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(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()
class CalibrateSpectrum(QWidget):
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 picked_from_range(self, type, min, max):
min=(self.fits_spectrum.spectrum.wavelength_index(min))
max=(self.fits_spectrum.spectrum.wavelength_index(max))
add_line = lambda x: self.spectrum_plot.add_line("x_axis_pick", self.fits_spectrum.spectrum.wavelengths[x], color='r')
set_x_value = lambda x: self.ui.point_x_axis.setValue(x)
if type != 'central':
subplot = SelectPlottedPoints(self.fits_spectrum.spectrum.fluxes, min, max+1, self.settings, type)
subplot.point.connect(add_line)
subplot.point.connect(set_x_value)
subplot.show()
return
point = min+(max-min)/2
self.ui.point_x_axis.setValue(point)
set_x_value(point)
add_line(point)
def pick_from_range(self, type):
self.spectrum_plot.add_span_selector('pick_x_axis', lambda min,max: self.picked_from_range(type, min, max),direction='horizontal')
def remove_calibration_point(self):
self.calibration_model.removeRow(self.ui.calibration_points.selectionModel().selectedIndexes()[0].row())
self.calculate_calibration()
def add_calibration_point_data(self, x_value, wavelength):
x_axis_item = QStandardItem("star" if x_value == 0 else "{}".format(x_value))
x_axis_item.setData(x_value)
wavelength_item = QStandardItem("{:.2f}".format(wavelength))
wavelength_item.setData(wavelength)
self.calibration_model.appendRow([x_axis_item, wavelength_item, QStandardItem("n/a")])
self.spectrum_plot.rm_element('x_axis_pick')
def picked_line(self, lines):
self.ui.point_wavelength.setValue(lines[0]['lambda'])
def add_calibration_point(self):
self.add_calibration_point_data(self.ui.point_x_axis.value(), 0 if self.ui.point_is_star.isChecked() else self.ui.point_wavelength.value())
self.calculate_calibration()
def calibration_points(self):
return [{'row': row, 'x': self.calibration_model.item(row, 0).data(), 'wavelength': self.calibration_model.item(row, 1).data()} for row in range(self.calibration_model.rowCount())]
def calculate_calibration(self, dispersion = None):
points_number = self.calibration_model.rowCount()
self.ui.set_dispersion.setEnabled(points_number == 1)
self.ui.dispersion.setEnabled(points_number == 1)
if points_number == 0:
self.fits_spectrum.reset()
self.lines_dialog.set_picker_enabled(False)
else:
self.lines_dialog.set_picker_enabled(True)
points = sorted(self.calibration_points(), key=lambda point: point['x'])
self.fits_spectrum.calibrate(points, dispersion if dispersion else self.ui.dispersion.value() )
for row, value in [(p['row'], "{:.2f}".format( p['wavelength']-self.fits_spectrum.spectrum.wavelengths[p['x']])) for p in points]:
self.calibration_model.item(row, 2).setText(value)
self.ui.dispersion.setValue(self.fits_spectrum.spectrum.dispersion())
self.fits_spectrum.plot_to(self.spectrum_plot.axes)
def save_spectrum(self):
if not self.project:
save_file_sticky('Save plot...', 'FITS file (.fit)', lambda f: self.save(f[0]), self.settings, CALIBRATED_PROFILE, [RAW_PROFILE])
return
self.project.add_file(Project.CALIBRATED_PROFILE, object_properties = self.object_properties, on_added=self.save)
def save(self, filename):
self.fits_spectrum.save(filename, self.calibration_points())
class CalibrateSpectrum(QWidget):
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 picked_from_range(self, type, min, max):
min = (self.fits_spectrum.spectrum.wavelength_index(min))
max = (self.fits_spectrum.spectrum.wavelength_index(max))
add_line = lambda x: self.spectrum_plot.add_line(
"x_axis_pick",
self.fits_spectrum.spectrum.wavelengths[x],
color='r')
set_x_value = lambda x: self.ui.point_x_axis.setValue(x)
if type != 'central':
subplot = SelectPlottedPoints(self.fits_spectrum.spectrum.fluxes,
min, max + 1, self.settings, type)
subplot.point.connect(add_line)
subplot.point.connect(set_x_value)
subplot.show()
return
point = min + (max - min) / 2
self.ui.point_x_axis.setValue(point)
set_x_value(point)
add_line(point)
def pick_from_range(self, type):
self.spectrum_plot.add_span_selector(
'pick_x_axis',
lambda min, max: self.picked_from_range(type, min, max),
direction='horizontal')
def remove_calibration_point(self):
self.calibration_model.removeRow(
self.ui.calibration_points.selectionModel().selectedIndexes()
[0].row())
self.calculate_calibration()
def add_calibration_point_data(self, x_value, wavelength):
x_axis_item = QStandardItem("star" if x_value ==
0 else "{}".format(x_value))
x_axis_item.setData(x_value)
wavelength_item = QStandardItem("{:.2f}".format(wavelength))
wavelength_item.setData(wavelength)
self.calibration_model.appendRow(
[x_axis_item, wavelength_item,
QStandardItem("n/a")])
self.spectrum_plot.rm_element('x_axis_pick')
def picked_line(self, lines):
self.ui.point_wavelength.setValue(lines[0]['lambda'])
def add_calibration_point(self):
self.add_calibration_point_data(
self.ui.point_x_axis.value(),
0 if self.ui.point_is_star.isChecked() else
self.ui.point_wavelength.value())
self.calculate_calibration()
def calibration_points(self):
return [{
'row': row,
'x': self.calibration_model.item(row, 0).data(),
'wavelength': self.calibration_model.item(row, 1).data()
} for row in range(self.calibration_model.rowCount())]
def calculate_calibration(self, dispersion=None):
points_number = self.calibration_model.rowCount()
self.ui.set_dispersion.setEnabled(points_number == 1)
self.ui.dispersion.setEnabled(points_number == 1)
if points_number == 0:
self.fits_spectrum.reset()
self.lines_dialog.set_picker_enabled(False)
else:
self.lines_dialog.set_picker_enabled(True)
points = sorted(self.calibration_points(),
key=lambda point: point['x'])
self.fits_spectrum.calibrate(
points,
dispersion if dispersion else self.ui.dispersion.value())
for row, value in [(p['row'], "{:.2f}".format(
p['wavelength'] -
self.fits_spectrum.spectrum.wavelengths[p['x']]))
for p in points]:
self.calibration_model.item(row, 2).setText(value)
self.ui.dispersion.setValue(self.fits_spectrum.spectrum.dispersion())
self.fits_spectrum.plot_to(self.spectrum_plot.axes)
def save_spectrum(self):
if not self.project:
save_file_sticky('Save plot...', 'FITS file (.fit)',
lambda f: self.save(f[0]), self.settings,
CALIBRATED_PROFILE, [RAW_PROFILE])
return
self.project.add_file(Project.CALIBRATED_PROFILE,
object_properties=self.object_properties,
on_added=self.save)
def save(self, filename):
self.fits_spectrum.save(filename, self.calibration_points())