Complete first pass (untested on hardware) of bg detect refactor.
This commit is contained in:
Julian Stirling
parent
2245d9357d
commit
fe1b84a922
10 changed files with 90 additions and 88 deletions
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@ -20,7 +20,11 @@ import piexif
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import labthings_fastapi as lt
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from labthings_fastapi.types.numpy import NDArray
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from openflexure_microscope_server.background_detect import BackgroundDetectLUV
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from openflexure_microscope_server.background_detect import (
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ColourChannelDetectLUV,
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BackgroundDetectAlgorithm,
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BackgroundDetectorStatus,
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)
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LOGGER = logging.getLogger(__name__)
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@ -166,7 +170,7 @@ class BaseCamera(lt.Thing):
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This must be run by all child camera classes.
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"""
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super().__init__()
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self.background_detectors = {"Colour Channels (LUV)": BackgroundDetectLUV()}
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self.background_detectors = {"Colour Channels (LUV)": ColourChannelDetectLUV()}
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self._detector_name = "Colour Channels (LUV)"
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def __enter__(self) -> None:
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@ -484,23 +488,36 @@ class BaseCamera(lt.Thing):
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self._detector_name = name
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@property
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def active_detector(self):
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def active_detector(self) -> BackgroundDetectAlgorithm:
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"""The active background detector instance."""
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return self.background_detectors[self.detector_name]
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@lt.thing_property
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def background_detector_status(self) -> BackgroundDetectorStatus:
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"""The status of the active detector for the UI."""
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return self.active_detector.status
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@lt.thing_setting
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def background_detector_data(self) -> str:
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"""The name of the active background selector."""
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"""The data for each background detector, used to save to disk."""
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data = {}
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for name, obj in self.background_detectors.items():
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bg_data = (
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None
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if obj.background_data is None
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else obj.background_data.model_dump()
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)
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data[name] = {
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"settings": obj.settings.model_dump(),
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"background_data": obj.background_data.model_dump(),
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"background_data": bg_data,
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}
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@detector_name.setter
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def detector_name(self, data: str) -> None:
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"""Validate and set detector_name."""
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"""Set the data for each detector. This should only be called on init.
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Do not call over HTTP. Would be good to have a way to make this private.
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"""
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for name, instance_data in data.items():
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if name in self.background_detectors:
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obj = self.background_detectors[name]
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@ -118,7 +118,7 @@ class StreamingPiCamera2(BaseCamera):
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:param camera_num: The number of the camera. This should generally be left as 0
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as most Raspberry Pi boards only support 1 camera.
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"""
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super().__init()
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super().__init__()
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self._setting_save_in_progress = False
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self.camera_num = camera_num
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self.camera_configs: dict[str, dict] = {}
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@ -58,7 +58,7 @@ class SimulatedCamera(BaseCamera):
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:param frame_interval: Nominally the time between frames on the MJPEG stream,
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however the rate may be slower due to calculation time for focus.
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"""
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super().__init()
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super().__init__()
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self.shape = shape
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self.glyph_shape = glyph_shape
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self.canvas_shape = canvas_shape
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@ -1,7 +1,7 @@
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"""The core sample scanning functionality for the OpenFlexure Microscope.
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SmartScan provides sample scanning functionality including automatic background
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detection (via the `BackgroundDetectThing`) and automatic path planning via
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detection (via the `CameraThing`) and automatic path planning via
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`scan_planners`. It manages the directories of past scans via `scan_directories`.
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It also controls external processes for live stitching composite images, and
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the creation of the final stitched images.
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@ -29,7 +29,6 @@ from openflexure_microscope_server import scan_planners
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# Things
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from .autofocus import AutofocusThing
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from .camera_stage_mapping import CameraStageMapper
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from .background_detect import BackgroundDetectThing
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from .camera import CameraDependency as CamDep
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from .stage import StageDependency as StageDep
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@ -37,9 +36,6 @@ CSMDep = lt.deps.direct_thing_client_dependency(
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CameraStageMapper, "/camera_stage_mapping/"
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)
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AutofocusDep = lt.deps.direct_thing_client_dependency(AutofocusThing, "/autofocus/")
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BackgroundDep = lt.deps.direct_thing_client_dependency(
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BackgroundDetectThing, "/background_detect/"
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)
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JPEGBlob = lt.blob.blob_type("image/jpeg")
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ZipBlob = lt.blob.blob_type("application/zip")
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@ -110,7 +106,6 @@ class SmartScanThing(lt.Thing):
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self._cam: Optional[CamDep] = None
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self._metadata_getter: Optional[lt.deps.GetThingStates] = None
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self._csm: Optional[CSMDep] = None
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self._background_detect: Optional[BackgroundDep] = None
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self._ongoing_scan: Optional[scan_directories.ScanDirectory] = None
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self._starting_position: Optional[Mapping[str, int]] = None
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self._capture_thread: Optional[ErrorCapturingThread] = None
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@ -128,14 +123,13 @@ class SmartScanThing(lt.Thing):
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cam: CamDep,
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metadata_getter: lt.deps.GetThingStates,
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csm: CSMDep,
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background_detect: BackgroundDep,
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scan_name: str = "",
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):
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"""Move the stage to cover an area, taking images that can be tiled together.
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The stage will move in a pattern that grows outwards from the starting point,
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stopping once it is surrounded by "background" (as detected by the
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background_detect Thing) or reaches the "max_range" measured in steps.
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camera Thing) or reaches the "max_range" measured in steps.
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"""
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got_lock = self._scan_lock.acquire(timeout=0.1)
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if not got_lock:
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@ -149,7 +143,6 @@ class SmartScanThing(lt.Thing):
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self._cam = cam
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self._metadata_getter = metadata_getter
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self._csm = csm
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self._background_detect = background_detect
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self._capture_thread = None
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self._scan_images_taken = 0
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@ -183,7 +176,6 @@ class SmartScanThing(lt.Thing):
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self._cam = None
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self._metadata_getter = None
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self._csm = None
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self._background_detect = None
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self._capture_thread = None
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self._ongoing_scan = None
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self._scan_images_taken = None
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@ -207,7 +199,7 @@ class SmartScanThing(lt.Thing):
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)
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if self.skip_background:
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if not self._background_detect.background_distributions:
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if not self._cam.background_detector_status.ready:
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raise RuntimeError(
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"Background is not set: you need to calibrate background detection."
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)
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@ -511,7 +503,7 @@ class SmartScanThing(lt.Thing):
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capture_image = True
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# If skipping background, take an image to check if current field of view is background
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if self._scan_data["skip_background"]:
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capture_image, bg_message = self._background_detect.image_is_sample()
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capture_image, bg_message = self._cam.image_is_sample()
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if not capture_image:
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route_planner.mark_location_visited(
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