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sematura_params.py
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sematura_params.py
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### User input for diffuse scattering analysis
###---------Parameters from Bragg data reduction---------###
alpha = 90.0 # alpha angle of unit cell
beta = 90.0 # beta angle of unit cell
gamma = 90.0 # gamma angle of unit cell
cella = 43.038 # length of unit cell along a axis
cellb = 52.574 # length of unit cell along b axis
cellc = 89.063 # length of unit cell along c axis
target_sg = str(19) # space group from Bragg data reduction
resolution = str(1.4) # maximum resolution for diffuse data integration
target_cell = (str(cella)+" "+str(cellb)+" "+str(cellc)+" "
+str(alpha)+" "+str(beta)+" "+str(gamma))
###---------------file and directory names---------------###
diffuse_lattice_prefix = 'cypa_sema_corrcomp'
image_prefix = 'set_1_1_'
lunus_image_prefix = 'set_1_1_lunus_'
image_dir = '/Users/student/diffuse_working'
phenix_dir = '/usr/local/phenix-dev-2499'
###-----------Choose files to use for indexing-----------###
indexing_one = str(1) # number of first file for indexing
indexing_two = str(45) # number of second file for indexing
indexing_three = str(90) # number of third file for indexing
###----------------Lunus input parameters----------------###
### image borders
windim_xmax =2363 # right border for processed image (pixels)
windim_xmin =10 # left border for processed image (pixels)
windim_ymax =2427 # top border for processed image (pixels)
windim_ymin =100 # bottom border for processed image (pixels)
### beamstop borders
punchim_xmax =2459 # right border of beam stop shadow (pixels)
punchim_xmin =1156 # left border of beam stop shadow (pixels)
punchim_ymax =1363 # top border of beam stop shadow (pixels)
punchim_ymin =1224 # bottom border of beam stop shadow (pixels)
### intensity thresholds
thrshim_max =10000 # maximum reliable intensity for detector (count)
thrshim_min =1 # minimum intensity for diffuse analysis (count)
### binning to remove Bragg peaks
modeim_bin_size =1 # mask bin for mode filtering (count)
modeim_kernel_width =20 # mask width for mode filtering (pixels)
### beam polarization correction
polarim_dist =182.87 # distance from sample to detector (mm)
polarim_offset =0.0 # ask Mike W.
polarim_polarization=0.8 # polarization fraction (0.0-1.0)
### solid-angle image normalization
normim_tilt_x =0.0 # ask Mike W.
normim_tilt_y =0.0 # ask Mike W.
### image scaling
reference_image_number =str(1) # reference for scaling
scale_inner_radius =99 # ask Mike W.
scale_outer_radius =799 # ask Mike W.