Merge branch 'old-fast-autofocus' into 'master'

Old fast autofocus

See merge request openflexure/openflexure-microscope-server!77

openflexure_microscope/api/default_extensions/autofocus.py

@@ -80,13 +80,19 @@ class JPEGSharpnessMonitor:
 
     def focus_rel(self, dz, backlash=False, **kwargs):
         self.keep_alive()
+        # Start time and position
         self.stage_times.append(time.time())
         self.stage_positions.append(self.stage.position)
+        # Main move
         self.stage.move_rel([0, 0, dz], backlash=backlash, **kwargs)
+        # End time and position
         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]
+        # Index of the data for this movement
+        data_index = len(self.stage_positions) - 2
+        # Final z position after move
+        final_z_position = self.stage_positions[-1][2]
+        return data_index, final_z_position
 
     def move_data(self, istart, istop=None):
         "Extract sharpness as a function of (interpolated) z"
@@ -218,19 +224,25 @@ def move_and_measure(microscope, dz):
         return m.data_dict()
 
 
-def fast_autofocus(microscope, dz=2000, backlash=None):
+def fast_autofocus(microscope, dz=2000):
     """Perform a down-up-down-up autofocus"""
-    with monitor_sharpness(
-        microscope
-    ) as m, microscope.camera.lock as _, microscope.stage.lock as _:
-        i, z = m.focus_rel(-dz / 2)
+    with microscope.camera.lock, microscope.stage.lock:
+        with monitor_sharpness(microscope) as m:
+            # Move to (-dz / 2) 
+            m.focus_rel(-dz / 2)
+            # Move to dz while monitoring sharpness
+            # i: Sharpness monitor index for this move
+            # z: Final z position after move
             i, z = m.focus_rel(dz)
+            # Get the z position with highest sharpness from the previous move (index i)
             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)
+            # Move all the way to the start so it's consistent
+            # Store final absolute z position from this return move 
+            i, z = m.focus_rel(-dz)  
+            # Move to the target position fz
+            # Can't do absolute move here yet so move by (fz - z)
             m.focus_rel(fz - z)
+            # Return all focus data
             return m.data_dict()
 
 
@@ -272,9 +284,8 @@ def fast_up_down_up_autofocus(
             might slightly hurt accuracy, but is unlikely to be a big issue.  Too big
             may cause you to overshoot, which is a problem.
     """
-    with monitor_sharpness(
-        microscope
-    ) as m, microscope.camera.lock as _, microscope.stage.lock as _:
+    with microscope.camera.lock, microscope.stage.lock:
+        with monitor_sharpness(microscope) as m:
             # Ensure the MJPEG stream has started
             microscope.camera.start_stream_recording()
 
@@ -346,7 +357,6 @@ class MoveAndMeasureAPI(ActionView):
         if microscope.has_real_stage():
             # Acquire microscope lock with 1s timeout
             with microscope.lock(timeout=1):
-                # Run fast_up_down_up_autofocus
                 return move_and_measure(microscope, dz=args.get("dz"))
 
         else:
@@ -384,8 +394,32 @@ class FastAutofocusAPI(ActionView):
     Run a fast autofocus
     """
 
+    args = {"dz": fields.Int(missing=2000, example=2000)}
+
+    def post(self, args):
+        microscope = find_component("org.openflexure.microscope")
+
+        if not microscope:
+            abort(503, "No microscope connected. Unable to autofocus.")
+
+        if microscope.has_real_stage():
+            logging.debug("Running autofocus...")
+            # Acquire microscope lock with 1s timeout
+            with microscope.lock(timeout=1):
+                # Run fast_autofocus
+                return fast_autofocus(microscope, dz=args.get("dz"))
+
+        else:
+            abort(503, "No stage connected. Unable to autofocus.")
+
+
+class UpDownUpAutofocusAPI(ActionView):
+    """
+    Run a fast up-down-up autofocus
+    """
+
     args = {
-        "dz": fields.Int(missing=2000),
+        "dz": fields.Int(missing=2000, example=2000),
         "backlash": fields.Int(missing=25, minimum=0),
     }
 
@@ -433,6 +467,9 @@ autofocus_extension_v2.add_view(AutofocusAPI, "/autofocus", endpoint="autofocus"
 autofocus_extension_v2.add_view(
     FastAutofocusAPI, "/fast_autofocus", endpoint="fast_autofocus"
 )
+autofocus_extension_v2.add_view(
+    UpDownUpAutofocusAPI, "/updownup_autofocus", endpoint="updownup_autofocus"
+)
 
 autofocus_extension_v2.add_view(
     MoveAndMeasureAPI, "/move_and_measure", endpoint="move_and_measure"

openflexure_microscope/api/default_extensions/scan.py

@@ -203,7 +203,7 @@ class ScanExtension(BaseExtension):
                 if autofocus_enabled:
                     if fast_autofocus:
                         # Run fast autofocus. Client should provide dz ~ 2000
-                        autofocus_extension.fast_up_down_up_autofocus(
+                        autofocus_extension.fast_autofocus(
                             microscope, dz=autofocus_dz
                         )
                     else: