Commit 65fc58c6 authored by Joel Collins's avatar Joel Collins
Browse files

Fixed scan to use newer fast autofocus

parent 945c7e4e

openflexure_microscope/api/default_extensions/autofocus.py

+11 −8
Original line number Diff line number Diff line 
from labthings.server.find import find_component

from labthings.server.extensions import BaseExtension

from labthings.server.view import View

from labthings.server.decorators import ThingAction, ThingProperty

from labthings.server.decorators import ThingAction, ThingProperty, marshal_task



from openflexure_microscope.devel import JsonResponse, request, jsonify, taskify, abort

from openflexure_microscope.utilities import set_properties
@@ -195,7 +195,7 @@ def move_and_find_focus(microscope, dz): 


def fast_autofocus(microscope, dz=2000, backlash=None):

    """Perform a down-up-down-up autofocus"""

    with monitor_sharpness(microscope) as m:

    with monitor_sharpness(microscope) as m, microscope.camera.lock:

        i, z = m.focus_rel(-dz / 2)

        i, z = m.focus_rel(dz)

        fz = m.sharpest_z_on_move(i)
@@ -208,7 +208,7 @@ def fast_autofocus(microscope, dz=2000, backlash=None): 




def fast_up_down_up_autofocus(

    microscope, dz=2000, target_z=0, initial_move_up=True, mini_backlash=150

    microscope, dz=2000, target_z=0, initial_move_up=True, mini_backlash=25

):

    """Autofocus by measuring on the way down, and moving back up with feedback.
@@ -239,7 +239,7 @@ def fast_up_down_up_autofocus( 
            from the starting position.  Mostly useful if you're able to combine

            the initial move with something else, e.g. moving to the next scan point.



        mini_backlash: (optional, default 50) is a small extra move made in step

        mini_backlash: (optional, default 25) is a small extra move made in step

            3 to help counteract backlash.  It should be small enough that you

            would always expect there to be greater backlash than this.  Too small

            might slightly hurt accuracy, but is unlikely to be a big issue.  Too big
@@ -305,6 +305,7 @@ class AutofocusAPI(View): 
    Run a standard autofocus

    """



    @marshal_task

    def post(self):

        payload = JsonResponse(request)

        microscope = find_component("org.openflexure.microscope")
@@ -320,7 +321,7 @@ class AutofocusAPI(View): 
            task = taskify(autofocus)(microscope, dz)



            # return a handle on the autofocus task

            return jsonify(task.state), 201

            return task



        else:

            abort(503, "No stage connected. Unable to autofocus.")
@@ -332,6 +333,7 @@ class FastAutofocusAPI(View): 
    Run a fast autofocus

    """



    @marshal_task

    def post(self):

        payload = JsonResponse(request)

        microscope = find_component("org.openflexure.microscope")
@@ -341,16 +343,16 @@ class FastAutofocusAPI(View): 


        # Figure out the parameters to use

        dz = payload.param("dz", default=2000, convert=int)

        backlash = payload.param("backlash", default=0, convert=int)

        backlash = payload.param("backlash", default=25, convert=int)

        if backlash < 0:

            backlash = 0



        if microscope.has_real_stage():

            logging.info("Running autofocus...")

            task = taskify(fast_autofocus)(microscope, dz, backlash=backlash)

            task = taskify(fast_up_down_up_autofocus)(microscope, dz=dz, mini_backlash=backlash)



            # return a handle on the autofocus task

            return jsonify(task.state), 201

            return task



        else:

            abort(503, "No stage connected. Unable to autofocus.")
@@ -361,6 +363,7 @@ autofocus_extension_v2 = BaseExtension( 
)



autofocus_extension_v2.add_method(fast_autofocus, "fast_autofocus")

autofocus_extension_v2.add_method(fast_up_down_up_autofocus, "fast_up_down_up_autofocus")

autofocus_extension_v2.add_method(autofocus, "autofocus")



autofocus_extension_v2.add_view(MeasureSharpnessAPI, "/measure_sharpness")

openflexure_microscope/api/default_extensions/scan.py

+4 −2
Original line number Diff line number Diff line
@@ -197,13 +197,15 @@ def tile( 
            # Refocus

            if autofocus_enabled:

                if fast_autofocus:

                    autofocus_extension.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

                    )

                else:

                    logging.debug("Running autofocus")

                    # Run slow autofocus. Client should provide dz ~ 50

                    autofocus_extension.autofocus(

                        range(-3 * autofocus_dz, 4 * autofocus_dz, autofocus_dz)

                    )