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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() 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""" """Perform a down-up-down-up autofocus"""
with monitor_sharpness( with microscope.camera.lock, microscope.stage.lock:
microscope with monitor_sharpness(microscope) as m:
) as m, microscope.camera.lock as _, microscope.stage.lock as _: 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)
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: m.focus_rel(fz - z)
i, z = m.focus_rel(fz - z - backlash) return m.data_dict()
m.focus_rel(fz - z)
return m.data_dict()
def fast_up_down_up_autofocus( 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 might slightly hurt accuracy, but is unlikely to be a big issue. Too big
may cause you to overshoot, which is a problem. may cause you to overshoot, which is a problem.
""" """
with monitor_sharpness( with microscope.camera.lock, microscope.stage.lock:
microscope with monitor_sharpness(microscope) as m:
) as m, microscope.camera.lock as _, microscope.stage.lock as _: # Ensure the MJPEG stream has started
# Ensure the MJPEG stream has started microscope.camera.start_stream_recording()
microscope.camera.start_stream_recording()
df = dz # TODO: refactor so I actually use dz in the code below! df = dz # TODO: refactor so I actually use dz in the code below!
logging.debug("Initial move") logging.debug("Initial move")
if initial_move_up: if initial_move_up:
m.focus_rel(df / 2) m.focus_rel(df / 2)
# move down # move down
logging.debug("Move down") logging.debug("Move down")
i, z = m.focus_rel(-df) i, z = m.focus_rel(-df)
# now inspect where the sharpest point is, and estimate the sharpness # now inspect where the sharpest point is, and estimate the sharpness
# (JPEG size) that we should find at the start of the Z stack # (JPEG size) that we should find at the start of the Z stack
_, jz, js = m.move_data(i) _, jz, js = m.move_data(i)
best_z = jz[np.argmax(js)] best_z = jz[np.argmax(js)]
# now move to the start of the z stack # now move to the start of the z stack
logging.debug("Move to the start of the z stack") logging.debug("Move to the start of the z stack")
i, z = m.focus_rel( i, z = m.focus_rel(
best_z + target_z - z + mini_backlash best_z + target_z - z + mini_backlash
) # takes us to the start of the stack ) # takes us to the start of the stack
# We've deliberately undershot - figure out how much further we should move based on the curve # We've deliberately undershot - figure out how much further we should move based on the curve
logging.debug("Calculate remining movement") logging.debug("Calculate remining movement")
current_js = m.jpeg_size() current_js = m.jpeg_size()
imax = np.argmax(js) # we want to crop out just the bit below the peak imax = np.argmax(js) # we want to crop out just the bit below the peak
js = js[imax:] # NB z is in DECREASING order js = js[imax:] # NB z is in DECREASING order
jz = jz[imax:] jz = jz[imax:]
inow = np.argmax( inow = np.argmax(
js < current_js js < current_js
) # use the curve we recorded to estimate our position ) # use the curve we recorded to estimate our position
# TODO: fancy interpolation stuff # TODO: fancy interpolation stuff
# So, the Z position corresponding to our current sharpness value is zs[inow] # So, the Z position corresponding to our current sharpness value is zs[inow]
# That means we should move forwards, by best_z - zs[inow] # That means we should move forwards, by best_z - zs[inow]
logging.debug("Correction move") logging.debug("Correction move")
correction_move = best_z + target_z - jz[inow] correction_move = best_z + target_z - jz[inow]
logging.debug( logging.debug(
"Fast autofocus scan: correcting backlash by moving {} steps".format( "Fast autofocus scan: correcting backlash by moving {} steps".format(
correction_move correction_move
)
) )
) m.focus_rel(correction_move)
m.focus_rel(correction_move) return m.data_dict()
return m.data_dict()
class MeasureSharpnessAPI(View): class MeasureSharpnessAPI(View):
@ -346,7 +341,6 @@ class MoveAndMeasureAPI(ActionView):
if microscope.has_real_stage(): if microscope.has_real_stage():
# Acquire microscope lock with 1s timeout # Acquire microscope lock with 1s timeout
with microscope.lock(timeout=1): with microscope.lock(timeout=1):
# Run fast_up_down_up_autofocus
return move_and_measure(microscope, dz=args.get("dz")) return move_and_measure(microscope, dz=args.get("dz"))
else: else:
@ -384,6 +378,30 @@ class FastAutofocusAPI(ActionView):
Run a fast autofocus 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 = { args = {
"dz": fields.Int(missing=2000), "dz": fields.Int(missing=2000),
"backlash": fields.Int(missing=25, minimum=0), "backlash": fields.Int(missing=25, minimum=0),