Reflections list calculation for any spacegroup : lattice parameters,...

Reflections list calculation for any spacegroup : lattice parameters, spacegroup and maximum sin(theta)/lambda are needed.

Content of the commit:

  zUtil_Cryst/gtCrystCalculateReflections :
      function to generate the reflection list for any spacegroup (using fable package xfab) and convert it from text file to matlab matrix
  zUtil_Cryst/gtCrystGetReflections :
      function to read output from gtCrystCalculateReflections and convert in matlab matrices
  zUtil_Python/create_reflections_list.py :
      python script for the calculation using xfab package

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

git-svn-id: https://svn.code.sf.net/p/dct/code/trunk@943 4c865b51-4357-4376-afb4-474e03ccb993

zUtil_Cryst/gtCrystCalculateReflections.m

+function [hkl, theta, output_file] = gtCrystCalculateReflections(latticepar, mintheta, maxtheta, sg, typelist, filename)
+% GTCRYSTCALCULATEREFLECTIONS  Calculate the reflections list using python 
+%                              from fable library (genhkl_all or genhkl_unique
+%                              scripts)
+%     [hkl, theta, output_file] = gtCrystCalculateReflections(latticepar, mintheta, maxtheta, sg, typelist, filename)
+%     ---------------------------------------------------------------------------------------------------------------
+%
+%     INPUT: 
+%       latticepar      = lattice parameters <double 1x6>
+%       mintheta        = minimum sin(theta)/lambda allowed <double> {0.0001}
+%       maxtheta        = maximum sin(theta)/lambda allowed <double>
+%       sg              = spacegroup number <int>
+%       typelist        = type of list <string> [{'all'}/'unique]
+%       filename = filename for output <string>
+%
+%     OUTPUT:
+%       hkl             = reflection list <double>
+%       theta           = theta value for each reflection <double>
+%       output_file     = path to the output filename <string>
+%
+%
+%     Version 001 03-12-2012 by LNervo
+
+
+if ~exist('latticepar','var') || isempty(latticepar)
+    load parameters;
+    latticepar = parameters.cryst(1).latticepar;
+end
+if ~exist('mintheta','var') || isempty(mintheta)
+    mintheta = 0.0001;
+end
+if ~exist('maxtheta','var') || isempty(maxtheta)
+    load parameters;
+    tmp = parameters.labgeo.detanglemax;
+    maxtheta = sind(tmp)/gtConvEnergyToWavelength(parameters.acq.energy);
+    clear tmp
+end
+if ~exist('sg','var') || isempty(sg)
+    load parameters;
+    sg = parameters.cryst(1).spacegroup;
+end
+if ~exist('typelist','var') || isempty(typelist)
+    typelist = 'all';
+end
+if ~exist('filename','var') || isempty(filename)
+    filename = 'reflections.txt';
+end
+
+latticepar_str = sprintf('%f ', latticepar);
+script_file = fullfile('/users/',getenv('USER'),'matlabDCT','zUtil_Python','create_reflections_list.py');
+
+cmd = sprintf('python26 %s %s %f %f %d %s %s',...
+              script_file,latticepar_str,mintheta,maxtheta,sg,typelist,filename);
+
+[~,msg]=unix(cmd);
+disp(msg)
+
+[hkl,sintheta] = gtCrystGetReflections(filename);
+
+if nargout > 1
+    load parameters;
+    energy = parameters.acq.energy;
+    theta = asind(sintheta)*gtConvEnergyToWavelength(energy);
+    
+    if nargout == 3
+        output_file = fullfile(pwd(),filename);
+    end
+end
+
+end % end of function

zUtil_Cryst/gtCrystGetReflections.m

+function [hkl, sintheta] = gtCrystGetReflections(filename)
+% GTCRYSTGETREFLECTIONS  Reads output file from gtCrystCalculateReflections
+%
+%     [hkl, sintheta] = gtCrystGetReflections(filename)
+%     -------------------------------------------------
+%
+%     INPUT:
+%       filename = output file from gtCrystCalculateReflections <string> 
+%
+%     OUTPUT:
+%       hkl      = generated reflections <double>
+%       sintheta = sin(theta)/lambda <double>
+%
+%
+%     Version 001 03-12-2012 by LNervo
+
+
+fid = fopen(filename,'r');
+C = textscan(fid,'%f %f %f %f',...
+                 'Delimiter','\n',...
+                 'CommentStyle','#');
+fclose(fid);
+
+hkl = cell2mat(C(:,1:3));
+
+if nargout == 2
+    sintheta = cell2mat(C(:,4));
+end
+
+end % end of function

zUtil_Python/create_reflections_list.py

+#!/usr/bin/python26
+
+'''
+Created on Dec 03, 2012
+@author: lnervo
+'''
+
+import sys, os, numpy as np
+
+from xfab import *
+from xfab import symmetry
+from xfab.symmetry import *
+from xfab.symmetry import tools
+
+index = 1;
+_a = float(sys.argv[index])
+_b = float(sys.argv[index+1])
+_c = float(sys.argv[3])
+_alpha = float(sys.argv[4])
+_beta  = float(sys.argv[5])
+_gamma = float(sys.argv[6])
+
+_mintheta = float(sys.argv[7])
+_maxtheta = float(sys.argv[8])
+_sgno = int(sys.argv[9])
+_type = sys.argv[10]
+_output = sys.argv[11]
+
+print("")
+print("    *** Input data ***")
+print("    lattice parameters: (%f,%f,%f,%f,%f,%f)"
+       % (_a, _b, _c, _alpha, _beta, _gamma))
+print("    sin(theta)/lambda range: %f,%f" % (_mintheta, _maxtheta))
+print("    spacegroup: %s" % _sgno)
+print("    type: %s" % _type)
+print("")
+print("Reflections list calculation...")
+
+if _type == 'all':
+    list = symmetry.tools.genhkl_all([_a,_b,_c,_alpha,_beta,_gamma],
+                                     _mintheta,_maxtheta,sgno=_sgno,
+                                     output_stl=True)
+elif _type == 'unique':
+    list = symmetry.tools.genhkl_unique([_a,_b,_c,_alpha,_beta,_gamma],
+                                        _mintheta,_maxtheta,sgno=_sgno,
+                                        output_stl=True)
+else:
+    print("Type not known...Existing")
+    list = None
+
+if list is not None:
+    print("...done!")
+    print("Saving reflections list in:\n    %s..." % _output)
+
+    with file(_output,'w') as outfile:
+        outfile.write('# Reflection list: {0}\n'.format(list.shape))
+        for data_hkl in list:
+            np.savetxt(outfile, data_hkl)
+            outfile.write('# New reflection\n')
+
+    print("...done!")