def __init__(self, fits_file, settings, project = None):
super(ImportImage, self).__init__()
self.settings = settings
self.fits_file = fits_file
self.project = project
try:
image_hdu_index = fits_file.index_of('IMAGE')
except KeyError:
image_hdu_index = 0
original_image = fits.ImageHDU(data=fits_file[image_hdu_index].data, header=fits_file[image_hdu_index].header, name='IMAGE')
for hdu in [h for h in self.fits_file if h.name == 'IMAGE']: self.fits_file.remove(hdu)
self.fits_file.append(original_image)
self.ui = Ui_ImportImage()
self.ui.setupUi(self)
self.rotate_dialog = RotateImageDialog(self.fits_file, image_hdu_index, project=project)
self.rotate_dialog.rotated.connect(self.rotated)
self.image_plot = QtCommons.nestWidget(self.ui.image_widget, QImPlotWidget(self.rotate_dialog.data_rotated, cmap='gray'))
self.spatial_plot = QtCommons.nestWidget(self.ui.spatial_plot_widget, QMathPlotWidget())
self.spectrum_plot = QtCommons.nestWidget(self.ui.spectrum_plot_widget, QMathPlotWidget())
self.image_view = self.image_plot.axes_image
self.toolbar = QToolBar('Image Toolbar')
self.toolbar.addAction(QIcon(':/rotate_20'), "Rotate", lambda: self.rotate_dialog.show())
self.toolbar.addAction(QIcon(':/save_20'), "Save", self.save_profile)
self.toolbar.addAction(QIcon(':/select_all_20'), "Select spectrum data", lambda: self.spatial_plot.add_span_selector('select_spectrum', self.spectrum_span_selected,direction='horizontal'))
self.toolbar.addAction(QIcon.fromTheme('edit-select-invert'), "Select background data", lambda: self.spatial_plot.add_span_selector('select_background', self.background_span_selected,direction='horizontal', rectprops = dict(facecolor='blue', alpha=0.5))).setEnabled(False)
#self.toolbar.addAction('Stack', self.show_stack_images_dialog)
self.toolbar.addSeparator()
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.rotated()
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']))
class FinishSpectrum(QWidget):
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 add_custom_line(self):
wl = QInputDialog.getDouble(self, "Custom Line", "Enter line wavelength in Å", self.fits_spectrum.spectrum.wavelengths[0],self.fits_spectrum.spectrum.wavelengths[0],self.fits_spectrum.spectrum.wavelengths[-1],3)
if not wl[1]: return
self.add_lines([{'name': 'Custom Line', 'lambda': wl[0]}])
def add_lines(self, lines):
for line in lines:
self.lines.append(ReferenceLine(line['name'], line['lambda'], self.profile_plot.axes, lambda line: self.lines.remove(line)))
def synthetize_img(wavelengths, fluxes):
f_fluxes = lambda f: math.pow(f, 3/5)
colors = [wavelength_to_rgb(w/10., f_fluxes(fluxes[i])) for i,w in enumerate(wavelengths)]
im_height = 150
colors = np.array(colors*im_height).reshape(im_height,len(colors),4)
return colors, im_height
def split_view(self):
figure = self.spectrum_plot.figure
figure.clear()
self.gs = gridspec.GridSpec(40,1)
self.profile_plot = figure.add_subplot(self.gs[0:-6])
self.synthetize = figure.add_subplot(self.gs[-3:-1], sharex = self.profile_plot)
self.synthetize.yaxis.set_visible(False)
self.synthetize.xaxis.set_visible(False)
self.draw()
def draw(self):
# self.profile_plot.clear()
if self.profile_line:
self.profile_line.remove()
self.profile_line = self.profile_plot.plot(self.spectrum.wavelengths, self.spectrum.fluxes, color='blue')[0]
self.synthetize.axes.set_axis_bgcolor('black')
with ThreadPoolExecutor(max_workers=1) as executor:
future = executor.submit(FinishSpectrum.synthetize_img, self.spectrum.wavelengths, self.spectrum.fluxes)
future.add_done_callback(lambda f: self.synthetize.imshow(f.result()[0], extent=[self.spectrum.wavelengths[0], self.spectrum.wavelengths[-1], 0, f.result()[1]]) )
self.profile_plot.axes.set_xlabel('wavelength (Å)')
self.profile_plot.axes.set_ylabel('relative flux')
self.profile_plot.axes.xaxis.set_major_locator(MaxNLocator(16)) # TODO: settings for customization?
self.profile_plot.axes.xaxis.set_minor_locator(MaxNLocator(200))
self.spectrum_plot.figure.canvas.draw()
self.gs.tight_layout(self.spectrum_plot.figure)
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 save_image(self, filename):
Notification('Image {} saved in {}'.format(os.path.basename(filename), os.path.dirname(filename)), title='File Saved', type='success', timeout=5)
self.spectrum_plot.figure.savefig(filename, bbox_inches='tight', dpi=300)
def save_finished_in_project(self):
self.project.add_file(Project.FINISHED_PROFILES, self.__save, self.object_properties)
def __save(self, filename):
self.fits_spectrum.save(filename, spectral_lines = self.lines, labels = self.labels)
def add_title(self):
title = self.object_properties.name if self.object_properties else 'Title - double click to edit'
self.add_label(text=title, coords=(self.spectrum.wavelengths[len(self.spectrum.wavelengths)/2-100], 0.95), fontsize=25, type='lineedit')
def add_fits_information_label(self):
info_text = "Object Name: {}, type: {}, spectral class: {}\nCoordinates: {}\nDate: {}\nObserver: {}\nEquipment: {}\nPosition: {}".format(
self.object_properties.name,
self.object_properties.type,
self.object_properties.sptype,
self.object_properties.printable_coordinates(),
self.object_properties.date.toString(),
self.object_properties.observer,
self.object_properties.equipment,
self.object_properties.position
)
self.add_label(info_text, type='textbox', coords=(self.spectrum.wavelengths[len(self.spectrum.wavelengths)/4*3], 0.80), fontsize=14)
self.profile_plot.figure.canvas.draw()
def add_label(self, text=None, type='textbox', coords = None, fontsize = 12, color='black'):
if not coords: coords = (self.spectrum.wavelengths[len(self.spectrum.wavelengths)/2], 0.5)
self.labels.append((type, MoveableLabel(text=text if text else 'Label - double click to edit', on_dblclick=lambda l: self.edit_label(l, type=type), x=coords[0], y=coords[1], fontsize=fontsize, color=color, axes=self.profile_plot.axes)))
self.profile_plot.figure.canvas.draw()
def edit_label(self, label, type='lineedit'):
def remove_label(self, label, dialog):
label.remove()
self.labels.remove([l for l in self.labels if l[1] == label][0])
self.profile_plot.figure.canvas.draw()
dialog.reject()
dialog = QDialog()
dialog.setWindowTitle("Edit Label")
dialog.setLayout(QVBoxLayout())
font_size = QSpinBox()
font_size.setValue(label.get_fontsize())
dialog.layout().addWidget(QLabel("Font Size"))
dialog.layout().addWidget(font_size)
text_edit = None
if type == 'lineedit':
text_edit = QLineEdit(label.get_text())
else:
text_edit = QTextEdit()
text_edit.setPlainText(label.get_text())
dialog.layout().addWidget(QLabel("Text"))
dialog.layout().addWidget(text_edit)
button_box = QDialogButtonBox(QDialogButtonBox.Ok | QDialogButtonBox.Cancel)
button_box.accepted.connect(dialog.accept)
button_box.rejected.connect(dialog.reject)
remove_button = QPushButton('Remove')
remove_button.clicked.connect(lambda: remove_label(self, label, dialog))
dialog.layout().addWidget(remove_button)
dialog.layout().addWidget(button_box)
if QDialog.Accepted != dialog.exec():
return
label.set_text(text_edit.text() if type=='lineedit' else text_edit.toPlainText())
label.set_fontsize(font_size.value())
label.axes.figure.canvas.draw()
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']))
class FinishSpectrum(QWidget):
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 add_custom_line(self):
wl = QInputDialog.getDouble(
self, "Custom Line", "Enter line wavelength in Å",
self.fits_spectrum.spectrum.wavelengths[0],
self.fits_spectrum.spectrum.wavelengths[0],
self.fits_spectrum.spectrum.wavelengths[-1], 3)
if not wl[1]: return
self.add_lines([{'name': 'Custom Line', 'lambda': wl[0]}])
def add_lines(self, lines):
for line in lines:
self.lines.append(
ReferenceLine(line['name'], line['lambda'],
self.profile_plot.axes,
lambda line: self.lines.remove(line)))
def synthetize_img(wavelengths, fluxes):
f_fluxes = lambda f: math.pow(f, 3 / 5)
colors = [
wavelength_to_rgb(w / 10., f_fluxes(fluxes[i]))
for i, w in enumerate(wavelengths)
]
im_height = 150
colors = np.array(colors * im_height).reshape(im_height, len(colors),
4)
return colors, im_height
def split_view(self):
figure = self.spectrum_plot.figure
figure.clear()
self.gs = gridspec.GridSpec(40, 1)
self.profile_plot = figure.add_subplot(self.gs[0:-6])
self.synthetize = figure.add_subplot(self.gs[-3:-1],
sharex=self.profile_plot)
self.synthetize.yaxis.set_visible(False)
self.synthetize.xaxis.set_visible(False)
self.draw()
def draw(self):
# self.profile_plot.clear()
if self.profile_line:
self.profile_line.remove()
self.profile_line = self.profile_plot.plot(self.spectrum.wavelengths,
self.spectrum.fluxes,
color='blue')[0]
self.synthetize.axes.set_facecolor('black')
with ThreadPoolExecutor(max_workers=1) as executor:
future = executor.submit(FinishSpectrum.synthetize_img,
self.spectrum.wavelengths,
self.spectrum.fluxes)
future.add_done_callback(lambda f: self.synthetize.imshow(
f.result()[0],
extent=[
self.spectrum.wavelengths[0], self.spectrum.wavelengths[
-1], 0,
f.result()[1]
]))
self.profile_plot.axes.set_xlabel('wavelength (Å)')
self.profile_plot.axes.set_ylabel('relative flux')
self.profile_plot.axes.xaxis.set_major_locator(
MaxNLocator(16)) # TODO: settings for customization?
self.profile_plot.axes.xaxis.set_minor_locator(MaxNLocator(200))
self.spectrum_plot.figure.canvas.draw()
self.gs.tight_layout(self.spectrum_plot.figure)
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 save_image(self, filename):
Notification('Image {} saved in {}'.format(os.path.basename(filename),
os.path.dirname(filename)),
title='File Saved',
type='success',
timeout=5)
self.spectrum_plot.figure.savefig(filename,
bbox_inches='tight',
dpi=300)
def save_finished_in_project(self):
self.project.add_file(Project.FINISHED_PROFILES, self.__save,
self.object_properties)
def __save(self, filename):
self.fits_spectrum.save(filename,
spectral_lines=self.lines,
labels=self.labels)
def add_title(self):
title = self.object_properties.name if self.object_properties else 'Title - double click to edit'
self.add_label(
text=title,
coords=(
self.spectrum.wavelengths[len(self.spectrum.wavelengths) / 2 -
100], 0.95),
fontsize=25,
type='lineedit')
def add_fits_information_label(self):
info_text = "Object Name: {}, type: {}, spectral class: {}\nCoordinates: {}\nDate: {}\nObserver: {}\nEquipment: {}\nPosition: {}".format(
self.object_properties.name, self.object_properties.type,
self.object_properties.sptype,
self.object_properties.printable_coordinates(),
self.object_properties.date.toString(),
self.object_properties.observer, self.object_properties.equipment,
self.object_properties.position)
self.add_label(
info_text,
type='textbox',
coords=(self.spectrum.wavelengths[len(self.spectrum.wavelengths) /
4 * 3], 0.80),
fontsize=14)
self.profile_plot.figure.canvas.draw()
def add_label(self,
text=None,
type='textbox',
coords=None,
fontsize=12,
color='black'):
if not coords:
coords = (
self.spectrum.wavelengths[len(self.spectrum.wavelengths) / 2],
0.5)
self.labels.append(
(type,
MoveableLabel(
text=text if text else 'Label - double click to edit',
on_dblclick=lambda l: self.edit_label(l, type=type),
x=coords[0],
y=coords[1],
fontsize=fontsize,
color=color,
axes=self.profile_plot.axes)))
self.profile_plot.figure.canvas.draw()
def edit_label(self, label, type='lineedit'):
def remove_label(self, label, dialog):
label.remove()
self.labels.remove([l for l in self.labels if l[1] == label][0])
self.profile_plot.figure.canvas.draw()
dialog.reject()
dialog = QDialog()
dialog.setWindowTitle("Edit Label")
dialog.setLayout(QVBoxLayout())
font_size = QSpinBox()
font_size.setValue(label.get_fontsize())
dialog.layout().addWidget(QLabel("Font Size"))
dialog.layout().addWidget(font_size)
text_edit = None
if type == 'lineedit':
text_edit = QLineEdit(label.get_text())
else:
text_edit = QTextEdit()
text_edit.setPlainText(label.get_text())
dialog.layout().addWidget(QLabel("Text"))
dialog.layout().addWidget(text_edit)
button_box = QDialogButtonBox(QDialogButtonBox.Ok
| QDialogButtonBox.Cancel)
button_box.accepted.connect(dialog.accept)
button_box.rejected.connect(dialog.reject)
remove_button = QPushButton('Remove')
remove_button.clicked.connect(
lambda: remove_label(self, label, dialog))
dialog.layout().addWidget(remove_button)
dialog.layout().addWidget(button_box)
if QDialog.Accepted != dialog.exec():
return
label.set_text(text_edit.text() if type ==
'lineedit' else text_edit.toPlainText())
label.set_fontsize(font_size.value())
label.axes.figure.canvas.draw()
