def testGenerator2(self):
# Test generator with a profile
EllipsoidModel = sasimport('sas.models.EllipsoidModel').EllipsoidModel
model = EllipsoidModel()
gen = SASGenerator("ellipsoid", model)
# Load the data using SAS tools
Loader = sasimport('sas.dataloader.loader').Loader
loader = Loader()
data = datafile("sas_ellipsoid_testdata.txt")
datainfo = loader.load(data)
profile = SASProfile(datainfo)
gen.setProfile(profile)
gen.scale.value = 1.0
gen.radius_a.value = 20
gen.radius_b.value = 400
gen.background.value = 0.01
y = gen(profile.xobs)
diff = profile.yobs - y
res = numpy.dot(diff, diff)
self.assertAlmostEqual(0, res)
return
def testParser1(self):
data = datafile("ni-q27r100-neutron.gr")
parser = PDFParser()
parser.parseFile(data)
meta = parser._meta
self.assertEqual(data, meta['filename'])
self.assertEqual(1, meta['nbanks'])
self.assertEqual('N', meta['stype'])
self.assertEqual(27, meta['qmax'])
self.assertEquals(300, meta.get('temperature'))
self.assertEquals(None, meta.get('qdamp'))
self.assertEquals(None, meta.get('qbroad'))
self.assertEquals(None, meta.get('spdiameter'))
self.assertEquals(None, meta.get('scale'))
self.assertEquals(None, meta.get('doping'))
x, y, dx, dy = parser.getData()
self.assertTrue(dx is None)
self.assertTrue(dy is None)
testx = numpy.linspace(0.01, 100, 10000)
diff = testx - x
res = numpy.dot(diff, diff)
self.assertAlmostEqual(0, res)
testy = numpy.array([1.144, 2.258, 3.312, 4.279, 5.135, 5.862, 6.445,
6.875, 7.150, 7.272])
diff = testy - y[:10]
res = numpy.dot(diff, diff)
self.assertAlmostEqual(0, res)
return
def testGenerator2(self):
# Test generator with a profile
EllipsoidModel = sasimport('sas.models.EllipsoidModel').EllipsoidModel
model = EllipsoidModel()
gen = SASGenerator("ellipsoid", model)
# Load the data using SAS tools
Loader = sasimport('sas.dataloader.loader').Loader
loader = Loader()
data = datafile("sas_ellipsoid_testdata.txt")
datainfo = loader.load(data)
profile = SASProfile(datainfo)
gen.setProfile(profile)
gen.scale.value = 1.0
gen.radius_a.value = 20
gen.radius_b.value = 400
gen.background.value = 0.01
y = gen(profile.xobs)
diff = profile.yobs - y
res = numpy.dot(diff, diff)
self.assertAlmostEqual(0, res)
return
def testLoadtxt(self):
"""Test the loadtxt method"""
prof = self.profile
data = datafile("testdata.txt")
def _test(p):
self.assertAlmostEqual(1e-2, p.x[0])
self.assertAlmostEqual(1.105784e-1, p.y[0])
self.assertAlmostEqual(1.802192e-3, p.dy[0])
# Test normal load
prof.loadtxt(data, usecols=(0,1,3))
_test(prof)
# Test trying to not set unpack
prof.loadtxt(data, usecols=(0,1,3), unpack = False)
_test(prof)
prof.loadtxt(data, float, '#', None, None, 0, (0,1,3), False)
_test(prof)
# Try not including dy
prof.loadtxt(data, usecols=(0,1))
self.assertAlmostEqual(1e-2, prof.x[0])
self.assertAlmostEqual(1.105784e-1, prof.y[0])
self.assertAlmostEqual(1, prof.dy[0])
# Try to include too little
self.assertRaises(ValueError, prof.loadtxt, data, usecols=(0,))
return
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 testGenerator2(self):
# Test generator with a profile
from sans.models.EllipsoidModel import EllipsoidModel
model = EllipsoidModel()
gen = sas.SASGenerator("ellipsoid", model)
# Load the data using SAS tools
from diffpy.srfit.sas.sasparser import _import_sans_Loader
Loader = _import_sans_Loader()
loader = Loader()
data = datafile("sas_ellipsoid_testdata.txt")
datainfo = loader.load(data)
profile = sas.SASProfile(datainfo)
gen.setProfile(profile)
gen.scale.value = 1.0
gen.radius_a.value = 20
gen.radius_b.value = 400
gen.background.value = 0.01
y = gen(profile.xobs)
diff = profile.yobs - y
res = numpy.dot(diff, diff)
self.assertAlmostEqual(0, res)
return
def testGenerator2(self):
# Test generator with a profile
from sans.models.EllipsoidModel import EllipsoidModel
model = EllipsoidModel()
gen = sas.SASGenerator("ellipsoid", model)
# Load the data using SAS tools
from diffpy.srfit.sas.sasparser import _import_sans_Loader
Loader = _import_sans_Loader()
loader = Loader()
data = datafile("sas_ellipsoid_testdata.txt")
datainfo = loader.load(data)
profile = sas.SASProfile(datainfo)
gen.setProfile(profile)
gen.scale.value = 1.0
gen.radius_a.value = 20
gen.radius_b.value = 400
gen.background.value = 0.01
y = gen(profile.xobs)
diff = profile.yobs - y
res = numpy.dot(diff, diff)
self.assertAlmostEqual(0, res)
return
def testParser1(self):
data = datafile("ni-q27r100-neutron.gr")
parser = PDFParser()
parser.parseFile(data)
meta = parser._meta
self.assertEqual(data, meta['filename'])
self.assertEqual(1, meta['nbanks'])
self.assertEqual('N', meta['stype'])
self.assertEqual(27, meta['qmax'])
self.assertEquals(300, meta.get('temperature'))
self.assertEquals(None, meta.get('qdamp'))
self.assertEquals(None, meta.get('qbroad'))
self.assertEquals(None, meta.get('spdiameter'))
self.assertEquals(None, meta.get('scale'))
self.assertEquals(None, meta.get('doping'))
x, y, dx, dy = parser.getData()
self.assertTrue(dx is None)
self.assertTrue(dy is None)
testx = numpy.linspace(0.01, 100, 10000)
diff = testx - x
res = numpy.dot(diff, diff)
self.assertAlmostEqual(0, res)
testy = numpy.array([1.144, 2.258, 3.312, 4.279, 5.135, 5.862, 6.445,
6.875, 7.150, 7.272])
diff = testy - y[:10]
res = numpy.dot(diff, diff)
self.assertAlmostEqual(0, res)
return
def testLoadtxt(self):
"""Test the loadtxt method"""
prof = self.profile
data = datafile("testdata.txt")
def _test(p):
self.assertAlmostEqual(1e-2, p.x[0])
self.assertAlmostEqual(1.105784e-1, p.y[0])
self.assertAlmostEqual(1.802192e-3, p.dy[0])
# Test normal load
prof.loadtxt(data, usecols=(0,1,3))
_test(prof)
# Test trying to not set unpack
prof.loadtxt(data, usecols=(0,1,3), unpack = False)
_test(prof)
prof.loadtxt(data, float, '#', None, None, 0, (0,1,3), False)
_test(prof)
# Try not including dy
prof.loadtxt(data, usecols=(0,1))
self.assertAlmostEqual(1e-2, prof.x[0])
self.assertAlmostEqual(1.105784e-1, prof.y[0])
self.assertAlmostEqual(1, prof.dy[0])
# Try to include too little
self.assertRaises(ValueError, prof.loadtxt, data, usecols=(0,))
return
def test_pickling(self):
"validate PDFContribution.residual() after pickling."
from itertools import chain
from diffpy.structure import loadStructure
pc = self.pc
pc.loadData(datafile("ni-q27r100-neutron.gr"))
ni = loadStructure(datafile("ni.cif"))
ni.Uisoequiv = 0.003
pc.addStructure('ni', ni)
pc.setCalculationRange(0, 10)
pc2 = pickle.loads(pickle.dumps(pc))
res0 = pc.residual()
self.assertTrue(numpy.array_equal(res0, pc2.residual()))
for p in chain(pc.iterPars('Uiso'), pc2.iterPars('Uiso')):
p.value = 0.004
res1 = pc.residual()
self.assertFalse(numpy.allclose(res0, res1))
self.assertTrue(numpy.array_equal(res1, pc2.residual()))
return
def test_pickling(self):
"validate PDFContribution.residual() after pickling."
from itertools import chain
from diffpy.structure import loadStructure
pc = self.pc
pc.loadData(datafile("ni-q27r100-neutron.gr"))
ni = loadStructure(datafile("ni.cif"))
ni.Uisoequiv = 0.003
pc.addStructure('ni', ni)
pc.setCalculationRange(0, 10)
pc2 = pickle.loads(pickle.dumps(pc))
res0 = pc.residual()
self.assertTrue(numpy.array_equal(res0, pc2.residual()))
for p in chain(pc.iterPars('Uiso'), pc2.iterPars('Uiso')):
p.value = 0.004
res1 = pc.residual()
self.assertFalse(numpy.allclose(res0, res1))
self.assertTrue(numpy.array_equal(res1, pc2.residual()))
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 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 test_savetxt(self):
"check PDFContribution.savetxt()"
from diffpy.structure import Structure
pc = self.pc
pc.loadData(datafile("si-q27r60-xray.gr"))
pc.setCalculationRange(0, 10)
pc.addStructure('empty', Structure())
fp = io.BytesIO()
self.assertRaises(SrFitError, pc.savetxt, fp)
pc.evaluate()
pc.savetxt(fp)
txt = fp.getvalue().decode()
nlines = len(txt.strip().split('\n'))
self.assertEqual(1001, nlines)
return
def test_savetxt(self):
"check PDFContribution.savetxt()"
from diffpy.structure import Structure
pc = self.pc
pc.loadData(datafile("si-q27r60-xray.gr"))
pc.setCalculationRange(0, 10)
pc.addStructure('empty', Structure())
fp = io.BytesIO()
self.assertRaises(SrFitError, pc.savetxt, fp)
pc.evaluate()
pc.savetxt(fp)
txt = fp.getvalue().decode()
nlines = len(txt.strip().split('\n'))
self.assertEqual(1001, nlines)
return
def testGenerator(self):
qmax = 27.0
gen = self.gen
gen.setScatteringType('N')
self.assertEqual('N', gen.getScatteringType())
gen.setQmax(qmax)
self.assertAlmostEqual(qmax, gen.getQmax())
from diffpy.Structure import PDFFitStructure
stru = PDFFitStructure()
ciffile = datafile("ni.cif")
stru.read(ciffile)
for i in range(4):
stru[i].Bisoequiv = 1
gen.setStructure(stru)
calc = gen._calc
# Test parameters
for par in gen.iterPars(recurse=False):
pname = par.name
defval = calc._getDoubleAttr(pname)
self.assertEquals(defval, par.getValue())
# Test setting values
par.setValue(1.0)
self.assertEquals(1.0, par.getValue())
par.setValue(defval)
self.assertEquals(defval, par.getValue())
r = numpy.arange(0, 10, 0.1)
y = gen(r)
# Now create a reference PDF. Since the calculator is testing its
# output, we just have to make sure we can calculate from the
# PDFGenerator interface.
from diffpy.srreal.pdfcalculator import PDFCalculator
calc = PDFCalculator()
calc.rstep = r[1] - r[0]
calc.rmin = r[0]
calc.rmax = r[-1] + 0.5 * calc.rstep
calc.qmax = qmax
calc.setScatteringFactorTableByType('N')
calc.eval(stru)
yref = calc.pdf
diff = y - yref
res = numpy.dot(diff, diff)
self.assertAlmostEquals(0, res)
return
def testGenerator(self):
qmax = 27.0
gen = PDFGenerator()
gen.setScatteringType('N')
self.assertEqual('N', gen.getScatteringType())
gen.setQmax(qmax)
self.assertAlmostEqual(qmax, gen.getQmax())
from diffpy.Structure import PDFFitStructure
stru = PDFFitStructure()
ciffile = datafile("ni.cif")
stru.read(ciffile)
for i in range(4):
stru[i].Bisoequiv = 1
gen.setStructure(stru)
calc = gen._calc
# Test parameters
for par in gen.iterPars(recurse = False):
pname = par.name
defval = calc._getDoubleAttr(pname)
self.assertEquals(defval, par.getValue())
# Test setting values
par.setValue(1.0)
self.assertEquals(1.0, par.getValue())
par.setValue(defval)
self.assertEquals(defval, par.getValue())
r = numpy.arange(0, 10, 0.1)
y = gen(r)
# Now create a reference PDF. Since the calculator is testing its
# output, we just have to make sure we can calculate from the
# PDFGenerator interface.
from diffpy.srreal.pdfcalculator import PDFCalculator
calc = PDFCalculator()
calc.rstep = r[1] - r[0]
calc.rmin = r[0]
calc.rmax = r[-1] + 0.5 * calc.rstep
calc.qmax = qmax
calc.setScatteringFactorTableByType('N')
calc.eval(stru)
yref = calc.pdf
diff = y - yref
res = numpy.dot(diff, diff)
self.assertAlmostEquals(0, res)
return
def testParser2(self):
data = datafile("si-q27r60-xray.gr")
parser = PDFParser()
parser.parseFile(data)
meta = parser._meta
self.assertEqual(data, meta['filename'])
self.assertEqual(1, meta['nbanks'])
self.assertEqual('X', meta['stype'])
self.assertEqual(27, meta['qmax'])
self.assertEquals(300, meta.get('temperature'))
self.assertEquals(None, meta.get('qdamp'))
self.assertEquals(None, meta.get('qbroad'))
self.assertEquals(None, meta.get('spdiameter'))
self.assertEquals(None, meta.get('scale'))
self.assertEquals(None, meta.get('doping'))
x, y, dx, dy = parser.getData()
testx = numpy.linspace(0.01, 60, 5999, endpoint=False)
diff = testx - x
res = numpy.dot(diff, diff)
self.assertAlmostEqual(0, res)
testy = numpy.array([
0.1105784, 0.2199684, 0.3270088, 0.4305913, 0.5296853, 0.6233606,
0.7108060, 0.7913456, 0.8644501, 0.9297440
])
diff = testy - y[:10]
res = numpy.dot(diff, diff)
self.assertAlmostEqual(0, res)
testdy = numpy.array([
0.001802192, 0.003521449, 0.005079115, 0.006404892, 0.007440527,
0.008142955, 0.008486813, 0.008466340, 0.008096858, 0.007416456
])
diff = testdy - dy[:10]
res = numpy.dot(diff, diff)
self.assertAlmostEqual(0, res)
self.assertTrue(dx is None)
return
def testParser2(self):
data = datafile("si-q27r60-xray.gr")
parser = PDFParser()
parser.parseFile(data)
meta = parser._meta
self.assertEqual(data, meta['filename'])
self.assertEqual(1, meta['nbanks'])
self.assertEqual('X', meta['stype'])
self.assertEqual(27, meta['qmax'])
self.assertEquals(300, meta.get('temperature'))
self.assertEquals(None, meta.get('qdamp'))
self.assertEquals(None, meta.get('qbroad'))
self.assertEquals(None, meta.get('spdiameter'))
self.assertEquals(None, meta.get('scale'))
self.assertEquals(None, meta.get('doping'))
x, y, dx, dy = parser.getData()
testx = numpy.linspace(0.01, 60, 5999, endpoint=False)
diff = testx - x
res = numpy.dot(diff, diff)
self.assertAlmostEqual(0, res)
testy = numpy.array([0.1105784, 0.2199684, 0.3270088, 0.4305913,
0.5296853, 0.6233606, 0.7108060, 0.7913456, 0.8644501, 0.9297440])
diff = testy - y[:10]
res = numpy.dot(diff, diff)
self.assertAlmostEqual(0, res)
testdy = numpy.array([0.001802192, 0.003521449, 0.005079115,
0.006404892, 0.007440527, 0.008142955, 0.008486813, 0.008466340,
0.008096858, 0.007416456])
diff = testdy - dy[:10]
res = numpy.dot(diff, diff)
self.assertAlmostEqual(0, res)
self.assertTrue(dx is None)
return
def makeLaMnO3_P1():
from diffpy.structure import Structure
stru = Structure()
stru.read(datafile('LaMnO3.stru'))
return stru