lower = mean - threshold
upper = mean + threshold
# single out the too low and too high pixels
too_low = img < lower[int_q]
too_hi = img > upper[int_q]
mask = mask * ~too_low * ~too_hi
return mask.astype(bool)
img_folder = '/mnt/bulk-data/research_data/USC_beamtime/APS_March_2016/S1/temp_exp'
cal_folder = '/mnt/bulk-data/research_data/USC_beamtime/APS_March_2016/Calibration/CeO2_25_3_12'
geo = Geometry()
geo.load(os.path.join(cal_folder, 'CeO2calibration_25-00004_sum.poni'))
lamda = geo.wavelength * 10 ** 10
print(lamda)
img = TiffStack(os.path.join(img_folder, 'd25_S6_VT-00000.tif'))[0]
mask = np.ones(img.shape, dtype=bool)
mask *= mask_edge(img.shape, 30)
r = geo.rArray((2048, 2048))
q = geo.qArray((2048, 2048))
rmax = np.max(r)
qmax = np.max(q)
pixel_size = geo.pixel1
distance = geo.dist
wavelength = lamda
lower = mean - threshold
upper = mean + threshold
# single out the too low and too high pixels
too_low = img < lower[int_q]
too_hi = img > upper[int_q]
mask = mask * ~too_low * ~too_hi
return mask.astype(bool)
img_folder = '/mnt/bulk-data/research_data/USC_beamtime/APS_March_2016/even_more_cells'
cal_folder = img_folder
geo = Geometry()
geo.load(os.path.join(cal_folder, 'CeO2_d25-00023.poni'))
lamda = geo.wavelength * 10 ** 10
print(lamda)
img = TiffStack(os.path.join(img_folder, 'S32_d25-00020.tif'))[0]
mask = np.ones(img.shape, dtype=bool)
mask *= mask_edge(img.shape, 30)
r = geo.rArray((2048, 2048))
q = geo.qArray((2048, 2048))
rmax = np.max(r)
qmax = np.max(q)
pixel_size = geo.pixel1
distance = geo.dist
wavelength = lamda
