Updated documentation to subclass-based extensions
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Joel Collins
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10 changed files with 249 additions and 318 deletions
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@ -4,60 +4,97 @@ from labthings import current_action, fields, find_component, update_action_prog
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from labthings.extensions import BaseExtension
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from labthings.views import ActionView
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# Used to convert our GUI dictionary into a complete eV extension GUI
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from openflexure_microscope.api.utilities.gui import build_gui
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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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# Used to convert our GUI dictionary into a complete eV extension GUI
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from openflexure_microscope.api.utilities.gui import build_gui
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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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# 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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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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# Add our API views
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self.add_view(TimelapseAPIView, "/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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# Add our GUI description
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gui_description = {
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"icon": "timelapse", # Name of an icon from https://material.io/resources/icons/
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"forms": [ # List of forms. Each form is a collapsible accordion panel
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{
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"name": "Start a timelapse", # Form title
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"route": "/timelapse", # The URL rule (as given by "add_view") of your submission view
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"isTask": True, # This forms submission starts a background task
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"isCollapsible": False, # This form cannot be collapsed into an accordion
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"submitLabel": "Start", # Label for the form submit button
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"schema": [ # List of dictionaries. Each element is a form component.
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{
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"fieldType": "numberInput",
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"name": "n_images", # Name of the view arg this value corresponds to
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"label": "Number of images",
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"min": 1, # HTML number input attribute
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"default": 5, # HTML number input attribute
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},
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{
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"fieldType": "numberInput",
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"name": "t_between",
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"label": "Time (seconds) between images",
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"min": 0.1, # HTML number input attribute
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"step": 0.1, # HTML number input attribute
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"default": 1, # HTML number input attribute
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},
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],
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}
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],
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}
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self.add_meta("gui", build_gui(gui_description, self))
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# Capture
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microscope.camera.capture(output)
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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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# Add system metadata
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output.put_metadata(microscope.metadata, system=True)
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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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# 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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# 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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# Wait for the specified time
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time.sleep(t_between)
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# Capture
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microscope.camera.capture(output)
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# Add system metadata
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output.put_metadata(microscope.metadata, system=True)
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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, running as a background task
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Take a series of images in a timelapse
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"""
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args = {
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@ -73,53 +110,10 @@ class TimelapseAPI(ActionView):
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# Find our microscope component
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microscope = find_component("org.openflexure.microscope")
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# Create and start "timelapse", running in a background task
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return timelapse(microscope, args.get("n_images"), args.get("t_between"))
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# Start "timelapse"
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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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## Extension GUI (OpenFlexure eV)
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# Alternate form without any dynamic parts
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extension_gui = {
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"icon": "timelapse", # Name of an icon from https://material.io/resources/icons/
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"forms": [ # List of forms. Each form is a collapsible accordion panel
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{
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"name": "Start a timelapse", # Form title
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"route": "/timelapse", # The URL rule (as given by "add_view") of your submission view
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"isTask": True, # This forms submission starts a background task
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"isCollapsible": False, # This form cannot be collapsed into an accordion
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"submitLabel": "Start", # Label for the form submit button
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"schema": [ # List of dictionaries. Each element is a form component.
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{
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"fieldType": "numberInput",
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"name": "n_images", # Name of the view arg this value corresponds to
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"label": "Number of images",
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"min": 1, # HTML number input attribute
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"default": 5, # HTML number input attribute
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},
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{
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"fieldType": "numberInput",
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"name": "t_between",
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"label": "Time (seconds) between images",
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"min": 0.1, # HTML number input attribute
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"step": 0.1, # HTML number input attribute
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"default": 1, # HTML number input attribute
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},
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],
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}
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],
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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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# Add OpenFlexure eV GUI to your extension
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my_extension.add_meta("gui", build_gui(extension_gui, my_extension))
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LABTHINGS_EXTENSIONS = (TimelapseExtension,)
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