| 1 | '''Development code to export a GSAS-II project as a CIF |
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| 2 | The heavy lifting is done in method export |
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| 3 | ''' |
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| 4 | |
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| 5 | import datetime as dt |
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| 6 | import os.path |
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| 7 | import GSASIIIO as G2IO |
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| 8 | import GSASIIgrid as G2gd |
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| 9 | #reload(G2gd) |
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| 10 | class ExportCIF(G2IO.ExportBaseclass): |
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| 11 | def __init__(self,G2frame): |
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| 12 | super(self.__class__,self).__init__( # fancy way to say <parentclass>.__init__ |
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| 13 | G2frame=G2frame, |
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| 14 | formatName = 'full CIF', |
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| 15 | longFormatName = 'Export project as complete CIF' |
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| 16 | ) |
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| 17 | self.author = '' |
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| 18 | |
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| 19 | def export(self,mode='full'): |
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| 20 | '''Export a CIF |
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| 21 | |
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| 22 | :param str mode: "full" (default) to create a complete CIF of project, |
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| 23 | "simple" for a simple CIF with only coordinates |
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| 24 | ''' |
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| 25 | def WriteCIFitem(name,value=''): |
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| 26 | if value: |
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| 27 | if "\n" in value or len(value)> 70: |
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| 28 | if name.strip(): print name |
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| 29 | print '; '+value |
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| 30 | print '; ' |
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| 31 | elif " " in value: |
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| 32 | if len(name)+len(value) > 65: |
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| 33 | print name,'\n ','"' + str(value) + '"' |
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| 34 | else: |
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| 35 | print name,' ','"' + str(value) + '"' |
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| 36 | else: |
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| 37 | if len(name)+len(value) > 65: |
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| 38 | print name,'\n ',value |
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| 39 | else: |
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| 40 | print name,' ',value |
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| 41 | else: |
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| 42 | print name |
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| 43 | |
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| 44 | def WriteAudit(): |
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| 45 | WriteCIFitem('_audit_creation_method', |
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| 46 | 'created in GSAS-II') |
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| 47 | WriteCIFitem('_audit_creation_date',self.CIFdate) |
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| 48 | if self.author: |
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| 49 | WriteCIFitem('_audit_author_name',self.author) |
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| 50 | WriteCIFitem('_audit_update_record', |
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| 51 | self.CIFdate+' Initial software-generated CIF') |
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| 52 | |
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| 53 | def WriteOverall(): |
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| 54 | '''TODO: Write out overall refinement information |
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| 55 | ''' |
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| 56 | WriteCIFitem('_pd_proc_info_datetime', self.CIFdate) |
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| 57 | WriteCIFitem('_pd_calc_method', 'Rietveld Refinement') |
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| 58 | #WriteCIFitem('_refine_ls_shift/su_max',DAT1) |
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| 59 | #WriteCIFitem('_refine_ls_shift/su_mean',DAT2) |
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| 60 | WriteCIFitem('_computing_structure_refinement','GSAS-II') |
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| 61 | #WriteCIFitem('_refine_ls_number_parameters',DAT1) |
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| 62 | #WriteCIFitem('_refine_ls_goodness_of_fit_all',DAT2) |
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| 63 | #WriteCIFitem('_refine_ls_number_restraints',TEXT(1:7)) |
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| 64 | # other things to consider reporting |
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| 65 | # _refine_ls_number_reflns |
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| 66 | # _refine_ls_goodness_of_fit_obs |
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| 67 | # _refine_ls_R_factor_all |
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| 68 | # _refine_ls_R_factor_obs |
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| 69 | # _refine_ls_wR_factor_all |
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| 70 | # _refine_ls_wR_factor_obs |
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| 71 | # _refine_ls_restrained_S_all |
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| 72 | # _refine_ls_restrained_S_obs |
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| 73 | |
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| 74 | # include an overall profile r-factor, if there is more than one powder histogram |
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| 75 | if self.npowder > 1: |
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| 76 | WriteCIFitem('\n# OVERALL POWDER R-FACTORS') |
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| 77 | #WriteCIFitem('_pd_proc_ls_prof_R_factor',TEXT(11:20)) |
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| 78 | #WriteCIFitem('_pd_proc_ls_prof_wR_factor',TEXT(1:10)) |
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| 79 | WriteCIFitem('_refine_ls_matrix_type','full') |
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| 80 | #WriteCIFitem('_refine_ls_matrix_type','userblocks') |
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| 81 | |
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| 82 | def WritePubTemplate(): |
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| 83 | '''TODO: insert the publication template ``template_publ.cif`` or some modified |
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| 84 | version for this project. Store this in the GPX file? |
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| 85 | ''' |
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| 86 | print "TODO: publication info goes here" |
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| 87 | |
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| 88 | def WritePhaseTemplate(): |
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| 89 | '''TODO: insert the phase template ``template_phase.cif`` or some modified |
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| 90 | version for this project |
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| 91 | ''' |
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| 92 | print "TODO: phase template info goes here" |
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| 93 | |
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| 94 | def WritePowderTemplate(): |
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| 95 | '''TODO: insert the phase template ``template_instrument.cif`` or some modified |
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| 96 | version for this project |
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| 97 | ''' |
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| 98 | print "TODO: powder histogram template info goes here" |
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| 99 | |
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| 100 | def WriteSnglXtalTemplate(): |
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| 101 | '''TODO: insert the single-crystal histogram template |
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| 102 | for this project |
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| 103 | ''' |
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| 104 | print "TODO: single-crystal histogram template info goes here" |
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| 105 | |
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| 106 | def WritePhaseInfo(phasenam): |
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| 107 | # see writepha.for |
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| 108 | print 'TODO: phase info for',phasenam,'goes here' |
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| 109 | # THINK: how to select publication flags for distances/angles? |
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| 110 | phasedict = self.GroupedParms['Phases'][phasenam] # pointer to current phase info |
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| 111 | WriteCIFitem('_pd_phase_name', phasenam) |
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| 112 | text = '?' |
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| 113 | for lbl in 'a','b','c': |
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| 114 | WriteCIFitem('_cell_length_'+lbl,text) |
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| 115 | for lbl in 'alpha','beta ','gamma': |
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| 116 | WriteCIFitem('_cell_angle_'+lbl,text) |
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| 117 | |
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| 118 | WriteCIFitem('_cell_volume',text) |
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| 119 | |
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| 120 | #print phasedict['Histograms'] |
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| 121 | # for key in phasedict['General']: |
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| 122 | # print key,'=',phasedict['General'][key] |
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| 123 | # print phasedict['pId'] |
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| 124 | |
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| 125 | #NSYS = (1,2,3,4,4,5,5,5,5,5,6,6,7,7) |
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| 126 | #SYST = ('','triclinic','monoclinic','orthorhombic','tetragonal','trigonal ','hexagonal','cubic') |
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| 127 | |
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| 128 | WriteCIFitem('_symmetry_cell_setting', |
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| 129 | phasedict['General']['SGData']['SGSys']) |
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| 130 | |
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| 131 | spacegroup = phasedict['General']['SGData']['SpGrp'].strip() |
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| 132 | # regularize capitalization and remove trailing H/R |
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| 133 | spacegroup = spacegroup[0].upper() + spacegroup[1:].lower().rstrip('rh ') |
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| 134 | WriteCIFitem('_symmetry_space_group_name_H-M',spacegroup) |
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| 135 | # generate symmetry operations including centering and center of symmetry |
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| 136 | WriteCIFitem('loop_ _symmetry_equiv_pos_site_id _symmetry_equiv_pos_as_xyz') |
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| 137 | |
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| 138 | # loop over histogram(s) used in this phase |
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| 139 | if not oneblock: |
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| 140 | # pointers to histograms used in this phase |
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| 141 | histlist = [] |
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| 142 | for hist in self.GroupedParms['Phases'][phasenam]['Histograms']: |
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| 143 | if self.GroupedParms['Phases'][phasenam]['Histograms'][hist]['Use']: |
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| 144 | if phasebyhistDict.get(hist): |
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| 145 | phasebyhistDict[hist].append(phasenam) |
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| 146 | else: |
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| 147 | phasebyhistDict[hist] = [phasenam,] |
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| 148 | blockid = datablockidDict.get(hist) |
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| 149 | if not blockid: |
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| 150 | print "Internal error: no block for data. Phase "+str( |
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| 151 | phasenam)+" histogram "+str(hist) |
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| 152 | histlist = [] |
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| 153 | break |
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| 154 | histlist.append(blockid) |
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| 155 | |
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| 156 | if len(histlist) == 0: |
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| 157 | WriteCIFitem('# Note: phase has no associated data') |
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| 158 | else: |
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| 159 | WriteCIFitem('loop_ _pd_block_diffractogram_id') |
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| 160 | for hist in histlist: |
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| 161 | WriteCIFitem('',hist) |
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| 162 | # TODO: sample/histogram profile information and other "HAP" info should be |
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| 163 | # reported in this loop, such as |
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| 164 | # _pd_proc_ls_pref_orient_corr |
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| 165 | # _pd_proc_ls_profile_function |
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| 166 | #txt = ' Spherical Harmonic ODF' + '\n spherical harmonic order='+'?' |
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| 167 | #IF ( ISAMSYM.EQ.1 ) THEN |
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| 168 | #txt += '\n No sample symmetry' |
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| 169 | #ELSE IF ( ISAMSYM.EQ.2 ) THEN |
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| 170 | #txt += ' The sample symmetry is: 2/m (shear texture)' |
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| 171 | #ELSE IF ( ISAMSYM.EQ.3 ) THEN |
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| 172 | #txt += ' The sample symmetry is: mmm (rolling texture)' |
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| 173 | #ELSE IF ( ISAMSYM.EQ.0 ) THEN |
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| 174 | #txt += ' The sample symmetry is: cylindrical (fiber texture)' |
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| 175 | #WriteCIFitem('_pd_proc_ls_pref_orient_corr',txt) |
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| 176 | else: |
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| 177 | # report all profile information here (include instrumental) |
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| 178 | # _pd_proc_ls_pref_orient_corr |
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| 179 | # _pd_proc_ls_profile_function |
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| 180 | pass |
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| 181 | |
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| 182 | WriteCIFitem('\n# ATOMIC COORDINATES AND DISPLACEMENT PARAMETERS') |
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| 183 | |
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| 184 | WriteCIFitem('loop_ '+ |
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| 185 | '\n\t_atom_site_type_symbol'+ |
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| 186 | '\n\t_atom_site_label'+ |
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| 187 | '\n\t_atom_site_fract_x'+ |
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| 188 | '\n\t_atom_site_fract_y'+ |
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| 189 | '\n\t_atom_site_fract_z'+ |
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| 190 | '\n\t_atom_site_occupancy'+ |
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| 191 | '\n\t_atom_site_thermal_displace_type'+ |
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| 192 | '\n\t_atom_site_U_iso_or_equiv'+ |
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| 193 | '\n\t_atom_site_symmetry_multiplicity') |
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| 194 | |
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| 195 | WriteCIFitem('loop_' + '\n\t_atom_site_aniso_label' + |
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| 196 | '\n\t_atom_site_aniso_U_11' + '\n\t_atom_site_aniso_U_12' + |
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| 197 | '\n\t_atom_site_aniso_U_13' + '\n\t_atom_site_aniso_U_22' + |
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| 198 | '\n\t_atom_site_aniso_U_23' + '\n\t_atom_site_aniso_U_33') |
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| 199 | |
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| 200 | # process the chemical formula: pick a Z value & generate molecular weight |
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| 201 | # find the maximum possible Z value |
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| 202 | |
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| 203 | # order the elements in "Hill" order: C, H, D, T & alphabetical or alphabetical |
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| 204 | if not oneblock: # in single block, this is combined with the scattering factors |
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| 205 | WriteCIFitem('loop_ _atom_type_symbol _atom_type_number_in_cell') |
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| 206 | |
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| 207 | WriteCIFitem('# If you change Z, be sure to change all 3 of the following') |
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| 208 | WriteCIFitem( '_chemical_formula_sum',text) |
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| 209 | #WRITE(TEXT,'(F15.2)') ATMASS |
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| 210 | WriteCIFitem( '_chemical_formula_weight',text) |
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| 211 | #WRITE(TEXT,'(I4)') Z |
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| 212 | WriteCIFitem( '_cell_formula_units_Z',text) |
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| 213 | |
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| 214 | #C now loop over interatomic distances for this phase |
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| 215 | WriteCIFitem('\n# MOLECULAR GEOMETRY') |
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| 216 | WriteCIFitem('loop_' + |
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| 217 | '\n\t_geom_bond_atom_site_label_1' + |
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| 218 | '\n\t_geom_bond_atom_site_label_2' + |
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| 219 | '\n\t_geom_bond_distance' + |
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| 220 | '\n\t_geom_bond_site_symmetry_1' + |
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| 221 | '\n\t_geom_bond_site_symmetry_2' + |
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| 222 | '\n\t_geom_bond_publ_flag') |
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| 223 | |
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| 224 | #C now loop over interatomic angles for this phase |
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| 225 | WriteCIFitem('loop_' + |
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| 226 | '\n\t_geom_angle_atom_site_label_1' + |
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| 227 | '\n\t_geom_angle_atom_site_label_2' + |
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| 228 | '\n\t_geom_angle_atom_site_label_3' + |
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| 229 | '\n\t_geom_angle' + |
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| 230 | '\n\t_geom_angle_site_symmetry_1' + |
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| 231 | '\n\t_geom_angle_site_symmetry_2' + |
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| 232 | '\n\t_geom_angle_site_symmetry_3' + |
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| 233 | '\n\t_geom_angle_publ_flag') |
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| 234 | |
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| 235 | def WritePowderData(histlbl): |
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| 236 | text = '?' |
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| 237 | histblk = self.GroupedParms['PWDR'][histlbl] |
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| 238 | print 'TODO: powder here data for',histblk["Sample Parameters"]['InstrName'] |
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| 239 | # see wrpowdhist.for & wrreflist.for |
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| 240 | |
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| 241 | refprx = '_refln.' # mm |
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| 242 | refprx = '_refln_' # normal |
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| 243 | |
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| 244 | if not oneblock: |
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| 245 | if not phasebyhistDict.get(histlbl): |
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| 246 | WriteCIFitem('\n# No phases associated with this data set') |
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| 247 | else: |
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| 248 | WriteCIFitem('\n# PHASE TABLE') |
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| 249 | WriteCIFitem('loop_' + |
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| 250 | '\n\t_pd_phase_id' + |
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| 251 | '\n\t_pd_phase_block_id' + |
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| 252 | '\n\t_pd_phase_mass_%') |
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| 253 | for phasenam in phasebyhistDict.get(histlbl): |
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| 254 | pass |
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| 255 | |
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| 256 | WriteCIFitem('\n# SCATTERING FACTOR INFO') |
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| 257 | WriteCIFitem('_diffrn_radiation_wavelength' ,text) |
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| 258 | #WriteCIFitem('_diffrn_radiation_type',text) |
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| 259 | #C always assume Ka1 & Ka2 if two wavelengths are present |
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| 260 | #WriteCIFitem('loop_' + |
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| 261 | # '\n\t_diffrn_radiation_wavelength' + |
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| 262 | # '\n\t_diffrn_radiation_wavelength_wt' + |
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| 263 | # '\n\t_diffrn_radiation_type' + |
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| 264 | # '\n\t_diffrn_radiation_wavelength_id') |
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| 265 | #WRITE LAM1,1.0,'K\\a~1~',1, LAM2,ratio,'K\\a~2~',2 |
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| 266 | |
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| 267 | WriteCIFitem('_pd_proc_ls_prof_R_factor','?') |
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| 268 | WriteCIFitem('_pd_proc_ls_prof_wR_factor','?') |
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| 269 | WriteCIFitem('_pd_proc_ls_prof_wR_expected','?') |
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| 270 | WriteCIFitem('_refine_ls_R_Fsqd_factor','?') |
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| 271 | |
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| 272 | #WriteCIFitem('_pd_meas_2theta_fixed',text) |
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| 273 | WriteCIFitem('_diffrn_radiation_probe','x-ray') |
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| 274 | WriteCIFitem('_diffrn_radiation_probe','neutron') |
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| 275 | WriteCIFitem('_diffrn_radiation_polarisn_ratio','?') |
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| 276 | |
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| 277 | WriteCIFitem('loop_ _atom_type_symbol') |
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| 278 | if oneblock: |
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| 279 | WriteCIFitem(' _atom_type_number_in_cell') |
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| 280 | #IF (HTYP(2:2) .eq. 'X' .AND. HTYP(3:3) .ne. 'E') THEN |
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| 281 | WriteCIFitem(' _atom_type_scat_dispersion_real') |
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| 282 | WriteCIFitem(' _atom_type_scat_dispersion_imag') |
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| 283 | for lbl in ('a1','a2','a3', 'a4', 'b1', 'b2', 'b3', 'b4', 'c'): |
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| 284 | WriteCIFitem(' _atom_type_scat_Cromer_Mann_'+lbl) |
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| 285 | #ELSEIF (HTYP(2:2) .eq. 'N') THEN |
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| 286 | WriteCIFitem(' _atom_type_scat_length_neutron') |
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| 287 | #ENDIF |
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| 288 | WriteCIFitem(' _atom_type_scat_source') |
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| 289 | |
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| 290 | #C document the background function used |
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| 291 | WriteCIFitem('_pd_proc_ls_background_function','?') |
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| 292 | |
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| 293 | WriteCIFitem('_exptl_absorpt_process_details','?') |
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| 294 | WriteCIFitem('_exptl_absorpt_correction_T_min','?') |
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| 295 | WriteCIFitem('_exptl_absorpt_correction_T_max','?') |
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| 296 | #C extinction |
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| 297 | #WRITE(IUCIF,'(A)') '# Extinction correction' |
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| 298 | #CALL WRVAL(IUCIF,'_gsas_exptl_extinct_corr_T_min',TEXT(1:10)) |
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| 299 | #CALL WRVAL(IUCIF,'_gsas_exptl_extinct_corr_T_max',TEXT(11:20)) |
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| 300 | |
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| 301 | if not oneblock: |
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| 302 | # instrumental profile terms go here |
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| 303 | WriteCIFitem('_pd_proc_ls_profile_function','?') |
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| 304 | |
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| 305 | WriteCIFitem('\n# STRUCTURE FACTOR TABLE') |
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| 306 | WriteCIFitem('loop_' + |
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| 307 | '\n\t' + refprx + 'index_h' + |
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| 308 | '\n\t' + refprx + 'index_k' + |
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| 309 | '\n\t' + refprx + 'index_l' + |
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| 310 | '\n\t_pd_refln_wavelength_id' + |
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| 311 | '\n\t_pd_refln_phase_id' + |
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| 312 | '\n\t' + refprx + 'status' + |
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| 313 | '\n\t' + refprx + 'F_squared_meas' + |
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| 314 | '\n\t' + refprx + 'F_squared_sigma' + |
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| 315 | '\n\t' + refprx + 'F_squared_calc' + |
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| 316 | '\n\t' + refprx + 'phase_calc' + |
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| 317 | '\n\t_pd_refln_d_spacing' + |
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| 318 | '\n\t_gsas_i100_meas') |
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| 319 | |
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| 320 | WriteCIFitem('_reflns_number_total', text) |
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| 321 | WriteCIFitem('_reflns_limit_h_min', text) |
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| 322 | WriteCIFitem('_reflns_limit_h_max', text) |
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| 323 | WriteCIFitem('_reflns_limit_k_min', text) |
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| 324 | WriteCIFitem('_reflns_limit_k_max', text) |
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| 325 | WriteCIFitem('_reflns_limit_l_min', text) |
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| 326 | WriteCIFitem('_reflns_limit_l_max', text) |
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| 327 | WriteCIFitem('_reflns_d_resolution_high', text) |
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| 328 | WriteCIFitem('_reflns_d_resolution_low', text) |
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| 329 | |
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| 330 | WriteCIFitem('\n# POWDER DATA TABLE') |
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| 331 | # is data fixed step? |
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| 332 | fixedstep = False |
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| 333 | # are ESDs sqrt(I) |
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| 334 | countsdata = False |
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| 335 | zero = 0.01 |
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| 336 | if fixedstep: |
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| 337 | WriteCIFitem('_pd_meas_2theta_range_min', text) |
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| 338 | WriteCIFitem('_pd_meas_2theta_range_max', text) |
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| 339 | WriteCIFitem('_pd_meas_2theta_range_inc', text) |
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| 340 | # zero correct |
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| 341 | if zero != 0.0: |
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| 342 | WriteCIFitem('_pd_proc_2theta_range_min', text) |
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| 343 | WriteCIFitem('_pd_proc_2theta_range_max', text) |
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| 344 | WriteCIFitem('_pd_proc_2theta_range_inc', text) |
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| 345 | WriteCIFitem('loop_' + |
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| 346 | '\n\t_pd_proc_d_spacing') |
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| 347 | #'_pd_meas_time_of_flight' |
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| 348 | if not fixedstep: |
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| 349 | if zero != 0.0: |
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| 350 | WriteCIFitem('\t_pd_proc_2theta_corrected') |
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| 351 | else: |
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| 352 | WriteCIFitem('\t_pd_meas_2theta_scan') |
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| 353 | if countsdata: |
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| 354 | WriteCIFitem('\t_pd_meas_counts_total') |
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| 355 | else: |
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| 356 | WriteCIFitem('\t_pd_meas_intensity_total') |
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| 357 | WriteCIFitem('\t_pd_proc_ls_weight') |
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| 358 | WriteCIFitem('\t_pd_proc_intensity_bkg_calc') |
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| 359 | WriteCIFitem('\t_pd_calc_intensity_total') |
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| 360 | if zero != 0.0: |
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| 361 | WriteCIFitem('_pd_proc_number_of_points', text) |
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| 362 | else: |
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| 363 | WriteCIFitem('_pd_meas_number_of_points', text) |
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| 364 | |
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| 365 | def WriteSingleXtalData(histlbl): |
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| 366 | histblk = self.GroupedParms['HKLF'][histlbl] |
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| 367 | print 'TODO: single xtal here data for',histblk["Instrument Parameters"][0]['InstrName'] |
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| 368 | # see wrreflist.for |
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| 369 | refprx = '_refln.' # mm |
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| 370 | refprx = '_refln_' # normal |
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| 371 | |
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| 372 | WriteCIFitem('\n# STRUCTURE FACTOR TABLE') |
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| 373 | WriteCIFitem('loop_' + |
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| 374 | '\n\t' + refprx + 'index_h' + |
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| 375 | '\n\t' + refprx + 'index_k' + |
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| 376 | '\n\t' + refprx + 'index_l' + |
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| 377 | '\n\t' + refprx + 'status' + |
|---|
| 378 | '\n\t' + refprx + 'F_squared_meas' + |
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| 379 | '\n\t' + refprx + 'F_squared_sigma' + |
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| 380 | '\n\t' + refprx + 'F_squared_calc' + |
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| 381 | '\n\t' + refprx + 'phase_calc') |
|---|
| 382 | WriteCIFitem('_reflns_number_total', text) |
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| 383 | WriteCIFitem('_reflns_number_observed', text) |
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| 384 | WriteCIFitem('_reflns_limit_h_min', text) |
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| 385 | WriteCIFitem('_reflns_limit_h_max', text) |
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| 386 | WriteCIFitem('_reflns_limit_k_min', text) |
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| 387 | WriteCIFitem('_reflns_limit_k_max', text) |
|---|
| 388 | WriteCIFitem('_reflns_limit_l_min', text) |
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| 389 | WriteCIFitem('_reflns_limit_l_max', text) |
|---|
| 390 | WriteCIFitem('_reflns_d_resolution_high', text) |
|---|
| 391 | WriteCIFitem('_reflns_d_resolution_low', text) |
|---|
| 392 | |
|---|
| 393 | #============================================================ |
|---|
| 394 | # the export process starts here |
|---|
| 395 | self.loadTree() |
|---|
| 396 | self.CIFdate = dt.datetime.strftime(dt.datetime.now(),"%Y-%m-%dT%H:%M") |
|---|
| 397 | # count phases, powder and single crystal histograms |
|---|
| 398 | self.nphase = len(self.GroupedParms.get("Phases",[])) |
|---|
| 399 | self.npowder = len(self.GroupedParms.get("PWDR",[])) |
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| 400 | self.nsingle = len(self.GroupedParms.get("HKLF",[])) |
|---|
| 401 | # is there anything to export? |
|---|
| 402 | if self.nphase + self.npowder + self.nsingle == 0: |
|---|
| 403 | self.G2frame.ErrorDialog( |
|---|
| 404 | 'Empty project', |
|---|
| 405 | 'No data or phases to include in CIF') |
|---|
| 406 | return |
|---|
| 407 | # is there a file name defined? |
|---|
| 408 | self.CIFname = os.path.splitext( |
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| 409 | os.path.split(self.G2frame.GSASprojectfile)[1] |
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| 410 | )[0] |
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| 411 | self.CIFname = self.CIFname.replace(' ','') |
|---|
| 412 | if not self.CIFname: |
|---|
| 413 | self.G2frame.ErrorDialog( |
|---|
| 414 | 'No GPX name', |
|---|
| 415 | 'Please save the project to provide a name') |
|---|
| 416 | return |
|---|
| 417 | # test for quick CIF mode or no data |
|---|
| 418 | self.quickmode = False |
|---|
| 419 | phasenam = phasenum = None # include all phases |
|---|
| 420 | if mode != "full" or self.npowder + self.nsingle == 0: |
|---|
| 421 | self.quickmode = True |
|---|
| 422 | oneblock = True |
|---|
| 423 | if self.nphase == 0: |
|---|
| 424 | self.G2frame.ErrorDialog( |
|---|
| 425 | 'No phase present', |
|---|
| 426 | 'Cannot create a coordinates CIF with no phases') |
|---|
| 427 | return |
|---|
| 428 | elif self.nphase > 1: # quick mode: choose one phase |
|---|
| 429 | choices = sorted(self.GroupedParms['Phases'].keys()) |
|---|
| 430 | phasenum = G2gd.ItemSelector(choices,self.G2frame) |
|---|
| 431 | if phasenum is None: return |
|---|
| 432 | phasenam = choices[phasenum] |
|---|
| 433 | # will this require a multiblock CIF? |
|---|
| 434 | elif self.nphase > 1: |
|---|
| 435 | oneblock = False |
|---|
| 436 | elif self.npowder + self.nsingle > 1: |
|---|
| 437 | oneblock = False |
|---|
| 438 | else: # one phase, one dataset, Full CIF |
|---|
| 439 | oneblock = True |
|---|
| 440 | |
|---|
| 441 | # make sure needed infomation is present |
|---|
| 442 | # get CIF author name -- required for full CIFs |
|---|
| 443 | try: |
|---|
| 444 | self.author = self.OverallParms['Controls'].get("Author",'').strip() |
|---|
| 445 | except KeyError: |
|---|
| 446 | pass |
|---|
| 447 | while not (self.author or self.quickmode): |
|---|
| 448 | dlg = G2gd.SingleStringDialog(self.G2frame,'Get CIF Author','Provide CIF Author name (Last, First)') |
|---|
| 449 | if not dlg.Show(): return # cancel was pressed |
|---|
| 450 | self.author = dlg.GetValue() |
|---|
| 451 | dlg.Destroy() |
|---|
| 452 | try: |
|---|
| 453 | self.OverallParms['Controls']["Author"] = self.author # save for future |
|---|
| 454 | except KeyError: |
|---|
| 455 | pass |
|---|
| 456 | self.shortauthorname = self.author.replace(',','').replace(' ','')[:20] |
|---|
| 457 | |
|---|
| 458 | # check the instrument name for every histogram |
|---|
| 459 | if not self.quickmode: |
|---|
| 460 | dictlist = [] |
|---|
| 461 | keylist = [] |
|---|
| 462 | lbllist = [] |
|---|
| 463 | invalid = 0 |
|---|
| 464 | key3 = 'InstrName' |
|---|
| 465 | for key in self.GroupedParms: |
|---|
| 466 | if key == 'Phases': continue |
|---|
| 467 | for key1 in self.GroupedParms[key]: |
|---|
| 468 | if key == "PWDR": |
|---|
| 469 | key2 = "Sample Parameters" |
|---|
| 470 | d = self.GroupedParms[key][key1][key2] |
|---|
| 471 | elif key == "HKLF": |
|---|
| 472 | key2 = "Instrument Parameters" |
|---|
| 473 | d = self.GroupedParms[key][key1][key2][0] |
|---|
| 474 | else: |
|---|
| 475 | raise Exception,"Unexpected histogram type for CIF: "+str(key) |
|---|
| 476 | |
|---|
| 477 | lbllist.append(key1) |
|---|
| 478 | dictlist.append(d) |
|---|
| 479 | keylist.append(key3) |
|---|
| 480 | instrname = d.get(key3) |
|---|
| 481 | if instrname is None: |
|---|
| 482 | d[key3] = '' |
|---|
| 483 | invalid += 1 |
|---|
| 484 | elif instrname.strip() == '': |
|---|
| 485 | invalid += 1 |
|---|
| 486 | if invalid: |
|---|
| 487 | msg = "" |
|---|
| 488 | if invalid > 1: msg = ( |
|---|
| 489 | "\n\nNote: it may be faster to set the name for\n" |
|---|
| 490 | "one histogram for each instrument and use the\n" |
|---|
| 491 | "File/Copy option to duplicate the name" |
|---|
| 492 | ) |
|---|
| 493 | if not G2gd.CallScrolledMultiEditor( |
|---|
| 494 | self.G2frame,dictlist,keylist, |
|---|
| 495 | prelbl=range(1,len(dictlist)+1), |
|---|
| 496 | postlbl=lbllist, |
|---|
| 497 | title='Instrument names', |
|---|
| 498 | header="Edit instrument names. Note that a non-blank\nname is required for all histograms"+msg, |
|---|
| 499 | ): return |
|---|
| 500 | |
|---|
| 501 | #====================================================================== |
|---|
| 502 | # Start writing the CIF - single block |
|---|
| 503 | #====================================================================== |
|---|
| 504 | if oneblock: |
|---|
| 505 | if phasenam is None: # if not already selected, select the first phase (should be one) |
|---|
| 506 | phasenam = self.GroupedParms['Phases'].keys()[0] |
|---|
| 507 | #print 'phasenam',phasenam |
|---|
| 508 | phaseblk = self.GroupedParms['Phases'][phasenam] # pointer to current phase info |
|---|
| 509 | # select data, should only be one set, but take whatever comes 1st |
|---|
| 510 | if not self.quickmode: |
|---|
| 511 | for key in self.GroupedParms: |
|---|
| 512 | if key == 'Phases': continue |
|---|
| 513 | for key1 in self.GroupedParms[key]: |
|---|
| 514 | histblk = self.GroupedParms[key][key1] |
|---|
| 515 | histkey = key1 |
|---|
| 516 | histtyp = key |
|---|
| 517 | if key == "PWDR": |
|---|
| 518 | instnam = histblk["Sample Parameters"]['InstrName'] |
|---|
| 519 | elif key == "HKLF": |
|---|
| 520 | instnam = histblk["Instrument Parameters"][0]['InstrName'] |
|---|
| 521 | break |
|---|
| 522 | break |
|---|
| 523 | instnam = instnam.replace(' ','') |
|---|
| 524 | WriteCIFitem('data_'+self.CIFname) |
|---|
| 525 | if not self.quickmode: # publication information |
|---|
| 526 | WriteCIFitem('_pd_block_id', |
|---|
| 527 | str(self.CIFdate) + "|" + str(self.CIFname) + "|" + |
|---|
| 528 | str(self.shortauthorname) + "|" + instnam) |
|---|
| 529 | WriteAudit() |
|---|
| 530 | WritePubTemplate() |
|---|
| 531 | WriteOverall() |
|---|
| 532 | # report the phase |
|---|
| 533 | WritePhaseTemplate() |
|---|
| 534 | WritePhaseInfo(phasenam) |
|---|
| 535 | if not self.quickmode: |
|---|
| 536 | if histtyp == "PWDR": |
|---|
| 537 | WritePowderTemplate() |
|---|
| 538 | WritePowderData(histkey) |
|---|
| 539 | else: |
|---|
| 540 | WriteSnglXtalTemplate() |
|---|
| 541 | WriteSingleXtalData(histkey) |
|---|
| 542 | else: |
|---|
| 543 | #====================================================================== |
|---|
| 544 | # Start writing the CIF - multiblock |
|---|
| 545 | #====================================================================== |
|---|
| 546 | # publication info |
|---|
| 547 | WriteCIFitem('\ndata_'+self.CIFname+'_publ') |
|---|
| 548 | WriteAudit() |
|---|
| 549 | WriteCIFitem('_pd_block_id', |
|---|
| 550 | str(self.CIFdate) + "|" + str(self.CIFname) + "|" + |
|---|
| 551 | str(self.shortauthorname) + "|Overall") |
|---|
| 552 | WritePubTemplate() |
|---|
| 553 | # overall info |
|---|
| 554 | WriteCIFitem('data_'+str(self.CIFname)+'_overall') |
|---|
| 555 | WriteOverall() |
|---|
| 556 | #============================================================ |
|---|
| 557 | WriteCIFitem('# POINTERS TO PHASE AND HISTOGRAM BLOCKS') |
|---|
| 558 | datablockidDict = {} # save block names here -- N.B. check for conflicts between phase & hist names (unlikely!) |
|---|
| 559 | # loop over phase blocks |
|---|
| 560 | if self.nphase > 1: |
|---|
| 561 | loopprefix = '' |
|---|
| 562 | WriteCIFitem('loop_ _pd_phase_block_id') |
|---|
| 563 | else: |
|---|
| 564 | loopprefix = '_pd_phase_block_id' |
|---|
| 565 | |
|---|
| 566 | for i,phasenam in enumerate(sorted(self.GroupedParms['Phases'].keys())): |
|---|
| 567 | datablockidDict[phasenam] = (str(self.CIFdate) + "|" + str(self.CIFname) + "|" + |
|---|
| 568 | 'phase_'+ str(i+1) + '|' + str(self.shortauthorname)) |
|---|
| 569 | WriteCIFitem(loopprefix,datablockidDict[phasenam]) |
|---|
| 570 | # loop over data blocks |
|---|
| 571 | i = 0 |
|---|
| 572 | if self.npowder + self.nsingle > 1: |
|---|
| 573 | loopprefix = '' |
|---|
| 574 | WriteCIFitem('loop_ _pd_block_diffractogram_id') |
|---|
| 575 | else: |
|---|
| 576 | loopprefix = '_pd_block_diffractogram_id' |
|---|
| 577 | for key in self.GroupedParms: |
|---|
| 578 | if key == 'Phases': continue |
|---|
| 579 | for key1 in self.GroupedParms[key]: |
|---|
| 580 | i += 1 |
|---|
| 581 | histblk = self.GroupedParms[key][key1] |
|---|
| 582 | if key == "PWDR": |
|---|
| 583 | instnam = histblk["Sample Parameters"]['InstrName'] |
|---|
| 584 | elif key == "HKLF": |
|---|
| 585 | instnam = histblk["Instrument Parameters"][0]['InstrName'] |
|---|
| 586 | instnam = instnam.replace(' ','') |
|---|
| 587 | if datablockidDict.get(key1): |
|---|
| 588 | print "Error: histogram name is duplicated: ",key1 |
|---|
| 589 | return |
|---|
| 590 | datablockidDict[key1] = (str(self.CIFdate) + "|" + str(self.CIFname) + "|" + |
|---|
| 591 | str(self.shortauthorname) + "|" + |
|---|
| 592 | instnam + "_hist_"+str(i)) |
|---|
| 593 | WriteCIFitem(loopprefix,datablockidDict[key1]) |
|---|
| 594 | #============================================================ |
|---|
| 595 | # loop over phases, exporting them |
|---|
| 596 | phasebyhistDict = {} # create a cross-reference to phases by histogram |
|---|
| 597 | for j,phasenam in enumerate(sorted(self.GroupedParms['Phases'].keys())): |
|---|
| 598 | i = j + 1 |
|---|
| 599 | WriteCIFitem('\ndata_'+self.CIFname+"_phase_"+str(i)) |
|---|
| 600 | print "debug, processing ",phasenam |
|---|
| 601 | WriteCIFitem('# Information for phase '+str(i)) |
|---|
| 602 | WriteCIFitem('_pd_block_id',datablockidDict[phasenam]) |
|---|
| 603 | # report the phase |
|---|
| 604 | WritePhaseTemplate() |
|---|
| 605 | WritePhaseInfo(phasenam) |
|---|
| 606 | |
|---|
| 607 | #============================================================ |
|---|
| 608 | # loop over histograms, exporting them |
|---|
| 609 | i = 0 |
|---|
| 610 | for key in self.GroupedParms: |
|---|
| 611 | if key == 'Phases': continue |
|---|
| 612 | for key1 in self.GroupedParms[key]: |
|---|
| 613 | i += 1 |
|---|
| 614 | histblk = self.GroupedParms[key][key1] |
|---|
| 615 | if key == "PWDR": |
|---|
| 616 | WriteCIFitem('\ndata_'+self.CIFname+"_pwd_"+str(i)) |
|---|
| 617 | elif key == "HKLF": |
|---|
| 618 | WriteCIFitem('\ndata_'+self.CIFname+"_sx_"+str(i)) |
|---|
| 619 | WriteCIFitem('# Information for histogram '+str(i)+': '+ |
|---|
| 620 | key1) |
|---|
| 621 | WriteCIFitem('_pd_block_id',datablockidDict[key1]) |
|---|
| 622 | if key == "PWDR": |
|---|
| 623 | WritePowderTemplate() |
|---|
| 624 | WritePowderData(key1) |
|---|
| 625 | else: |
|---|
| 626 | WriteSnglXtalTemplate() |
|---|
| 627 | WriteSingleXtalData(key1) |
|---|
| 628 | |
|---|
| 629 | # TODO: how to report _pd_proc_ls_peak_cutoff? |
|---|
| 630 | WriteCIFitem('#--' + 15*'eof--' + '#') |
|---|
| 631 | |
|---|
