def phases(self, value):
if isinstance(value, Phase):
value = Phases('Phases', value)
if not isinstance(value, Phases):
raise ValueError
self._phases = value
self._borg.map.add_edge(self, value)
self._phases.interface = self.interface
def __init__(self,
phases: Union[Phase, Phases] = None,
parameters=None,
pattern=None,
calculator=None,
interface=None,
name: str = 'easySample'):
if isinstance(phases, Phase):
phases = Phases('Phases', phases)
elif phases is None:
phases = Phases('Phases')
if not isinstance(phases, Phases):
raise AttributeError('`phases` must be a Crystal or Crystals')
if parameters is None:
parameters = Instrument1DCWParameters.default()
if pattern is None:
pattern = Pattern1D.default()
super(Sample, self).__init__(name,
_phases=phases,
_parameters=parameters,
_pattern=pattern)
self.filename = os.path.join(tempfile.gettempdir(),
'easydiffraction_temp.cif')
print(f"Temp CIF: {self.filename}")
self.output_index = None
if calculator is not None:
self.interface = calculator
elif interface is not None:
self.interface = interface
else:
self.interface = InterfaceFactory()
def __init__(self,
name: str = '',
job_type=None,
datastore: xr.Dataset = None,
phases: Union[Phase, Phases] = None,
parameters=None,
pattern=None,
interface=None):
if isinstance(phases, Phase):
phases = Phases('Phases', phases)
elif phases is None:
phases = Phases('Phases')
if not isinstance(phases, Phases):
raise AttributeError('`phases` must be a Crystal or Crystals')
if parameters is None:
parameters = job_type.pattern_class.default()
if pattern is None:
pattern = job_type.instrumental_parameter_class.default()
super(_PowderBase, self).__init__(name,
_phases=phases,
_parameters=parameters,
_pattern=pattern)
self.__constituting_classes = job_type
self.__dataset = datastore
self.datastore = DataContainer.prepare(self.__dataset,
*job_type.datastore_classes)
self.filename = os.path.join(tempfile.gettempdir(),
'easydiffraction_temp.cif')
self.output_index = None
self.interface = interface
__author__ = 'github.com/wardsimon'
__version__ = '0.0.1'
from easyCore import np
from easyDiffractionLib.sample import Sample
from easyDiffractionLib import Phases
from easyDiffractionLib.interface import InterfaceFactory
from easyDiffractionLib.Elements.Experiments.Experiment import Pars1D
from easyDiffractionLib.Elements.Experiments.Pattern import Pattern1D
from easyDiffractionLib.Elements.Backgrounds.Point import PointBackground, BackgroundPoint
from easyCore.Fitting.Fitting import Fitter
from easyCore.Datasets.xarray import xr
interface = InterfaceFactory()
c = Phases.from_cif_file('PbSO4.cif')
S = Sample(phases=c,
parameters=Pars1D.default(),
pattern=Pattern1D.default(),
interface=interface)
file_path = 'PbSO4_neutrons_short.xye'
data_x, data_y, data_e = np.loadtxt(file_path, unpack=True)
data_set = xr.Dataset()
data_set.easyCore.add_coordinate('tth', data_x)
data_set.easyCore.add_variable('I', ['tth'], data_y)
data_set.easyCore.sigma_attach('I', data_e)
S.parameters.wavelength = 1.912
S.parameters.u_resolution = 1.4
__author__ = 'github.com/wardsimon'
__version__ = '0.0.1'
from easyCore import np
from easyDiffractionLib.sample import Sample
from easyDiffractionLib import Phase, Phases
from easyDiffractionLib.interface import InterfaceFactory
from easyDiffractionLib.Profiles.P1D import Instrument1DCWParameters
import matplotlib.pyplot as plt
i = InterfaceFactory()
c = Phases.from_cif_file('tests/SrTiO3.cif')
S = Sample(phases=c, parameters=Instrument1DCWParameters.default(), interface=i)
x_data = np.linspace(5, 150, 10000)
y_data = i.fit_func(x_data)
i.switch('CrysPy')
S._updateInterface()
y_data2 = np.array(i.fit_func(x_data))
fig = plt.figure()
axprops = dict()
ax1 = fig.add_axes([0.1, 0.5, 0.8, 0.4], **axprops)
ax1.plot(x_data, y_data, label="CrysFML")
calculator = Calculator()
calculator.switch('CrysPy')
atom = Site.from_pars(label="Cl1",
specie='Cl',
fract_x=0.1250,
fract_y=0.1670,
fract_z=0.1070)
atom.add_adp('Uiso', Uiso=0.0)
phase = Phase(name="p1")
phase.spacegroup.space_group_HM_name = "P 42/n c m"
phase.add_atom(atom)
phases = Phases()
phases.append(phase)
parameters = CWParams.default()
parameters.length_a = 8.56
parameters.length_c = 6.12
parameters.length_b = 8.56
parameters.resolution_u = 0.1447
parameters.resolution_v = -0.4252
parameters.resolution_w = 0.3864
parameters.resolution_x = 0.0
parameters.resolution_y = 0.0
pattern = Powder1DParameters.default()
pattern.zero_shift = 0.0
def phasesAsCif(self, phases_as_cif):
if self._phases_as_cif == phases_as_cif:
return
self._sample.phases = Phases.from_cif_str(phases_as_cif)
def addSampleFromCif(self, cif_url):
cif_path = generalizePath(cif_url)
borg.stack.enabled = False
self._sample.phases = Phases.from_cif_file(cif_path)
borg.stack.enabled = True