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This commit is contained in:
Joel Collins 2020-04-28 13:20:38 +01:00
parent ed8057ce04
commit 9646058c37
14 changed files with 381 additions and 201 deletions
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33
openflexure_microscope/api/default_extensions/autofocus.py
View file

@ -51,7 +51,9 @@ class JPEGSharpnessMonitor:
def start(self):
"Start monitoring sharpness by looking at JPEG size"
if not self.camera.stream_active:
logging.warn("Autofocus sharpness monitor was started but the camera isn't streaming. Attempting to start the stream...")
logging.warn(
"Autofocus sharpness monitor was started but the camera isn't streaming. Attempting to start the stream..."
)
self.camera.start_stream_recording()
self.background_thread = Thread(target=self._measure_jpegs)
self.background_thread.start()
@ -106,7 +108,9 @@ class JPEGSharpnessMonitor:
stop = np.argmax(jpeg_times > stage_times[1])
except ValueError as e:
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?")
raise ValueError(
"No images were captured during the move of the stage. Perhaps the camera is not streaming images?"
)
else:
raise e
if stop < 1:
@ -120,7 +124,9 @@ class JPEGSharpnessMonitor:
"""Return the z position of the sharpest image on a given move"""
jt, 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?")
raise ValueError(
"No images were captured during the move of the stage. Perhaps the camera is not streaming images?"
)
return jz[np.argmax(js)]
def data_dict(self):
@ -212,7 +218,9 @@ def move_and_find_focus(microscope, dz):
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:
with monitor_sharpness(
microscope
) as m, microscope.camera.lock, microscope.stage.lock:
i, z = m.focus_rel(-dz / 2)
i, z = m.focus_rel(dz)
fz = m.sharpest_z_on_move(i)
@ -262,7 +270,9 @@ def fast_up_down_up_autofocus(
might slightly hurt accuracy, but is unlikely to be a big issue. Too big
may cause you to overshoot, which is a problem.
"""
with monitor_sharpness(microscope) as m, microscope.camera.lock, microscope.stage.lock:
with monitor_sharpness(
microscope
) as m, microscope.camera.lock, microscope.stage.lock:
# Ensure the MJPEG stream has started
microscope.camera.start_stream_recording()
@ -372,7 +382,9 @@ class FastAutofocusAPI(View):
if microscope.has_real_stage():
logging.debug("Running autofocus...")
task = taskify(fast_up_down_up_autofocus)(microscope, dz=dz, mini_backlash=backlash)
task = taskify(fast_up_down_up_autofocus)(
microscope, dz=dz, mini_backlash=backlash
)
# return a handle on the autofocus task
return task
@ -382,12 +394,15 @@ class FastAutofocusAPI(View):
autofocus_extension_v2 = BaseExtension(
"org.openflexure.autofocus", version="2.0.0",
description="Actions to move the microscope in Z and pick the point with the sharpest image."
"org.openflexure.autofocus",
version="2.0.0",
description="Actions to move the microscope in Z and pick the point with the sharpest image.",
)
autofocus_extension_v2.add_method(fast_autofocus, "fast_autofocus")
autofocus_extension_v2.add_method(fast_up_down_up_autofocus, "fast_up_down_up_autofocus")
autofocus_extension_v2.add_method(
fast_up_down_up_autofocus, "fast_up_down_up_autofocus"
)
autofocus_extension_v2.add_method(autofocus, "autofocus")
autofocus_extension_v2.add_view(MeasureSharpnessAPI, "/measure_sharpness")