pymmcore superset providing improved APIs, event handling, and a pure python acquisition engine
Project description
pymmcore-plus
pymmcore-plus extends pymmcore
(python bindings for the C++ micro-manager
core) with a number of
features designed to facilitate working with Micro-manager in pure python/C
environments.
pymmcore_plus.CMMCorePlusis a drop-in replacement subclass ofpymmcore.CMMCorethat provides a number of helpful overrides and additional convenience functions beyond the standard CMMCore API. See CMMCorePlus documentation for details.pymmcore-plusincludes an acquisition engine that drives micro-manager for conventional multi-dimensional experiments. It accepts an MDASequence from useq-schema for experiment design/declaration.- Adds a callback
system that adapts
the CMMCore callback object to an existing python event loop (such as Qt, or
perhaps asyncio/etc...). The
CMMCorePlusclass also fixes a number of "missed" events that are not currently emitted by the CMMCore API.
Documentation
https://pymmcore-plus.github.io/pymmcore-plus/
Why not just use pymmcore directly?
pymmcore is (and should probably remain) a thin SWIG wrapper for the C++ code at the core of the Micro-Manager project. It is sufficient to control micromanager via python, but lacks some "niceties" that python users are accustomed to. This library:
- extends the
pymmcore.CMMCoreobject with additional methods - fixes emission of a number of events in
MMCore. - provide proper python interfaces for various objects like
ConfigurationandMetadata. - provides an object-oriented API for Devices and their properties.
- uses more interpretable
Enumsrather thanintfor various constants - improves docstrings and type annotations.
- generally feel more pythonic (note however,
camelCasemethod names from the CMMCore API are not substituted withsnake_case).
How does this relate to Pycro-Manager?
Pycro-Manager is an impressive library written by Henry Pinkard designed to make it easier to work with and control the Java Micro-manager application using python. As such, it requires Java to be installed and running in the background (either via the micro-manager GUI application directly, or via a headless process). The python half communicates with the Java half using ZeroMQ messaging.
In brief: while Pycro-Manager provides a python API to control the Java
Micro-manager application (which in turn controls the C++ core), pymmcore-plus
provides a python API to control the C++ core directly, without the need for
Java in the loop. Each has its own advantages and disadvantages! With
pycro-manager you immediately get the entire existing micro-manager ecosystem
and GUI application. With pymmcore-plus you don't need to install Java, and you
have direct access to the memory buffers used by the C++ core, but the GUI
side of things is far less mature.
Quickstart
Install
from pip
pip install pymmcore-plus
# or, add the [cli] extra if you wish to use the `mmcore` command line tool:
pip install "pymmcore-plus[cli]"
# add the [io] extra if you wish to use the tiff or zarr writers
pip install "pymmcore-plus[io]"
from conda
conda install -c conda-forge pymmcore-plus
dev version from github
pip install 'pymmcore-plus[cli] @ git+https://github.com/pymmcore-plus/pymmcore-plus'
Usually, you'll then want to install the device adapters. Assuming you've
installed with pip install "pymmcore-plus[cli]", you can run:
mmcore install
(you can also download these manually from micro-manager.org)
See installation documentation for more details.
Usage
Then use the core object as you would pymmcore.CMMCore...
but with more features :smile:
from pymmcore_plus import CMMCorePlus
core = CMMCorePlus()
...
Examples
See a number of usage examples in the documentation.
You can find some basic python scripts in the examples directory of this repository
Contributing
Contributions are welcome! See contributing guide.
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