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 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 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 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(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()