PycroManagerControl.imjoy.html

<config lang="json">
{
  "name": "PycroManagerControl",
  "type": "native-python",
  "version": "0.1.0",
  "description": "Microscope control with PycroManager",
  "tags": [],
  "ui": "",
  "cover": "",
  "inputs": null,
  "outputs": null,
  "flags": [],
  "icon": "extension",
  "api_version": "0.1.8",
  "env": "",
  "permissions": [],
  "requirements": ["pycromanager", "numpy"],
  "dependencies": []
}
</config>

<script lang="python">
import time
from imjoy import api
import numpy as np
from pycromanager import Bridge


class MyMicroscope():
    async def setup(self):
        bridge = Bridge()
        self._core = bridge.get_core()
        exposure = self._core.get_exposure()
        api.showMessage('MMcore loaded, exposure: ' + str(exposure))

    def snap_image(self):
        if self._core.is_sequence_running():
            self._core.stop_sequence_acquisition()
        self._core.snap_image()
        tagged_image = self._core.get_tagged_image()
        image_array = np.reshape(tagged_image.pix, newshape=[-1, tagged_image.tags['Height'], tagged_image.tags['Width']])
        image_array = (image_array/image_array.max()*255).astype('uint8')
        return image_array
    
    def get_image(self):
        # we can also check remaining with getRemainingImageCount()
        tagged_image = self._core.get_tagged_image()
        image_array = np.reshape(tagged_image.pix, newshape=[-1, tagged_image.tags['Height'], tagged_image.tags['Width']])
        image_array = (image_array/image_array.max()*255).astype('uint8')
        return image_array

    def get_device_properties(self):
        core = self._core
        devices = core.get_loaded_devices()
        devices = [devices.get(i) for i in range(devices.size())]
        device_items = []
        for device in devices:
            names = core.get_device_property_names(device)
            props = [names.get(i) for i in range(names.size())]
            property_items = []
            for prop in props:
                value = core.get_property(device, prop)
                is_read_only = core.is_property_read_only(device, prop)
                if core.has_property_limits(device, prop):
                    lower = core.get_property_lower_limit(device, prop)
                    upper = core.get_property_upper_limit(device, prop)
                    allowed = {"type": "range", "min": lower, "max": upper, "readOnly": is_read_only}
                else:
                    allowed = core.get_allowed_property_values(device, prop)
                    allowed = {"type": "enum", "options": [allowed.get(i) for i in range(allowed.size())], "readOnly": is_read_only}
                property_items.append({"device": device, "name": prop, "value": value, "allowed": allowed})
                # print('===>', device, prop, value, allowed)
            if len(property_items) > 0:
                device_items.append({"name": device, "value": "{} properties".format(len(props)), "items": property_items})
        return device_items

    async def run(self, ctx):
        mmcore_api = {
            "_rintf": True,
            "snapImage": self.snap_image,
            "getImage": self.get_image,
            "getDeviceProperties": self.get_device_properties,
            "getCameraDevice": self._core.get_camera_device,
            "setCameraDevice": self._core.set_camera_device,
            "startContinuousSequenceAcquisition": self._core.start_continuous_sequence_acquisition,
            "stopSequenceAcquisition": self._core.stop_sequence_acquisition,
            "setExposure": self._core.set_exposure,
            "getExposure": self._core.get_exposure,
            "setProperty": self._core.set_property,
            "getProperty": self._core.get_property
        }
        viewer = await api.createWindow(src='https://gist.github.com/oeway/f59c1d1c49c94a831e5e21ba4c6111dd', data={'mmcore': mmcore_api})

api.export(MyMicroscope())
</script>