rahix/openflexure-microscope-server
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

Blackened everything

Browse source
This commit is contained in:
Joel Collins 2019-09-15 14:17:52 +01:00
parent e213647217
commit 5966ce29be
57 changed files with 1938 additions and 1414 deletions
Download patch file Download diff file Expand all files Collapse all files

45
openflexure_microscope/plugins/default/autofocus/plugin.py
View file

@ -10,15 +10,16 @@ from .api import MeasureSharpnessAPI, AutofocusAPI, FastAutofocusAPI
from openflexure_microscope.devel import MicroscopePlugin
class AutofocusPlugin(MicroscopePlugin):
"""
Basic autofocus plugin
"""
api_views = {
'/measure_sharpness': MeasureSharpnessAPI,
'/autofocus': AutofocusAPI,
'/fast_autofocus': FastAutofocusAPI,
"/measure_sharpness": MeasureSharpnessAPI,
"/autofocus": AutofocusAPI,
"/fast_autofocus": FastAutofocusAPI,
}
### SLOW AUTOFOCUS
@ -70,21 +71,24 @@ class AutofocusPlugin(MicroscopePlugin):
m.focus_rel(dz)
return m.sharpest_z_on_move(0)
def fast_autofocus(self, dz=2000, backlash=None):
"""Perform a down-up-down-up autofocus"""
with self.monitor_sharpness() as m:
i, z = m.focus_rel(-dz/2)
i, z = m.focus_rel(-dz / 2)
i, z = m.focus_rel(dz)
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:
i, z = m.focus_rel(fz - z - backlash)
m.focus_rel(fz - z)
return m.data_dict()
def fast_up_down_up_autofocus(self, dz=2000, target_z=0, initial_move_up=True, mini_backlash=150):
def fast_up_down_up_autofocus(
self, dz=2000, target_z=0, initial_move_up=True, mini_backlash=150
):
"""Autofocus by measuring on the way down, and moving back up with feedback.
This autofocus method is very efficient, as it only passes the peak once.
@ -124,32 +128,41 @@ class AutofocusPlugin(MicroscopePlugin):
# Ensure the MJPEG stream has started
self.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!
if initial_move_up:
m.focus_rel(df/2)
m.focus_rel(df / 2)
# 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+target_z], jz[::-1], js[::-1]) #NB jz is decreasing
target_s = np.interp(
[best_z + target_z], jz[::-1], js[::-1]
) # NB jz is decreasing
# now 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
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
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
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
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 + target_z - jz[inow]
logging.debug("Fast autofocus scan: correcting backlash by moving {} steps".format(correction_move))
logging.debug(
"Fast autofocus scan: correcting backlash by moving {} steps".format(
correction_move
)
)
m.focus_rel(correction_move)
return m.data_dict()