Restructured fast autofocus into main autofocus plugin

openflexure_microscope/plugins/default/autofocus/plugin.py

@@ -1,11 +1,13 @@
 import time
+import logging
 import numpy as np
+from contextlib import contextmanager
 
 from openflexure_microscope.plugins import MicroscopePlugin
 from openflexure_microscope.utilities import set_properties
 
-from .focus_utils import sharpness_sum_lap2
-from .api import MeasureSharpnessAPI, AutofocusAPI
+from .focus_utils import sharpness_sum_lap2, JPEGSharpnessMonitor
+from .api import MeasureSharpnessAPI, AutofocusAPI, FastAutofocusAPI
 
 
 class AutofocusPlugin(MicroscopePlugin):
@@ -16,8 +18,11 @@ class AutofocusPlugin(MicroscopePlugin):
     api_views = {
         '/measure_sharpness': MeasureSharpnessAPI,
         '/autofocus': AutofocusAPI,
+        '/fast_autofocus': FastAutofocusAPI,
     }
 
+    ### SLOW AUTOFOCUS
+
     def autofocus(self, dz, settle=0.5, metric_fn=sharpness_sum_lap2):
         """Perform a simple autofocus routine.
         The stage is moved to z positions (relative to current position) in dz,
@@ -46,4 +51,39 @@ class AutofocusPlugin(MicroscopePlugin):
 
     def measure_sharpness(self, metric_fn=sharpness_sum_lap2):
         """Measure the sharpness of the camera's current view."""
-        return metric_fn(self.microscope.camera.array(use_video_port=True, resize=(640, 480)))
+        return metric_fn(self.microscope.camera.array(use_video_port=True))
+
+    ### 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()