def parse_formulas(self, text):
self.parameters_dictionary.clear()
is_empty = False
try:
congruence.checkEmptyString(text, "")
except:
is_empty = True
if not is_empty:
lines = text.splitlines()
for i in range(len(lines)):
is_line_empty = False
try:
congruence.checkEmptyString(lines[i], "")
except:
is_line_empty = True
if not is_line_empty:
data = lines[i].strip().split("=")
if len(data) != 2: raise ValueError("Free Output Parameters, malformed line:" + str(i+1))
name = data[0].strip()
expression = data[1].strip()
self.set_parameter_expression(name, expression)
def create_fitter(cls,
fitter_name=FitterName.MINPACK,
additional_data=None):
congruence.checkEmptyString(fitter_name, "Fitter Name")
if fitter_name == FitterName.MINPACK:
return FitterMinpack()
else:
raise ValueError("Fitter name <" + fitter_name +
"> not recognized")
def append_fit_initialization(self):
if self.use_structure == 0:
crystal_structure = CrystalStructure.init_cube(a0=self.widget.populate_parameter_in_widget(self, "a", self.get_parameters_prefix()),
symmetry=self.cb_symmetry.currentText(),
progressive=self.get_parameter_progressive())
self.widget.fit_global_parameters.fit_initialization.crystal_structures.append(crystal_structure)
self.widget.fit_global_parameters.evaluate_functions() # in case that a is a function of other parameters
crystal_structure.parse_reflections(self.reflections, progressive=self.get_parameter_progressive())
elif self.use_structure == 1:
crystal_structure = CrystalStructure.init_cube(a0=self.widget.populate_parameter_in_widget(self, "a", self.get_parameters_prefix()),
symmetry=self.cb_symmetry.currentText(),
use_structure=True,
formula=congruence.checkEmptyString(self.formula, "Chemical Formula"),
intensity_scale_factor=self.widget.populate_parameter_in_widget(self, "intensity_scale_factor", self.get_parameters_prefix()),
progressive=self.get_parameter_progressive())
self.widget.fit_global_parameters.fit_initialization.crystal_structures.append(crystal_structure)
self.widget.fit_global_parameters.evaluate_functions() # in case that a is a function of other parameters
crystal_structure.parse_reflections(self.reflections, progressive=self.get_parameter_progressive())
#intensities will be ignored
for reflection in crystal_structure.get_reflections():
reflection.intensity.fixed = True
if not self.widget.fit_global_parameters.fit_initialization is None \
and not self.widget.fit_global_parameters.fit_initialization.diffraction_patterns is None:
diffraction_pattern = self.widget.fit_global_parameters.fit_initialization.diffraction_patterns[self.index]
if not diffraction_pattern.wavelength.function:
wavelength = diffraction_pattern.wavelength.value
s_min = diffraction_pattern.get_diffraction_point(0).s
s_max = diffraction_pattern.get_diffraction_point(-1).s
excluded_reflections = crystal_structure.get_congruence_check(wavelength=wavelength,
min_value=s_min,
max_value=s_max)
if not excluded_reflections is None:
text_before = "The following reflections lie outside the diffraction pattern nr " + str(self.index+1) + ":"
text = ""
for reflection in excluded_reflections:
text += "[" + str(reflection.h) + ", " + str(reflection.k) + ", " + str(reflection.l) +"]\n"
text_after = "Proceed anyway?"
if not ConfirmTextDialog.confirm_text("Confirm Structure", text,
text_after=text_after, text_before=text_before,
width=350, parent=self): return
return crystal_structure
def set_data(self, crystal_structure):
self.widget.populate_fields_in_widget(self, "a", crystal_structure.a)
self.use_structure = 1 if crystal_structure.use_structure else 0
if self.use_structure == 0:
existing_crystal_structure = CrystalStructure.init_cube(
a0=self.widget.populate_parameter_in_widget(
self, "a", self.get_parameters_prefix()),
symmetry=self.cb_symmetry.currentText(),
progressive=self.get_parameter_progressive())
elif self.use_structure == 1:
self.widget.populate_fields_in_widget(
self, "intensity_scale_factor",
crystal_structure.intensity_scale_factor)
existing_crystal_structure = CrystalStructure.init_cube(
a0=self.widget.populate_parameter_in_widget(
self, "a", self.get_parameters_prefix()),
symmetry=self.cb_symmetry.currentText(),
use_structure=True,
formula=congruence.checkEmptyString(self.formula,
"Chemical Formula"),
intensity_scale_factor=self.widget.
populate_parameter_in_widget(self, "intensity_scale_factor",
self.get_parameters_prefix()),
progressive=self.get_parameter_progressive())
if not self.text_area.toPlainText().strip() == "":
existing_crystal_structure.parse_reflections(
self.text_area.toPlainText(),
progressive=self.get_parameter_progressive())
simmetries = Symmetry.tuple()
for index in range(0, len(simmetries)):
if simmetries[index] == crystal_structure.symmetry:
self.symmetry = index
for reflection in crystal_structure.get_reflections():
existing_reflection = existing_crystal_structure.existing_reflection(
reflection.h, reflection.k, reflection.l)
if existing_reflection is None:
existing_crystal_structure.add_reflection(reflection)
else:
existing_reflection.intensity.value = reflection.intensity.value
text = ""
for reflection in existing_crystal_structure.get_reflections():
text += reflection.to_row() + "\n"
self.text_area.setText(text)
def parse_reflections(self, text, progressive=""):
congruence.checkEmptyString(text, "Reflections")
lines = text.splitlines()
reflections = []
for i in range(len(lines)):
congruence.checkEmptyString(lines[i],
"Reflections: line " + str(i + 1))
if not lines[i].strip().startswith("#"):
data = lines[i].strip().split(",")
if len(data) < 4:
raise ValueError("Reflections, malformed line: " +
str(i + 1))
h = int(data[0].strip())
k = int(data[1].strip())
l = int(data[2].strip())
if ":=" in data[3].strip():
intensity_data = data[3].strip().split(":=")
if len(intensity_data) == 2:
intensity_name = intensity_data[0].strip()
function_value = intensity_data[1].strip()
else:
intensity_name = None
function_value = data[3].strip()
if intensity_name is None:
intensity_name = CrystalStructure.get_parameters_prefix(
) + progressive + "I" + str(h) + str(k) + str(l)
elif not intensity_name.startswith(
CrystalStructure.get_parameters_prefix()):
intensity_name = CrystalStructure.get_parameters_prefix(
) + progressive + intensity_name
reflection = Reflection(h,
k,
l,
intensity=FitParameter(
parameter_name=intensity_name,
function=True,
function_value=function_value))
else:
intensity_data = data[3].strip().split()
if len(intensity_data) == 2:
intensity_name = intensity_data[0].strip()
intensity_value = float(intensity_data[1])
else:
intensity_name = None
intensity_value = float(data[3])
boundary = None
fixed = False
if len(data) > 4:
min_value = PARAM_HWMIN
max_value = PARAM_HWMAX
for j in range(4, len(data)):
boundary_data = data[j].strip().split()
if boundary_data[0] == "min":
min_value = float(boundary_data[1].strip())
elif boundary_data[0] == "max":
max_value = float(boundary_data[1].strip())
elif boundary_data[0] == "fixed":
fixed = True
if not fixed:
if min_value != PARAM_HWMIN or max_value != PARAM_HWMAX:
boundary = Boundary(min_value=min_value,
max_value=max_value)
else:
boundary = Boundary()
if intensity_name is None:
intensity_name = CrystalStructure.get_parameters_prefix(
) + progressive + "I" + str(h) + str(k) + str(l)
elif not intensity_name.startswith(
CrystalStructure.get_parameters_prefix()):
intensity_name = CrystalStructure.get_parameters_prefix(
) + progressive + intensity_name
reflection = Reflection(h,
k,
l,
intensity=FitParameter(
parameter_name=intensity_name,
value=intensity_value,
fixed=fixed,
boundary=boundary))
reflections.append(reflection)
self.reflections = reflections
self.update_reflections()
