Timelapse extension

I made a little timelapse extension following the documentation and the example there (OpenFlexure eV GUI — OpenFlexure Microscope Software documentation)

However, I got some sort of error that the .camera.new_image() method didn’t exist, so I modified my code a bit. It takes timelapse images now, but the images/experiment folders are not shown in the gallery on microscope.local. Also I’d like to add the metadata, but not sure how to use the .put_metadata() method

import time  # Used in our timelapse function
import os # Used to make the experiment folders

from labthings import current_action, fields, find_component, update_action_progress
from labthings.extensions import BaseExtension
from labthings.views import ActionView

# Used in our timelapse function
from openflexure_microscope.captures.capture_manager import generate_basename

# Used to convert our GUI dictionary into a complete eV extension GUI
from openflexure_microscope.api.utilities.gui import build_gui



# Create the extension class
class TimelapseExtension(BaseExtension):
    def __init__(self):
        # Superclass init function
        super().__init__("org.openflexure.timelapse-extension", version="0.1")

        # Add our API views
        self.add_view(TimelapseAPIView, "/timelapse")

        # 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
                            "placeholder": "Enter number of images",
                            #"default": 5,  # HTML number input attribute
                        },
                        {
                            "fieldType": "numberInput",
                            "name": "t_between",
                            "label": "Time (seconds) between images",
                            "min": 0.1,  # HTML number input attribute
                            "step": 1,  # HTML number input attribute
                            "placeholder": "Enter time",
                            #"default": 1,  # HTML number input attribute
                        },
                        {
                            "fieldType": "textInput",
                            "name": "experiment_name",
                            "label": "Experiment Name",
                            "placeholder": "Enter folder name for experiment",
                            #"default": "test",
                        },
                    ],
                }
            ],
        }
        self.add_meta("gui", build_gui(gui_description, self))

    def timelapse(self, microscope, n_images, t_between, experiment_name):
        """
        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
            experiment_name: Name for the folder in which the images shall be saved
        """

        os.makedirs(f"/var/openflexure/data/micrographs/{experiment_name}", exist_ok=False)

        # 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, basename creates a name based on the current time
                base_file_name = generate_basename()
                filename = f"/var/openflexure/data/micrographs/{experiment_name}/{base_file_name}_image{n}.jpg"

                # Capture
                microscope.camera.capture(filename)

                # Add system metadata
                #output.put_metadata(microscope.metadata, system=True)

                # Update task progress (only does anything 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 TimelapseAPIView(ActionView):
    """
    Take a series of images in a timelapse
    """

    args = {
        "n_images": fields.Integer(
            required=True, metadata={"example": 5, "description": "Number of images"}
        ),
        "t_between": fields.Number(
            load_default=1,
            metadata={"example": 1, "description": "Time (seconds) between images"},
        ),
        "experiment_name": fields.String(
            required=True, metadata={"example": "test", "description": "Folder name for experiment"}
        )
    }

    def post(self, args):
        # Find our microscope component
        microscope = find_component("org.openflexure.microscope")

        # Start "timelapse"
        return self.extension.timelapse(
            microscope, args.get("n_images"), args.get("t_between"), args.get("experiment_name")
        )


LABTHINGS_EXTENSIONS = (TimelapseExtension,)

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