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)
