Included Richards autofocus plugin in defaults

openflexure_microscope/plugins/default/api.py

@@ -1,6 +1,9 @@
-from openflexure_microscope.api.v1.views import MicroscopeViewPlugin
+import numpy as np
 
-from flask import request, Response, escape
+from openflexure_microscope.api.v1.views import MicroscopeViewPlugin
+from openflexure_microscope.api.utilities import JsonPayload
+
+from flask import request, Response, escape, jsonify
 
 import logging
 
@@ -17,3 +20,21 @@ class IdentifyAPI(MicroscopeViewPlugin):
         """
         data = self.microscope.plugin.default.identify()  # Call a method from our plugin, using the full route
         return Response(escape(data))
+
+class MeasureSharpnessAPI(MicroscopeViewPlugin):
+    def post(self):
+        payload = JsonPayload(request)
+        return jsonify({'sharpness': self.plugin.measure_sharpness()})
+
+class AutofocusAPI(MicroscopeViewPlugin):
+    def post(self):
+        payload = JsonPayload(request)
+        
+        # Figure out the range of z values to use
+        dz = payload.param("dz", default=np.linspace(-300,300,7), convert=np.array)
+
+        print("Running autofocus...")
+        task = self.microscope.task.start(self.plugin.autofocus, dz)
+
+        # return a handle on the autofocus task
+        return jsonify(task.state, 202)

openflexure_microscope/plugins/default/focus_utils.py

@@ -0,0 +1,21 @@
+import numpy as np
+from scipy import ndimage
+
+def decimate_to(shape, image):
+    """Decimate an image to reduce its size if it's too big."""
+    decimation = np.max(np.ceil(np.array(image.shape, dtype=np.float)[:len(shape)]/np.array(shape)))
+    return image[::int(decimation), ::int(decimation), ...]
+
+def sharpness_sum_lap2(rgb_image):
+    """Return an image sharpness metric: sum(laplacian(image)**")"""
+    #image_bw=np.mean(decimate_to((1000,1000), rgb_image),2)
+    image_bw=np.mean(rgb_image, 2)
+    image_lap=ndimage.filters.laplace(image_bw)
+    return np.mean(image_lap.astype(np.float)**4)
+
+def sharpness_edge(image):
+    """Return a sharpness metric optimised for vertical lines"""
+    gray = np.mean(image.astype(float), 2)
+    n = 20
+    edge = np.array([[-1]*n + [1]*n])
+    return np.sum([np.sum(ndimage.filters.convolve(gray,W)**2) for W in [edge, edge.T]])

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)))