Merge branch 'fast-autofocus' into 'master'

Added fast autofocus to default plugins

See merge request openflexure/openflexure-microscope-server!6

openflexure_microscope/camera/pi.py

@@ -366,6 +366,7 @@ class StreamingCamera(BaseCamera):
                     self.stream,
                     format='mjpeg',
                     quality=self.config['jpeg_quality'],
+                    bitrate=-1, # RWB: disable bitrate control
                     splitter_port=splitter_port)
             except picamera.exc.PiCameraAlreadyRecording:
                 logging.info("Error while starting preview: Recording already running.")

openflexure_microscope/plugins/default/fast_autofocus/__init__.py

@@ -0,0 +1,168 @@
+import time
+import numpy as np
+import threading
+
+from openflexure_microscope.plugins import MicroscopePlugin
+from openflexure_microscope.utilities import set_properties
+from openflexure_microscope.api.v1.views import MicroscopeViewPlugin
+from openflexure_microscope.api.utilities import JsonPayload
+from flask import request, jsonify, abort, current_app
+import logging
+from contextlib import contextmanager
+
+class JPEGSharpnessMonitor():
+    def __init__(self, microscope, timeout=60):
+        self.microscope = microscope
+        self.camera = microscope.camera
+        self.stage = microscope.stage
+        self.jpeg_sizes = []
+        self.jpeg_times = []
+        self.stage_positions = []
+        self.stage_times = []
+        self.stop_event = threading.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()
+            
+    def should_stop(self):
+        import time
+        return time.time() - self.kept_alive > self.timeout
+    
+    def keep_alive(self):
+        import time
+        self.kept_alive = time.time()
+    
+    def start(self):
+        "Start monitoring sharpness by looking at JPEG size"
+        self.background_thread = threading.Thread(target=self._measure_jpegs)
+        self.background_thread.start()
+        return self
+        
+    def stop(self):
+        "Stop the background thread"
+        self.stop_event.set()
+        self.background_thread.join()
+        
+    def _measure_jpegs(self):
+        "Function that runs in a background thread to record sharpness"
+        logging.info("Starting sharpness measurement in background thread")
+        self.keep_alive()
+        while not self.stop_event.is_set() and not self.should_stop():
+            self.jpeg_sizes.append(self.jpeg_size())
+            self.jpeg_times.append(time.time())
+        if self.stop_event.is_set():
+            logging.info("Cleanly stopped sharpness measurement in background thread")
+        if self.should_stop():
+            logging.info("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())
+
+
+    def focus_rel(self, dz, backlash=False, **kwargs):
+        self.keep_alive()
+        self.stage_times.append(time.time())
+        self.stage_positions.append(self.stage.position)
+        self.stage.move_rel([0, 0, dz], backlash=backlash, **kwargs)
+        self.stage_times.append(time.time())
+        self.stage_positions.append(self.stage.position)
+        i = len(self.stage_positions) - 2
+        return i, self.stage_positions[-1][2]
+        
+    def move_data(self, istart, istop=None):
+        "Extract sharpness as a function of (interpolated) z"
+        global np, logging
+        if istop is None:
+            istop = istart + 2
+        jpeg_times = np.array(self.jpeg_times)
+        jpeg_sizes = np.array(self.jpeg_sizes)
+        stage_times = np.array(self.stage_times)[istart:istop]
+        stage_zs = np.array(self.stage_positions)[istart:istop, 2]
+        start = np.argmax(jpeg_times > stage_times[0])
+        stop = np.argmax(jpeg_times > stage_times[1])
+        if stop < 1:
+            stop = len(jpeg_times)
+            logging.debug("changing stop to {}".format(stop))
+        jpeg_times = jpeg_times[start:stop]
+        jpeg_zs = np.interp(jpeg_times, stage_times, stage_zs)
+        return jpeg_times, jpeg_zs, jpeg_sizes[start:stop]
+
+    def sharpest_z_on_move(self, index):
+        """Return the z position of the sharpest image on a given move"""
+        jt, jz, js = self.move_data(index)
+        return jz[np.argmax(js)]
+    
+    def data_dict(self):
+        """Return the gathered data as a single convenient dictionary"""
+        data = {}
+        for k in ['jpeg_times', 'jpeg_sizes', 'stage_times', 'stage_positions']:
+            data[k] = getattr(self, k)
+        return data
+
+class FastAutofocusAPI(MicroscopeViewPlugin):
+    def post(self):
+        payload = JsonPayload(request)
+        
+        # Figure out the parameters to use
+        dz = payload.param("dz", default=2000, convert=int)
+        backlash = payload.param("backlash", default=None, convert=int)
+        if backlash < 0:
+            backlash = None
+
+        print("Running autofocus...")
+        task = self.microscope.task.start(self.plugin.fast_autofocus, dz, backlash=backlash)
+
+        # return a handle on the autofocus task
+        return jsonify(task.state), 202
+
+        
+
+class Plugin(MicroscopePlugin):
+    """
+    Plugin to provide fast autofocus
+    """
+    JPEGSharpnessMonitor = JPEGSharpnessMonitor # make the class available
+    def sharpness_monitor(self):
+        return JPEGSharpnessMonitor(self.microscope)
+
+    @contextmanager
+    def monitor_sharpness(self):
+        m = self.sharpness_monitor()
+        m.start()
+        try:
+            yield m
+        finally:
+            m.stop()
+
+    def move_and_find_focus(self, dz):
+        """Make a relative Z move and return the peak sharpness position"""
+        with self.monitor_sharpness() as m:
+            m.focus_rel(dz)
+            return m.sharpest_z_on_move(0)
+
+
+    def fast_autofocus(self, dz=2000, backlash=None):
+        """Perform a down-up-down-up autofocus"""
+        with self.monitor_sharpness() as m:
+            i, z = m.focus_rel(-dz/2)
+            i, z = m.focus_rel(dz)
+            fz = m.sharpest_z_on_move(i)
+            if backlash is None:
+                i, z = m.focus_rel(-dz) # move all the way to the start so it's consistent
+            else:
+                i, z = m.focus_rel(fz - z - backlash)
+            m.focus_rel(fz - z)
+            return m.data_dict()
+
+
+    api_views = {
+            '/fast_autofocus': FastAutofocusAPI,
+    }
+