Framework to enable acquisition, analysis, visualization of computational microscopy workflows
record Order (recOrder): A framework for live-processing birefringence data
pypi install coming soon!
recOrder is a framework to enable microscopy acquisition, analysis, and visualization pipelines. In particular it is developed to accelerate computational microscopy workflows.
recOrder is an abstraction on top of the pyqt5 backend that simplifies pyqt5's signal/slot mechanism. recOrder enables a traditional 'publish-subscribe' pattern through simple function decorations. It does not use QtDBus, and thus does not require installation of D-bus for your OS.
please see the examples for a sense of how to construct a program. In particular, look at "example_reconstruct_order"
Create a new conda environment (optional, but recommended)
Install conda package management system by installing anaconda or miniconda (https://conda.io/). Creating a conda environment dedicated to ReconstructOrder will avoid version conflicts among packages required by ReconstructOrder and packages required by other python software.conda create -n <your-environment-name> python=3.7 conda activate <your-environment-name>
pip install via pypi
There are three primary modules in this framework
And one program construction module:
Acquisition, analysis and visualization contain one base class named
Program contains one class that connects any number of the earlier three modules together.
The typical pattern of usage is to define a class that inherits any of the above bases:
class MyTestClass(AcquisitionBase): def __init__(self): super().__init__()
Next, to have a class's method broadcast or receive on a channel, simply decorate it:
class MyAcquisitionClass(AcquisitionBase): def __init__(self): super().__init__() @AcquisitionBase.emitter(channel=0) def broadcast_to_channel(): pass @AcquisitionBase.receiver(channel=1) der receive_from_channel(from_signal): pass
If you want the same method to both receive and broadcast on a channel, use bidirectional:
class MyVisualizationClass(VisualizeBase): def __init__(self): super().__init__() @VisualizeBase.bidirectional(emitter_channel=1, receiver_channel=0): def emit_and_receive_from_channels(from_signal): pass
####Note, a method does not need to return a value to emit a signal. However, a method needs to declare parameter in order to receive a signal.
Finally, to build and run an entire program, use the program class:
acq = MyAcquisitionClass() vis = MyVisualizationClass() program = Program(acquire=acq, visualize=vis) program.build()
Any number of primary modules can be instantiated and passed to the "program" builder: program = Program(acquire=<acquisition_module>, analyze=<analysis_module>, visualize=<visualization_module>) Upon calling "program.build()", signals will be connected and the program is run.
For computational microscopy workflows, there are additionally four datastructures and some microscope control utilities:
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