class FindDialog(NXDialog):
def __init__(self, parent=None):
super().__init__(parent)
self.select_entry(self.choose_entry)
default = NXSettings().settings['nxreduce']
self.parameters = GridParameters()
self.parameters.add('threshold', default['threshold'], 'Threshold')
self.parameters.add('first', default['first'], 'First Frame')
self.parameters.add('last', default['last'], 'Last Frame')
self.parameters.add('min_pixels', default['min_pixels'],
'Minimum Pixels in Peak')
self.parameters.grid()
self.find_button = NXPushButton('Find Peaks', self.find_peaks)
self.find_layout = self.make_layout(self.action_buttons(
('Find Peaks', self.find_peaks), ('List Peaks', self.list_peaks)),
align='center')
self.set_layout(self.entry_layout,
self.close_layout(save=True, progress=True))
self.set_title('Find Peaks')
self.reduce = None
self.refine = None
self.peaks_box = None
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
@property
def threshold(self):
try:
return int(self.parameters['threshold'].value)
except Exception as error:
report_error("Finding Peaks", error)
@property
def first(self):
try:
return int(self.parameters['first'].value)
except Exception as error:
report_error("Finding Peaks", error)
@property
def last(self):
try:
return int(self.parameters['last'].value)
except Exception as error:
report_error("Finding Peaks", error)
@property
def min_pixels(self):
try:
return int(self.parameters['min_pixels'].value)
except Exception as error:
report_error("Finding Peaks", error)
def find_peaks(self):
if is_file_locked(self.reduce.data_file):
return
self.start_thread()
self.reduce = NXReduce(self.entry,
threshold=self.threshold,
first=self.first,
last=self.last,
min_pixels=self.min_pixels,
find=True,
overwrite=True,
gui=True)
self.reduce.moveToThread(self.thread)
self.reduce.start.connect(self.start_progress)
self.reduce.update.connect(self.update_progress)
self.reduce.result.connect(self.get_peaks)
self.reduce.stop.connect(self.stop)
self.thread.started.connect(self.reduce.nxfind)
self.thread.start()
def get_peaks(self, peaks):
self.peaks = peaks
self.status_message.setText(f'{len(self.peaks)} peaks found')
self.status_message.setVisible(True)
self.refine.xp = np.array([peak.x for peak in peaks])
self.refine.yp = np.array([peak.y for peak in peaks])
self.refine.zp = np.array([peak.z for peak in peaks])
self.refine.intensity = np.array([peak.intensity for peak in peaks])
self.refine.polar_angle, self.refine.azimuthal_angle = (
self.refine.calculate_angles(self.refine.xp, self.refine.yp))
self.update_table()
def stop(self):
self.stop_progress()
if self.thread and self.thread.isRunning():
self.reduce.stopped = True
self.stop_thread()
def list_peaks(self):
if self.peaks_box in self.mainwindow.dialogs:
self.update_table()
return
self.peaks_box = NXDialog(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.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)
self.peaks_box.set_layout(self.table_view,
self.close_buttons(close=True))
self.peaks_box.set_title(f'{self.refine.name} Peak Table')
self.peaks_box.adjustSize()
self.peaks_box.show()
self.plotview = None
def update_table(self):
if self.peaks_box not in self.mainwindow.dialogs:
return
elif self.table_model is None:
self.close_peaks_box()
self.list_peaks()
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.table_view.resizeColumnsToContents()
self.peaks_box.set_title(f'{self.refine.name} Peak Table')
self.peaks_box.adjustSize()
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 'Peak Plot' in self.plotviews:
self.plotview = self.plotviews['Peak Plot']
else:
self.plotview = NXPlotView('Peak Plot')
self.plotview.plot(data[zslab], log=True)
self.plotview.ax.set_title(f'{data.nxtitle}: Peak {i}')
self.plotview.ztab.maxbox.setValue(z)
self.plotview.aspect = 'equal'
self.plotview.crosshairs(x, y, color='r', linewidth=0.5)
def close_peaks_box(self):
try:
self.peaks_box.close()
except Exception:
pass
self.peaks_box = None
def accept(self):
try:
self.reduce.write_peaks(self.peaks)
self.reduce.record('nxfind',
threshold=self.threshold,
first_frame=self.first,
last_frame=self.last,
min_pixels=self.min_pixels,
peak_number=len(self.peaks))
self.reduce.record_end('nxfind')
super().accept()
except Exception as error:
report_error("Finding Peaks", error)
def reject(self):
self.stop()
super().reject()
class OrientationDialog(BaseDialog):
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 update_parameters(self):
self.parameters['phi_start'].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['polar'].value = self.refine.polar_max
self.parameters['polar_tolerance'].value = self.refine.polar_tolerance
self.parameters['peak_tolerance'].value = self.refine.peak_tolerance
def get_phi(self):
return (self.parameters['phi_start'].value,
self.parameters['phi_step'].value)
def set_phi(self):
self.refine.phi_start, self.refine.phi_step = self.get_phi()
def get_chi(self):
return self.parameters['chi'].value
def set_chi(self):
self.refine.chi = self.get_chi()
def get_omega(self):
return self.parameters['omega'].value
def set_omega(self):
self.refine.omega = self.get_omega()
@property
def polar_max(self):
return self.parameters['polar'].value
def set_polar_max(self):
self.refine.polar_max = self.polar_max
def get_polar_tolerance(self):
return self.parameters['polar_tolerance'].value
def set_polar_tolerance(self):
self.refine.polar_tolerance = self.get_polar_tolerance()
def get_peak_tolerance(self):
return self.parameters['peak_tolerance'].value
def set_peak_tolerance(self):
self.refine.peak_tolerance = self.get_peak_tolerance()
def generate_grains(self):
self.set_polar_max()
self.refine.generate_grains()
if self.refine.grains is not None:
self.layout.insertLayout(2, self.grain_layout)
self.grain_combo.clear()
for i in range(len(self.refine.grains)):
self.grain_combo.addItem('Grain %s' % i)
self.grain_combo.setCurrentIndex(0)
self.set_grain()
def set_grain(self):
try:
grain = self.refine.grains[self.get_grain()]
self.grain_textbox.setText('%s peaks; Score: %.4f'
% (len(grain), grain.score))
self.refine.Umat = grain.Umat
self.refine.primary = grain.primary
self.refine.secondary = grain.secondary
self.get_score()
except:
self.grain_textbox.setText('')
def get_grain(self):
return int(self.grain_combo.currentText().split()[-1])
def list_peaks(self):
self.refine.phi = self.get_phi()
self.refine.chi = self.get_chi()
self.refine.omega = self.get_omega()
if self.refine.grains is not None:
grain = self.refine.grains[self.get_grain()]
self.refine.Umat = grain.Umat
self.list_orientations()
else:
self.list_orientations()
def get_score(self):
if self.refine.Umat is not None:
self.score = self.refine.score()
self.result_textbox.setText('%s peaks; Score: %.4f'
% (len(self.refine.idx), self.score))
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 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 refine_orientation(self):
idx = self.refine.idx
intensities = self.refine.intensity[idx]
sigma = np.average(intensities) / intensities
p0 = self.set_parameters(idx)
def diffs(p):
self.get_parameters(p)
UBimat = np.linalg.inv(self.refine.UBmat)
Q = [UBimat * self.Gvec[i] for i in idx]
dQ = Q - np.rint(Q)
return np.array([np.linalg.norm(self.refine.Bmat*np.matrix(dQ[i]))
for i in idx]) / sigma
popt, C, info, msg, success = leastsq(diffs, p0, full_output=1)
self.get_parameters(popt)
self.update_lattice()
self.update_table()
self.status_text.setText('Score: %.4f' % self.refine.score())
def restore_orientation(self):
self.refine.Umat = self.Umat
for par in self.lattice.values():
par.value = par.init_value
self.update_table()
def update_table(self):
self.refine.hkl_tolerance = np.float32(self.tolerance_box.text())
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 update_lattice(self):
self.lattice['a'].value = self.refine.a
self.lattice['b'].value = self.refine.b
self.lattice['c'].value = self.refine.c
self.lattice['alpha'].value = self.refine.alpha
self.lattice['beta'].value = self.refine.beta
self.lattice['gamma'].value = self.refine.gamma
def set_parameters(self, idx):
x, y, z = self.refine.xp[idx], self.refine.yp[idx], self.refine.zp[idx]
self.Gvec = [self.refine.Gvec(xx,yy,zz) for xx,yy,zz in zip(x,y,z)]
self.Umat = self.refine.Umat
pars = []
for par in self.lattice.values():
par.init_value = par.value
if par.vary:
pars.append(par.value)
p0 = np.zeros(shape=(len(pars)+9), dtype=np.float32)
p0[:len(pars)] = pars
p0[len(pars):] = np.ravel(self.refine.Umat)
return p0
def get_parameters(self, p):
i = 0
for par in self.lattice.values():
if par.vary:
par.value = p[i]
i += 1
self.refine.a, self.refine.b, self.refine.c, \
self.refine.alpha, self.refine.beta, self.refine.gamma = \
[par.value for par in self.lattice.values()]
self.refine.set_symmetry()
self.refine.Umat = np.matrix(p[i:]).reshape(3,3)
def save_orientation(self):
self.write_parameters()
def write_parameters(self):
try:
self.refine.write_parameters()
except NeXusError as error:
report_error('Defining Orientation', error)
class OrientationDialog(BaseDialog):
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 update_parameters(self):
self.parameters['phi_start'].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['polar'].value = self.refine.polar_max
self.parameters['polar_tolerance'].value = self.refine.polar_tolerance
self.parameters['peak_tolerance'].value = self.refine.peak_tolerance
def get_phi(self):
return (self.parameters['phi_start'].value,
self.parameters['phi_step'].value)
def set_phi(self):
self.refine.phi_start, self.refine.phi_step = self.get_phi()
def get_chi(self):
return self.parameters['chi'].value
def set_chi(self):
self.refine.chi = self.get_chi()
def get_omega(self):
return self.parameters['omega'].value
def set_omega(self):
self.refine.omega = self.get_omega()
@property
def polar_max(self):
return self.parameters['polar'].value
def set_polar_max(self):
self.refine.polar_max = self.polar_max
def get_polar_tolerance(self):
return self.parameters['polar_tolerance'].value
def set_polar_tolerance(self):
self.refine.polar_tolerance = self.get_polar_tolerance()
def get_peak_tolerance(self):
return self.parameters['peak_tolerance'].value
def set_peak_tolerance(self):
self.refine.peak_tolerance = self.get_peak_tolerance()
def generate_grains(self):
self.set_polar_max()
self.refine.generate_grains()
if self.refine.grains is not None:
self.layout.insertLayout(2, self.grain_layout)
self.grain_combo.clear()
for i in range(len(self.refine.grains)):
self.grain_combo.addItem('Grain %s' % i)
self.grain_combo.setCurrentIndex(0)
self.set_grain()
def set_grain(self):
try:
grain = self.refine.grains[self.get_grain()]
self.grain_textbox.setText('%s peaks; Score: %.4f' %
(len(grain), grain.score))
self.refine.Umat = grain.Umat
self.refine.primary = grain.primary
self.refine.secondary = grain.secondary
self.get_score()
except:
self.grain_textbox.setText('')
def get_grain(self):
return int(self.grain_combo.currentText().split()[-1])
def list_peaks(self):
self.refine.phi = self.get_phi()
self.refine.chi = self.get_chi()
self.refine.omega = self.get_omega()
if self.refine.grains is not None:
grain = self.refine.grains[self.get_grain()]
self.refine.Umat = grain.Umat
self.list_orientations()
else:
self.list_orientations()
def get_score(self):
if self.refine.Umat is not None:
self.score = self.refine.score()
self.result_textbox.setText('%s peaks; Score: %.4f' %
(len(self.refine.idx), self.score))
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 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 refine_orientation(self):
idx = self.refine.idx
intensities = self.refine.intensity[idx]
sigma = np.average(intensities) / intensities
p0 = self.set_parameters(idx)
def diffs(p):
self.get_parameters(p)
UBimat = np.linalg.inv(self.refine.UBmat)
Q = [UBimat * self.Gvec[i] for i in idx]
dQ = Q - np.rint(Q)
return np.array([
np.linalg.norm(self.refine.Bmat * np.matrix(dQ[i]))
for i in idx
]) / sigma
popt, C, info, msg, success = leastsq(diffs, p0, full_output=1)
self.get_parameters(popt)
self.update_lattice()
self.update_table()
self.status_text.setText('Score: %.4f' % self.refine.score())
def restore_orientation(self):
self.refine.Umat = self.Umat
for par in self.lattice.values():
par.value = par.init_value
self.update_table()
def update_table(self):
self.refine.hkl_tolerance = np.float32(self.tolerance_box.text())
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 update_lattice(self):
self.lattice['a'].value = self.refine.a
self.lattice['b'].value = self.refine.b
self.lattice['c'].value = self.refine.c
self.lattice['alpha'].value = self.refine.alpha
self.lattice['beta'].value = self.refine.beta
self.lattice['gamma'].value = self.refine.gamma
def set_parameters(self, idx):
x, y, z = self.refine.xp[idx], self.refine.yp[idx], self.refine.zp[idx]
self.Gvec = [
self.refine.Gvec(xx, yy, zz) for xx, yy, zz in zip(x, y, z)
]
self.Umat = self.refine.Umat
pars = []
for par in self.lattice.values():
par.init_value = par.value
if par.vary:
pars.append(par.value)
p0 = np.zeros(shape=(len(pars) + 9), dtype=np.float32)
p0[:len(pars)] = pars
p0[len(pars):] = np.ravel(self.refine.Umat)
return p0
def get_parameters(self, p):
i = 0
for par in self.lattice.values():
if par.vary:
par.value = p[i]
i += 1
self.refine.a, self.refine.b, self.refine.c, \
self.refine.alpha, self.refine.beta, self.refine.gamma = \
[par.value for par in self.lattice.values()]
self.refine.set_symmetry()
self.refine.Umat = np.matrix(p[i:]).reshape(3, 3)
def save_orientation(self):
self.write_parameters()
def write_parameters(self):
try:
self.refine.write_parameters()
except NeXusError as error:
report_error('Defining Orientation', error)
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
class RefineLatticeDialog(NXDialog):
def __init__(self, parent=None):
super().__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.parameters.grid()
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_buttons = self.action_buttons(
('Refine Orientation Matrix', self.refine_orientation),
('Remove Orientation Matrix', self.remove_orientation))
self.lattice_buttons = self.action_buttons(
('Plot', self.plot_lattice), ('List', self.list_peaks),
('Update', self.update_scaling), ('Save', self.write_parameters))
self.set_layout(self.entry_layout, 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.orient_box = None
self.update_box = None
self.fit_report = []
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 report_score(self):
try:
self.status_message.setText(f'Score: {self.refine.score():.4f}')
if self.peaks_box in self.mainwindow.dialogs:
self.status_text.setText(f'Score: {self.refine.score():.4f}')
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['peak_tolerance'].value = self.refine.peak_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_tolerance = self.get_polar_tolerance()
self.refine.peak_tolerance = self.get_peak_tolerance()
def write_parameters(self):
if self.entry.nxfilemode == 'r':
display_message("NeXus file opened as readonly")
return
elif ('nxrefine' in self.entry
or 'orientation_matrix' in self.entry['instrument/detector']):
if not self.confirm_action('Overwrite existing refinement?'):
return
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_start('nxrefine')
reduce.record('nxrefine', fit_report='\n'.join(self.fit_report))
reduce.logger.info('Orientation refined in NeXpy')
reduce.record_end('nxrefine')
root = self.entry.nxroot
entries = [
entry for entry in root.entries
if entry != 'entry' and entry != self.entry.nxname
]
if entries and self.confirm_action(
f'Copy orientation to other entries? ({", ".join(entries)})',
answer='yes'):
om = self.entry['instrument/detector/orientation_matrix']
for entry in entries:
root[entry]['instrument/detector/orientation_matrix'] = om
self.define_data()
if len(self.paths) > 0:
self.update_scaling()
def update_scaling(self):
self.define_data()
if len(self.paths) == 0:
display_message("Refining Lattice", "No data groups to update")
if self.update_box in self.mainwindow.dialogs:
try:
self.update_box.close()
except Exception:
pass
self.update_box = NXDialog(parent=self)
self.update_box.set_title('Update Scaling Factors')
self.update_box.setMinimumWidth(300)
self.update_box.set_layout(
self.paths.grid(header=('', 'Data Groups', '')),
self.update_box.close_layout())
self.update_box.close_box.accepted.connect(self.update_data)
self.update_box.show()
def define_data(self):
def is_valid(data):
try:
valid_axes = [['Ql', 'Qk', 'Qh'], ['l', 'k', 'h'],
['z', 'y', 'x']]
axis_names = [axis.nxname for axis in data.nxaxes]
return axis_names in valid_axes
except Exception:
return False
root = self.entry.nxroot
self.paths = GridParameters()
i = 0
for entry in root.NXentry:
for data in [d for d in entry.NXdata if is_valid(d)]:
i += 1
self.paths.add(i, data.nxpath, i, True, width=200)
def update_data(self):
try:
for path in [
self.paths[p].value for p in self.paths
if self.paths[p].vary
]:
data = self.entry.nxroot[path]
if [axis.nxname for axis in data.nxaxes] == ['z', 'y', 'x']:
lp = self.refine.lattice_parameters
else:
lp = self.refine.reciprocal_lattice_parameters
for i, axis in enumerate(data.nxaxes):
data[axis.nxname].attrs['scaling_factor'] = lp[2 - i]
data.attrs['angles'] = lp[5:2:-1]
self.update_box.close()
except NeXusError as error:
report_error("Updating Groups", error)
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_polar_tolerance(self):
return self.parameters['polar_tolerance'].value
def get_peak_tolerance(self):
return self.parameters['peak_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=f'{self.refine.name} Peak Angles'),
xmax=self.get_polar_max())
except NeXusError as error:
report_error('Plotting Lattice', error)
def plot_rings(self):
plotview = get_plotview()
plotview.vlines(self.refine.two_thetas,
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_lattice_parameters()
try:
self.refine.refine_angles(**self.refined)
except NeXusError as error:
report_error('Refining Lattice', error)
self.parameters.status_message.setText('')
return
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)
self.update_table()
def refine_hkls(self):
self.parameters.status_message.setText('Fitting...')
self.parameters.status_message.repaint()
self.mainwindow.app.app.processEvents()
self.transfer_parameters()
try:
self.refine.refine_hkls(**self.refined)
except NeXusError as error:
report_error('Refining Lattice', error)
self.parameters.status_message.setText('')
return
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)
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)
self.update_table()
def remove_orientation(self):
self.refine.Umat = None
self.report_score()
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 in self.mainwindow.dialogs:
self.update_table()
return
self.peaks_box = NXDialog(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.make_rings()
self.ring_list = self.refine.get_ring_list()
if self.refine.primary is None:
self.refine.primary = 0
if self.refine.secondary is None:
self.refine.secondary = 1
self.primary_box = NXLineEdit(self.refine.primary,
width=80,
align='right')
self.secondary_box = NXLineEdit(self.refine.secondary,
width=80,
align='right')
orient_button = NXPushButton('Orient', self.choose_peaks)
orient_layout = self.make_layout(NXLabel('Primary'),
self.primary_box,
NXLabel('Secondary'),
self.secondary_box,
'stretch',
orient_button,
align='right')
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)
self.status_text = NXLabel(f'Score: {self.refine.score():.4f}')
self.tolerance_box = NXLineEdit(self.refine.hkl_tolerance,
width=80,
slot=self.update_table,
align='right')
self.tolerance_box.setMaxLength(5)
export_button = NXPushButton('Export', self.export_peaks)
save_button = NXPushButton('Save', self.save_orientation)
close_button = NXPushButton('Close', self.close_peaks_box)
close_layout = self.make_layout(self.status_text, 'stretch',
NXLabel('Threshold'),
self.tolerance_box, 'stretch',
export_button, save_button,
close_button)
self.peaks_box.set_layout(orient_layout, self.table_view, close_layout)
self.peaks_box.set_title(f'{self.refine.name} Peak Table')
self.peaks_box.adjustSize()
self.peaks_box.show()
self.plotview = None
def update_table(self):
if self.peaks_box not in self.mainwindow.dialogs:
return
elif self.table_model is None:
self.close_peaks_box()
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.ring_list = self.refine.get_ring_list()
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.peaks_box.set_title(f'{self.refine.name} Peak Table')
self.peaks_box.adjustSize()
self.peaks_box.setVisible(True)
self.report_score()
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 'Peak Plot' in self.plotviews:
self.plotview = self.plotviews['Peak Plot']
else:
self.plotview = NXPlotView('Peak Plot')
self.plotview.plot(data[zslab], log=True)
self.plotview.ax.set_title(f'{data.nxtitle}: Peak {i}')
self.plotview.ztab.maxbox.setValue(z)
self.plotview.aspect = 'equal'
self.plotview.crosshairs(x, y, color='r', linewidth=0.5)
@property
def primary(self):
return int(self.primary_box.text())
@property
def secondary(self):
return int(self.secondary_box.text())
def choose_peaks(self):
try:
if self.orient_box in self.mainwindow.dialogs:
self.orient_box.close()
except Exception:
pass
self.orient_box = NXDialog(self)
self.peak_parameters = GridParameters()
self.peak_parameters.add('primary',
self.primary,
'Primary',
readonly=True)
self.peak_parameters.add('secondary',
self.secondary,
'Secondary',
readonly=True)
self.peak_parameters.add('angle',
self.refine.angle_peaks(
self.primary, self.secondary),
'Angle (deg)',
readonly=True)
self.peak_parameters.add('primary_hkl',
self.ring_list[self.refine.rp[self.primary]],
'Primary HKL',
slot=self.choose_secondary_grid)
self.orient_box.set_layout(
self.peak_parameters.grid(header=False, spacing=5),
self.action_buttons(('Orient', self.orient)),
self.orient_box.close_buttons(close=True))
self.orient_box.set_title('Orient Lattice')
self.orient_box.show()
try:
self.setup_secondary_grid()
except NeXusError as error:
report_error("Refining Lattice", error)
self.orient_box.close()
def setup_secondary_grid(self):
ps_angle = self.refine.angle_peaks(self.primary, self.secondary)
n_phkl = len(self.ring_list[self.refine.rp[self.primary]])
self.hkl_parameters = [GridParameters() for i in range(n_phkl)]
min_diff = self.get_peak_tolerance()
min_p = None
min_hkl = None
for i in range(n_phkl):
phkl = eval(self.peak_parameters['primary_hkl'].box.items()[i])
for hkls in self.rings[self.refine.rp[self.secondary]][1]:
for hkl in hkls:
hkl_angle = self.refine.angle_hkls(phkl, hkl)
diff = abs(ps_angle - hkl_angle)
if diff < self.get_peak_tolerance():
self.hkl_parameters[i].add(str(hkl),
hkl_angle,
str(hkl),
vary=False,
readonly=True)
if diff < min_diff:
min_diff = diff
min_p = i
min_hkl = str(hkl)
self.orient_box.insert_layout(
i + 1, self.hkl_parameters[i].grid(
header=['HKL', 'Angle (deg)', 'Select'], spacing=5))
if min_hkl is None:
raise NeXusError("No matching peaks found")
self.peak_parameters['primary_hkl'].box.setCurrentIndex(min_p)
self.hkl_parameters[min_p][min_hkl].vary = True
self.choose_secondary_grid()
def choose_secondary_grid(self):
box = self.peak_parameters['primary_hkl'].box
for i in [i for i in range(box.count()) if i != box.currentIndex()]:
self.hkl_parameters[i].hide_grid()
self.hkl_parameters[box.currentIndex()].show_grid()
@property
def primary_hkl(self):
return eval(self.peak_parameters['primary_hkl'].value)
@property
def secondary_hkl(self):
for hkls in self.hkl_parameters:
for hkl in hkls:
if hkls[hkl].vary is True:
return eval(hkls[hkl].name)
def orient(self):
self.refine.primary = self.primary
self.refine.secondary = self.secondary
self.refine.Umat = self.refine.get_UBmat(self.primary, self.secondary,
self.primary_hkl,
self.secondary_hkl)
self.update_table()
def export_peaks(self):
peaks = list(
zip(*[
p for p in self.table_model.peak_list
if p[-1] < self.get_hkl_tolerance()
]))
idx = NXfield(peaks[0], name='index')
x = NXfield(peaks[1], name='x')
y = NXfield(peaks[2], name='y')
z = NXfield(peaks[3], name='z')
pol = NXfield(peaks[4], name='polar_angle', units='degree')
azi = NXfield(peaks[5], name='azimuthal_angle', units='degree')
polarization = self.refine.get_polarization()
intensity = NXfield(peaks[6] / polarization[y, x], name='intensity')
H = NXfield(peaks[7], name='H', units='rlu')
K = NXfield(peaks[8], name='K', units='rlu')
L = NXfield(peaks[9], name='L', units='rlu')
diff = NXfield(peaks[10], name='diff')
peaks_data = NXdata(intensity, idx, diff, H, K, L, pol, azi, x, y, z)
export_dialog = ExportDialog(peaks_data, parent=self)
export_dialog.show()
def save_orientation(self):
self.write_parameters()
def close_peaks_box(self):
try:
self.peaks_box.close()
except Exception:
pass
self.peaks_box = None
def accept(self):
if 'transform' not in self.entry:
if self.confirm_action("Set up transforms?", answer="yes"):
self.treeview.select_node(self.entry)
from . import transform_data
transform_data.show_dialog()
super().accept()