def setUp(self):
self.img_data = ImgData()
self.img_data.load('Data/LaB6_p49_40keV_006.tif')
self.calibration_data = CalibrationData(self.img_data)
self.calibration_data.calibrant.load_file('Data/Calibrants/LaB6.D')
self.calibration_data.calibrant.set_wavelength(0.31 * 1e-10)
self.calibration_data.load('Data/LaB6_p49_40keV_006.poni')
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.img_data = ImgData()
self.img_data.load('Data/Mg2SiO4_ambient_001.tif')
self.calibration_data = CalibrationData(self.img_data)
self.calibration_data.load('Data/calibration.poni')
self.mask_data = MaskData()
self.mask_data.load_mask('Data/test.mask')
self.spectrum_data = SpectrumData()
class CombinedDataTest(unittest.TestCase):
def setUp(self):
self.img_data = ImgData()
self.img_data.load('Data/LaB6_p49_40keV_006.tif')
self.calibration_data = CalibrationData(self.img_data)
self.calibration_data.calibrant.load_file('Data/Calibrants/LaB6.D')
self.calibration_data.calibrant.set_wavelength(0.31 * 1e-10)
self.calibration_data.load('Data/LaB6_p49_40keV_006.poni')
def test_recalibration(self):
self.calibration_data.recalibrate()
plt.imshow(self.img_data.img_data)
plt.plot(self.calibration_data.geometry.data[:, 0], self.calibration_data.geometry.data[:, 1], 'g.')
plt.savefig('Results/recalib_massif.jpg')
self.calibration_data.recalibrate('blob')
plt.figure(2)
plt.imshow(self.img_data.img_data)
plt.plot(self.calibration_data.geometry.data[:, 0], self.calibration_data.geometry.data[:, 1], 'g.')
plt.savefig('Results/recalib_blob.jpg')
self.calibration_data.recalibrate('blob')
plt.figure(3)
plt.imshow(self.img_data.img_data)
plt.plot(self.calibration_data.geometry.data[:, 0], self.calibration_data.geometry.data[:, 1], 'g.')
plt.savefig('Results/recalib_blob2.jpg')
class CombinedDataTest(unittest.TestCase):
def setUp(self):
self.img_data = ImgData()
self.img_data.load('Data/LaB6_p49_40keV_006.tif')
self.calibration_data = CalibrationData(self.img_data)
self.calibration_data.calibrant.load_file('Data/Calibrants/LaB6.D')
self.calibration_data.calibrant.set_wavelength(0.31 * 1e-10)
self.calibration_data.load('Data/LaB6_p49_40keV_006.poni')
def test_recalibration(self):
self.calibration_data.recalibrate()
plt.imshow(self.img_data.img_data)
plt.plot(self.calibration_data.geometry.data[:, 0],
self.calibration_data.geometry.data[:, 1], 'g.')
plt.savefig('Results/recalib_massif.jpg')
self.calibration_data.recalibrate('blob')
plt.figure(2)
plt.imshow(self.img_data.img_data)
plt.plot(self.calibration_data.geometry.data[:, 0],
self.calibration_data.geometry.data[:, 1], 'g.')
plt.savefig('Results/recalib_blob.jpg')
self.calibration_data.recalibrate('blob')
plt.figure(3)
plt.imshow(self.img_data.img_data)
plt.plot(self.calibration_data.geometry.data[:, 0],
self.calibration_data.geometry.data[:, 1], 'g.')
plt.savefig('Results/recalib_blob2.jpg')
class MaskUnitTest(unittest.TestCase):
def setUp(self):
self.img_data = ImgData()
self.calibration_data = CalibrationData(self.img_data)
def tearDown(self):
pass
def test_loading_calibration_gives_right_pixel_size(self):
self.calibration_data.spectrum_geometry.load("Data/calibration_PE.poni")
self.assertEqual(self.calibration_data.spectrum_geometry.pixel1, 0.0002)
self.calibration_data.load("Data/calibration_PE.poni")
self.assertEqual(self.calibration_data.spectrum_geometry.pixel1, 0.0002)
def __init__(self, app):
self.splash_img = QtGui.QPixmap("UiFiles/splash.png")
self.splash_screen = QtGui.QSplashScreen(
self.splash_img, QtCore.Qt.WindowStaysOnTopHint)
self.splash_screen.show()
app.processEvents()
time.sleep(1)
app.processEvents()
self.view = MainView()
#create data
self.img_data = ImgData()
self.calibration_data = CalibrationData(self.img_data)
self.mask_data = MaskData()
self.spectrum_data = SpectrumData()
self.phase_data = PhaseData()
self.load_directories()
#create controller
self.calibration_controller = CalibrationController(
self.working_dir, self.view.calibration_widget, self.img_data,
self.mask_data, self.calibration_data)
self.mask_controller = MaskController(self.working_dir,
self.view.mask_widget,
self.img_data, self.mask_data)
self.integration_controller = IntegrationController(
self.working_dir, self.view.integration_widget, self.img_data,
self.mask_data, self.calibration_data, self.spectrum_data,
self.phase_data)
self.create_signals()
self.set_title()
self.raise_window()
self.splash_screen.finish(self.view)
def setUp(self):
self.img_data = ImgData()
self.img_data.load('Data/LaB6_p49_40keV_006.tif')
self.calibration_data = CalibrationData(self.img_data)
self.calibration_data.calibrant.load_file('Data/Calibrants/LaB6.D')
self.calibration_data.calibrant.set_wavelength(0.31 * 1e-10)
self.calibration_data.load('Data/LaB6_p49_40keV_006.poni')
def __init__(self):
self.view = MainView()
#create data
self.img_data = ImgData()
self.calibration_data = CalibrationData(self.img_data)
self.mask_data = MaskData()
self.spectrum_data = SpectrumData()
self.phase_data = PhaseData()
self.load_directories()
#create controller
self.calibration_controller = CalibrationController(
self.working_dir, self.view.calibration_widget, self.img_data,
self.calibration_data)
self.mask_controller = MaskController(self.working_dir,
self.view.mask_widget,
self.img_data, self.mask_data)
self.integration_controller = IntegrationController(
self.working_dir, self.view.integration_widget, self.img_data,
self.mask_data, self.calibration_data, self.spectrum_data,
self.phase_data)
self.create_signals()
self.raise_window()
def __init__(self):
self.view = MainView()
#create data
self.img_data = ImgData()
self.calibration_data = CalibrationData(self.img_data)
self.mask_data = MaskData()
self.spectrum_data = SpectrumData()
self.phase_data = PhaseData()
self.settings_directory = os.path.join(os.path.expanduser("~"), '.Dioptas')
self.working_directories = {'calibration': '', 'mask': '', 'image': '', 'spectrum': '', 'overlay': '',
'phase': ''}
self.load_settings()
#create controller
self.calibration_controller = CalibrationController(self.working_directories,
self.view.calibration_widget,
self.img_data,
self.mask_data,
self.calibration_data)
self.mask_controller = MaskController(self.working_directories,
self.view.mask_widget,
self.img_data,
self.mask_data)
self.integration_controller = IntegrationController(self.working_directories,
self.view.integration_widget,
self.img_data,
self.mask_data,
self.calibration_data,
self.spectrum_data,
self.phase_data)
self.create_signals()
self.set_title()
self.raise_window(self.view)
def setUp(self):
self.img_data = ImgData()
self.img_data.load('Data/Mg2SiO4_ambient_001.tif')
self.calibration_data = CalibrationData(self.img_data)
self.calibration_data.load('Data/calibration.poni')
self.mask_data = MaskData()
self.mask_data.mask_ellipse(500, 500, 100, 100)
self.spectrum_data = SpectrumData()
def setUp(self):
self.app = QtGui.QApplication(sys.argv)
self.image_data = ImgData()
self.calibration_data = CalibrationData(self.image_data)
self.calibration_data._calibrants_working_dir = 'Data/Calibrants'
self.calibration_controller = CalibrationController(img_data=self.image_data, \
calibration_data=self.calibration_data)
class CombinedDataTest(unittest.TestCase):
def setUp(self):
self.img_data = ImgData()
self.img_data.load('Data/Mg2SiO4_ambient_001.tif')
self.calibration_data = CalibrationData(self.img_data)
self.calibration_data.load('Data/calibration.poni')
self.mask_data = MaskData()
self.mask_data.mask_ellipse(500, 500, 100, 100)
self.spectrum_data = SpectrumData()
def test_dependencies(self):
tth1, int1 = self.calibration_data.integrate_1d()
self.img_data.load_next_file()
self.assertEqual(os.path.abspath(self.img_data.filename),
os.path.abspath('Data/Mg2SiO4_ambient_002.tif'))
tth2, int2 = self.calibration_data.integrate_1d()
self.assertFalse(np.array_equal(int1, int2))
plt.figure(1)
plt.plot(tth1, int1)
plt.plot(tth2, int2)
plt.savefig('Results/dependencies1.png')
tth3, int3 = self.calibration_data.integrate_1d(mask=self.mask_data.get_mask())
self.assertFalse(np.array_equal(int2, int3))
plt.figure(2)
plt.plot(tth2, int2)
plt.plot(tth3, int3)
plt.savefig('Results/dependencies2.png')
tth4, int4 = self.calibration_data.integrate_1d(polarization_factor=0.90, mask=None)
plt.figure(3)
plt.plot(tth2, int2)
plt.plot(tth4, int4)
plt.savefig('Results/dependencies3.png')
tth5, int5 = self.calibration_data.integrate_1d(polarization_factor=.5, mask=None)
plt.figure(4)
plt.plot(tth4, int4)
plt.plot(tth5, int5)
plt.savefig('Results/dependencies4.png')
def test_automatism(self):
def integrate_and_set_spectrum():
tth, I = self.calibration_data.integrate_1d()
self.spectrum_data.set_spectrum(tth, I, self.img_data.filename)
self.img_data.subscribe(integrate_and_set_spectrum)
y1 = self.spectrum_data.spectrum.data[1]
self.img_data.load_next_file()
y2 = self.spectrum_data.spectrum.data[1]
self.assertFalse(np.array_equal(y1, y2))
class CombinedDataTest(unittest.TestCase):
def setUp(self):
self.img_data = ImgData()
self.img_data.load('Data/Mg2SiO4_ambient_001.tif')
self.calibration_data = CalibrationData(self.img_data)
self.calibration_data.load('Data/calibration.poni')
self.mask_data = MaskData()
self.mask_data.load_mask('Data/test.mask')
self.spectrum_data = SpectrumData()
def test_dependencies(self):
tth1, int1 = self.calibration_data.integrate_1d()
self.img_data.load_next()
tth2, int2 = self.calibration_data.integrate_1d()
self.assertFalse(np.array_equal(int1, int2))
plt.figure(1)
plt.plot(tth1, int1)
plt.plot(tth2, int2)
plt.savefig('Results/dependencies1.jpg')
tth3, int3 = self.calibration_data.integrate_1d(mask=self.mask_data.get_mask())
self.assertFalse(np.array_equal(int2, int3))
plt.figure(2)
plt.plot(tth2, int2)
plt.plot(tth3, int3)
plt.savefig('Results/dependencies2.jpg')
tth4, int4 = self.calibration_data.integrate_1d(polarization_factor=0.90, mask=None)
plt.figure(3)
plt.plot(tth2, int2)
plt.plot(tth4, int4)
plt.savefig('Results/dependencies3.jpg')
tth5, int5 = self.calibration_data.integrate_1d(polarization_factor=.5, mask=None)
plt.figure(4)
plt.plot(tth4, int4)
plt.plot(tth5, int5)
plt.savefig('Results/dependencies4.jpg')
def test_automatism(self):
def integrate_and_set_spectrum():
tth, I = self.calibration_data.integrate_1d()
self.spectrum_data.set_spectrum(tth, I, self.img_data.filename)
self.img_data.subscribe(integrate_and_set_spectrum)
y1 = self.spectrum_data.spectrum.data[1]
self.img_data.load_next()
y2 = self.spectrum_data.spectrum.data[1]
self.assertFalse(np.array_equal(y1, y2))
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,
working_dir,
view=None,
img_data=None,
mask_data=None,
calibration_data=None,
spectrum_data=None,
phase_data=None):
self.working_dir = working_dir
if view == None:
self.view = IntegrationView()
else:
self.view = view
if img_data == None:
self.img_data = ImgData()
else:
self.img_data = img_data
if mask_data == None:
self.mask_data = MaskData()
else:
self.mask_data = mask_data
if calibration_data == None:
self.calibration_data = CalibrationData(self.img_data)
else:
self.calibration_data = calibration_data
if spectrum_data == None:
self.spectrum_data = SpectrumData()
else:
self.spectrum_data = spectrum_data
if phase_data == None:
self.phase_data = PhaseData()
else:
self.phase_data = phase_data
self.create_sub_controller()
self.view.setWindowState(self.view.windowState()
& ~QtCore.Qt.WindowMinimized
| QtCore.Qt.WindowActive)
self.view.activateWindow()
self.view.raise_()
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 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')
def setUp(self):
self.img_data = ImgData()
self.calibration_data = CalibrationData(self.img_data)
class MainController(object):
"""
Creates a the main controller for Dioptas. Loads all the data objects and connects them with the other controllers
"""
def __init__(self):
self.view = MainView()
#create data
self.img_data = ImgData()
self.calibration_data = CalibrationData(self.img_data)
self.mask_data = MaskData()
self.spectrum_data = SpectrumData()
self.phase_data = PhaseData()
self.settings_directory = os.path.join(os.path.expanduser("~"), '.Dioptas')
self.working_directories = {'calibration': '', 'mask': '', 'image': '', 'spectrum': '', 'overlay': '',
'phase': ''}
self.load_settings()
#create controller
self.calibration_controller = CalibrationController(self.working_directories,
self.view.calibration_widget,
self.img_data,
self.mask_data,
self.calibration_data)
self.mask_controller = MaskController(self.working_directories,
self.view.mask_widget,
self.img_data,
self.mask_data)
self.integration_controller = IntegrationController(self.working_directories,
self.view.integration_widget,
self.img_data,
self.mask_data,
self.calibration_data,
self.spectrum_data,
self.phase_data)
self.create_signals()
self.set_title()
self.raise_window(self.view)
@staticmethod
def raise_window(widget):
widget.show()
widget.setWindowState(widget.windowState() & ~QtCore.Qt.WindowMinimized | QtCore.Qt.WindowActive)
widget.activateWindow()
widget.raise_()
def create_signals(self):
self.view.tabWidget.currentChanged.connect(self.tab_changed)
self.view.closeEvent = self.close_event
self.img_data.subscribe(self.set_title)
self.spectrum_data.subscribe(self.set_title)
def tab_changed(self, ind):
if ind == 2:
self.mask_data.set_supersampling()
self.integration_controller.image_controller.plot_mask()
self.integration_controller.view.calibration_lbl.setText(self.calibration_data.calibration_name)
auto_scale_previous = self.integration_controller.image_controller._auto_scale
self.integration_controller.image_controller._auto_scale = False
self.integration_controller.spectrum_controller.image_changed()
self.integration_controller.image_controller.update_img()
self.integration_controller.image_controller._auto_scale = auto_scale_previous
elif ind == 1:
self.mask_controller.plot_mask()
self.mask_controller.plot_image()
elif ind == 0:
self.calibration_controller.plot_mask()
try:
self.calibration_controller.update_calibration_parameter_in_view()
except (TypeError, AttributeError):
pass
def set_title(self):
img_filename = os.path.basename(self.img_data.filename)
spec_filename = os.path.basename(self.spectrum_data.spectrum_filename)
calibration_name = self.calibration_data.calibration_name
str = 'Dioptas ' + __VERSION__
if img_filename is '' and spec_filename is '':
self.view.setWindowTitle(str + u' - © 2014 C. Prescher')
self.view.integration_widget.img_frame.setWindowTitle(str + u' - © 2014 C. Prescher')
return
if img_filename is not '' or spec_filename is not '':
str += ' - ['
if img_filename is not '':
str += img_filename
elif img_filename is '' and spec_filename is not '':
str += spec_filename
if not img_filename == spec_filename:
str += ', ' + spec_filename
if calibration_name is not None:
str += ', calibration: ' + calibration_name
str += ']'
str += u' - © 2014 C. Prescher'
self.view.setWindowTitle(str)
self.view.integration_widget.img_frame.setWindowTitle(str)
def load_settings(self):
if os.path.exists(self.settings_directory):
self.load_directories()
self.load_xml_settings()
def load_directories(self):
working_directories_path = os.path.join(self.settings_directory, 'working_directories.csv')
if os.path.exists(working_directories_path):
reader = csv.reader(open(working_directories_path, 'r'))
self.working_directories = dict(x for x in reader)
def load_xml_settings(self):
xml_settings_path = os.path.join(self.settings_directory, "settings.xml")
if os.path.exists(xml_settings_path):
tree = ET.parse(xml_settings_path)
root = tree.getroot()
filenames = root.find("filenames")
calibration_path=filenames.find("calibration").text
if os.path.exists(str(calibration_path)):
self.calibration_data.load(calibration_path)
def save_settings(self):
if not os.path.exists(self.settings_directory):
os.mkdir(self.settings_directory)
self.save_directories()
self.save_xml_settings()
def save_directories(self):
working_directories_path = os.path.join(self.settings_directory, 'working_directories.csv')
writer = csv.writer(open(working_directories_path, 'w'))
for key, value in list(self.working_directories.items()):
writer.writerow([key, value])
writer.writerow([key, value])
def save_xml_settings(self):
root = ET.Element("DioptasSettings")
filenames = ET.SubElement(root, "filenames")
calibration_filename = ET.SubElement(filenames, "calibration")
calibration_filename.text = self.calibration_data.filename
tree = ET.ElementTree(root)
tree.write(os.path.join(self.settings_directory, "settings.xml"))
def close_event(self, _):
self.save_settings()
QtGui.QApplication.closeAllWindows()
QtGui.QApplication.quit()