def testParser(self):
data = datafile("sas_ascii_test_1.txt")
parser = SASParser()
parser.parseFile(data)
x, y, dx, dy = parser.getData()
testx = numpy.array([0.002618, 0.007854, 0.01309, 0.01832, 0.02356,
0.02879, 0.03402, 0.03925, 0.04448, 0.0497])
diff = testx - x
res = numpy.dot(diff, diff)
self.assertAlmostEqual(0, res)
testy = numpy.array([ 0.02198, 0.02201, 0.02695, 0.02645, 0.03024,
0.3927, 7.305, 17.43, 13.43, 8.346])
diff = testy - y
res = numpy.dot(diff, diff)
self.assertAlmostEqual(0, res)
testdy = numpy.array([ 0.002704, 0.001643, 0.002452, 0.001769,
0.001531, 0.1697, 1.006, 0.5351, 0.3677, 0.191])
diff = testdy - dy
res = numpy.dot(diff, diff)
self.assertAlmostEqual(0, res)
testdx = numpy.array([0.0004091, 0.005587, 0.005598, 0.005624,
0.005707, 0.005975, 0.006264, 0.006344, 0.006424, 0.006516])
diff = testdx - dx
res = numpy.dot(diff, diff)
self.assertAlmostEqual(0, res)
return
def makeRecipe(datname):
"""Create a fitting recipe for ellipsoidal SAS data."""
## The Profile
# This will be used to store the observed and calculated I(Q) data.
profile = Profile()
# Load data and add it to the Profile. We use a SASParser to load the data
# properly and pass the metadata along.
parser = SASParser()
parser.parseFile(datname)
profile.loadParsedData(parser)
## The ProfileGenerator
# The SASGenerator is for configuring and calculating a SAS profile. We use
# a sans model to configure and serve as the calculation engine of the
# generator. This allows us to use the full sans model creation
# capabilities, and tie this into SrFit when we want to fit a model to
# data. The documentation for the various sans models can be found at
# http://danse.chem.utk.edu/sansview.html.
from sans.models.EllipsoidModel import EllipsoidModel
model = EllipsoidModel()
generator = SASGenerator("generator", model)
## The FitContribution
# Here we associate the Profile and ProfileGenerator, as has been done
# before.
contribution = FitContribution("ellipsoid")
contribution.addProfileGenerator(generator)
contribution.setProfile(profile, xname="q")
# We want to fit the log of the signal to the log of the data so that the
# higher-Q information remains significant. There are no I(Q) uncertainty
# values with the data, so we do not need to worry about the effect this
# will have on the estimated parameter uncertainties.
contribution.setResidualEquation("log(eq) - log(y)")
## Make the FitRecipe and add the FitContribution.
recipe = FitRecipe()
recipe.addContribution(contribution)
## Configure the fit variables
# The SASGenerator uses the parameters from the params and dispersion
# attribues of the model. These vary from model to model, but are adopted
# as SrFit Parameters within the generator. Whereas the dispersion
# parameters are accessible as, e.g. "radius.width", within the
# SASGenerator these are named like "radius_width".
#
# We want to fit the scale factor, radii and background factors.
recipe.addVar(generator.scale, 1)
recipe.addVar(generator.radius_a, 50)
recipe.addVar(generator.radius_b, 500)
recipe.addVar(generator.background, 0)
# Give the recipe away so it can be used!
return recipe
def makeRecipe(datname):
"""Create a fitting recipe for ellipsoidal SAS data."""
## The Profile
# This will be used to store the observed and calculated I(Q) data.
profile = Profile()
# Load data and add it to the Profile. We use a SASParser to load the data
# properly and pass the metadata along.
parser = SASParser()
parser.parseFile(datname)
profile.loadParsedData(parser)
## The ProfileGenerator
# The SASGenerator is for configuring and calculating a SAS profile. We use
# a sans model to configure and serve as the calculation engine of the
# generator. This allows us to use the full sans model creation
# capabilities, and tie this into SrFit when we want to fit a model to
# data. The documentation for the various sans models can be found at
# http://danse.chem.utk.edu/sansview.html.
from sans.models.EllipsoidModel import EllipsoidModel
model = EllipsoidModel()
generator = SASGenerator("generator", model)
## The FitContribution
# Here we associate the Profile and ProfileGenerator, as has been done
# before.
contribution = FitContribution("ellipsoid")
contribution.addProfileGenerator(generator)
contribution.setProfile(profile, xname = "q")
# We want to fit the log of the signal to the log of the data so that the
# higher-Q information remains significant. There are no I(Q) uncertainty
# values with the data, so we do not need to worry about the effect this
# will have on the estimated parameter uncertainties.
contribution.setResidualEquation("log(eq) - log(y)")
## Make the FitRecipe and add the FitContribution.
recipe = FitRecipe()
recipe.addContribution(contribution)
## Configure the fit variables
# The SASGenerator uses the parameters from the params and dispersion
# attribues of the model. These vary from model to model, but are adopted
# as SrFit Parameters within the generator. Whereas the dispersion
# parameters are accessible as, e.g. "radius.width", within the
# SASGenerator these are named like "radius_width".
#
# We want to fit the scale factor, radii and background factors.
recipe.addVar(generator.scale, 1)
recipe.addVar(generator.radius_a, 50)
recipe.addVar(generator.radius_b, 500)
recipe.addVar(generator.background, 0)
# Give the recipe away so it can be used!
return recipe
def makeRecipe(ciffile, grdata, iqdata):
"""Make complex-modeling recipe where I(q) and G(r) are fit
simultaneously.
The fit I(q) is fed into the calculation of G(r), which provides feedback
for the fit parameters of both.
"""
# Create a PDF contribution as before
pdfprofile = Profile()
pdfparser = PDFParser()
pdfparser.parseFile(grdata)
pdfprofile.loadParsedData(pdfparser)
pdfprofile.setCalculationRange(xmin = 0.1, xmax = 20)
pdfcontribution = FitContribution("pdf")
pdfcontribution.setProfile(pdfprofile, xname = "r")
pdfgenerator = PDFGenerator("G")
pdfgenerator.setQmax(30.0)
stru = loadCrystal(ciffile)
pdfgenerator.setStructure(stru)
pdfcontribution.addProfileGenerator(pdfgenerator)
pdfcontribution.setResidualEquation("resv")
# Create a SAS contribution as well. We assume the nanoparticle is roughly
# elliptical.
sasprofile = Profile()
sasparser = SASParser()
sasparser.parseFile(iqdata)
sasprofile.loadParsedData(sasparser)
if all(sasprofile.dy == 0):
sasprofile.dy[:] = 1
sascontribution = FitContribution("sas")
sascontribution.setProfile(sasprofile)
from sas.models.EllipsoidModel import EllipsoidModel
model = EllipsoidModel()
sasgenerator = SASGenerator("generator", model)
sascontribution.addProfileGenerator(sasgenerator)
sascontribution.setResidualEquation("resv")
# Now we set up a characteristic function calculator that depends on the
# sas model.
cfcalculator = SASCF("f", model)
# Register the calculator with the pdf contribution and define the fitting
# equation.
pdfcontribution.registerCalculator(cfcalculator)
# The PDF for a nanoscale crystalline is approximated by
# Gnano = f * Gcryst
pdfcontribution.setEquation("f * G")
# Moving on
recipe = FitRecipe()
recipe.addContribution(pdfcontribution)
recipe.addContribution(sascontribution)
# PDF
phase = pdfgenerator.phase
for par in phase.sgpars:
recipe.addVar(par)
recipe.addVar(pdfgenerator.scale, 1)
recipe.addVar(pdfgenerator.delta2, 0)
# SAS
recipe.addVar(sasgenerator.scale, 1, name = "iqscale")
recipe.addVar(sasgenerator.radius_a, 10)
recipe.addVar(sasgenerator.radius_b, 10)
# Even though the cfcalculator and sasgenerator depend on the same sas
# model, we must still constrain the cfcalculator Parameters so that it is
# informed of changes in the refined parameters.
recipe.constrain(cfcalculator.radius_a, "radius_a")
recipe.constrain(cfcalculator.radius_b, "radius_b")
return recipe
def makeRecipe(ciffile, grdata, iqdata):
"""Make complex-modeling recipe where I(q) and G(r) are fit
simultaneously.
The fit I(q) is fed into the calculation of G(r), which provides feedback
for the fit parameters of both.
"""
# Create a PDF contribution as before
pdfprofile = Profile()
pdfparser = PDFParser()
pdfparser.parseFile(grdata)
pdfprofile.loadParsedData(pdfparser)
pdfprofile.setCalculationRange(xmin = 0.1, xmax = 20)
pdfcontribution = FitContribution("pdf")
pdfcontribution.setProfile(pdfprofile, xname = "r")
pdfgenerator = PDFGenerator("G")
pdfgenerator.setQmax(30.0)
stru = CreateCrystalFromCIF(file(ciffile))
pdfgenerator.setStructure(stru)
pdfcontribution.addProfileGenerator(pdfgenerator)
pdfcontribution.setResidualEquation("resv")
# Create a SAS contribution as well. We assume the nanoparticle is roughly
# elliptical.
sasprofile = Profile()
sasparser = SASParser()
sasparser.parseFile(iqdata)
sasprofile.loadParsedData(sasparser)
sascontribution = FitContribution("sas")
sascontribution.setProfile(sasprofile)
from sans.models.EllipsoidModel import EllipsoidModel
model = EllipsoidModel()
sasgenerator = SASGenerator("generator", model)
sascontribution.addProfileGenerator(sasgenerator)
sascontribution.setResidualEquation("resv")
# Now we set up a characteristic function calculator that depends on the
# sas model.
cfcalculator = SASCF("f", model)
# Register the calculator with the pdf contribution and define the fitting
# equation.
pdfcontribution.registerCalculator(cfcalculator)
# The PDF for a nanoscale crystalline is approximated by
# Gnano = f * Gcryst
pdfcontribution.setEquation("f * G")
# Moving on
recipe = FitRecipe()
recipe.addContribution(pdfcontribution)
recipe.addContribution(sascontribution)
# PDF
phase = pdfgenerator.phase
for par in phase.sgpars:
recipe.addVar(par)
recipe.addVar(pdfgenerator.scale, 1)
recipe.addVar(pdfgenerator.delta2, 0)
# SAS
recipe.addVar(sasgenerator.scale, 1, name = "iqscale")
recipe.addVar(sasgenerator.radius_a, 10)
recipe.addVar(sasgenerator.radius_b, 10)
# Even though the cfcalculator and sasgenerator depend on the same sas
# model, we must still constrain the cfcalculator Parameters so that it is
# informed of changes in the refined parameters.
recipe.constrain(cfcalculator.radius_a, "radius_a")
recipe.constrain(cfcalculator.radius_b, "radius_b")
return recipe