pymmcore superset providing improved APIs, event connection, 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.CMMCorePlusincludes arun_mdamethod (name may change) "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).
What about Pycro-Manager?
Pycro-Manager is a library 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.
Quickstart
Install
# from pip
pip install pymmcore-plus
# from conda
conda install -c conda-forge pymmcore-plus
# or from source tree
pip install git+https://github.com/pymmcore-plus/pymmcore-plus.git
Usually, you'll then want to install the device adapters (though you can also download these manually from micro-manager.org):
mmcore install
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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