Commit caf553db authored by Joel Collins's avatar Joel Collins
Browse files

Moved capture management into separate object

parent 1a6088a8

openflexure_microscope/api/app.py

+2 −0
Original line number Diff line number Diff line
@@ -57,6 +57,7 @@ logger.setLevel(logging.INFO) 
# Log server paths being used

logging.info(f"Running with data path {OPENFLEXURE_VAR_PATH}")



print("Creating app")

# Create flask app

app, labthing = create_app(

    __name__,
@@ -175,5 +176,6 @@ atexit.register(cleanup) 
if __name__ == "__main__":

    from labthings.server.wsgi import Server



    print("Starting OpenFlexure Microscope Server...")

    server = Server(app)

    server.run(host="::", port=5000, debug=False, zeroconf=True)

openflexure_microscope/api/default_extensions/autostorage.py

+15 −15
Original line number Diff line number Diff line
@@ -6,8 +6,8 @@ from labthings.server.find import find_component 


from openflexure_microscope.paths import settings_file_path, check_rw

from openflexure_microscope.config import OpenflexureSettingsFile

from openflexure_microscope.camera.base import BASE_CAPTURE_PATH

from openflexure_microscope.camera.capture import build_captures_from_exif

from openflexure_microscope.captures.capture_manager import BASE_CAPTURE_PATH

from openflexure_microscope.captures.capture import build_captures_from_exif



from openflexure_microscope.api.utilities.gui import build_gui
@@ -37,17 +37,17 @@ def get_permissive_locations(): 
    ]





def get_current_location(camera):

    return camera.paths.get("default")

def get_current_location(capture_manager):

    return capture_manager.paths.get("default")





def set_current_location(camera, location: str):

def set_current_location(capture_manager, location: str):

    if not os.path.isdir(location):

        os.makedirs(location)

    logging.debug("Updating location...")

    camera.paths.update({"default": location})

    capture_manager.paths.update({"default": location})

    logging.debug("Rebuilding captures...")

    camera.rebuild_captures()

    capture_manager.rebuild_captures()

    logging.debug("Capture location changed successfully.")
@@ -93,7 +93,7 @@ class AutostorageExtension(BaseExtension): 
        )



        # We'll store a reference to a camera object, who's capture paths will be modified

        self.camera = None

        self.capture_manager = None



        self.initial_location = get_default_location()
@@ -107,9 +107,9 @@ class AutostorageExtension(BaseExtension): 
            logging.debug(f"Autostorage extension bound to camera {self.camera}")



            # Store a reference to the camera

            self.camera = microscope_obj.camera

            self.capture_manager = microscope_obj.captures

            # Store the initial storage location

            self.initial_location = get_current_location(self.camera)

            self.initial_location = get_current_location(self.capture_manager)



            # If preferred path does not exist, or cannot be written to

            self.check_location(self.initial_location)
@@ -118,20 +118,20 @@ class AutostorageExtension(BaseExtension): 


    def check_location(self, location=None):

        if not location:

            location = get_current_location(self.camera)

            location = get_current_location(self.capture_manager)

        # If preferred path does not exist, or cannot be written to

        if not (os.path.isdir(location) and check_rw(location)):

            logging.error(

                f"Preferred capture path {location} is missing or cannot be written to. Restoring defaults."

            )

            # Reset the storage location to default

            set_current_location(self.camera, get_default_location())

            set_current_location(self.capture_manager, get_default_location())



    def get_locations(self):

        if self.camera:

            locations = get_all_locations()



            current_location = get_current_location(self.camera)

            current_location = get_current_location(self.capture_manager)

            if current_location not in locations.values():

                locations.update({"Custom": current_location})

            # Add location from the cameras settings file
@@ -140,7 +140,7 @@ class AutostorageExtension(BaseExtension): 
            return {}



    def get_preferred_key(self):

        current = get_current_location(self.camera)

        current = get_current_location(self.capture_manager)

        locations = self.get_locations()



        matches = [k for k, v in locations.items() if v == current]
@@ -157,7 +157,7 @@ class AutostorageExtension(BaseExtension): 
            raise KeyError(f"No location named {new_path_key}")



        location = self.get_locations().get(new_path_key)

        set_current_location(self.camera, location)

        set_current_location(self.capture_manager, location)



    def key_to_title(self, path_key: str):

        if not path_key in self.get_locations().keys():

openflexure_microscope/api/default_extensions/scan.py

+9 −19
Original line number Diff line number Diff line
@@ -85,27 +85,17 @@ def capture( 
    filename = "{}_{}_{}_{}".format(basename, *microscope.stage.position)

    folder = "SCAN_{}".format(basename)



    # Create output object

    output = microscope.camera.new_image(

        temporary=temporary, filename=filename, folder=folder

    )



    # Capture

    microscope.camera.capture(

        output.file, use_video_port=use_video_port, resize=resize, bayer=bayer

    # Do capture

    return microscope.capture(

        filename=filename,

        folder=folder,

        temporary=temporary,

        use_video_port=use_video_port, resize=resize, bayer=bayer,

        annotations=annotations,

        tags=tags,

        metadata=metadata

    )



    # Inject system metadata

    output.put_metadata({"instrument": microscope.metadata})



    # Insert custom metadata

    output.put_metadata(metadata)



    # Insert custom metadata

    output.put_annotations(annotations)

    # Insert custom tags

    output.put_tags(tags)





### Scanning

openflexure_microscope/api/example_extensions/custom_element/__init__.py

+0 −2
Original line number Diff line number Diff line
@@ -7,8 +7,6 @@ from labthings.core.utilities import path_relative_to 


from openflexure_microscope.paths import settings_file_path, check_rw

from openflexure_microscope.config import OpenflexureSettingsFile

from openflexure_microscope.camera.base import BASE_CAPTURE_PATH

from openflexure_microscope.camera.capture import build_captures_from_exif



from openflexure_microscope.api.utilities.gui import build_gui

openflexure_microscope/api/microscope.py

+1 −1
Original line number Diff line number Diff line
@@ -7,6 +7,6 @@ default_microscope = Microscope() 


# Restore loaded capture array to camera object

logging.debug("Restoring captures...")

default_microscope.camera.rebuild_captures()

default_microscope.captures.rebuild_captures()



logging.debug("Microscope successfully attached!")