Moved capture management into separate object
This commit is contained in:
parent
1a6088a816
commit
caf553db7a
14 changed files with 302 additions and 227 deletions
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@ -57,6 +57,7 @@ logger.setLevel(logging.INFO)
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# Log server paths being used
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# Log server paths being used
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logging.info(f"Running with data path {OPENFLEXURE_VAR_PATH}")
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logging.info(f"Running with data path {OPENFLEXURE_VAR_PATH}")
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print("Creating app")
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# Create flask app
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# Create flask app
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app, labthing = create_app(
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app, labthing = create_app(
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__name__,
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__name__,
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@ -175,5 +176,6 @@ atexit.register(cleanup)
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if __name__ == "__main__":
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if __name__ == "__main__":
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from labthings.server.wsgi import Server
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from labthings.server.wsgi import Server
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print("Starting OpenFlexure Microscope Server...")
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server = Server(app)
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server = Server(app)
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server.run(host="::", port=5000, debug=False, zeroconf=True)
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server.run(host="::", port=5000, debug=False, zeroconf=True)
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@ -6,8 +6,8 @@ from labthings.server.find import find_component
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from openflexure_microscope.paths import settings_file_path, check_rw
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from openflexure_microscope.paths import settings_file_path, check_rw
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from openflexure_microscope.config import OpenflexureSettingsFile
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from openflexure_microscope.config import OpenflexureSettingsFile
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from openflexure_microscope.camera.base import BASE_CAPTURE_PATH
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from openflexure_microscope.captures.capture_manager import BASE_CAPTURE_PATH
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from openflexure_microscope.camera.capture import build_captures_from_exif
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from openflexure_microscope.captures.capture import build_captures_from_exif
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from openflexure_microscope.api.utilities.gui import build_gui
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from openflexure_microscope.api.utilities.gui import build_gui
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@ -37,17 +37,17 @@ def get_permissive_locations():
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]
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]
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def get_current_location(camera):
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def get_current_location(capture_manager):
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return camera.paths.get("default")
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return capture_manager.paths.get("default")
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def set_current_location(camera, location: str):
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def set_current_location(capture_manager, location: str):
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if not os.path.isdir(location):
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if not os.path.isdir(location):
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os.makedirs(location)
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os.makedirs(location)
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logging.debug("Updating location...")
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logging.debug("Updating location...")
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camera.paths.update({"default": location})
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capture_manager.paths.update({"default": location})
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logging.debug("Rebuilding captures...")
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logging.debug("Rebuilding captures...")
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camera.rebuild_captures()
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capture_manager.rebuild_captures()
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logging.debug("Capture location changed successfully.")
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logging.debug("Capture location changed successfully.")
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@ -93,7 +93,7 @@ class AutostorageExtension(BaseExtension):
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)
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)
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# We'll store a reference to a camera object, who's capture paths will be modified
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# We'll store a reference to a camera object, who's capture paths will be modified
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self.camera = None
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self.capture_manager = None
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self.initial_location = get_default_location()
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self.initial_location = get_default_location()
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@ -107,9 +107,9 @@ class AutostorageExtension(BaseExtension):
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logging.debug(f"Autostorage extension bound to camera {self.camera}")
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logging.debug(f"Autostorage extension bound to camera {self.camera}")
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# Store a reference to the camera
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# Store a reference to the camera
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self.camera = microscope_obj.camera
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self.capture_manager = microscope_obj.captures
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# Store the initial storage location
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# Store the initial storage location
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self.initial_location = get_current_location(self.camera)
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self.initial_location = get_current_location(self.capture_manager)
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# If preferred path does not exist, or cannot be written to
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# If preferred path does not exist, or cannot be written to
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self.check_location(self.initial_location)
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self.check_location(self.initial_location)
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@ -118,20 +118,20 @@ class AutostorageExtension(BaseExtension):
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def check_location(self, location=None):
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def check_location(self, location=None):
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if not location:
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if not location:
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location = get_current_location(self.camera)
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location = get_current_location(self.capture_manager)
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# If preferred path does not exist, or cannot be written to
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# If preferred path does not exist, or cannot be written to
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if not (os.path.isdir(location) and check_rw(location)):
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if not (os.path.isdir(location) and check_rw(location)):
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logging.error(
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logging.error(
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f"Preferred capture path {location} is missing or cannot be written to. Restoring defaults."
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f"Preferred capture path {location} is missing or cannot be written to. Restoring defaults."
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)
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)
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# Reset the storage location to default
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# Reset the storage location to default
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set_current_location(self.camera, get_default_location())
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set_current_location(self.capture_manager, get_default_location())
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def get_locations(self):
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def get_locations(self):
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if self.camera:
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if self.camera:
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locations = get_all_locations()
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locations = get_all_locations()
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current_location = get_current_location(self.camera)
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current_location = get_current_location(self.capture_manager)
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if current_location not in locations.values():
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if current_location not in locations.values():
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locations.update({"Custom": current_location})
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locations.update({"Custom": current_location})
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# Add location from the cameras settings file
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# Add location from the cameras settings file
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@ -140,7 +140,7 @@ class AutostorageExtension(BaseExtension):
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return {}
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return {}
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def get_preferred_key(self):
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def get_preferred_key(self):
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current = get_current_location(self.camera)
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current = get_current_location(self.capture_manager)
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locations = self.get_locations()
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locations = self.get_locations()
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matches = [k for k, v in locations.items() if v == current]
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matches = [k for k, v in locations.items() if v == current]
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@ -157,7 +157,7 @@ class AutostorageExtension(BaseExtension):
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raise KeyError(f"No location named {new_path_key}")
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raise KeyError(f"No location named {new_path_key}")
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location = self.get_locations().get(new_path_key)
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location = self.get_locations().get(new_path_key)
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set_current_location(self.camera, location)
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set_current_location(self.capture_manager, location)
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def key_to_title(self, path_key: str):
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def key_to_title(self, path_key: str):
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if not path_key in self.get_locations().keys():
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if not path_key in self.get_locations().keys():
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@ -85,27 +85,17 @@ def capture(
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filename = "{}_{}_{}_{}".format(basename, *microscope.stage.position)
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filename = "{}_{}_{}_{}".format(basename, *microscope.stage.position)
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folder = "SCAN_{}".format(basename)
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folder = "SCAN_{}".format(basename)
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# Create output object
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# Do capture
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output = microscope.camera.new_image(
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return microscope.capture(
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temporary=temporary, filename=filename, folder=folder
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filename=filename,
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folder=folder,
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temporary=temporary,
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use_video_port=use_video_port, resize=resize, bayer=bayer,
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annotations=annotations,
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tags=tags,
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metadata=metadata
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)
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)
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# Capture
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microscope.camera.capture(
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output.file, use_video_port=use_video_port, resize=resize, bayer=bayer
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)
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# Inject system metadata
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output.put_metadata({"instrument": microscope.metadata})
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# Insert custom metadata
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output.put_metadata(metadata)
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# Insert custom metadata
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output.put_annotations(annotations)
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# Insert custom tags
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output.put_tags(tags)
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### Scanning
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### Scanning
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@ -7,8 +7,6 @@ from labthings.core.utilities import path_relative_to
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from openflexure_microscope.paths import settings_file_path, check_rw
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from openflexure_microscope.paths import settings_file_path, check_rw
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from openflexure_microscope.config import OpenflexureSettingsFile
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from openflexure_microscope.config import OpenflexureSettingsFile
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from openflexure_microscope.camera.base import BASE_CAPTURE_PATH
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from openflexure_microscope.camera.capture import build_captures_from_exif
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from openflexure_microscope.api.utilities.gui import build_gui
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from openflexure_microscope.api.utilities.gui import build_gui
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@ -7,6 +7,6 @@ default_microscope = Microscope()
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# Restore loaded capture array to camera object
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# Restore loaded capture array to camera object
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logging.debug("Restoring captures...")
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logging.debug("Restoring captures...")
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default_microscope.camera.rebuild_captures()
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default_microscope.captures.rebuild_captures()
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logging.debug("Microscope successfully attached!")
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logging.debug("Microscope successfully attached!")
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@ -63,26 +63,16 @@ class CaptureAPI(View):
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# Explicitally acquire lock (prevents empty files being created if lock is unavailable)
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# Explicitally acquire lock (prevents empty files being created if lock is unavailable)
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with microscope.camera.lock:
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with microscope.camera.lock:
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output = microscope.camera.new_image(
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return microscope.capture(
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temporary=args.get("temporary"), filename=args.get("filename")
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filename=args.get("filename"),
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)
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temporary=args.get("temporary"),
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microscope.camera.capture(
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output.file,
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use_video_port=args.get("use_video_port"),
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use_video_port=args.get("use_video_port"),
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resize=resize,
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resize=resize,
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bayer=args.get("bayer"),
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bayer=args.get("bayer"),
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annotations=args.get("annotations"),
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tags=args.get("tags")
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)
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)
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# Inject system metadata
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output.put_metadata({"instrument": microscope.metadata})
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# Insert custom metadata
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output.put_annotations(args.get("annotations"))
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# Insert custom tags
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output.put_tags(args.get("tags"))
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return output
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@ThingAction
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@ThingAction
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@ -10,43 +10,11 @@ import threading
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import gevent
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import gevent
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from abc import ABCMeta, abstractmethod
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from abc import ABCMeta, abstractmethod
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from collections import OrderedDict
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from .capture import CaptureObject, build_captures_from_exif
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from openflexure_microscope.utilities import entry_by_uuid
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from labthings.core.lock import StrictLock
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from labthings.core.lock import StrictLock
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from labthings.core.event import ClientEvent
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from labthings.core.event import ClientEvent
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from openflexure_microscope.paths import data_file_path
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BASE_CAPTURE_PATH = data_file_path("micrographs")
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TEMP_CAPTURE_PATH = os.path.join(BASE_CAPTURE_PATH, "tmp")
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def last_entry(object_list: list):
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"""Return the last entry of a list, if the list contains items."""
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if object_list: # If any images have been captured
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return object_list[-1] # Return the latest captured image
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else:
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return None
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def generate_basename():
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"""Return a default filename based on the capture datetime"""
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return datetime.datetime.now().strftime("%Y-%m-%d_%H-%M-%S")
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def generate_numbered_basename(obj_list: list) -> str:
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initial_basename = generate_basename()
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basename = initial_basename
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# Handle clashing
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iterator = 1
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while basename in [obj.basename for obj in obj_list]:
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basename = initial_basename + "_{}".format(iterator)
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iterator += 1
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return basename
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class BaseCamera(metaclass=ABCMeta):
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class BaseCamera(metaclass=ABCMeta):
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"""
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"""
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self.stream_active = False
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self.stream_active = False
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self.record_active = False
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self.record_active = False
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self.paths = {"default": BASE_CAPTURE_PATH, "temp": TEMP_CAPTURE_PATH}
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# Capture data
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self.images = OrderedDict()
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self.videos = OrderedDict()
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@property
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@property
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@abstractmethod
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@abstractmethod
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def configuration(self):
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def configuration(self):
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@ -104,7 +66,7 @@ class BaseCamera(metaclass=ABCMeta):
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@abstractmethod
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@abstractmethod
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def read_settings(self) -> dict:
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def read_settings(self) -> dict:
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"""Return the current settings as a dictionary"""
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"""Return the current settings as a dictionary"""
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return {"paths": self.paths}
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return {}
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def __enter__(self):
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def __enter__(self):
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"""Create camera on context enter."""
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"""Create camera on context enter."""
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@ -127,134 +89,6 @@ class BaseCamera(metaclass=ABCMeta):
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self.stop_worker()
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self.stop_worker()
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logging.info("Closed {}".format(self))
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logging.info("Closed {}".format(self))
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def clear_tmp(self):
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"""
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Removes all files in the temporary capture directories
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"""
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if os.path.isdir(self.paths["temp"]):
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logging.info("Clearing {}...".format(self.paths["temp"]))
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shutil.rmtree(self.paths["temp"])
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logging.debug("Cleared {}.".format(self.paths["temp"]))
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def rebuild_captures(self):
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self.images = build_captures_from_exif(self.paths["default"])
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# RETURNING CAPTURES
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@property
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def image(self):
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"""Return the latest captured image."""
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return last_entry(self.images.values())
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@property
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def video(self):
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"""Return the latest recorded video."""
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return last_entry(self.videos.values())
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def image_from_id(self, image_id):
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"""Return an image StreamObject with a matching ID."""
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logging.warning("image_from_id is deprecated. Access captures as a dictionary.")
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return entry_by_uuid(image_id, self.images.values())
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def video_from_id(self, video_id):
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"""Return a video StreamObject with a matching ID."""
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logging.warning("video_from_id is deprecated. Access captures as a dictionary.")
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return entry_by_uuid(video_id, self.videos.values())
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# CREATING NEW CAPTURES
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def new_image(
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self,
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temporary: bool = True,
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filename: str = None,
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folder: str = "",
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fmt: str = "jpeg",
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):
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"""
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Create a new image capture object.
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Args:
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temporary (bool): Should the data be deleted after session ends.
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Creating the capture with a content manager sets this to true.
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filename (str): Name of the stored file. Defaults to timestamp.
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folder (str): Name of the folder in which to store the capture.
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fmt (str): Format of the capture.
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"""
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# Generate file name
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if not filename:
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filename = generate_numbered_basename(self.images.values())
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logging.debug(filename)
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filename = "{}.{}".format(filename, fmt)
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# Generate folder
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base_folder = self.paths["temp"] if temporary else self.paths["default"]
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folder = os.path.join(base_folder, folder)
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# Generate file path
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filepath = os.path.join(folder, filename)
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# Create capture object
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output = CaptureObject(filepath=filepath)
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# Insert a temporary tag if temporary
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if temporary:
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output.put_tags(["temporary"])
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# Update capture list
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capture_key = str(output.id)
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logging.debug(f"Adding image {output} with key {capture_key}")
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self.images[capture_key] = output
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return output
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def new_video(
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self,
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temporary: bool = False,
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||||||
filename: str = None,
|
|
||||||
folder: str = "",
|
|
||||||
fmt: str = "h264",
|
|
||||||
):
|
|
||||||
|
|
||||||
"""
|
|
||||||
Create a new video capture object.
|
|
||||||
|
|
||||||
Args:
|
|
||||||
temporary (bool): Should the data be deleted after session ends.
|
|
||||||
Creating the capture with a content manager sets this to true.
|
|
||||||
filename (str): Name of the stored file. Defaults to timestamp.
|
|
||||||
folder (str): Name of the folder in which to store the capture.
|
|
||||||
fmt (str): Format of the capture.
|
|
||||||
"""
|
|
||||||
# TODO: Remove the redundancy here
|
|
||||||
|
|
||||||
# Generate file name
|
|
||||||
if not filename:
|
|
||||||
filename = generate_numbered_basename(self.videos.values())
|
|
||||||
logging.debug(filename)
|
|
||||||
filename = "{}.{}".format(filename, fmt)
|
|
||||||
|
|
||||||
# Generate folder
|
|
||||||
base_folder = self.paths["temp"] if temporary else self.paths["default"]
|
|
||||||
folder = os.path.join(base_folder, folder)
|
|
||||||
|
|
||||||
# Generate file path
|
|
||||||
filepath = os.path.join(folder, filename)
|
|
||||||
|
|
||||||
# Create capture object
|
|
||||||
output = CaptureObject(filepath=filepath)
|
|
||||||
# Insert a temporary tag if temporary
|
|
||||||
if temporary:
|
|
||||||
output.put_tags(["temporary"])
|
|
||||||
|
|
||||||
# Update capture list
|
|
||||||
capture_key = str(output.id)
|
|
||||||
logging.debug(f"Adding video {output} with key {capture_key}")
|
|
||||||
self.videos[capture_key] = output
|
|
||||||
|
|
||||||
return output
|
|
||||||
|
|
||||||
# START AND STOP WORKER THREAD
|
# START AND STOP WORKER THREAD
|
||||||
|
|
||||||
def start_worker(self, timeout: int = 5) -> bool:
|
def start_worker(self, timeout: int = 5) -> bool:
|
||||||
|
|
|
||||||
|
|
@ -17,7 +17,8 @@ import logging
|
||||||
# Type hinting
|
# Type hinting
|
||||||
from typing import Tuple
|
from typing import Tuple
|
||||||
|
|
||||||
from openflexure_microscope.camera.base import BaseCamera, CaptureObject
|
from openflexure_microscope.camera.base import BaseCamera
|
||||||
|
from openflexure_microscope.captures import CaptureObject
|
||||||
|
|
||||||
|
|
||||||
"""
|
"""
|
||||||
|
|
|
||||||
|
|
@ -41,7 +41,8 @@ import picamera.array
|
||||||
# Type hinting
|
# Type hinting
|
||||||
from typing import Tuple
|
from typing import Tuple
|
||||||
|
|
||||||
from .base import BaseCamera, CaptureObject
|
from openflexure_microscope.camera.base import BaseCamera
|
||||||
|
from openflexure_microscope.captures import CaptureObject
|
||||||
|
|
||||||
# Richard's fix gain
|
# Richard's fix gain
|
||||||
from .set_picamera_gain import set_analog_gain, set_digital_gain
|
from .set_picamera_gain import set_analog_gain, set_digital_gain
|
||||||
|
|
|
||||||
3
openflexure_microscope/captures/__init__.py
Normal file
3
openflexure_microscope/captures/__init__.py
Normal file
|
|
@ -0,0 +1,3 @@
|
||||||
|
from .capture_manager import CaptureManager
|
||||||
|
from .capture import CaptureObject
|
||||||
|
from . import capture_manager, capture
|
||||||
193
openflexure_microscope/captures/capture_manager.py
Normal file
193
openflexure_microscope/captures/capture_manager.py
Normal file
|
|
@ -0,0 +1,193 @@
|
||||||
|
import os
|
||||||
|
import datetime
|
||||||
|
import shutil
|
||||||
|
import logging
|
||||||
|
from collections import OrderedDict
|
||||||
|
|
||||||
|
from labthings.core.lock import StrictLock
|
||||||
|
|
||||||
|
from openflexure_microscope.utilities import entry_by_uuid
|
||||||
|
from openflexure_microscope.paths import data_file_path
|
||||||
|
|
||||||
|
from .capture import CaptureObject, build_captures_from_exif
|
||||||
|
|
||||||
|
BASE_CAPTURE_PATH = data_file_path("micrographs")
|
||||||
|
TEMP_CAPTURE_PATH = os.path.join(BASE_CAPTURE_PATH, "tmp")
|
||||||
|
|
||||||
|
|
||||||
|
def last_entry(object_list: list):
|
||||||
|
"""Return the last entry of a list, if the list contains items."""
|
||||||
|
if object_list: # If any images have been captured
|
||||||
|
return object_list[-1] # Return the latest captured image
|
||||||
|
else:
|
||||||
|
return None
|
||||||
|
|
||||||
|
|
||||||
|
def generate_basename():
|
||||||
|
"""Return a default filename based on the capture datetime"""
|
||||||
|
return datetime.datetime.now().strftime("%Y-%m-%d_%H-%M-%S")
|
||||||
|
|
||||||
|
|
||||||
|
def generate_numbered_basename(obj_list: list) -> str:
|
||||||
|
initial_basename = generate_basename()
|
||||||
|
basename = initial_basename
|
||||||
|
# Handle clashing
|
||||||
|
iterator = 1
|
||||||
|
while basename in [obj.basename for obj in obj_list]:
|
||||||
|
basename = initial_basename + "_{}".format(iterator)
|
||||||
|
iterator += 1
|
||||||
|
|
||||||
|
return basename
|
||||||
|
|
||||||
|
|
||||||
|
class CaptureManager:
|
||||||
|
def __init__(self):
|
||||||
|
self.paths = {"default": BASE_CAPTURE_PATH, "temp": TEMP_CAPTURE_PATH}
|
||||||
|
|
||||||
|
self.lock = StrictLock(timeout=1, name="Captures")
|
||||||
|
|
||||||
|
# Capture data
|
||||||
|
self.images = OrderedDict()
|
||||||
|
self.videos = OrderedDict()
|
||||||
|
|
||||||
|
# FILE MANAGEMENT
|
||||||
|
|
||||||
|
def clear_tmp(self):
|
||||||
|
"""
|
||||||
|
Removes all files in the temporary capture directories
|
||||||
|
"""
|
||||||
|
|
||||||
|
if os.path.isdir(self.paths["temp"]):
|
||||||
|
logging.info("Clearing {}...".format(self.paths["temp"]))
|
||||||
|
shutil.rmtree(self.paths["temp"])
|
||||||
|
logging.debug("Cleared {}.".format(self.paths["temp"]))
|
||||||
|
|
||||||
|
def rebuild_captures(self):
|
||||||
|
self.images = build_captures_from_exif(self.paths["default"])
|
||||||
|
|
||||||
|
def update_settings(self, config: dict):
|
||||||
|
"""Update settings from a config dictionary"""
|
||||||
|
with self.lock:
|
||||||
|
# Apply valid config params to camera object
|
||||||
|
for key, value in config.items(): # For each provided setting
|
||||||
|
if hasattr(self, key): # If the instance has a matching property
|
||||||
|
setattr(self, key, value) # Set to the target value
|
||||||
|
|
||||||
|
def read_settings(self) -> dict:
|
||||||
|
"""Return the current settings as a dictionary"""
|
||||||
|
return {"paths": self.paths}
|
||||||
|
|
||||||
|
# RETURNING CAPTURES
|
||||||
|
|
||||||
|
@property
|
||||||
|
def image(self):
|
||||||
|
"""Return the latest captured image."""
|
||||||
|
return last_entry(self.images.values())
|
||||||
|
|
||||||
|
@property
|
||||||
|
def video(self):
|
||||||
|
"""Return the latest recorded video."""
|
||||||
|
return last_entry(self.videos.values())
|
||||||
|
|
||||||
|
def image_from_id(self, image_id):
|
||||||
|
"""Return an image StreamObject with a matching ID."""
|
||||||
|
logging.warning("image_from_id is deprecated. Access captures as a dictionary.")
|
||||||
|
return entry_by_uuid(image_id, self.images.values())
|
||||||
|
|
||||||
|
def video_from_id(self, video_id):
|
||||||
|
"""Return a video StreamObject with a matching ID."""
|
||||||
|
logging.warning("video_from_id is deprecated. Access captures as a dictionary.")
|
||||||
|
return entry_by_uuid(video_id, self.videos.values())
|
||||||
|
|
||||||
|
# CREATING NEW CAPTURES
|
||||||
|
|
||||||
|
def new_image(
|
||||||
|
self,
|
||||||
|
temporary: bool = True,
|
||||||
|
filename: str = None,
|
||||||
|
folder: str = "",
|
||||||
|
fmt: str = "jpeg",
|
||||||
|
):
|
||||||
|
|
||||||
|
"""
|
||||||
|
Create a new image capture object.
|
||||||
|
|
||||||
|
Args:
|
||||||
|
temporary (bool): Should the data be deleted after session ends.
|
||||||
|
Creating the capture with a content manager sets this to true.
|
||||||
|
filename (str): Name of the stored file. Defaults to timestamp.
|
||||||
|
folder (str): Name of the folder in which to store the capture.
|
||||||
|
fmt (str): Format of the capture.
|
||||||
|
"""
|
||||||
|
|
||||||
|
# Generate file name
|
||||||
|
if not filename:
|
||||||
|
filename = generate_numbered_basename(self.images.values())
|
||||||
|
logging.debug(filename)
|
||||||
|
filename = "{}.{}".format(filename, fmt)
|
||||||
|
|
||||||
|
# Generate folder
|
||||||
|
base_folder = self.paths["temp"] if temporary else self.paths["default"]
|
||||||
|
folder = os.path.join(base_folder, folder)
|
||||||
|
|
||||||
|
# Generate file path
|
||||||
|
filepath = os.path.join(folder, filename)
|
||||||
|
|
||||||
|
# Create capture object
|
||||||
|
output = CaptureObject(filepath=filepath)
|
||||||
|
# Insert a temporary tag if temporary
|
||||||
|
if temporary:
|
||||||
|
output.put_tags(["temporary"])
|
||||||
|
|
||||||
|
# Update capture list
|
||||||
|
capture_key = str(output.id)
|
||||||
|
logging.debug(f"Adding image {output} with key {capture_key}")
|
||||||
|
self.images[capture_key] = output
|
||||||
|
|
||||||
|
return output
|
||||||
|
|
||||||
|
def new_video(
|
||||||
|
self,
|
||||||
|
temporary: bool = False,
|
||||||
|
filename: str = None,
|
||||||
|
folder: str = "",
|
||||||
|
fmt: str = "h264",
|
||||||
|
):
|
||||||
|
|
||||||
|
"""
|
||||||
|
Create a new video capture object.
|
||||||
|
|
||||||
|
Args:
|
||||||
|
temporary (bool): Should the data be deleted after session ends.
|
||||||
|
Creating the capture with a content manager sets this to true.
|
||||||
|
filename (str): Name of the stored file. Defaults to timestamp.
|
||||||
|
folder (str): Name of the folder in which to store the capture.
|
||||||
|
fmt (str): Format of the capture.
|
||||||
|
"""
|
||||||
|
# TODO: Remove the redundancy here
|
||||||
|
|
||||||
|
# Generate file name
|
||||||
|
if not filename:
|
||||||
|
filename = generate_numbered_basename(self.videos.values())
|
||||||
|
logging.debug(filename)
|
||||||
|
filename = "{}.{}".format(filename, fmt)
|
||||||
|
|
||||||
|
# Generate folder
|
||||||
|
base_folder = self.paths["temp"] if temporary else self.paths["default"]
|
||||||
|
folder = os.path.join(base_folder, folder)
|
||||||
|
|
||||||
|
# Generate file path
|
||||||
|
filepath = os.path.join(folder, filename)
|
||||||
|
|
||||||
|
# Create capture object
|
||||||
|
output = CaptureObject(filepath=filepath)
|
||||||
|
# Insert a temporary tag if temporary
|
||||||
|
if temporary:
|
||||||
|
output.put_tags(["temporary"])
|
||||||
|
|
||||||
|
# Update capture list
|
||||||
|
capture_key = str(output.id)
|
||||||
|
logging.debug(f"Adding video {output} with key {capture_key}")
|
||||||
|
self.videos[capture_key] = output
|
||||||
|
|
||||||
|
return output
|
||||||
|
|
@ -5,6 +5,9 @@ Defines a microscope object, binding a camera and stage with basic functionality
|
||||||
import logging
|
import logging
|
||||||
import pkg_resources
|
import pkg_resources
|
||||||
import uuid
|
import uuid
|
||||||
|
from typing import Tuple
|
||||||
|
|
||||||
|
from openflexure_microscope.captures import CaptureManager
|
||||||
|
|
||||||
from openflexure_microscope.stage.mock import MissingStage
|
from openflexure_microscope.stage.mock import MissingStage
|
||||||
from openflexure_microscope.camera.mock import MissingCamera
|
from openflexure_microscope.camera.mock import MissingCamera
|
||||||
|
|
@ -33,6 +36,8 @@ class Microscope:
|
||||||
self.id = uuid.uuid4()
|
self.id = uuid.uuid4()
|
||||||
self.name = self.id
|
self.name = self.id
|
||||||
|
|
||||||
|
self.captures = CaptureManager()
|
||||||
|
|
||||||
self.fov = [0, 0] #: Microscope field-of-view in stage motor steps
|
self.fov = [0, 0] #: Microscope field-of-view in stage motor steps
|
||||||
|
|
||||||
# Store settings and configuration files
|
# Store settings and configuration files
|
||||||
|
|
@ -47,6 +52,7 @@ class Microscope:
|
||||||
|
|
||||||
self.camera = None #: Currently connected camera object
|
self.camera = None #: Currently connected camera object
|
||||||
self.stage = None #: Currently connected stage object
|
self.stage = None #: Currently connected stage object
|
||||||
|
|
||||||
self.setup(self.configuration_file.load()) # Attach components
|
self.setup(self.configuration_file.load()) # Attach components
|
||||||
|
|
||||||
# Apply settings loaded from file
|
# Apply settings loaded from file
|
||||||
|
|
@ -75,6 +81,7 @@ class Microscope:
|
||||||
"""
|
"""
|
||||||
|
|
||||||
### Detector
|
### Detector
|
||||||
|
print("Creating camera")
|
||||||
if configuration.get("camera"):
|
if configuration.get("camera"):
|
||||||
camera_type = configuration["camera"].get("type")
|
camera_type = configuration["camera"].get("type")
|
||||||
if camera_type in ("PiCamera", "PiCameraStreamer"):
|
if camera_type in ("PiCamera", "PiCameraStreamer"):
|
||||||
|
|
@ -85,6 +92,7 @@ class Microscope:
|
||||||
logging.warning("No compatible camera hardware found.")
|
logging.warning("No compatible camera hardware found.")
|
||||||
|
|
||||||
### Stage
|
### Stage
|
||||||
|
print("Creating stage")
|
||||||
if configuration.get("stage"):
|
if configuration.get("stage"):
|
||||||
stage_type = configuration["stage"].get("type")
|
stage_type = configuration["stage"].get("type")
|
||||||
stage_port = configuration["stage"].get("port")
|
stage_port = configuration["stage"].get("port")
|
||||||
|
|
@ -95,6 +103,7 @@ class Microscope:
|
||||||
logging.error(e)
|
logging.error(e)
|
||||||
logging.warning("No compatible Sangaboard hardware found.")
|
logging.warning("No compatible Sangaboard hardware found.")
|
||||||
|
|
||||||
|
print("Handling fallbacks")
|
||||||
### Fallbacks
|
### Fallbacks
|
||||||
if not self.camera:
|
if not self.camera:
|
||||||
self.camera = MissingCamera()
|
self.camera = MissingCamera()
|
||||||
|
|
@ -102,6 +111,7 @@ class Microscope:
|
||||||
self.stage = MissingStage()
|
self.stage = MissingStage()
|
||||||
|
|
||||||
### Locks
|
### Locks
|
||||||
|
print("Creating locks")
|
||||||
if hasattr(self.camera, "lock"):
|
if hasattr(self.camera, "lock"):
|
||||||
self.lock.locks.append(self.camera.lock)
|
self.lock.locks.append(self.camera.lock)
|
||||||
if hasattr(self.stage, "lock"):
|
if hasattr(self.stage, "lock"):
|
||||||
|
|
@ -144,11 +154,14 @@ class Microscope:
|
||||||
|
|
||||||
# If attached to a camera
|
# If attached to a camera
|
||||||
if ("camera" in settings) and self.camera:
|
if ("camera" in settings) and self.camera:
|
||||||
self.camera.update_settings(settings["camera"])
|
self.camera.update_settings(settings.get("camera", {}))
|
||||||
|
|
||||||
# If attached to a stage
|
# If attached to a stage
|
||||||
if ("stage" in settings) and self.stage:
|
if ("stage" in settings) and self.stage:
|
||||||
self.stage.update_settings(settings["stage"])
|
self.stage.update_settings(settings.get("stage", {}))
|
||||||
|
|
||||||
|
# Capture manager
|
||||||
|
self.captures.update_settings(settings.get("captures", {}))
|
||||||
|
|
||||||
# Microscope settings
|
# Microscope settings
|
||||||
if "id" in settings:
|
if "id" in settings:
|
||||||
|
|
@ -207,6 +220,10 @@ class Microscope:
|
||||||
settings_current_stage = self.stage.read_settings()
|
settings_current_stage = self.stage.read_settings()
|
||||||
settings_current["stage"] = settings_current_stage
|
settings_current["stage"] = settings_current_stage
|
||||||
|
|
||||||
|
# Capture manager
|
||||||
|
settings_current_captures = self.captures.read_settings()
|
||||||
|
settings_current["captures"] = settings_current_captures
|
||||||
|
|
||||||
settings_full = self.settings_file.merge(settings_current)
|
settings_full = self.settings_file.merge(settings_current)
|
||||||
|
|
||||||
if full:
|
if full:
|
||||||
|
|
@ -260,3 +277,49 @@ class Microscope:
|
||||||
}
|
}
|
||||||
|
|
||||||
return system_metadata
|
return system_metadata
|
||||||
|
|
||||||
|
def capture(
|
||||||
|
self,
|
||||||
|
filename: str = None,
|
||||||
|
folder: str = "",
|
||||||
|
temporary: bool = False,
|
||||||
|
use_video_port: bool = False,
|
||||||
|
resize: Tuple[int, int] = None,
|
||||||
|
bayer: bool = True,
|
||||||
|
fmt: str = "jpeg",
|
||||||
|
annotations: dict = None,
|
||||||
|
tags: list = None,
|
||||||
|
metadata: dict = None
|
||||||
|
):
|
||||||
|
if not annotations:
|
||||||
|
annotations = {}
|
||||||
|
if not metadata:
|
||||||
|
metadata = {}
|
||||||
|
if not tags:
|
||||||
|
tags = []
|
||||||
|
|
||||||
|
with self.camera.lock:
|
||||||
|
# Create output object
|
||||||
|
output = self.captures.new_image(
|
||||||
|
temporary=temporary, filename=filename, folder=folder, fmt=fmt
|
||||||
|
)
|
||||||
|
|
||||||
|
# Capture to output object
|
||||||
|
self.camera.capture(
|
||||||
|
output.file,
|
||||||
|
use_video_port=use_video_port,
|
||||||
|
resize=resize,
|
||||||
|
bayer=bayer,
|
||||||
|
fmt=fmt
|
||||||
|
)
|
||||||
|
|
||||||
|
# Inject system metadata
|
||||||
|
output.put_metadata({"instrument": self.metadata})
|
||||||
|
# Insert custom metadata
|
||||||
|
output.put_metadata(metadata)
|
||||||
|
# Insert custom metadata
|
||||||
|
output.put_annotations(annotations)
|
||||||
|
# Insert custom tags
|
||||||
|
output.put_tags(tags)
|
||||||
|
|
||||||
|
return output
|
||||||
|
|
@ -1,6 +1,6 @@
|
||||||
from openflexure_microscope.rescue.monitor_timeout import launch_timeout_test_process
|
from openflexure_microscope.rescue.monitor_timeout import launch_timeout_test_process
|
||||||
from openflexure_microscope.camera.capture import build_captures_from_exif
|
from openflexure_microscope.captures.capture_manager import BASE_CAPTURE_PATH
|
||||||
from openflexure_microscope.camera.base import BASE_CAPTURE_PATH
|
from openflexure_microscope.captures.capture import build_captures_from_exif
|
||||||
from openflexure_microscope.config import user_settings
|
from openflexure_microscope.config import user_settings
|
||||||
|
|
||||||
import logging
|
import logging
|
||||||
|
|
@ -10,7 +10,7 @@ def check_capture_rebuild(timeout=10):
|
||||||
logging.info("Loading user settings...")
|
logging.info("Loading user settings...")
|
||||||
settings = user_settings.load()
|
settings = user_settings.load()
|
||||||
|
|
||||||
cap_path = str(settings.get("camera", {}).get("paths", {}).get("default"))
|
cap_path = str(settings.get("captures", {}).get("paths", {}).get("default"))
|
||||||
logging.info(f"Capture path found: {cap_path}")
|
logging.info(f"Capture path found: {cap_path}")
|
||||||
if not cap_path:
|
if not cap_path:
|
||||||
logging.error(
|
logging.error(
|
||||||
|
|
|
||||||
Loading…
Add table
Add a link
Reference in a new issue