cmi_plugins

CMI Plugins

Here you will find community developed functions and IPython plugins related to the DiffPy-CMI complex modeling framework. CMI Plugins require that the parent cmi_exchange directory is in the Python module path, so that any given plugin can be imported in Python using

import cmi_plugins.SomeName

See the Python Path Instructions for details on adding the cmi_exchange directory to Python path.

Contents

cmi_plugins.ipy_gaussianfit

IPython extension to fit a Gaussian peak to a set of data using the SrFit framework. Provides GaussianFit class and fitGaussian function.

To activate in an IPython session use %load_ext cmi_plugins.ipy_gaussianfit. For use in Python scripts import the code as cmi_plugins.ipy_gaussianfit.

To try out the class execute the following commands:

from cmi_plugins.ipy_gaussianfit import GaussianFit
import numpy as np

x = np.arange(-10, 10, 0.1)
x0, sig = -2, 1.5
noise = 0.2 * np.ones_like(x)
y = np.exp(-0.5*(x-x0)**2/sig**2) + noise * np.random.randn(*x.shape)
gfit = GaussianFit(x, y, noise)
gfit.refine()
gfit.plot()

x, y, dy are the data to be fitted with Gaussian peak (dy may be omitted) A, sig, and x0 are initial values. If omitted the program will estimate their starting values.

More information on IPython

IPython extensions are importable IPython modules that can modify the behavior of the shell to add functionality. They are activated from the IPython command line by running

%load_ext python_name_of_extenstion

To have certain extensions available at startup first make sure that the IPython user profile exists and determine its location by running in a system shell

ipython profile create     # create default user profile
ipython locate profile     # print location of user profile

Edit the ipython_config.py file in the profile directory and modify the c.InteractiveShellApp.extensions variable as necessary. See IPython documentation for an exhaustive details.