def __init__(self,
working_dir,
view=None,
img_data=None,
calibration_data=None):
self.working_dir = working_dir
if view == None:
self.view = CalibrationView()
else:
self.view = view
if img_data == None:
self.data = ImgData()
else:
self.data = img_data
if calibration_data == None:
self.calibration_data = CalibrationData(self.data)
else:
self.calibration_data = calibration_data
self.data.subscribe(self.plot_image)
self.view.set_start_values(self.calibration_data.start_values)
self._first_plot = True
self.create_signals()
self.load_calibrants_list()
self.raise_window()
def setUp(self):
self.app = QtGui.QApplication(sys.argv)
self.img_data = ImgData()
self.mask_data = MaskData()
self.calibration_data = CalibrationData(self.img_data)
self.calibration_data._calibrants_working_dir = 'Data/Calibrants'
self.calibration_view = CalibrationView()
self.working_dir = {}
self.calibration_controller = CalibrationController(working_dir=self.working_dir,
img_data=self.img_data,
mask_data=self.mask_data,
view=self.calibration_view,
calibration_data=self.calibration_data)
def __init__(self):
super(MainView, self).__init__(None)
self.setupUi(self)
self.calibration_widget = CalibrationView()
self.mask_widget = MaskView()
self.integration_widget = IntegrationView()
self.calibration_layout = QtGui.QHBoxLayout()
self.calibration_layout.setContentsMargins(0, 0, 0, 0)
self.calibration_tab.setLayout(self.calibration_layout)
self.calibration_layout.addWidget(self.calibration_widget)
self.mask_layout = QtGui.QHBoxLayout()
self.mask_layout.setContentsMargins(0, 0, 0, 0)
self.mask_tab.setLayout(self.mask_layout)
self.mask_layout.addWidget(self.mask_widget)
self.integration_layout = QtGui.QHBoxLayout()
self.integration_layout.setContentsMargins(0, 0, 0, 0)
self.integration_tab.setLayout(self.integration_layout)
self.integration_layout.addWidget(self.integration_widget)
def __init__(self, working_dir, view=None, img_data=None, calibration_data=None):
self.working_dir = working_dir
if view == None:
self.view = CalibrationView()
else:
self.view = view
if img_data == None:
self.data = ImgData()
else:
self.data = img_data
if calibration_data == None:
self.calibration_data = CalibrationData(self.data)
else:
self.calibration_data = calibration_data
self.data.subscribe(self.plot_image)
self.view.set_start_values(self.calibration_data.start_values)
self._first_plot = True
self.create_signals()
self.load_calibrants_list()
self.raise_window()
class CalibrationController(object):
def __init__(self, working_dir, view=None, img_data=None, calibration_data=None):
self.working_dir = working_dir
if view == None:
self.view = CalibrationView()
else:
self.view = view
if img_data == None:
self.data = ImgData()
else:
self.data = img_data
if calibration_data == None:
self.calibration_data = CalibrationData(self.data)
else:
self.calibration_data = calibration_data
self.data.subscribe(self.plot_image)
self.view.set_start_values(self.calibration_data.start_values)
self._first_plot = True
self.create_signals()
self.load_calibrants_list()
self.raise_window()
def raise_window(self):
self.view.show()
self.view.setWindowState(self.view.windowState() & ~QtCore.Qt.WindowMinimized | QtCore.Qt.WindowActive)
self.view.activateWindow()
self.view.raise_()
def create_signals(self):
self.create_transformation_signals()
self.create_txt_box_signals()
self.view.calibrant_cb.currentIndexChanged.connect(self.load_calibrant)
self.connect_click_function(self.view.load_file_btn, self.load_file)
self.connect_click_function(self.view.save_calibration_btn, self.save_calibration)
self.connect_click_function(self.view.load_calibration_btn, self.load_calibration)
self.connect_click_function(self.view.integrate_btn, self.calibrate)
self.connect_click_function(self.view.refine_btn, self.refine)
self.view.img_view.add_left_click_observer(self.search_peaks)
self.connect_click_function(self.view.clear_peaks_btn, self.clear_peaks_btn_click)
def create_transformation_signals(self):
self.connect_click_function(self.view.rotate_m90_btn, self.data.rotate_img_m90)
self.connect_click_function(self.view.rotate_m90_btn, self.clear_peaks_btn_click)
self.connect_click_function(self.view.rotate_p90_btn, self.data.rotate_img_p90)
self.connect_click_function(self.view.rotate_p90_btn, self.clear_peaks_btn_click)
self.connect_click_function(self.view.invert_horizontal_btn, self.data.flip_img_horizontally)
self.connect_click_function(self.view.invert_horizontal_btn, self.clear_peaks_btn_click)
self.connect_click_function(self.view.invert_vertical_btn, self.data.flip_img_vertically)
self.connect_click_function(self.view.invert_vertical_btn, self.clear_peaks_btn_click)
self.connect_click_function(self.view.reset_transformations_btn, self.data.reset_img_transformations)
self.connect_click_function(self.view.reset_transformations_btn, self.clear_peaks_btn_click)
self.view.connect(self.view.f2_wavelength_cb, QtCore.SIGNAL('clicked()'), self.wavelength_cb_changed)
self.view.connect(self.view.pf_wavelength_cb, QtCore.SIGNAL('clicked()'), self.wavelength_cb_changed)
def create_txt_box_signals(self):
self.connect_click_function(self.view.f2_update_btn, self.update_f2_btn_click)
self.connect_click_function(self.view.pf_update_btn, self.update_pyFAI_btn_click)
def update_f2_btn_click(self):
fit2d_parameter = self.view.get_fit2d_parameter()
self.calibration_data.geometry.setFit2D(directDist=fit2d_parameter['directDist'],
centerX=fit2d_parameter['centerX'],
centerY=fit2d_parameter['centerY'],
tilt=fit2d_parameter['tilt'],
tiltPlanRotation=fit2d_parameter['tiltPlanRotation'],
pixelX=fit2d_parameter['pixelX'],
pixelY=fit2d_parameter['pixelY'])
self.calibration_data.geometry.wavelength = fit2d_parameter['wavelength']
self.calibration_data.polarization_factor = fit2d_parameter['polarization_factor']
self.calibration_data.is_calibrated = True
self.update_all()
def update_pyFAI_btn_click(self):
pyFAI_parameter = self.view.get_pyFAI_parameter()
self.calibration_data.geometry.setPyFAI(dist=pyFAI_parameter['dist'],
poni1=pyFAI_parameter['poni1'],
poni2=pyFAI_parameter['poni2'],
rot1=pyFAI_parameter['rot1'],
rot2=pyFAI_parameter['rot2'],
rot3=pyFAI_parameter['rot3'],
pixel1=pyFAI_parameter['pixel1'],
pixel2=pyFAI_parameter['pixel2'])
self.calibration_data.geometry.wavelength = pyFAI_parameter['wavelength']
self.calibration_data.polarization_factor = pyFAI_parameter['polarization_factor']
self.calibration_data.is_calibrated = True
self.update_all()
def load_file(self, filename=None):
if filename is None:
filename = str(QtGui.QFileDialog.getOpenFileName(self.view, caption="Load Calibration Image",
directory=self.working_dir['image']))
if filename is not '':
self.working_dir['image'] = os.path.dirname(filename)
self.data.load(filename)
def load_calibrants_list(self):
self._calibrants_file_list = []
self._calibrants_file_names_list = []
for file in os.listdir(self.calibration_data._calibrants_working_dir):
if file.endswith('.D'):
self._calibrants_file_list.append(file)
self._calibrants_file_names_list.append(file.split('.')[:-1][0])
self.view.calibrant_cb.blockSignals(True)
self.view.calibrant_cb.clear()
self.view.calibrant_cb.addItems(self._calibrants_file_names_list)
self.view.calibrant_cb.blockSignals(False)
self.view.calibrant_cb.setCurrentIndex(7) # to LaB6
self.load_calibrant()
def load_calibrant(self, wavelength_from='start_values'):
current_index = self.view.calibrant_cb.currentIndex()
filename = os.path.join(self.calibration_data._calibrants_working_dir,
self._calibrants_file_list[current_index])
self.calibration_data.set_calibrant(filename)
wavelength = 0
if wavelength_from == 'start_values':
start_values = self.view.get_start_values()
wavelength = start_values['wavelength']
elif wavelength_from == 'pyFAI':
pyFAI_parameter, _ = self.calibration_data.get_calibration_parameter()
if pyFAI_parameter['wavelength'] is not 0:
wavelength = pyFAI_parameter['wavelength']
else:
start_values = self.view.get_start_values()
wavelength = start_values['wavelength']
else:
start_values = self.view.get_start_values()
wavelength = start_values['wavelength']
self.calibration_data.calibrant.setWavelength_change2th(wavelength)
self.view.spectrum_view.plot_vertical_lines(np.array(self.calibration_data.calibrant.get_2th()) / np.pi * 180,
name=self._calibrants_file_names_list[current_index])
def set_calibrant(self, index):
self.view.calibrant_cb.setCurrentIndex(index)
self.load_calibrant()
def plot_image(self):
if self._first_plot:
self.view.img_view.plot_image(self.data.get_img_data(), True)
self.view.img_view.auto_range()
self._first_plot = False
else:
self.view.img_view.plot_image(self.data.get_img_data(), False)
self.view.set_img_filename(self.data.filename)
def connect_click_function(self, emitter, function):
self.view.connect(emitter, QtCore.SIGNAL('clicked()'), function)
def search_peaks(self, x, y):
peak_ind = self.view.peak_num_sb.value()
if self.view.automatic_peak_search_rb.isChecked():
points = self.calibration_data.find_peaks_automatic(x, y, peak_ind - 1)
else:
search_size = np.int(self.view.search_size_sb.value())
points = self.calibration_data.find_peak(x, y, search_size, peak_ind - 1)
if len(points):
self.plot_points(points)
if self.view.automatic_peak_num_inc_cb.checkState():
self.view.peak_num_sb.setValue(peak_ind + 1)
def plot_points(self, points=None):
if points == None:
try:
points = self.calibration_data.get_point_array()
except IndexError:
points = []
if len(points):
self.view.img_view.add_scatter_data(points[:, 0] + 0.5, points[:, 1] + 0.5)
def clear_peaks_btn_click(self):
self.calibration_data.clear_peaks()
self.view.img_view.clear_scatter_plot()
self.view.peak_num_sb.setValue(1)
def wavelength_cb_changed(self):
self.calibration_data.fit_wavelength = self.view.f2_wavelength_cb.isChecked()
def calibrate(self):
self.load_calibrant() #load the right calibration file...
self.calibration_data.set_start_values(self.view.get_start_values())
self.calibration_data.calibrate()
self.update_calibration_parameter()
if self.view.options_automatic_refinement_cb.isChecked():
self.refine()
self.update_all()
def refine(self):
self.clear_peaks_btn_click()
self.load_calibrant(wavelength_from='pyFAI') #load right calibration file
# get options
algorithm = str(self.view.options_peaksearch_algorithm_cb.currentText())
delta_tth = np.float(self.view.options_delta_tth_txt.text())
intensity_min_factor = np.float(self.view.options_intensity_mean_factor_sb.value())
intensity_max = np.float(self.view.options_intensity_limit_txt.text())
num_rings = self.view.options_num_rings_sb.value()
self.calibration_data.search_peaks_on_ring(0, delta_tth, algorithm, intensity_min_factor, intensity_max)
self.calibration_data.search_peaks_on_ring(1, delta_tth, algorithm, intensity_min_factor, intensity_max)
try:
self.calibration_data.refine()
except IndexError:
print 'Did not find any Points with the specified parameters for the first two rings!'
self.plot_points()
for i in xrange(num_rings - 2):
points = self.calibration_data.search_peaks_on_ring(i + 2, delta_tth, algorithm, intensity_min_factor,
intensity_max)
self.plot_points(points)
QtGui.QApplication.processEvents()
QtGui.QApplication.processEvents()
try:
self.calibration_data.refine()
except IndexError:
print 'Did not find enough points with the specified parameters!'
self.calibration_data.integrate()
self.update_all()
def load_calibration(self, filename=None):
if filename is None:
filename = str(QtGui.QFileDialog.getOpenFileName(self.view, caption="Load calibration...",
directory=self.working_dir['calibration'],
filter='*.poni'))
if filename is not '':
self.working_dir['calibration'] = os.path.dirname(filename)
self.calibration_data.load(filename)
self.update_all()
def update_all(self):
if not self._first_plot:
self.calibration_data.integrate_1d()
self.calibration_data.integrate_2d()
self.view.cake_view.plot_image(self.calibration_data.cake_img, True)
self.view.spectrum_view.plot_data(self.calibration_data.tth, self.calibration_data.int)
self.view.spectrum_view.plot_vertical_lines(np.array(self.calibration_data.calibrant.get_2th()) /
np.pi * 180)
self.view.spectrum_view.view_box.autoRange()
if self.view.tab_widget.currentIndex() == 0:
self.view.tab_widget.setCurrentIndex(1)
if self.view.ToolBox.currentIndex() is not 2 or \
self.view.ToolBox.currentIndex() is not 3:
self.view.ToolBox.setCurrentIndex(2)
self.update_calibration_parameter()
def update_calibration_parameter(self):
pyFAI_parameter, fit2d_parameter = self.calibration_data.get_calibration_parameter()
self.view.set_calibration_parameters(pyFAI_parameter, fit2d_parameter)
def save_calibration(self, filename=None):
if filename is None:
filename = str(QtGui.QFileDialog.getSaveFileName(self.view, "Save calibration...",
self.working_dir['calibration'], '*.poni'))
if filename is not '':
self.working_dir['calibration'] = os.path.dirname(filename)
self.calibration_data.geometry.save(filename)
class CalibrationControllerTest(unittest.TestCase):
def setUp(self):
self.app = QtGui.QApplication(sys.argv)
self.img_data = ImgData()
self.mask_data = MaskData()
self.calibration_data = CalibrationData(self.img_data)
self.calibration_data._calibrants_working_dir = 'Data/Calibrants'
self.calibration_view = CalibrationView()
self.working_dir = {}
self.calibration_controller = CalibrationController(working_dir=self.working_dir,
img_data=self.img_data,
mask_data=self.mask_data,
view=self.calibration_view,
calibration_data=self.calibration_data)
def tearDown(self):
del self.app
def test_automatic_calibration1(self):
self.calibration_controller.load_img('Data/LaB6_p49_40keV_006.tif')
self.calibration_controller.search_peaks(1179.6, 1129.4)
self.calibration_controller.search_peaks(1268.5, 1119.8)
self.calibration_controller.view.sv_wavelength_txt.setText('0.31')
self.calibration_controller.view.sv_distance_txt.setText('200')
self.calibration_controller.view.sv_pixel_width_txt.setText('79')
self.calibration_controller.view.sv_pixel_height_txt.setText('79')
self.calibration_controller.view.calibrant_cb.setCurrentIndex(7)
self.calibration_controller.calibrate()
self.calibration_controller.view.cake_view.set_vertical_line_pos(1419.8, 653.4)
def test_automatic_calibration2(self):
self.calibration_controller.load_img('Data/LaB6_WOS_30keV_005.tif')
self.calibration_controller.search_peaks(1245.2, 1919.3)
self.calibration_controller.search_peaks(1334.0, 1823.7)
self.calibration_controller.view.sv_wavelength_txt.setText('0.3344')
self.calibration_controller.view.sv_distance_txt.setText('500')
self.calibration_controller.view.sv_pixel_width_txt.setText('200')
self.calibration_controller.view.sv_pixel_height_txt.setText('200')
self.calibration_controller.view.calibrant_cb.setCurrentIndex(7)
self.calibration_controller.calibrate()
self.calibration_controller.view.cake_view.set_vertical_line_pos(206.5, 171.6)
def test_automatic_calibration3(self):
self.calibration_controller.load_img('Data/CeO2_Oct24_2014_001_0000.tif')
QTest.mouseClick(self.calibration_view.automatic_peak_num_inc_cb, QtCore.Qt.LeftButton)
self.assertFalse(self.calibration_view.automatic_peak_num_inc_cb.isChecked())
self.calibration_controller.search_peaks(517.664434674, 647.529865592)
self.calibration_controller.search_peaks(667.380513299, 525.252854758)
self.calibration_controller.search_peaks(671.110095329, 473.571503774)
self.calibration_controller.search_peaks(592.788872703, 350.495296791)
self.calibration_controller.search_peaks(387.395462348, 390.987901686)
self.calibration_controller.search_peaks(367.94835605, 554.290314848)
self.calibration_controller.view.sv_wavelength_txt.setText('0.406626')
self.calibration_controller.view.sv_distance_txt.setText('200')
self.calibration_controller.view.sv_pixel_width_txt.setText('172')
self.calibration_controller.view.sv_pixel_height_txt.setText('172')
self.calibration_controller.view.calibrant_cb.setCurrentIndex(4)
start_values = self.calibration_view.get_start_values()
self.assertAlmostEqual(start_values['wavelength'], 0.406626e-10)
self.assertAlmostEqual(start_values['pixel_height'], 172e-6)
self.assertAlmostEqual(start_values['pixel_width'], 172e-6)
self.calibration_controller.load_calibrant()
self.assertAlmostEqual(self.calibration_data.calibrant.wavelength, 0.406626e-10)
QTest.mouseClick(self.calibration_view.integrate_btn, QtCore.Qt.LeftButton)
calibration_parameter = self.calibration_data.get_calibration_parameter()[0]
self.assertAlmostEqual(calibration_parameter['dist'], .2086, places=4)
def test_automatic_calibration_with_supersampling(self):
self.calibration_controller.load_img('Data/LaB6_p49_40keV_006.tif')
self.calibration_controller.search_peaks(1179.6, 1129.4)
self.calibration_controller.search_peaks(1268.5, 1119.8)
self.calibration_controller.view.sv_wavelength_txt.setText('0.31')
self.calibration_controller.view.sv_distance_txt.setText('200')
self.calibration_controller.view.sv_pixel_width_txt.setText('79')
self.calibration_controller.view.sv_pixel_height_txt.setText('79')
self.calibration_controller.view.calibrant_cb.setCurrentIndex(7)
self.img_data.set_supersampling(2)
self.calibration_data.set_supersampling(2)
self.calibration_controller.calibrate()
def test_automatic_calibration_with_supersampling_and_mask(self):
self.calibration_controller.load_img('Data/LaB6_p49_40keV_006.tif')
self.calibration_controller.search_peaks(1179.6, 1129.4)
self.calibration_controller.search_peaks(1268.5, 1119.8)
self.calibration_controller.view.sv_wavelength_txt.setText('0.31')
self.calibration_controller.view.sv_distance_txt.setText('200')
self.calibration_controller.view.sv_pixel_width_txt.setText('79')
self.calibration_controller.view.sv_pixel_height_txt.setText('79')
self.calibration_controller.view.calibrant_cb.setCurrentIndex(7)
self.img_data.set_supersampling(2)
self.mask_data.mask_below_threshold(self.img_data._img_data, 1)
self.mask_data.set_supersampling(2)
self.calibration_data.set_supersampling(2)
self.calibration_controller.view.use_mask_cb.setChecked(True)
self.calibration_controller.calibrate()
def test_calibrating_one_image_size_and_loading_different_image_size(self):
self.calibration_controller.load_img('Data/LaB6_p49_40keV_006.tif')
self.calibration_controller.search_peaks(1179.6, 1129.4)
self.calibration_controller.search_peaks(1268.5, 1119.8)
self.calibration_controller.view.sv_wavelength_txt.setText('0.31')
self.calibration_controller.view.sv_distance_txt.setText('200')
self.calibration_controller.view.sv_pixel_width_txt.setText('79')
self.calibration_controller.view.sv_pixel_height_txt.setText('79')
self.calibration_controller.view.calibrant_cb.setCurrentIndex(7)
self.calibration_controller.view.options_automatic_refinement_cb.setChecked(False)
self.calibration_controller.view.use_mask_cb.setChecked(True)
self.calibration_controller.calibrate()
self.calibration_data.integrate_1d()
self.calibration_data.integrate_2d()
self.calibration_controller.load_img('Data/CeO2_Pilatus1M.tif')
self.calibration_data.integrate_1d()
self.calibration_data.integrate_2d()
def test_loading_and_saving_of_calibration_files(self):
self.calibration_controller.load_calibration('Data/calibration.poni')
self.calibration_controller.save_calibration('Data/calibration.poni')
class CalibrationController(object):
def __init__(self,
working_dir,
view=None,
img_data=None,
calibration_data=None):
self.working_dir = working_dir
if view == None:
self.view = CalibrationView()
else:
self.view = view
if img_data == None:
self.data = ImgData()
else:
self.data = img_data
if calibration_data == None:
self.calibration_data = CalibrationData(self.data)
else:
self.calibration_data = calibration_data
self.data.subscribe(self.plot_image)
self.view.set_start_values(self.calibration_data.start_values)
self._first_plot = True
self.create_signals()
self.load_calibrants_list()
self.raise_window()
def raise_window(self):
self.view.show()
self.view.setWindowState(self.view.windowState()
& ~QtCore.Qt.WindowMinimized
| QtCore.Qt.WindowActive)
self.view.activateWindow()
self.view.raise_()
def create_signals(self):
self.create_transformation_signals()
self.create_txt_box_signals()
self.view.calibrant_cb.currentIndexChanged.connect(self.load_calibrant)
self.connect_click_function(self.view.load_file_btn, self.load_file)
self.connect_click_function(self.view.save_calibration_btn,
self.save_calibration)
self.connect_click_function(self.view.load_calibration_btn,
self.load_calibration)
self.connect_click_function(self.view.integrate_btn, self.calibrate)
self.connect_click_function(self.view.refine_btn, self.refine)
self.view.img_view.add_left_click_observer(self.search_peaks)
self.connect_click_function(self.view.clear_peaks_btn,
self.clear_peaks_btn_click)
def create_transformation_signals(self):
self.connect_click_function(self.view.rotate_m90_btn,
self.data.rotate_img_m90)
self.connect_click_function(self.view.rotate_m90_btn,
self.clear_peaks_btn_click)
self.connect_click_function(self.view.rotate_p90_btn,
self.data.rotate_img_p90)
self.connect_click_function(self.view.rotate_p90_btn,
self.clear_peaks_btn_click)
self.connect_click_function(self.view.invert_horizontal_btn,
self.data.flip_img_horizontally)
self.connect_click_function(self.view.invert_horizontal_btn,
self.clear_peaks_btn_click)
self.connect_click_function(self.view.invert_vertical_btn,
self.data.flip_img_vertically)
self.connect_click_function(self.view.invert_vertical_btn,
self.clear_peaks_btn_click)
self.connect_click_function(self.view.reset_transformations_btn,
self.data.reset_img_transformations)
self.connect_click_function(self.view.reset_transformations_btn,
self.clear_peaks_btn_click)
self.view.connect(self.view.f2_wavelength_cb,
QtCore.SIGNAL('clicked()'),
self.wavelength_cb_changed)
self.view.connect(self.view.pf_wavelength_cb,
QtCore.SIGNAL('clicked()'),
self.wavelength_cb_changed)
def create_txt_box_signals(self):
self.connect_click_function(self.view.f2_update_btn,
self.update_f2_btn_click)
self.connect_click_function(self.view.pf_update_btn,
self.update_pyFAI_btn_click)
def update_f2_btn_click(self):
fit2d_parameter = self.view.get_fit2d_parameter()
self.calibration_data.geometry.setFit2D(
directDist=fit2d_parameter['directDist'],
centerX=fit2d_parameter['centerX'],
centerY=fit2d_parameter['centerY'],
tilt=fit2d_parameter['tilt'],
tiltPlanRotation=fit2d_parameter['tiltPlanRotation'],
pixelX=fit2d_parameter['pixelX'],
pixelY=fit2d_parameter['pixelY'])
self.calibration_data.geometry.wavelength = fit2d_parameter[
'wavelength']
self.calibration_data.polarization_factor = fit2d_parameter[
'polarization_factor']
self.calibration_data.is_calibrated = True
self.update_all()
def update_pyFAI_btn_click(self):
pyFAI_parameter = self.view.get_pyFAI_parameter()
self.calibration_data.geometry.setPyFAI(
dist=pyFAI_parameter['dist'],
poni1=pyFAI_parameter['poni1'],
poni2=pyFAI_parameter['poni2'],
rot1=pyFAI_parameter['rot1'],
rot2=pyFAI_parameter['rot2'],
rot3=pyFAI_parameter['rot3'],
pixel1=pyFAI_parameter['pixel1'],
pixel2=pyFAI_parameter['pixel2'])
self.calibration_data.geometry.wavelength = pyFAI_parameter[
'wavelength']
self.calibration_data.polarization_factor = pyFAI_parameter[
'polarization_factor']
self.calibration_data.is_calibrated = True
self.update_all()
def load_file(self, filename=None):
if filename is None:
filename = str(
QtGui.QFileDialog.getOpenFileName(
self.view,
caption="Load Calibration Image",
directory=self.working_dir['image']))
if filename is not '':
self.working_dir['image'] = os.path.dirname(filename)
self.data.load(filename)
def load_calibrants_list(self):
self._calibrants_file_list = []
self._calibrants_file_names_list = []
for file in os.listdir(self.calibration_data._calibrants_working_dir):
if file.endswith('.D'):
self._calibrants_file_list.append(file)
self._calibrants_file_names_list.append(
file.split('.')[:-1][0])
self.view.calibrant_cb.blockSignals(True)
self.view.calibrant_cb.clear()
self.view.calibrant_cb.addItems(self._calibrants_file_names_list)
self.view.calibrant_cb.blockSignals(False)
self.view.calibrant_cb.setCurrentIndex(7) # to LaB6
self.load_calibrant()
def load_calibrant(self, wavelength_from='start_values'):
current_index = self.view.calibrant_cb.currentIndex()
filename = os.path.join(self.calibration_data._calibrants_working_dir,
self._calibrants_file_list[current_index])
self.calibration_data.set_calibrant(filename)
wavelength = 0
if wavelength_from == 'start_values':
start_values = self.view.get_start_values()
wavelength = start_values['wavelength']
elif wavelength_from == 'pyFAI':
pyFAI_parameter, _ = self.calibration_data.get_calibration_parameter(
)
if pyFAI_parameter['wavelength'] is not 0:
wavelength = pyFAI_parameter['wavelength']
else:
start_values = self.view.get_start_values()
wavelength = start_values['wavelength']
else:
start_values = self.view.get_start_values()
wavelength = start_values['wavelength']
self.calibration_data.calibrant.setWavelength_change2th(wavelength)
self.view.spectrum_view.plot_vertical_lines(
np.array(self.calibration_data.calibrant.get_2th()) / np.pi * 180,
name=self._calibrants_file_names_list[current_index])
def set_calibrant(self, index):
self.view.calibrant_cb.setCurrentIndex(index)
self.load_calibrant()
def plot_image(self):
if self._first_plot:
self.view.img_view.plot_image(self.data.get_img_data(), True)
self.view.img_view.auto_range()
self._first_plot = False
else:
self.view.img_view.plot_image(self.data.get_img_data(), False)
self.view.set_img_filename(self.data.filename)
def connect_click_function(self, emitter, function):
self.view.connect(emitter, QtCore.SIGNAL('clicked()'), function)
def search_peaks(self, x, y):
peak_ind = self.view.peak_num_sb.value()
if self.view.automatic_peak_search_rb.isChecked():
points = self.calibration_data.find_peaks_automatic(
x, y, peak_ind - 1)
else:
search_size = np.int(self.view.search_size_sb.value())
points = self.calibration_data.find_peak(x, y, search_size,
peak_ind - 1)
if len(points):
self.plot_points(points)
if self.view.automatic_peak_num_inc_cb.checkState():
self.view.peak_num_sb.setValue(peak_ind + 1)
def plot_points(self, points=None):
if points == None:
try:
points = self.calibration_data.get_point_array()
except IndexError:
points = []
if len(points):
self.view.img_view.add_scatter_data(points[:, 0] + 0.5,
points[:, 1] + 0.5)
def clear_peaks_btn_click(self):
self.calibration_data.clear_peaks()
self.view.img_view.clear_scatter_plot()
self.view.peak_num_sb.setValue(1)
def wavelength_cb_changed(self):
self.calibration_data.fit_wavelength = self.view.f2_wavelength_cb.isChecked(
)
def calibrate(self):
self.load_calibrant() #load the right calibration file...
self.calibration_data.set_start_values(self.view.get_start_values())
self.calibration_data.calibrate()
self.update_calibration_parameter()
if self.view.options_automatic_refinement_cb.isChecked():
self.refine()
self.update_all()
def refine(self):
self.clear_peaks_btn_click()
self.load_calibrant(
wavelength_from='pyFAI') #load right calibration file
# get options
algorithm = str(
self.view.options_peaksearch_algorithm_cb.currentText())
delta_tth = np.float(self.view.options_delta_tth_txt.text())
intensity_min_factor = np.float(
self.view.options_intensity_mean_factor_sb.value())
intensity_max = np.float(self.view.options_intensity_limit_txt.text())
num_rings = self.view.options_num_rings_sb.value()
self.calibration_data.search_peaks_on_ring(0, delta_tth, algorithm,
intensity_min_factor,
intensity_max)
self.calibration_data.search_peaks_on_ring(1, delta_tth, algorithm,
intensity_min_factor,
intensity_max)
try:
self.calibration_data.refine()
except IndexError:
print 'Did not find any Points with the specified parameters for the first two rings!'
self.plot_points()
for i in xrange(num_rings - 2):
points = self.calibration_data.search_peaks_on_ring(
i + 2, delta_tth, algorithm, intensity_min_factor,
intensity_max)
self.plot_points(points)
QtGui.QApplication.processEvents()
QtGui.QApplication.processEvents()
try:
self.calibration_data.refine()
except IndexError:
print 'Did not find enough points with the specified parameters!'
self.calibration_data.integrate()
self.update_all()
def load_calibration(self, filename=None):
if filename is None:
filename = str(
QtGui.QFileDialog.getOpenFileName(
self.view,
caption="Load calibration...",
directory=self.working_dir['calibration'],
filter='*.poni'))
if filename is not '':
self.working_dir['calibration'] = os.path.dirname(filename)
self.calibration_data.load(filename)
self.update_all()
def update_all(self):
if not self._first_plot:
self.calibration_data.integrate_1d()
self.calibration_data.integrate_2d()
self.view.cake_view.plot_image(self.calibration_data.cake_img,
True)
self.view.spectrum_view.plot_data(self.calibration_data.tth,
self.calibration_data.int)
self.view.spectrum_view.plot_vertical_lines(
np.array(self.calibration_data.calibrant.get_2th()) / np.pi *
180)
self.view.spectrum_view.view_box.autoRange()
if self.view.tab_widget.currentIndex() == 0:
self.view.tab_widget.setCurrentIndex(1)
if self.view.ToolBox.currentIndex() is not 2 or \
self.view.ToolBox.currentIndex() is not 3:
self.view.ToolBox.setCurrentIndex(2)
self.update_calibration_parameter()
def update_calibration_parameter(self):
pyFAI_parameter, fit2d_parameter = self.calibration_data.get_calibration_parameter(
)
self.view.set_calibration_parameters(pyFAI_parameter, fit2d_parameter)
def save_calibration(self, filename=None):
if filename is None:
filename = str(
QtGui.QFileDialog.getSaveFileName(
self.view, "Save calibration...",
self.working_dir['calibration'], '*.poni'))
if filename is not '':
self.working_dir['calibration'] = os.path.dirname(filename)
self.calibration_data.geometry.save(filename)
