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Refactored fast_autofocus

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This commit is contained in:
Joel Collins 2020-10-19 18:17:29 +01:00
parent 2186bf7aaa
commit 51ff132633
1 changed files with 22 additions and 6 deletions
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28
openflexure_microscope/api/default_extensions/autofocus.py
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@ -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"
@ -222,11 +228,21 @@ def fast_autofocus(microscope, dz=2000):
"""Perform a down-up-down-up autofocus""" """Perform a down-up-down-up autofocus"""
with microscope.camera.lock, microscope.stage.lock: with microscope.camera.lock, microscope.stage.lock:
with monitor_sharpness(microscope) as m: with monitor_sharpness(microscope) as m:
i, z = m.focus_rel(-dz / 2) # Move to (-dz / 2)
m.focus_rel(-dz / 2)
# Move to dz while monitoring sharpness
# i: Sharpness monitor index for this move
# z: Final z position after move
i, z = m.focus_rel(dz) i, z = m.focus_rel(dz)
# Get the z position with highest sharpness from the previous move (index i)
fz = m.sharpest_z_on_move(i) fz = m.sharpest_z_on_move(i)
i, z = m.focus_rel(-dz) # move all the way to the start so it's consistent # Move all the way to the start so it's consistent
# 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) m.focus_rel(fz - z)
# Return all focus data
return m.data_dict() return m.data_dict()
@ -378,7 +394,7 @@ class FastAutofocusAPI(ActionView):
Run a fast autofocus Run a fast autofocus
""" """
args = {"dz": fields.Int(missing=2000)} args = {"dz": fields.Int(missing=2000, example=2000)}
def post(self, args): def post(self, args):
microscope = find_component("org.openflexure.microscope") microscope = find_component("org.openflexure.microscope")
@ -403,7 +419,7 @@ class UpDownUpAutofocusAPI(ActionView):
""" """
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),
} }