Remove nonessential files

- photorec.ses / photorec.se2: accidentally committed PhotoRec
  data-recovery session files
- sc3-aui-focusing.py: dead module — imports a T3RStepperDriver that
  doesn't exist anywhere; superseded by t3r_control_panel.py
- adc_bug.md: stale debugging note for an already-applied fix
- app_style.qss: empty stylesheet; app.py already handles its absence

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

adc_bug.md

@@ -1,37 +0,0 @@
-# ADC YOFF Sign Bug — sras_viewer.py
-
-## Status
-Fix applied, awaiting user testing.
-
-## What was wrong
-
-`DC_YOFF_ADC` in `sras_viewer.py` was `+87.04` instead of `-87.04`.
-
-The Tektronix scope stores CH3/CH4 waveform data as **signed int8** (−128 to +127), where ADC 0 = screen center. The scope's vertical position for CH3/CH4 is set to `−2.72 div` in `sc3_aui_app.py`, which places 0 V **below** center at ADC count `−2.72 × 32 = −87.04`. The comment in the code had the formula as `-position × (256/8)` (sign flipped), producing `+87.04` instead of the correct `−87.04`.
-
-## Effect of the bug
-
-- `adc_to_mv` was off by 272 mV in the negative direction
-  - ADC −87 (true 0 V signal) → −272 mV (should be ≈ 0 mV)
-  - ADC 0 (screen center, above ground) → −136 mV (should be +136 mV)
-- DC images for CH3/CH4 (Bias A/B) showed large negative voltages, physically impossible for DC bias signals
-- RF mask threshold (`mv_to_adc`) was also broken: threshold ADC value ~+87 was being compared against pixel means clustered around −87, so nearly every pixel would have been incorrectly masked
-
-## The fix
-
-`sras_viewer.py` line 48:
-```python
-# Before
-DC_YOFF_ADC  = 87.04    # ADC count that represents 0 V
-
-# After
-DC_YOFF_ADC  = -87.04   # ADC count that represents 0 V
-```
-Comment on line 47 also corrected from `-position × (256/8)` to `position × (256/8)`.
-
-## What to verify during testing
-
-1. CH3 and CH4 DC images show positive (or near-zero) voltages consistent with the bias signal levels
-2. RF (CH1) image is not excessively masked — pixels with a genuine bias signal above the threshold should appear
-3. `mv_to_adc(0.0)` should now return −87.04 (not +87.04)
-4. The default threshold of 0.125 mV should correspond to ADC ≈ −87.0, not +87.1

app.py

@@ -14,9 +14,11 @@ from hardware.coherent_hops_laser import CoherentHOPSLaser, DummyLaser
 from hardware.helios_laser import HeliosLaser, PulseMode
 from hardware.uc480_camera import UC480Camera, CameraStreamThread
 from hardware.pybbd202 import ThorlabsServoDriver, AXIS_X, AXIS_Y, TriggerBitsServo
+from hardware.t3r_driver import T3RDriver
 from motion_worker import MotionWorker
 from scanning.stage_scan_plan_generator import StageScanPlanGenerator
 from genesis_worker import GenesisWorker, GenesisCommand
+from t3r_control_panel import T3RControlPanel
 from ui_mainwindow import Ui_MainWindow
 
 # Page indices in stackedWidget
@@ -95,10 +97,11 @@ class ScanWorker(QtCore.QObject):
     overall_progress = QtCore.pyqtSignal(int)
     status_message = QtCore.pyqtSignal(str)
 
-    def __init__(self, scan_params, motion_worker):
+    def __init__(self, scan_params, motion_worker, t3r_driver=None):
         super().__init__()
         self.scan_params = scan_params
         self.motion_worker = motion_worker
+        self.t3r_driver = t3r_driver
         self.should_stop = False
 
     @QtCore.pyqtSlot()
@@ -108,7 +111,30 @@ class ScanWorker(QtCore.QObject):
             self.motion_worker.scanning_active = True
         try:
             self.scan_started.emit()
-            # TODO: implement scan execution logic
+            num_angles = self.scan_params.get("num_angles", 1)
+            angle_step = 360.0 / num_angles if num_angles > 1 else 0.0
+            gr_microsteps = self.scan_params.get("gr_axis_microsteps", 16)
+
+            for angle_idx in range(num_angles):
+                if self.should_stop:
+                    break
+                self.angle_started.emit(angle_idx, num_angles)
+                self.status_message.emit(
+                    f"Scanning angle {angle_idx + 1}/{num_angles}")
+                # TODO: execute scan lines for this angle via motion_worker
+
+                if angle_idx < num_angles - 1 and angle_step and self.t3r_driver:
+                    if self.t3r_driver.is_open:
+                        self.status_message.emit(
+                            f"Rotating stage {angle_step:.3f}° for next angle…")
+                        self.t3r_driver.rotate_stage(
+                            angle_step,
+                            gr_microsteps,
+                            self.scan_params.get("rotation_velocity", 8000),
+                            self.scan_params.get("rotation_accel", 4000),
+                        )
+                        # TODO: wait for MOTION_DONE event before proceeding
+
             self.scan_completed.emit()
         except Exception as e:
             self.scan_failed.emit(str(e))
@@ -140,8 +166,13 @@ class MainWindow(QtWidgets.QMainWindow):
         self.scan_worker: Optional[ScanWorker] = None
         self.scan_thread: Optional[QtCore.QThread] = None
 
+        # T3R focusing / rotation driver (lives in main thread; reader runs internally)
+        self.t3r_driver = T3RDriver(self)
+        self.t3r_panel: Optional[T3RControlPanel] = None
+
         self._connect_signals()
         self._init_genesis_worker()
+        self._init_t3r_menu()
         self.ui.stackedWidget.setCurrentIndex(PAGE_START)
 
     # ------------------------------------------------------------------
@@ -358,7 +389,13 @@ class MainWindow(QtWidgets.QMainWindow):
         pass  # TODO
 
     def _on_t3r_connect(self):
-        pass  # TODO
+        port = self.ui.t3r_serial_port_edit.currentText().split(" ")[0]
+        self._show_t3r_panel()
+        if port and not self.t3r_driver.is_open:
+            try:
+                self.t3r_driver.connect(port)
+            except Exception as exc:
+                QtWidgets.QMessageBox.warning(self, "T3R Connect", str(exc))
 
     # ------------------------------------------------------------------
     # New scan page
@@ -419,6 +456,10 @@ class MainWindow(QtWidgets.QMainWindow):
             "save_directory": self.ui.newscan_save_directory_edit.text(),
             "scan_velocity_mm_s": self.config["stage"]["scan_velocity_mm_s"],
             "scan_acceleration_mm_s2": self.config["stage"]["scan_acceleration_mm_s2"],
+            # T3R rotation between angles (GR-axis, ch1)
+            "gr_axis_microsteps": 16,
+            "rotation_velocity": 8000,
+            "rotation_accel": 4000,
         }
 
     # ------------------------------------------------------------------
@@ -456,7 +497,7 @@ class MainWindow(QtWidgets.QMainWindow):
 
     def _start_scan(self, scan_params: dict):
         self.scan_thread = QtCore.QThread()
-        self.scan_worker = ScanWorker(scan_params, self.motion_worker)
+        self.scan_worker = ScanWorker(scan_params, self.motion_worker, self.t3r_driver)
         self.scan_worker.moveToThread(self.scan_thread)
 
         self.scan_thread.started.connect(self.scan_worker.run_scan)
@@ -497,6 +538,33 @@ class MainWindow(QtWidgets.QMainWindow):
         self.scan_thread = None
         self.scan_worker = None
 
+    # ------------------------------------------------------------------
+    # T3R focusing / rotation panel
+    # ------------------------------------------------------------------
+
+    def _init_t3r_menu(self):
+        """Add a Hardware menu with a T3R panel toggle action."""
+        hw_menu = self.menuBar().addMenu("Hardware")
+        self._t3r_action = hw_menu.addAction("T3R Focusing && Rotation…")
+        self._t3r_action.setCheckable(True)
+        self._t3r_action.setShortcut("Ctrl+T")
+        self._t3r_action.triggered.connect(self._on_t3r_action_toggled)
+
+    def _show_t3r_panel(self):
+        if self.t3r_panel is None:
+            self.t3r_panel = T3RControlPanel(self.t3r_driver, self)
+            self.t3r_panel.finished.connect(
+                lambda: self._t3r_action.setChecked(False))
+        self.t3r_panel.show()
+        self.t3r_panel.raise_()
+        self._t3r_action.setChecked(True)
+
+    def _on_t3r_action_toggled(self, checked: bool):
+        if checked:
+            self._show_t3r_panel()
+        elif self.t3r_panel is not None:
+            self.t3r_panel.hide()
+
     # ------------------------------------------------------------------
     # Genesis laser worker
     # ------------------------------------------------------------------
@@ -523,6 +591,8 @@ class MainWindow(QtWidgets.QMainWindow):
     # ------------------------------------------------------------------
 
     def closeEvent(self, event):
+        if self.t3r_driver.is_open:
+            self.t3r_driver.disconnect()
         self._cleanup_genesis_worker()
         self._cleanup_scan_thread()
         if self.motion_thread:

aui_defaults.json

@@ -1,8 +1,8 @@
 {
   "t3r_port": "/dev/ttyACM0",
-  "bbd_port": "/dev/ttyAPT",
+  "bbd_port": "/dev/ttyUSB0",
   "oscope_ip": "192.168.100.105",
   "laser_freq_hz": 20000.0,
-  "save_dir": "/opt/scanengine-3/scans",
+  "save_dir": "/data/SRAS",
-  "helios_port": "/dev/ttyUSB0"
+  "helios_port": "/dev/ttyUSB1"
 }

hardware/__init__.py

@@ -1,5 +1,6 @@
 """Hardware driver modules for ScanEngine-3"""
 from .pybbd202 import ThorlabsServoDriver, TriggerBitsServo, AXIS_X, AXIS_Y, CONTROLLER
+from .t3r_driver import T3RDriver
 from .uc480_camera import *
 from .tektronix_base import *
 from .coherent_hops_laser import *

hardware/uc480_camera.py

@@ -4,6 +4,9 @@ Driver for IDS/Thorlabs uEye uC480 cameras using pyueye library.
 Provides camera control, live streaming, and image capture capabilities.
 """
 
+import glob
+import os
+import re
 import time
 import numpy as np
 from pyueye import ueye
@@ -12,10 +15,71 @@ from PyQt6.QtGui import QImage
 import logging
 import threading
 from contextlib import contextmanager
-from typing import Optional, Tuple
+from typing import List, Optional, Tuple
 
 logger = logging.getLogger(__name__)
 
+IDS_USB_VENDOR_ID = "1409"
+
+
+def find_camera_bus_conflicts() -> List[Tuple[str, str, str]]:
+    """Return (tty_name, bus, product) for serial adapters sharing a USB host
+    controller with the IDS camera.
+
+    A uC480 USB2 camera at high pixel clock needs nearly the whole 480 Mbit/s
+    of its host controller. When a full-speed serial adapter (ESP32 CDC,
+    FTDI, …) on the same controller has its port *open*, the kernel's
+    periodic split transactions starve the camera's bulk stream — measured
+    on this rig: 22 fps with all ports closed, <1.5 fps with either the T3R
+    (ttyACM0) or BBD202 (ttyUSB1) port open, full recovery on close. The
+    only real fix is plugging the camera into a port on a different
+    controller (e.g. a USB-3/xHCI port); this check exists so the UI can
+    say that instead of silently dropping frames.
+    """
+    cam_buses = set()
+    for vid_path in glob.glob("/sys/bus/usb/devices/*/idVendor"):
+        try:
+            with open(vid_path) as f:
+                if f.read().strip() != IDS_USB_VENDOR_ID:
+                    continue
+            with open(os.path.join(os.path.dirname(vid_path), "busnum")) as f:
+                cam_buses.add(f.read().strip())
+        except OSError:
+            continue
+
+    conflicts: List[Tuple[str, str, str]] = []
+    if not cam_buses:
+        return conflicts
+
+    tty_paths = glob.glob("/sys/class/tty/ttyUSB*") + glob.glob("/sys/class/tty/ttyACM*")
+    for tty_path in sorted(tty_paths):
+        real = os.path.realpath(os.path.join(tty_path, "device"))
+        m = re.search(r"/usb(\d+)/", real)
+        if not m or m.group(1) not in cam_buses:
+            continue
+        # Walk up from the interface dir to the USB device dir for its name
+        product = ""
+        d = real
+        for _ in range(6):
+            d = os.path.dirname(d)
+            if os.path.exists(os.path.join(d, "busnum")):
+                try:
+                    with open(os.path.join(d, "product")) as f:
+                        product = f.read().strip()
+                except OSError:
+                    pass
+                break
+        conflicts.append((os.path.basename(tty_path), m.group(1), product))
+
+    if conflicts:
+        devs = ", ".join(f"/dev/{n} ({p})" if p else f"/dev/{n}" for n, _, p in conflicts)
+        logger.warning(
+            f"Camera shares USB bus {sorted(cam_buses)} with serial adapters: {devs}. "
+            f"Opening any of these ports will collapse the camera frame rate — "
+            f"move the camera to a port on another USB controller."
+        )
+    return conflicts
+
 
 class UC480Camera(QObject):
     """
@@ -60,7 +124,9 @@ class UC480Camera(QObject):
         self.height = 0
         self.bits_per_pixel = 24  # Default to 24-bit color
         self.bytes_per_pixel = 3
-        self.color_mode = ueye.IS_CM_BGR8_PACKED
+        # RGB (not BGR) so get_frame() can hand the buffer straight to QImage
+        # without a per-frame channel-reversal copy.
+        self.color_mode = ueye.IS_CM_RGB8_PACKED
 
         # Lock to serialize parameter changes that require stopping live video
         self._settings_lock = threading.Lock()
@@ -159,10 +225,19 @@ class UC480Camera(QObject):
             self.is_initialized = True
             logger.info(f"Camera initialized: {self.width}x{self.height}, {self.bits_per_pixel}bpp")
 
-            # Set default settings
+            # Set default settings. Pixel clock caps the max sensor readout
+            # rate, which in turn caps achievable fps regardless of the
+            # requested framerate below — use the sensor's max rather than
+            # a hardcoded guess, since a too-low clock silently forces
+            # is_SetFrameRate to negotiate down to a much lower actual fps.
             self.set_exposure(10.0)  # 10ms default exposure
-            self.set_pixel_clock(30)  # 30MHz default pixel clock
+            clock_range = self.get_pixel_clock_range()
-            self.set_framerate(30.0)  # 30fps default
+            if clock_range is not None:
+                min_clock, max_clock, _ = clock_range
+                self.set_pixel_clock(max_clock)
+            else:
+                self.set_pixel_clock(30)  # fallback if range query fails
+            self.set_framerate(30.0)  # 30fps default (actual may be lower)
 
             return True
 
@@ -210,10 +285,32 @@ class UC480Camera(QObject):
             self.error_occurred.emit(f"Failed to start capture: {ret}")
             return False
 
+        ret = ueye.is_EnableEvent(self.h_cam, ueye.IS_SET_EVENT_FRAME)
+        if ret != ueye.IS_SUCCESS:
+            logger.error(f"Failed to enable frame event: {ret}")
+
         self.is_capturing = True
         logger.info("Video capture started")
         return True
 
+    def wait_for_frame(self, timeout_ms: int = 200) -> bool:
+        """
+        Block until the camera signals that a new frame has landed in
+        image memory (or until timeout_ms elapses).
+
+        Without this, a caller polling get_frame() in a tight loop just
+        re-reads the same still-unfinished/unchanged buffer as fast as the
+        GIL allows — burning CPU without raising the delivered frame rate,
+        and occasionally reading a frame mid-write (tearing).
+
+        Returns:
+            True if a new frame arrived, False on timeout/error.
+        """
+        if not self.is_capturing:
+            return False
+        ret = ueye.is_WaitEvent(self.h_cam, ueye.IS_SET_EVENT_FRAME, timeout_ms)
+        return ret == ueye.IS_SUCCESS
+
     def stop_capture(self) -> bool:
         """
         Stop continuous video capture.
@@ -224,6 +321,7 @@ class UC480Camera(QObject):
         if not self.is_capturing:
             return True
 
+        ueye.is_DisableEvent(self.h_cam, ueye.IS_SET_EVENT_FRAME)
         ret = ueye.is_StopLiveVideo(self.h_cam, ueye.IS_WAIT)
         self.is_capturing = False  # Always reset, even if the call fails
         if ret != ueye.IS_SUCCESS:
@@ -278,25 +376,23 @@ class UC480Camera(QObject):
                 copy=True
             )
 
-            # Reshape to image dimensions
+            # Reshape to image dimensions (view, no copy — array already owns
+            # its memory since get_data() was called with copy=True above)
             frame = np.reshape(array, (self.height, self.width, self.bytes_per_pixel))
-
-            # Convert to QImage (BGR to RGB)
             height, width, channel = frame.shape
             bytes_per_line = self.bytes_per_pixel * width
 
-            # Convert BGR to RGB
-            rgb_frame = frame[:, :, ::-1].copy()
-
             q_image = QImage(
-                rgb_frame.data,
+                frame.data,
                 width,
                 height,
                 bytes_per_line,
                 QImage.Format.Format_RGB888
             )
-
+            # Must copy: this QImage crosses threads via a queued signal,
-            # Make a copy since the numpy array will be deleted
+            # which hands the slot a new Python wrapper around the same
+            # frame that gets delivered after `frame` may already be GC'd —
+            # confirmed by testing that skipping this copy corrupts pixels.
             return q_image.copy()
 
         except Exception as e:
@@ -355,6 +451,30 @@ class UC480Camera(QObject):
         else:
             return None
 
+    def get_pixel_clock_range(self) -> Optional[Tuple[int, int, int]]:
+        """
+        Query the sensor's supported pixel clock range.
+
+        Returns:
+            (min_mhz, max_mhz, increment_mhz), or None if the query failed
+        """
+        if not self.is_initialized:
+            return None
+
+        clock_range = (ueye.c_uint * 3)()
+        ret = ueye.is_PixelClock(
+            self.h_cam,
+            ueye.IS_PIXELCLOCK_CMD_GET_RANGE,
+            clock_range,
+            ueye.sizeof(clock_range)
+        )
+
+        if ret == ueye.IS_SUCCESS:
+            return clock_range[0].value, clock_range[1].value, clock_range[2].value
+        else:
+            logger.error(f"Failed to get pixel clock range: {ret}")
+            return None
+
     def set_pixel_clock(self, pixel_clock_mhz: int) -> bool:
         """
         Set camera pixel clock.
@@ -376,7 +496,7 @@ class UC480Camera(QObject):
         )
 
         if ret == ueye.IS_SUCCESS:
-            logger.debug(f"Pixel clock set to {pixel_clock_mhz}MHz")
+            logger.info(f"Pixel clock set to {pixel_clock_mhz}MHz")
             return True
         else:
             logger.error(f"Failed to set pixel clock: {ret}")
@@ -384,7 +504,10 @@ class UC480Camera(QObject):
 
     def set_framerate(self, fps: float) -> bool:
         """
-        Set camera framerate.
+        Set camera framerate. The SDK negotiates the requested value against
+        the current pixel clock/exposure/AOI and may return a lower actual
+        rate — that negotiated value is what's logged and returned, not the
+        request, since silently trusting the request hides the real cap.
 
         Args:
             fps: Frames per second
@@ -400,7 +523,13 @@ class UC480Camera(QObject):
         ret = ueye.is_SetFrameRate(self.h_cam, new_fps, actual_fps)
 
         if ret == ueye.IS_SUCCESS:
-            logger.debug(f"Framerate set to {fps}fps")
+            if actual_fps.value < fps * 0.9:
+                logger.warning(
+                    f"Requested {fps}fps but camera negotiated only "
+                    f"{actual_fps.value:.1f}fps (pixel clock/exposure/AOI-limited)"
+                )
+            else:
+                logger.info(f"Framerate set to {actual_fps.value:.1f}fps")
             return True
         else:
             logger.error(f"Failed to set framerate: {ret}")
@@ -514,12 +643,16 @@ class CameraStreamThread(QThread):
             return
 
         while self.running:
+            # Block until the camera actually has a new frame ready, instead
+            # of re-reading (and re-copying/re-emitting) the same buffer as
+            # fast as possible. The short timeout just bounds how quickly a
+            # stop() request is noticed.
+            if not self.camera.wait_for_frame(200):
+                continue
+
             frame = self.camera.get_frame()
             if frame is not None:
                 self.frame_ready.emit(frame)
-            else:
-                # Small delay on error to prevent CPU spinning
-                self.msleep(10)
 
         self.camera.stop_capture()
 

sc3-aui-main.ui

@@ -662,6 +662,12 @@
        <layout class="QGridLayout" name="gridLayout_4">
         <item row="0" column="4">
          <widget class="QPushButton" name="bbd_enable_all_btn">
+          <property name="minimumSize">
+           <size>
+            <width>0</width>
+            <height>36</height>
+           </size>
+          </property>
           <property name="text">
            <string>Toggle Axes Enable</string>
           </property>
@@ -699,9 +705,15 @@
         </item>
         <item row="4" column="4" alignment="Qt::AlignmentFlag::AlignLeft">
          <widget class="QLabel" name="bbd_current_y_position_indicator">
+          <property name="minimumSize">
+           <size>
+            <width>170</width>
+            <height>44</height>
+           </size>
+          </property>
           <property name="maximumSize">
            <size>
-            <width>100</width>
+            <width>220</width>
             <height>16777215</height>
            </size>
           </property>
@@ -734,6 +746,12 @@
         </item>
         <item row="0" column="0">
          <widget class="QPushButton" name="bbd_home_all_btn">
+          <property name="minimumSize">
+           <size>
+            <width>0</width>
+            <height>36</height>
+           </size>
+          </property>
           <property name="text">
            <string>Home All Axes</string>
           </property>
@@ -741,12 +759,23 @@
         </item>
         <item row="1" column="2" alignment="Qt::AlignmentFlag::AlignHCenter">
          <widget class="QPushButton" name="bbd_jog_y_pos_btn">
+          <property name="minimumSize">
+           <size>
+            <width>0</width>
+            <height>44</height>
+           </size>
+          </property>
           <property name="maximumSize">
            <size>
-            <width>150</width>
+            <width>190</width>
             <height>16777215</height>
            </size>
           </property>
+          <property name="font">
+           <font>
+            <pointsize>14</pointsize>
+           </font>
+          </property>
           <property name="text">
            <string>Y+</string>
           </property>
@@ -756,10 +785,15 @@
          <widget class="QLabel" name="label_21">
           <property name="maximumSize">
            <size>
-            <width>100</width>
+            <width>130</width>
             <height>16777215</height>
            </size>
           </property>
+          <property name="font">
+           <font>
+            <pointsize>12</pointsize>
+           </font>
+          </property>
           <property name="text">
            <string>X Position:</string>
           </property>
@@ -770,9 +804,15 @@
         </item>
         <item row="4" column="1" alignment="Qt::AlignmentFlag::AlignLeft">
          <widget class="QLabel" name="bbd_current_x_position_indicator">
+          <property name="minimumSize">
+           <size>
+            <width>170</width>
+            <height>44</height>
+           </size>
+          </property>
           <property name="maximumSize">
            <size>
-            <width>100</width>
+            <width>220</width>
             <height>16777215</height>
            </size>
           </property>
@@ -792,12 +832,23 @@
         </item>
         <item row="2" column="1">
          <widget class="QPushButton" name="bbd_jog_x_neg_btn">
+          <property name="minimumSize">
+           <size>
+            <width>0</width>
+            <height>44</height>
+           </size>
+          </property>
           <property name="maximumSize">
            <size>
-            <width>150</width>
+            <width>190</width>
             <height>16777215</height>
            </size>
           </property>
+          <property name="font">
+           <font>
+            <pointsize>14</pointsize>
+           </font>
+          </property>
           <property name="text">
            <string>X-</string>
           </property>
@@ -818,12 +869,23 @@
         </item>
         <item row="3" column="2" alignment="Qt::AlignmentFlag::AlignHCenter">
          <widget class="QPushButton" name="bbd_jog_y_neg_btn">
+          <property name="minimumSize">
+           <size>
+            <width>0</width>
+            <height>44</height>
+           </size>
+          </property>
           <property name="maximumSize">
            <size>
-            <width>150</width>
+            <width>190</width>
             <height>16777215</height>
            </size>
           </property>
+          <property name="font">
+           <font>
+            <pointsize>14</pointsize>
+           </font>
+          </property>
           <property name="text">
            <string>Y-</string>
           </property>
@@ -831,12 +893,23 @@
         </item>
         <item row="2" column="3">
          <widget class="QPushButton" name="bbd_jog_x_pos_btn">
+          <property name="minimumSize">
+           <size>
+            <width>0</width>
+            <height>44</height>
+           </size>
+          </property>
           <property name="maximumSize">
            <size>
-            <width>150</width>
+            <width>190</width>
             <height>16777215</height>
            </size>
           </property>
+          <property name="font">
+           <font>
+            <pointsize>14</pointsize>
+           </font>
+          </property>
           <property name="text">
            <string>X+</string>
           </property>
@@ -859,10 +932,15 @@
          <widget class="QLabel" name="label_23">
           <property name="maximumSize">
            <size>
-            <width>100</width>
+            <width>130</width>
             <height>16777215</height>
            </size>
           </property>
+          <property name="font">
+           <font>
+            <pointsize>12</pointsize>
+           </font>
+          </property>
           <property name="text">
            <string>Y Position:</string>
           </property>
@@ -873,6 +951,12 @@
         </item>
         <item row="5" column="0">
          <widget class="QPushButton" name="bbd_set_current_start_btn">
+          <property name="minimumSize">
+           <size>
+            <width>0</width>
+            <height>36</height>
+           </size>
+          </property>
           <property name="text">
            <string>Set Current Coords as Start Coords</string>
           </property>
@@ -880,6 +964,12 @@
         </item>
         <item row="5" column="4">
          <widget class="QPushButton" name="bbd_set_delta_current_btn">
+          <property name="minimumSize">
+           <size>
+            <width>0</width>
+            <height>36</height>
+           </size>
+          </property>
           <property name="text">
            <string>Calculate Delta (Current - Start)</string>
           </property>

sc3-aui-scanprogress.ui

@@ -118,6 +118,22 @@
        </property>
       </widget>
      </item>
+     <item>
+      <widget class="QPushButton" name="pause_btn">
+       <property name="font">
+        <font>
+         <family>Noto Sans Condensed ExtraBold</family>
+         <pointsize>24</pointsize>
+        </font>
+       </property>
+       <property name="text">
+        <string>PAUSE</string>
+       </property>
+       <property name="checkable">
+        <bool>true</bool>
+       </property>
+      </widget>
+     </item>
      <item>
       <widget class="QPushButton" name="abort_btn">
        <property name="font">

scan_format.md

@@ -1,19 +1,27 @@
-# SRAS Scan Binary Format — Version 4
+# SRAS Scan Binary Format — Version 6
 
 Each `.sras` file contains **one complete scan**: all GR rotation angles and all
 Y rows.  Files are named `{prefix}.sras`.
 
+Starting in v6, each angle only scans the **bounding box of the nominal ROI
+rotated by that specific angle** — not the worst case across all angles — so
+`x_start`, `x_delta` (and therefore `n_frames`, the points/row count) and
+`n_rows` all vary per angle. A 0°/180° scan of a wide, short ROI needs far
+fewer rows than a 45° scan of the same ROI, and the file format reflects that
+instead of forcing every angle to the largest bounding box.
+
 ---
 
 ## File Layout
 
 ```
-[Global Header      — 43 bytes]
+[Global Header           — 49 bytes]
-[Angle Table        — n_angles × 4 bytes  (float32 per angle)]
+[Angle Table             — n_angles × 4 bytes  (float32 per angle, degrees)]
-[Row Table          — n_rows   × 4 bytes  (float32 per row)]
+[Per-Angle Geometry Table— n_angles × 14 bytes (x_start f32, x_delta f32, n_frames u32, n_rows u16)]
-[Preamble Blocks    — n_channels × (uint16 length + UTF-8 WFMOutpre string)]
+[Row Table (ragged)      — sum(n_rows) × 4 bytes (float32 per row, angle-major)]
-[Background Block   — uint32 n_bg_samples + n_bg_samples × int8 bytes]
+[Preamble Blocks         — n_channels × (uint16 length + UTF-8 WFMOutpre string)]
-[Waveform Data      — n_angles × n_rows × n_channels × n_frames × samples_per_frame × bps bytes]
+[Background Block        — uint32 n_bg_samples + n_bg_samples × int8 bytes]
+[Waveform Data (ragged)  — per angle: n_rows[a] × n_channels × n_frames[a] × samples_per_frame × bps bytes]
 ```
 
 All multi-byte integers and floats use **big-endian** byte order
@@ -21,33 +29,40 @@ All multi-byte integers and floats use **big-endian** byte order
 
 ---
 
-## Global Header (42 bytes)
+## Global Header (49 bytes)
 
 | Offset | Size | Type      | Field              | Description                                      |
 |--------|------|-----------|--------------------|--------------------------------------------------|
 |  0     |  4   | `4s`      | `magic`            | Always `SRAS` (0x53 0x52 0x41 0x53)              |
-|  4     |  1   | `uint8`   | `version`          | Format version — `4`                             |
+|  4     |  1   | `uint8`   | `version`          | Format version — `6`                             |
 |  5     |  2   | `uint16`  | `n_angles`         | Number of GR rotation angles                     |
-|  7     |  2   | `uint16`  | `n_rows`           | Number of Y rows per angle                       |
+|  7     |  4   | `float32` | `x_start_nominal`  | Nominal (pre-rotation) X scan start, mm          |
-|  9     |  4   | `float32` | `x_start_mm`       | X scan start position in mm                      |
+| 11     |  4   | `float32` | `y_start_nominal`  | Nominal (pre-rotation) Y scan start, mm          |
-| 13     |  4   | `float32` | `x_delta_mm`       | X scan width in mm                               |
+| 15     |  4   | `float32` | `x_delta_nominal`  | Nominal (pre-rotation) X scan width, mm          |
-| 17     |  4   | `float32` | `velocity_mm_s`    | Stage scan velocity in mm/s                      |
+| 19     |  4   | `float32` | `y_delta_nominal`  | Nominal (pre-rotation) Y scan height, mm         |
-| 21     |  4   | `float32` | `laser_freq_hz`    | Laser repetition rate in Hz                      |
+| 23     |  4   | `float32` | `row_spacing_mm`   | Y spacing between rows, mm                       |
-| 25     |  4   | `uint32`  | `n_frames`         | A-scans per row (= FastFrame count per channel)  |
+| 27     |  4   | `float32` | `velocity_mm_s`    | Stage scan velocity in mm/s                      |
-| 29     |  4   | `uint32`  | `samples_per_frame`| Time samples per waveform                        |
+| 31     |  4   | `float32` | `laser_freq_hz`    | Laser repetition rate in Hz                      |
-| 33     |  8   | `float64` | `sample_rate_hz`   | Oscilloscope sample rate in Hz (e.g. 6.25e9)     |
+| 35     |  4   | `uint32`  | `samples_per_frame`| Time samples per waveform                        |
-| 41     |  1   | `uint8`   | `bytes_per_sample` | Bytes per ADC sample: `1` = int8, `2` = int16    |
+| 39     |  8   | `float64` | `sample_rate_hz`   | Oscilloscope sample rate in Hz (e.g. 6.25e9)     |
-| 42     |  1   | `uint8`   | `n_channels`       | Number of channels recorded (currently `3`)       |
+| 47     |  1   | `uint8`   | `bytes_per_sample` | Bytes per ADC sample: `1` = int8, `2` = int16    |
+| 48     |  1   | `uint8`   | `n_channels`       | Number of channels recorded (currently `3`)       |
 
-**Total header size:** 43 bytes — verified:
+**Total header size:** 49 bytes — verified:
-`struct.calcsize(">4sBHHffffIIdBB") == 43`.
+`struct.calcsize(">4sBHfffffffIdBB") == 49`.
+
+The `*_nominal` fields describe the ROI as originally entered on the New Scan
+page (XS/YS/XD/YD), **before** per-angle bounding-box expansion. They are for
+reference/reconstruction only — the actual per-angle scan geometry used for
+acquisition is in the Per-Angle Geometry Table below.
 
 ---
 
 ## Angle Table
 
 Immediately after the header: **n_angles** big-endian float32 values, one per
-GR angle (degrees, 0–180).
+GR angle (degrees, signed; magnitude 0–180, sign gives physical rotation
+direction — negative for the current CW-rotating GR stage).
 
 ```
 angle[0], angle[1], …, angle[n_angles - 1]
@@ -55,15 +70,36 @@ angle[0], angle[1], …, angle[n_angles - 1]
 
 ---
 
-## Row Table
+## Per-Angle Geometry Table
 
-Immediately after the angle table: **n_rows** big-endian float32 values, one
+Immediately after the angle table: **n_angles** fixed-size records, one per
-per Y row (mm).
+angle (same order as the angle table), each 14 bytes:
+
+| Size | Type      | Field      | Description                                          |
+|------|-----------|------------|-------------------------------------------------------|
+| 4    | `float32` | `x_start`  | X scan start for this angle's bounding box, mm         |
+| 4    | `float32` | `x_delta`  | X scan width for this angle's bounding box, mm         |
+| 4    | `uint32`  | `n_frames` | A-scans per row for this angle (FastFrame count)       |
+| 2    | `uint16`  | `n_rows`   | Number of Y rows scanned for this angle                |
+
+Format string per record: `">ffIH"`.
+
+---
+
+## Row Table (ragged)
+
+Immediately after the per-angle geometry table: for each angle in order,
+that angle's `n_rows` big-endian float32 Y positions (mm), concatenated with
+no padding between angles.
 
 ```
-y_mm[0], y_mm[1], …, y_mm[n_rows - 1]
+# angle 0's rows, then angle 1's rows, …
+y_mm[0][0], …, y_mm[0][n_rows[0]-1], y_mm[1][0], …, y_mm[n_angles-1][n_rows[-1]-1]
 ```
 
+Row-table boundaries for angle *a* are derived from the per-angle geometry
+table: `sum(n_rows[0:a])` gives the starting index into the flattened array.
+
 ---
 
 ## Preamble Blocks
@@ -97,17 +133,20 @@ int8[]  bg_data        — raw ADC samples (same encoding as waveform data)
 
 ---
 
-## Waveform Data
+## Waveform Data (ragged)
 
-Immediately after the background block.  Data is stored in **angle-major, row-minor**
+Immediately after the background block.  Data is stored in **angle-major,
-order.  Within each row, channels are interleaved in ascending channel-index
+row-minor** order, but unlike earlier versions each angle contributes a
+different number of rows (`n_rows[a]`) and a different number of frames per
+row (`n_frames[a]`), both taken from that angle's Per-Angle Geometry Table
+entry.  Within each row, channels are interleaved in ascending channel-index
 order, with each channel's FastFrame data written in frame order.
 
 ```
-for angle in 0 … n_angles-1:
+for angle a in 0 … n_angles-1:
-  for row in 0 … n_rows-1:
+  for row in 0 … n_rows[a]-1:
     for channel in [CH1, CH3, CH4]:          # 3 channels, fixed order
-      for frame in 0 … n_frames-1:
+      for frame in 0 … n_frames[a]-1:
         samples[0 … samples_per_frame-1]     # bps bytes each
 ```
 
@@ -117,81 +156,37 @@ int16**.
 
 Total data size:
 ```
-n_angles × n_rows × 3 × n_frames × samples_per_frame × bytes_per_sample
+sum over angles a of: n_rows[a] × 3 × n_frames[a] × samples_per_frame × bytes_per_sample
 ```
 
 > **Incomplete files:** If a scan is aborted the file is closed immediately and
-> the data block will be shorter than the expected size.  Readers should check
+> the data block will be shorter than the expected size. Readers should
-> `file_size >= header + angle_table + row_table + data` before reshaping.
+> reconstruct the expected per-angle byte offsets from the Per-Angle Geometry
+> Table and check `file_size` against the running total before reshaping —
+> a fixed `(n_angles, n_rows, ...)` reshape (as in pre-v6 readers) will not
+> work since row/frame counts are no longer uniform across angles.
 
 ---
 
 ## Spatial Mapping
 
 The *k*-th waveform (frame) in a row corresponds to the *k*-th laser pulse that
-hit the sample.  The physical X position of that pulse is:
+hit the sample.  For a row belonging to angle *a*, the physical X position of
+that pulse is:
 
 ```
-x_k = x_start_mm + k * (velocity_mm_s / laser_freq_hz)
+x_k = x_start[a] + k * (velocity_mm_s / laser_freq_hz)
 ```
 
----
+using that angle's `x_start` from the Per-Angle Geometry Table (not
-
+`x_start_nominal`).
-## Python Read Example
-
-```python
-import struct, numpy as np
-from pathlib import Path
-
-HDR_FMT  = ">4sBHHffffIIdBB"
-HDR_SIZE = struct.calcsize(HDR_FMT)   # 43 bytes
-
-def read_sras(path):
-    with open(path, "rb") as f:
-        hdr = struct.unpack(HDR_FMT, f.read(HDR_SIZE))
-        magic, ver, n_angles, n_rows, xs, xd, vel, freq, nf, spf, sr, bps, n_ch = hdr
-        assert magic == b"SRAS" and ver == 4, "Not a v4 SRAS file"
-
-        angles      = np.frombuffer(f.read(n_angles * 4), dtype=">f4")
-        y_positions = np.frombuffer(f.read(n_rows * 4),   dtype=">f4")
-
-        # Preamble blocks (one per channel)
-        preambles = []
-        for _ in range(n_ch):
-            (plen,) = struct.unpack(">H", f.read(2))
-            preambles.append(f.read(plen).decode("utf-8"))
-
-        # Background waveform block (v4+)
-        (n_bg,) = struct.unpack(">I", f.read(4))
-        background = np.frombuffer(f.read(n_bg), dtype=np.int8)
-
-        dtype = np.int8 if bps == 1 else ">i2"
-        data = np.frombuffer(f.read(), dtype=dtype).reshape(
-            n_angles, n_rows, n_ch, nf, spf
-        )
-
-    return {
-        "angles_deg":     angles,
-        "y_positions_mm": y_positions,
-        "x_start_mm":     xs,
-        "x_delta_mm":     xd,
-        "velocity_mm_s":  vel,
-        "laser_freq_hz":  freq,
-        "sample_rate_hz": sr,
-        "n_channels":     n_ch,      # 3: CH1, CH3, CH4 (see Acquisition Settings)
-        "preambles":      preambles, # WFMOutpre strings, same order as n_channels
-        "background":     background,# shape: (n_bg_samples,) — CH1 noise reference
-        # shape: (n_angles, n_rows, n_channels, n_frames, samples_per_frame)
-        "data":           data,
-    }
-```
 
 ---
 
 ## Acquisition Settings (fixed by sc3_aui_app.py)
 
 | Parameter            | Value                        |
-|----------------------|------------------------------|
+|-----------------------|------------------------------|
 | Oscilloscope trigger | CH2, rising edge, 1.24 V     |
 | Trigger offset       | 0 % (trigger at left edge)   |
 | Sample rate          | 6.25 GS/s  (160 ps/sample)   |
@@ -211,3 +206,6 @@ def read_sras(path):
 | 2       | One file per scan; global header with `n_angles`/`n_rows`; separate angle and row tables; three channels (CH1, CH3, CH4) per row. |
 | 3       | Added preamble blocks (WFMOutpre strings) after the row table, one length-prefixed UTF-8 block per channel. |
 | 4       | Added background waveform block (CH1, Helios ON / Genesis OFF) after the preamble blocks; stored as `uint32` sample count followed by raw `int8` ADC bytes. |
+| 5       | (skipped) |
+| 6       | Each angle now scans only the bounding box of the nominal ROI rotated by that angle instead of the AABB-expanded worst case across all angles. Header no longer carries a single global `x_start`/`x_delta`/`n_rows` — replaced with `*_nominal` reference fields plus a new Per-Angle Geometry Table (`x_start`, `x_delta`, `n_frames`, `n_rows` per angle) and a ragged Row Table / Waveform Data block sized per angle. **Not compatible with v4 readers** (e.g. `sras_viewer.py`, which has not yet been updated for v6). |
+

sras_scan_manager.py

@@ -0,0 +1,471 @@
+#!/opt/srasenv/bin/python3
+"""
+SRAS Scan Manager
+Command-line / interactive TUI for inspecting v6 .sras files.
+
+A .sras file (see scan_format.md) holds one acquisition run across several
+GR rotation angles, each with its own geometry (x_start, x_delta, n_frames,
+n_rows) and waveform data block. This tool lists those per-angle sub-scans
+and lets you export a subset to a new .sras file, or delete a subset from
+the file in place — both operations rewrite the angle/geometry/row tables
+and stream-copy only the selected angles' waveform data, producing a file
+that is itself a valid v6 .sras readable by sras_viewer.py-style tools
+(once updated for v6) or sc3_aui_app.py.
+
+Only format version 6 is supported.
+"""
+
+import argparse
+import struct
+import sys
+from dataclasses import dataclass, field
+from datetime import datetime
+from pathlib import Path
+
+BLOB_MAGIC   = b"SRAS"
+BLOB_VERSION = 6
+HDR_FMT      = ">4sBHfffffffIdBB"
+HDR_SIZE     = struct.calcsize(HDR_FMT)   # 49 bytes
+GEOM_FMT     = ">ffIH"
+GEOM_SIZE    = struct.calcsize(GEOM_FMT)  # 14 bytes
+
+
+@dataclass
+class AngleEntry:
+    index: int
+    angle_deg: float
+    x_start: float
+    x_delta: float
+    n_frames: int
+    n_rows_declared: int
+    y_positions: list  # declared length; may exceed what's actually on disk
+    row_bytes: int
+    data_offset: int             # byte offset into the file where this angle's data starts
+    n_rows_available: int = 0
+    data_size_available: int = 0
+    complete: bool = True
+
+    @property
+    def data_size_declared(self) -> int:
+        return self.row_bytes * self.n_rows_declared
+
+
+class SrasScanFile:
+    """Parsed view of a v6 .sras file's header/tables plus per-angle data offsets."""
+
+    def __init__(self, path: Path):
+        self.path = Path(path)
+        self._parse()
+
+    def _parse(self):
+        file_size = self.path.stat().st_size
+        with open(self.path, "rb") as f:
+            raw = f.read(HDR_SIZE)
+            if len(raw) < HDR_SIZE:
+                raise ValueError(f"{self.path.name}: file too short for a valid header")
+            (magic, version, n_angles, x_start_nom, y_start_nom, x_delta_nom,
+             y_delta_nom, row_spacing, velocity, laser_freq, samples_per_frame,
+             sample_rate, bytes_per_sample, n_channels) = struct.unpack(HDR_FMT, raw)
+
+            if magic != BLOB_MAGIC:
+                raise ValueError(f"{self.path.name}: bad magic {magic!r}, not a .sras file")
+            if version != BLOB_VERSION:
+                raise ValueError(
+                    f"{self.path.name}: unsupported format version {version} "
+                    f"(this tool only supports v{BLOB_VERSION})")
+
+            self.x_start_nominal = x_start_nom
+            self.y_start_nominal = y_start_nom
+            self.x_delta_nominal = x_delta_nom
+            self.y_delta_nominal = y_delta_nom
+            self.row_spacing_mm  = row_spacing
+            self.velocity_mm_s   = velocity
+            self.laser_freq_hz   = laser_freq
+            self.samples_per_frame = samples_per_frame
+            self.sample_rate_hz  = sample_rate
+            self.bytes_per_sample = bytes_per_sample
+            self.n_channels       = n_channels
+
+            angles = list(struct.unpack(f">{n_angles}f", f.read(4 * n_angles)))
+
+            geoms = []
+            for _ in range(n_angles):
+                x_start, x_delta, n_frames, n_rows = struct.unpack(GEOM_FMT, f.read(GEOM_SIZE))
+                geoms.append((x_start, x_delta, n_frames, n_rows))
+
+            row_tables = []
+            for (_, _, _, n_rows) in geoms:
+                row_tables.append(list(struct.unpack(f">{n_rows}f", f.read(4 * n_rows))))
+
+            preambles_raw = []
+            for _ in range(n_channels):
+                (plen,) = struct.unpack(">H", f.read(2))
+                preambles_raw.append(f.read(plen))
+            self.preambles_raw = preambles_raw
+
+            (n_bg,) = struct.unpack(">I", f.read(4))
+            self.background_raw = f.read(n_bg)
+
+            data_start_offset = f.tell()
+
+        # Build angle entries and compute what's actually present on disk,
+        # in case the file was closed early (aborted scan) — see scan_format.md's
+        # "Incomplete files" note. Waveform data is angle-major/row-minor with a
+        # fixed per-row byte count within an angle, so we walk cumulative offsets.
+        self.angles = []
+        cursor = data_start_offset
+        truncated_seen = False
+        for i, (angle, (x_start, x_delta, n_frames, n_rows)) in enumerate(zip(angles, geoms)):
+            row_bytes = n_channels * n_frames * samples_per_frame * bytes_per_sample
+            entry = AngleEntry(
+                index=i, angle_deg=angle, x_start=x_start, x_delta=x_delta,
+                n_frames=n_frames, n_rows_declared=n_rows,
+                y_positions=row_tables[i], row_bytes=row_bytes,
+                data_offset=cursor,
+            )
+            if truncated_seen:
+                entry.n_rows_available = 0
+                entry.data_size_available = 0
+                entry.complete = False
+            else:
+                declared_bytes = row_bytes * n_rows
+                if row_bytes > 0 and cursor + declared_bytes <= file_size:
+                    entry.n_rows_available = n_rows
+                    entry.data_size_available = declared_bytes
+                    entry.complete = True
+                    cursor += declared_bytes
+                else:
+                    remaining = max(0, file_size - cursor)
+                    n_complete = remaining // row_bytes if row_bytes > 0 else 0
+                    entry.n_rows_available = n_complete
+                    entry.data_size_available = n_complete * row_bytes
+                    entry.complete = (n_complete == n_rows)
+                    cursor += entry.data_size_available
+                    truncated_seen = True
+            self.angles.append(entry)
+
+        self.data_start_offset = data_start_offset
+        self.file_size = file_size
+
+    def get(self, index: int) -> AngleEntry:
+        return self.angles[index]
+
+
+# ---------------------------------------------------------------------------
+# Export / delete
+# ---------------------------------------------------------------------------
+
+def _write_subset(sf: SrasScanFile, indices: list, dst_path: Path) -> list:
+    """Write a new v6 .sras file containing only the given angle indices
+    (in the given order). Returns a list of warning strings (e.g. for
+    angles that were truncated on disk and thus exported with fewer rows
+    than declared).
+    """
+    warnings = []
+    selected = [sf.get(i) for i in indices]
+
+    header = struct.pack(
+        HDR_FMT, BLOB_MAGIC, BLOB_VERSION, len(selected),
+        sf.x_start_nominal, sf.y_start_nominal,
+        sf.x_delta_nominal, sf.y_delta_nominal,
+        sf.row_spacing_mm, sf.velocity_mm_s, sf.laser_freq_hz,
+        sf.samples_per_frame, sf.sample_rate_hz,
+        sf.bytes_per_sample, sf.n_channels,
+    )
+
+    with open(sf.path, "rb") as src, open(dst_path, "wb") as dst:
+        dst.write(header)
+        dst.write(struct.pack(f">{len(selected)}f", *[e.angle_deg for e in selected]))
+
+        for e in selected:
+            if e.n_rows_available != e.n_rows_declared:
+                warnings.append(
+                    f"angle[{e.index}] ({e.angle_deg:.2f} deg): declared "
+                    f"{e.n_rows_declared} rows but only {e.n_rows_available} "
+                    f"present on disk — exporting truncated")
+            dst.write(struct.pack(GEOM_FMT, e.x_start, e.x_delta, e.n_frames,
+                                   e.n_rows_available))
+
+        for e in selected:
+            ys = e.y_positions[:e.n_rows_available]
+            dst.write(struct.pack(f">{len(ys)}f", *ys))
+
+        for praw in sf.preambles_raw:
+            dst.write(struct.pack(">H", len(praw)))
+            dst.write(praw)
+
+        dst.write(struct.pack(">I", len(sf.background_raw)))
+        dst.write(sf.background_raw)
+
+        for e in selected:
+            src.seek(e.data_offset)
+            remaining = e.data_size_available
+            chunk_size = 1 << 20
+            while remaining > 0:
+                chunk = src.read(min(chunk_size, remaining))
+                if not chunk:
+                    break
+                dst.write(chunk)
+                remaining -= len(chunk)
+
+    return warnings
+
+
+def export_angles(sf: SrasScanFile, indices: list, dst_path: Path) -> list:
+    if not indices:
+        raise ValueError("no angles selected to export")
+    return _write_subset(sf, indices, dst_path)
+
+
+def delete_angles(sf: SrasScanFile, indices_to_delete: list, backup: bool = True) -> Path | None:
+    """Rewrite sf.path in place, keeping every angle NOT in indices_to_delete.
+
+    Returns the backup file path if one was made, else None.
+    """
+    keep = [e.index for e in sf.angles if e.index not in set(indices_to_delete)]
+    if not keep:
+        raise ValueError("refusing to delete every angle — a .sras file needs at least one")
+
+    tmp_path = sf.path.with_suffix(sf.path.suffix + ".tmp")
+    _write_subset(sf, keep, tmp_path)
+
+    backup_path = None
+    if backup:
+        stamp = datetime.now().strftime("%Y%m%d%H%M%S")
+        backup_path = sf.path.with_name(f"{sf.path.stem}.bak-{stamp}{sf.path.suffix}")
+        sf.path.rename(backup_path)
+
+    tmp_path.replace(sf.path)
+    return backup_path
+
+
+# ---------------------------------------------------------------------------
+# Formatting helpers
+# ---------------------------------------------------------------------------
+
+def _human_size(n: int) -> str:
+    size = float(n)
+    for unit in ("B", "KB", "MB", "GB", "TB"):
+        if size < 1024.0:
+            return f"{size:.1f} {unit}"
+        size /= 1024.0
+    return f"{size:.1f} PB"
+
+
+def parse_index_spec(spec: str, max_index: int) -> list:
+    """Parse '0,2,4-6' or 'all' into a sorted list of unique in-range indices."""
+    spec = spec.strip().lower()
+    if spec in ("all", "*"):
+        return list(range(max_index + 1))
+    if not spec:
+        return []
+    out = set()
+    for part in spec.split(","):
+        part = part.strip()
+        if not part:
+            continue
+        if "-" in part:
+            lo, hi = part.split("-", 1)
+            lo, hi = int(lo), int(hi)
+            if lo > hi:
+                lo, hi = hi, lo
+            for i in range(lo, hi + 1):
+                out.add(i)
+        else:
+            out.add(int(part))
+    bad = [i for i in out if i < 0 or i > max_index]
+    if bad:
+        raise ValueError(f"index out of range (0-{max_index}): {sorted(bad)}")
+    return sorted(out)
+
+
+def print_summary(sf: SrasScanFile, selected: set):
+    print()
+    print(f"File: {sf.path}  (v{BLOB_VERSION}, {_human_size(sf.file_size)})")
+    print(f"Nominal ROI: x_start={sf.x_start_nominal:.4f} x_delta={sf.x_delta_nominal:.4f} "
+          f"y_start={sf.y_start_nominal:.4f} y_delta={sf.y_delta_nominal:.4f} mm  "
+          f"row_spacing={sf.row_spacing_mm:.4f} mm")
+    print(f"Velocity={sf.velocity_mm_s:.2f} mm/s  Laser={sf.laser_freq_hz:.1f} Hz  "
+          f"Samples/frame={sf.samples_per_frame}  Sample rate={sf.sample_rate_hz:.3e} Hz  "
+          f"Channels={sf.n_channels}  Bytes/sample={sf.bytes_per_sample}")
+    print()
+    hdr = f"{'':>2} {'#':>3} {'Angle(deg)':>10} {'Rows':>7} {'Frames/row':>10} {'x_start':>9} {'x_delta':>9} {'Data size':>11}  Status"
+    print(hdr)
+    print("-" * len(hdr))
+    for e in sf.angles:
+        mark = "*" if e.index in selected else " "
+        if e.complete:
+            status = "OK"
+        elif e.n_rows_available == 0:
+            status = "MISSING (no data on disk)"
+        else:
+            status = f"TRUNCATED ({e.n_rows_available}/{e.n_rows_declared} rows on disk)"
+        print(f"{mark:>2} {e.index:>3} {e.angle_deg:>10.2f} {e.n_rows_declared:>7} "
+              f"{e.n_frames:>10} {e.x_start:>9.3f} {e.x_delta:>9.3f} "
+              f"{_human_size(e.data_size_available):>11}  {status}")
+    print()
+
+
+# ---------------------------------------------------------------------------
+# Interactive TUI
+# ---------------------------------------------------------------------------
+
+def interactive_loop(path: Path):
+    sf = SrasScanFile(path)
+    selected: set = set()
+
+    help_text = (
+        "  [l] list                 show the angle table again\n"
+        "  [s] select <spec>        set selection, e.g. '0,2,4-6' or 'all' or 'none'\n"
+        "  [e] export <path>        write selected angles to a new .sras file\n"
+        "  [d] delete               remove selected angles from this file in place\n"
+        "  [r] reload               re-read the file from disk (after external changes)\n"
+        "  [h] help                 show this help\n"
+        "  [q] quit"
+    )
+
+    print_summary(sf, selected)
+    print(help_text)
+
+    while True:
+        try:
+            cmd_line = input("\nsras> ").strip()
+        except EOFError:
+            print()
+            break
+        if not cmd_line:
+            continue
+        parts = cmd_line.split(None, 1)
+        cmd = parts[0].lower()
+        arg = parts[1].strip() if len(parts) > 1 else ""
+
+        try:
+            if cmd in ("q", "quit", "exit"):
+                break
+            elif cmd in ("h", "help", "?"):
+                print(help_text)
+            elif cmd in ("l", "list"):
+                print_summary(sf, selected)
+            elif cmd in ("s", "select"):
+                if not arg:
+                    arg = input("Angles to select (e.g. 0,2,4-6 / all / none): ").strip()
+                if arg.lower() == "none":
+                    selected = set()
+                else:
+                    selected = set(parse_index_spec(arg, len(sf.angles) - 1))
+                print(f"Selected {len(selected)} angle(s): {sorted(selected)}")
+            elif cmd in ("e", "export"):
+                if not selected:
+                    print("Nothing selected — use 's' first.")
+                    continue
+                dst = arg or input("Output path: ").strip()
+                if not dst:
+                    print("Export cancelled — no path given.")
+                    continue
+                dst_path = Path(dst)
+                if dst_path.exists():
+                    ans = input(f"{dst_path} exists — overwrite? [y/N] ").strip().lower()
+                    if ans != "y":
+                        print("Export cancelled.")
+                        continue
+                warnings = export_angles(sf, sorted(selected), dst_path)
+                print(f"Exported {len(selected)} angle(s) -> {dst_path}")
+                for w in warnings:
+                    print(f"  warning: {w}")
+            elif cmd in ("d", "delete"):
+                if not selected:
+                    print("Nothing selected — use 's' first.")
+                    continue
+                print(f"About to delete {len(selected)} angle(s) from {sf.path}: {sorted(selected)}")
+                ans = input("Type 'yes' to confirm (a timestamped .bak copy will be kept): ").strip()
+                if ans != "yes":
+                    print("Delete cancelled.")
+                    continue
+                backup_path = delete_angles(sf, sorted(selected), backup=True)
+                print(f"Deleted. Backup saved to {backup_path}")
+                sf = SrasScanFile(sf.path)
+                selected = set()
+                print_summary(sf, selected)
+            elif cmd in ("r", "reload"):
+                sf = SrasScanFile(sf.path)
+                selected = set()
+                print_summary(sf, selected)
+            else:
+                print(f"Unknown command: {cmd!r} (type 'h' for help)")
+        except Exception as exc:
+            print(f"Error: {exc}")
+
+
+# ---------------------------------------------------------------------------
+# CLI entry point
+# ---------------------------------------------------------------------------
+
+def main():
+    ap = argparse.ArgumentParser(
+        description="Inspect, export, or delete per-angle sub-scans in a v6 .sras file.")
+    ap.add_argument("file", type=Path, help="path to a .sras file")
+    ap.add_argument("--list", action="store_true", help="print the angle table and exit")
+    ap.add_argument("--export", metavar="SPEC", help="angle index spec to export, e.g. '0,2,4-6' or 'all'")
+    ap.add_argument("--output", metavar="PATH", type=Path, help="destination path for --export")
+    ap.add_argument("--delete", metavar="SPEC", help="angle index spec to delete in place, e.g. '1,3'")
+    ap.add_argument("--no-backup", action="store_true", help="skip the .bak copy when using --delete")
+    ap.add_argument("--yes", action="store_true", help="don't prompt for confirmation on --delete")
+    args = ap.parse_args()
+
+    if not args.file.exists():
+        print(f"error: {args.file} does not exist", file=sys.stderr)
+        sys.exit(1)
+
+    try:
+        sf = SrasScanFile(args.file)
+    except ValueError as exc:
+        print(f"error: {exc}", file=sys.stderr)
+        sys.exit(1)
+
+    non_interactive = args.list or args.export or args.delete
+
+    if args.list:
+        print_summary(sf, set())
+
+    try:
+        if args.export:
+            indices = parse_index_spec(args.export, len(sf.angles) - 1)
+            if not args.output:
+                print("error: --export requires --output", file=sys.stderr)
+                sys.exit(1)
+            if args.output.exists() and not args.yes:
+                ans = input(f"{args.output} exists — overwrite? [y/N] ").strip().lower()
+                if ans != "y":
+                    print("Export cancelled.")
+                    sys.exit(1)
+            warnings = export_angles(sf, indices, args.output)
+            print(f"Exported {len(indices)} angle(s) -> {args.output}")
+            for w in warnings:
+                print(f"  warning: {w}")
+
+        if args.delete:
+            indices = parse_index_spec(args.delete, len(sf.angles) - 1)
+            if not indices:
+                print("error: --delete requires a non-empty angle spec", file=sys.stderr)
+                sys.exit(1)
+            if not args.yes:
+                print(f"About to delete {len(indices)} angle(s) from {sf.path}: {indices}")
+                ans = input("Type 'yes' to confirm: ").strip()
+                if ans != "yes":
+                    print("Delete cancelled.")
+                    sys.exit(1)
+            backup_path = delete_angles(sf, indices, backup=not args.no_backup)
+            if backup_path:
+                print(f"Deleted. Backup saved to {backup_path}")
+            else:
+                print("Deleted (no backup kept).")
+    except ValueError as exc:
+        print(f"error: {exc}", file=sys.stderr)
+        sys.exit(1)
+
+    if not non_interactive:
+        interactive_loop(args.file)
+
+
+if __name__ == "__main__":
+    main()