class RefineLatticeDialog(BaseDialog):
def __init__(self, parent=None):
super(RefineLatticeDialog, self).__init__(parent)
self.select_entry(self.choose_entry)
self.refine = NXRefine(self.entry)
self.refine.read_parameters()
self.parameters = GridParameters()
self.parameters.add('symmetry', self.refine.symmetries, 'Symmetry',
None, self.set_symmetry)
self.parameters.add('a', self.refine.a, 'Unit Cell - a (Ang)', True)
self.parameters.add('b', self.refine.b, 'Unit Cell - b (Ang)', True)
self.parameters.add('c', self.refine.c, 'Unit Cell - c (Ang)', True)
self.parameters.add('alpha', self.refine.alpha, 'Unit Cell - alpha (deg)', False)
self.parameters.add('beta', self.refine.beta, 'Unit Cell - beta (deg)', False)
self.parameters.add('gamma', self.refine.gamma, 'Unit Cell - gamma (deg)', False)
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_start', self.refine.phi_start, 'Phi Start (deg)', False)
self.parameters.add('phi_step', self.refine.phi_step, 'Phi Step (deg)')
self.parameters.add('chi_start', self.refine.chi_start, 'Chi Start (deg)', False)
self.parameters.add('chi_step', self.refine.chi_step, 'Chi Step (deg)')
self.parameters.add('omega_start', self.refine.omega_start, 'Omega Start (deg)', False)
self.parameters.add('omega_step', self.refine.omega_step, 'Omega Step (deg)')
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.parameters.add('orientation_matrix', False, 'Orientation Matrix', False)
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.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.lattice_buttons,
self.close_buttons())
self.parameters.grid_layout.setVerticalSpacing(1)
self.set_title('Refining Lattice')
self.parameters['symmetry'].value = self.refine.symmetry
self.set_symmetry()
self.peaks_box = None
def choose_entry(self):
self.refine = NXRefine(self.entry)
self.update_parameters()
def update_parameters(self):
self.parameters['a'].value = self.refine.a
self.parameters['b'].value = self.refine.b
self.parameters['c'].value = self.refine.c
self.parameters['alpha'].value = self.refine.alpha
self.parameters['beta'].value = self.refine.beta
self.parameters['gamma'].value = self.refine.gamma
self.parameters['wavelength'].value = self.refine.wavelength
self.parameters['distance'].value = self.refine.distance
self.parameters['yaw'].value = self.refine.yaw
self.parameters['pitch'].value = self.refine.pitch
self.parameters['roll'].value = self.refine.roll
self.parameters['xc'].value = self.refine.xc
self.parameters['yc'].value = self.refine.yc
self.parameters['phi_start'].value = self.refine.phi_start
self.parameters['phi_step'].value = self.refine.phi_step
self.parameters['chi_start'].value = self.refine.chi_start
self.parameters['chi_step'].value = self.refine.chi_step
self.parameters['omega_start'].value = self.refine.omega_start
self.parameters['omega_step'].value = self.refine.omega_step
self.parameters['polar'].value = self.refine.polar_max
self.parameters['polar_tolerance'].value = self.refine.polar_tolerance
try:
self.refine.polar_angles, self.refine.azimuthal_angles = \
self.refine.calculate_angles(self.refine.xp, self.refine.yp)
except Exception:
pass
def transfer_parameters(self):
self.refine.a, self.refine.b, self.refine.c, \
self.refine.alpha, self.refine.beta, self.refine.gamma = \
self.get_lattice_parameters()
self.refine.set_symmetry()
self.refine.wavelength = self.get_wavelength()
self.refine.distance = self.get_distance()
self.refine.yaw, self.refine.pitch, self.refine.roll = self.get_tilts()
self.refine.xc, self.refine.yc = self.get_centers()
self.refine.phi_start, self.refine.phi_step = self.get_phi()
self.refine.chi_start, self.refine.chi_step = self.get_chi()
self.refine.omega_start, self.refine.omega_step = self.get_omega()
self.refine.polar_max = self.get_polar_max()
self.refine.polar_tol = self.get_tolerance()
self.refine.polar_angles
def write_parameters(self):
self.transfer_parameters()
polar_angles, azimuthal_angles = self.refine.calculate_angles(
self.refine.xp, self.refine.yp)
self.refine.write_angles(polar_angles, azimuthal_angles)
self.refine.write_parameters()
def get_symmetry(self):
return self.parameters['symmetry'].value
def set_symmetry(self):
self.refine.symmetry = self.get_symmetry()
self.refine.set_symmetry()
self.update_parameters()
if self.refine.symmetry == 'cubic':
self.parameters['b'].vary = False
self.parameters['c'].vary = False
self.parameters['alpha'].vary = False
self.parameters['beta'].vary = False
self.parameters['gamma'].vary = False
elif self.refine.symmetry == 'tetragonal':
self.parameters['b'].vary = False
self.parameters['alpha'].vary = False
self.parameters['beta'].vary = False
self.parameters['gamma'].vary = False
elif self.refine.symmetry == 'orthorhombic':
self.parameters['alpha'].vary = False
self.parameters['beta'].vary = False
self.parameters['gamma'].vary = False
elif self.refine.symmetry == 'hexagonal':
self.parameters['b'].vary = False
self.parameters['alpha'].vary = False
self.parameters['beta'].vary = False
self.parameters['gamma'].vary = False
elif self.refine.symmetry == 'monoclinic':
self.parameters['alpha'].vary = False
self.parameters['gamma'].vary = False
def get_lattice_parameters(self):
return (self.parameters['a'].value,
self.parameters['b'].value,
self.parameters['c'].value,
self.parameters['alpha'].value,
self.parameters['beta'].value,
self.parameters['gamma'].value)
def get_wavelength(self):
return self.parameters['wavelength'].value
def get_distance(self):
return self.parameters['distance'].value
def get_tilts(self):
return (self.parameters['yaw'].value,
self.parameters['pitch'].value,
self.parameters['roll'].value)
def get_centers(self):
return self.parameters['xc'].value, self.parameters['yc'].value
def get_polar_max(self):
return self.parameters['polar'].value
def set_polar_max(self):
self.refine.polar_max = self.get_polar_max()
def get_tolerance(self):
return self.parameters['polar_tolerance'].value
def get_phi(self):
return (self.parameters['phi_start'].value,
self.parameters['phi_step'].value)
def get_chi(self):
return (self.parameters['chi_start'].value,
self.parameters['chi_step'].value)
def get_omega(self):
return (self.parameters['omega_start'].value,
self.parameters['omega_step'].value)
def get_hkl_tolerance(self):
try:
return np.float32(self.tolerance_box.text())
except Exception:
return self.refine.hkl_tolerance
def plot_lattice(self):
self.transfer_parameters()
self.set_polar_max()
self.plot_peaks()
self.plot_rings()
def plot_peaks(self):
try:
x, y = self.refine.xp[self.refine.idx], self.refine.yp[self.refine.idx]
polar_angles, azimuthal_angles = self.refine.calculate_angles(x, y)
if polar_angles[0] > polar_angles[-1]:
polar_angles = polar_angles[::-1]
azimuthal_angles = azimuthal_angles[::-1]
azimuthal_field = NXfield(azimuthal_angles, name='azimuthal_angle')
azimuthal_field.long_name = 'Azimuthal Angle'
polar_field = NXfield(polar_angles, name='polar_angle')
polar_field.long_name = 'Polar Angle'
plotview = get_plotview()
plotview.plot(NXdata(azimuthal_field, polar_field, title='Peak Angles'))
except NeXusError as error:
report_error('Plotting Lattice', error)
def plot_rings(self, polar_max=None):
if polar_max is None:
polar_max = self.refine.polar_max
peaks = self.refine.calculate_rings(polar_max)
plotview = get_plotview()
plotview.vlines(peaks, colors='r', linestyles='dotted')
plotview.draw()
def plot_peak(self, i):
x, y, z = self.refine.xp[i], self.refine.yp[i], self.refine.zp[i]/10.0
xmin, xmax = max(0,int(x)-200), min(int(x)+200,data.v.shape[2])
ymin, ymax = max(0,int(y)-200), min(int(y)+200,data.v.shape[1])
zmin, zmax = max(0.0,z-20.0), min(z+20.0, 360.0)
xslab=np.s_[zmin:zmax,ymin:ymax,x]
yslab=np.s_[zmin:zmax,y,xmin:xmax]
zslab=np.s_[z,ymin:ymax,xmin:xmax]
pvz.plot(data[zslab], log=True)
pvz.crosshairs(x, y)
pvy.plot(data[yslab], log=True)
pvy.crosshairs(x, z)
pvx.plot(data[xslab], log=True)
pvx.crosshairs(y, z)
def refine_angles(self):
self.parameters['orientation_matrix'].vary = False
self.parameters['phi_start'].vary = False
self.parameters['chi_start'].vary = False
self.parameters['omega_start'].vary = False
self.parameters.refine_parameters(self.angle_residuals)
self.update_parameters()
def angle_residuals(self, p):
self.parameters.get_parameters(p)
self.transfer_parameters()
polar_angles, _ = self.refine.calculate_angles(self.refine.x, self.refine.y)
rings = self.refine.calculate_rings()
residuals = np.array([find_nearest(rings, polar_angle) - polar_angle
for polar_angle in polar_angles])
return np.sum(residuals**2)
def refine_hkls(self):
self.parameters.refine_parameters(self.hkl_residuals)
self.update_parameters()
if self.peaks_box is None:
self.list_peaks()
else:
self.update_table()
def hkl_residuals(self, p):
self.parameters.get_parameters(p)
self.transfer_parameters()
return self.refine.score(self.refine.idx)
def restore_parameters(self):
self.parameters.restore_parameters()
self.transfer_parameters()
def reset_parameters(self):
self.refine.read_parameters()
self.update_parameters()
def list_peaks(self):
if self.peaks_box is not None:
self.update_table()
return
self.peaks_box = BaseDialog(self)
self.peaks_box.setMinimumWidth(600)
self.peaks_box.setMinimumHeight(600)
header = ['i', 'x', 'y', 'z', 'Polar', 'Azi', 'Intensity',
'H', 'K', 'L', 'Diff']
peak_list = self.refine.get_peaks()
self.refine.assign_rings()
self.rings = self.refine.get_ring_hkls()
orient_layout = QtGui.QHBoxLayout()
if self.refine.primary is None:
self.refine.primary = 0
if self.refine.secondary is None:
self.refine.secondary = 1
self.primary_box = QtGui.QLineEdit(str(self.refine.primary))
self.primary_box.setAlignment(QtCore.Qt.AlignRight)
self.primary_box.setFixedWidth(80)
self.secondary_box = QtGui.QLineEdit(str(self.refine.secondary))
self.secondary_box.setAlignment(QtCore.Qt.AlignRight)
self.secondary_box.setFixedWidth(80)
orient_button = QtGui.QPushButton('Orient')
orient_button.clicked.connect(self.orient)
orient_layout.addStretch()
orient_layout.addWidget(QtGui.QLabel('Primary'))
orient_layout.addWidget(self.primary_box)
orient_layout.addWidget(QtGui.QLabel('Secondary'))
orient_layout.addWidget(self.secondary_box)
orient_layout.addStretch()
orient_layout.addWidget(orient_button)
self.table_view = QtGui.QTableView()
self.table_model = NXTableModel(self, peak_list, header)
self.table_view.setModel(self.table_model)
self.table_view.resizeColumnsToContents()
self.table_view.horizontalHeader().stretchLastSection()
self.table_view.setSelectionBehavior(QtGui.QAbstractItemView.SelectRows)
self.table_view.doubleClicked.connect(self.plot_peak)
self.table_view.setSortingEnabled(True)
self.table_view.sortByColumn(0, QtCore.Qt.AscendingOrder)
layout = QtGui.QVBoxLayout()
layout.addLayout(orient_layout)
layout.addWidget(self.table_view)
close_layout = QtGui.QHBoxLayout()
self.status_text = QtGui.QLabel('Score: %.4f' % self.refine.score())
self.tolerance_box = QtGui.QLineEdit(str(self.refine.hkl_tolerance))
self.tolerance_box.setAlignment(QtCore.Qt.AlignRight)
self.tolerance_box.setMaxLength(5)
self.tolerance_box.editingFinished.connect(self.update_table)
self.tolerance_box.setFixedWidth(80)
save_button = QtGui.QPushButton('Save Orientation')
save_button.clicked.connect(self.save_orientation)
close_button = QtGui.QPushButton('Close Window')
close_button.clicked.connect(self.close_peaks_box)
close_layout.addWidget(self.status_text)
close_layout.addStretch()
close_layout.addWidget(QtGui.QLabel('Threshold'))
close_layout.addWidget(self.tolerance_box)
close_layout.addStretch()
close_layout.addWidget(save_button)
close_layout.addStretch()
close_layout.addWidget(close_button)
layout.addLayout(close_layout)
self.peaks_box.setLayout(layout)
self.peaks_box.setWindowTitle('%s Peak Table' % self.entry.nxtitle)
self.peaks_box.adjustSize()
self.peaks_box.show()
self.plotview = None
def update_table(self):
self.transfer_parameters()
self.refine.hkl_tolerance = self.get_hkl_tolerance()
self.table_model.peak_list = self.refine.get_peaks()
rows, columns = len(self.table_model.peak_list), 11
self.table_model.dataChanged.emit(self.table_model.createIndex(0, 0),
self.table_model.createIndex(rows-1, columns-1))
self.status_text.setText('Score: %.4f' % self.refine.score())
def plot_peak(self):
row = self.table_view.currentIndex().row()
data = self.entry.data
x, y, z = [self.table_view.model().peak_list[row][i] for i in range(1, 4)]
xmin, xmax = max(0,x-200), min(x+200,data.nxsignal.shape[2])
ymin, ymax = max(0,y-200), min(y+200,data.nxsignal.shape[1])
zmin, zmax = max(0,z-200), min(z+200,data.nxsignal.shape[0])
zslab=np.s_[z,ymin:ymax,xmin:xmax]
if self.plotview is None:
self.plotview = NXPlotView('X-Y Projection')
self.plotview.plot(data[zslab], log=True)
self.plotview.crosshairs(x, y)
def orient(self):
self.refine.primary = int(self.primary_box.text())
self.refine.secondary = int(self.secondary_box.text())
self.refine.Umat = self.refine.get_UBmat(self.refine.primary,
self.refine.secondary) \
* self.refine.Bimat
self.update_table()
def save_orientation(self):
self.write_parameters()
def close_peaks_box(self):
self.peaks_box.close()
self.peaks_box = None
class RefineLatticeDialog(BaseDialog):
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()
def report_score(self):
try:
self.status_message.setText('Score: %.4f' % self.refine.score())
except Exception as error:
pass
def update_parameters(self):
self.parameters['a'].value = self.refine.a
self.parameters['b'].value = self.refine.b
self.parameters['c'].value = self.refine.c
self.parameters['alpha'].value = self.refine.alpha
self.parameters['beta'].value = self.refine.beta
self.parameters['gamma'].value = self.refine.gamma
self.parameters['wavelength'].value = self.refine.wavelength
self.parameters['distance'].value = self.refine.distance
self.parameters['yaw'].value = self.refine.yaw
self.parameters['pitch'].value = self.refine.pitch
self.parameters['roll'].value = self.refine.roll
self.parameters['xc'].value = self.refine.xc
self.parameters['yc'].value = self.refine.yc
self.parameters['phi'].value = self.refine.phi
self.parameters['phi_step'].value = self.refine.phi_step
self.parameters['chi'].value = self.refine.chi
self.parameters['omega'].value = self.refine.omega
self.parameters['twotheta'].value = self.refine.twotheta
self.parameters['gonpitch'].value = self.refine.gonpitch
self.parameters['polar'].value = self.refine.polar_max
self.parameters['polar_tolerance'].value = self.refine.polar_tolerance
self.parameters['symmetry'].value = self.refine.symmetry
try:
self.refine.polar_angles, self.refine.azimuthal_angles = \
self.refine.calculate_angles(self.refine.xp, self.refine.yp)
except Exception:
pass
self.report_score()
def transfer_parameters(self):
self.refine.a, self.refine.b, self.refine.c, \
self.refine.alpha, self.refine.beta, self.refine.gamma = \
self.get_lattice_parameters()
self.refine.set_symmetry()
self.refine.wavelength = self.get_wavelength()
self.refine.distance = self.get_distance()
self.refine.yaw, self.refine.pitch, self.refine.roll = self.get_tilts()
self.refine.xc, self.refine.yc = self.get_centers()
self.refine.phi, self.refine.phi_step = self.get_phi()
self.refine.chi, self.refine.omega, self.refine.twotheta, \
self.refine.gonpitch = self.get_angles()
self.refine.polar_max = self.get_polar_max()
self.refine.polar_tol = self.get_tolerance()
def write_parameters(self):
self.transfer_parameters()
polar_angles, azimuthal_angles = self.refine.calculate_angles(
self.refine.xp, self.refine.yp)
self.refine.write_angles(polar_angles, azimuthal_angles)
self.refine.write_parameters()
reduce = NXReduce(self.entry)
reduce.record('nxrefine', fit_report='\n'.join(self.fit_report))
root = self.entry.nxroot
entries = [entry for entry in root.entries if entry != 'entry']
if entries and self.confirm_action(
'Copy orientation to other entries? (%s)' %
(', '.join(entries))):
om = self.entry['instrument/detector/orientation_matrix']
for entry in entries:
root[entry]['instrument/detector/orientation_matrix'] = om
def get_symmetry(self):
return self.parameters['symmetry'].value
def set_symmetry(self):
self.refine.symmetry = self.get_symmetry()
self.refine.set_symmetry()
self.update_parameters()
if self.refine.symmetry == 'cubic':
self.parameters['b'].vary = False
self.parameters['c'].vary = False
self.parameters['alpha'].vary = False
self.parameters['beta'].vary = False
self.parameters['gamma'].vary = False
elif self.refine.symmetry == 'tetragonal':
self.parameters['b'].vary = False
self.parameters['alpha'].vary = False
self.parameters['beta'].vary = False
self.parameters['gamma'].vary = False
elif self.refine.symmetry == 'orthorhombic':
self.parameters['alpha'].vary = False
self.parameters['beta'].vary = False
self.parameters['gamma'].vary = False
elif self.refine.symmetry == 'hexagonal':
self.parameters['b'].vary = False
self.parameters['alpha'].vary = False
self.parameters['beta'].vary = False
self.parameters['gamma'].vary = False
elif self.refine.symmetry == 'monoclinic':
self.parameters['alpha'].vary = False
self.parameters['gamma'].vary = False
def get_lattice_parameters(self):
return (self.parameters['a'].value, self.parameters['b'].value,
self.parameters['c'].value, self.parameters['alpha'].value,
self.parameters['beta'].value, self.parameters['gamma'].value)
def set_lattice_parameters(self):
symmetry = self.get_symmetry()
if symmetry == 'cubic':
self.parameters['b'].value = self.parameters['a'].value
self.parameters['c'].value = self.parameters['a'].value
self.parameters['alpha'].value = 90.0
self.parameters['beta'].value = 90.0
self.parameters['gamma'].value = 90.0
self.parameters['a'].enable(vary=True)
self.parameters['b'].disable(vary=False)
self.parameters['c'].disable(vary=False)
self.parameters['alpha'].disable(vary=False)
self.parameters['beta'].disable(vary=False)
self.parameters['gamma'].disable(vary=False)
elif symmetry == 'tetragonal':
self.parameters['b'].value = self.parameters['a'].value
self.parameters['alpha'].value = 90.0
self.parameters['beta'].value = 90.0
self.parameters['gamma'].value = 90.0
self.parameters['a'].enable(vary=True)
self.parameters['b'].disable(vary=False)
self.parameters['c'].enable(vary=True)
self.parameters['alpha'].disable(vary=False)
self.parameters['beta'].disable(vary=False)
self.parameters['gamma'].disable(vary=False)
elif symmetry == 'orthorhombic':
self.parameters['alpha'].value = 90.0
self.parameters['beta'].value = 90.0
self.parameters['gamma'].value = 90.0
self.parameters['a'].enable(vary=True)
self.parameters['b'].enable(vary=True)
self.parameters['c'].enable(vary=True)
self.parameters['alpha'].disable(vary=False)
self.parameters['beta'].disable(vary=False)
self.parameters['gamma'].disable(vary=False)
elif symmetry == 'hexagonal':
self.parameters['b'].value = self.parameters['a'].value
self.parameters['alpha'].value = 90.0
self.parameters['beta'].value = 90.0
self.parameters['gamma'].value = 120.0
self.parameters['a'].enable(vary=True)
self.parameters['b'].disable(vary=False)
self.parameters['c'].enable(vary=True)
self.parameters['alpha'].disable(vary=False)
self.parameters['beta'].disable(vary=False)
self.parameters['gamma'].disable(vary=False)
elif symmetry == 'monoclinic':
self.parameters['alpha'].value = 90.0
self.parameters['gamma'].value = 90.0
self.parameters['a'].enable(vary=True)
self.parameters['b'].enable(vary=True)
self.parameters['c'].enable(vary=True)
self.parameters['alpha'].disable(vary=False)
self.parameters['beta'].enable(vary=True)
self.parameters['gamma'].disable(vary=False)
else:
self.parameters['a'].enable(vary=True)
self.parameters['b'].enable(vary=True)
self.parameters['c'].enable(vary=True)
self.parameters['alpha'].enable(vary=True)
self.parameters['beta'].enable(vary=True)
self.parameters['gamma'].enable(vary=True)
def get_wavelength(self):
return self.parameters['wavelength'].value
def get_distance(self):
return self.parameters['distance'].value
def get_tilts(self):
return (self.parameters['yaw'].value, self.parameters['pitch'].value,
self.parameters['roll'].value)
def get_centers(self):
return self.parameters['xc'].value, self.parameters['yc'].value
def get_phi(self):
return (self.parameters['phi'].value,
self.parameters['phi_step'].value)
def get_angles(self):
return (self.parameters['chi'].value, self.parameters['omega'].value,
self.parameters['twotheta'].value,
self.parameters['gonpitch'].value)
def get_polar_max(self):
return self.parameters['polar'].value
def set_polar_max(self):
self.refine.polar_max = self.get_polar_max()
def get_tolerance(self):
return self.parameters['polar_tolerance'].value
def get_hkl_tolerance(self):
try:
return np.float32(self.tolerance_box.text())
except Exception:
return self.refine.hkl_tolerance
def plot_lattice(self):
self.transfer_parameters()
self.set_polar_max()
self.plot_peaks()
self.plot_rings()
def plot_peaks(self):
try:
x, y = (self.refine.xp[self.refine.idx],
self.refine.yp[self.refine.idx])
polar_angles, azimuthal_angles = self.refine.calculate_angles(x, y)
if polar_angles[0] > polar_angles[-1]:
polar_angles = polar_angles[::-1]
azimuthal_angles = azimuthal_angles[::-1]
azimuthal_field = NXfield(azimuthal_angles, name='azimuthal_angle')
azimuthal_field.long_name = 'Azimuthal Angle'
polar_field = NXfield(polar_angles, name='polar_angle')
polar_field.long_name = 'Polar Angle'
plotview = get_plotview()
plotview.plot(
NXdata(azimuthal_field, polar_field, title='Peak Angles'))
except NeXusError as error:
report_error('Plotting Lattice', error)
def plot_rings(self, polar_max=None):
if polar_max is None:
polar_max = self.refine.polar_max
peaks = self.refine.calculate_rings(polar_max)
plotview = get_plotview()
plotview.vlines(peaks, colors='r', linestyles='dotted')
plotview.draw()
@property
def refined(self):
refined = {}
for p in self.parameters:
if self.parameters[p].vary:
refined[p] = True
return refined
def refine_angles(self):
self.parameters.status_message.setText('Fitting...')
self.parameters.status_message.repaint()
self.mainwindow.app.app.processEvents()
self.parameters['phi'].vary = False
self.transfer_parameters()
self.set_symmetry()
self.refine.refine_angles(**self.refined)
self.parameters.result = self.refine.result
self.parameters.fit_report = self.refine.fit_report
self.fit_report.append(self.refine.fit_report)
self.update_parameters()
self.parameters.status_message.setText(self.parameters.result.message)
if self.peaks_box and self.peaks_box.isVisible():
self.update_table()
def refine_hkls(self):
self.parameters.status_message.setText('Fitting...')
self.parameters.status_message.repaint()
self.mainwindow.app.app.processEvents()
self.set_symmetry()
self.transfer_parameters()
self.refine.refine_hkls(**self.refined)
self.parameters.result = self.refine.result
self.parameters.fit_report = self.refine.fit_report
self.fit_report.append(self.refine.fit_report)
self.update_parameters()
self.parameters.status_message.setText(self.parameters.result.message)
if self.peaks_box and self.peaks_box.isVisible():
self.update_table()
def refine_orientation(self):
self.parameters.status_message.setText('Fitting...')
self.parameters.status_message.repaint()
self.mainwindow.app.app.processEvents()
self.transfer_parameters()
self.refine.refine_orientation_matrix()
self.parameters.result = self.refine.result
self.parameters.fit_report = self.refine.fit_report
self.fit_report.append(self.refine.fit_report)
self.update_parameters()
self.parameters.status_message.setText(self.parameters.result.message)
if self.peaks_box and self.peaks_box.isVisible():
self.update_table()
def restore_parameters(self):
self.refine.restore_parameters()
self.update_parameters()
try:
self.fit_report.pop()
except IndexError:
pass
def reset_parameters(self):
self.refine.read_parameters()
self.update_parameters()
self.set_symmetry()
try:
self.fit_report.pop()
except IndexError:
pass
def list_peaks(self):
if self.peaks_box is not None and self.table_model is not None:
self.update_table()
return
self.peaks_box = BaseDialog(self)
self.peaks_box.setMinimumWidth(600)
self.peaks_box.setMinimumHeight(600)
header = [
'i', 'x', 'y', 'z', 'Polar', 'Azi', 'Intensity', 'H', 'K', 'L',
'Diff'
]
peak_list = self.refine.get_peaks()
self.refine.assign_rings()
self.rings = self.refine.get_ring_hkls()
orient_layout = QtWidgets.QHBoxLayout()
if self.refine.primary is None:
self.refine.primary = 0
if self.refine.secondary is None:
self.refine.secondary = 1
self.primary_box = QtWidgets.QLineEdit(str(self.refine.primary))
self.primary_box.setAlignment(QtCore.Qt.AlignRight)
self.primary_box.setFixedWidth(80)
self.secondary_box = QtWidgets.QLineEdit(str(self.refine.secondary))
self.secondary_box.setAlignment(QtCore.Qt.AlignRight)
self.secondary_box.setFixedWidth(80)
orient_button = QtWidgets.QPushButton('Orient')
orient_button.clicked.connect(self.orient)
orient_layout.addStretch()
orient_layout.addWidget(QtWidgets.QLabel('Primary'))
orient_layout.addWidget(self.primary_box)
orient_layout.addWidget(QtWidgets.QLabel('Secondary'))
orient_layout.addWidget(self.secondary_box)
orient_layout.addStretch()
orient_layout.addWidget(orient_button)
self.table_view = QtWidgets.QTableView()
self.table_model = NXTableModel(self, peak_list, header)
self.table_view.setModel(self.table_model)
self.table_view.resizeColumnsToContents()
self.table_view.horizontalHeader().stretchLastSection()
self.table_view.setSelectionBehavior(
QtWidgets.QAbstractItemView.SelectRows)
self.table_view.doubleClicked.connect(self.plot_peak)
self.table_view.setSortingEnabled(True)
self.table_view.sortByColumn(0, QtCore.Qt.AscendingOrder)
layout = QtWidgets.QVBoxLayout()
layout.addLayout(orient_layout)
layout.addWidget(self.table_view)
close_layout = QtWidgets.QHBoxLayout()
self.status_text = QtWidgets.QLabel('Score: %.4f' %
self.refine.score())
self.tolerance_box = QtWidgets.QLineEdit(str(
self.refine.hkl_tolerance))
self.tolerance_box.setAlignment(QtCore.Qt.AlignRight)
self.tolerance_box.setMaxLength(5)
self.tolerance_box.editingFinished.connect(self.update_table)
self.tolerance_box.setFixedWidth(80)
save_button = QtWidgets.QPushButton('Save Orientation')
save_button.clicked.connect(self.save_orientation)
close_button = QtWidgets.QPushButton('Close Window')
close_button.clicked.connect(self.close_peaks_box)
close_layout.addWidget(self.status_text)
close_layout.addStretch()
close_layout.addWidget(QtWidgets.QLabel('Threshold'))
close_layout.addWidget(self.tolerance_box)
close_layout.addStretch()
close_layout.addWidget(save_button)
close_layout.addStretch()
close_layout.addWidget(close_button)
layout.addLayout(close_layout)
self.peaks_box.setLayout(layout)
self.peaks_box.setWindowTitle('%s Peak Table' % self.entry.nxtitle)
self.peaks_box.adjustSize()
self.peaks_box.show()
self.plotview = None
def update_table(self):
if self.peaks_box is None:
self.list_peaks()
self.transfer_parameters()
self.refine.hkl_tolerance = self.get_hkl_tolerance()
self.table_model.peak_list = self.refine.get_peaks()
self.refine.assign_rings()
self.rings = self.refine.get_ring_hkls()
rows, columns = len(self.table_model.peak_list), 11
self.table_model.dataChanged.emit(
self.table_model.createIndex(0, 0),
self.table_model.createIndex(rows - 1, columns - 1))
self.table_view.resizeColumnsToContents()
self.status_text.setText('Score: %.4f' % self.refine.score())
self.peaks_box.setWindowTitle('%s Peak Table' % self.entry.nxtitle)
self.peaks_box.setVisible(True)
def plot_peak(self):
row = self.table_view.currentIndex().row()
data = self.entry.data
i, x, y, z = [
self.table_view.model().peak_list[row][i] for i in range(4)
]
signal = data.nxsignal
xmin, xmax = max(0, x - 200), min(x + 200, signal.shape[2])
ymin, ymax = max(0, y - 200), min(y + 200, signal.shape[1])
zmin, zmax = max(0, z - 20), min(z + 20, signal.shape[0])
zslab = np.s_[zmin:zmax, ymin:ymax, xmin:xmax]
if self.plotview is None:
self.plotview = NXPlotView('Peak Plot')
self.plotview.plot(data[zslab], log=True)
self.plotview.ax.set_title('%s: Peak %s' % (data.nxtitle, i))
self.plotview.ztab.maxbox.setValue(z)
self.plotview.aspect = 'equal'
self.plotview.crosshairs(x, y, color='r', linewidth=0.5)
def orient(self):
self.refine.primary = int(self.primary_box.text())
self.refine.secondary = int(self.secondary_box.text())
self.refine.Umat = (
self.refine.get_UBmat(self.refine.primary, self.refine.secondary) *
self.refine.Bimat)
self.update_table()
def save_orientation(self):
self.write_parameters()
def close_peaks_box(self):
self.peaks_box.close()
self.peaks_box = None
def list_orientations(self):
message_box = BaseDialog(self)
message_box.setMinimumWidth(600)
message_box.setMinimumHeight(600)
header = ['i', 'x', 'y', 'z', 'Polar', 'Azi', 'Intensity',
'H', 'K', 'L', 'Diff']
peak_list = self.refine.get_peaks()
self.refine.assign_rings()
self.rings = self.refine.get_ring_hkls()
orient_layout = QtWidgets.QHBoxLayout()
if self.refine.primary is None:
self.refine.primary = 0
if self.refine.secondary is None:
self.refine.secondary = 1
self.primary_box = QtWidgets.QLineEdit(str(self.refine.primary))
self.primary_box.setAlignment(QtCore.Qt.AlignRight)
self.primary_box.setFixedWidth(80)
self.secondary_box = QtWidgets.QLineEdit(str(self.refine.secondary))
self.secondary_box.setAlignment(QtCore.Qt.AlignRight)
self.secondary_box.setFixedWidth(80)
orient_button = QtWidgets.QPushButton('Orient')
orient_button.clicked.connect(self.orient)
refine_button = QtWidgets.QPushButton('Refine')
refine_button.clicked.connect(self.refine_orientation)
restore_button = QtWidgets.QPushButton('Restore')
restore_button.clicked.connect(self.restore_orientation)
orient_layout.addStretch()
orient_layout.addWidget(QtWidgets.QLabel('Primary'))
orient_layout.addWidget(self.primary_box)
orient_layout.addWidget(QtWidgets.QLabel('Secondary'))
orient_layout.addWidget(self.secondary_box)
orient_layout.addStretch()
orient_layout.addWidget(orient_button)
orient_layout.addWidget(refine_button)
orient_layout.addWidget(restore_button)
grid = QtWidgets.QGridLayout()
grid.setSpacing(10)
self.lattice = GridParameters()
self.lattice.add('a', self.refine.a, 'a', False)
self.lattice.add('b', self.refine.b, 'b', False)
self.lattice.add('c', self.refine.c, 'c', False)
self.lattice.add('alpha', self.refine.alpha, 'alpha', False)
self.lattice.add('beta', self.refine.beta, 'beta', False)
self.lattice.add('gamma', self.refine.gamma, 'gamma', False)
p = self.lattice['a']
p.box.setFixedWidth(80)
label, value, checkbox = p.label, p.value, p.vary
grid.addWidget(p.label, 0, 0, QtCore.Qt.AlignRight)
grid.addWidget(p.box, 0, 1, QtCore.Qt.AlignHCenter)
grid.addWidget(p.checkbox, 0, 2, QtCore.Qt.AlignHCenter)
p = self.lattice['b']
p.box.setFixedWidth(80)
label, value, checkbox = p.label, p.value, p.vary
grid.addWidget(p.label, 0, 3, QtCore.Qt.AlignRight)
grid.addWidget(p.box, 0, 4, QtCore.Qt.AlignHCenter)
grid.addWidget(p.checkbox, 0, 5, QtCore.Qt.AlignHCenter)
p = self.lattice['c']
p.box.setFixedWidth(80)
label, value, checkbox = p.label, p.value, p.vary
grid.addWidget(p.label, 0, 6, QtCore.Qt.AlignRight)
grid.addWidget(p.box, 0, 7, QtCore.Qt.AlignHCenter)
grid.addWidget(p.checkbox, 0, 8, QtCore.Qt.AlignHCenter)
p = self.lattice['alpha']
p.box.setFixedWidth(80)
label, value, checkbox = p.label, p.value, p.vary
grid.addWidget(p.label, 1, 0, QtCore.Qt.AlignRight)
grid.addWidget(p.box, 1, 1, QtCore.Qt.AlignHCenter)
grid.addWidget(p.checkbox, 1, 2, QtCore.Qt.AlignHCenter)
p = self.lattice['beta']
p.box.setFixedWidth(80)
label, value, checkbox = p.label, p.value, p.vary
grid.addWidget(p.label, 1, 3, QtCore.Qt.AlignRight)
grid.addWidget(p.box, 1, 4, QtCore.Qt.AlignHCenter)
grid.addWidget(p.checkbox, 1, 5, QtCore.Qt.AlignHCenter)
p = self.lattice['gamma']
p.box.setFixedWidth(80)
label, value, checkbox = p.label, p.value, p.vary
grid.addWidget(p.label, 1, 6, QtCore.Qt.AlignRight)
grid.addWidget(p.box, 1, 7, QtCore.Qt.AlignHCenter)
grid.addWidget(p.checkbox, 1, 8, QtCore.Qt.AlignHCenter)
self.table_view = QtWidgets.QTableView()
self.table_model = NXTableModel(self, peak_list, header)
self.table_view.setModel(self.table_model)
self.table_view.resizeColumnsToContents()
self.table_view.horizontalHeader().stretchLastSection()
self.table_view.setSelectionBehavior(QtWidgets.QAbstractItemView.SelectRows)
self.table_view.doubleClicked.connect(self.plot_peak)
self.table_view.setSortingEnabled(True)
self.table_view.sortByColumn(0, QtCore.Qt.AscendingOrder)
layout = QtWidgets.QVBoxLayout()
layout.addLayout(orient_layout)
layout.addLayout(grid)
layout.addWidget(self.table_view)
close_layout = QtWidgets.QHBoxLayout()
self.status_text = QtWidgets.QLabel('Score: %.4f' % self.refine.score())
self.tolerance_box = QtWidgets.QLineEdit(str(self.refine.hkl_tolerance))
self.tolerance_box.setAlignment(QtCore.Qt.AlignRight)
self.tolerance_box.setMaxLength(5)
self.tolerance_box.editingFinished.connect(self.update_table)
self.tolerance_box.setFixedWidth(80)
save_button = QtWidgets.QPushButton('Save Orientation')
save_button.clicked.connect(self.save_orientation)
close_button = QtWidgets.QPushButton('Close Window')
close_button.clicked.connect(message_box.close)
close_layout.addWidget(self.status_text)
close_layout.addStretch()
close_layout.addWidget(QtWidgets.QLabel('Threshold'))
close_layout.addWidget(self.tolerance_box)
close_layout.addStretch()
close_layout.addWidget(save_button)
close_layout.addStretch()
close_layout.addWidget(close_button)
layout.addLayout(close_layout)
message_box.setLayout(layout)
message_box.setWindowTitle('%s Peak Table' % self.entry.nxtitle)
message_box.adjustSize()
message_box.show()
self.plotview = None
def list_orientations(self):
message_box = BaseDialog(self)
message_box.setMinimumWidth(600)
message_box.setMinimumHeight(600)
header = [
'i', 'x', 'y', 'z', 'Polar', 'Azi', 'Intensity', 'H', 'K', 'L',
'Diff'
]
peak_list = self.refine.get_peaks()
self.refine.assign_rings()
self.rings = self.refine.get_ring_hkls()
orient_layout = QtWidgets.QHBoxLayout()
if self.refine.primary is None:
self.refine.primary = 0
if self.refine.secondary is None:
self.refine.secondary = 1
self.primary_box = QtWidgets.QLineEdit(str(self.refine.primary))
self.primary_box.setAlignment(QtCore.Qt.AlignRight)
self.primary_box.setFixedWidth(80)
self.secondary_box = QtWidgets.QLineEdit(str(self.refine.secondary))
self.secondary_box.setAlignment(QtCore.Qt.AlignRight)
self.secondary_box.setFixedWidth(80)
orient_button = QtWidgets.QPushButton('Orient')
orient_button.clicked.connect(self.orient)
refine_button = QtWidgets.QPushButton('Refine')
refine_button.clicked.connect(self.refine_orientation)
restore_button = QtWidgets.QPushButton('Restore')
restore_button.clicked.connect(self.restore_orientation)
orient_layout.addStretch()
orient_layout.addWidget(QtWidgets.QLabel('Primary'))
orient_layout.addWidget(self.primary_box)
orient_layout.addWidget(QtWidgets.QLabel('Secondary'))
orient_layout.addWidget(self.secondary_box)
orient_layout.addStretch()
orient_layout.addWidget(orient_button)
orient_layout.addWidget(refine_button)
orient_layout.addWidget(restore_button)
grid = QtWidgets.QGridLayout()
grid.setSpacing(10)
self.lattice = GridParameters()
self.lattice.add('a', self.refine.a, 'a', False)
self.lattice.add('b', self.refine.b, 'b', False)
self.lattice.add('c', self.refine.c, 'c', False)
self.lattice.add('alpha', self.refine.alpha, 'alpha', False)
self.lattice.add('beta', self.refine.beta, 'beta', False)
self.lattice.add('gamma', self.refine.gamma, 'gamma', False)
p = self.lattice['a']
p.box.setFixedWidth(80)
label, value, checkbox = p.label, p.value, p.vary
grid.addWidget(p.label, 0, 0, QtCore.Qt.AlignRight)
grid.addWidget(p.box, 0, 1, QtCore.Qt.AlignHCenter)
grid.addWidget(p.checkbox, 0, 2, QtCore.Qt.AlignHCenter)
p = self.lattice['b']
p.box.setFixedWidth(80)
label, value, checkbox = p.label, p.value, p.vary
grid.addWidget(p.label, 0, 3, QtCore.Qt.AlignRight)
grid.addWidget(p.box, 0, 4, QtCore.Qt.AlignHCenter)
grid.addWidget(p.checkbox, 0, 5, QtCore.Qt.AlignHCenter)
p = self.lattice['c']
p.box.setFixedWidth(80)
label, value, checkbox = p.label, p.value, p.vary
grid.addWidget(p.label, 0, 6, QtCore.Qt.AlignRight)
grid.addWidget(p.box, 0, 7, QtCore.Qt.AlignHCenter)
grid.addWidget(p.checkbox, 0, 8, QtCore.Qt.AlignHCenter)
p = self.lattice['alpha']
p.box.setFixedWidth(80)
label, value, checkbox = p.label, p.value, p.vary
grid.addWidget(p.label, 1, 0, QtCore.Qt.AlignRight)
grid.addWidget(p.box, 1, 1, QtCore.Qt.AlignHCenter)
grid.addWidget(p.checkbox, 1, 2, QtCore.Qt.AlignHCenter)
p = self.lattice['beta']
p.box.setFixedWidth(80)
label, value, checkbox = p.label, p.value, p.vary
grid.addWidget(p.label, 1, 3, QtCore.Qt.AlignRight)
grid.addWidget(p.box, 1, 4, QtCore.Qt.AlignHCenter)
grid.addWidget(p.checkbox, 1, 5, QtCore.Qt.AlignHCenter)
p = self.lattice['gamma']
p.box.setFixedWidth(80)
label, value, checkbox = p.label, p.value, p.vary
grid.addWidget(p.label, 1, 6, QtCore.Qt.AlignRight)
grid.addWidget(p.box, 1, 7, QtCore.Qt.AlignHCenter)
grid.addWidget(p.checkbox, 1, 8, QtCore.Qt.AlignHCenter)
self.table_view = QtWidgets.QTableView()
self.table_model = NXTableModel(self, peak_list, header)
self.table_view.setModel(self.table_model)
self.table_view.resizeColumnsToContents()
self.table_view.horizontalHeader().stretchLastSection()
self.table_view.setSelectionBehavior(
QtWidgets.QAbstractItemView.SelectRows)
self.table_view.doubleClicked.connect(self.plot_peak)
self.table_view.setSortingEnabled(True)
self.table_view.sortByColumn(0, QtCore.Qt.AscendingOrder)
layout = QtWidgets.QVBoxLayout()
layout.addLayout(orient_layout)
layout.addLayout(grid)
layout.addWidget(self.table_view)
close_layout = QtWidgets.QHBoxLayout()
self.status_text = QtWidgets.QLabel('Score: %.4f' %
self.refine.score())
self.tolerance_box = QtWidgets.QLineEdit(str(
self.refine.hkl_tolerance))
self.tolerance_box.setAlignment(QtCore.Qt.AlignRight)
self.tolerance_box.setMaxLength(5)
self.tolerance_box.editingFinished.connect(self.update_table)
self.tolerance_box.setFixedWidth(80)
save_button = QtWidgets.QPushButton('Save Orientation')
save_button.clicked.connect(self.save_orientation)
close_button = QtWidgets.QPushButton('Close Window')
close_button.clicked.connect(message_box.close)
close_layout.addWidget(self.status_text)
close_layout.addStretch()
close_layout.addWidget(QtWidgets.QLabel('Threshold'))
close_layout.addWidget(self.tolerance_box)
close_layout.addStretch()
close_layout.addWidget(save_button)
close_layout.addStretch()
close_layout.addWidget(close_button)
layout.addLayout(close_layout)
message_box.setLayout(layout)
message_box.setWindowTitle('%s Peak Table' % self.entry.nxtitle)
message_box.adjustSize()
message_box.show()
self.plotview = None