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Separate "classic" fast AF from up-down-up AF

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This commit is contained in:
Joel Collins 2020-10-19 17:59:07 +01:00
parent e6913b23e2
commit 4ceb6bcafe
1 changed files with 72 additions and 54 deletions
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126
openflexure_microscope/api/default_extensions/autofocus.py
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@ -218,20 +218,16 @@ def move_and_measure(microscope, dz):
return m.data_dict()
def fast_autofocus(microscope, dz=2000, backlash=None):
def fast_autofocus(microscope, dz=2000):
"""Perform a down-up-down-up autofocus"""
with monitor_sharpness(
microscope
) as m, microscope.camera.lock as _, microscope.stage.lock as _:
i, z = m.focus_rel(-dz / 2)
i, z = m.focus_rel(dz)
fz = m.sharpest_z_on_move(i)
if backlash is None:
with microscope.camera.lock, microscope.stage.lock:
with monitor_sharpness(microscope) as m:
i, z = m.focus_rel(-dz / 2)
i, z = m.focus_rel(dz)
fz = m.sharpest_z_on_move(i)
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()
m.focus_rel(fz - z)
return m.data_dict()
def fast_up_down_up_autofocus(
@ -272,52 +268,51 @@ def fast_up_down_up_autofocus(
might slightly hurt accuracy, but is unlikely to be a big issue. Too big
may cause you to overshoot, which is a problem.
"""
with monitor_sharpness(
microscope
) as m, microscope.camera.lock as _, microscope.stage.lock as _:
# Ensure the MJPEG stream has started
microscope.camera.start_stream_recording()
with microscope.camera.lock, microscope.stage.lock:
with monitor_sharpness(microscope) as m:
# Ensure the MJPEG stream has started
microscope.camera.start_stream_recording()
df = dz # TODO: refactor so I actually use dz in the code below!
logging.debug("Initial move")
if initial_move_up:
m.focus_rel(df / 2)
# move down
logging.debug("Move down")
i, z = m.focus_rel(-df)
# now inspect where the sharpest point is, and estimate the sharpness
# (JPEG size) that we should find at the start of the Z stack
_, jz, js = m.move_data(i)
best_z = jz[np.argmax(js)]
df = dz # TODO: refactor so I actually use dz in the code below!
logging.debug("Initial move")
if initial_move_up:
m.focus_rel(df / 2)
# move down
logging.debug("Move down")
i, z = m.focus_rel(-df)
# now inspect where the sharpest point is, and estimate the sharpness
# (JPEG size) that we should find at the start of the Z stack
_, jz, js = m.move_data(i)
best_z = jz[np.argmax(js)]
# now move to the start of the z stack
logging.debug("Move to the start of the z stack")
i, z = m.focus_rel(
best_z + target_z - z + mini_backlash
) # takes us to the start of the stack
# now move to the start of the z stack
logging.debug("Move to the start of the z stack")
i, z = m.focus_rel(
best_z + target_z - z + mini_backlash
) # takes us to the start of the stack
# We've deliberately undershot - figure out how much further we should move based on the curve
logging.debug("Calculate remining movement")
current_js = m.jpeg_size()
imax = np.argmax(js) # we want to crop out just the bit below the peak
js = js[imax:] # NB z is in DECREASING order
jz = jz[imax:]
inow = np.argmax(
js < current_js
) # use the curve we recorded to estimate our position
# TODO: fancy interpolation stuff
# We've deliberately undershot - figure out how much further we should move based on the curve
logging.debug("Calculate remining movement")
current_js = m.jpeg_size()
imax = np.argmax(js) # we want to crop out just the bit below the peak
js = js[imax:] # NB z is in DECREASING order
jz = jz[imax:]
inow = np.argmax(
js < current_js
) # use the curve we recorded to estimate our position
# TODO: fancy interpolation stuff
# So, the Z position corresponding to our current sharpness value is zs[inow]
# That means we should move forwards, by best_z - zs[inow]
logging.debug("Correction move")
correction_move = best_z + target_z - jz[inow]
logging.debug(
"Fast autofocus scan: correcting backlash by moving {} steps".format(
correction_move
# So, the Z position corresponding to our current sharpness value is zs[inow]
# That means we should move forwards, by best_z - zs[inow]
logging.debug("Correction move")
correction_move = best_z + target_z - jz[inow]
logging.debug(
"Fast autofocus scan: correcting backlash by moving {} steps".format(
correction_move
)
)
)
m.focus_rel(correction_move)
return m.data_dict()
m.focus_rel(correction_move)
return m.data_dict()
class MeasureSharpnessAPI(View):
@ -346,7 +341,6 @@ class MoveAndMeasureAPI(ActionView):
if microscope.has_real_stage():
# Acquire microscope lock with 1s timeout
with microscope.lock(timeout=1):
# Run fast_up_down_up_autofocus
return move_and_measure(microscope, dz=args.get("dz"))
else:
@ -384,6 +378,30 @@ class FastAutofocusAPI(ActionView):
Run a fast autofocus
"""
args = {"dz": fields.Int(missing=2000)}
def post(self, args):
microscope = find_component("org.openflexure.microscope")
if not microscope:
abort(503, "No microscope connected. Unable to autofocus.")
if microscope.has_real_stage():
logging.debug("Running autofocus...")
# Acquire microscope lock with 1s timeout
with microscope.lock(timeout=1):
# Run fast_autofocus
return fast_autofocus(microscope, dz=args.get("dz"))
else:
abort(503, "No stage connected. Unable to autofocus.")
class UpDownUpAutofocusAPI(ActionView):
"""
Run a fast up-down-up autofocus
"""
args = {
"dz": fields.Int(missing=2000),
"backlash": fields.Int(missing=25, minimum=0),