def setUp(self):
""" initialize data"""
self.data1=Loader().load("cyl_400_20.txt")
self.data2=Loader().load("cyl_400_40.txt")
# Receives the type of model for the fitting
from sas.models.CylinderModel import CylinderModel
cyl1 = CylinderModel()
cyl1.name = "C1"
self.model1 = Model(cyl1)
self.model1.set(scale= 1.0)
self.model1.set(radius=18)
self.model1.set(length=200)
self.model1.set(sldCyl=3e-006, sldSolv=0.0)
self.model1.set(background=0.0)
cyl2 = CylinderModel()
cyl2.name = "C2"
self.model2 = Model(cyl2)
self.model2.set(scale= 1.0)
self.model2.set(radius=37)
self.model2.set(length=300)
self.model2.set(sldCyl=3e-006, sldSolv=0.0)
self.model2.set(background=0.0)
def setUp(self):
""" initialize data"""
self.data1 = Loader().load("cyl_400_20.txt")
self.data2 = Loader().load("cyl_400_40.txt")
# Receives the type of model for the fitting
from sas.models.CylinderModel import CylinderModel
cyl1 = CylinderModel()
cyl1.name = "C1"
self.model1 = Model(cyl1)
self.model1.set(scale=1.0)
self.model1.set(radius=18)
self.model1.set(length=200)
self.model1.set(sldCyl=3e-006, sldSolv=0.0)
self.model1.set(background=0.0)
cyl2 = CylinderModel()
cyl2.name = "C2"
self.model2 = Model(cyl2)
self.model2.set(scale=1.0)
self.model2.set(radius=37)
self.model2.set(length=300)
self.model2.set(sldCyl=3e-006, sldSolv=0.0)
self.model2.set(background=0.0)
def test2(self):
""" fit 2 data and 2 model with no constrainst"""
#load data
l = Loader()
data1 = l.load("testdata_line.txt")
data1.name = data1.filename
data2 = l.load("testdata_line1.txt")
data2.name = data2.filename
#Importing the Fit module
fitter = Fit('bumps')
# Receives the type of model for the fitting
model11 = LineModel()
model11.name = "M1"
model22 = LineModel()
model11.name = "M2"
model1 = Model(model11, data1)
model2 = Model(model22, data2)
pars1 = ['A', 'B']
fitter.set_data(data1, 1)
fitter.set_model(model1, 1, pars1)
fitter.select_problem_for_fit(id=1, value=0)
fitter.set_data(data2, 2)
fitter.set_model(model2, 2, pars1)
fitter.select_problem_for_fit(id=2, value=0)
try:
result1, = fitter.fit(handler=FitHandler())
except RuntimeError, msg:
assert str(msg) == "Nothing to fit"
def fit_single(self, fitter_name, isdream=False):
fitter = Fit(fitter_name)
data = Loader().load("testdata_line.txt")
data.name = data.filename
fitter.set_data(data, 1)
# Receives the type of model for the fitting
model1 = LineModel()
model1.name = "M1"
model = Model(model1, data)
pars1 = ['A', 'B']
fitter.set_model(model, 1, pars1)
fitter.select_problem_for_fit(id=1, value=1)
result1, = fitter.fit(handler=FitHandler())
# The target values were generated from the following statements
p, s, fx = result1.pvec, result1.stderr, result1.fitness
#print "p0,p1,s0,s1,fx = %g, %g, %g, %g, %g"%(p[0],p[1],s[0],s[1],fx)
p0, p1, s0, s1, fx_ = 3.68353, 2.61004, 0.336186, 0.105244, 1.20189
if isdream:
# Dream is not a minimizer: just check that the fit is within
# uncertainty
self.assertTrue(abs(p[0] - p0) <= s0)
self.assertTrue(abs(p[1] - p1) <= s1)
else:
self.assertTrue(abs(p[0] - p0) <= 1e-5)
self.assertTrue(abs(p[1] - p1) <= 1e-5)
self.assertTrue(abs(fx - fx_) <= 1e-5)
def test_without_resolution(self):
""" Simple cylinder model fit """
out=Loader().load("cyl_400_20.txt")
# This data file has not error, add them
#out.dy = out.y
fitter = Fit()
fitter.set_data(out,1)
# Receives the type of model for the fitting
model1 = CylinderModel()
model1.setParam("scale", 1.0)
model1.setParam("radius",18)
model1.setParam("length", 397)
model1.setParam("sldCyl",3e-006 )
model1.setParam("sldSolv",0.0 )
model1.setParam("background", 0.0)
model = Model(model1)
pars1 =['length','radius','scale']
fitter.set_model(model,1,pars1)
# What the hell is this line for?
fitter.select_problem_for_fit(id=1,value=1)
result1, = fitter.fit()
#print "result1",result1
self.assert_(result1)
self.assertTrue(len(result1.pvec) > 0)
self.assertTrue(len(result1.stderr) > 0)
self.assertTrue( math.fabs(result1.pvec[0]-400.0)/3.0 < result1.stderr[0] )
self.assertTrue( math.fabs(result1.pvec[1]-20.0)/3.0 < result1.stderr[1] )
self.assertTrue( math.fabs(result1.pvec[2]-1)/3.0 < result1.stderr[2] )
self.assertTrue( result1.fitness < 1.0 )
def test4(self):
""" fit 2 data concatenates with limited range of x and one model """
#load data
l = Loader()
data1 = l.load("testdata_line.txt")
data1.name = data1.filename
data2 = l.load("testdata_line1.txt")
data2.name = data2.filename
# Receives the type of model for the fitting
model1 = LineModel()
model1.name = "M1"
model1.setParam("A", 1.0)
model1.setParam("B", 1.0)
model = Model(model1, data1)
pars1 = ['A', 'B']
#Importing the Fit module
fitter = Fit('bumps')
fitter.set_data(data1, 1, qmin=0, qmax=7)
fitter.set_model(model, 1, pars1)
fitter.set_data(data2, 1, qmin=1, qmax=10)
fitter.select_problem_for_fit(id=1, value=1)
result2, = fitter.fit(handler=FitHandler())
self.assert_(result2)
self.assertTrue(
math.fabs(result2.pvec[0] - 4) / 3 <= result2.stderr[0])
self.assertTrue(
math.fabs(result2.pvec[1] - 2.5) / 3 <= result2.stderr[1])
self.assertTrue(result2.fitness / len(data1.x) < 2)
def test_slit(self):
smear = smear_selection(self.data_slit)
#self.assertEqual(smear.__class__.__name__, 'SlitSmearer')
#self.assertEqual(smear.__class__.__name__, 'PySmearer')
fitter = Fit()
# Data: right now this is the only way to set the smearer object
# We should improve that and have a way to get access to the
# data for a given fit.
fitter.set_data(self.data_slit,1)
fitter.fit_arrange_dict[1].data_list[0].smearer = smear
fitter.fit_arrange_dict[1].data_list[0].qmax = 0.003
# Model
fitter.set_model(Model(self.sphere),1, ['radius','scale'])
fitter.select_problem_for_fit(id=1,value=1)
result1, = fitter.fit()
#print "v",result1.pvec
#print "dv",result1.stderr
#print "chisq(v)",result1.fitness
numpy.testing.assert_allclose(result1.pvec, [2323.466,0.22137], rtol=0.001)
def test_reso(self):
# Let the data module find out what smearing the
# data needs
smear = smear_selection(self.data_res)
#self.assertEqual(smear.__class__.__name__, 'QSmearer')
#self.assertEqual(smear.__class__.__name__, 'PySmearer')
# Fit
fitter = Fit()
# Data: right now this is the only way to set the smearer object
# We should improve that and have a way to get access to the
# data for a given fit.
fitter.set_data(self.data_res,1)
fitter.fit_arrange_dict[1].data_list[0].smearer = smear
# Model: maybe there's a better way to do this.
# Ideally we should have to create a new model from our sas model.
fitter.set_model(Model(self.sphere),1, ['radius','scale', 'background'])
# Why do we have to do this...?
fitter.select_problem_for_fit(id=1,value=1)
# Perform the fit (might take a while)
result1, = fitter.fit()
#print "v",result1.pvec
#print "dv",result1.stderr
#print "chisq(v)",result1.fitness
self.assertTrue( math.fabs(result1.pvec[0]-5000) < 20 )
self.assertTrue( math.fabs(result1.pvec[1]-0.48) < 0.02 )
self.assertTrue( math.fabs(result1.pvec[2]-0.060) < 0.002 )
def test_slit(self):
smear = smear_selection(self.data_slit)
self.assertEqual(smear.__class__.__name__, 'SlitSmearer')
fitter = Fit('bumps')
# Data: right now this is the only way to set the smearer object
# We should improve that and have a way to get access to the
# data for a given fit.
fitter.set_data(self.data_slit, 1)
fitter._engine.fit_arrange_dict[1].data_list[0].smearer = smear
fitter._engine.fit_arrange_dict[1].data_list[0].qmax = 0.003
# Model
fitter.set_model(Model(self.sphere), 1, ['radius', 'scale'])
fitter.select_problem_for_fit(id=1, value=1)
result1, = fitter.fit()
#print "v",result1.pvec
#print "dv",result1.stderr
#print "chisq(v)",result1.fitness
self.assertTrue(math.fabs(result1.pvec[0] - 2340) < 20)
self.assertTrue(math.fabs(result1.pvec[1] - 0.010) < 0.002)
def test_constraints(self):
""" fit 2 data and 2 model with 1 constrainst"""
#load data
l = Loader()
data1= l.load("testdata_line.txt")
data1.name = data1.filename
data2= l.load("testdata_cst.txt")
data2.name = data2.filename
# Receives the type of model for the fitting
model11 = LineModel()
model11.name= "line"
model11.setParam("A", 1.0)
model11.setParam("B",1.0)
model22 = Constant()
model22.name= "cst"
model22.setParam("value", 1.0)
model1 = Model(model11,data1)
model2 = Model(model22,data2)
model1.set(A=4)
model1.set(B=3)
# Constraint the constant value to be equal to parameter B (the real value is 2.5)
#model2.set(value='line.B')
pars1= ['A','B']
pars2= ['value']
#Importing the Fit module
fitter = Fit()
fitter.set_data(data1,1)
fitter.set_model(model1,1,pars1)
fitter.set_data(data2,2,smearer=None)
fitter.set_model(model2,2,pars2,constraints=[("value","line.B")])
fitter.select_problem_for_fit(id=1,value=1)
fitter.select_problem_for_fit(id=2,value=1)
R1,R2 = fitter.fit(handler=FitHandler())
self.assertTrue( math.fabs(R1.pvec[0]-4.0)/3. <= R1.stderr[0])
self.assertTrue( math.fabs(R1.pvec[1]-2.5)/3. <= R1.stderr[1])
self.assertTrue( R1.fitness/(len(data1.x)+len(data2.x)) < 2)
def test_constraints(self):
""" fit 2 data and 2 model with 1 constrainst"""
#load data
l = Loader()
data1 = l.load("testdata_line.txt")
data1.name = data1.filename
data2 = l.load("testdata_cst.txt")
data2.name = data2.filename
# Receives the type of model for the fitting
model11 = LineModel()
model11.name = "line"
model11.setParam("A", 1.0)
model11.setParam("B", 1.0)
model22 = Constant()
model22.name = "cst"
model22.setParam("value", 1.0)
model1 = Model(model11, data1)
model2 = Model(model22, data2)
model1.set(A=4)
model1.set(B=3)
# Constraint the constant value to be equal to parameter B (the real value is 2.5)
#model2.set(value='line.B')
pars1 = ['A', 'B']
pars2 = ['value']
#Importing the Fit module
fitter = Fit('bumps')
fitter.set_data(data1, 1)
fitter.set_model(model1, 1, pars1)
fitter.set_data(data2, 2, smearer=None)
fitter.set_model(model2, 2, pars2, constraints=[("value", "line.B")])
fitter.select_problem_for_fit(id=1, value=1)
fitter.select_problem_for_fit(id=2, value=1)
R1, R2 = fitter.fit(handler=FitHandler())
self.assertTrue(math.fabs(R1.pvec[0] - 4.0) / 3. <= R1.stderr[0])
self.assertTrue(math.fabs(R1.pvec[1] - 2.5) / 3. <= R1.stderr[1])
self.assertTrue(R1.fitness / (len(data1.x) + len(data2.x)) < 2)
def test_bad_pars(self):
fitter = Fit('bumps')
data = Loader().load("testdata_line.txt")
data.name = data.filename
fitter.set_data(data, 1)
model1 = LineModel()
model1.name = "M1"
model = Model(model1, data)
pars1 = ['param1', 'param2']
try:
fitter.set_model(model, 1, pars1)
except ValueError, exc:
#print "ValueError was correctly raised: "+str(msg)
assert str(exc).startswith('parameter param1')
def _dispersion(self, fitter):
# Load data
# This data is for a cylinder with
# length=400, radius=20, radius disp=5, scale=1e-10
out = Loader().load("cyl_400_20_disp5r.txt")
out.dy = numpy.zeros(len(out.y))
for i in range(len(out.y)):
out.dy[i] = math.sqrt(out.y[i])
# Receives the type of model for the fitting
model1 = CylinderModel()
model1.setParam("scale", 10.0)
model1.setParam("radius", 18)
model1.setParam("length", 397)
model1.setParam("sldCyl", 3e-006)
model1.setParam("sldSolv", 0.0)
model1.setParam("background", 0.0)
# Dispersion parameters
model1.dispersion['radius']['width'] = 0.25
model1.dispersion['radius']['npts'] = 50
model = Model(model1)
pars1 = ['length', 'radius', 'scale', 'radius.width']
fitter.set_data(out, 1)
fitter.set_model(model, 1, pars1)
fitter.select_problem_for_fit(id=1, value=1)
#import time; T0 = time.time()
result1, = fitter.fit()
#print "time",time.time()-T0,fitter._engine.__class__.__name__
self.assert_(result1)
self.assertTrue(len(result1.pvec) > 0)
self.assertTrue(len(result1.stderr) > 0)
#print [z for z in zip(result1.param_list,result1.pvec,result1.stderr)]
self.assertTrue(
math.fabs(result1.pvec[0] - 399.8) / 3.0 < result1.stderr[0])
self.assertTrue(
math.fabs(result1.pvec[1] - 17.5) / 3.0 < result1.stderr[1])
self.assertTrue(
math.fabs(result1.pvec[2] - 11.1) / 3.0 < result1.stderr[2])
self.assertTrue(
math.fabs(result1.pvec[3] - 0.276) / 3.0 < result1.stderr[3])
self.assertTrue(result1.fitness < 1.0)
def test_cyl_times_square(self):
""" Simple cylinder model fit """
out = Loader().load("cyl_400_20.txt")
data = Data1D(x=out.x, y=out.y, dx=out.dx, dy=out.dy)
# Receives the type of model for the fitting
model1 = MultiplicationModel(CylinderModel(), SquareWellStructure())
model1.setParam('background', 0.0)
model1.setParam('sldCyl', 3e-006)
model1.setParam('sldSolv', 0.0)
model1.setParam('length', 420)
model1.setParam('radius', 40)
model1.setParam('scale_factor', 2)
model1.setParam('volfraction', 0.04)
model1.setParam('welldepth', 1.5)
model1.setParam('wellwidth', 1.2)
model = Model(model1)
pars1 = ['length', 'radius', 'scale_factor']
fitter = Fit('bumps')
fitter.set_data(data, 1)
fitter.set_model(model, 1, pars1)
fitter.select_problem_for_fit(id=1, value=1)
result1, = fitter.fit()
self.assert_(result1)
self.assertTrue(len(result1.pvec) >= 0)
self.assertTrue(len(result1.stderr) >= 0)
#print "results",list(zip(result1.pvec, result1.stderr))
self.assertTrue(
math.fabs(result1.pvec[0] - 612) / 3.0 <= result1.stderr[0])
self.assertTrue(
math.fabs(result1.pvec[1] - 20.3) / 3.0 <= result1.stderr[1])
self.assertTrue(
math.fabs(result1.pvec[2] - 25) / 3.0 <= result1.stderr[2])
self.assertTrue(result1.fitness / len(data.x) < 1.0)
class TestSimultaneousFit(unittest.TestCase):
""" test simultaneous fitting """
def setUp(self):
""" initialize data"""
self.data1=Loader().load("cyl_400_20.txt")
self.data2=Loader().load("cyl_400_40.txt")
# Receives the type of model for the fitting
from sas.models.CylinderModel import CylinderModel
cyl1 = CylinderModel()
cyl1.name = "C1"
self.model1 = Model(cyl1)
self.model1.set(scale= 1.0)
self.model1.set(radius=18)
self.model1.set(length=200)
self.model1.set(sldCyl=3e-006, sldSolv=0.0)
self.model1.set(background=0.0)
cyl2 = CylinderModel()
cyl2.name = "C2"
self.model2 = Model(cyl2)
self.model2.set(scale= 1.0)
self.model2.set(radius=37)
self.model2.set(length=300)
self.model2.set(sldCyl=3e-006, sldSolv=0.0)
self.model2.set(background=0.0)
def test_constrained_bumps(self):
""" Simultaneous cylinder model fit """
self._run_fit(Fit('bumps'))
#@unittest.skip("")
def _run_fit(self, fitter):
result1, result2 = self._fit(fitter)
self.assert_(result1)
self.assertTrue(len(result1.pvec)>0)
self.assertTrue(len(result1.stderr)>0)
for n, v, dv in zip(result1.param_list, result1.pvec, result1.stderr):
#print "%s M1.%s = %s +/- %s"%(fitter._engine.__class__.__name__,n,v,dv)
if n == "length":
self.assertTrue( math.fabs(v-400.0)/3.0 < dv )
elif n=='radius':
self.assertTrue( math.fabs(v-20.0)/3.0 < dv )
elif n=='scale':
self.assertTrue( math.fabs(v-1.0)/3.0 < dv )
for n, v, dv in zip(result2.param_list, result2.pvec, result2.stderr):
#print "%s M2.%s = %s +/- %s"%(fitter._engine.__class__.__name__,n,v,dv)
if n=='radius':
self.assertTrue( math.fabs(v-40.0)/3.0 < dv )
elif n=='scale':
self.assertTrue( math.fabs(v-1.0)/3.0 < dv )
def _fit(self, fitter):
""" return fit result """
fitter.set_data(self.data1,1)
fitter.set_model(self.model1, 1, ['length','radius','scale'])
fitter.set_data(self.data2,2)
fitter.set_model(self.model2, 2, ['length','radius','scale'],
constraints=[("length","C1.length")])
fitter.select_problem_for_fit(id=1,value=1)
fitter.select_problem_for_fit(id=2,value=1)
return fitter.fit()
class TestSimultaneousFit(unittest.TestCase):
""" test simultaneous fitting """
def setUp(self):
""" initialize data"""
self.data1 = Loader().load("cyl_400_20.txt")
self.data2 = Loader().load("cyl_400_40.txt")
# Receives the type of model for the fitting
from sas.models.CylinderModel import CylinderModel
cyl1 = CylinderModel()
cyl1.name = "C1"
self.model1 = Model(cyl1)
self.model1.set(scale=1.0)
self.model1.set(radius=18)
self.model1.set(length=200)
self.model1.set(sldCyl=3e-006, sldSolv=0.0)
self.model1.set(background=0.0)
cyl2 = CylinderModel()
cyl2.name = "C2"
self.model2 = Model(cyl2)
self.model2.set(scale=1.0)
self.model2.set(radius=37)
self.model2.set(length=300)
self.model2.set(sldCyl=3e-006, sldSolv=0.0)
self.model2.set(background=0.0)
def test_constrained_bumps(self):
""" Simultaneous cylinder model fit """
self._run_fit(Fit())
# @unittest.skip("")
def _run_fit(self, fitter):
result1, result2 = self._fit(fitter)
self.assert_(result1)
self.assertTrue(len(result1.pvec) > 0)
self.assertTrue(len(result1.stderr) > 0)
for n, v, dv in zip(result1.param_list, result1.pvec, result1.stderr):
if n == "length":
self.assertTrue(math.fabs(v - 400.0) / 3.0 < dv)
elif n == "radius":
self.assertTrue(math.fabs(v - 20.0) / 3.0 < dv)
elif n == "scale":
self.assertTrue(math.fabs(v - 1.0) / 3.0 < dv)
for n, v, dv in zip(result2.param_list, result2.pvec, result2.stderr):
if n == "radius":
self.assertTrue(math.fabs(v - 40.0) / 3.0 < dv)
elif n == "scale":
self.assertTrue(math.fabs(v - 1.0) / 3.0 < dv)
def _fit(self, fitter):
""" return fit result """
fitter.set_data(self.data1, 1)
fitter.set_model(self.model1, 1, ["length", "radius", "scale"])
fitter.set_data(self.data2, 2)
fitter.set_model(self.model2, 2, ["length", "radius", "scale"], constraints=[("length", "C1.length")])
fitter.select_problem_for_fit(id=1, value=1)
fitter.select_problem_for_fit(id=2, value=1)
return fitter.fit()