n_frames), dtype=np.float32) dc4_buf = np.zeros((n_angles, n_rows, n_frames), dtype=np.float32) dc3_buf = np.zeros((n_angles, n_rows, n_frames), dtype=np.float32) for _ in range(n_stored): (aidx,) = struct.unpack(">H", f.read(2)) if aidx >= n_angles: break freq_buf[aidx] = np.frombuffer( f.read(img_bytes), dtype=">f4").reshape(n_rows, n_frames) dc4_buf[aidx] = np.frombuffer( f.read(img_bytes), dtype=">f4").reshape(n_rows, n_frames) dc3_buf[aidx] = np.frombuffer( f.read(img_bytes), dtype=">f4").reshape(n_rows, n_frames) self.precomputed_freq_mhz = freq_buf self.precomputed_dc4_mv = dc4_buf self.precomputed_dc3_mv = dc3_buf # ------------------------------------------------------------------ # v6 parsing (per-angle geometry, ragged waveform blocks) # ------------------------------------------------------------------ def _parse_v6(self): with open(self.path, "rb") as f: fields = struct.unpack(HDR_FMT_V6, f.read(HDR_SIZE_V6)) (magic, ver, n_angles, x_start_nom, y_start_nom, x_delta_nom, y_delta_nom, row_spacing, vel, freq, spf, sr, bps, n_ch) = fields n_angles_declared = n_angles self.velocity_mm_s = float(vel) self.laser_freq_hz = float(freq) self.samples_per_frame = spf self.sample_rate_hz = float(sr) self.bytes_per_sample = bps self.n_channels = n_ch # Reference-only fields: the ROI as entered before per-angle # bounding-box expansion. Actual per-angle geometry used for # rendering comes from the Per-Angle Geometry Table below. self.x_start_nominal_mm = float(x_start_nom) self.y_start_nominal_mm = float(y_start_nom) self.x_delta_nominal_mm = float(x_delta_nom) self.y_delta_nominal_mm = float(y_delta_nom) self.row_spacing_mm = float(row_spacing) self.n_frames_header = None self.frame_count_mismatch = False self.n_frames_remainder = 0 angles = np.frombuffer(f.read(n_angles * 4), dtype=">f4").astype(np.float32) x_start = np.empty(n_angles, dtype=np.float64) n_frames = np.empty(n_angles, dtype=np.int64) n_rows = np.empty(n_angles, dtype=np.int64) for a in range(n_angles): xs, xd, nf, nr = struct.unpack(GEO_FMT_V6, f.read(GEO_SIZE_V6)) x_start[a] = xs n_frames[a] = nf n_rows[a] = nr y_pos_per_angle = [] for a in range(n_angles): nr = int(n_rows[a]) y_pos_per_angle.append( np.frombuffer(f.read(nr * 4), dtype=">f4").astype(np.float32)) preambles = [] for _ in range(n_ch): (length,) = struct.unpack(">H", f.read(2)) preambles.append(f.read(length).decode("utf-8")) self.preambles = preambles self.ch_ymult_mv = [] 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() self._data_offset = data_offset # ---- 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] # Precomputed-image cache (v7 only). Ragged per-angle lists — unlike # v5's dense (n_angles, n_rows, n_frames) arrays, v6/v7 geometry # varies per angle, so each entry is its own (n_rows[a], n_frames[a]) # array or None if that angle isn't cached yet. self.precomputed_freq_mhz: list[np.ndarray | None] = [None] * n_complete self.precomputed_dc4_mv: list[np.ndarray | None] = [None] * n_complete self.precomputed_dc3_mv: list[np.ndarray | None] = [None] * n_complete self.precomputed_bg_sub: bool = False if self.version == 7 and offset < file_size: self._parse_cach_section(offset) # ------------------------------------------------------------------ # v7 cache tail (CACH section: precomputed DC / FFT images) # ------------------------------------------------------------------ def _cache_tail_offset(self) -> int: """Deterministic file offset where the CACH tail starts (or would start), derived purely from the header + Per-Angle Geometry Table — independent of whether a cache tail is actually present. Used by both the parser and the in-place writer.""" n_ch = self.n_channels spf = self.samples_per_frame bps = self.bytes_per_sample waveform_bytes = int(sum( int(self.n_rows[a]) * n_ch * int(self.n_frames[a]) * spf * bps for a in range(self.n_angles) )) return self._data_offset + waveform_bytes def _parse_cach_section(self, offset: int): """Parse the v7 CACH tail that holds precomputed DC/FFT images.""" with open(self.path, "rb") as f: f.seek(offset) header_raw = f.read(CACH_HDR_SIZE) if len(header_raw) < CACH_HDR_SIZE: return magic, cach_version, block_flags = struct.unpack(CACH_HDR_FMT, header_raw) if magic != CACH_MAGIC or cach_version != CACH_VERSION: return if block_flags & CACH_FLAG_DC: sdcb_raw = f.read(SDCB_HDR_SIZE) if len(sdcb_raw) < SDCB_HDR_SIZE: return sdcb_magic, _reserved, n_stored = struct.unpack(SDCB_HDR_FMT, sdcb_raw) if sdcb_magic != SDCB_MAGIC: return for _ in range(n_stored): (angle_idx,) = struct.unpack(">H", f.read(2)) if angle_idx >= self.n_angles: break px = int(self.n_rows[angle_idx]) * int(self.n_frames[angle_idx]) shape = (int(self.n_rows[angle_idx]), int(self.n_frames[angle_idx])) self.precomputed_dc3_mv[angle_idx] = np.frombuffer( f.read(px * 4), dtype=">f4").reshape(shape) self.precomputed_dc4_mv[angle_idx] = np.frombuffer( f.read(px * 4), dtype=">f4").reshape(shape) if block_flags & CACH_FLAG_FFT: sfft_raw = f.read(SFFT_HDR_SIZE) if len(sfft_raw) < SFFT_HDR_SIZE: return sfft_magic, flags, n_stored = struct.unpack(SFFT_HDR_FMT, sfft_raw) if sfft_magic != SFFT_MAGIC: return self.precomputed_bg_sub = bool(flags & SFFT_FLAG_BG_SUB) for _ in range(n_stored): (angle_idx,) = struct.unpack(">H", f.read(2)) if angle_idx >= self.n_angles: break px = int(self.n_rows[angle_idx]) * int(self.n_frames[angle_idx]) shape = (int(self.n_rows[angle_idx]), int(self.n_frames[angle_idx])) self.precomputed_freq_mhz[angle_idx] = np.frombuffer( f.read(px * 4), dtype=">f4").reshape(shape) def write_v7_cache(self, *, new_dc3_mv: list[np.ndarray | None] | None = None, new_dc4_mv: list[np.ndarray | None] | None = None, new_freq_mhz: list[np.ndarray | None] | None = None, new_bg_sub: bool | None = None): """Store computed DC and/or FFT images into this file's CACH tail, in place, converting a v6 source to v7 (or updating an existing v7 file). Only the block(s) passed in are recomputed; whichever block isn't passed is carried forward unchanged from whatever this ``SrasFile`` already has in memory (from parsing, or a prior write in this same session) — its bytes are never re-read from disk. The waveform data itself is never touched: the cache tail always starts at ``_cache_tail_offset()``, a fixed offset derived from the header and geometry table alone. """ if self.version not in (6, 7): raise ValueError( f"write_v7_cache only supports v6/v7 source files, got v{self.version}") final_dc3 = new_dc3_mv if new_dc3_mv is not None else self.precomputed_dc3_mv final_dc4 = new_dc4_mv if new_dc4_mv is not None else self.precomputed_dc4_mv final_freq = new_freq_mhz if new_freq_mhz is not None else self.precomputed_freq_mhz final_bg_sub = new_bg_sub if new_bg_sub is not None else self.precomputed_bg_sub dc_entries = [a for a in range(self.n_angles) if final_dc3[a] is not None] fft_entries = [a for a in range(self.n_angles) if final_freq[a] is not None] block_flags = 0 if dc_entries: block_flags |= CACH_FLAG_DC if fft_entries: block_flags |= CACH_FLAG_FFT payload = bytearray() payload += struct.pack(CACH_HDR_FMT, CACH_MAGIC, CACH_VERSION, block_flags) if dc_entries: payload += struct.pack(SDCB_HDR_FMT, SDCB_MAGIC, 0, len(dc_entries)) for a in dc_entries: payload += struct.pack(">H", a) payload += final_dc3[a].astype(">f4").tobytes() payload += final_dc4[a].astype(">f4").tobytes() if fft_entries: fft_flags = SFFT_FLAG_BG_SUB if final_bg_sub else 0 payload += struct.pack(SFFT_HDR_FMT, SFFT_MAGIC, fft_flags, len(fft_entries)) for a in fft_entries: payload += struct.pack(">H", a) payload += final_freq[a].astype(">f4").tobytes() cache_offset = self._cache_tail_offset() with open(self.path, "r+b") as f: f.seek(cache_offset) f.write(payload) f.truncate() f.flush() os.fsync(f.fileno()) # Version-byte flip last: if the process dies before this point, # the file is still readable as plain v6 (v6 parsing only # bounds-checks per-angle offset+nbytes <= file_size, it never # asserts exactly how many bytes follow the last angle) — so an # interrupted write can never corrupt the file, only leave # harmless trailing bytes that the next successful write # overwrites via this same deterministic cache_offset. f.seek(4) f.write(struct.pack("B", 7)) f.flush() os.fsync(f.fileno()) self.version = 7 self.precomputed_dc3_mv = final_dc3 self.precomputed_dc4_mv = final_dc4 self.precomputed_freq_mhz = final_freq self.precomputed_bg_sub = final_bg_sub # ------------------------------------------------------------------ # 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 _cached_dc_mv(sras: SrasFile, angle_idx: int, ch_idx: int) -> np.ndarray | None: """Return a v7-cached DC image (mV, already converted) for (angle_idx, ch_idx) if the file's CACH section has it, else None. Only applies to the ragged v6/v7 list representation of ``precomputed_dc3_mv``/``precomputed_dc4_mv`` — v5's dense PREC arrays don't track per-angle validity (unstored angles are left at 0.0 rather than a sentinel), so they're intentionally not consulted here. """ store = sras.precomputed_dc3_mv if ch_idx == CH3_IDX else sras.precomputed_dc4_mv if isinstance(store, list) and angle_idx < len(store): return store[angle_idx] return None 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 precomputed peak-frequency images for this angle (v5's dense per-file PREC section, or v7's ragged per-angle CACH section), and zero-padding is not active, and the bg-sub flag matches, the stored image is 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: precomputed images (v5 PREC or v7 CACH) ---------------- # v5 stores a dense (n_angles, n_rows, n_frames) ndarray (uniform # geometry); v6/v7 store a ragged list, one entry per angle (None where # that angle hasn't been cached), since geometry varies per angle. freq_store = sras.precomputed_freq_mhz if isinstance(freq_store, list): angle_cached = angle_idx < len(freq_store) and freq_store[angle_idx] is not None else: angle_cached = freq_store is not None can_use_precomputed = ( angle_cached 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 = freq_store[angle_idx].copy() # DC4 mask, in priority order: already-cached DC block, caller- # supplied image, or a fresh (cheap — no FFT) recompute. dc4_store = sras.precomputed_dc4_mv if isinstance(dc4_store, list): dc4_img = _cached_dc_mv(sras, angle_idx, CH4_IDX) else: dc4_img = dc4_store[angle_idx] if dc4_store is not None else None if dc4_img is None: if dc4_mv is not None: dc4_img = dc4_mv else: dc4_img = adc_to_mv(compute_dc_image(sras, angle_idx, CH4_IDX), sras.ch_ymult_mv[CH4_IDX], sras.ch_yoff_adc[CH4_IDX], sras.ch_yzero_mv[CH4_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 # --------------------------------------------------------------------------- # Angle alignment (Fusion menu) # # Puts every angle's images onto one shared, zero-padded pixel grid using a # rigid transform only (rotation + translation, never scale). Rotation for # angle `a` is the *known* scan-angle delta relative to a reference angle — # never searched. Only the residual translation is found, via FFT phase # correlation of each angle's binarized CH4 ("dc-mask") image. # # Rotation is done in physical mm space rather than on raw pixel indices: # the x-pixel pitch (SrasFile.pixel_x_mm) is file-wide constant but the # y-pixel pitch (row spacing) can differ from it, and for v6 files can even # vary per angle. Rotating the raw index grid directly would implicitly # assume square pixels and shear a non-square-pixel image — an unwanted # effective anisotropic scale. Instead each angle gets one affine that maps # shared-canvas pixel index -> mm -> undo rotation/shift -> that angle's own # local mm -> that angle's own raw pixel index, matching the output->input # convention scipy.ndimage.affine_transform expects. # --------------------------------------------------------------------------- @dataclass class AngleTransform: rotation_deg: float shift_mm: tuple[float, float] # (dx_mm, dy_mm) found by phase correlation matrix: np.ndarray # (2,2): canvas (row,col) -> this angle's raw (row,col) offset: np.ndarray # (2,) @dataclass class AlignmentResult: ref_angle_idx: int dc_threshold_mv: float canvas_shape: tuple[int, int] # (n_rows, n_cols) canvas_dx_mm: float canvas_dy_mm: float canvas_origin_mm: tuple[float, float] # mm at canvas pixel index (0, 0) per_angle: dict[int, AngleTransform] def _pixel_pitch_mm(sras: SrasFile, angle_idx: int) -> tuple[float, float]: """(dx, dy) mm/pixel for one angle: dx is the file-wide constant pixel_x_mm; dy is this angle's own row spacing (assumed uniform, same assumption _redraw_image already makes when it builds the display extent).""" dx = sras.pixel_x_mm y = sras.y_positions_mm(angle_idx) dy = float(y[1] - y[0]) if len(y) > 1 else 1.0 return dx, dy def _bbox_center_mm(sras: SrasFile, angle_idx: int) -> tuple[float, float]: x = sras.x_axis_mm(angle_idx) y = sras.y_positions_mm(angle_idx) return float((x[0] + x[-1]) / 2.0), float((y[0] + y[-1]) / 2.0) def _bbox_corners_mm(sras: SrasFile, angle_idx: int) -> np.ndarray: """4 corners (x, y) of this angle's raw mm bounding box, shape (4, 2).""" x = sras.x_axis_mm(angle_idx) y = sras.y_positions_mm(angle_idx) return np.array([[xx, yy] for xx in (x[0], x[-1]) for yy in (y[0], y[-1])]) def _rotation_matrix(theta_deg: float) -> np.ndarray: t = np.radians(theta_deg) c, s = np.cos(t), np.sin(t) return np.array([[c, -s], [s, c]]) # CCW rotation acting on (x, y) def _build_affine_canvas_to_raw(sras: SrasFile, angle_idx: int, ref_idx: int, shift_mm: tuple[float, float], canvas_dx: float, canvas_dy: float, canvas_origin_mm: tuple[float, float] ) -> tuple[np.ndarray, np.ndarray]: """matrix, offset s.t. raw_index = matrix @ [row_out, col_out] + offset, matching scipy.ndimage.affine_transform's output->input convention. Pipeline (all mm unless noted): [X;Y] = A_out @ [row_out;col_out] + b_out # canvas idx -> ref-frame mm [lx;ly] = R(theta)^T @ ([X;Y]-c_ref-shift) + c_a # undo rotation+shift -> angle a's local mm [row;col] = D @ ([lx;ly] - [x_start_a; y0_a]) # local mm -> angle a's raw idx where theta = angles_deg[angle_idx] - angles_deg[ref_idx], c_ref/c_a are each angle's own raw-bbox mm centroid (the rotation pivot — this keeps rotated content centered, minimizing required canvas padding), and A_out/D are the index<->mm scaling matrices for the canvas pitch and this angle's own native pitch respectively. """ theta = float(sras.angles_deg[angle_idx] - sras.angles_deg[ref_idx]) Rinv = _rotation_matrix(theta).T cx_a, cy_a = _bbox_center_mm(sras, angle_idx) cx_ref, cy_ref = _bbox_center_mm(sras, ref_idx) dx_a, dy_a = _pixel_pitch_mm(sras, angle_idx) x0_a = float(sras.x_start_mm[angle_idx]) y0_a = float(sras.y_positions_mm(angle_idx)[0]) A_out = np.array([[0.0, canvas_dx], [canvas_dy, 0.0]]) # [row,col] -> [X,Y] b_out = np.array(canvas_origin_mm, dtype=np.float64) D = np.array([[0.0, 1.0 / dy_a], [1.0 / dx_a, 0.0]]) # [x,y] -> [row,col] shift = np.array(shift_mm, dtype=np.float64) c_ref_v = np.array([cx_ref, cy_ref]) c_a_v = np.array([cx_a, cy_a]) origin_a = np.array([x0_a, y0_a]) matrix = D @ Rinv @ A_out offset = D @ Rinv @ (b_out - c_ref_v - shift) + D @ (c_a_v - origin_a) return matrix, offset def apply_alignment(result: AlignmentResult, angle_idx: int, img: np.ndarray, order: int = 0) -> np.ndarray: """Resample any already-computed 2D image for `angle_idx` (same shape as that angle's raw (n_rows, n_frames) — e.g. compute_dc_image / compute_rf_image output) onto the shared alignment canvas. order=0 (nearest) avoids blending real data with zero-padding or with masked-out (0-valued) CH1/velocity pixels at mask edges. Channel- agnostic: the same per-angle transform (found from the CH4 mask) works for any channel's image of that angle.""" t = result.per_angle[angle_idx] return scipy_ndimage.affine_transform( img.astype(np.float32, copy=False), t.matrix, offset=t.offset, output_shape=result.canvas_shape, order=order, mode="constant", cval=0.0) def _block_mean_downsample(img: np.ndarray, factor: int) -> np.ndarray: if factor <= 1: return img h, w = img.shape h2, w2 = (h // factor) * factor, (w // factor) * factor trimmed = img[:h2, :w2] return trimmed.reshape(h2 // factor, factor, w2 // factor, factor).mean(axis=(1, 3)) def _phase_correlate_shift(ref_img: np.ndarray, mov_img: np.ndarray) -> tuple[int, int]: """FFT normalized cross-power-spectrum phase correlation. Returns the integer (dr, dc) pixel shift of mov_img relative to ref_img; both must be the same shape. Risk: if the true shift is near +/- half the array size, wraparound can bias the peak — mitigated by the generous margin_frac padding in _working_canvas_for_pair, which keeps the true residual shift small relative to the correlation canvas.""" F1 = scipy_fft.fft2(ref_img.astype(np.float64)) F2 = scipy_fft.fft2(mov_img.astype(np.float64)) R = F1 * np.conj(F2) R /= np.maximum(np.abs(R), 1e-12) corr = scipy_fft.ifft2(R).real dr, dc = np.unravel_index(np.argmax(corr), corr.shape) h, w = corr.shape if dr > h // 2: dr -= h if dc > w // 2: dc -= w return int(dr), int(dc) def _working_canvas_for_pair(sras: SrasFile, ref_idx: int, a_idx: int, dx: float, dy: float, margin_frac: float = 0.3 ) -> tuple[tuple[float, float], tuple[int, int]]: """Union of the reference's own raw bbox and angle a's raw bbox rotated (about its own center) into the ref frame with zero shift, padded by margin_frac on each side — sized generously so the true phase- correlation shift lands well inside the canvas (see _phase_correlate_shift's wraparound note).""" theta = float(sras.angles_deg[a_idx] - sras.angles_deg[ref_idx]) R = _rotation_matrix(theta) c_a = np.array(_bbox_center_mm(sras, a_idx)) c_ref = np.array(_bbox_center_mm(sras, ref_idx)) pts = list(_bbox_corners_mm(sras, ref_idx)) for corner in _bbox_corners_mm(sras, a_idx): pts.append(R @ (corner - c_a) + c_ref) pts = np.array(pts) x_min, y_min = pts.min(axis=0) x_max, y_max = pts.max(axis=0) pad_x, pad_y = (x_max - x_min) * margin_frac, (y_max - y_min) * margin_frac x_min, x_max = x_min - pad_x, x_max + pad_x y_min, y_max = y_min - pad_y, y_max + pad_y n_cols = int(np.ceil((x_max - x_min) / dx)) + 1 n_rows = int(np.ceil((y_max - y_min) / abs(dy))) + 1 origin = (x_min, y_min if dy > 0 else y_max) return origin, (n_rows, n_cols) def _compute_angle_alignment(sras: SrasFile, ref_angle_idx: int, dc_threshold_mv: float, progress_cb=None) -> AlignmentResult: """Top-level alignment driver. Runs on a background thread (see AngleAlignmentWorker) — deliberately recomputes CH4 DC images from scratch via compute_dc_image rather than reading the GUI-thread _dc_cache dict, since background-thread workers must not touch GUI-thread-owned caches (BatchCacheWorker follows the same rule).""" n = sras.n_angles # already the *complete*-angle count for aborted v6 scans dx_ref, dy_ref = _pixel_pitch_mm(sras, ref_angle_idx) # ---- Step 1: binarized CH4 mask per angle, native per-angle grid ----- masks: dict[int, np.ndarray] = {} for a in range(n): dc4 = adc_to_mv(compute_dc_image(sras, a, CH4_IDX), sras.ch_ymult_mv[CH4_IDX], sras.ch_yoff_adc[CH4_IDX], sras.ch_yzero_mv[CH4_IDX]) masks[a] = (dc4 >= dc_threshold_mv).astype(np.float32) if progress_cb: progress_cb(int((a + 1) / n * 25)) # ---- Step 2: coarse correlation stage (downsample first, then rotate) # Downsampling before affine_transform (not after) is what keeps this # tractable for a v6 scan with thousands of rows/frames per angle. max_dim = max(max(m.shape) for m in masks.values()) factor = max(1, int(np.ceil(max_dim / 1024))) dx_c, dy_c = dx_ref * factor, dy_ref * factor masks_small = {a: _block_mean_downsample(m, factor) for a, m in masks.items()} shifts_mm: dict[int, tuple[float, float]] = {ref_angle_idx: (0.0, 0.0)} for a in range(n): if a == ref_angle_idx: continue work_origin, work_shape = _working_canvas_for_pair( sras, ref_angle_idx, a, dx_c, dy_c, margin_frac=0.3) # Coarse canvas->raw affine at native pitch, then rescale by /factor # so it maps coarse-canvas idx -> coarse (downsampled) raw idx — # exact for block-mean downsampling (up to the trimmed remainder). m_a, o_a = _build_affine_canvas_to_raw( sras, a, ref_angle_idx, (0.0, 0.0), dx_c, dy_c, work_origin) m_ref, o_ref = _build_affine_canvas_to_raw( sras, ref_angle_idx, ref_angle_idx, (0.0, 0.0), dx_c, dy_c, work_origin) rotated_a = scipy_ndimage.affine_transform( masks_small[a], m_a / factor, offset=o_a / factor, output_shape=work_shape, order=0, mode="constant", cval=0.0) embedded_ref = scipy_ndimage.affine_transform( masks_small[ref_angle_idx], m_ref / factor, offset=o_ref / factor, output_shape=work_shape, order=0, mode="constant", cval=0.0) dr, dc = _phase_correlate_shift(embedded_ref, rotated_a) shifts_mm[a] = (dc * dx_c, dr * dy_c) if progress_cb: progress_cb(25 + int((a + 1) / n * 50)) # ---- Step 3: union bounding box over all angles (rotation+shift applied) corners_ref_frame = [] for a in range(n): theta = float(sras.angles_deg[a] - sras.angles_deg[ref_angle_idx]) R = _rotation_matrix(theta) c_a = np.array(_bbox_center_mm(sras, a)) c_ref = np.array(_bbox_center_mm(sras, ref_angle_idx)) shift = np.array(shifts_mm[a]) for corner in _bbox_corners_mm(sras, a): corners_ref_frame.append(R @ (corner - c_a) + c_ref + shift) corners_ref_frame = np.array(corners_ref_frame) x_min, y_min = corners_ref_frame.min(axis=0) x_max, y_max = corners_ref_frame.max(axis=0) n_cols = int(np.ceil((x_max - x_min) / dx_ref)) + 1 n_rows = int(np.ceil((y_max - y_min) / abs(dy_ref))) + 1 canvas_origin_mm = (float(x_min), float(y_min if dy_ref > 0 else y_max)) canvas_shape = (n_rows, n_cols) # ---- Step 4: final per-angle full-resolution affine (canvas -> raw idx) per_angle: dict[int, AngleTransform] = {} for a in range(n): matrix, offset = _build_affine_canvas_to_raw( sras, a, ref_angle_idx, shifts_mm[a], dx_ref, dy_ref, canvas_origin_mm) theta = float(sras.angles_deg[a] - sras.angles_deg[ref_angle_idx]) per_angle[a] = AngleTransform(theta, shifts_mm[a], matrix, offset) if progress_cb: progress_cb(75 + int((a + 1) / n * 25)) return AlignmentResult(ref_angle_idx, dc_threshold_mv, canvas_shape, dx_ref, dy_ref, canvas_origin_mm, per_angle) # --------------------------------------------------------------------------- # 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: use the v7 cache if this angle is already # stored (already mV), else compute fresh and convert. cached = _cached_dc_mv(self._sras, self._angle, self._ch) if cached is not None: self.finished.emit(cached) return 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 cached_dc3 = _cached_dc_mv(self._sras, a, CH3_IDX) cached_dc4 = _cached_dc_mv(self._sras, a, CH4_IDX) if cached_dc3 is not None and cached_dc4 is not None: self.angle_done.emit(a, cached_dc3, cached_dc4) continue 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 BatchCacheWorker(QObject): """Batch-computes and stores DC or FFT images into each of *paths*'s v7 CACH tail, in place — converting v6 sources to v7 on first use, or updating an existing v7 file's cache blocks without disturbing whatever the other block already holds. *mode* is ``"dc"`` (CH3/CH4 mean images) or ``"fft"`` (CH1 peak-frequency images, unmasked — masking is applied at display time, same as v5's PREC convention). Emits ``progress(int)`` (0–100, weighted by total angle count across the whole batch), ``file_done(str, str)`` (path, error message or "" on success) after each file so one file's failure doesn't abort the batch, and ``finished()`` once every file has been attempted. """ progress = pyqtSignal(int) file_done = pyqtSignal(str, str) finished = pyqtSignal() def __init__(self, paths: list[str], mode: str, apply_bg_sub: bool): super().__init__() self._paths = paths self._mode = mode self._apply_bg_sub = apply_bg_sub def run(self): # Pass 1: quick open of each file just to weight progress by total # angle count. Don't hold every file's memmap open at once — reopen # fresh per file in pass 2 below. total_angles = 0 for path in self._paths: try: total_angles += SrasFile(path).n_angles except Exception: pass # unreadable files are reported properly in pass 2 total_angles = max(total_angles, 1) done_angles = 0 for path in self._paths: try: sras = SrasFile(path) if sras.version not in (6, 7): self.file_done.emit( path, f"unsupported version {sras.version} — only " "v6/v7 files can be batch-cached") continue n = sras.n_angles if self._mode == "dc": new_dc3 = [None] * n new_dc4 = [None] * n for a in range(n): new_dc3[a] = adc_to_mv( compute_dc_image(sras, a, CH3_IDX), sras.ch_ymult_mv[CH3_IDX], sras.ch_yoff_adc[CH3_IDX], sras.ch_yzero_mv[CH3_IDX]) new_dc4[a] = adc_to_mv( compute_dc_image(sras, a, CH4_IDX), sras.ch_ymult_mv[CH4_IDX], sras.ch_yoff_adc[CH4_IDX], sras.ch_yzero_mv[CH4_IDX]) done_angles += 1 self.progress.emit(int(done_angles / total_angles * 100)) sras.write_v7_cache(new_dc3_mv=new_dc3, new_dc4_mv=new_dc4) else: effective_bg = self._apply_bg_sub and sras.background is not None new_freq = [None] * n for a in range(n): new_freq[a] = compute_rf_image( sras, a, dc_threshold_mv=-1e9, # mask nothing apply_bg_sub=effective_bg) done_angles += 1 self.progress.emit(int(done_angles / total_angles * 100)) sras.write_v7_cache(new_freq_mhz=new_freq, new_bg_sub=effective_bg) self.file_done.emit(path, "") except Exception as exc: self.file_done.emit(path, str(exc)) self.finished.emit() class AngleAlignmentWorker(QObject): """Computes rotation+translation alignment for every angle in *sras*, referenced to *ref_angle_idx*, from each angle's binarized CH4 mask. Rotation is analytic (from sras.angles_deg); only translation is found by phase correlation. Uses the same progress(int)/finished(...) worker shape as the other background-thread workers in this file. """ progress = pyqtSignal(int) # 0–100 finished = pyqtSignal(object, str) # AlignmentResult|None, error msg ("" = success) def __init__(self, sras: SrasFile, ref_angle_idx: int, dc_threshold_mv: float): super().__init__() self._sras = sras self._ref = ref_angle_idx self._threshold = dc_threshold_mv def run(self): try: result = _compute_angle_alignment( self._sras, self._ref, self._threshold, progress_cb=lambda pct: self.progress.emit(pct)) self.finished.emit(result, "") except Exception as exc: self.finished.emit(None, 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 # Convert menu: batch DC/FFT compute-and-store (v6 -> v7) self._batch_thread: QThread | None = None self._batch_worker: BatchCacheWorker | None = None self._batch_errors: list[str] = [] self._batch_progress_dlg: QProgressDialog | 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 # Angle alignment ("Fusion" menu) self._alignment_result: AlignmentResult | None = None self._alignment_thread: QThread | None = None self._alignment_worker: AngleAlignmentWorker | None = None self._alignment_generation: int = 0 self._aligned_cache: dict[tuple, np.ndarray] = {} 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) # Aligned View (Fusion → Angle Alignment result) self.chk_aligned_view = QCheckBox("Aligned View (Fusion)") self.chk_aligned_view.setChecked(False) self.chk_aligned_view.setEnabled(False) self.chk_aligned_view.setToolTip( "Show the current angle/channel resampled onto the shared,\n" "rotation+translation-aligned canvas from Fusion → Angle\n" "Alignment. Uncheck to see the raw per-angle scan grid." ) self.chk_aligned_view.toggled.connect(self._on_aligned_view_toggled) vl.addWidget(self.chk_aligned_view) # 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) fusion_menu = menubar.addMenu("&Fusion") self._alignment_act = QAction("Angle &Alignment", self) self._alignment_act.setStatusTip( "Compute a rotation+translation alignment across all angles " "(from CH4 masks) and enable Aligned View. Requires >1 angle.") self._alignment_act.setEnabled(False) self._alignment_act.triggered.connect(self._on_angle_alignment) fusion_menu.addAction(self._alignment_act) convert_menu = menubar.addMenu("&Convert") self._batch_dc_act = QAction("Batch Compute DC and &Store…", self) self._batch_dc_act.setStatusTip( "Select .sras files and compute+store DC images (CH3/CH4 mean) " "for every angle, converting v6 files to v7 in place.") self._batch_dc_act.triggered.connect(lambda: self._on_batch_compute("dc")) convert_menu.addAction(self._batch_dc_act) self._batch_fft_act = QAction("Batch Compute FFT and Sto&re…", self) self._batch_fft_act.setStatusTip( "Select .sras files and compute+store FFT peak-frequency images " "for every angle, converting v6 files to v7 in place.") self._batch_fft_act.triggered.connect(lambda: self._on_batch_compute("fft")) convert_menu.addAction(self._batch_fft_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("") # Same for any alignment result — belongs to the previous file's # geometry. Bump the generation counter so a still-running # alignment worker's result is discarded when it lands (see # _on_alignment_done). self._alignment_result = None self._aligned_cache = {} self._alignment_generation += 1 self.chk_aligned_view.blockSignals(True) self.chk_aligned_view.setChecked(False) self.chk_aligned_view.setEnabled(False) self.chk_aligned_view.blockSignals(False) # 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 isinstance(s.precomputed_freq_mhz, np.ndarray): 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 in (6, 7): notes.append("v6/v7 format: rows / frames / x_start are per-angle") if s.version == 7: n_dc = sum(1 for x in s.precomputed_dc4_mv if x is not None) n_fft = sum(1 for x in s.precomputed_freq_mhz if x is not None) if n_dc or n_fft: bg_note = " (bg-sub)" if s.precomputed_bg_sub else " (no bg-sub)" notes.append( f"v7: cached DC ({n_dc}/{s.n_angles} angles), " f"FFT ({n_fft}/{s.n_angles} angles{bg_note if n_fft else ''}) " "— display is instant for cached angles") else: notes.append("v7 format: no cache blocks stored yet") 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) # Batch Convert actions: pick their own files, independent of # whatever's currently open — only gated on no batch already running can_batch = self._batch_thread is None self._batch_dc_act.setEnabled(can_batch) self._batch_fft_act.setEnabled(can_batch) # Angle alignment: needs >1 angle and no alignment already running can_align = (enabled and s is not None and s.n_angles > 1 and self._alignment_thread is None) self._alignment_act.setEnabled(can_align) self.chk_aligned_view.setEnabled( enabled and self._alignment_result is not None) 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: # Deliberately always the raw per-angle grid, even when # Aligned View is on: _on_export_roi_csv also exports on the # raw grid (never synthetically-resampled pixels), so this # readout must match what Export ROI actually writes. 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 # ------------------------------------------------------------------ # Aligned View (Fusion) display helpers # ------------------------------------------------------------------ def _aligned_cache_key(self, angle_idx: int, ch_idx: int) -> tuple: """Mirrors _fft_cache's key granularity so a stale aligned image is never shown after bg_sub/threshold/pad/grating changes.""" if ch_idx in CH1_DERIVED_MODES: return (angle_idx, ch_idx, self.chk_bg_sub.isChecked(), self._current_n_fft(), self.spin_threshold_mv.value(), self.spin_grating_um.value() if ch_idx == VELOCITY_MODE_IDX else None) return (angle_idx, ch_idx) def _aligned_canvas_axes(self) -> tuple[np.ndarray, np.ndarray]: r = self._alignment_result n_rows, n_cols = r.canvas_shape x_axis = r.canvas_origin_mm[0] + np.arange(n_cols) * r.canvas_dx_mm y_axis = r.canvas_origin_mm[1] + np.arange(n_rows) * r.canvas_dy_mm return x_axis, y_axis def _get_aligned_display_image(self, raw_img: np.ndarray, angle_idx: int, ch_idx: int) -> np.ndarray: key = self._aligned_cache_key(angle_idx, ch_idx) cached = self._aligned_cache.get(key) if cached is None: cached = apply_alignment(self._alignment_result, angle_idx, raw_img) self._aligned_cache[key] = cached return cached 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 ch_idx = self._current_ch aligned = (self.chk_aligned_view.isChecked() and self._alignment_result is not None and angle_idx in self._alignment_result.per_angle) if aligned: display_img = self._get_aligned_display_image(img, angle_idx, ch_idx) x_axis, y_axis = self._aligned_canvas_axes() else: display_img = img 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(display_img.min()), float(display_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() 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}°" if aligned: title += " [Aligned]" self.image_canvas.show_image( display_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"| {display_img.shape[1]} × {display_img.shape[0]} px | {unit}" f"{' | Aligned' if aligned else ''}" ) # ------------------------------------------------------------------ # 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 angle_idx = self._current_angle if (self.chk_aligned_view.isChecked() and self._alignment_result is not None and angle_idx in self._alignment_result.per_angle): # The click landed on the shared aligned canvas — invert the # same canvas->raw affine used to display it back to a raw # (row, frame) index before looking up the waveform. t = self._alignment_result.per_angle[angle_idx] raw = t.matrix @ np.array([row_idx, frame_idx], dtype=np.float64) + t.offset row_idx, frame_idx = int(round(raw[0])), int(round(raw[1])) n_rows_a = int(self._sras.n_rows[angle_idx]) n_frames_a = int(self._sras.n_frames[angle_idx]) if not (0 <= row_idx < n_rows_a and 0 <= frame_idx < n_frames_a): self.statusBar().showMessage( "No source waveform here (padding region of the aligned canvas).") 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, angle_idx, row_idx, frame_idx, apply_bg_sub=self.chk_bg_sub.isChecked(), ) else: self.wave_canvas.show_dc_waveform( self._sras, angle_idx, 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 # ------------------------------------------------------------------ # Convert menu: batch DC/FFT compute-and-store (v6 -> v7) # ------------------------------------------------------------------ def _on_batch_compute(self, mode: str): if self._batch_thread is not None: return label = "DC" if mode == "dc" else "FFT" paths, _ = QFileDialog.getOpenFileNames( self, f"Select .sras files to batch-compute {label}", "", "SRAS files (*.sras);;All files (*)", ) if not paths: return if self._batch_thread is not None: return # a second trigger snuck in while the file dialog was open apply_bg = self.chk_bg_sub.isChecked() self._batch_errors = [] # Claim self._batch_thread before anything below that can pump the # Qt event loop — see the comment in _start_compute for why. self._batch_worker = BatchCacheWorker(paths, mode, apply_bg) self._batch_thread = QThread() self._batch_worker.moveToThread(self._batch_thread) self._batch_thread.started.connect(self._batch_worker.run) self._batch_worker.progress.connect(self._on_batch_progress) self._batch_worker.file_done.connect(self._on_batch_file_done) self._batch_worker.finished.connect(lambda paths=paths: self._on_batch_finished(paths)) self._batch_worker.finished.connect(self._batch_thread.quit) self._batch_thread.finished.connect(self._on_batch_thread_finished) self._batch_dc_act.setEnabled(False) self._batch_fft_act.setEnabled(False) self._batch_progress_dlg = QProgressDialog( f"Batch computing {label} for {len(paths)} file(s)…", "", 0, 100, self) self._batch_progress_dlg.setWindowTitle("Please wait…") self._batch_progress_dlg.setCancelButton(None) self._batch_progress_dlg.setWindowModality(Qt.WindowModality.WindowModal) self._batch_progress_dlg.setMinimumDuration(300) self._batch_progress_dlg.show() self._batch_thread.start() def _on_batch_progress(self, pct: int): if self._batch_progress_dlg is not None: self._batch_progress_dlg.setValue(pct) def _on_batch_file_done(self, path: str, err: str): if err: self._batch_errors.append(f"{Path(path).name} — {err}") if self._batch_progress_dlg is not None: self._batch_progress_dlg.setLabelText(f"Processed {Path(path).name}…") def _on_batch_finished(self, paths: list[str]): if self._batch_progress_dlg is not None: self._batch_progress_dlg.close() self._batch_progress_dlg = None n_total = len(paths) n_failed = len(self._batch_errors) n_ok = n_total - n_failed if n_failed: summary = (f"Batch store: {n_ok}/{n_total} file(s) updated, " f"{n_failed} failed: {'; '.join(self._batch_errors)}") else: summary = f"Batch store: {n_ok}/{n_total} file(s) updated." self.statusBar().showMessage(summary) self._batch_errors = [] # If the currently-open file was in this batch, reload it so the # GUI picks up the newly-written v7 cache instead of stale state. if self._sras is not None and str(self._sras.path) in paths: self._load_file(str(self._sras.path)) def _on_batch_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._batch_thread is not None: self._batch_thread.wait() self._batch_thread = None self._batch_dc_act.setEnabled(True) self._batch_fft_act.setEnabled(True) # ------------------------------------------------------------------ # Fusion: angle alignment # ------------------------------------------------------------------ def _on_angle_alignment(self): if self._sras is None or self._sras.n_angles <= 1: return if self._alignment_thread is not None: return ref_idx = 0 threshold_mv = self.spin_threshold_mv.value() generation = self._alignment_generation # Claim self._alignment_thread before anything below that can pump # the Qt event loop — see the comment in _start_compute for why. self._alignment_worker = AngleAlignmentWorker(self._sras, ref_idx, threshold_mv) self._alignment_thread = QThread() self._alignment_worker.moveToThread(self._alignment_thread) self._alignment_thread.started.connect(self._alignment_worker.run) self._alignment_worker.progress.connect(self._on_alignment_progress) self._alignment_worker.finished.connect( lambda result, err, g=generation: self._on_alignment_done(g, result, err)) self._alignment_worker.finished.connect(self._alignment_thread.quit) self._alignment_thread.finished.connect(self._on_alignment_thread_finished) self._alignment_act.setEnabled(False) self._show_progress( f"Computing angle alignment ({self._sras.n_angles} angles, " f"ref=angle 0, CH4 mask ≥ {threshold_mv:.3f} mV)…" ) self._alignment_thread.start() def _on_alignment_progress(self, pct: int): if self._progress_dlg is not None: self._progress_dlg.setValue(pct) def _on_alignment_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._alignment_thread is not None: self._alignment_thread.wait() self._alignment_thread = None self._update_controls_enabled(self._sras is not None) def _on_alignment_done(self, generation: int, result, error_msg: str): self._close_progress() if generation != self._alignment_generation: return # a new file was loaded while this was computing — discard if error_msg: self.statusBar().showMessage(f"Angle alignment failed: {error_msg}") return self._alignment_result = result self._aligned_cache = {} self.chk_aligned_view.setEnabled(True) self.chk_aligned_view.blockSignals(True) self.chk_aligned_view.setChecked(True) self.chk_aligned_view.blockSignals(False) nr, nc = result.canvas_shape self.statusBar().showMessage( f"Angle alignment computed ({self._sras.n_angles} angles, " f"canvas {nc}×{nr} px).") self._refresh_display() def _on_aligned_view_toggled(self, checked: bool): if self._current_image is not None: self._redraw_image(self._current_image) # ------------------------------------------------------------------ # 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", "_batch_thread", "_dc_precompute_thread", "_alignment_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()