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

Code cleanup

Browse source
This commit is contained in:
Joel Collins 2020-10-14 14:56:29 +00:00
parent 2bfb988460
commit 994e83dbeb
46 changed files with 261 additions and 318 deletions
Download patch file Download diff file Expand all files Collapse all files

26
openflexure_microscope/api/default_extensions/autofocus.py
View file

@ -6,10 +6,10 @@ from threading import Event, Thread
import numpy as np
from labthings import current_action, fields, find_component
from labthings.extensions import BaseExtension
from labthings.views import ActionView, PropertyView, View
from labthings.views import ActionView, View
from scipy import ndimage
from openflexure_microscope.devel import JsonResponse, abort, request
from openflexure_microscope.devel import abort
from openflexure_microscope.utilities import set_properties
### Autofocus utilities
@ -36,19 +36,15 @@ class JPEGSharpnessMonitor:
return self.background_thread.is_alive()
def should_stop(self):
import time
return time.time() - self.kept_alive > self.timeout
def keep_alive(self):
import time
self.kept_alive = time.time()
def start(self):
"Start monitoring sharpness by looking at JPEG size"
if not self.camera.stream_active:
logging.warn(
logging.warning(
"Autofocus sharpness monitor was started but the camera isn't streaming. Attempting to start the stream..."
)
self.camera.start_stream_recording()
@ -66,7 +62,7 @@ class JPEGSharpnessMonitor:
"Function that runs in a background thread to record sharpness"
logging.debug("Starting sharpness measurement in background thread")
self.keep_alive()
logging.debug(f"_measure_jpegs stop_event: {self.stop_event.is_set()}")
logging.debug("_measure_jpegs stop_event: %s", self.stop_event.is_set())
while not self.stop_event.is_set() and not self.should_stop():
size_now = self.jpeg_size()
time_now = time.time()
@ -107,7 +103,7 @@ class JPEGSharpnessMonitor:
if np.sum(jpeg_times > stage_times[0]) == 0:
raise ValueError(
"No images were captured during the move of the stage. Perhaps the camera is not streaming images?"
)
) from e
else:
raise e
if stop < 1:
@ -119,7 +115,7 @@ class JPEGSharpnessMonitor:
def sharpest_z_on_move(self, index):
"""Return the z position of the sharpest image on a given move"""
jt, jz, js = self.move_data(index)
_, jz, js = self.move_data(index)
if len(js) == 0:
raise ValueError(
"No images were captured during the move of the stage. Perhaps the camera is not streaming images?"
@ -226,7 +222,7 @@ def fast_autofocus(microscope, dz=2000, backlash=None):
"""Perform a down-up-down-up autofocus"""
with monitor_sharpness(
microscope
) as m, microscope.camera.lock, microscope.stage.lock:
) as m, microscope.camera.lock as _, microscope.stage.lock as _:
i, z = m.focus_rel(-dz / 2)
i, z = m.focus_rel(dz)
fz = m.sharpest_z_on_move(i)
@ -278,7 +274,7 @@ def fast_up_down_up_autofocus(
"""
with monitor_sharpness(
microscope
) as m, microscope.camera.lock, microscope.stage.lock:
) as m, microscope.camera.lock as _, microscope.stage.lock as _:
# Ensure the MJPEG stream has started
microscope.camera.start_stream_recording()
@ -291,12 +287,8 @@ def fast_up_down_up_autofocus(
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
logging.debug("Get target_s")
jt, jz, js = m.move_data(i)
_, 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
# now move to the start of the z stack
logging.debug("Move to the start of the z stack")