Commit a4f6bc7d authored by Joel Collins's avatar Joel Collins
Browse files

Fixed scanning fast autofocus

parent ab7f3c3d

openflexure_microscope/api/default_extensions/scan.py

+8 −24
Original line number Diff line number Diff line
@@ -166,25 +166,19 @@ def tile( 
    else:

        autofocus_enabled = False



    z_stack_dz = (

        grid[2] * stride_size[2] if grid[2] > 1 else 0

    )  # shorthand for Z stack range



    # Construct an x-y grid (worry about z later)

    x_y_grid = construct_grid(initial_position, stride_size[:2], grid[:2], style=style)



    # Keep the initial Z position the same as our current position

    next_z = initial_position[2]

    if fast_autofocus:  # If fast autofocus is enabled, make

        next_z += autofocus_dz / 2  # sure we start from the top of the range

    initial_z = next_z  # Save this value for use in raster scans

    initial_z = initial_position[2]

    next_z = initial_z  # Save this value for use in raster scans



    # Now step through each point in the x-y coordinate array

    for line in x_y_grid:

        # If rastering, rather than snake (or eventually spiral)

        # Return focus to initial position

        if style == "raster":

            next_z = initial_z

            next_z = initial_z  # Reset z position at start of each new row

            logging.debug("Returning to initial z position")

            microscope.stage.move_abs(

                [line[0][0], line[0][1], next_z]
@@ -199,10 +193,7 @@ def tile( 
                if fast_autofocus:

                    # Run fast autofocus. Client should provide dz ~ 2000

                    autofocus_extension.fast_up_down_up_autofocus(

                        microscope,

                        dz=autofocus_dz,

                        target_z=-z_stack_dz / 2.0,  # Finish below the focus

                        initial_move_up=False,  # We're already at the top of the scan

                        microscope, dz=autofocus_dz

                    )

                else:

                    # Run slow autofocus. Client should provide dz ~ 50
@@ -236,7 +227,6 @@ def tile( 
                    temporary=temporary,

                    step_size=stride_size[2],

                    steps=grid[2],

                    return_to_start=not fast_autofocus,

                    use_video_port=use_video_port,

                    resize=resize,

                    bayer=bayer,
@@ -246,14 +236,6 @@ def tile( 
                )

            # Make sure we use our current best estimate of focus (i.e. the current position) next point

            next_z = microscope.stage.position[2]

            if fast_autofocus:

                next_z += (

                    autofocus_dz / 2

                )  # Fast autofocus requires us to start at the top of the range

                if grid[2] > 1:

                    next_z -= int(

                        grid[2] / 2.0 * stride_size[2]

                    )  # Z stacking means we're higher up to start with



    logging.debug("Returning to {}".format(initial_position))

    microscope.stage.move_abs(initial_position)
@@ -277,15 +259,17 @@ def stack( 


    # Store initial position

    initial_position = microscope.stage.position

    logging.debug(f"Starting z-stack from position {microscope.stage.position}")



    with microscope.lock:

        # Move to center scan

        logging.debug("Moving to starting position")

        logging.debug("Moving to z-stack starting position")

        microscope.stage.move_rel([0, 0, int((-step_size * steps) / 2)])

        logging.debug(f"Starting scan from position {microscope.stage.position}")



        for i in range(steps):

            time.sleep(0.1)

            logging.debug("Capturing...")

            logging.debug(f"Capturing from position {microscope.stage.position}")

            capture(

                microscope,

                basename,