Commit 51ff1326 authored by Joel Collins's avatar Joel Collins
Browse files

Refactored fast_autofocus

parent 2186bf7a
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+22 −6
Original line number Diff line number Diff line
@@ -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),
    }