diff --git a/openflexure_microscope/api/default_extensions/autofocus.py b/openflexure_microscope/api/default_extensions/autofocus.py index cee79dcf..803e95ae 100644 --- a/openflexure_microscope/api/default_extensions/autofocus.py +++ b/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" @@ -222,11 +228,21 @@ def fast_autofocus(microscope, dz=2000): """Perform a down-up-down-up autofocus""" with microscope.camera.lock, microscope.stage.lock: with monitor_sharpness(microscope) as m: - i, z = m.focus_rel(-dz / 2) + # 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) - i, z = m.focus_rel(-dz) # move all the way to the start so it's consistent + # 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() @@ -378,7 +394,7 @@ class FastAutofocusAPI(ActionView): Run a fast autofocus """ - args = {"dz": fields.Int(missing=2000)} + args = {"dz": fields.Int(missing=2000, example=2000)} def post(self, args): microscope = find_component("org.openflexure.microscope") @@ -403,7 +419,7 @@ class UpDownUpAutofocusAPI(ActionView): """ args = { - "dz": fields.Int(missing=2000), + "dz": fields.Int(missing=2000, example=2000), "backlash": fields.Int(missing=25, minimum=0), }