140 lines
4.7 KiB
Python
140 lines
4.7 KiB
Python
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, ActionView
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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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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, update_task_progress
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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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## Extension methods
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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)
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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_task_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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"""
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Take a series of images in a timelapse, running as a background task
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"""
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@use_args(
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{
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"n_images": fields.Integer(
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required=True, example=5, description="Number of images"
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),
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"t_between": fields.Number(
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missing=1, example=1, description="Time (seconds) between images"
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),
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}
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)
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def post(self, args):
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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(
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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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