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Refactored fast autofocus

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Tidied up the fast autofocus code, including moving the bulk of the
new code from the `scan` plugin into `autofocus` and updating it to
reflect the fact that the autofocus plugin now merges both old and
new functionality (i.e. fast_autofocus is no longer a separate
plugin).  Also fixed a bug that caused it to overshoot on scans.
This commit is contained in:
Richard Bowman 2019-04-08 19:56:29 +01:00
parent 7e83d724b8
commit 7aea6291c7
2 changed files with 69 additions and 37 deletions
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39
openflexure_microscope/plugins/default/scan/plugin.py
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@ -125,11 +125,10 @@ class ScanPlugin(MicroscopePlugin):
else:
autofocus_enabled = False
if fast_autofocus and not hasattr(self.microscope.plugin, 'default_fast_autofocus'):
logging.error("Can't use fast autofocus in the scan - the plugin is missing or disabled.")
if fast_autofocus and not hasattr(self.microscope.plugin.default_autofocus, 'monitor_sharpness'):
logging.error("Can't use fast autofocus in the scan - the default plugin doesn't support monitor_sharpness; maybe it is too old?")
fast_autofocus = False
z_stack_dz = grid[2] * step_size[2] if grid[2] > 1 else 0 # shorthand for Z stack range
sweep_to_scan_offset = 50 #TODO: make this a parameter, or calibrate it better! too small isn't a big problem, too big causes issues.
# Construct an x-y grid (worry about z later)
x_y_grid = construct_grid(
@ -161,34 +160,12 @@ class ScanPlugin(MicroscopePlugin):
# Refocus
if autofocus_enabled:
if fast_autofocus:
# TODO: put this in the fast autofocus plugin!
with self.microscope.plugin.default_fast_autofocus.monitor_sharpness() as m:
df = autofocus_dz
# 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
jt, jz, js = m.move_data(i)
best_z = jz[np.argmax(js)]
target_s = np.interp([best_z+z_stack_dz/2.0], jz[::-1], js[::-1]) #NB jz is decreasing
# now move to the start of the z stack
i, z = m.focus_rel(best_z - z + z_stack_dz/2.0 + sweep_to_scan_offset) # takes us to the start of the stack
# We've deliberately undershot - figure out how much further we should move based on the curve
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]
correction_move = best_z - jz[inow] - z_stack_dz/2.0
logging.debug("Fast autofocus scan: correcting backlash by moving {} steps".format(correction_move))
m.focus_rel(correction_move)
self.microscope.plugin.default_autofocus.fast_up_down_up_autofocus(
dz=autofocus_dz,
target_z=-z_stack_dz/2.0, # Finish below the focus
initial_move_up=False, # We're already at the top of the scan
)
#TODO: save the focus data for future reference? Use it for diagnostics?
else:
logging.debug("Running autofocus")
self.microscope.plugin.default_autofocus.autofocus(