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#!/usr/bin/env python
import pycbf
# Some cbf helper functions - obj would be a cbf_handle_struct object
def writewavelength(obj,wavelength):
obj.set_wavelength(float(wavelength))
def writecellpar(obj,cifname,value):
obj.find_category("cell")
obj.find_column(cifname)
obj.set_value(value)
def writecell(obj,cell):
"""
call with cell = (a,b,c,alpha,beta,gamma)
"""
obj.find_category("cell")
obj.find_column("length_a")
obj.set_value(str(cell[0]))
obj.find_column("length_b")
obj.set_value(str(cell[1]))
obj.find_column("length_c")
obj.set_value(str(cell[2]))
obj.find_column("angle_alpha")
obj.set_value(str(cell[3]))
obj.find_column("angle_beta")
obj.set_value(str(cell[4]))
obj.find_column("angle_gamma")
obj.set_value(str(cell[5]))
def writeUB(obj,ub):
"""
call with ub that can be indexed ub[i][j]
"""
obj.find_category("diffrn_orient_matrix")
for i in (1,2,3):
for j in (1,2,3):
obj.find_column("UB[%d][%d]"%(i,j))
obj.set_value(str(ub[i-1][j-1]))
def writedistance(obj,distance):
obj.set_axis_setting("DETECTOR_Z",float(distance),0.)
def writebeam_x_mm(obj,cen):
obj.set_axis_setting("DETECTOR_X",float(cen),0.)
def writebeam_y_mm(obj,cen):
obj.set_axis_setting("DETECTOR_Y",float(cen),0.)
def writeSPECcmd(obj,s):
obj.find_category("diffrn_measurement")
obj.find_column("details")
obj.set_value(s)
def writeSPECscan(obj,s):
obj.find_category("diffrn_scan")
obj.find_column("id")
obj.set_value("SCAN%s"%(s))
obj.find_category("diffrn_scan_axis")
obj.find_column("scan_id")
obj.rewind_row()
for i in range(obj.count_rows()):
obj.select_row(i)
obj.set_value("SCAN%s"%(s))
obj.find_category("diffrn_scan_frame")
obj.find_column("scan_id")
obj.rewind_row()
obj.set_value("SCAN%s"%(s))
def writepixelsize_y_mm(obj,s):
"""
Units are mm for cif
"""
# element number = assume this is first and only detector
element_number = 0
# axis number = faster or slower... ? Need to check precedence ideally...
obj.find_category("array_structure_list")
obj.find_column("axis_set_id")
obj.find_row("ELEMENT_Y")
obj.find_column("precedence")
axis_number = obj.get_integervalue()
obj.set_pixel_size(element_number, axis_number, float(s) )
obj.find_category("array_structure_list_axis")
obj.find_column("axis_id")
obj.find_row("ELEMENT_Y")
obj.find_column("displacement")
obj.set_doublevalue("%.6g",float(s)/2.0)
obj.find_column("displacement_increment")
obj.set_doublevalue("%.6g",float(s))
def writepixelsize_x_mm(obj,s):
# element number = assume this is first and only detector
element_number = 0
# axis number = faster or slower... ? Need to check precedence ideally...
obj.find_category("array_structure_list")
obj.find_column("axis_set_id")
obj.find_row("ELEMENT_X")
obj.find_column("precedence")
axis_number = obj.get_integervalue()
obj.set_pixel_size(element_number, axis_number, float(s) )
obj.find_category("array_structure_list_axis")
obj.find_column("axis_id")
obj.find_row("ELEMENT_X")
obj.find_column("displacement")
obj.set_doublevalue("%.6g",float(s)/2.0)
obj.find_column("displacement_increment")
obj.set_doublevalue("%.6g",float(s))
def writeintegrationtime(obj,s):
obj.find_category("diffrn_scan_frame")
obj.find_column("integration_time")
obj.set_value(str(s).replace("\000",""))
def writenfast(obj,s):
obj.find_category("array_structure_list")
obj.find_column("index")
obj.find_row("1")
obj.find_column("dimension")
obj.set_value(str(s))
def writenslow(obj,s):
obj.find_category("array_structure_list")
obj.find_column("index")
obj.find_row("2")
obj.find_column("dimension")
obj.set_value(str(s))
functiondict = {
"lambda" : writewavelength,
"beam_x_mm" : writebeam_x_mm,
"beam_y_mm" : writebeam_y_mm,
"distance" : writedistance,
"UB" : writeUB,
"cell" : writecell,
"cmd" : writeSPECcmd,
"scan" : writeSPECscan,
"nfast" : writenfast,
"nslow" : writenslow,
"pixelsize_y_mm" : writepixelsize_y_mm,
"pixelsize_x_mm" : writepixelsize_x_mm,
"integration_time_sec" : writeintegrationtime,
"tth" : lambda obj,value : obj.set_axis_setting(
"DETECTOR_TWO_THETA_VERTICAL",float(value),0.),
"chi" : lambda obj,value : obj.set_axis_setting(
"GONIOMETER_CHI",float(value),0.),
"th" : lambda obj,value : obj.set_axis_setting(
"GONIOMETER_THETA",float(value),0.),
"phi" : lambda obj,value : obj.set_axis_setting(
"GONIOMETER_PHI",float(value),0.),
"lc_a" : lambda obj,value : writecellpar(obj,"length_a",value),
"lc_b" : lambda obj,value : writecellpar(obj,"length_b",value),
"lc_c" : lambda obj,value : writecellpar(obj,"length_c",value),
"lc_al" : lambda obj,value : writecellpar(obj,"angle_alpha",value),
"lc_be" : lambda obj,value : writecellpar(obj,"angle_beta",value),
"lc_ga" : lambda obj,value : writecellpar(obj,"angle_gamma",value)
}
"""
#
# Not implementing these for now
lc_ra
lc_rc 0.4742
lc_rb 1.16
energy 13
cp_phi -180
alpha 7.3716
lc_ral 90
cp_tth -180
lc_rga 90
beta 17.572
omega -2.185
h 0.21539
k 0.01957
l 5.9763
cp_chi -180
lc_rbe 90
cp_th -180
azimuth 0
"""
# Finally a class for creating header files.
# It reads a template and then offers a processfile command
# for running over a file series
class cifheader:
def __init__(self,templatefile):
self.cbf=pycbf.cbf_handle_struct()
self.cbf.read_template(templatefile)
from readmarheader import marheaderreader
self.marheaderreader = marheaderreader()
def processfile(self,filename, outfile=None,
format="mccd",
**kwds):
outfile=outfile.replace(format,"cif")
if format == "mccd":
items = self.marheaderreader.get_header(filename)
if format == "bruker":
pass
if format == "edf":
pass
self.items=items
# Take the image header items as default
self.updateitems(items)
# Allow them to be overridden
self.updateitems(kwds)
# Write the file
self.writefile(outfile)
def writefile(self,filename):
self.cbf.write_file(filename,pycbf.CIF,pycbf.MIME_HEADERS,
pycbf.ENC_BASE64)
def updateitems(self,dict):
names = list(dict.keys())
for name in names:
value = dict[name]
# use a dictionary of functions
if name in functiondict:
# print("calling",functiondict[name],value)
functiondict[name](*(self.cbf,value))
else:
#print("ignoring",name,value)
pass
if __name__=="__main__":
import sys
obj=cifheader("xmas_cif_template.cif")
ub = [[0.11, 0.12, 0.13] , [0.21, 0.22, 0.23], [0.31, 0.32, 0.33]]
for filename in sys.argv[1:]:
fileout = filename.split("/")[-1]
obj.processfile(filename, outfile=fileout, UB=ub, distance=123.456)
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