def __init__(self, name="fit", conclass=FitContribution):
"""Initialization."""
FitRecipe.__init__(self, name)
self.fithooks[0].verbose = 3
contribution = conclass("contribution")
self.profile = Profile()
contribution.setProfile(self.profile)
self.addContribution(contribution)
self.results = FitResults(self, update=False)
# Adopt all the FitContribution methods
public = [
aname for aname in dir(contribution)
if aname not in dir(self) and not aname.startswith("_")
]
for mname in public:
method = getattr(contribution, mname)
setattr(self, mname, method)
return
def setUp(self):
self.recipe = FitRecipe("recipe")
self.recipe.fithooks[0].verbose = 0
# Set up the Profile
self.profile = Profile()
x = linspace(0, pi, 10)
y = sin(x)
self.profile.setObservedProfile(x, y)
# Set up the FitContribution
self.fitcontribution = FitContribution("cont")
self.fitcontribution.setProfile(self.profile)
self.fitcontribution.setEquation("A*sin(k*x + c)")
self.fitcontribution.A.setValue(1)
self.fitcontribution.k.setValue(1)
self.fitcontribution.c.setValue(0)
self.recipe.addContribution(self.fitcontribution)
return
def setUp(self):
self.recipe = recipe = FitRecipe("recipe")
recipe.newVar("A", 0)
recipe.newVar("sig", 0)
recipe.newVar("x0", 0)
self.filename = datafile("results.res")
self.Aval = 5.77619823e-01
self.sigval = -9.22758690e-01
self.x0val = 6.12422115e+00
return
def testConstrainSpaceGroup(self):
"""Make sure that all Parameters are constrained properly.
This tests constrainSpaceGroup from
diffpy.srfit.structure.sgconstraints, which is performed automatically
when an ObjCrystCrystalParSet is created.
"""
pi = numpy.pi
occryst = makeLaMnO3()
stru = ObjCrystCrystalParSet(occryst.GetName(), occryst)
# Make sure we actually create the constraints
stru._constrainSpaceGroup()
# Make the space group parameters individually
stru.sgpars.latpars
stru.sgpars.xyzpars
stru.sgpars.adppars
# Check the orthorhombic lattice
l = stru.getLattice()
self.assertTrue( l.alpha.const )
self.assertTrue( l.beta.const )
self.assertTrue( l.gamma.const )
self.assertEquals(pi/2, l.alpha.getValue())
self.assertEquals(pi/2, l.beta.getValue())
self.assertEquals(pi/2, l.gamma.getValue())
self.assertFalse( l.a.const )
self.assertFalse( l.b.const )
self.assertFalse( l.c.const )
self.assertEquals(0, len(l._constraints))
# Now make sure the scatterers are constrained properly
scatterers = stru.getScatterers()
la = scatterers[0]
self.assertFalse(la.x.const)
self.assertFalse(la.y.const)
self.assertTrue(la.z.const)
self.assertEquals(0, len(la._constraints))
mn = scatterers[1]
self.assertTrue(mn.x.const)
self.assertTrue(mn.y.const)
self.assertTrue(mn.z.const)
self.assertEquals(0, len(mn._constraints))
o1 = scatterers[2]
self.assertFalse(o1.x.const)
self.assertFalse(o1.y.const)
self.assertTrue(o1.z.const)
self.assertEquals(0, len(o1._constraints))
o2 = scatterers[3]
self.assertFalse(o2.x.const)
self.assertFalse(o2.y.const)
self.assertFalse(o2.z.const)
self.assertEquals(0, len(o2._constraints))
# Make sure we can't constrain these
self.assertRaises(ValueError, mn.constrain, mn.x, "y")
self.assertRaises(ValueError, mn.constrain, mn.y, "z")
self.assertRaises(ValueError, mn.constrain, mn.z, "x")
# Nor can we make them into variables
from diffpy.srfit.fitbase.fitrecipe import FitRecipe
f = FitRecipe()
self.assertRaises(ValueError, f.addVar, mn.x)
return
class TestFitRecipe(unittest.TestCase):
def setUp(self):
self.recipe = FitRecipe("recipe")
self.recipe.fithooks[0].verbose = 0
# Set up the Profile
self.profile = Profile()
x = linspace(0, pi, 10)
y = sin(x)
self.profile.setObservedProfile(x, y)
# Set up the FitContribution
self.fitcontribution = FitContribution("cont")
self.fitcontribution.setProfile(self.profile)
self.fitcontribution.setEquation("A*sin(k*x + c)")
self.fitcontribution.A.setValue(1)
self.fitcontribution.k.setValue(1)
self.fitcontribution.c.setValue(0)
self.recipe.addContribution(self.fitcontribution)
return
def testFixFree(self):
recipe = self.recipe
con = self.fitcontribution
recipe.addVar(con.A, 2, tag="tagA")
recipe.addVar(con.k, 1, tag="tagk")
recipe.addVar(con.c, 0)
recipe.newVar("B", 0)
self.assertTrue(recipe.isFree(recipe.A))
recipe.fix("tagA")
self.assertFalse(recipe.isFree(recipe.A))
recipe.free("tagA")
self.assertTrue(recipe.isFree(recipe.A))
recipe.fix("A")
self.assertFalse(recipe.isFree(recipe.A))
recipe.free("A")
self.assertTrue(recipe.isFree(recipe.A))
recipe.fix(recipe.A)
self.assertFalse(recipe.isFree(recipe.A))
recipe.free(recipe.A)
self.assertTrue(recipe.isFree(recipe.A))
recipe.fix(recipe.A)
self.assertFalse(recipe.isFree(recipe.A))
recipe.free("all")
self.assertTrue(recipe.isFree(recipe.A))
self.assertTrue(recipe.isFree(recipe.k))
self.assertTrue(recipe.isFree(recipe.c))
self.assertTrue(recipe.isFree(recipe.B))
recipe.fix(recipe.A, "tagk", c=3)
self.assertFalse(recipe.isFree(recipe.A))
self.assertFalse(recipe.isFree(recipe.k))
self.assertFalse(recipe.isFree(recipe.c))
self.assertTrue(recipe.isFree(recipe.B))
self.assertEquals(3, recipe.c.value)
recipe.fix("all")
self.assertFalse(recipe.isFree(recipe.A))
self.assertFalse(recipe.isFree(recipe.k))
self.assertFalse(recipe.isFree(recipe.c))
self.assertFalse(recipe.isFree(recipe.B))
self.assertRaises(ValueError, recipe.free, "junk")
self.assertRaises(ValueError, recipe.fix, tagA=1)
self.assertRaises(ValueError, recipe.fix, "junk")
return
def testVars(self):
"""Test to see if variables are added and removed properly."""
recipe = self.recipe
con = self.fitcontribution
recipe.addVar(con.A, 2)
recipe.addVar(con.k, 1)
recipe.addVar(con.c, 0)
recipe.newVar("B", 0)
names = recipe.getNames()
self.assertEquals(names, ["A", "k", "c", "B"])
values = recipe.getValues()
self.assertTrue((values == [2, 1, 0, 0]).all())
# Constrain a parameter to the B-variable to give it a value
p = Parameter("Bpar", -1)
recipe.constrain(recipe.B, p)
values = recipe.getValues()
self.assertTrue((values == [2, 1, 0]).all())
recipe.delVar(recipe.B)
recipe.fix(recipe.k)
names = recipe.getNames()
self.assertEquals(names, ["A", "c"])
values = recipe.getValues()
self.assertTrue((values == [2, 0]).all())
recipe.fix("all")
names = recipe.getNames()
self.assertEquals(names, [])
values = recipe.getValues()
self.assertTrue((values == []).all())
recipe.free("all")
names = recipe.getNames()
self.assertEquals(3, len(names))
self.assertTrue("A" in names)
self.assertTrue("k" in names)
self.assertTrue("c" in names)
values = recipe.getValues()
self.assertEquals(3, len(values))
self.assertTrue(0 in values)
self.assertTrue(1 in values)
self.assertTrue(2 in values)
return
def testResidual(self):
"""Test the residual and everything that can change it."""
# With thing set up as they are, the residual should be 0
res = self.recipe.residual()
self.assertAlmostEquals(0, dot(res, res))
# Change the c value to 1 so that the equation evaluates as sin(x+1)
x = self.profile.x
y = sin(x + 1)
self.recipe.cont.c.setValue(1)
res = self.recipe.residual()
self.assertTrue(array_equal(y - self.profile.y, res))
# Try some constraints
# Make c = 2*A, A = Avar
var = self.recipe.newVar("Avar")
self.recipe.constrain(self.fitcontribution.c, "2*A",
{"A": self.fitcontribution.A})
self.assertEquals(2, self.fitcontribution.c.value)
self.recipe.constrain(self.fitcontribution.A, var)
self.assertEquals(1, var.getValue())
self.assertEquals(self.recipe.cont.A.getValue(), var.getValue())
# c is constrained to a constrained parameter.
self.assertEquals(2, self.fitcontribution.c.value)
# The equation should evaluate to sin(x+2)
x = self.profile.x
y = sin(x + 2)
res = self.recipe.residual()
self.assertTrue(array_equal(y - self.profile.y, res))
# Now try some restraints. We want c to be exactly zero. It should give
# a penalty of (c-0)**2, which is 4 in this case
r1 = self.recipe.restrain(self.fitcontribution.c, 0, 0, 1)
self.recipe._ready = False
res = self.recipe.residual()
chi2 = 4 + dot(y - self.profile.y, y - self.profile.y)
self.assertAlmostEqual(chi2, dot(res, res))
# Clear the constraint and restore the value of c to 0. This should
# give us chi2 = 0 again.
self.recipe.unconstrain(self.fitcontribution.c)
self.fitcontribution.c.setValue(0)
res = self.recipe.residual([self.recipe.cont.A.getValue()])
chi2 = 0
self.assertAlmostEqual(chi2, dot(res, res))
# Remove the restraint and variable
self.recipe.unrestrain(r1)
self.recipe.delVar(self.recipe.Avar)
self.recipe._ready = False
res = self.recipe.residual()
chi2 = 0
self.assertAlmostEqual(chi2, dot(res, res))
# Add constraints at the fitcontribution level.
self.fitcontribution.constrain(self.fitcontribution.c, "2*A")
# This should evaluate to sin(x+2)
x = self.profile.x
y = sin(x + 2)
res = self.recipe.residual()
self.assertTrue(array_equal(y - self.profile.y, res))
# Add a restraint at the fitcontribution level.
r1 = self.fitcontribution.restrain(self.fitcontribution.c, 0, 0, 1)
self.recipe._ready = False
# The chi2 is the same as above, plus 4
res = self.recipe.residual()
x = self.profile.x
y = sin(x + 2)
chi2 = 4 + dot(y - self.profile.y, y - self.profile.y)
self.assertAlmostEqual(chi2, dot(res, res))
# Remove those
self.fitcontribution.unrestrain(r1)
self.recipe._ready = False
self.fitcontribution.unconstrain(self.fitcontribution.c)
self.fitcontribution.c.setValue(0)
res = self.recipe.residual()
chi2 = 0
self.assertAlmostEqual(chi2, dot(res, res))
# Now try to use the observed profile inside of the equation
# Set the equation equal to the data
self.fitcontribution.setEquation("y")
res = self.recipe.residual()
self.assertAlmostEquals(0, dot(res, res))
# Now add the uncertainty. This should give dy/dy = 1 for the residual
self.fitcontribution.setEquation("y+dy")
res = self.recipe.residual()
self.assertAlmostEquals(len(res), dot(res, res))
return