Updated documentation to subclass-based extensions
This commit is contained in:
Joel Collins
parent
7a849c725a
commit
bacc111a87
10 changed files with 249 additions and 318 deletions
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@ -2,35 +2,35 @@ from labthings import find_component
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from labthings.extensions import BaseExtension
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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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# Create the extension class
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class MyExtension(BaseExtension):
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def __init__(self):
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# Superclass init function
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super().__init__("com.myname.myextension", version="0.0.0")
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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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def identify(self):
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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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return response
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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(self, 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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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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LABTHINGS_EXTENSIONS = (MyExtension,)
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@ -1,41 +0,0 @@
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from labthings import find_component
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from labthings.extensions import BaseExtension
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# Create the extension class
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class MyExtension(BaseExtension):
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def __init__(self):
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# Create some instance variable
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self.state_variable = "An example of a persistant instance variable"
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# Superclass init function
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super().__init__("com.myname.myextension", version="0.0.0")
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def identify(self):
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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(self, 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 = MyExtension()
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@ -2,42 +2,44 @@ from labthings import fields, find_component
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from labthings.extensions import BaseExtension
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from labthings.views import View
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## Extension methods
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# Create the extension class
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class MyExtension(BaseExtension):
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def __init__(self):
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# Superclass init function
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super().__init__("com.myname.myextension", version="0.0.0")
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# Add our API Views (defined below MyExtension)
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self.add_view(ExampleIdentifyView, "/identify")
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self.add_view(ExampleRenameView, "/rename")
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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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def identify(self, 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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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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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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def rename(self, 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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return self.extension.identify(microscope)
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class ExampleRenameView(View):
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@ -53,21 +55,10 @@ class ExampleRenameView(View):
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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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self.extension.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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return self.extension.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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LABTHINGS_EXTENSIONS = (MyExtension,)
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@ -2,7 +2,22 @@ from labthings import Schema, fields, find_component
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from labthings.extensions import BaseExtension
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from labthings.views import View
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## Extension methods
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# Create the extension class
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class MyExtension(BaseExtension):
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def __init__(self):
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# Superclass init function
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super().__init__("com.myname.myextension", version="0.0.0")
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# Add our API Views (defined below MyExtension)
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self.add_view(ExampleIdentifyView, "/identify")
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self.add_view(ExampleRenameView, "/rename")
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def rename(self, 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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# Define which properties of a Microscope object we care about,
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@ -15,18 +30,7 @@ class MicroscopeIdentifySchema(Schema):
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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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schema = MicroscopeIdentifySchema()
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@ -54,21 +58,11 @@ class ExampleRenameView(View):
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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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self.extension.rename(microscope, new_name)
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# Return our microscope object,
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# let schema 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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LABTHINGS_EXTENSIONS = (MyExtension,)
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@ -2,7 +2,22 @@ from labthings import Schema, fields, find_component
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from labthings.extensions import BaseExtension
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from labthings.views import PropertyView
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## Extension methods
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# Create the extension class
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class MyExtension(BaseExtension):
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def __init__(self):
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# Superclass init function
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super().__init__("com.myname.myextension", version="0.0.0")
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# Add our API Views (defined below MyExtension)
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self.add_view(ExampleIdentifyView, "/identify")
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self.add_view(ExampleRenameView, "/rename")
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def rename(self, 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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# Define which properties of a Microscope object we care about,
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@ -15,16 +30,7 @@ class MicroscopeIdentifySchema(Schema):
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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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## Extension viewss
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# Since we only have a GET method here, it'll register as a read-only property
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class ExampleIdentifyView(PropertyView):
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@ -68,21 +74,11 @@ class ExampleRenameView(PropertyView):
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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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self.extension.rename(microscope, new_name)
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# Return our microscope object,
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# let schema 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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LABTHINGS_EXTENSIONS = (MyExtension,)
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@ -5,7 +5,22 @@ from labthings import Schema, fields, find_component
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from labthings.extensions import BaseExtension
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from labthings.views import ActionView, PropertyView
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## Extension methods
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# Create the extension class
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class MyExtension(BaseExtension):
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def __init__(self):
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# Superclass init function
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super().__init__("com.myname.myextension", version="0.0.0")
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# Add our API Views (defined below MyExtension)
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self.add_view(ExampleIdentifyView, "/identify")
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self.add_view(ExampleRenameView, "/rename")
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def rename(self, 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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# Define which properties of a Microscope object we care about,
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@ -18,15 +33,6 @@ class MicroscopeIdentifySchema(Schema):
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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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@ -71,7 +77,7 @@ class ExampleRenameView(PropertyView):
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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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self.extension.rename(microscope, new_name)
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# Return our microscope object,
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# let schema handle formatting the output
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@ -109,15 +115,4 @@ class QuickCaptureAPI(ActionView):
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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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LABTHINGS_EXTENSIONS = (MyExtension,)
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@ -7,52 +7,59 @@ from labthings.views import ActionView
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# Used in our timelapse function
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from openflexure_microscope.captures.capture_manager import generate_basename
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## Extension methods
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# Create the extension class
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class TimelapseExtension(BaseExtension):
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def __init__(self):
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# Superclass init function
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super().__init__("org.openflexure.timelapse-extension", version="0.0.0")
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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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# Add our API views
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self.add_view(TimelapseAPIView, "/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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def timelapse(self, 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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# 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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# Elegantly handle action cancellation
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if current_action() and current_action().stopped:
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return
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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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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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# Capture
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microscope.camera.capture(output)
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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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# Elegantly handle action cancellation
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if current_action() and current_action().stopped:
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return
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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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# Add system metadata
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output.put_metadata(microscope.metadata, system=True)
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# Capture
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microscope.camera.capture(output)
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# Update task progress (only does anyting if the function is running in a LabThings task)
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progress_pct = ((n + 1) / n_images) * 100 # Progress, in percent
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update_action_progress(progress_pct)
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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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# Update task progress (only does anyting if the function is running in a LabThings task)
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progress_pct = ((n + 1) / n_images) * 100 # Progress, in percent
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update_action_progress(progress_pct)
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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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class TimelapseAPI(ActionView):
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class TimelapseAPIView(ActionView):
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"""
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Take a series of images in a timelapse
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"""
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@ -71,16 +78,9 @@ class TimelapseAPI(ActionView):
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microscope = find_component("org.openflexure.microscope")
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# Start "timelapse"
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return timelapse(microscope, args.get("n_images"), args.get("t_between"))
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return self.extension.timelapse(
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microscope, args.get("n_images"), args.get("t_between")
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)
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## Create extension
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# Create your extension object
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my_extension = BaseExtension("com.myname.timelapse-extension", version="0.0.0")
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# Add methods to your extension
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my_extension.add_method(timelapse, "timelapse")
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# Add API views to your extension
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my_extension.add_view(TimelapseAPI, "/timelapse")
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LABTHINGS_EXTENSIONS = (TimelapseExtension,)
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|
@ -4,60 +4,97 @@ from labthings import current_action, fields, find_component, update_action_prog
|
|||
from labthings.extensions import BaseExtension
|
||||
from labthings.views import ActionView
|
||||
|
||||
# Used to convert our GUI dictionary into a complete eV extension GUI
|
||||
from openflexure_microscope.api.utilities.gui import build_gui
|
||||
|
||||
# Used in our timelapse function
|
||||
from openflexure_microscope.captures.capture_manager import generate_basename
|
||||
|
||||
## Extension methods
|
||||
# Used to convert our GUI dictionary into a complete eV extension GUI
|
||||
from openflexure_microscope.api.utilities.gui import build_gui
|
||||
|
||||
|
||||
def timelapse(microscope, n_images, t_between):
|
||||
"""
|
||||
Save a set of images in a timelapse
|
||||
# Create the extension class
|
||||
class TimelapseExtension(BaseExtension):
|
||||
def __init__(self):
|
||||
# Superclass init function
|
||||
super().__init__("org.openflexure.timelapse-extension", version="0.0.0")
|
||||
|
||||
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)
|
||||
# Add our API views
|
||||
self.add_view(TimelapseAPIView, "/timelapse")
|
||||
|
||||
# Take exclusive control over both the camera and stage
|
||||
with microscope.camera.lock, microscope.stage.lock:
|
||||
for n in range(n_images):
|
||||
# Elegantly handle action cancellation
|
||||
if current_action() and current_action().stopped:
|
||||
return
|
||||
# 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
|
||||
)
|
||||
# Add our GUI description
|
||||
gui_description = {
|
||||
"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
|
||||
"route": "/timelapse", # The URL rule (as given by "add_view") of your submission view
|
||||
"isTask": True, # This forms submission starts a background task
|
||||
"isCollapsible": False, # This form cannot be collapsed into an accordion
|
||||
"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
|
||||
},
|
||||
],
|
||||
}
|
||||
],
|
||||
}
|
||||
self.add_meta("gui", build_gui(gui_description, self))
|
||||
|
||||
# Capture
|
||||
microscope.camera.capture(output)
|
||||
def timelapse(self, microscope, n_images, t_between):
|
||||
"""
|
||||
Save a set of images in a timelapse
|
||||
|
||||
# Add system metadata
|
||||
output.put_metadata(microscope.metadata, system=True)
|
||||
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)
|
||||
|
||||
# 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_action_progress(progress_pct)
|
||||
# Take exclusive control over both the camera and stage
|
||||
with microscope.camera.lock, microscope.stage.lock:
|
||||
for n in range(n_images):
|
||||
# Elegantly handle action cancellation
|
||||
if current_action() and current_action().stopped:
|
||||
return
|
||||
# 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
|
||||
)
|
||||
|
||||
# Wait for the specified time
|
||||
time.sleep(t_between)
|
||||
# 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_action_progress(progress_pct)
|
||||
|
||||
# Wait for the specified time
|
||||
time.sleep(t_between)
|
||||
|
||||
|
||||
## Extension views
|
||||
|
||||
|
||||
class TimelapseAPI(ActionView):
|
||||
class TimelapseAPIView(ActionView):
|
||||
"""
|
||||
Take a series of images in a timelapse, running as a background task
|
||||
Take a series of images in a timelapse
|
||||
"""
|
||||
|
||||
args = {
|
||||
|
|
@ -73,53 +110,10 @@ class TimelapseAPI(ActionView):
|
|||
# Find our microscope component
|
||||
microscope = find_component("org.openflexure.microscope")
|
||||
|
||||
# Create and start "timelapse", running in a background task
|
||||
return timelapse(microscope, args.get("n_images"), args.get("t_between"))
|
||||
# Start "timelapse"
|
||||
return self.extension.timelapse(
|
||||
microscope, args.get("n_images"), args.get("t_between")
|
||||
)
|
||||
|
||||
|
||||
## 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
|
||||
"route": "/timelapse", # The URL rule (as given by "add_view") of your submission view
|
||||
"isTask": True, # This forms submission starts a background task
|
||||
"isCollapsible": False, # This form cannot be collapsed into an accordion
|
||||
"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.timelapse-extension", 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))
|
||||
LABTHINGS_EXTENSIONS = (TimelapseExtension,)
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue