def test_morph(self):
"""check MorphChain.morph()
"""
# Define the morphs
config = {
"rmin": 1,
"rmax": 6,
"rstep": 0.1,
"scale": 3.0,
}
mgrid = MorphRGrid()
mscale = MorphScale()
chain = MorphChain(config, mgrid, mscale)
xobj, yobj, xref, yref = chain(self.xobj, self.yobj, self.xref,
self.yref)
self.assertTrue((xobj == xref).all())
self.assertAlmostEqual(xobj[0], 1.0)
self.assertAlmostEqual(xobj[-1], 4.9)
self.assertAlmostEqual(xobj[1] - xobj[0], 0.1)
self.assertAlmostEqual(xobj[0], mgrid.rmin)
self.assertAlmostEqual(xobj[-1], mgrid.rmax - mgrid.rstep)
self.assertAlmostEqual(xobj[1] - xobj[0], mgrid.rstep)
self.assertTrue(numpy.allclose(yobj, yref))
return
def test_refine_chain(self):
"""refine a chain
"""
# Give this some texture
self.yobj[30:] = 5
self.yref[33:] = 15
# Define the morphs
config = {"scale": 1.0, "stretch": 0.0}
mscale = MorphScale(config)
mstretch = MorphStretch(config)
chain = MorphChain(config, mscale, mstretch)
refiner = Refiner(chain, self.xobj, self.yobj, self.xref, self.yref)
res = refiner.refine()
# Compare the objective to the reference. Note that due to
# interpolation, there will be issues at the boundary of the step
# function.
xobj, yobj, xref, yref = chain.xyallout
err = 15. * 2
res = sum(numpy.fabs(yref - yobj))
self.assertTrue(res < err)
self.assertAlmostEqual(chain.scale, 3, 2)
self.assertAlmostEqual(chain.stretch, 0.1, 2)
return
def test_refine(self):
config = {
"scale": 1.0,
"stretch": 0,
"smear": 0,
"baselineslope": -4 * numpy.pi * 0.0917132
}
# Note that scale must go first, since it does not commute with the
# PDF <--> RDF conversion.
chain = MorphChain(config)
chain.append(MorphScale())
chain.append(MorphStretch())
chain.append(MorphXtalPDFtoRDF())
chain.append(MorphSmear())
chain.append(MorphXtalRDFtoPDF())
refiner = Refiner(chain, self.xobj, self.yobj, self.xref, self.yref)
# Do this as two-stage fit. First refine amplitude parameters, and then
# position parameters.
res = refiner.refine("scale", "smear")
res = refiner.refine("scale", "stretch", "smear")
xobj, yobj, xref, yref = chain.xyallout
# We want the fit good to 1%. We will disregard the last bit of the
# fit, since we know we have unavoidable edge effects there.
sel = xobj < 9.5
yrsel = yref[sel]
diff = yrsel - yobj[sel]
rw = (numpy.dot(diff, diff) / numpy.dot(yrsel, yrsel))**0.5
self.assertTrue(rw < 0.01)
return