def __set_ref(self, index): self.reference = self.files_model.item(index).data() self.rotate_dialog = RotateImageDialog(self.fits_file, 0) self.rotate_dialog.rotated.connect(self.__rotated) indexes = lambda data: (int(len(data)/4), int(len(data)/4*3)) self.__set_reference_indexes(indexes(self.reference['profile']), indexes(self.reference['spatial']) ) #self.reference_indexes = { 'h': indexes(self.reference['profile']), 'v': indexes(self.reference['spatial']) } for data in self.__files_data() : self.align(data)
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()
class StackImages(QWidget): def __init__(self, fits_file, settings): QWidget.__init__(self) self.fits_file = fits_file self.ui = Ui_StackImages() self.ui.setupUi(self) self.settings = settings self.degrees = 0. # TODO self.files_model = QStandardItemModel() self.files_model.setHorizontalHeaderLabels(['File', 'Quality', 'Align']) self.ui.files.setModel(self.files_model) self.__add_file_to_model(fits_file) self.plot = QtCommons.nestWidget(self.ui.plot, QImPlotWidget(self.__files_data()[0]['data'], cmap='gray')) self.__set_ref(0) self.toolbar = QToolBar() self.add = self.toolbar.addAction('Add', lambda: open_files_sticky('Open FITS Images',FITS_IMG_EXTS, self.__open, settings, IMPORT_IMG, parent=self )) self.remove = self.toolbar.addAction('Remove', self.__remove_selected_rows) self.reference_action = self.toolbar.addAction('Reference', lambda: self.__set_ref(self.ui.files.selectionModel().selectedRows()[0].row() ) ) self.toolbar.addAction('Select alignment region', lambda: self.plot.add_rectangle_selector('select_align', self.__alignment_region_selected)) self.toolbar.addAction('Rotate', lambda: self.rotate_dialog.show() ) self.ui.files.selectionModel().selectionChanged.connect(lambda sel, unsel: self.__selection_changed() ) self.ui.files.clicked.connect(lambda index: self.__draw_image(index.row())) #self.accepted.connect(self.stack) self.__selection_changed() def __selection_changed(self): sel = len(self.ui.files.selectionModel().selectedRows()) self.remove.setEnabled(sel) self.reference_action.setEnabled(sel == 1) def __draw_image(self,index): image_view = self.plot.axes_image image_view.set_data(self.files_model.item(index).data()['data']) image_view.figure.canvas.draw() def __open(self, files): existing_files = [d['file'] for d in self.__files_data()] progress = QProgressDialog("Loading files", None, 0, len(files), self); progress.setWindowModality(Qt.WindowModal); progress.show() for index, file in enumerate(files): progress.setValue(index+1) QApplication.instance().processEvents() if file not in existing_files: self.__add_file(fits.open(file)) def __row_index(self, data): return [i for i, d in enumerate(self.__files_data()) if d['file'] == data['file']][0] def __add_file_to_model(self, fits_file): item = QStandardItem(os.path.basename(fits_file.filename())) data = fits_file[0].data data = scipy.ndimage.interpolation.rotate(data, self.degrees, reshape=True, order=5, mode='constant') spatial = data.sum(1) profile = data.sum(0) roots = UnivariateSpline(range(0, len(spatial)), spatial-np.max(spatial)/2, s=0.2, k=3).roots() quality = roots[1]-roots[0] item.setData({'file': fits_file.filename(), 'fits': fits_file, 'data': data, 'spatial': spatial, 'profile': profile, 'quality': quality}) offset = QStandardItem('N/A') # TODO quality_item = QStandardItem("") self.files_model.appendRow([item, quality_item, offset]) return item def __add_file(self, fits_file): item = self.__add_file_to_model(fits_file) if self.files_model.rowCount() == 1: self.__set_ref(0) else: self.align(item.data()) self.__update_qualities() def __update_qualities(self): qualities = [d['quality'] for d in self.__files_data()] self.qualities = (min(qualities), max(qualities)) for index in range(0, self.files_model.rowCount()): self.files_model.item(index, 1).setText("{}%".format(self.__quality_percent(self.files_model.item(index).data()['quality']))) def __quality_percent(self, quality): return 100. - (100. * (quality-self.qualities[0]) / (self.qualities[1]-self.qualities[0])) def align(self, data): if data['file'] == self.reference['file']: self.__update_offset(data, (0, 0)) return offset_range = lambda n: range(1-int(n), int(n)-1) offsets = lambda name, indexes: [ (pearsonr(self.reference[name][indexes[0]:indexes[1]], data[name][indexes[0]-offset:indexes[1]-offset] )[0], offset) for offset in offset_range(indexes[0]) ] x_offset = sorted(offsets('profile', self.reference_indexes['h']), key=lambda x: x[0])[-1] y_offset = sorted(offsets('spatial', self.reference_indexes['v']), key=lambda y: y[0])[-1] self.__update_offset(data, (x_offset[1], y_offset[1])) def __update_offset(self, data, offset): row = self.__row_index(data) self.files_model.item(row, 2).setText('{}, {}'.format(offset[0], offset[1])) data.update({'offset': {'x': offset[0], 'y': offset[1]}}) self.files_model.item(row).setData(data) def __files_data(self): return [self.files_model.item(i).data() for i in range(0, self.files_model.rowCount())] def __remove_selected_rows(self): for row in sorted([r.row() for r in self.ui.files.selectionModel().selectedRows()], reverse=True): self.files_model.removeRows(row, 1) if self.files_model.rowCount() == 0: return if len([f for f in self.__files_data() if f['file'] == self.reference['file']]) == 0: self.__set_ref(0) def __set_ref(self, index): self.reference = self.files_model.item(index).data() self.rotate_dialog = RotateImageDialog(self.fits_file, 0) self.rotate_dialog.rotated.connect(self.__rotated) indexes = lambda data: (int(len(data)/4), int(len(data)/4*3)) self.__set_reference_indexes(indexes(self.reference['profile']), indexes(self.reference['spatial']) ) #self.reference_indexes = { 'h': indexes(self.reference['profile']), 'v': indexes(self.reference['spatial']) } for data in self.__files_data() : self.align(data) def __rotated(self): self.degrees = self.rotate_dialog.degrees() for index in range(0, self.files_model.rowCount()): self.files_model.removeRow(index) self.__add_file(self.fits_file) self.__draw_image(0) def __alignment_region_selected(self, eclick, erelease): self.__set_reference_indexes((eclick.xdata, erelease.xdata), (eclick.ydata, erelease.ydata)) def __set_reference_indexes(self, x, y): self.reference_indexes = { 'h': x, 'v': y } self.__draw_reference_rect() def __draw_reference_rect(self): self.plot.rm_element('reference_indexes') x, y = self.reference_indexes['h'], self.reference_indexes['v'] rect = Rectangle((x[0], y[0]), x[1]-x[0], y[1]-y[0], fill=True, alpha=0.3, color='green') self.plot.figure.axes[0].add_artist(rect) self.plot.add_element(rect, 'reference_indexes') self.plot.figure.canvas.draw() def stack(self): dataset = self.__files_data() median = MedianStacker(dataset).median() self.fits_file[0].data = median
class ImportImage(QWidget): def icon(): return QIcon(':/image_20') ACTION_TEXT = 'Import Image' def pick(on_ok, settings): open_file_sticky('Open FITS Image',FITS_IMG_EXTS, on_ok, settings, IMPORT_IMG ) 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 rotated(self): self.image_view.set_data(self.rotate_dialog.data_rotated) self.image_view.axes.relim() self.image_view.axes.autoscale_view() self.image_view.set_extent([self.rotate_dialog.data_rotated.shape[1],0, self.rotate_dialog.data_rotated.shape[0],0]) self.image_view.figure.canvas.draw() self.draw_plot(self.spectrum_plot.axes, self.spectrum_profile()) self.draw_plot(self.spatial_plot.axes, self.spatial_profile()) def background_span_selected(self, min, max): self.background_span_selection = (min, max) self.spatial_plot.add_span('background_window', min, max, 'v', facecolor='gray', alpha=0.5) self.image_plot.add_span('background_window', min, max, 'h', facecolor='red', alpha=0.5, clip_on=True) self.draw_plot(self.spectrum_plot.axes, self.spectrum_profile()) def spectrum_span_selected(self, min, max): self.spectrum_span_selection = (min, max) self.spatial_plot.add_span('spectrum_window', min, max, 'v', facecolor='g', alpha=0.5) self.image_plot.add_span('spectrum_window', min, max, 'h', facecolor='y', alpha=0.25, clip_on=True) self.draw_plot(self.spectrum_plot.axes, self.spectrum_profile()) def draw_plot(self, axes, data): axes.clear() axes.plot(data) axes.figure.tight_layout() axes.figure.canvas.draw() def spatial_profile(self): return self.rotate_dialog.data_rotated.sum(1) def spectrum_profile(self): return self.rotate_dialog.data_rotated[self.spectrum_span_selection[0]:self.spectrum_span_selection[1]+1,:].sum(0) if hasattr(self, 'spectrum_span_selection') else self.rotate_dialog.data_rotated.sum(0) def save(self, save_file): data = self.spectrum_profile() data -= np.amin(data) data /= np.amax(data) hdu = self.fits_file[0] hdu.data = data hdu.header['ORIGIN'] = 'PySpectrum' self.fits_file.writeto(save_file, clobber=True) def save_profile(self): if not self.project: save_file_sticky('Save plot...', 'FITS file (.fit)', lambda f: self.save(f[0]), self.settings, RAW_PROFILE ) return if not self.object_properties.name: QMessageBox.information(self, 'Save FITS', 'Please set file information (name, date, etc) using the Object Properties button before saving') return file_path = self.project.add_file(Project.RAW_PROFILE, object_properties = self.object_properties, on_added=self.save)