Moved example extension and switched to includes
This commit is contained in:
jtc42
parent
d2780f5541
commit
1115d00a18
12 changed files with 117 additions and 397 deletions
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from labthings.server.extensions import BaseExtension
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from labthings.server.find import find_component
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def identify():
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"""
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Demonstrate access to Microscope.camera, and Microscope.stage
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"""
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microscope = find_component("org.openflexure.microscope")
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response = (
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f"My name is {microscope.name}. "
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f"My parent camera is {microscope.camera}, "
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f"and my parent stage is {microscope.stage}."
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)
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return response
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def rename(new_name):
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"""
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Rename the microscope
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"""
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microscope = find_component("org.openflexure.microscope")
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microscope.name = new_name
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microscope.save_settings()
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# Create your extension object
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my_extension = BaseExtension("com.myname.myextension", version="0.0.0")
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# Add methods to your extension
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my_extension.add_method(identify, "identify")
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my_extension.add_method(rename, "rename")
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@ -1,74 +0,0 @@
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from labthings.server.extensions import BaseExtension
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from labthings.server.find import find_component
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from labthings.server.view import View
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from labthings.server.decorators import use_body
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from labthings.server import fields
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## Extension methods
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def identify(microscope):
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"""
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Demonstrate access to Microscope.camera, and Microscope.stage
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"""
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response = (
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f"My name is {microscope.name}. "
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f"My parent camera is {microscope.camera}, "
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f"and my parent stage is {microscope.stage}."
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)
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return response
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def rename(microscope, new_name):
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"""
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Rename the microscope
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"""
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microscope.name = new_name
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microscope.save_settings()
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## Extension views
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class ExampleIdentifyView(View):
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def get(self):
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# Find our microscope component
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microscope = find_component("org.openflexure.microscope")
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# Return our identify function's output
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return identify(microscope)
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class ExampleRenameView(View):
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# Expect a request parameter called "name", which is a string. Pass to argument "args".
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@use_body(fields.String(required=True, example="My Example Microscope"))
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def post(self, body):
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# Look for our new name in the request body
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new_name = body
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# Find our microscope component
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microscope = find_component("org.openflexure.microscope")
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# Pass microscope and new name to our rename function
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rename(microscope, new_name)
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# Return our identify function's output
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return identify(microscope)
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## Create extension
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# Create your extension object
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my_extension = BaseExtension("com.myname.myextension", version="0.0.0")
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# Add methods to your extension
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my_extension.add_method(identify, "identify")
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my_extension.add_method(rename, "rename")
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# Add API views to your extension
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my_extension.add_view(ExampleIdentifyView, "/identify")
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my_extension.add_view(ExampleRenameView, "/rename")
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from labthings.server.extensions import BaseExtension
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from labthings.server.find import find_component
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from labthings.server.view import View
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from labthings.server.decorators import use_args, marshal_with
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from labthings.server.schema import Schema
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from labthings.server import fields
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## Extension methods
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# Define which properties of a Microscope object we care about,
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# and what types they should be converted to
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class MicroscopeIdentifySchema(Schema):
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name = fields.String() # Microscopes name
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id = fields.UUID() # Microscopes unique ID
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status = fields.Dict() # Status dictionary
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camera = fields.String() # Camera object (represented as a string)
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stage = fields.String() # Stage object (represented as a string)
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def rename(microscope, new_name):
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"""
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Rename the microscope
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"""
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microscope.name = new_name
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microscope.save_settings()
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## Extension views
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class ExampleIdentifyView(View):
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# Format our returned object using MicroscopeIdentifySchema
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@marshal_with(MicroscopeIdentifySchema())
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def get(self):
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# Find our microscope component
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microscope = find_component("org.openflexure.microscope")
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# Return our microscope object,
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# let @marshal_with handle formatting the output
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return microscope
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class ExampleRenameView(View):
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# Format our returned object using MicroscopeIdentifySchema
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@marshal_with(MicroscopeIdentifySchema())
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# Expect a request parameter called "name", which is a string. Pass to argument "args".
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@use_args({"name": fields.String(required=True, example="My Example Microscope")})
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def post(self, args):
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# Look for our "name" parameter in the request arguments
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new_name = args.get("name")
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# Find our microscope component
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microscope = find_component("org.openflexure.microscope")
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# Pass microscope and new name to our rename function
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rename(microscope, new_name)
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# Return our microscope object,
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# let @marshal_with handle formatting the output
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return microscope
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## Create extension
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# Create your extension object
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my_extension = BaseExtension("com.myname.myextension", version="0.0.0")
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# Add methods to your extension
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my_extension.add_method(rename, "rename")
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# Add API views to your extension
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my_extension.add_view(ExampleIdentifyView, "/identify")
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my_extension.add_view(ExampleRenameView, "/rename")
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@ -1,97 +0,0 @@
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from labthings.server.extensions import BaseExtension
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from labthings.server.find import find_component
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from labthings.server.view import View
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from labthings.server.decorators import (
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use_args,
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marshal_with,
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ThingProperty,
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PropertySchema,
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)
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from labthings.server.schema import Schema
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from labthings.server import fields
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## Extension methods
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# Define which properties of a Microscope object we care about,
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# and what types they should be converted to
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class MicroscopeIdentifySchema(Schema):
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name = fields.String() # Microscopes name
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id = fields.UUID() # Microscopes unique ID
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status = fields.Dict() # Status dictionary
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camera = fields.String() # Camera object (represented as a string)
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stage = fields.String() # Stage object (represented as a string)
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def rename(microscope, new_name):
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"""
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Rename the microscope
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"""
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microscope.name = new_name
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microscope.save_settings()
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## Extension views
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# Since we only have a GET method here, it'll register as a read-only property
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@ThingProperty
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class ExampleIdentifyView(View):
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# Format our returned object using MicroscopeIdentifySchema
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@marshal_with(MicroscopeIdentifySchema())
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def get(self):
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"""
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Show identifying information about the current microscope object
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"""
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# Find our microscope component
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microscope = find_component("org.openflexure.microscope")
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# Return our microscope object,
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# let @marshal_with handle formatting the output
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return microscope
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@ThingProperty
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# We can use a single schema for all methods if the input and output will be formatted identically
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# Eg. Here, we will always expect a "name" string argument, and always return a "name" string attribute
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@PropertySchema({"name": fields.String(required=True, example="My Example Microscope")})
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class ExampleRenameView(View):
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def get(self):
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"""
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Show the current microscope name
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"""
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# Find our microscope component
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microscope = find_component("org.openflexure.microscope")
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return microscope
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def post(self, args):
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"""
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Change the current microscope name
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"""
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# Look for our "name" parameter in the request arguments
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new_name = args.get("name")
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# Find our microscope component
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microscope = find_component("org.openflexure.microscope")
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# Pass microscope and new name to our rename function
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rename(microscope, new_name)
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# Return our microscope object,
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# let @marshal_with handle formatting the output
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return microscope
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## Create extension
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# Create your extension object
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my_extension = BaseExtension("com.myname.myextension", version="0.0.0")
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# Add methods to your extension
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my_extension.add_method(rename, "rename")
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# Add API views to your extension
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my_extension.add_view(ExampleIdentifyView, "/identify")
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my_extension.add_view(ExampleRenameView, "/rename")
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@ -1,133 +0,0 @@
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from labthings.server.extensions import BaseExtension
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from labthings.server.find import find_component
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from labthings.server.view import View
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from labthings.server.decorators import (
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use_args,
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marshal_with,
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ThingProperty,
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PropertySchema,
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ThingAction,
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doc_response,
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)
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from labthings.server.schema import Schema
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from labthings.server import fields
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from flask import send_file # Used to send images from our server
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import io # Used in our capture action
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## Extension methods
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# Define which properties of a Microscope object we care about,
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# and what types they should be converted to
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class MicroscopeIdentifySchema(Schema):
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name = fields.String() # Microscopes name
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id = fields.UUID() # Microscopes unique ID
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status = fields.Dict() # Status dictionary
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camera = fields.String() # Camera object (represented as a string)
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stage = fields.String() # Stage object (represented as a string)
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def rename(microscope, new_name):
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"""
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Rename the microscope
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"""
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microscope.name = new_name
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microscope.save_settings()
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## Extension views
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# Since we only have a GET method here, it'll register as a read-only property
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@ThingProperty
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class ExampleIdentifyView(View):
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# Format our returned object using MicroscopeIdentifySchema
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@marshal_with(MicroscopeIdentifySchema())
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def get(self):
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"""
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Show identifying information about the current microscope object
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"""
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# Find our microscope component
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microscope = find_component("org.openflexure.microscope")
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# Return our microscope object,
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# let @marshal_with handle formatting the output
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return microscope
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@ThingProperty
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# We can use a single schema for all methods if the input and output will be formatted identically
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# Eg. Here, we will always expect a "name" string argument, and always return a "name" string attribute
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@PropertySchema({"name": fields.String(required=True, example="My Example Microscope")})
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class ExampleRenameView(View):
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def get(self):
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"""
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Show the current microscope name
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"""
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# Find our microscope component
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microscope = find_component("org.openflexure.microscope")
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return microscope
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def post(self, args):
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"""
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Change the current microscope name
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"""
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# Look for our "name" parameter in the request arguments
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new_name = args.get("name")
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# Find our microscope component
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microscope = find_component("org.openflexure.microscope")
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# Pass microscope and new name to our rename function
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rename(microscope, new_name)
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# Return our microscope object,
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# let @marshal_with handle formatting the output
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return microscope
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@ThingAction
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class QuickCaptureAPI(View):
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"""
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Take an image capture and return it without saving
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"""
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# Expect a "use_video_port" boolean, which defaults to True if none is given
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@use_args({"use_video_port": fields.Boolean(missing=True)})
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# Our success response (200) returns an image (image/jpeg mimetype)
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@doc_response(200, mimetype="image/jpeg")
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def post(self, args):
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"""
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Take a non-persistant image capture.
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"""
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# Find our microscope component
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microscope = find_component("org.openflexure.microscope")
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# Open a BytesIO stream to be destroyed once request has returned
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with io.BytesIO() as stream:
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# Capture to our stream object
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microscope.camera.capture(stream, use_video_port=args.get("use_video_port"))
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# Rewind the stream
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stream.seek(0)
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# Return our image data using Flasks send_file function
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return send_file(io.BytesIO(stream.read()), mimetype="image/jpeg")
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## Create extension
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# Create your extension object
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my_extension = BaseExtension("com.myname.myextension", version="0.0.0")
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# Add methods to your extension
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my_extension.add_method(rename, "rename")
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# Add API views to your extension
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my_extension.add_view(ExampleIdentifyView, "/identify")
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my_extension.add_view(ExampleRenameView, "/rename")
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my_extension.add_view(QuickCaptureAPI, "/quick-capture")
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@ -1,203 +0,0 @@
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from labthings.server.extensions import BaseExtension
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from labthings.server.find import find_component
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from labthings.server.view import View
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from labthings.server.decorators import (
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use_args,
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marshal_with,
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ThingProperty,
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PropertySchema,
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ThingAction,
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doc_response,
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marshal_task,
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)
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from labthings.server.schema import Schema
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from labthings.server import fields
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from flask import send_file # Used to send images from our server
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import io # Used in our capture action
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import time # Used in our timelapse function
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# Used in our timelapse function
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from openflexure_microscope.camera.base import generate_basename
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# Used to run our timelapse in a background thread
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from labthings.core.tasks import taskify
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## Extension methods
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# Define which properties of a Microscope object we care about,
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# and what types they should be converted to
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class MicroscopeIdentifySchema(Schema):
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name = fields.String() # Microscopes name
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id = fields.UUID() # Microscopes unique ID
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status = fields.Dict() # Status dictionary
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camera = fields.String() # Camera object (represented as a string)
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stage = fields.String() # Stage object (represented as a string)
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def rename(microscope, new_name):
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"""
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Rename the microscope
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"""
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microscope.name = new_name
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microscope.save_settings()
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def timelapse(microscope, n_images, t_between):
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"""
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Save a set of images in a timelapse
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Args:
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microscope: Microscope object
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n_images (int): Number of images to take
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t_between (int/float): Time, in seconds, between sequential captures
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"""
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base_file_name = generate_basename()
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folder = "TIMELAPSE_{}".format(base_file_name)
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# Take exclusive control over both the camera and stage
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with microscope.camera.lock, microscope.stage.lock:
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for n in range(n_images):
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# Generate a filename
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filename = f"{base_file_name}_image{n}"
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# Create a file to save the image to
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output = microscope.camera.new_image(
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filename=filename, folder=folder, temporary=False
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)
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# Capture
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microscope.camera.capture(output.file)
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# Add system metadata
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output.put_metadata(microscope.metadata, system=True)
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# Wait for the specified time
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time.sleep(t_between)
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## Extension views
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# Since we only have a GET method here, it'll register as a read-only property
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@ThingProperty
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class ExampleIdentifyView(View):
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# Format our returned object using MicroscopeIdentifySchema
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@marshal_with(MicroscopeIdentifySchema())
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def get(self):
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"""
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Show identifying information about the current microscope object
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"""
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# Find our microscope component
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microscope = find_component("org.openflexure.microscope")
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# Return our microscope object,
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# let @marshal_with handle formatting the output
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return microscope
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@ThingProperty
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# We can use a single schema for all methods if the input and output will be formatted identically
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# Eg. Here, we will always expect a "name" string argument, and always return a "name" string attribute
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@PropertySchema({"name": fields.String(required=True, example="My Example Microscope")})
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class ExampleRenameView(View):
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def get(self):
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"""
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Show the current microscope name
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"""
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# Find our microscope component
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microscope = find_component("org.openflexure.microscope")
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return microscope
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def post(self, args):
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"""
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Change the current microscope name
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"""
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# Look for our "name" parameter in the request arguments
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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")
|
||||
|
||||
|
||||
@ThingAction
|
||||
class TimelapseAPI(View):
|
||||
"""
|
||||
Take a series of images in a timelapse, running as a background task
|
||||
"""
|
||||
|
||||
@marshal_task # Shorthand for marshaling with a pre-made Task object schema
|
||||
@use_args(
|
||||
{
|
||||
"n_images": fields.Integer(
|
||||
required=True, example=5, description="Number of images"
|
||||
),
|
||||
"t_between": fields.Number(
|
||||
missing=1, example=1, description="Time (seconds) between images"
|
||||
),
|
||||
}
|
||||
)
|
||||
def post(self, args):
|
||||
# Find our microscope component
|
||||
microscope = find_component("org.openflexure.microscope")
|
||||
|
||||
# Create and start "timelapse", running in a background task
|
||||
task = taskify(timelapse)(
|
||||
microscope, args.get("n_images"), args.get("t_between")
|
||||
)
|
||||
|
||||
return task
|
||||
|
||||
|
||||
## 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")
|
||||
my_extension.add_view(TimelapseAPI, "/timelapse")
|
||||
|
|
@ -1,146 +0,0 @@
|
|||
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,
|
||||
marshal_task,
|
||||
)
|
||||
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
|
||||
import time # Used in our timelapse function
|
||||
|
||||
# Used in our timelapse function
|
||||
from openflexure_microscope.camera.base import generate_basename
|
||||
|
||||
# Used to run our timelapse in a background thread
|
||||
from labthings.core.tasks import taskify, update_task_progress
|
||||
|
||||
# Used to convert our GUI dictionary into a complete eV extension GUI
|
||||
from openflexure_microscope.api.utilities.gui import build_gui
|
||||
|
||||
## Extension methods
|
||||
|
||||
|
||||
def timelapse(microscope, n_images, t_between):
|
||||
"""
|
||||
Save a set of images in a timelapse
|
||||
|
||||
Args:
|
||||
microscope: Microscope object
|
||||
n_images (int): Number of images to take
|
||||
t_between (int/float): Time, in seconds, between sequential captures
|
||||
"""
|
||||
base_file_name = generate_basename()
|
||||
folder = "TIMELAPSE_{}".format(base_file_name)
|
||||
|
||||
# Take exclusive control over both the camera and stage
|
||||
with microscope.camera.lock, microscope.stage.lock:
|
||||
for n in range(n_images):
|
||||
# Generate a filename
|
||||
filename = f"{base_file_name}_image{n}"
|
||||
# Create a file to save the image to
|
||||
output = microscope.camera.new_image(
|
||||
filename=filename, folder=folder, temporary=False
|
||||
)
|
||||
|
||||
# Capture
|
||||
microscope.camera.capture(output)
|
||||
|
||||
# Add system metadata
|
||||
output.put_metadata(microscope.metadata, system=True)
|
||||
|
||||
# Update task progress (only does anyting if the function is running in a LabThings task)
|
||||
progress_pct = ((n + 1) / n_images) * 100 # Progress, in percent
|
||||
update_task_progress(progress_pct)
|
||||
|
||||
# Wait for the specified time
|
||||
time.sleep(t_between)
|
||||
|
||||
|
||||
## Extension views
|
||||
|
||||
|
||||
@ThingAction
|
||||
class TimelapseAPI(View):
|
||||
"""
|
||||
Take a series of images in a timelapse, running as a background task
|
||||
"""
|
||||
|
||||
@marshal_task # Shorthand for marshaling with a pre-made Task object schema
|
||||
@use_args(
|
||||
{
|
||||
"n_images": fields.Integer(
|
||||
required=True, example=5, description="Number of images"
|
||||
),
|
||||
"t_between": fields.Number(
|
||||
missing=1, example=1, description="Time (seconds) between images"
|
||||
),
|
||||
}
|
||||
)
|
||||
def post(self, args):
|
||||
# Find our microscope component
|
||||
microscope = find_component("org.openflexure.microscope")
|
||||
|
||||
# Create and start "timelapse", running in a background task
|
||||
task = taskify(timelapse)(
|
||||
microscope, args.get("n_images"), args.get("t_between")
|
||||
)
|
||||
|
||||
return task
|
||||
|
||||
|
||||
## Extension GUI (OpenFlexure eV)
|
||||
# Alternate form without any dynamic parts
|
||||
extension_gui = {
|
||||
"icon": "timelapse", # Name of an icon from https://material.io/resources/icons/
|
||||
"forms": [ # List of forms. Each form is a collapsible accordion panel
|
||||
{
|
||||
"name": "Start a timelapse", # Form title
|
||||
"isCollapsible": False, # This form cannot be collapsed into an accordion
|
||||
"isTask": True, # This forms submission starts a background task
|
||||
"route": "/timelapse", # The URL rule (as given by "add_view") of your submission view
|
||||
"submitLabel": "Start", # Label for the form submit button
|
||||
"schema": [ # List of dictionaries. Each element is a form component.
|
||||
{
|
||||
"fieldType": "numberInput",
|
||||
"name": "n_images", # Name of the view arg this value corresponds to
|
||||
"label": "Number of images",
|
||||
"min": 1, # HTML number input attribute
|
||||
"default": 5, # HTML number input attribute
|
||||
},
|
||||
{
|
||||
"fieldType": "numberInput",
|
||||
"name": "t_between",
|
||||
"label": "Time (seconds) between images",
|
||||
"min": 0.1, # HTML number input attribute
|
||||
"step": 0.1, # HTML number input attribute
|
||||
"default": 1, # HTML number input attribute
|
||||
},
|
||||
],
|
||||
}
|
||||
],
|
||||
}
|
||||
|
||||
|
||||
## 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(timelapse, "timelapse")
|
||||
|
||||
# Add API views to your extension
|
||||
my_extension.add_view(TimelapseAPI, "/timelapse")
|
||||
|
||||
# Add OpenFlexure eV GUI to your extension
|
||||
my_extension.add_meta("gui", build_gui(extension_gui, my_extension))
|
||||
Loading…
Add table
Add a link
Reference in a new issue