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Functional z stack Thing

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jaknapper 2025-04-16 09:40:14 +01:00
parent 327a87e344
commit 1f3211e3ee
3 changed files with 182 additions and 41 deletions
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83
src/openflexure_microscope_server/things/smart_scan.py
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@ -34,6 +34,7 @@ from openflexure_microscope_server.utilities import ErrorCapturingThread
from openflexure_microscope_server.things.autofocus import AutofocusThing
from openflexure_microscope_server.things.camera_stage_mapping import CameraStageMapper
from openflexure_microscope_server.things.background_detect import BackgroundDetectThing
from openflexure_microscope_server.things.z_stack import ZStackThing
from openflexure_microscope_server import scan_planners
CSMDep = direct_thing_client_dependency(CameraStageMapper, "/camera_stage_mapping/")
@ -41,7 +42,7 @@ AutofocusDep = direct_thing_client_dependency(AutofocusThing, "/autofocus/")
BackgroundDep = direct_thing_client_dependency(
BackgroundDetectThing, "/background_detect/"
)
ZStackDep = direct_thing_client_dependency(ZStackThing, "/z_stack/")
IMAGE_REGEX = re.compile(r"-?[0-9]+_-?[0-9]+\.jpeg$")
@ -159,6 +160,7 @@ 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._z_stack: Optional[ZStackDep] = 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
@ -175,6 +177,7 @@ class SmartScanThing(Thing):
metadata_getter: GetThingStates,
csm: CSMDep,
background_detect: BackgroundDep,
z_stack: ZStackDep,
scan_name: str = "",
):
"""Move the stage to cover an area, taking images that can be tiled together.
@ -198,6 +201,7 @@ class SmartScanThing(Thing):
self._csm = csm
self._background_detect = background_detect
self._capture_thread = None
self._z_stack = z_stack
self._scan_images_taken = 0
# Don't set self._scan_data dictionary. This is done at the start of _run_scan
@ -232,6 +236,7 @@ class SmartScanThing(Thing):
self._ongoing_scan_name = None
self._scan_images_taken = None
self._scan_data = None
self._z_stack = None
self._scan_lock.release()
@_scan_running
@ -586,22 +591,24 @@ 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 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
self.create_zip_of_scan(
logger=self._scan_logger,
scan_name=self._ongoing_scan_name,
download_zip=False,
)
# 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
self.create_zip_of_scan(
logger=self._scan_logger,
scan_name=self._ongoing_scan_name,
download_zip=False,
)
name = f"image_{new_pos_xyz[0]}_{new_pos_xyz[1]}.jpg"
jpeg_path = os.path.join(self._ongoing_scan_images_dir, name)
self._capture_thread, acquired = self._start_capture_thread(jpeg_path)
# jpeg_path = os.path.join(self._ongoing_scan_images_dir, name)
self._z_stack.smart_stack(images_dir = self._ongoing_scan_images_dir)
# self._capture_thread = self._start_capture_thread(jpeg_path)
# wait until the image is acquired
acquired.wait()
# acquired.wait()
@_scan_running
def _try_autofocus(
@ -659,31 +666,31 @@ class SmartScanThing(Thing):
f"Waited {wait_time:.1f}s for the previous capture to finish saving."
)
@_scan_running
def _start_capture_thread(
self, jpeg_path: str
) -> tuple[ErrorCapturingThread, Event]:
"""
Start the capture thread.
# @_scan_running
# def _start_capture_thread(
# self, jpeg_path: str
# ) -> tuple[ErrorCapturingThread, Event]:
# """
# Start the capture thread.
Args:
jpeg_path, the path to save the image once aquired
# Args:
# jpeg_path, the path to save the image once aquired
Return the thread and an event that will be set when the image is aquired
"""
acquired = Event()
time.sleep(0.2)
# Return the thread and an event that will be set when the image is aquired
# """
# time.sleep(0.2)
# Acquire the image in a thread, and continue once it's acquired
# (i.e. leave saving in the background) Use ErrorCapturingThread
# intead of Thread. This will raise errors in the calling thread
# only when join() is called, allowing us to handle this appropriately.
capture_thread = ErrorCapturingThread(
target=self._capture_and_save,
kwargs={"acquired": acquired, "jpeg_path": jpeg_path},
)
capture_thread.start()
return capture_thread, acquired
# # Acquire the image in a thread, and continue once it's acquired
# # (i.e. leave saving in the background) Use ErrorCapturingThread
# # intead of Thread. This will raise errors in the calling thread
# # only when join() is called, allowing us to handle this appropriately.
# capture_thread = ErrorCapturingThread(
# # target=self._capture_and_save,
# target=self._z_stack.smart_stack(),
# kwargs={"images_dir": self._ongoing_scan_images_dir},
# )
# capture_thread.start()
# return capture_thread
@_scan_running
def _return_to_starting_position(self):
@ -1241,7 +1248,3 @@ class SmartScanThing(Thing):
"""List the relative paths of all files and folders in the zip folder specified"""
scan_zip = zipfile.ZipFile(zip_path)
return [os.path.normpath(i) for i in scan_zip.namelist()]
class CaptureError(RuntimeError):
"""An error trying to capture from Picamera"""