def copy(self, other=None):
"""Copy self to other. if other is None, create new instance
other -- ref to other object
returns reference to copied object
"""
# check arguments
if other is None:
other = FitDataSet(self.name)
PDFDataSet.copy(self, other)
if isinstance(other, FitDataSet):
# assigned attributes
other._fitrmin = self._fitrmin
other._fitrmax = self._fitrmax
other._fitrstep = self._fitrstep
other._rcalc_changed = self._rcalc_changed
# copied attributes
other.constraints = copy.deepcopy(self.constraints)
other.initial = copy.deepcopy(self.initial)
other.refined = copy.deepcopy(self.refined)
# must also update the sampling on the new object
st = self.getFitSamplingType()
other.setFitSamplingType(st, self.fitrstep)
return other
def copy(self, other=None):
"""Copy self to other. if other is None, create new instance
other -- ref to other object
returns reference to copied object
"""
# check arguments
if other is None:
other = FitDataSet(self.name)
PDFDataSet.copy(self, other)
if isinstance(other, FitDataSet):
# assigned attributes
other._fitrmin = self._fitrmin
other._fitrmax = self._fitrmax
other._fitrstep = self._fitrstep
other._rcalc_changed = self._rcalc_changed
# copied attributes
other.constraints = copy.deepcopy(self.constraints)
other.initial = copy.deepcopy(self.initial)
other.refined = copy.deepcopy(self.refined)
# must also update the sampling on the new object
st = self.getFitSamplingType()
other.setFitSamplingType(st, self.fitrstep)
return other
def __setattr__(self, name, value):
"""Assign refinable variables to self.initial.
"""
if name in PDFDataSet.refinableVars:
self.initial[name] = value
else:
PDFDataSet.__setattr__(self, name, value)
return
def __setattr__(self, name, value):
"""Assign refinable variables to self.initial.
"""
if name in PDFDataSet.refinableVars:
self.initial[name] = value
else:
PDFDataSet.__setattr__(self, name, value)
return
def writeObs(self, filename):
"""Write observed PDF data to a file.
filename -- name of file to write to
No return value.
"""
PDFDataSet.write(self, filename)
return
def writeObs(self, filename):
"""Write observed PDF data to a file.
filename -- name of file to write to
No return value.
"""
PDFDataSet.write(self, filename)
return
def readObsStr(self, datastring):
"""Read experimental PDF data from a string
datastring -- string of raw data
returns self
"""
PDFDataSet.readStr(self, datastring)
self._updateRcalcRange()
return self
def readObs(self, filename):
"""Load experimental PDF data from PDFGetX2 or PDFGetN gr file.
filename -- file to read from
returns self
"""
PDFDataSet.read(self, filename)
self._updateRcalcRange()
return self
def __init__(self, name):
"""Initialize FitDataSet.
name -- name of the data set. It must be a unique identifier.
"""
self.initial = {}
self.refined = {}
PDFDataSet.__init__(self, name)
self.clear()
return
def __init__(self, name):
"""Initialize FitDataSet.
name -- name of the data set. It must be a unique identifier.
"""
self.initial = {}
self.refined = {}
PDFDataSet.__init__(self, name)
self.clear()
return
def readObs(self, filename):
"""Load experimental PDF data from PDFGetX2 or PDFGetN gr file.
filename -- file to read from
returns self
"""
PDFDataSet.read(self, filename)
self._updateRcalcRange()
return self
def readObsStr(self, datastring):
"""Read experimental PDF data from a string
datastring -- string of raw data
returns self
"""
PDFDataSet.readStr(self, datastring)
self._updateRcalcRange()
return self
def _resampledPDFDataSet(self):
"""Return instance of PDFDataSet with resampled observed data.
Helper method for writeResampledObs and writeResampledObsStr.
"""
resampled = PDFDataSet(self.name)
self.copy(resampled)
resampled.robs = self.rcalc
resampled.drobs = len(self.rcalc) * [0.0]
resampled.Gobs = self.Gtrunc
resampled.dGobs = self.dGtrunc
return resampled
def clear(self):
"""Reset all data members to initial empty values.
"""
PDFDataSet.clear(self)
self._rcalc_changed = True
self._rcalc = []
self._Gcalc = []
self._dGcalc = []
self._Gtrunc = []
self._dGtrunc = []
self._crw = []
self._fitrmin = None
self._fitrmax = None
self._fitrstep = None
self.constraints = {}
self.refined = {}
return
def clear(self):
"""Reset all data members to initial empty values.
"""
PDFDataSet.clear(self)
self._rcalc_changed = True
self._rcalc = []
self._Gcalc = []
self._dGcalc = []
self._Gtrunc = []
self._dGtrunc = []
self._crw = []
self._fitrmin = 0.5
self._fitrmax = None
self._fitrstep = None
self.constraints = {}
self.refined = {}
return
def _resampledPDFDataSet(self):
"""Return instance of PDFDataSet with resampled observed data.
Helper method for writeResampledObs and writeResampledObsStr.
"""
resampled = PDFDataSet(self.name)
self.copy(resampled)
resampled.robs = self.rcalc
resampled.drobs = len(self.rcalc) * [0.0]
resampled.Gobs = self.Gtrunc
resampled.dGobs = self.dGtrunc
return resampled
class TestPDFDataSet(unittest.TestCase):
def setUp(self):
self.pdfds = PDFDataSet('test data set')
return
def tearDown(self):
self.pdfds = None
return
# def test___init__(self):
# """check PDFDataSet.__init__()
# """
# return
#
# def test_clear(self):
# """check PDFDataSet.clear()
# """
# return
#
# def test_setvar(self):
# """check PDFDataSet.setvar()
# """
# return
#
# def test_getvar(self):
# """check PDFDataSet.getvar()
# """
# return
#
def test_read(self):
"""check PDFDataSet.read()
"""
# neutron data -------------------------------------------------
fn_550K = datafile('550K.gr')
self.pdfds.read(fn_550K)
self.assertEqual('N', self.pdfds.stype)
self.assertEqual(32.0, self.pdfds.qmax)
# there are 2000 points in the file
npts = len(self.pdfds.robs)
self.assertEqual(2000, npts)
# drobs are all zero
self.assertEqual(npts*[0.0], self.pdfds.drobs)
# dGobs should be defined
self.assertTrue(min(self.pdfds.dGobs) > 0)
# x-ray data ---------------------------------------------------
fx_Ni = datafile('Ni_2-8.chi.gr')
self.pdfds.read(fx_Ni)
self.assertEqual('X', self.pdfds.stype)
self.assertEqual(40.0, self.pdfds.qmax)
# there are 2000 points in the file
npts = len(self.pdfds.robs)
self.assertEqual(2000, npts)
# drobs are all zero
self.assertEqual(npts*[0.0], self.pdfds.drobs)
# dGobs should be defined
self.assertTrue(min(self.pdfds.dGobs) > 0)
return
def test_readStr(self):
"""check PDFDataSet.readStr()
"""
# read Ni xray data, but invalidate the last dGobs
fx_Ni = datafile('Ni_2-8.chi.gr')
sNi = open(fx_Ni).read()
lastdGobs = sNi.rstrip().rindex(' ')
sNi_no_dGobs = sNi[:lastdGobs] + " -1.3e-3"
self.pdfds.readStr(sNi_no_dGobs)
# there are 2000 points in the file
npts = len(self.pdfds.robs)
self.assertEqual(2000, npts)
# dGobs should be all zero
self.assertEqual(npts*[0.0], self.pdfds.dGobs)
return
class TestPDFDataSet(unittest.TestCase):
def setUp(self):
self.pdfds = PDFDataSet('test data set')
return
def tearDown(self):
self.pdfds = None
return
# def test___init__(self):
# """check PDFDataSet.__init__()
# """
# return
#
# def test_clear(self):
# """check PDFDataSet.clear()
# """
# return
#
# def test_setvar(self):
# """check PDFDataSet.setvar()
# """
# return
#
# def test_getvar(self):
# """check PDFDataSet.getvar()
# """
# return
#
def test_read(self):
"""check PDFDataSet.read()
"""
# neutron data -------------------------------------------------
fn_550K = datafile('550K.gr')
self.pdfds.read(fn_550K)
self.assertEqual('N', self.pdfds.stype)
self.assertEqual(32.0, self.pdfds.qmax)
# there are 2000 points in the file
npts = len(self.pdfds.robs)
self.assertEqual(2000, npts)
# drobs are all zero
self.assertEqual(npts*[0.0], self.pdfds.drobs)
# dGobs should be defined
self.failUnless(min(self.pdfds.dGobs) > 0)
# x-ray data ---------------------------------------------------
fx_Ni = datafile('Ni_2-8.chi.gr')
self.pdfds.read(fx_Ni)
self.assertEqual('X', self.pdfds.stype)
self.assertEqual(40.0, self.pdfds.qmax)
# there are 2000 points in the file
npts = len(self.pdfds.robs)
self.assertEqual(2000, npts)
# drobs are all zero
self.assertEqual(npts*[0.0], self.pdfds.drobs)
# dGobs should be defined
self.failUnless(min(self.pdfds.dGobs) > 0)
return
def test_readStr(self):
"""check PDFDataSet.readStr()
"""
# read Ni xray data, but invalidate the last dGobs
fx_Ni = datafile('Ni_2-8.chi.gr')
sNi = open(fx_Ni).read()
lastdGobs = sNi.rstrip().rindex(' ')
sNi_no_dGobs = sNi[:lastdGobs] + " -1.3e-3"
self.pdfds.readStr(sNi_no_dGobs)
# there are 2000 points in the file
npts = len(self.pdfds.robs)
self.assertEqual(2000, npts)
# dGobs should be all zero
self.assertEqual(npts*[0.0], self.pdfds.dGobs)
return
def writeObsStr(self):
"""String representation of observed PDF data.
Return data string.
"""
return PDFDataSet.writeStr(self)
def setUp(self):
self.pdfds = PDFDataSet('test data set')
return
def setUp(self):
self.pdfds = PDFDataSet('test data set')
return
def writeObsStr(self):
"""String representation of observed PDF data.
Return data string.
"""
return PDFDataSet.writeStr(self)
