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Merge branch 'old-fast-autofocus' into 'master'

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Old fast autofocus

See merge request openflexure/openflexure-microscope-server!77
This commit is contained in:
Joel Collins 2020-10-19 17:24:44 +00:00
commit b9bed71272
2 changed files with 96 additions and 59 deletions
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153
openflexure_microscope/api/default_extensions/autofocus.py
View file

@ -80,13 +80,19 @@ class JPEGSharpnessMonitor:
def focus_rel(self, dz, backlash=False, **kwargs): def focus_rel(self, dz, backlash=False, **kwargs):
self.keep_alive() self.keep_alive()
# Start time and position
self.stage_times.append(time.time()) self.stage_times.append(time.time())
self.stage_positions.append(self.stage.position) self.stage_positions.append(self.stage.position)
# Main move
self.stage.move_rel([0, 0, dz], backlash=backlash, **kwargs) self.stage.move_rel([0, 0, dz], backlash=backlash, **kwargs)
# End time and position
self.stage_times.append(time.time()) self.stage_times.append(time.time())
self.stage_positions.append(self.stage.position) self.stage_positions.append(self.stage.position)
i = len(self.stage_positions) - 2 # Index of the data for this movement
return i, self.stage_positions[-1][2] data_index = len(self.stage_positions) - 2
# Final z position after move
final_z_position = self.stage_positions[-1][2]
return data_index, final_z_position
def move_data(self, istart, istop=None): def move_data(self, istart, istop=None):
"Extract sharpness as a function of (interpolated) z" "Extract sharpness as a function of (interpolated) z"
@ -218,20 +224,26 @@ 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 _: # Move to (-dz / 2)
i, z = m.focus_rel(-dz / 2) m.focus_rel(-dz / 2)
i, z = m.focus_rel(dz) # Move to dz while monitoring sharpness
fz = m.sharpest_z_on_move(i) # i: Sharpness monitor index for this move
if backlash is None: # z: Final z position after move
i, z = m.focus_rel(-dz) # move all the way to the start so it's consistent i, z = m.focus_rel(dz)
else: # Get the z position with highest sharpness from the previous move (index i)
i, z = m.focus_rel(fz - z - backlash) fz = m.sharpest_z_on_move(i)
m.focus_rel(fz - z) # Move all the way to the start so it's consistent
return m.data_dict() # Store final absolute z position from this return move
i, z = m.focus_rel(-dz)
# Move to the target position fz
# Can't do absolute move here yet so move by (fz - z)
m.focus_rel(fz - z)
# Return all focus data
return m.data_dict()
def fast_up_down_up_autofocus( def fast_up_down_up_autofocus(
@ -272,52 +284,51 @@ 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 +357,6 @@ 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:
@ -384,8 +394,32 @@ class FastAutofocusAPI(ActionView):
Run a fast autofocus Run a fast autofocus
""" """
args = {"dz": fields.Int(missing=2000, example=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, example=2000),
"backlash": fields.Int(missing=25, minimum=0), "backlash": fields.Int(missing=25, minimum=0),
} }
@ -433,6 +467,9 @@ autofocus_extension_v2.add_view(AutofocusAPI, "/autofocus", endpoint="autofocus"
autofocus_extension_v2.add_view( autofocus_extension_v2.add_view(
FastAutofocusAPI, "/fast_autofocus", endpoint="fast_autofocus" FastAutofocusAPI, "/fast_autofocus", endpoint="fast_autofocus"
) )
autofocus_extension_v2.add_view(
UpDownUpAutofocusAPI, "/updownup_autofocus", endpoint="updownup_autofocus"
)
autofocus_extension_v2.add_view( autofocus_extension_v2.add_view(
MoveAndMeasureAPI, "/move_and_measure", endpoint="move_and_measure" MoveAndMeasureAPI, "/move_and_measure", endpoint="move_and_measure"

2
openflexure_microscope/api/default_extensions/scan.py
View file

@ -203,7 +203,7 @@ class ScanExtension(BaseExtension):
if autofocus_enabled: if autofocus_enabled:
if fast_autofocus: if fast_autofocus:
# Run fast autofocus. Client should provide dz ~ 2000 # Run fast autofocus. Client should provide dz ~ 2000
autofocus_extension.fast_up_down_up_autofocus( autofocus_extension.fast_autofocus(
microscope, dz=autofocus_dz microscope, dz=autofocus_dz
) )
else: else: