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 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)