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Fixed scan to use newer fast autofocus

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

@ -1,7 +1,7 @@
from labthings.server.find import find_component from labthings.server.find import find_component
from labthings.server.extensions import BaseExtension from labthings.server.extensions import BaseExtension
from labthings.server.view import View 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.devel import JsonResponse, request, jsonify, taskify, abort
from openflexure_microscope.utilities import set_properties 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): def fast_autofocus(microscope, dz=2000, backlash=None):
"""Perform a down-up-down-up autofocus""" """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 / 2)
i, z = m.focus_rel(dz) i, z = m.focus_rel(dz)
fz = m.sharpest_z_on_move(i) 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( 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. """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 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. 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 3 to help counteract backlash. It should be small enough that you
would always expect there to be greater backlash than this. Too small 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 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 Run a standard autofocus
""" """
@marshal_task
def post(self): def post(self):
payload = JsonResponse(request) payload = JsonResponse(request)
microscope = find_component("org.openflexure.microscope") microscope = find_component("org.openflexure.microscope")
@ -320,7 +321,7 @@ class AutofocusAPI(View):
task = taskify(autofocus)(microscope, dz) task = taskify(autofocus)(microscope, dz)
# return a handle on the autofocus task # return a handle on the autofocus task
return jsonify(task.state), 201 return task
else: else:
abort(503, "No stage connected. Unable to autofocus.") abort(503, "No stage connected. Unable to autofocus.")
@ -332,6 +333,7 @@ class FastAutofocusAPI(View):
Run a fast autofocus Run a fast autofocus
""" """
@marshal_task
def post(self): def post(self):
payload = JsonResponse(request) payload = JsonResponse(request)
microscope = find_component("org.openflexure.microscope") microscope = find_component("org.openflexure.microscope")
@ -341,16 +343,16 @@ class FastAutofocusAPI(View):
# Figure out the parameters to use # Figure out the parameters to use
dz = payload.param("dz", default=2000, convert=int) 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: if backlash < 0:
backlash = 0 backlash = 0
if microscope.has_real_stage(): if microscope.has_real_stage():
logging.info("Running autofocus...") 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 a handle on the autofocus task
return jsonify(task.state), 201 return task
else: else:
abort(503, "No stage connected. Unable to autofocus.") 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_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_method(autofocus, "autofocus")
autofocus_extension_v2.add_view(MeasureSharpnessAPI, "/measure_sharpness") autofocus_extension_v2.add_view(MeasureSharpnessAPI, "/measure_sharpness")

6
openflexure_microscope/api/default_extensions/scan.py
View file

@ -197,13 +197,15 @@ def tile(
# Refocus # Refocus
if autofocus_enabled: if autofocus_enabled:
if fast_autofocus: 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, dz=autofocus_dz,
target_z=-z_stack_dz / 2.0, # Finish below the focus target_z=-z_stack_dz / 2.0, # Finish below the focus
initial_move_up=False, # We're already at the top of the scan initial_move_up=False, # We're already at the top of the scan
) )
else: else:
logging.debug("Running autofocus") # Run slow autofocus. Client should provide dz ~ 50
autofocus_extension.autofocus( autofocus_extension.autofocus(
range(-3 * autofocus_dz, 4 * autofocus_dz, autofocus_dz) range(-3 * autofocus_dz, 4 * autofocus_dz, autofocus_dz)
) )