def open_fits(self, filename): fits_file = fits.open(filename) fits_spectrum = FitsSpectrum(fits_file) self.spectrum_name = fits_spectrum.name() self.spectrum = fits_spectrum.spectrum self.undo.set_spectrum(self.spectrum) self.spectrum.normalize_to_max() if self.spectrum.dispersion() <0.4: print("dispersion too high ({}), reducing spectrum resolution".format(self.spectrum.dispersion())) self.spectrum.resample(self.spectrum.dispersion() / 0.4) self.draw()
def instrument_response(self, filename): print("Applying instrument response {}".format(filename)) instrument_response_file = fits.open(filename) instrument_response = FitsSpectrum(instrument_response_file) response = instrument_response.spectrum response.normalize_to_max() range = (max(response.wavelengths[0], self.spectrum.wavelengths[0]), min(response.wavelengths[-1], self.spectrum.wavelengths[-1])) self.spectrum.cut(self.spectrum.wavelength_index(range[0]), self.spectrum.wavelength_index(range[1])) spline = InterpolatedUnivariateSpline(response.wavelengths, response.fluxes) response_data = [spline(x) for x in self.spectrum.wavelengths] self.spectrum.fluxes /= response_data self.spectrum.normalize_to_max() self.draw()
def __init__(self, fits_file, settings, database, project=None): super(CalibrateSpectrum, self).__init__() self.project = project self.settings = settings self.fits_spectrum = FitsSpectrum(fits_file) self.fits_spectrum.spectrum.normalize_to_max() self.fits_file = fits_file self.ui = Ui_CalibrateSpectrum() self.ui.setupUi(self) self.toolbar = QToolBar('Calibration Toolbar') self.toolbar.setToolButtonStyle(Qt.ToolButtonTextBesideIcon) self.ui.x_axis_pick.setMenu(QMenu()) self.ui.x_axis_pick.menu().addAction( "Maximum from range").triggered.connect( lambda: self.pick_from_range('maximum')) self.ui.x_axis_pick.menu().addAction( "Minimum from range").triggered.connect( lambda: self.pick_from_range('minimum')) self.ui.x_axis_pick.menu().addAction( "Central value from range").triggered.connect( lambda: self.pick_from_range('central')) self.ui.wavelength_pick.clicked.connect( lambda: self.lines_dialog.show()) save_action = self.toolbar.addAction(QIcon(':/save_20'), 'Save', self.save_spectrum) self.spectrum_plot = QtCommons.nestWidget(self.ui.spectrum_plot_widget, QMathPlotWidget()) self.reference_spectra_dialog = ReferenceSpectraDialog(database) self.reference_spectra_dialog.setup_menu(self.toolbar, self.spectrum_plot.axes, settings) self.object_properties = ObjectProperties(self.fits_file, project=project) self.object_properties_dialog = ObjectPropertiesDialog( settings, self.object_properties) self.toolbar.addAction("Object properties", self.object_properties_dialog.show) self.calibration_model = QStandardItemModel() self.calibration_model.setHorizontalHeaderLabels( ["x-axis", "wavelength", "error"]) self.ui.calibration_points.setModel(self.calibration_model) self.ui.calibration_points.selectionModel().selectionChanged.connect( lambda selected, deselected: self.ui.remove_calibration_point. setEnabled(len(selected.indexes()) > 0)) self.ui.add_calibration_point.clicked.connect( self.add_calibration_point) self.ui.remove_calibration_point.setEnabled(False) self.ui.remove_calibration_point.clicked.connect( self.remove_calibration_point) if project and project.avg_dispersion(): self.ui.set_dispersion.setMenu(QMenu()) self.ui.set_dispersion.menu().addAction('From input value', self.calculate_calibration) self.ui.set_dispersion.menu().addAction( 'From Project', lambda: self.calculate_calibration(project.avg_dispersion())) else: self.ui.set_dispersion.clicked.connect(self.calculate_calibration) self.ui.point_is_star.toggled.connect( lambda checked: self.ui.wavelength_pick.setEnabled(not checked)) self.ui.point_is_star.toggled.connect( lambda checked: self.ui.point_wavelength.setEnabled(not checked)) self.fits_spectrum.plot_to(self.spectrum_plot.axes) self.toolbar.addSeparator() self.toolbar.addAction("Zoom", self.spectrum_plot.select_zoom) self.toolbar.addAction( "Reset Zoom", lambda: self.spectrum_plot.reset_zoom( self.fits_spectrum.spectrum.wavelengths, self.fits_spectrum.spectrum.fluxes.min(), self.fits_spectrum.spectrum.fluxes.max())) self.toolbar.addSeparator() self.lines_dialog = LinesDialog(database, settings, self.spectrum_plot, enable_picker=False, selection_mode='single') self.lines_dialog.lines.connect(self.picked_line) hdu_calibration_points = [ h for h in self.fits_file if h.name == FitsSpectrum.CALIBRATION_DATA ] if len(hdu_calibration_points) > 0: for point in hdu_calibration_points[-1].data: self.add_calibration_point_data(point[0], point[1]) self.calculate_calibration()
def __init__(self, fits_file, settings, database, project=None): super(FinishSpectrum, self).__init__() self.settings = settings self.ui = Ui_FinishSpectrum() self.ui.setupUi(self) self.profile_line = None self.project = project self.fits_spectrum = FitsSpectrum(fits_file) self.undo = Undo(self.fits_spectrum.spectrum, self.draw) try: fits_file.index_of('ORIGINAL_DATA') except KeyError: hdu = fits.ImageHDU(data=fits_file[0].data, header=fits_file[0].header, name='ORIGINAL_DATA') fits_file.append(hdu) self.fits_spectrum.spectrum.normalize_to_max() self.spectrum = self.fits_spectrum.spectrum self.spectrum_plot = QtCommons.nestWidget(self.ui.plot, QMathPlotWidget()) self.spectrum_plot.mouse_moved.connect( Instances.MainWindow.print_coordinates) self.split_view() self.toolbar = QToolBar('Finish Spectrum Toolbar') if project: instrument_response_action = QtCommons.addToolbarPopup( self.toolbar, "Instrument Response") instrument_response_action.menu().addAction( 'From FITS file...', lambda: open_file_sticky( 'Open Instrument Response Profile', FITS_EXTS, lambda f: self.instrument_response(f[ 0]), settings, MATH_OPERATION, [RAW_PROFILE])) for instrument_response in project.get_instrument_responses(): print("Adding instrument response {}".format( instrument_response)) instrument_response_action.menu().addAction( os.path.basename(instrument_response[1]), lambda: self.instrument_response(instrument_response[1])) else: self.toolbar.addAction( 'Instrument Response', lambda: open_file_sticky( 'Open Instrument Response Profile', FITS_EXTS, lambda f: self.instrument_response(f[ 0]), settings, MATH_OPERATION, [RAW_PROFILE])) self.toolbar.addAction( "Zoom", lambda: self.spectrum_plot.select_zoom(self.profile_plot.axes)) self.toolbar.addAction( "Reset Zoom", lambda: self.spectrum_plot.reset_zoom( self.spectrum.wavelengths, self.spectrum.fluxes.min(), self.spectrum.fluxes.max(), self.profile_plot.axes)) remove_action = QtCommons.addToolbarPopup(self.toolbar, "Remove") remove_action.menu().addAction( "Before point", lambda: spectrum_trim_dialog(self.spectrum, 'before', self.profile_plot.axes, lambda: self.draw(), self, before_removal=self.undo.save_undo)) remove_action.menu().addAction( "After point", lambda: spectrum_trim_dialog(self.spectrum, 'after', self.profile_plot.axes, lambda: self.draw(), self, before_removal=self.undo.save_undo)) self.undo.add_actions(self.toolbar) self.toolbar.addSeparator() self.reference_spectra_dialog = ReferenceSpectraDialog( database, self.fits_spectrum.spectrum) self.reference_spectra_dialog.setup_menu(self.toolbar, self.profile_plot.axes, settings) lines_menu = QtCommons.addToolbarPopup(self.toolbar, "Spectral Lines..") lines_menu.menu().addAction('Lines Database', lambda: self.lines_dialog.show()) lines_menu.menu().addAction('Custom line', self.add_custom_line) labels_action = QtCommons.addToolbarPopup(self.toolbar, "Labels..") self.object_properties = ObjectProperties(fits_file, project=project) labels_action.menu().addAction('Title', self.add_title) if self.object_properties: labels_action.menu().addAction('Information from FITS file', self.add_fits_information_label) labels_action.menu().addAction('Custom', self.add_label) self.object_properties_dialog = ObjectPropertiesDialog( settings, self.object_properties) self.toolbar.addAction("Object properties", self.object_properties_dialog.show) self.labels, self.lines = [], [] for label in self.fits_spectrum.labels(): self.add_label(text=label['text'], coords=label['coords'], type=label['type'], fontsize=label['fontsize']) self.toolbar.addSeparator() if project: self.toolbar.addAction( QIcon(':/image_20'), "Export Image...", lambda: QtCommons.save_file( 'Export plot to image', 'PNG (*.png);;PDF (*.pdf);;PostScript (*.ps);;SVG (*.svg)', lambda f: self.save_image(f[0]), project.directory_path(Project.EXPORTED_IMAGES))) self.toolbar.addAction(QIcon(':/save_20'), 'Save', self.save_finished_in_project) else: self.toolbar.addAction( QIcon(':/image_20'), "Export Image...", lambda: save_file_sticky( 'Export plot to image', 'PNG (*.png);;PDF (*.pdf);;PostScript (*.ps);;SVG (*.svg)', lambda f: self.save_image(f[0]), self.settings, EXPORT_IMAGES, [CALIBRATED_PROFILE])) self.toolbar.addAction( QIcon(':/save_20'), 'Save', lambda: save_file_sticky( 'Save plot...', 'FITS file (.fit)', lambda f: self.__save( f[0]), self.settings, CALIBRATED_PROFILE)) self.lines_dialog = LinesDialog(database, settings, self.spectrum_plot, self.profile_plot.axes) self.lines_dialog.lines.connect(self.add_lines) for line in self.fits_spectrum.lines_labels(): self.lines.append( ReferenceLine(line['text'], line['wavelength'], self.profile_plot.axes, lambda line: self.lines.remove(line), show_wavelength=line['display_wavelength'], fontsize=line['fontsize'], position=line['position']))
def __open_reference(self, file, axes): fits_spectrum = FitsSpectrum(fits.open(file)) self.__open(fits_spectrum.spectrum, axes)