Python client code for the OpenFlexure Microscope
A Python client for the OpenFlexure Microscope.
The OpenFlexure Microscope is most often controlled by two pieces of software - the OpenFlexure Microscope Server, which is written in Python and runs on the embedded Raspberry Pi, and OpenFlexure Connect which is a graphical interface written in Electron, that can be run either on the Raspberry Pi, or on another computer via a network connection. However, if you want to write your own scripts to perform particular experiments or protocols, it's useful not to have to embed these into the the OpenFlexure Microscope Server or package them up as plugins. This library exists to make it easy to control your microscope from a simple Python script that can run either on the Raspberry Pi, or over the network. I particularly like to use it from a Jupyter notebook on my laptop, because it allows me to plot graphs and display images as I go.
This module can be installed with
pip install openflexure-microscope-client, or by cloning the repository and running
Connect to your microscope
You can connect to the microscope either by specifying a hostname or IP address, or using mDNS. If your network is relatively simple, and if you can see your microscope in the "nearby devices" section of Connect, then mDNS is a zero-faff way of connecting to your microscope:
import openflexure_microscope_client as ofm_client microscope = ofm_client.find_first_microscope()
If your network is more complicated, or you know the address of your microscope, you can connect using the hostname or IP address. By default, your microscope will declare itself as
microscope.local though this also relies on mDNS so if the method above doesn't work,
microscope.local may also not work.
microscope = ofm_client.MicroscopeClient("example.host.name")
Check the connection
Usually, I run a few commands to check my microscope is working properly:
pos = microscope.position starting_pos = pos.copy() pos['x'] += 100 microscope.move(pos) assert microscope.position == pos pos['x'] -= 100 microscope.move(pos) assert microscope.position == starting_pos # Check the microscope will autofocus ret = microscope.autofocus() # Acquire an image for sanity-checking too image = microscope.grab_image() f, ax = plt.subplots(1,1) ax.imshow(np.array(image)) #print(image.metadata) print("Active microscope extensions") for k in microscope.extensions.keys(): print(k)
After running this block, you should see a list of extensions that are currently active, and a picture taken by the microscope. Given that we just autofocused, this image should be nice and sharp!
There are a few basic commands built in as methods of the
positionis a property that returns a dictionary with
'z'components, giving the position of the stage.
get_position_array()returns a 3-element
numpyarray with the same position in it.
move(position)accepts either a 3-element array or a dictionary as returned by
position, and performs an absolute move
move_rel(displacement)performs a relative move (i.e. supplying 0 will not move that axis)
capture_image()will take a new image from the camera and return it as a
grab_image()will return the next image the camera sends in its MJPEG preview stream (i.e. it's quicker but lower quality than
grab_image_array()returns the image as a
autofocus()runs the fast autofocus routine, just like clicking the "autofocus" button in Connect
To run methods provided by the microscope extensions, you can use the
extensions dictionary, to make
The dependencies are managed using poetry, so once you have cloned the repository, you can set up a virtual environment with
There are some basic tests that can be run using
pytest. This needs to be within the environment installed above, so use
poetry run pytest. These mostly need to connect to a microscope; the easiest way to test this automatically is to build
openflexure-microscope-server and run it locally - this will create a local dummy microscope server. Some tests will be skipped because they need microscope hardware, but it should at least verify most of the URLs. Running the tests requires you to have started that server already - it will not be started automatically.
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Hashes for openflexure-microscope-client-0.1.6.tar.gz
Hashes for openflexure_microscope_client-0.1.6-py3-none-any.whl