class CalibrationModelTest(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.app = QtGui.QApplication([])
@classmethod
def tearDownClass(cls):
cls.app.quit()
cls.app.deleteLater()
def setUp(self):
self.img_model = ImgModel()
self.calibration_model = CalibrationModel(self.img_model)
def tearDown(self):
del self.img_model
if hasattr(self.calibration_model, 'cake_geometry'):
del self.calibration_model.cake_geometry
del self.calibration_model.spectrum_geometry
del self.calibration_model
gc.collect()
def test_loading_calibration_gives_right_pixel_size(self):
self.calibration_model.spectrum_geometry.load(os.path.join(data_path, 'CeO2_Pilatus1M.poni'))
self.assertEqual(self.calibration_model.spectrum_geometry.pixel1, 0.000172)
self.calibration_model.load(os.path.join(data_path, 'LaB6_40keV_MarCCD.poni'))
self.assertEqual(self.calibration_model.spectrum_geometry.pixel1, 0.000079)
def test_find_peaks_automatic(self):
self.load_pilatus_1M_and_find_peaks()
self.assertEqual(len(self.calibration_model.points), 6)
for points in self.calibration_model.points:
self.assertGreater(len(points), 0)
def test_find_peak(self):
"""
Tests the find_peak function for several maxima and pick points
"""
points_and_pick_points = [
[[30, 50], [31, 49]],
[[30, 50], [34, 46]],
[[5, 5], [3, 3]],
[[298, 298], [299, 299]]
]
for data in points_and_pick_points:
self.img_model._img_data = np.zeros((300, 300))
point = data[0]
pick_point = data[1]
self.img_model._img_data[point[0], point[1]] = 100
peak_point = self.calibration_model.find_peak(pick_point[0], pick_point[1], 10, 0)
self.assertEqual(peak_point[0][0], point[0])
self.assertEqual(peak_point[0][1], point[1])
def test_search_peaks_on_ring(self):
"""
Tests to search on the first ring of the calibrant after an inital calibration
"""
pass
def load_pilatus_1M_and_find_peaks(self):
self.img_model.load(os.path.join(data_path, 'CeO2_Pilatus1M.tif'))
self.calibration_model.find_peaks_automatic(517.664434674, 647.529865592, 0)
self.calibration_model.find_peaks_automatic(667.380513299, 525.252854758, 1)
self.calibration_model.find_peaks_automatic(671.110095329, 473.571503774, 2)
self.calibration_model.find_peaks_automatic(592.788872703, 350.495296791, 3)
self.calibration_model.find_peaks_automatic(387.395462348, 390.987901686, 4)
self.calibration_model.find_peaks_automatic(367.94835605, 554.290314848, 5)
def test_calibration_with_supersampling(self):
self.load_pilatus_1M_and_find_peaks()
self.calibration_model.set_calibrant(os.path.join(calibrant_path, 'LaB6.D'))
self.calibration_model.calibrate()
normal_poni1 = self.calibration_model.spectrum_geometry.poni1
self.img_model.set_supersampling(2)
self.calibration_model.set_supersampling(2)
self.calibration_model.calibrate()
self.assertAlmostEqual(normal_poni1, self.calibration_model.spectrum_geometry.poni1, places=5)
def test_calibration1(self):
self.img_model.load(os.path.join(data_path, 'LaB6_40keV_MarCCD.tif'))
self.calibration_model.find_peaks_automatic(1179.6, 1129.4, 0)
self.calibration_model.find_peaks_automatic(1268.5, 1119.8, 1)
self.calibration_model.set_calibrant(os.path.join(calibrant_path, 'LaB6.D'))
self.calibration_model.calibrate()
self.assertGreater(self.calibration_model.spectrum_geometry.poni1, 0)
self.assertAlmostEqual(self.calibration_model.spectrum_geometry.dist, 0.18, delta=0.01)
self.assertGreater(self.calibration_model.cake_geometry.poni1, 0)
def test_calibration2(self):
self.img_model.load(os.path.join(data_path, 'LaB6_OffCenter_PE.tif'))
self.calibration_model.find_peaks_automatic(1245.2, 1919.3, 0)
self.calibration_model.find_peaks_automatic(1334.0, 1823.7, 1)
self.calibration_model.start_values['dist'] = 500e-3
self.calibration_model.start_values['pixel_height'] = 200e-6
self.calibration_model.start_values['pixel_width'] = 200e-6
self.calibration_model.set_calibrant(os.path.join(calibrant_path, 'LaB6.D'))
self.calibration_model.calibrate()
self.assertGreater(self.calibration_model.spectrum_geometry.poni1, 0)
self.assertAlmostEqual(self.calibration_model.spectrum_geometry.dist, 0.500, delta=0.01)
self.assertGreater(self.calibration_model.cake_geometry.poni1, 0)
def test_calibration3(self):
self.load_pilatus_1M_and_find_peaks()
self.calibration_model.start_values['wavelength'] = 0.406626e-10
self.calibration_model.start_values['pixel_height'] = 172e-6
self.calibration_model.start_values['pixel_width'] = 172e-6
self.calibration_model.set_calibrant(os.path.join(calibrant_path, 'LaB6.D'))
self.calibration_model.calibrate()
self.assertGreater(self.calibration_model.spectrum_geometry.poni1, 0)
self.assertAlmostEqual(self.calibration_model.spectrum_geometry.dist, 0.100, delta=0.02)
self.assertGreater(self.calibration_model.cake_geometry.poni1, 0)
def test_get_pixel_ind(self):
self.img_model.load(os.path.join(data_path, 'image_001.tif'))
self.calibration_model.load(os.path.join(data_path, 'LaB6_40keV_MarCCD.poni'))
self.calibration_model.integrate_1d(1000)
tth_array = self.calibration_model.spectrum_geometry.ttha
azi_array = self.calibration_model.spectrum_geometry.chia
for i in range(100):
ind1 = np.random.random_integers(0, 2023)
ind2 = np.random.random_integers(0, 2023)
tth = tth_array[ind1, ind2]
azi = azi_array[ind1, ind2]
result_ind1, result_ind2 = self.calibration_model.get_pixel_ind(tth, azi)
self.assertAlmostEqual(ind1, result_ind1, places=3)
self.assertAlmostEqual(ind2, result_ind2, places=3)
class CbnAbsorptionCorrectionOptimizationTest(unittest.TestCase):
def setUp(self):
# creating Data objects
self.img_data = ImgModel()
self.img_data.load("Data/CbnCorrectionOptimization/Mg2SiO4_091.tif")
self.calibration_data = CalibrationModel(self.img_data)
self.calibration_data.load("Data/CbnCorrectionOptimization/LaB6_40keV side.poni")
self.mask_data = MaskModel()
self.mask_data.load_mask("Data/CbnCorrectionOptimization/Mg2SiO4_91_combined.mask")
# creating the ObliqueAngleDetectorAbsorptionCorrection
_, fit2d_parameter = self.calibration_data.get_calibration_parameter()
detector_tilt = fit2d_parameter['tilt']
detector_tilt_rotation = fit2d_parameter['tiltPlanRotation']
self.tth_array = self.calibration_data.spectrum_geometry.twoThetaArray((2048, 2048))
self.azi_array = self.calibration_data.spectrum_geometry.chiArray((2048, 2048))
self.oiadac_correction = ObliqueAngleDetectorAbsorptionCorrection(
self.tth_array, self.azi_array,
detector_thickness=40,
absorption_length=465.5,
tilt=detector_tilt,
rotation=detector_tilt_rotation,
)
self.img_data.add_img_correction(self.oiadac_correction, "oiadac")
def tearDown(self):
del self.calibration_data.cake_geometry
del self.calibration_data.spectrum_geometry
def test_the_world(self):
params = Parameters()
params.add("diamond_thickness", value=2, min=1.9, max=2.3)
params.add("seat_thickness", value=5.3, min=4.0, max=6.6, vary=False)
params.add("small_cbn_seat_radius", value=0.2, min=0.10, max=0.5, vary=True)
params.add("large_cbn_seat_radius", value=1.95, min=1.85, max=2.05, vary=False)
params.add("tilt", value=3.3, min=0, max=8)
params.add("tilt_rotation", value=0, min=-15, max=+15)
params.add("cbn_abs_length", value=14.05, min=12, max=16)
region = [8, 26]
self.tth_array = 180.0 / np.pi * self.tth_array
self.azi_array = 180.0 / np.pi * self.azi_array
def fcn2min(params):
cbn_correction = CbnCorrection(
tth_array=self.tth_array,
azi_array=self.azi_array,
diamond_thickness=params['diamond_thickness'].value,
seat_thickness=params['seat_thickness'].value,
small_cbn_seat_radius=params['small_cbn_seat_radius'].value,
large_cbn_seat_radius=params['large_cbn_seat_radius'].value,
tilt=params['tilt'].value,
tilt_rotation=params['tilt_rotation'].value,
cbn_abs_length=params["cbn_abs_length"].value
)
self.img_data.add_img_correction(cbn_correction, "cbn")
tth, int = self.calibration_data.integrate_1d(mask=self.mask_data.get_mask())
self.img_data.delete_img_correction("cbn")
ind = np.where((tth > region[0]) & (tth < region[1]))
int = gaussian_filter1d(int, 20)
return (np.diff(int[ind])) ** 2
def output_values(param1, iteration, residual):
report_fit(param1)
result = minimize(fcn2min, params, iter_cb=output_values)
report_fit(params)
# plotting result:
cbn_correction = CbnCorrection(
tth_array=self.tth_array,
azi_array=self.azi_array,
diamond_thickness=params['diamond_thickness'].value,
seat_thickness=params['seat_thickness'].value,
small_cbn_seat_radius=params['small_cbn_seat_radius'].value,
large_cbn_seat_radius=params['large_cbn_seat_radius'].value,
tilt=params['tilt'].value,
tilt_rotation=params['tilt_rotation'].value,
cbn_abs_length=params['cbn_abs_length'].value
)
self.img_data.add_img_correction(cbn_correction, "cbn")
tth, int = self.calibration_data.integrate_1d(mask=self.mask_data.get_mask())
ind = np.where((tth > region[0]) & (tth < region[1]))
tth = tth[ind]
int = int[ind]
int_smooth = gaussian_filter1d(int, 10)
int_diff1 = np.diff(int)
int_diff1_smooth = np.diff(int_smooth)
int_diff2 = np.diff(int_diff1)
int_diff2_smooth = np.diff(int_diff1_smooth)
plt.figure()
plt.subplot(3, 1, 1)
plt.plot(tth, int)
plt.plot(tth, int_smooth)
plt.subplot(3, 1, 2)
plt.plot(int_diff1)
plt.plot(int_diff1_smooth)
plt.subplot(3, 1, 3)
plt.plot(int_diff2)
plt.plot(int_diff2_smooth)
plt.savefig("Results/optimize_cbn_absorption.png", dpi=300)
os.system("open " + "Results/optimize_cbn_absorption.png")
class CalibrationControllerTest(unittest.TestCase):
def setUp(self):
self.app = QtGui.QApplication(sys.argv)
self.img_model = ImgModel()
self.mask_model = MaskModel()
self.calibration_model = CalibrationModel(self.img_model)
self.calibration_model._calibrants_working_dir = os.path.join(data_path, 'calibrants')
self.calibration_widget = CalibrationWidget()
self.working_dir = {}
self.calibration_controller = CalibrationController(working_dir=self.working_dir,
img_model=self.img_model,
mask_model=self.mask_model,
widget=self.calibration_widget,
calibration_model=self.calibration_model)
def tearDown(self):
del self.img_model
del self.calibration_model.cake_geometry
del self.calibration_model.spectrum_geometry
del self.calibration_model
del self.app
gc.collect()
def load_pilatus_1M_and_pick_peaks(self):
self.calibration_controller.load_img(os.path.join(data_path,'CeO2_Pilatus1M.tif'))
QTest.mouseClick(self.calibration_widget.automatic_peak_num_inc_cb, QtCore.Qt.LeftButton)
self.assertFalse(self.calibration_widget.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_widget.sv_wavelength_txt.setText('0.406626')
self.calibration_widget.sv_distance_txt.setText('200')
self.calibration_widget.sv_pixel_width_txt.setText('172')
self.calibration_widget.sv_pixel_height_txt.setText('172')
calibrant_index = self.calibration_widget.calibrant_cb.findText('CeO2')
self.calibration_widget.calibrant_cb.setCurrentIndex(calibrant_index)
self.mask_model.set_dimension(self.img_model.img_data.shape)
def test_automatic_calibration1(self):
self.calibration_controller.load_img(os.path.join(data_path,'LaB6_40keV_MarCCD.tif'))
self.calibration_controller.search_peaks(1179.6, 1129.4)
self.calibration_controller.search_peaks(1268.5, 1119.8)
self.calibration_controller.widget.sv_wavelength_txt.setText('0.31')
self.calibration_controller.widget.sv_distance_txt.setText('200')
self.calibration_controller.widget.sv_pixel_width_txt.setText('79')
self.calibration_controller.widget.sv_pixel_height_txt.setText('79')
calibrant_index = self.calibration_widget.calibrant_cb.findText('LaB6')
self.calibration_controller.widget.calibrant_cb.setCurrentIndex(calibrant_index)
self.calibration_controller.calibrate()
self.calibration_controller.widget.cake_view.set_vertical_line_pos(1419.8, 653.4)
def test_automatic_calibration2(self):
self.calibration_controller.load_img(os.path.join(data_path,'LaB6_OffCenter_PE.tif'))
self.calibration_controller.search_peaks(1245.2, 1919.3)
self.calibration_controller.search_peaks(1334.0, 1823.7)
self.calibration_controller.widget.sv_wavelength_txt.setText('0.3344')
self.calibration_controller.widget.sv_distance_txt.setText('500')
self.calibration_controller.widget.sv_pixel_width_txt.setText('200')
self.calibration_controller.widget.sv_pixel_height_txt.setText('200')
calibrant_index = self.calibration_widget.calibrant_cb.findText('LaB6')
self.calibration_controller.widget.calibrant_cb.setCurrentIndex(calibrant_index)
self.calibration_controller.calibrate()
self.calibration_controller.widget.cake_view.set_vertical_line_pos(206.5, 171.6)
def test_automatic_calibration3(self):
self.load_pilatus_1M_and_pick_peaks()
start_values = self.calibration_widget.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_model.calibrant.wavelength, 0.406626e-10)
QTest.mouseClick(self.calibration_widget.integrate_btn, QtCore.Qt.LeftButton)
calibration_parameter = self.calibration_model.get_calibration_parameter()[0]
self.assertAlmostEqual(calibration_parameter['dist'], .2086, places=4)
def test_automatic_calibration_with_supersampling(self):
self.load_pilatus_1M_and_pick_peaks()
self.img_model.set_supersampling(2)
self.calibration_model.set_supersampling(2)
self.calibration_controller.calibrate()
def test_automatic_calibration_with_supersampling_and_mask(self):
self.load_pilatus_1M_and_pick_peaks()
self.img_model.set_supersampling(2)
self.mask_model.mask_below_threshold(self.img_model._img_data, 1)
self.mask_model.set_supersampling(2)
self.calibration_model.set_supersampling(2)
self.calibration_controller.widget.use_mask_cb.setChecked(True)
self.calibration_controller.calibrate()
def test_calibrating_one_image_size_and_loading_different_image_size(self):
self.load_pilatus_1M_and_pick_peaks()
self.calibration_controller.calibrate()
self.calibration_model.integrate_1d()
self.calibration_model.integrate_2d()
self.calibration_controller.load_img(os.path.join(data_path, 'CeO2_Pilatus1M.tif'))
self.calibration_model.integrate_1d()
self.calibration_model.integrate_2d()
def test_loading_and_saving_of_calibration_files(self):
self.calibration_controller.load_calibration(os.path.join(data_path, 'LaB6_40keV_MarCCD.poni'))
self.calibration_controller.save_calibration(os.path.join(data_path, 'calibration.poni'))
self.assertTrue(os.path.exists(os.path.join(data_path, 'calibration.poni')))
os.remove(os.path.join(data_path, 'calibration.poni'))
