def setUp(self):
_file_path = os.path.dirname(__file__)
self.folder = os.path.abspath(
os.path.join(_file_path, '../../ResoFit/data/_mock_data_for_test'))
self.data_file = os.path.join(self.folder,
'_data_calibration_fitting_test.txt')
self.spectra_file = os.path.join(
self.folder, '_spectra_calibration_fitting_test.txt')
energy_min = 7
energy_max = 150
energy_step = 0.01
layer_1 = 'U'
thickness_1 = 0.075
density_1 = None
layer = Layer()
layer.add_layer(layer=layer_1,
thickness_mm=thickness_1,
density_gcm3=density_1)
self.calibration = Calibration(data_file=self.data_file,
spectra_file=self.spectra_file,
layer=layer,
energy_min=energy_min,
energy_max=energy_max,
energy_step=energy_step,
folder=self.folder,
database=self.database)
image_end = 2700 # Can be omitted or =None
# norm_to_file = 'ob_1.csv' #'Ag.csv'
# norm_to_file = 'Ag.csv'
norm_to_file = 'ob_all.csv'
baseline = False
each_step = False
norm_factor = 1.2
source_to_detector_m = 16.126845685903064 # 16#16.445359069030175#16.447496101100739
offset_us = -12112.431834715671 # 0#2.7120797253959119#2.7355447625559037
# Calibrate the peak positions
calibration = Calibration(data_file=data_file,
spectra_file=spectra_file,
layer=layers,
energy_min=energy_min,
energy_max=energy_max,
energy_step=energy_step,
folder=folder,
baseline=baseline)
calibration.experiment.norm_to(norm_to_file, norm_factor=norm_factor)
calibration.experiment.slice(start=image_start, end=image_end)
calibrate_result = calibration.calibrate(
source_to_detector_m=source_to_detector_m,
offset_us=offset_us,
vary='all',
each_step=each_step)
calibration.index_peak(thres_exp=0.05,
min_dist_exp=2,
min_dist_map=5,
image_start = None # Can be omitted or =None
image_end = None # Can be omitted or =None
norm_to_file = 'run_33_resonance_ob.txt' #None # 'sphere_background_1.csv'
baseline = True
each_step = False
repeat = 1
source_to_detector_m = 15.4318 # 16#16.445359069030175#16.447496101100739
offset_us = 2.7 # 0#2.7120797253959119#2.7355447625559037
# Calibrate the peak positions
calibration = Calibration(data_file=data_file,
spectra_file=spectra_file,
layer=layer,
energy_min=energy_min,
energy_max=energy_max,
energy_step=energy_step,
norm_factor=repeat,
folder=folder,
baseline=baseline)
calibration.norm_to(norm_to_file)
calibration.slice(slice_start=image_start, slice_end=image_end)
calibrate_result = calibration.calibrate(
source_to_detector_m=source_to_detector_m,
offset_us=offset_us,
vary='all',
each_step=each_step)
calibration.plot()
# experiment.slice(start=image_start)
# experiment.find_peak(x_type=x_type, y_type=y_type, thres=0.07, min_dist=50)
# experiment.plot(x_type=x_type, y_type=y_type, plot_with_baseline=True)
# print(experiment.o_peak)
# plt.xlim(left=0, right=300)
# plt.show()
# Calibrate the peak positions
calibration = Calibration(data_file=data_file,
spectra_file=spectra_file,
layer=layers,
energy_min=energy_min,
energy_max=energy_max,
energy_step=energy_step,
folder=folder,
exp_source_to_detector_m=source_to_detector_m,
exp_offset_us=offset_us,
database=database,
baseline=baseline,
baseline_deg=baseline_deg,
x_type=x_type,
y_type=y_type
)
calibration.experiment.norm_to(norm_to_file, norm_factor=norm_factor)
calibration.experiment.slice(start=image_start, end=image_end)
calibrate_result = calibration.calibrate(source_to_detector_m=source_to_detector_m,
offset_us=offset_us,
vary='source_to_detector',
# vary='all',
each_step=each_step)
# x_type = 'lambda'
# x_type = 'energy'
x_type = 'number'
# x_type = 'time'
# y_type = 'transmission'
y_type = 'attenuation'
# Calibrate the peak positions
calibration = Calibration(data_file=data_file,
spectra_file=spectra_file,
layer=layers,
energy_min=energy_min,
energy_max=energy_max,
energy_step=energy_step,
folder=folder,
exp_source_to_detector_m=source_to_detector_m,
exp_offset_us=offset_us,
database=database,
baseline=baseline,
baseline_deg=baseline_deg,
x_type=x_type,
y_type=y_type)
calibration.experiment.norm_to(file=norm_to_file, norm_factor=norm_factor)
calibration.experiment.slice(start=image_start, end=image_end)
calibrate_result = calibration.calibrate(
source_to_detector_m=source_to_detector_m,
offset_us=offset_us,
vary='all',
each_step=each_step)
image_end = 2720 # Can be omitted or =None
# norm_to_file = 'ob_1.csv' #'Ag.csv'
# norm_to_file = 'Ag.csv'
norm_to_file = 'ob_all.csv'
baseline = False
each_step = True
repeat = 1.2
source_to_detector_m = 16.126845685903064 # 16#16.445359069030175#16.447496101100739
offset_us = -12112.431834715671 # 0#2.7120797253959119#2.7355447625559037
# Calibrate the peak positions
calibration = Calibration(data_file=data_file,
spectra_file=spectra_file,
layer=layers,
energy_min=energy_min,
energy_max=energy_max,
energy_step=energy_step,
folder=folder,
baseline=baseline)
calibration.experiment.norm_to(norm_to_file)
calibration.experiment.slice(start=image_start, end=image_end)
calibration.experiment.plot(
x_type='energy',
source_to_detector_m=source_to_detector_m,
offset_us=offset_us,
logx=True,
)
# calibrate_result = calibration.calibrate(source_to_detector_m=source_to_detector_m,
# offset_us=offset_us,