rahix/openflexure-microscope-server
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

Fixed scan to use newer fast autofocus

Browse source
This commit is contained in:
Joel Collins 2020-01-30 14:22:03 +00:00
parent 945c7e4e27
commit 65fc58c651
2 changed files with 15 additions and 10 deletions
Download patch file Download diff file Expand all files Collapse all files

19
openflexure_microscope/api/default_extensions/autofocus.py
View file

@ -1,7 +1,7 @@
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")