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Fixing capture_thread variable and autofocus logic

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This commit is contained in:
Julian Stirling 2025-04-14 00:03:39 +01:00
parent 2ced848695
commit 7f46bc2d9b
1 changed files with 20 additions and 22 deletions
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42
src/openflexure_microscope_server/things/smart_scan.py
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@ -175,6 +175,7 @@ class SmartScanThing(Thing):
self._background_detect: Optional[BackgroundDep] = None
self._ongoing_scan_name: Optional[str] = None
self._starting_position: Optional[Mapping[str, int]] = None
self._capture_thread: Optional[ErrorCapturingThread] = None
self._scan_images_taken: Optional[int] = None
# TODO Scan data is a dict during refactoring, should become a dataclass
self._scan_data: Optional[dict] = None
@ -212,6 +213,7 @@ class SmartScanThing(Thing):
self._metadata_getter = metadata_getter
self._csm = csm
self._background_detect = background_detect
self._capture_thread = None
self._scan_images_taken = 0
# Don't set self._scan_data dictionary. This is done at the start of _run_scan
@ -241,6 +243,7 @@ class SmartScanThing(Thing):
self._metadata_getter = None
self._csm = None
self._background_detect = None
self._capture_thread = None
self._ongoing_scan_name = None
self._scan_images_taken = None
self._scan_data = None
@ -499,8 +502,6 @@ class SmartScanThing(Thing):
# cancel by user.
scan_successful = True
capture_thread = None
try:
self._set_scan_data()
self._save_scan_inputs_jons()
@ -530,10 +531,10 @@ class SmartScanThing(Thing):
)
raise e
finally:
if capture_thread:
if self._capture_thread:
# If the capture thread had an error we capture it here
try:
capture_thread.join()
self._capture_thread.join()
except Exception as e:
# If the scan has already ended due to an exception we will
# ignore any exceptions, but if it appeared to be successful
@ -563,8 +564,6 @@ class SmartScanThing(Thing):
planner_settings=planner_settings,
)
capture_thread = None
# At the start of the loop, we simultaneously capture an image and move to the next scan point.
# We skip capturing on the first run, because we've not focused yet - and also we skip capturing if
# it looks like background.
@ -600,8 +599,8 @@ class SmartScanThing(Thing):
)
# wait for the previous capture to be saved, i.e. don't leave more than one image saving in the background
if capture_thread:
self._wait_for_capture_thread(capture_thread)
if self._capture_thread:
self._wait_for_capture_thread()
# increment capure counter as thread has completed
self._scan_images_taken += 1
# Add it to the incremental zip
@ -613,7 +612,7 @@ class SmartScanThing(Thing):
name = f"image_{new_pos_xyz[0]}_{new_pos_xyz[1]}.jpg"
jpeg_path = os.path.join(self._ongoing_scan_images_dir, name)
capture_thread, acquired = self._start_capture_thread(jpeg_path)
self._capture_thread, acquired = self._start_capture_thread(jpeg_path)
# wait until the image is acquired
acquired.wait()
@ -635,25 +634,23 @@ class SmartScanThing(Thing):
Return False if failed after 3 tries - the position will be the initial estimate
"""
attempts = 0
max_attempts = 3
dz = self._scan_data["autofocus_dz"]
while attempts < 3:
while attempts < max_attempts:
attempts += 1
# Base on first run otherwise we move to estimated_z
start = "base" if attempts == 0 else "centre"
_, jpeg_sizes = self._autofocus.looping_autofocus(
dz=self._scan_data["autofocus_dz"], start=start
)
_, jpeg_sizes = self._autofocus.looping_autofocus(dz=dz, start="base")
current_height = self._stage.position["z"]
time.sleep(0.2)
autofocus_sharp_enough = self._autofocus.verify_focus_sharpness(
sweep_sizes=jpeg_sizes, camera=CamDep, threshold=0.92
)
# Not sharp enough, nobe to start and try again
# Not sharp enough, go to start and try again
if not autofocus_sharp_enough:
self._stage.move_absolute(z=this_xyz[2])
z = this_xyz[2] - dz / 2 if attempts < max_attempts else this_xyz[2]
self._stage.move_absolute(z=z)
continue
# No previous positions to compare against return success
@ -675,7 +672,8 @@ class SmartScanThing(Thing):
return True
# Shifted to far move to start and try again
self._stage.move_absolute(z=this_xyz[2])
z = this_xyz[2] - dz / 2 if attempts < max_attempts else this_xyz[2]
self._stage.move_absolute(z=z)
self._scan_logger.info(
"The focus has shifted further than we expect: retrying."
)
@ -684,18 +682,18 @@ class SmartScanThing(Thing):
return False
@_scan_running
def _wait_for_capture_thread(self, capture_thread: ErrorCapturingThread) -> None:
def _wait_for_capture_thread(self) -> None:
"""
Wait for the capture thread to be complete.
"""
wait_start = time.time()
thread_was_alive = capture_thread.is_alive()
thread_was_alive = self._capture_thread.is_alive()
# If the capture thread has thrown an exception it will be raised
# when join is called, this will cause the scan to end. If we want
# to retry captures at a later date this is where we will need to
# catch the IOError or CaptureError from the thread.
capture_thread.join()
self._capture_thread.join()
time.sleep(0.2)
if thread_was_alive:
wait_time = time.time() - wait_start