def choose_entry(self):
self.refine = NXRefine(self.entry)
if 'peaks' in self.entry:
if self.layout.count() == 2:
self.insert_layout(1, self.parameters.grid(header=False))
self.insert_layout(2, self.action_buttons)
self.update_parameters()
else:
self.display_message("Calculating Angles",
"No peaks have been found in this entry")
def choose_entry(self):
self.refine = NXRefine(self.root['entry'])
if self.layout.count() == 2:
self.insert_layout(1, self.parameters.grid(header=False))
if sgtbx:
self.insert_layout(
2,
self.make_layout(self.import_button,
self.import_checkbox,
align='center'))
self.update_parameters()
def accept(self):
try:
if 'transform' in self.entry and not self.overwrite:
self.display_message(
"Preparing Transform",
f"Transform group already exists in {self.entry.nxname}")
return
if (self.mask and 'masked_transform' in self.entry
and not self.overwrite):
self.display_message(
"Preparing Transform",
"Masked transform group already exists in "
f"{self.entry.nxname}")
return
output_file = self.get_output_file()
settings_file = self.get_settings_file()
self.write_parameters(output_file, settings_file)
self.refine.prepare_transform(output_file)
if self.mask:
masked_output_file = self.get_output_file(mask=True)
self.refine.prepare_transform(masked_output_file, mask=True)
self.refine.write_settings(settings_file)
if self.copy:
root = self.entry.nxroot
for entry in [
e for e in root
if e != 'entry' and e != self.entry.nxname
]:
if 'transform' in root[entry] and not self.overwrite:
self.display_message(
"Preparing Transform",
f"Transform group already exists in {entry}")
return
if (self.mask and 'masked_transform' in root[entry]
and not self.overwrite):
self.display_message(
"Preparing Transform",
f"Masked transform group already exists in {entry}"
)
return
self.refine = NXRefine(root[entry])
output_file = self.get_output_file(entry=root[entry])
settings_file = self.get_settings_file(entry=root[entry])
self.write_parameters(output_file, settings_file)
self.refine.prepare_transform(output_file)
if self.mask:
masked_output_file = self.get_output_file(
mask=True, entry=root[entry])
self.refine.prepare_transform(masked_output_file,
mask=True)
self.refine.write_settings(settings_file)
super().accept()
except NeXusError as error:
report_error("Preparing Data Transform", error)
def initialize_grid(self):
self.refine = NXRefine(self.entry)
self.refine.initialize_grid()
self.start_h_box.setText('%g' % self.refine.h_start)
self.step_h_box.setText('%g' % self.refine.h_step)
self.stop_h_box.setText('%g' % self.refine.h_stop)
self.start_k_box.setText('%g' % self.refine.k_start)
self.step_k_box.setText('%g' % self.refine.k_step)
self.stop_k_box.setText('%g' % self.refine.k_stop)
self.start_l_box.setText('%g' % self.refine.l_start)
self.step_l_box.setText('%g' % self.refine.l_step)
self.stop_l_box.setText('%g' % self.refine.l_stop)
def accept(self):
try:
if 'transform' in self.entry and not self.overwrite:
self.display_message(
'Preparing Transform',
'Transform group already exists in %s' % self.entry.nxname)
return
if self.mask and 'masked_transform' in self.entry and not self.overwrite:
self.display_message(
'Preparing Transform',
'Masked transform group already exists in %s' %
self.entry.nxname)
return
output_file = self.get_output_file()
settings_file = self.get_settings_file()
self.write_parameters(output_file, settings_file)
self.refine.prepare_transform(output_file)
if self.mask:
masked_output_file = self.get_output_file(mask=True)
self.refine.prepare_transform(masked_output_file, mask=True)
self.refine.write_settings(settings_file)
if self.copy:
root = self.entry.nxroot
for entry in [
e for e in root
if e != 'entry' and e != self.entry.nxname
]:
if 'transform' in root[entry] and not self.overwrite:
self.display_message(
'Preparing Transform',
'Transform group already exists in %s' % entry)
return
if self.mask and 'masked_transform' in root[
entry] and not self.overwrite:
self.display_message(
'Preparing Transform',
'Masked transform group already exists in %s' %
entry)
return
self.refine = NXRefine(root[entry])
output = output_file.replace(self.entry.nxname, entry)
settings = settings_file.replace(self.entry.nxname, entry)
self.write_parameters(output, settings)
self.refine.prepare_transform(output)
if self.mask:
output = masked_output_file.replace(
self.entry.nxname, entry)
self.refine.prepare_transform(output, mask=True)
self.refine.write_settings(settings)
super(TransformDialog, self).accept()
except NeXusError as error:
report_error("Preparing Data Transform", error)
def __init__(self, parent=None):
super(TransformDialog, self).__init__(parent)
self.select_entry(self.initialize_grid)
self.refine = NXRefine()
grid = QtWidgets.QGridLayout()
grid.setSpacing(10)
header_font = QtGui.QFont()
header_font.setBold(True)
start_label = QtWidgets.QLabel('Start')
start_label.setFont(header_font)
grid.addWidget(start_label, 0, 1)
step_label = QtWidgets.QLabel('Step')
step_label.setFont(header_font)
grid.addWidget(step_label, 0, 2)
stop_label = QtWidgets.QLabel('Stop')
stop_label.setFont(header_font)
grid.addWidget(stop_label, 0, 3)
grid.addWidget(QtWidgets.QLabel('H:'), 1, 0)
grid.addWidget(QtWidgets.QLabel('K:'), 2, 0)
grid.addWidget(QtWidgets.QLabel('L:'), 3, 0)
self.start_h_box = QtWidgets.QLineEdit()
self.step_h_box = QtWidgets.QLineEdit()
self.stop_h_box = QtWidgets.QLineEdit()
grid.addWidget(self.start_h_box, 1, 1)
grid.addWidget(self.step_h_box, 1, 2)
grid.addWidget(self.stop_h_box, 1, 3)
self.start_k_box = QtWidgets.QLineEdit()
self.step_k_box = QtWidgets.QLineEdit()
self.stop_k_box = QtWidgets.QLineEdit()
grid.addWidget(self.start_k_box, 2, 1)
grid.addWidget(self.step_k_box, 2, 2)
grid.addWidget(self.stop_k_box, 2, 3)
self.start_l_box = QtWidgets.QLineEdit()
self.step_l_box = QtWidgets.QLineEdit()
self.stop_l_box = QtWidgets.QLineEdit()
grid.addWidget(self.start_l_box, 3, 1)
grid.addWidget(self.step_l_box, 3, 2)
grid.addWidget(self.stop_l_box, 3, 3)
self.set_layout(
self.entry_layout, grid,
self.checkboxes(
('copy', 'Copy to all entries', True),
('mask', 'Create masked transform group', True),
('overwrite', 'Overwrite existing transforms', False)),
self.close_buttons(save=True))
self.setWindowTitle('Transforming Data')
try:
self.initialize_grid()
except Exception:
pass
def __init__(self, parent=None):
super().__init__(parent)
self.select_root(self.choose_entry)
self.refine = NXRefine()
self.parameters = GridParameters()
self.parameters.add('space_group',
self.refine.space_group,
'Space Group',
slot=self.set_groups)
self.parameters.add('laue_group', self.refine.laue_groups,
'Laue Group')
self.parameters.add('symmetry',
self.refine.symmetries,
'Symmetry',
slot=self.set_lattice_parameters)
self.parameters.add('centring', self.refine.centrings, 'Cell Centring')
self.parameters.add('a',
self.refine.a,
'Unit Cell - a (Ang)',
slot=self.set_lattice_parameters)
self.parameters.add('b',
self.refine.b,
'Unit Cell - b (Ang)',
slot=self.set_lattice_parameters)
self.parameters.add('c',
self.refine.c,
'Unit Cell - c (Ang)',
slot=self.set_lattice_parameters)
self.parameters.add('alpha',
self.refine.alpha,
'Unit Cell - alpha (deg)',
slot=self.set_lattice_parameters)
self.parameters.add('beta',
self.refine.beta,
'Unit Cell - beta (deg)',
slot=self.set_lattice_parameters)
self.parameters.add('gamma',
self.refine.gamma,
'Unit Cell - gamma (deg)',
slot=self.set_lattice_parameters)
self.parameters['laue_group'].value = self.refine.laue_group
self.parameters['symmetry'].value = self.refine.symmetry
self.parameters['centring'].value = self.refine.centring
self.import_button = NXPushButton('Import CIF', self.import_cif)
self.import_checkbox = NXCheckBox('Update Lattice Parameters')
self.set_layout(self.root_layout, self.close_buttons(save=True))
self.set_title('Defining Lattice')
def choose_entry(self):
if self.layout.count() == 2:
self.insert_layout(1, self.parameters.grid_layout)
self.insert_layout(2, self.find_layout)
self.reduce = NXReduce(self.entry)
self.refine = NXRefine(self.entry)
self.refine.polar_max = self.refine.two_theta_max()
if self.reduce.first is not None:
self.parameters['first'].value = self.reduce.first
if self.reduce.last:
self.parameters['last'].value = self.reduce.last
else:
try:
self.parameters['last'].value = self.reduce.shape[0]
except Exception:
pass
self.parameters['threshold'].value = self.reduce.threshold
def __init__(self, parent=None):
super().__init__(parent)
self.select_entry(self.choose_entry)
self.refine = NXRefine()
self.parameters = GridParameters()
self.parameters.add('wavelength', self.refine.wavelength,
'Wavelength (Ang)')
self.parameters.add('distance', self.refine.distance,
'Detector Distance (mm)')
self.parameters.add('xc', self.refine.xc, 'Beam Center - x')
self.parameters.add('yc', self.refine.yc, 'Beam Center - y')
self.parameters.add('pixel', self.refine.pixel_size, 'Pixel Size (mm)')
self.action_buttons = self.action_buttons(
('Plot', self.plot_lattice), ('Save', self.write_parameters))
self.set_layout(self.entry_layout, self.close_buttons())
self.set_title('Calculate Angles')
def choose_entry(self):
try:
refine = NXRefine(self.entry)
if refine.xp is None:
raise NeXusError("No peaks in entry")
except NeXusError as error:
report_error("Refining Lattice", error)
return
self.refine = refine
if self.layout.count() == 2:
self.insert_layout(1, self.Qgrid)
self.insert_layout(
2,
self.checkboxes(('copy', 'Copy to all entries', True),
('mask', 'Create masked transforms', True),
('overwrite', 'Overwrite transforms', False)))
self.refine.initialize_grid()
self.update_grid()
def choose_entry(self):
try:
refine = NXRefine(self.entry)
if refine.xp is None:
raise NeXusError("No peaks in entry")
except NeXusError as error:
report_error("Refining Lattice", error)
return
self.refine = refine
self.set_title(f"Refining {self.refine.name}")
if self.layout.count() == 2:
self.insert_layout(1, self.parameters.grid_layout)
self.insert_layout(2, self.refine_buttons)
self.insert_layout(3, self.orientation_buttons)
self.insert_layout(4, self.parameters.report_layout())
self.insert_layout(5, self.lattice_buttons)
self.update_parameters()
self.update_table()
def __init__(self, parent=None):
super(LatticeDialog, self).__init__(parent)
self.select_entry(self.choose_entry)
self.refine = NXRefine()
self.parameters = GridParameters()
self.parameters.add('symmetry',
self.refine.symmetries,
'Symmetry',
slot=self.set_lattice_parameters)
self.parameters.add('centring', self.refine.centrings, 'Cell Centring')
self.parameters.add('a',
self.refine.a,
'Unit Cell - a (Ang)',
slot=self.set_lattice_parameters)
self.parameters.add('b',
self.refine.b,
'Unit Cell - b (Ang)',
slot=self.set_lattice_parameters)
self.parameters.add('c',
self.refine.c,
'Unit Cell - c (Ang)',
slot=self.set_lattice_parameters)
self.parameters.add('alpha',
self.refine.alpha,
'Unit Cell - alpha (deg)',
slot=self.set_lattice_parameters)
self.parameters.add('beta',
self.refine.beta,
'Unit Cell - beta (deg)',
slot=self.set_lattice_parameters)
self.parameters.add('gamma',
self.refine.gamma,
'Unit Cell - gamma (deg)',
slot=self.set_lattice_parameters)
self.parameters['symmetry'].value = self.refine.symmetry
self.parameters['centring'].value = self.refine.centring
action_buttons = self.action_buttons(('Plot', self.plot_lattice),
('Save', self.write_parameters))
self.set_layout(self.entry_layout, self.parameters.grid(),
action_buttons, self.close_buttons())
self.set_title('Defining Lattice')
def __init__(self, parent=None):
super(OrientationDialog, self).__init__(parent)
self.select_entry(self.choose_entry)
self.refine = NXRefine(self.entry)
self.refine.read_parameters()
self.parameters = GridParameters()
self.parameters.add('phi_start', self.refine.phi, 'Phi Start (deg)')
self.parameters.add('phi_step', self.refine.phi_step, 'Phi Step (deg)')
self.parameters.add('chi', self.refine.chi, 'Chi (deg)')
self.parameters.add('omega', self.refine.omega, 'Omega (deg)')
self.parameters.add('polar', self.refine.polar_max,
'Max. Polar Angle (deg)')
self.parameters.add('polar_tolerance', self.refine.polar_tolerance,
'Polar Angle Tolerance')
self.parameters.add('peak_tolerance', self.refine.peak_tolerance,
'Peak Angle Tolerance')
action_buttons = self.action_buttons(
('Generate Grains', self.generate_grains),
('List Peaks', self.list_peaks))
self.grain_layout = QtWidgets.QHBoxLayout()
self.grain_combo = QtWidgets.QComboBox()
self.grain_combo.setSizeAdjustPolicy(
QtWidgets.QComboBox.AdjustToContents)
self.grain_combo.currentIndexChanged.connect(self.set_grain)
self.grain_textbox = QtWidgets.QLabel()
self.grain_layout.addWidget(self.grain_combo)
self.grain_layout.addStretch()
self.grain_layout.addWidget(self.grain_textbox)
bottom_layout = QtWidgets.QHBoxLayout()
self.result_textbox = QtWidgets.QLabel()
bottom_layout.addWidget(self.result_textbox)
bottom_layout.addStretch()
bottom_layout.addWidget(self.close_buttons())
self.set_layout(self.entry_layout, self.parameters.grid(),
action_buttons, bottom_layout)
self.set_title('Defining Orientation')
def choose_entry(self):
self.refine = NXRefine(self.entry)
self.update_parameters()
def __init__(self, parent=None):
super(RefineLatticeDialog, self).__init__(parent)
self.select_entry(self.choose_entry)
self.refine = NXRefine()
self.parameters = GridParameters()
self.parameters.add('symmetry', self.refine.symmetries, 'Symmetry',
None, self.set_lattice_parameters)
self.parameters.add('a',
self.refine.a,
'Unit Cell - a (Ang)',
False,
slot=self.set_lattice_parameters)
self.parameters.add('b',
self.refine.b,
'Unit Cell - b (Ang)',
False,
slot=self.set_lattice_parameters)
self.parameters.add('c',
self.refine.c,
'Unit Cell - c (Ang)',
False,
slot=self.set_lattice_parameters)
self.parameters.add('alpha',
self.refine.alpha,
'Unit Cell - alpha (deg)',
False,
slot=self.set_lattice_parameters)
self.parameters.add('beta',
self.refine.beta,
'Unit Cell - beta (deg)',
False,
slot=self.set_lattice_parameters)
self.parameters.add('gamma',
self.refine.gamma,
'Unit Cell - gamma (deg)',
False,
slot=self.set_lattice_parameters)
self.parameters.add('wavelength', self.refine.wavelength,
'Wavelength (Ang)', False)
self.parameters.add('distance', self.refine.distance, 'Distance (mm)',
False)
self.parameters.add('yaw', self.refine.yaw, 'Yaw (deg)', False)
self.parameters.add('pitch', self.refine.pitch, 'Pitch (deg)', False)
self.parameters.add('roll', self.refine.roll, 'Roll (deg)')
self.parameters.add('xc', self.refine.xc, 'Beam Center - x', False)
self.parameters.add('yc', self.refine.yc, 'Beam Center - y', False)
self.parameters.add('phi', self.refine.phi, 'Phi Start (deg)', False)
self.parameters.add('phi_step', self.refine.phi_step, 'Phi Step (deg)')
self.parameters.add('chi', self.refine.chi, 'Chi (deg)', False)
self.parameters.add('omega', self.refine.omega, 'Omega (deg)', False)
self.parameters.add('twotheta', self.refine.twotheta,
'Two Theta (deg)')
self.parameters.add('gonpitch', self.refine.gonpitch,
'Goniometer Pitch (deg)', False)
self.parameters.add('polar', self.refine.polar_max,
'Max. Polar Angle (deg)', None, self.set_polar_max)
self.parameters.add('polar_tolerance', self.refine.polar_tolerance,
'Polar Angle Tolerance')
self.parameters.add('peak_tolerance', self.refine.peak_tolerance,
'Peak Angle Tolerance')
self.set_symmetry()
self.refine_buttons = self.action_buttons(
('Refine Angles', self.refine_angles),
('Refine HKLs', self.refine_hkls),
('Restore', self.restore_parameters),
('Reset', self.reset_parameters))
self.orientation_button = self.action_buttons(
('Refine Orientation Matrix', self.refine_orientation))
self.lattice_buttons = self.action_buttons(
('Plot', self.plot_lattice), ('List', self.list_peaks),
('Save', self.write_parameters))
self.set_layout(self.entry_layout, self.parameters.grid(),
self.refine_buttons, self.orientation_button,
self.parameters.report_layout(), self.lattice_buttons,
self.close_layout())
self.parameters.grid_layout.setVerticalSpacing(1)
self.layout.setSpacing(2)
self.set_title('Refining Lattice')
self.peaks_box = None
self.table_model = None
self.fit_report = []
def choose_entry(self):
self.refine = NXRefine(self.entry)
self.update_parameters()
if self.peaks_box:
self.update_table()