Restructured fast autofocus into main autofocus plugin

openflexure_microscope/plugins/default/autofocus/focus_utils.py

@@ -1,6 +1,104 @@
+import time
 import numpy as np
+import threading
+import logging
 from scipy import ndimage
 
+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
 
 def decimate_to(shape, image):
     """Decimate an image to reduce its size if it's too big."""