Loading openflexure_microscope/api/example_extensions/doc_example/01_basic_structure.py 0 → 100644 +36 −0 Original line number Diff line number Diff line from labthings.server.extensions import BaseExtension from labthings.server.find import find_component def identify(): """ Demonstrate access to Microscope.camera, and Microscope.stage """ microscope = find_component("org.openflexure.microscope") parent_camera = microscope.camera parent_stage = microscope.stage response = "My parent camera is {}, and my parent stage is {}.".format( parent_camera, parent_stage ) return response def rename(new_name): """ Rename the microscope """ microscope = find_component("org.openflexure.microscope") microscope.name = new_name microscope.save_settings() # Create your extension object my_extension = BaseExtension("com.myname.myextension", version="0.0.0") # Add methods to your extension my_extension.add_method(identify, "identify") my_extension.add_method(rename, "rename") openflexure_microscope/api/example_extensions/doc_example/02_adding_views.py 0 → 100644 +74 −0 Original line number Diff line number Diff line from labthings.server.extensions import BaseExtension from labthings.server.find import find_component from labthings.server.view import View from labthings.server.decorators import use_args from labthings.server import fields ## Extension methods def identify(microscope): """ Demonstrate access to Microscope.camera, and Microscope.stage """ response = ( f"My name is {microscope.name}. " f"My parent camera is {microscope.camera}, " f"and my parent stage is {microscope.stage}." ) return response def rename(microscope, new_name): """ Rename the microscope """ microscope.name = new_name microscope.save_settings() ## Extension views class ExampleIdentifyView(View): def get(self): # Find our microscope component microscope = find_component("org.openflexure.microscope") # Return our identify function's output return identify(microscope) class ExampleRenameView(View): # Expect a request parameter called "name", which is a string. Pass to argument "args". @use_args({"name": fields.String(required=True, example="My Example Microscope")}) def post(self, args): # Look for our "name" parameter in the request arguments new_name = args.get("name") # Find our microscope component microscope = find_component("org.openflexure.microscope") # Pass microscope and new name to our rename function rename(microscope, new_name) # Return our identify function's output return identify(microscope) ## Create extension # Create your extension object my_extension = BaseExtension("com.myname.myextension", version="0.0.0") # Add methods to your extension my_extension.add_method(identify, "identify") my_extension.add_method(rename, "rename") # Add API views to your extension my_extension.add_view(ExampleIdentifyView, "/identify") my_extension.add_view(ExampleRenameView, "/rename") openflexure_microscope/api/example_extensions/doc_example/03_marshaling_data.py 0 → 100644 +76 −0 Original line number Diff line number Diff line from labthings.server.extensions import BaseExtension from labthings.server.find import find_component from labthings.server.view import View from labthings.server.decorators import use_args, marshal_with from labthings.server.schema import Schema from labthings.server import fields ## Extension methods # Define which properties of a Microscope object we care about, # and what types they should be converted to class MicroscopeIdentifySchema(Schema): name = fields.String() # Microscopes name id = fields.UUID() # Microscopes unique ID status = fields.Dict() # Status dictionary camera = fields.String() # Camera object (represented as a string) stage = fields.String() # Stage object (represented as a string) def rename(microscope, new_name): """ Rename the microscope """ microscope.name = new_name microscope.save_settings() ## Extension views class ExampleIdentifyView(View): # Format our returned object using MicroscopeIdentifySchema @marshal_with(MicroscopeIdentifySchema()) def get(self): # Find our microscope component microscope = find_component("org.openflexure.microscope") # Return our microscope object, # let @marshal_with handle formatting the output return microscope class ExampleRenameView(View): # Format our returned object using MicroscopeIdentifySchema @marshal_with(MicroscopeIdentifySchema()) # Expect a request parameter called "name", which is a string. Pass to argument "args". @use_args({"name": fields.String(required=True, example="My Example Microscope")}) def post(self, args): # Look for our "name" parameter in the request arguments new_name = args.get("name") # Find our microscope component microscope = find_component("org.openflexure.microscope") # Pass microscope and new name to our rename function rename(microscope, new_name) # Return our microscope object, # let @marshal_with handle formatting the output return microscope ## Create extension # Create your extension object my_extension = BaseExtension("com.myname.myextension", version="0.0.0") # Add methods to your extension my_extension.add_method(rename, "rename") # Add API views to your extension my_extension.add_view(ExampleIdentifyView, "/identify") my_extension.add_view(ExampleRenameView, "/rename") openflexure_microscope/api/example_extensions/doc_example/04_properties.py 0 → 100644 +97 −0 Original line number Diff line number Diff line from labthings.server.extensions import BaseExtension from labthings.server.find import find_component from labthings.server.view import View from labthings.server.decorators import ( use_args, marshal_with, ThingProperty, PropertySchema, ) from labthings.server.schema import Schema from labthings.server import fields ## Extension methods # Define which properties of a Microscope object we care about, # and what types they should be converted to class MicroscopeIdentifySchema(Schema): name = fields.String() # Microscopes name id = fields.UUID() # Microscopes unique ID status = fields.Dict() # Status dictionary camera = fields.String() # Camera object (represented as a string) stage = fields.String() # Stage object (represented as a string) def rename(microscope, new_name): """ Rename the microscope """ microscope.name = new_name microscope.save_settings() ## Extension views # Since we only have a GET method here, it'll register as a read-only property @ThingProperty class ExampleIdentifyView(View): # Format our returned object using MicroscopeIdentifySchema @marshal_with(MicroscopeIdentifySchema()) def get(self): """ Show identifying information about the current microscope object """ # Find our microscope component microscope = find_component("org.openflexure.microscope") # Return our microscope object, # let @marshal_with handle formatting the output return microscope @ThingProperty # We can use a single schema for all methods if the input and output will be formatted identically # Eg. Here, we will always expect a "name" string argument, and always return a "name" string attribute @PropertySchema({"name": fields.String(required=True, example="My Example Microscope")}) class ExampleRenameView(View): def get(self): """ Show the current microscope name """ # Find our microscope component microscope = find_component("org.openflexure.microscope") return microscope def post(self, args): """ Change the current microscope name """ # Look for our "name" parameter in the request arguments new_name = args.get("name") # Find our microscope component microscope = find_component("org.openflexure.microscope") # Pass microscope and new name to our rename function rename(microscope, new_name) # Return our microscope object, # let @marshal_with handle formatting the output return microscope ## Create extension # Create your extension object my_extension = BaseExtension("com.myname.myextension", version="0.0.0") # Add methods to your extension my_extension.add_method(rename, "rename") # Add API views to your extension my_extension.add_view(ExampleIdentifyView, "/identify") my_extension.add_view(ExampleRenameView, "/rename") openflexure_microscope/api/example_extensions/doc_example/05_actions.py 0 → 100644 +133 −0 Original line number Diff line number Diff line from labthings.server.extensions import BaseExtension from labthings.server.find import find_component from labthings.server.view import View from labthings.server.decorators import ( use_args, marshal_with, ThingProperty, PropertySchema, ThingAction, doc_response, ) from labthings.server.schema import Schema from labthings.server import fields from flask import send_file # Used to send images from our server import io # Used in our capture action ## Extension methods # Define which properties of a Microscope object we care about, # and what types they should be converted to class MicroscopeIdentifySchema(Schema): name = fields.String() # Microscopes name id = fields.UUID() # Microscopes unique ID status = fields.Dict() # Status dictionary camera = fields.String() # Camera object (represented as a string) stage = fields.String() # Stage object (represented as a string) def rename(microscope, new_name): """ Rename the microscope """ microscope.name = new_name microscope.save_settings() ## Extension views # Since we only have a GET method here, it'll register as a read-only property @ThingProperty class ExampleIdentifyView(View): # Format our returned object using MicroscopeIdentifySchema @marshal_with(MicroscopeIdentifySchema()) def get(self): """ Show identifying information about the current microscope object """ # Find our microscope component microscope = find_component("org.openflexure.microscope") # Return our microscope object, # let @marshal_with handle formatting the output return microscope @ThingProperty # We can use a single schema for all methods if the input and output will be formatted identically # Eg. Here, we will always expect a "name" string argument, and always return a "name" string attribute @PropertySchema({"name": fields.String(required=True, example="My Example Microscope")}) class ExampleRenameView(View): def get(self): """ Show the current microscope name """ # Find our microscope component microscope = find_component("org.openflexure.microscope") return microscope def post(self, args): """ Change the current microscope name """ # Look for our "name" parameter in the request arguments new_name = args.get("name") # Find our microscope component microscope = find_component("org.openflexure.microscope") # Pass microscope and new name to our rename function rename(microscope, new_name) # Return our microscope object, # let @marshal_with handle formatting the output return microscope @ThingAction class QuickCaptureAPI(View): """ Take an image capture and return it without saving """ # Expect a "use_video_port" boolean, which defaults to True if none is given @use_args({"use_video_port": fields.Boolean(missing=True)}) # Our success response (200) returns an image (image/jpeg mimetype) @doc_response(200, mimetype="image/jpeg") def post(self, args): """ Take a non-persistant image capture. """ # Find our microscope component microscope = find_component("org.openflexure.microscope") # Open a BytesIO stream to be destroyed once request has returned with io.BytesIO() as stream: # Capture to our stream object microscope.camera.capture(stream, use_video_port=args.get("use_video_port")) # Rewind the stream stream.seek(0) # Return our image data using Flasks send_file function return send_file(io.BytesIO(stream.read()), mimetype="image/jpeg") ## Create extension # Create your extension object my_extension = BaseExtension("com.myname.myextension", version="0.0.0") # Add methods to your extension my_extension.add_method(rename, "rename") # Add API views to your extension my_extension.add_view(ExampleIdentifyView, "/identify") my_extension.add_view(ExampleRenameView, "/rename") my_extension.add_view(QuickCaptureAPI, "/quick-capture") Loading
openflexure_microscope/api/example_extensions/doc_example/01_basic_structure.py 0 → 100644 +36 −0 Original line number Diff line number Diff line from labthings.server.extensions import BaseExtension from labthings.server.find import find_component def identify(): """ Demonstrate access to Microscope.camera, and Microscope.stage """ microscope = find_component("org.openflexure.microscope") parent_camera = microscope.camera parent_stage = microscope.stage response = "My parent camera is {}, and my parent stage is {}.".format( parent_camera, parent_stage ) return response def rename(new_name): """ Rename the microscope """ microscope = find_component("org.openflexure.microscope") microscope.name = new_name microscope.save_settings() # Create your extension object my_extension = BaseExtension("com.myname.myextension", version="0.0.0") # Add methods to your extension my_extension.add_method(identify, "identify") my_extension.add_method(rename, "rename")
openflexure_microscope/api/example_extensions/doc_example/02_adding_views.py 0 → 100644 +74 −0 Original line number Diff line number Diff line from labthings.server.extensions import BaseExtension from labthings.server.find import find_component from labthings.server.view import View from labthings.server.decorators import use_args from labthings.server import fields ## Extension methods def identify(microscope): """ Demonstrate access to Microscope.camera, and Microscope.stage """ response = ( f"My name is {microscope.name}. " f"My parent camera is {microscope.camera}, " f"and my parent stage is {microscope.stage}." ) return response def rename(microscope, new_name): """ Rename the microscope """ microscope.name = new_name microscope.save_settings() ## Extension views class ExampleIdentifyView(View): def get(self): # Find our microscope component microscope = find_component("org.openflexure.microscope") # Return our identify function's output return identify(microscope) class ExampleRenameView(View): # Expect a request parameter called "name", which is a string. Pass to argument "args". @use_args({"name": fields.String(required=True, example="My Example Microscope")}) def post(self, args): # Look for our "name" parameter in the request arguments new_name = args.get("name") # Find our microscope component microscope = find_component("org.openflexure.microscope") # Pass microscope and new name to our rename function rename(microscope, new_name) # Return our identify function's output return identify(microscope) ## Create extension # Create your extension object my_extension = BaseExtension("com.myname.myextension", version="0.0.0") # Add methods to your extension my_extension.add_method(identify, "identify") my_extension.add_method(rename, "rename") # Add API views to your extension my_extension.add_view(ExampleIdentifyView, "/identify") my_extension.add_view(ExampleRenameView, "/rename")
openflexure_microscope/api/example_extensions/doc_example/03_marshaling_data.py 0 → 100644 +76 −0 Original line number Diff line number Diff line from labthings.server.extensions import BaseExtension from labthings.server.find import find_component from labthings.server.view import View from labthings.server.decorators import use_args, marshal_with from labthings.server.schema import Schema from labthings.server import fields ## Extension methods # Define which properties of a Microscope object we care about, # and what types they should be converted to class MicroscopeIdentifySchema(Schema): name = fields.String() # Microscopes name id = fields.UUID() # Microscopes unique ID status = fields.Dict() # Status dictionary camera = fields.String() # Camera object (represented as a string) stage = fields.String() # Stage object (represented as a string) def rename(microscope, new_name): """ Rename the microscope """ microscope.name = new_name microscope.save_settings() ## Extension views class ExampleIdentifyView(View): # Format our returned object using MicroscopeIdentifySchema @marshal_with(MicroscopeIdentifySchema()) def get(self): # Find our microscope component microscope = find_component("org.openflexure.microscope") # Return our microscope object, # let @marshal_with handle formatting the output return microscope class ExampleRenameView(View): # Format our returned object using MicroscopeIdentifySchema @marshal_with(MicroscopeIdentifySchema()) # Expect a request parameter called "name", which is a string. Pass to argument "args". @use_args({"name": fields.String(required=True, example="My Example Microscope")}) def post(self, args): # Look for our "name" parameter in the request arguments new_name = args.get("name") # Find our microscope component microscope = find_component("org.openflexure.microscope") # Pass microscope and new name to our rename function rename(microscope, new_name) # Return our microscope object, # let @marshal_with handle formatting the output return microscope ## Create extension # Create your extension object my_extension = BaseExtension("com.myname.myextension", version="0.0.0") # Add methods to your extension my_extension.add_method(rename, "rename") # Add API views to your extension my_extension.add_view(ExampleIdentifyView, "/identify") my_extension.add_view(ExampleRenameView, "/rename")
openflexure_microscope/api/example_extensions/doc_example/04_properties.py 0 → 100644 +97 −0 Original line number Diff line number Diff line from labthings.server.extensions import BaseExtension from labthings.server.find import find_component from labthings.server.view import View from labthings.server.decorators import ( use_args, marshal_with, ThingProperty, PropertySchema, ) from labthings.server.schema import Schema from labthings.server import fields ## Extension methods # Define which properties of a Microscope object we care about, # and what types they should be converted to class MicroscopeIdentifySchema(Schema): name = fields.String() # Microscopes name id = fields.UUID() # Microscopes unique ID status = fields.Dict() # Status dictionary camera = fields.String() # Camera object (represented as a string) stage = fields.String() # Stage object (represented as a string) def rename(microscope, new_name): """ Rename the microscope """ microscope.name = new_name microscope.save_settings() ## Extension views # Since we only have a GET method here, it'll register as a read-only property @ThingProperty class ExampleIdentifyView(View): # Format our returned object using MicroscopeIdentifySchema @marshal_with(MicroscopeIdentifySchema()) def get(self): """ Show identifying information about the current microscope object """ # Find our microscope component microscope = find_component("org.openflexure.microscope") # Return our microscope object, # let @marshal_with handle formatting the output return microscope @ThingProperty # We can use a single schema for all methods if the input and output will be formatted identically # Eg. Here, we will always expect a "name" string argument, and always return a "name" string attribute @PropertySchema({"name": fields.String(required=True, example="My Example Microscope")}) class ExampleRenameView(View): def get(self): """ Show the current microscope name """ # Find our microscope component microscope = find_component("org.openflexure.microscope") return microscope def post(self, args): """ Change the current microscope name """ # Look for our "name" parameter in the request arguments new_name = args.get("name") # Find our microscope component microscope = find_component("org.openflexure.microscope") # Pass microscope and new name to our rename function rename(microscope, new_name) # Return our microscope object, # let @marshal_with handle formatting the output return microscope ## Create extension # Create your extension object my_extension = BaseExtension("com.myname.myextension", version="0.0.0") # Add methods to your extension my_extension.add_method(rename, "rename") # Add API views to your extension my_extension.add_view(ExampleIdentifyView, "/identify") my_extension.add_view(ExampleRenameView, "/rename")
openflexure_microscope/api/example_extensions/doc_example/05_actions.py 0 → 100644 +133 −0 Original line number Diff line number Diff line from labthings.server.extensions import BaseExtension from labthings.server.find import find_component from labthings.server.view import View from labthings.server.decorators import ( use_args, marshal_with, ThingProperty, PropertySchema, ThingAction, doc_response, ) from labthings.server.schema import Schema from labthings.server import fields from flask import send_file # Used to send images from our server import io # Used in our capture action ## Extension methods # Define which properties of a Microscope object we care about, # and what types they should be converted to class MicroscopeIdentifySchema(Schema): name = fields.String() # Microscopes name id = fields.UUID() # Microscopes unique ID status = fields.Dict() # Status dictionary camera = fields.String() # Camera object (represented as a string) stage = fields.String() # Stage object (represented as a string) def rename(microscope, new_name): """ Rename the microscope """ microscope.name = new_name microscope.save_settings() ## Extension views # Since we only have a GET method here, it'll register as a read-only property @ThingProperty class ExampleIdentifyView(View): # Format our returned object using MicroscopeIdentifySchema @marshal_with(MicroscopeIdentifySchema()) def get(self): """ Show identifying information about the current microscope object """ # Find our microscope component microscope = find_component("org.openflexure.microscope") # Return our microscope object, # let @marshal_with handle formatting the output return microscope @ThingProperty # We can use a single schema for all methods if the input and output will be formatted identically # Eg. Here, we will always expect a "name" string argument, and always return a "name" string attribute @PropertySchema({"name": fields.String(required=True, example="My Example Microscope")}) class ExampleRenameView(View): def get(self): """ Show the current microscope name """ # Find our microscope component microscope = find_component("org.openflexure.microscope") return microscope def post(self, args): """ Change the current microscope name """ # Look for our "name" parameter in the request arguments new_name = args.get("name") # Find our microscope component microscope = find_component("org.openflexure.microscope") # Pass microscope and new name to our rename function rename(microscope, new_name) # Return our microscope object, # let @marshal_with handle formatting the output return microscope @ThingAction class QuickCaptureAPI(View): """ Take an image capture and return it without saving """ # Expect a "use_video_port" boolean, which defaults to True if none is given @use_args({"use_video_port": fields.Boolean(missing=True)}) # Our success response (200) returns an image (image/jpeg mimetype) @doc_response(200, mimetype="image/jpeg") def post(self, args): """ Take a non-persistant image capture. """ # Find our microscope component microscope = find_component("org.openflexure.microscope") # Open a BytesIO stream to be destroyed once request has returned with io.BytesIO() as stream: # Capture to our stream object microscope.camera.capture(stream, use_video_port=args.get("use_video_port")) # Rewind the stream stream.seek(0) # Return our image data using Flasks send_file function return send_file(io.BytesIO(stream.read()), mimetype="image/jpeg") ## Create extension # Create your extension object my_extension = BaseExtension("com.myname.myextension", version="0.0.0") # Add methods to your extension my_extension.add_method(rename, "rename") # Add API views to your extension my_extension.add_view(ExampleIdentifyView, "/identify") my_extension.add_view(ExampleRenameView, "/rename") my_extension.add_view(QuickCaptureAPI, "/quick-capture")
