Loading openflexure_microscope/api/default_extensions/autofocus.py +75 −55 Original line number Diff line number Diff line import logging import time from collections import namedtuple from contextlib import contextmanager from threading import Event, Thread import numpy as np from labthings import current_action, fields, find_component Loading @@ -14,80 +14,100 @@ from openflexure_microscope.utilities import set_properties ### Autofocus utilities # Class to store a frames metadata TrackerFrame = namedtuple("TrackerFrame", ["size", "time"]) class FrameTracker(object): """ A file-like object used to analyse MJPEG frames. Instead of analysing a load of real MJPEG frames after they've been stored in a BytesIO stream, we tell the camera to write frames to this class instead. We then do analysis as the frames are written, and discard the heavier image data. """ def __init__(self): # Array of TrackerFrame objects self.frames = [] self.last = None def write(self, s): # Store the incoming frame metadata # Discards the actual frame image data # NOTE: This could be used for smarter processing # E.g. different sharpness metrics frame = TrackerFrame(size=len(s), time=time.time()) self.frames.append(frame) self.last = frame def flush(self): # Called at end of recording pass class JPEGSharpnessMonitor: def __init__(self, microscope, timeout=60): def __init__(self, microscope): self.microscope = microscope self.camera = microscope.camera self.stage = microscope.stage self.jpeg_sizes = [] self.jpeg_times = [] self.recording_start_time = None self.stage_positions = [] self.stage_times = [] self.stop_event = Event() self.timeout = timeout self.keep_alive() self.background_thread = None def is_alive(self): if self.background_thread is None: return False else: return self.background_thread.is_alive() self.jpeg_times = [] self.jpeg_sizes = [] def should_stop(self): return time.time() - self.kept_alive > self.timeout # Splitter port 3 is reserved for autofocus self.splitter_port = 3 self.stream = FrameTracker() def keep_alive(self): self.kept_alive = time.time() def stop_recording(self): logging.info("Stopping recording for autofocus...") self.camera.camera.stop_recording(splitter_port=self.splitter_port) logging.info("Stopped recording for autofocus!") def start(self): "Start monitoring sharpness by looking at JPEG size" if not self.camera.stream_active: logging.warning( "Autofocus sharpness monitor was started but the camera isn't streaming. Attempting to start the stream..." # Log the recording start time self.recording_start_time = time.time() # Start the stream recording self.camera.camera.start_recording( self.stream, format="mjpeg", quality=100, # Use best quality (we don't store the frames anyway!) bitrate=-1, # RWB: disable bitrate control # (bitrate control makes JPEG size less good as a focus # metric) splitter_port=self.splitter_port, ) self.camera.start_stream_recording() self.background_thread = Thread(target=self._measure_jpegs) self.background_thread.start() return self logging.info("Started recording for autofocus") def stop(self): "Stop the background thread" self.stop_event.set() logging.info("Joining JPEG thread") self.background_thread.join() def _measure_jpegs(self): "Function that runs in a background thread to record sharpness" logging.debug("Starting sharpness measurement in background thread") self.keep_alive() logging.debug("_measure_jpegs stop_event: %s", self.stop_event.is_set()) while not self.stop_event.is_set() and not self.should_stop(): size_now = self.jpeg_size() time_now = time.time() self.jpeg_sizes.append(size_now) self.jpeg_times.append(time_now) logging.info("Exited JPEG measure loop") if self.stop_event.is_set(): logging.debug("Cleanly stopped sharpness measurement in background thread") if self.should_stop(): logging.debug("Sharpness measurement timed out and has stopped") def jpeg_size(self): """Return the size of a frame from the MJPEG stream""" return len(self.camera.get_frame()) self.stop_recording() logging.info("Stopped recording for autofocus") def focus_rel(self, dz, backlash=False, **kwargs): self.keep_alive() # Start time and position # Store the start time and position self.stage_times.append(time.time()) self.stage_positions.append(self.stage.position) # Main move self.stage.move_rel([0, 0, dz], backlash=backlash, **kwargs) # End time and position # Store the end time and position self.stage_times.append(time.time()) self.stage_positions.append(self.stage.position) # Retrieve frame data for frame in self.stream.frames: # Make timestamp absolute Unix time self.jpeg_times.append(frame.time) self.jpeg_sizes.append(frame.size) # Index of the data for this movement data_index = len(self.stage_positions) - 2 # Final z position after move Loading Loading @@ -309,7 +329,7 @@ def fast_up_down_up_autofocus( # We've deliberately undershot - figure out how much further we should move based on the curve logging.debug("Calculate remining movement") current_js = m.jpeg_size() current_js = m.stream.last.size imax = np.argmax(js) # we want to crop out just the bit below the peak js = js[imax:] # NB z is in DECREASING order jz = jz[imax:] Loading Loading
openflexure_microscope/api/default_extensions/autofocus.py +75 −55 Original line number Diff line number Diff line import logging import time from collections import namedtuple from contextlib import contextmanager from threading import Event, Thread import numpy as np from labthings import current_action, fields, find_component Loading @@ -14,80 +14,100 @@ from openflexure_microscope.utilities import set_properties ### Autofocus utilities # Class to store a frames metadata TrackerFrame = namedtuple("TrackerFrame", ["size", "time"]) class FrameTracker(object): """ A file-like object used to analyse MJPEG frames. Instead of analysing a load of real MJPEG frames after they've been stored in a BytesIO stream, we tell the camera to write frames to this class instead. We then do analysis as the frames are written, and discard the heavier image data. """ def __init__(self): # Array of TrackerFrame objects self.frames = [] self.last = None def write(self, s): # Store the incoming frame metadata # Discards the actual frame image data # NOTE: This could be used for smarter processing # E.g. different sharpness metrics frame = TrackerFrame(size=len(s), time=time.time()) self.frames.append(frame) self.last = frame def flush(self): # Called at end of recording pass class JPEGSharpnessMonitor: def __init__(self, microscope, timeout=60): def __init__(self, microscope): self.microscope = microscope self.camera = microscope.camera self.stage = microscope.stage self.jpeg_sizes = [] self.jpeg_times = [] self.recording_start_time = None self.stage_positions = [] self.stage_times = [] self.stop_event = Event() self.timeout = timeout self.keep_alive() self.background_thread = None def is_alive(self): if self.background_thread is None: return False else: return self.background_thread.is_alive() self.jpeg_times = [] self.jpeg_sizes = [] def should_stop(self): return time.time() - self.kept_alive > self.timeout # Splitter port 3 is reserved for autofocus self.splitter_port = 3 self.stream = FrameTracker() def keep_alive(self): self.kept_alive = time.time() def stop_recording(self): logging.info("Stopping recording for autofocus...") self.camera.camera.stop_recording(splitter_port=self.splitter_port) logging.info("Stopped recording for autofocus!") def start(self): "Start monitoring sharpness by looking at JPEG size" if not self.camera.stream_active: logging.warning( "Autofocus sharpness monitor was started but the camera isn't streaming. Attempting to start the stream..." # Log the recording start time self.recording_start_time = time.time() # Start the stream recording self.camera.camera.start_recording( self.stream, format="mjpeg", quality=100, # Use best quality (we don't store the frames anyway!) bitrate=-1, # RWB: disable bitrate control # (bitrate control makes JPEG size less good as a focus # metric) splitter_port=self.splitter_port, ) self.camera.start_stream_recording() self.background_thread = Thread(target=self._measure_jpegs) self.background_thread.start() return self logging.info("Started recording for autofocus") def stop(self): "Stop the background thread" self.stop_event.set() logging.info("Joining JPEG thread") self.background_thread.join() def _measure_jpegs(self): "Function that runs in a background thread to record sharpness" logging.debug("Starting sharpness measurement in background thread") self.keep_alive() logging.debug("_measure_jpegs stop_event: %s", self.stop_event.is_set()) while not self.stop_event.is_set() and not self.should_stop(): size_now = self.jpeg_size() time_now = time.time() self.jpeg_sizes.append(size_now) self.jpeg_times.append(time_now) logging.info("Exited JPEG measure loop") if self.stop_event.is_set(): logging.debug("Cleanly stopped sharpness measurement in background thread") if self.should_stop(): logging.debug("Sharpness measurement timed out and has stopped") def jpeg_size(self): """Return the size of a frame from the MJPEG stream""" return len(self.camera.get_frame()) self.stop_recording() logging.info("Stopped recording for autofocus") def focus_rel(self, dz, backlash=False, **kwargs): self.keep_alive() # Start time and position # Store the start time and position self.stage_times.append(time.time()) self.stage_positions.append(self.stage.position) # Main move self.stage.move_rel([0, 0, dz], backlash=backlash, **kwargs) # End time and position # Store the end time and position self.stage_times.append(time.time()) self.stage_positions.append(self.stage.position) # Retrieve frame data for frame in self.stream.frames: # Make timestamp absolute Unix time self.jpeg_times.append(frame.time) self.jpeg_sizes.append(frame.size) # Index of the data for this movement data_index = len(self.stage_positions) - 2 # Final z position after move Loading Loading @@ -309,7 +329,7 @@ def fast_up_down_up_autofocus( # We've deliberately undershot - figure out how much further we should move based on the curve logging.debug("Calculate remining movement") current_js = m.jpeg_size() current_js = m.stream.last.size imax = np.argmax(js) # we want to crop out just the bit below the peak js = js[imax:] # NB z is in DECREASING order jz = jz[imax:] Loading
