#!/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)