fix estimate of standard deviations reported from PDFgui project

estimatepdfguiesds.py

#!/usr/bin/env python

import sys
import numpy

def getfitesd(fit):
    import cStringIO
    from diffpy.pdffit2 import redirect_stdout
    # throw away any output from pdffit2
    redirect_stdout(cStringIO.StringIO())
    # set nyquist spacing for every dataset and redo the fit
    for ds in fit.datasets:
        ds.setFitSamplingType('Nyquist')
    fit.run()
    N = sum([len(ds.Gdiff) for ds in fit.datasets])
    ssq = sum([numpy.dot(ds.Gdiff, ds.Gdiff) for ds in fit.datasets])
    P = len([p for p in fit.parameters.values() if not p.fixed])
    dG = numpy.sqrt(ssq / (N - P))
    return dict(N=N, P=P, dG=dG, ssq=ssq)


def processddpfile(filename):
    from diffpy.pdfgui.tui import LoadProject
    print "Loading PDFgui project %r" % filename
    prj = LoadProject(filename)
    for fit in prj.getFits():
        print fit.name
        e = getfitesd(fit)
        print "    number of datapoints on Nyquist grid N = %(N)i" % e
        print "    number of refined parameters P = %(P)i" % e
        print "    sum of squares on Nyquist grid = %(ssq)g" % e
        print "    estimated uncertainty dG = %(dG)g" % e
    return


if __name__ == '__main__':
    for f in sys.argv[1:]:
        processddpfile(f)