Included Richards autofocus plugin in defaults

openflexure_microscope/plugins/default/plugin.py

@@ -1,6 +1,11 @@
-from openflexure_microscope.plugins import MicroscopePlugin
+import time
+import numpy as np
 
-from .api import IdentifyAPI
+from openflexure_microscope.plugins import MicroscopePlugin
+from openflexure_microscope.utilities import set_properties
+
+from .focus_utils import sharpness_sum_lap2
+from .api import IdentifyAPI, MeasureSharpnessAPI, AutofocusAPI
 
 
 class Plugin(MicroscopePlugin):
@@ -10,6 +15,8 @@ class Plugin(MicroscopePlugin):
 
     api_views = {
         '/identify': IdentifyAPI,
+        '/measure_sharpness': MeasureSharpnessAPI,
+        '/autofocus': AutofocusAPI,
     }
 
     def identify(self):
@@ -18,5 +25,34 @@ class Plugin(MicroscopePlugin):
         """
 
         response = "My parent camera is {}, and my parent stage is {}.".format(self.microscope.camera, self.microscope.stage)
-        print(response)
         return response
+
+    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,
+        and at each position an image is captured and the sharpness function 
+        evaulated.  We then move back to the position where the sharpness was
+        highest.  No interpolation is performed.
+        dz is assumed to be in ascending order (starting at -ve values)
+        """
+        camera = self.microscope.camera
+        stage = self.microscope.stage
+
+        with set_properties(stage, backlash=256), stage.lock, camera.lock:
+            sharpnesses = []
+            positions = []
+            camera.annotate_text = ""
+
+            for i in stage.scan_z(dz, return_to_start=False):
+                positions.append(stage.position[2])
+                time.sleep(settle)
+                sharpnesses.append(self.measure_sharpness(metric_fn))
+
+            newposition = positions[np.argmax(sharpnesses)]
+            stage.focus_rel(newposition - stage.position[2])
+
+        return positions, sharpnesses
+
+    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)))