def get_hkl(self,
x_array: np.ndarray = None,
idx=0,
phase_name=None,
encoded_name=False) -> dict:
# Do we need to re-run a calculation to get the HKL's
do_run = False
old_x = self.additional_data.get("ivar", np.array(()))
if not np.array_equal(old_x, x_array):
do_run = True
if do_run and x_array is not None:
_ = self.calculate(x_array)
# Collate and return
if phase_name is None:
known_phases = list(self.known_phases.values())
phase_name = known_phases[idx]
phase_data = self.additional_data.get(phase_name, {})
return phase_data.get(
"hkl",
{
"ttheta": np.array([]),
"h": np.array([]),
"k": np.array([]),
"l": np.array([]),
},
)
def polarized_update(func, crystals, profiles, peak_dat, scales, x_str):
up = np.array([profile.intensity_up_total for profile in profiles])
down = np.array([profile.intensity_down_total for profile in profiles])
dependent = np.array([func(u, d) for u, d in zip(up, down)])
output = {}
for idx, profile in enumerate(profiles):
output.update({
crystals[idx].data_name: {
"hkl": {
x_str: getattr(peak_dat[idx], "numpy_" + x_str),
"h": peak_dat[idx].numpy_index_h,
"k": peak_dat[idx].numpy_index_k,
"l": peak_dat[idx].numpy_index_l,
},
"profile": scales[idx] * dependent[idx, :] / normalization,
"components": {
"total": dependent[idx, :],
"up": up[idx, :],
"down": down[idx, :],
},
"profile_scale": scales[idx],
"func": func,
}
})
return dependent, output
def get_parameters(self) -> List[Parameter]:
""""
Redefine get_parameters so that the returned values are in the correct order
"""
list_pars = np.array(super(PointBackground, self).get_parameters())
idx = np.array([item.x.raw_value for item in self]).argsort()
return list_pars[idx].tolist()
def __init__(self,
name: str = 'Series',
x: Union[np.ndarray, list] = None,
y: Union[np.ndarray, list] = None,
e: Union[np.ndarray, list] = None,
data_type: str = 'simulation',
x_label: str = 'x',
y_label: str = 'y'):
if not isinstance(data_type, str):
raise AttributeError
self._datatype = None
self.data_type = data_type
if x is None:
x = np.array([])
if y is None:
y = np.array([])
if e is None:
e = np.zeros_like(x)
self.name = name
if not isinstance(x, np.ndarray):
x = np.array(x)
if not isinstance(y, np.ndarray):
y = np.array(y)
self.x = x
self.y = y
self.e = e
self.x_label = x_label
self.y_label = y_label
self._color = None
def __index_contents(self):
"""
Index the contents
"""
x = np.array([item.power.raw_value for item in self])
idx = x.argsort()
y = np.array([item.amp.raw_value for item in self])
self._sorted_self = {'idx': idx, 'power': x[idx], 'amp': y[idx]}
def y_sorted_points(self) -> np.ndarray:
"""
Get the stored y-values based on the sorted x-values
:return: Sorted y-values
:rtype: np.ndarray
"""
idx = np.array([item.x.raw_value for item in self]).argsort()
y = np.array([item.y.raw_value for item in self])
return y[idx]
def _setAsXml(self):
start_time = timeit.default_timer()
if self._background_as_obj is None:
self._background_as_xml = dicttoxml({}, attr_type=False).decode()
else:
background = np.array([item.as_dict() for item in self._background_as_obj])
point_index = np.array([item.x.raw_value for item in self._background_as_obj]).argsort()
self._background_as_xml = dicttoxml(background[point_index], attr_type=False).decode()
print("+ _setAsXml: {0:.3f} s".format(timeit.default_timer() - start_time))
self.asXmlChanged.emit()
def nonPolarized_update(crystal_name,
diffraction_pattern,
reflection_list,
job_info,
scales=1):
dependent = diffraction_pattern.ycalc
hkltth = np.array([[*reflection_list[i].hkl, reflection_list[i].stl]
for i in range(reflection_list.nref)])
output = {
crystal_name: {
"hkl": {
"ttheta":
np.rad2deg(np.arcsin(hkltth[:, 3] * job_info.lambdas[0])) *
2,
"h":
hkltth[:, 0],
"k":
hkltth[:, 1],
"l":
hkltth[:, 2],
},
"profile": scales * dependent,
"components": {
"total": dependent
},
"profile_scale": scales,
}
}
return dependent, output
def x_sorted_points(self) -> np.ndarray:
"""
Get the stored x-values as a sorted array
:return: Sorted x-values
:rtype: np.ndarray
"""
x = np.array([item.x.raw_value for item in self])
x.sort()
return x
def _parse_operator(self, obj: V, *args, **kwargs) -> Number:
value = obj.raw_value
if isinstance(value, list):
value = np.array(value)
self.aeval.symtable["value1"] = value
self.aeval.symtable["value2"] = self.value
try:
self.aeval.eval(f"value3 = value1 {self.operator} value2")
logic = self.aeval.symtable["value3"]
if isinstance(logic, np.ndarray):
value[not logic] = self.aeval.symtable["value2"]
else:
if not logic:
value = self.aeval.symtable["value2"]
except Exception as e:
raise e
finally:
self.aeval.symtable.clear()
return value
def nonPolarized_update(crystals, profiles, peak_dat, scales, x_str):
dependent = np.array([profile.intensity_total for profile in profiles])
output = {}
for idx, profile in enumerate(profiles):
output.update({
crystals[idx].data_name: {
"hkl": {
x_str: getattr(peak_dat[idx], "numpy_" + x_str),
"h": peak_dat[idx].numpy_index_h,
"k": peak_dat[idx].numpy_index_k,
"l": peak_dat[idx].numpy_index_l,
},
"profile": scales[idx] * dependent[idx, :] / normalization,
"components": {
"total": dependent[idx, :]
},
"profile_scale": scales[idx],
}
})
return dependent, output
def _feature_generator(radiation='N', exp_type='CW', sample_type='powder', dimensionality='1D'):
radiation_options = exp_type_strings['radiation_options']
if radiation not in radiation_options:
raise AttributeError(f'"{radiation}" is not supported, only: {radiation_options}')
exp_type_options = exp_type_strings['exp_type_options']
if exp_type not in exp_type_options:
raise AttributeError(f'"{exp_type}" is not supported, only: {exp_type_options}')
dimensional_options = exp_type_strings['dimensional_options']
if dimensionality not in dimensional_options:
raise AttributeError(f'"{dimensionality}" is not supported, only: {dimensional_options}')
sample_options = exp_type_strings['sample_options']
if sample_type not in sample_options:
raise AttributeError(f'"{sample_type}" is not supported, only: {sample_options}')
features = [''.join(item) for item in np.array(np.meshgrid(radiation_options,
sample_options,
dimensional_options,
exp_type_options)).T.reshape(-1,
len(exp_type_strings)).tolist()]
feature_dict = dict.fromkeys(features, False)
return feature_dict
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")
ax1.legend()
axprops['sharex'] = ax1
# axprops['sharey'] = ax1
# force x axes to remain in register, even with toolbar navigation
ax2 = fig.add_axes([0.1, 0.1, 0.8, 0.4], **axprops)
ax2.plot(x_data, y_data2, label="Cryspy")
ax2.legend()
fig.show()
fig.savefig('CFML_Cryspy.png')
def fit(self,
fitter,
*args,
fit_kwargs: dict = None,
fn_kwargs: dict = None,
vectorize: bool = False,
dask: str = 'forbidden',
**kwargs) -> FitResults:
"""
Perform a fit on the given DataArray. This fit utilises a given fitter from `easyCore.Fitting.Fitter`, though
there are a few differences to a standard easyCore fit. In particular, key-word arguments to control the
optimisation algorithm go in the `fit_kwargs` dictionary, fit function key-word arguments go in the `fn_kwargs`
and given key-word arguments control the `xarray.apply_ufunc` function.
:param fitter: Fitting object which controls the fitting
:type fitter: easyCore.Fitting.Fitter
:param args: Arguments to go to the fit function
:type args: Any
:param dask: Dask control string. See `xarray.apply_ufunc` documentation
:type dask: str
:param fit_kwargs: Dictionary of key-word arguments to be supplied to the Fitting control
:type fit_kwargs: dict
:param fn_kwargs: Dictionary of key-words to be supplied to the fit function
:type fn_kwargs: dict
:param vectorize: Should the fit function be given dependents in a single object or split
:type vectorize: bool
:param kwargs: Key-word arguments for `xarray.apply_ufunc`. See `xarray.apply_ufunc` documentation
:type kwargs: Any
:return: Results of the fit
:rtype: FitResults
"""
# Deal with any kwargs which has been given
if fn_kwargs is None:
fn_kwargs = {}
if fit_kwargs is None:
fit_kwargs = {}
old_fit_func = fitter.fit_function
# Wrap and broadcast
bdims, f = self.fit_prep(fitter.fit_function)
dims = self._obj.dims
# Find which coords we need
if isinstance(dims, dict):
dims = list(dims.keys())
# Wrap the wrap in a callable
def local_fit_func(x, *args, **kwargs):
"""
Function which will be called by the fitter. This will deal with sending the function the correct data.
"""
kwargs['vectorize'] = vectorize
res = xr.apply_ufunc(f,
*bdims,
*args,
dask=dask,
kwargs=fn_kwargs,
**kwargs)
if dask != 'forbidden':
res.compute()
return res.stack(all_x=dims)
# Set the new callable to the fitter and initialize
fitter.initialize(fitter.fit_object, local_fit_func)
# Make easyCore.Fitting.Fitter compatible `x`
x_for_fit = xr.concat(bdims, dim='fit_dim')
x_for_fit = x_for_fit.stack(all_x=[d.name for d in bdims])
try:
# Deal with any sigmas if supplied
if fit_kwargs.get('weights', None) is not None:
fit_kwargs['weights'] = xr.DataArray(
np.array(fit_kwargs['weights']),
dims=['all_x'],
coords={'all_x': x_for_fit.all_x})
# Try to perform a fit
f_res = fitter.fit(x_for_fit, self._obj.stack(all_x=dims),
**fit_kwargs)
f_res = check_sanity_single(f_res)
finally:
# Reset the fit function on the fitter to the old fit function.
fitter.fit_function = old_fit_func
return f_res
def add_variable(self,
variable_name,
variable_coordinates: Union[str, List[str]],
variable_values: Union[List[T_], np.ndarray],
variable_sigma: Union[List[T_], np.ndarray] = None,
unit: str = '',
auto_sigma: bool = False):
"""
Create a DataArray from known coordinates and data, assign it to the dataset under a given name. Variances can
be calculated assuming gaussian distribution to 1 sigma.
:param variable_name: Name of the DataArray which will be created and added to the dataset
:type variable_name: str
:param variable_coordinates: List of coordinates used in the supplied data array.
:type variable_coordinates: str, List[str]
:param variable_values: Numpy or list of data which will be assigned to the DataArray
:type variable_values: Union[numpy.ndarray, list]
:param variable_sigma: If the sigmas of the dataset are known, they can be supplied here.
:type variable_sigma: Union[numpy.ndarray, list]
:param unit: Unit associated with the DataArray
:type unit: str
:param auto_sigma: Should the sigma DataArray be automatically calculated assuming gaussian probability?
:type auto_sigma: bool
:return: None
:rtype: None
"""
# Check if a user has supplied a coordinate as a string. Make it a list of strings
if isinstance(variable_coordinates, str):
variable_coordinates = [variable_coordinates]
# The variable_coordinates can be any iterable object. Though we would assume list/tuple
if not isinstance(variable_coordinates, Iterable):
raise ValueError(
'The variable coordinates must be a list of strings')
# Check to see if the user want to assign a coordinate which does not exist yet.
known_keys = self._obj.coords.keys()
for dimension in variable_coordinates:
if dimension not in known_keys:
raise ValueError(
f'The supplied coordinate `{dimension}` must first be defined.'
)
# Create the dataset.
self._obj[variable_name] = (variable_coordinates, variable_values)
# Deal with sigmas
if variable_sigma is not None:
# CASE 1, user has supplied sigmas
if isinstance(variable_sigma, Callable):
# CASE 1-1, The sigmas are created by some kind of generator
self.sigma_generator(variable_name, variable_sigma)
elif isinstance(variable_sigma, np.ndarray):
# CASE 1-2, The sigmas are a numpy arrays
self.sigma_attach(variable_name, variable_sigma)
elif isinstance(variable_sigma, list):
# CASE 1-3, We have been given a list. Make it a numpy array
self.sigma_attach(variable_name, np.array(variable_sigma))
else:
raise ValueError(
'User supplied sigmas must be of the form; Callable fn, numpy array, list'
)
else:
# CASE 2, No sigmas have been supplied.
if auto_sigma:
# CASE 2-1, Automatically generate the sigmas using gaussian probability
self.sigma_generator(variable_name)
# Set units for the newly created DataArray
self._obj.attrs['units'][variable_name] = ureg.Unit(unit)
# If a sigma has been attached, attempt to work out the units.
if unit and variable_sigma is None and auto_sigma:
self._obj.attrs['units'][self.sigma_label_prefix +
variable_name] = ureg.Unit(unit +
' ** 0.5')
else:
if auto_sigma:
self._obj.attrs['units'][self.sigma_label_prefix +
variable_name] = ureg.Unit('')
def _loadProject(self):
"""
"""
path = generalizePath(self.project_load_filepath)
if not os.path.isfile(path):
print("Failed to find project: '{0}'".format(path))
return
with open(path, 'r') as xml_file:
descr: dict = json.load(xml_file)
interface_name = descr.get('interface', None)
if interface_name is not None:
old_interface_name = self._interface.current_interface_name
if old_interface_name != interface_name:
self._interface.switch(interface_name)
self._sample = Sample.from_dict(descr['sample'])
self._sample.interface = self._interface
# send signal to tell the proxy we changed phases
self.phasesEnabled.emit()
self.phasesAsObjChanged.emit()
self.structureParametersChanged.emit()
# experiment
if 'experiments' in descr:
self.experimentLoaded(True)
self.experimentSkipped(False)
self._data.experiments[0].x = np.array(descr['experiments'][0])
self._data.experiments[0].y = np.array(descr['experiments'][1])
self._data.experiments[0].e = np.array(descr['experiments'][2])
self._experiment_data = self._data.experiments[0]
self.experiments = [{'name': descr['project_info']['experiments']}]
self.setCurrentExperimentDatasetName(
descr['project_info']['experiments'])
# send signal to tell the proxy we changed experiment
self.experimentDataAdded.emit()
self.parametersChanged.emit()
self.experimentLoadedChanged.emit()
else:
# delete existing experiment
self.removeExperiment()
self.experimentLoaded(False)
if descr['experiment_skipped']:
self.experimentSkipped(True)
self.experimentSkippedChanged.emit()
# project info
self._project_info = descr['project_info']
new_minimizer_settings = descr.get('minimizer', None)
if new_minimizer_settings is not None:
new_engine = new_minimizer_settings['engine']
new_method = new_minimizer_settings['method']
new_engine_index = self.parent.minimizerNames().index(new_engine)
self.currentMinimizerIndex.emit(new_engine_index)
new_method_index = self.parent.minimizerMethodNames().index(
new_method)
self.currentMinimizerMethodIndex.emit(new_method_index)
self.parent.fitLogic.fitter.fit_object = self._sample
self.resetUndoRedoStack.emit()
self.setProjectCreated(True)