Extending PyFibre

PyFibre can be extended using the Envisage plugin framework. We provide the PyFibrePlugin class, designed to be used to support additional image formats. Each plugin may contribute objects to support multiple image formats.

PyFibre Factories

Each plugin contributes a set of IMultiImageFactory classes that contains:

1. An image file type, provided by a class that fulfils the IMultiImage interface.

2. A reader for the image file type, provided by a class that fulfils the IMultiImageReader interface.

3. An analysis script for image file type, provided by a class that fulfils the IMultiImageAnalysis interface.

In practice, a developer should use the following abstract base classes:

BaseMultiImage

Represents a stack of images that contain each signal for a given position. Provides the IMultiImage interface and requires the following methods to be implemented:

@classmethod
def verify_stack(cls, image_stack):
    """Perform verification that image_stack is allowed by this
    subclass of BaseMultiImage. Returns either True or False, depending
    on whether the image_stack argument is correctly formatted.
    """

def preprocess_images(self):
    """Implement operations that are used to pre-process
    the image_stack before analysis.
    """

BaseMultiImageReader

Is able to load an image file or a set of images files as a BaseMultiImage object. Provides the IMultiImageReader interface, and requires the following methods to be implemented

def collate_files(self, filenames):
    """From a given list of file names, returns a dictionary where each entry
    represents the files required to create an instance of a multi image.
    Each key will be passed on as the name of the multi image, used during
    further PyFibre operations. Each value could be passed in as the `filenames`
    argument to the class `create_image_stack` method.

    Returns
    -------
    image_dict: dict(str, list of str)
        Dictionary containing file references as keys and a list of
        files able to be loaded in as an image stack as values
    """

def load_image(self, filename):
    """Load a single image from a file"""

def can_load(self, filename):
    """Perform check to see whether file is formatted
    correctly to be loaded"""

BaseMultiImageAnalyser

Contains analysis scripts for a specific BaseMultiImage class. Provides the IMultiImageAnalysis interface, and requires the following methods to be implemented

def image_analysis(self, *args, **kwargs):
    """Perform analysis on data"""

def create_metrics(self, *args, **kwargs):
    """Create metrics from multi-image components that can be
    generated upon end of analysis"""

def create_figures(self, *args, **kwargs):
    """Create figures from multi-image components that can be
    generated upon end of analysis"""

Creating a Plugin

All plugin classes must

• Inherit from pyfibre.api.BasePyFibrePlugin

from pyfibre.api import BasePyFibrePlugin

class ExamplePlugin(BasePyFibrePlugin):
"""This is an example of plugin for PyFibre."""

• Implement the methods get_name() and get_version() to return appropriate values.

def get_name(self):
    return "My example plugin"

def get_version(self):
    return 0

• Implement a method get_multi_image_factories() returning a list of all contributed classes that provide the IMultiImageFactory interface.

def get_multi_image_factories(self):
    return [
        ExampleMultiImageFactory
    ]

Install the Plugin

In order for PyFibre to recognize the plugin, it must be installed as a package in the deployment edm environment, using the entry point namespace pyfibre.plugins. This can be performed using pip and an appropriate setup.py file, that employs the setuptools package.

A basic example setup.py file is therefore shown below

from setuptools import setup, find_packages

setup(
    name="my_example_plugin",
    version=0,
    entry_points={
        "pyfibre.plugins": [
            "my_example = "
            "my_example.example_plugin:ExamplePlugin",
    ]
    },
    # Automatically looks for file directories containing __init__.py files
    # to be included in package
    packages=find_packages(),
)

Running the following command line instruction from the same directory as setup.py will then install the package in the deployed environment

edm run -e pyfibre-py36 -- pip install -e .