def view_logs(self): if self.grid is None: raise NeXusError('Need to update status') dialog = BaseDialog(self) dialog.setMinimumWidth(800) dialog.setMinimumHeight(600) scans = [os.path.basename(scan) for scan in self.scans] self.scan_combo = dialog.select_box(scans, slot=self.refreshview) self.entry_combo = dialog.select_box(self.entries, slot=self.refreshview) self.program_combo = dialog.select_box(self.programs, slot=self.refreshview) self.defaultview = None self.output_box = dialog.editor() self.output_box.setStyleSheet('font-family: monospace;') self.output_box.setLineWrapMode(QtWidgets.QPlainTextEdit.NoWrap) dialog.set_layout( dialog.make_layout(self.scan_combo, self.entry_combo, self.program_combo), self.output_box, dialog.action_buttons(('View Server Logs', self.serverview), ('View Workflow Logs', self.logview), ('View Workflow Output', self.outview), ('View Database', self.databaseview)), dialog.close_buttons(close=True)) dialog.setWindowTitle("'%s' Logs" % self.sample) self.view_dialog = dialog self.view_dialog.show()
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
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 list_orientations(self): message_box = BaseDialog(self) message_box.setMinimumWidth(600) message_box.setMinimumHeight(600) header = ['i', 'x', 'y', 'z', 'Polar', 'Azi', 'Intensity', 'H', 'K', 'L', 'Diff'] peak_list = self.refine.get_peaks() self.refine.assign_rings() self.rings = self.refine.get_ring_hkls() orient_layout = QtWidgets.QHBoxLayout() if self.refine.primary is None: self.refine.primary = 0 if self.refine.secondary is None: self.refine.secondary = 1 self.primary_box = QtWidgets.QLineEdit(str(self.refine.primary)) self.primary_box.setAlignment(QtCore.Qt.AlignRight) self.primary_box.setFixedWidth(80) self.secondary_box = QtWidgets.QLineEdit(str(self.refine.secondary)) self.secondary_box.setAlignment(QtCore.Qt.AlignRight) self.secondary_box.setFixedWidth(80) orient_button = QtWidgets.QPushButton('Orient') orient_button.clicked.connect(self.orient) refine_button = QtWidgets.QPushButton('Refine') refine_button.clicked.connect(self.refine_orientation) restore_button = QtWidgets.QPushButton('Restore') restore_button.clicked.connect(self.restore_orientation) orient_layout.addStretch() orient_layout.addWidget(QtWidgets.QLabel('Primary')) orient_layout.addWidget(self.primary_box) orient_layout.addWidget(QtWidgets.QLabel('Secondary')) orient_layout.addWidget(self.secondary_box) orient_layout.addStretch() orient_layout.addWidget(orient_button) orient_layout.addWidget(refine_button) orient_layout.addWidget(restore_button) grid = QtWidgets.QGridLayout() grid.setSpacing(10) self.lattice = GridParameters() self.lattice.add('a', self.refine.a, 'a', False) self.lattice.add('b', self.refine.b, 'b', False) self.lattice.add('c', self.refine.c, 'c', False) self.lattice.add('alpha', self.refine.alpha, 'alpha', False) self.lattice.add('beta', self.refine.beta, 'beta', False) self.lattice.add('gamma', self.refine.gamma, 'gamma', False) p = self.lattice['a'] p.box.setFixedWidth(80) label, value, checkbox = p.label, p.value, p.vary grid.addWidget(p.label, 0, 0, QtCore.Qt.AlignRight) grid.addWidget(p.box, 0, 1, QtCore.Qt.AlignHCenter) grid.addWidget(p.checkbox, 0, 2, QtCore.Qt.AlignHCenter) p = self.lattice['b'] p.box.setFixedWidth(80) label, value, checkbox = p.label, p.value, p.vary grid.addWidget(p.label, 0, 3, QtCore.Qt.AlignRight) grid.addWidget(p.box, 0, 4, QtCore.Qt.AlignHCenter) grid.addWidget(p.checkbox, 0, 5, QtCore.Qt.AlignHCenter) p = self.lattice['c'] p.box.setFixedWidth(80) label, value, checkbox = p.label, p.value, p.vary grid.addWidget(p.label, 0, 6, QtCore.Qt.AlignRight) grid.addWidget(p.box, 0, 7, QtCore.Qt.AlignHCenter) grid.addWidget(p.checkbox, 0, 8, QtCore.Qt.AlignHCenter) p = self.lattice['alpha'] p.box.setFixedWidth(80) label, value, checkbox = p.label, p.value, p.vary grid.addWidget(p.label, 1, 0, QtCore.Qt.AlignRight) grid.addWidget(p.box, 1, 1, QtCore.Qt.AlignHCenter) grid.addWidget(p.checkbox, 1, 2, QtCore.Qt.AlignHCenter) p = self.lattice['beta'] p.box.setFixedWidth(80) label, value, checkbox = p.label, p.value, p.vary grid.addWidget(p.label, 1, 3, QtCore.Qt.AlignRight) grid.addWidget(p.box, 1, 4, QtCore.Qt.AlignHCenter) grid.addWidget(p.checkbox, 1, 5, QtCore.Qt.AlignHCenter) p = self.lattice['gamma'] p.box.setFixedWidth(80) label, value, checkbox = p.label, p.value, p.vary grid.addWidget(p.label, 1, 6, QtCore.Qt.AlignRight) grid.addWidget(p.box, 1, 7, QtCore.Qt.AlignHCenter) grid.addWidget(p.checkbox, 1, 8, QtCore.Qt.AlignHCenter) self.table_view = QtWidgets.QTableView() self.table_model = NXTableModel(self, peak_list, header) self.table_view.setModel(self.table_model) self.table_view.resizeColumnsToContents() self.table_view.horizontalHeader().stretchLastSection() self.table_view.setSelectionBehavior(QtWidgets.QAbstractItemView.SelectRows) self.table_view.doubleClicked.connect(self.plot_peak) self.table_view.setSortingEnabled(True) self.table_view.sortByColumn(0, QtCore.Qt.AscendingOrder) layout = QtWidgets.QVBoxLayout() layout.addLayout(orient_layout) layout.addLayout(grid) layout.addWidget(self.table_view) close_layout = QtWidgets.QHBoxLayout() self.status_text = QtWidgets.QLabel('Score: %.4f' % self.refine.score()) self.tolerance_box = QtWidgets.QLineEdit(str(self.refine.hkl_tolerance)) self.tolerance_box.setAlignment(QtCore.Qt.AlignRight) self.tolerance_box.setMaxLength(5) self.tolerance_box.editingFinished.connect(self.update_table) self.tolerance_box.setFixedWidth(80) save_button = QtWidgets.QPushButton('Save Orientation') save_button.clicked.connect(self.save_orientation) close_button = QtWidgets.QPushButton('Close Window') close_button.clicked.connect(message_box.close) close_layout.addWidget(self.status_text) close_layout.addStretch() close_layout.addWidget(QtWidgets.QLabel('Threshold')) close_layout.addWidget(self.tolerance_box) close_layout.addStretch() close_layout.addWidget(save_button) close_layout.addStretch() close_layout.addWidget(close_button) layout.addLayout(close_layout) message_box.setLayout(layout) message_box.setWindowTitle('%s Peak Table' % self.entry.nxtitle) message_box.adjustSize() message_box.show() self.plotview = None
def list_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
class RefineLatticeDialog(BaseDialog): def __init__(self, parent=None): super(RefineLatticeDialog, self).__init__(parent) self.select_entry(self.choose_entry) self.refine = NXRefine() self.parameters = GridParameters() self.parameters.add('symmetry', self.refine.symmetries, 'Symmetry', None, self.set_lattice_parameters) self.parameters.add('a', self.refine.a, 'Unit Cell - a (Ang)', False, slot=self.set_lattice_parameters) self.parameters.add('b', self.refine.b, 'Unit Cell - b (Ang)', False, slot=self.set_lattice_parameters) self.parameters.add('c', self.refine.c, 'Unit Cell - c (Ang)', False, slot=self.set_lattice_parameters) self.parameters.add('alpha', self.refine.alpha, 'Unit Cell - alpha (deg)', False, slot=self.set_lattice_parameters) self.parameters.add('beta', self.refine.beta, 'Unit Cell - beta (deg)', False, slot=self.set_lattice_parameters) self.parameters.add('gamma', self.refine.gamma, 'Unit Cell - gamma (deg)', False, slot=self.set_lattice_parameters) self.parameters.add('wavelength', self.refine.wavelength, 'Wavelength (Ang)', False) self.parameters.add('distance', self.refine.distance, 'Distance (mm)', False) self.parameters.add('yaw', self.refine.yaw, 'Yaw (deg)', False) self.parameters.add('pitch', self.refine.pitch, 'Pitch (deg)', False) self.parameters.add('roll', self.refine.roll, 'Roll (deg)') self.parameters.add('xc', self.refine.xc, 'Beam Center - x', False) self.parameters.add('yc', self.refine.yc, 'Beam Center - y', False) self.parameters.add('phi', self.refine.phi, 'Phi Start (deg)', False) self.parameters.add('phi_step', self.refine.phi_step, 'Phi Step (deg)') self.parameters.add('chi', self.refine.chi, 'Chi (deg)', False) self.parameters.add('omega', self.refine.omega, 'Omega (deg)', False) self.parameters.add('twotheta', self.refine.twotheta, 'Two Theta (deg)') self.parameters.add('gonpitch', self.refine.gonpitch, 'Goniometer Pitch (deg)', False) self.parameters.add('polar', self.refine.polar_max, 'Max. Polar Angle (deg)', None, self.set_polar_max) self.parameters.add('polar_tolerance', self.refine.polar_tolerance, 'Polar Angle Tolerance') self.parameters.add('peak_tolerance', self.refine.peak_tolerance, 'Peak Angle Tolerance') self.set_symmetry() self.refine_buttons = self.action_buttons( ('Refine Angles', self.refine_angles), ('Refine HKLs', self.refine_hkls), ('Restore', self.restore_parameters), ('Reset', self.reset_parameters)) self.orientation_button = self.action_buttons( ('Refine Orientation Matrix', self.refine_orientation)) self.lattice_buttons = self.action_buttons( ('Plot', self.plot_lattice), ('List', self.list_peaks), ('Save', self.write_parameters)) self.set_layout(self.entry_layout, self.parameters.grid(), self.refine_buttons, self.orientation_button, self.parameters.report_layout(), self.lattice_buttons, self.close_layout()) self.parameters.grid_layout.setVerticalSpacing(1) self.layout.setSpacing(2) self.set_title('Refining Lattice') self.peaks_box = None self.table_model = None self.fit_report = [] def choose_entry(self): self.refine = NXRefine(self.entry) self.update_parameters() if self.peaks_box: self.update_table() def report_score(self): try: self.status_message.setText('Score: %.4f' % self.refine.score()) except Exception as error: pass def update_parameters(self): self.parameters['a'].value = self.refine.a self.parameters['b'].value = self.refine.b self.parameters['c'].value = self.refine.c self.parameters['alpha'].value = self.refine.alpha self.parameters['beta'].value = self.refine.beta self.parameters['gamma'].value = self.refine.gamma self.parameters['wavelength'].value = self.refine.wavelength self.parameters['distance'].value = self.refine.distance self.parameters['yaw'].value = self.refine.yaw self.parameters['pitch'].value = self.refine.pitch self.parameters['roll'].value = self.refine.roll self.parameters['xc'].value = self.refine.xc self.parameters['yc'].value = self.refine.yc self.parameters['phi'].value = self.refine.phi self.parameters['phi_step'].value = self.refine.phi_step self.parameters['chi'].value = self.refine.chi self.parameters['omega'].value = self.refine.omega self.parameters['twotheta'].value = self.refine.twotheta self.parameters['gonpitch'].value = self.refine.gonpitch self.parameters['polar'].value = self.refine.polar_max self.parameters['polar_tolerance'].value = self.refine.polar_tolerance self.parameters['symmetry'].value = self.refine.symmetry try: self.refine.polar_angles, self.refine.azimuthal_angles = \ self.refine.calculate_angles(self.refine.xp, self.refine.yp) except Exception: pass self.report_score() def transfer_parameters(self): self.refine.a, self.refine.b, self.refine.c, \ self.refine.alpha, self.refine.beta, self.refine.gamma = \ self.get_lattice_parameters() self.refine.set_symmetry() self.refine.wavelength = self.get_wavelength() self.refine.distance = self.get_distance() self.refine.yaw, self.refine.pitch, self.refine.roll = self.get_tilts() self.refine.xc, self.refine.yc = self.get_centers() self.refine.phi, self.refine.phi_step = self.get_phi() self.refine.chi, self.refine.omega, self.refine.twotheta, \ self.refine.gonpitch = self.get_angles() self.refine.polar_max = self.get_polar_max() self.refine.polar_tol = self.get_tolerance() def write_parameters(self): self.transfer_parameters() polar_angles, azimuthal_angles = self.refine.calculate_angles( self.refine.xp, self.refine.yp) self.refine.write_angles(polar_angles, azimuthal_angles) self.refine.write_parameters() reduce = NXReduce(self.entry) reduce.record('nxrefine', fit_report='\n'.join(self.fit_report)) root = self.entry.nxroot entries = [entry for entry in root.entries if entry != 'entry'] if entries and self.confirm_action( 'Copy orientation to other entries? (%s)' % (', '.join(entries))): om = self.entry['instrument/detector/orientation_matrix'] for entry in entries: root[entry]['instrument/detector/orientation_matrix'] = om def get_symmetry(self): return self.parameters['symmetry'].value def set_symmetry(self): self.refine.symmetry = self.get_symmetry() self.refine.set_symmetry() self.update_parameters() if self.refine.symmetry == 'cubic': self.parameters['b'].vary = False self.parameters['c'].vary = False self.parameters['alpha'].vary = False self.parameters['beta'].vary = False self.parameters['gamma'].vary = False elif self.refine.symmetry == 'tetragonal': self.parameters['b'].vary = False self.parameters['alpha'].vary = False self.parameters['beta'].vary = False self.parameters['gamma'].vary = False elif self.refine.symmetry == 'orthorhombic': self.parameters['alpha'].vary = False self.parameters['beta'].vary = False self.parameters['gamma'].vary = False elif self.refine.symmetry == 'hexagonal': self.parameters['b'].vary = False self.parameters['alpha'].vary = False self.parameters['beta'].vary = False self.parameters['gamma'].vary = False elif self.refine.symmetry == 'monoclinic': self.parameters['alpha'].vary = False self.parameters['gamma'].vary = False def get_lattice_parameters(self): return (self.parameters['a'].value, self.parameters['b'].value, self.parameters['c'].value, self.parameters['alpha'].value, self.parameters['beta'].value, self.parameters['gamma'].value) def set_lattice_parameters(self): symmetry = self.get_symmetry() if symmetry == 'cubic': self.parameters['b'].value = self.parameters['a'].value self.parameters['c'].value = self.parameters['a'].value self.parameters['alpha'].value = 90.0 self.parameters['beta'].value = 90.0 self.parameters['gamma'].value = 90.0 self.parameters['a'].enable(vary=True) self.parameters['b'].disable(vary=False) self.parameters['c'].disable(vary=False) self.parameters['alpha'].disable(vary=False) self.parameters['beta'].disable(vary=False) self.parameters['gamma'].disable(vary=False) elif symmetry == 'tetragonal': self.parameters['b'].value = self.parameters['a'].value self.parameters['alpha'].value = 90.0 self.parameters['beta'].value = 90.0 self.parameters['gamma'].value = 90.0 self.parameters['a'].enable(vary=True) self.parameters['b'].disable(vary=False) self.parameters['c'].enable(vary=True) self.parameters['alpha'].disable(vary=False) self.parameters['beta'].disable(vary=False) self.parameters['gamma'].disable(vary=False) elif symmetry == 'orthorhombic': self.parameters['alpha'].value = 90.0 self.parameters['beta'].value = 90.0 self.parameters['gamma'].value = 90.0 self.parameters['a'].enable(vary=True) self.parameters['b'].enable(vary=True) self.parameters['c'].enable(vary=True) self.parameters['alpha'].disable(vary=False) self.parameters['beta'].disable(vary=False) self.parameters['gamma'].disable(vary=False) elif symmetry == 'hexagonal': self.parameters['b'].value = self.parameters['a'].value self.parameters['alpha'].value = 90.0 self.parameters['beta'].value = 90.0 self.parameters['gamma'].value = 120.0 self.parameters['a'].enable(vary=True) self.parameters['b'].disable(vary=False) self.parameters['c'].enable(vary=True) self.parameters['alpha'].disable(vary=False) self.parameters['beta'].disable(vary=False) self.parameters['gamma'].disable(vary=False) elif symmetry == 'monoclinic': self.parameters['alpha'].value = 90.0 self.parameters['gamma'].value = 90.0 self.parameters['a'].enable(vary=True) self.parameters['b'].enable(vary=True) self.parameters['c'].enable(vary=True) self.parameters['alpha'].disable(vary=False) self.parameters['beta'].enable(vary=True) self.parameters['gamma'].disable(vary=False) else: self.parameters['a'].enable(vary=True) self.parameters['b'].enable(vary=True) self.parameters['c'].enable(vary=True) self.parameters['alpha'].enable(vary=True) self.parameters['beta'].enable(vary=True) self.parameters['gamma'].enable(vary=True) def get_wavelength(self): return self.parameters['wavelength'].value def get_distance(self): return self.parameters['distance'].value def get_tilts(self): return (self.parameters['yaw'].value, self.parameters['pitch'].value, self.parameters['roll'].value) def get_centers(self): return self.parameters['xc'].value, self.parameters['yc'].value def get_phi(self): return (self.parameters['phi'].value, self.parameters['phi_step'].value) def get_angles(self): return (self.parameters['chi'].value, self.parameters['omega'].value, self.parameters['twotheta'].value, self.parameters['gonpitch'].value) def get_polar_max(self): return self.parameters['polar'].value def set_polar_max(self): self.refine.polar_max = self.get_polar_max() def get_tolerance(self): return self.parameters['polar_tolerance'].value def get_hkl_tolerance(self): try: return np.float32(self.tolerance_box.text()) except Exception: return self.refine.hkl_tolerance def plot_lattice(self): self.transfer_parameters() self.set_polar_max() self.plot_peaks() self.plot_rings() def plot_peaks(self): try: x, y = (self.refine.xp[self.refine.idx], self.refine.yp[self.refine.idx]) polar_angles, azimuthal_angles = self.refine.calculate_angles(x, y) if polar_angles[0] > polar_angles[-1]: polar_angles = polar_angles[::-1] azimuthal_angles = azimuthal_angles[::-1] azimuthal_field = NXfield(azimuthal_angles, name='azimuthal_angle') azimuthal_field.long_name = 'Azimuthal Angle' polar_field = NXfield(polar_angles, name='polar_angle') polar_field.long_name = 'Polar Angle' plotview = get_plotview() plotview.plot( NXdata(azimuthal_field, polar_field, title='Peak Angles')) except NeXusError as error: report_error('Plotting Lattice', error) def plot_rings(self, polar_max=None): if polar_max is None: polar_max = self.refine.polar_max peaks = self.refine.calculate_rings(polar_max) plotview = get_plotview() plotview.vlines(peaks, colors='r', linestyles='dotted') plotview.draw() @property def refined(self): refined = {} for p in self.parameters: if self.parameters[p].vary: refined[p] = True return refined def refine_angles(self): self.parameters.status_message.setText('Fitting...') self.parameters.status_message.repaint() self.mainwindow.app.app.processEvents() self.parameters['phi'].vary = False self.transfer_parameters() self.set_symmetry() self.refine.refine_angles(**self.refined) self.parameters.result = self.refine.result self.parameters.fit_report = self.refine.fit_report self.fit_report.append(self.refine.fit_report) self.update_parameters() self.parameters.status_message.setText(self.parameters.result.message) if self.peaks_box and self.peaks_box.isVisible(): self.update_table() def refine_hkls(self): self.parameters.status_message.setText('Fitting...') self.parameters.status_message.repaint() self.mainwindow.app.app.processEvents() self.set_symmetry() self.transfer_parameters() self.refine.refine_hkls(**self.refined) self.parameters.result = self.refine.result self.parameters.fit_report = self.refine.fit_report self.fit_report.append(self.refine.fit_report) self.update_parameters() self.parameters.status_message.setText(self.parameters.result.message) if self.peaks_box and self.peaks_box.isVisible(): self.update_table() def refine_orientation(self): self.parameters.status_message.setText('Fitting...') self.parameters.status_message.repaint() self.mainwindow.app.app.processEvents() self.transfer_parameters() self.refine.refine_orientation_matrix() self.parameters.result = self.refine.result self.parameters.fit_report = self.refine.fit_report self.fit_report.append(self.refine.fit_report) self.update_parameters() self.parameters.status_message.setText(self.parameters.result.message) if self.peaks_box and self.peaks_box.isVisible(): self.update_table() def restore_parameters(self): self.refine.restore_parameters() self.update_parameters() try: self.fit_report.pop() except IndexError: pass def reset_parameters(self): self.refine.read_parameters() self.update_parameters() self.set_symmetry() try: self.fit_report.pop() except IndexError: pass def list_peaks(self): if self.peaks_box is not None and self.table_model is not None: self.update_table() return self.peaks_box = BaseDialog(self) self.peaks_box.setMinimumWidth(600) self.peaks_box.setMinimumHeight(600) header = [ 'i', 'x', 'y', 'z', 'Polar', 'Azi', 'Intensity', 'H', 'K', 'L', 'Diff' ] peak_list = self.refine.get_peaks() self.refine.assign_rings() self.rings = self.refine.get_ring_hkls() orient_layout = QtWidgets.QHBoxLayout() if self.refine.primary is None: self.refine.primary = 0 if self.refine.secondary is None: self.refine.secondary = 1 self.primary_box = QtWidgets.QLineEdit(str(self.refine.primary)) self.primary_box.setAlignment(QtCore.Qt.AlignRight) self.primary_box.setFixedWidth(80) self.secondary_box = QtWidgets.QLineEdit(str(self.refine.secondary)) self.secondary_box.setAlignment(QtCore.Qt.AlignRight) self.secondary_box.setFixedWidth(80) orient_button = QtWidgets.QPushButton('Orient') orient_button.clicked.connect(self.orient) orient_layout.addStretch() orient_layout.addWidget(QtWidgets.QLabel('Primary')) orient_layout.addWidget(self.primary_box) orient_layout.addWidget(QtWidgets.QLabel('Secondary')) orient_layout.addWidget(self.secondary_box) orient_layout.addStretch() orient_layout.addWidget(orient_button) self.table_view = QtWidgets.QTableView() self.table_model = NXTableModel(self, peak_list, header) self.table_view.setModel(self.table_model) self.table_view.resizeColumnsToContents() self.table_view.horizontalHeader().stretchLastSection() self.table_view.setSelectionBehavior( QtWidgets.QAbstractItemView.SelectRows) self.table_view.doubleClicked.connect(self.plot_peak) self.table_view.setSortingEnabled(True) self.table_view.sortByColumn(0, QtCore.Qt.AscendingOrder) layout = QtWidgets.QVBoxLayout() layout.addLayout(orient_layout) layout.addWidget(self.table_view) close_layout = QtWidgets.QHBoxLayout() self.status_text = QtWidgets.QLabel('Score: %.4f' % self.refine.score()) self.tolerance_box = QtWidgets.QLineEdit(str( self.refine.hkl_tolerance)) self.tolerance_box.setAlignment(QtCore.Qt.AlignRight) self.tolerance_box.setMaxLength(5) self.tolerance_box.editingFinished.connect(self.update_table) self.tolerance_box.setFixedWidth(80) save_button = QtWidgets.QPushButton('Save Orientation') save_button.clicked.connect(self.save_orientation) close_button = QtWidgets.QPushButton('Close Window') close_button.clicked.connect(self.close_peaks_box) close_layout.addWidget(self.status_text) close_layout.addStretch() close_layout.addWidget(QtWidgets.QLabel('Threshold')) close_layout.addWidget(self.tolerance_box) close_layout.addStretch() close_layout.addWidget(save_button) close_layout.addStretch() close_layout.addWidget(close_button) layout.addLayout(close_layout) self.peaks_box.setLayout(layout) self.peaks_box.setWindowTitle('%s Peak Table' % self.entry.nxtitle) self.peaks_box.adjustSize() self.peaks_box.show() self.plotview = None def update_table(self): if self.peaks_box is None: self.list_peaks() self.transfer_parameters() self.refine.hkl_tolerance = self.get_hkl_tolerance() self.table_model.peak_list = self.refine.get_peaks() self.refine.assign_rings() self.rings = self.refine.get_ring_hkls() rows, columns = len(self.table_model.peak_list), 11 self.table_model.dataChanged.emit( self.table_model.createIndex(0, 0), self.table_model.createIndex(rows - 1, columns - 1)) self.table_view.resizeColumnsToContents() self.status_text.setText('Score: %.4f' % self.refine.score()) self.peaks_box.setWindowTitle('%s Peak Table' % self.entry.nxtitle) self.peaks_box.setVisible(True) def plot_peak(self): row = self.table_view.currentIndex().row() data = self.entry.data i, x, y, z = [ self.table_view.model().peak_list[row][i] for i in range(4) ] signal = data.nxsignal xmin, xmax = max(0, x - 200), min(x + 200, signal.shape[2]) ymin, ymax = max(0, y - 200), min(y + 200, signal.shape[1]) zmin, zmax = max(0, z - 20), min(z + 20, signal.shape[0]) zslab = np.s_[zmin:zmax, ymin:ymax, xmin:xmax] if self.plotview is None: self.plotview = NXPlotView('Peak Plot') self.plotview.plot(data[zslab], log=True) self.plotview.ax.set_title('%s: Peak %s' % (data.nxtitle, i)) self.plotview.ztab.maxbox.setValue(z) self.plotview.aspect = 'equal' self.plotview.crosshairs(x, y, color='r', linewidth=0.5) def orient(self): self.refine.primary = int(self.primary_box.text()) self.refine.secondary = int(self.secondary_box.text()) self.refine.Umat = ( self.refine.get_UBmat(self.refine.primary, self.refine.secondary) * self.refine.Bimat) self.update_table() def save_orientation(self): self.write_parameters() def close_peaks_box(self): self.peaks_box.close() self.peaks_box = None
def view_logs(self): if self.grid is None: raise NeXusError('Need to update status') dialog = BaseDialog(self) dialog.setMinimumWidth(800) dialog.setMinimumHeight(600) scans = [os.path.basename(scan) for scan in self.scans] self.scan_combo = dialog.select_box(scans, slot=self.refreshview) self.entry_combo = dialog.select_box(self.entries, slot=self.refreshview) self.program_combo = dialog.select_box(self.programs, slot=self.refreshview) self.defaultview = None self.output_box = dialog.editor() self.output_box.setStyleSheet('font-family: monospace;') self.output_box.setLineWrapMode(QtWidgets.QPlainTextEdit.NoWrap) dialog.set_layout( dialog.make_layout(self.scan_combo, self.entry_combo, self.program_combo), self.output_box, dialog.action_buttons(('View Server Logs', self.serverview), ('View Workflow Logs', self.logview), ('View Workflow Output', self.outview), ('View Database', self.databaseview)), dialog.close_buttons(close=True)) dialog.setWindowTitle("'%s' Logs" % self.sample) self.view_dialog = dialog self.view_dialog.show()
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