Commit 4eef909d authored by Joel Collins's avatar Joel Collins
Browse files

Check for missing devices

parent cc931cc5

openflexure_microscope/plugins/v2/autofocus.py

+14 −11
Original line number Diff line number Diff line
@@ -2,13 +2,7 @@ from openflexure_microscope.common.labthings import find_device 
from openflexure_microscope.common.labthings.plugins import BasePlugin

from openflexure_microscope.microscope import Microscope



from openflexure_microscope.devel import (

    JsonResponse,

    request,

    jsonify,

    taskify,

    abort,

)

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

from openflexure_microscope.utilities import set_properties



from flask.views import MethodView
@@ -22,6 +16,7 @@ from contextlib import contextmanager 


### Autofocus utilities





class JPEGSharpnessMonitor:

    def __init__(self, microscope, timeout=60):

        self.microscope = microscope
@@ -148,10 +143,12 @@ def sharpness_edge(image): 


### Autofocus plugin





def measure_sharpness(microscope, metric_fn=sharpness_sum_lap2):

    """Measure the sharpness of the camera's current view."""

    return metric_fn(microscope.camera.array(use_video_port=True))





def autofocus(microscope, dz, settle=0.5, metric_fn=sharpness_sum_lap2):

    """Perform a simple autofocus routine.

    The stage is moved to z positions (relative to current position) in dz,
@@ -203,16 +200,13 @@ def fast_autofocus(microscope, dz=2000, backlash=None): 
        i, z = m.focus_rel(dz)

        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

            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)

        m.focus_rel(fz - z)

        return m.data_dict()







def fast_up_down_up_autofocus(

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

):
@@ -299,6 +293,9 @@ class MeasureSharpnessAPI(MethodView): 
    def post(self):

        microscope = find_device("openflexure_microscope")



        if not microscope:

            abort(503, "No microscope connected. Unable to measure sharpness.")



        return jsonify({"sharpness": measure_sharpness(microscope)})
@@ -311,6 +308,9 @@ class AutofocusAPI(MethodView): 
        payload = JsonResponse(request)

        microscope = find_device("openflexure_microscope")



        if not microscope:

            abort(503, "No microscope connected. Unable to autofocus.")



        # Figure out the range of z values to use

        dz = payload.param("dz", default=np.linspace(-300, 300, 7), convert=np.array)
@@ -334,6 +334,9 @@ class FastAutofocusAPI(MethodView): 
        payload = JsonResponse(request)

        microscope = find_device("openflexure_microscope")



        if not microscope:

            abort(503, "No microscope connected. Unable to autofocus.")



        # Figure out the parameters to use

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

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