Пример #1
0
def main():
    """
    NAME
        zeq_magic_redo.py
   
    DESCRIPTION
        Calculate principal components through demagnetization data using bounds and calculation type stored in "redo" file
  
    SYNTAX
        zeq_magic_redo.py [command line options]

    OPTIONS
        -h prints help message
        -usr USER:   identify user, default is ""
        -f: specify input file, default is magic_measurements.txt
        -F: specify output file, default is zeq_specimens.txt
        -fre  REDO: specify redo file, default is "zeq_redo"
        -fsa  SAMPFILE: specify er_samples format file, default is "er_samples.txt"
        -A : don't average replicate measurements, default is yes
        -crd [s,g,t] : 
             specify coordinate system [s,g,t]  [default is specimen coordinates]
                 are specimen, geographic, and tilt corrected respectively
             NB: you must have a SAMPFILE in this directory to rotate from specimen coordinates
        -leg:  attaches "Recalculated from original measurements; supercedes published results. " to comment field
    INPUTS
        zeq_redo format file is:
        specimen_name calculation_type[DE-BFL,DE-BFL-A,DE-BFL-O,DE-BFP,DE-FM]  step_min step_max component_name[A,B,C]
    """
    dir_path='.'
    INCL=["LT-NO","LT-AF-Z","LT-T-Z","LT-M-Z"] # looking for demag data
    beg,end,pole,geo,tilt,askave,save=0,0,[],0,0,0,0
    user,doave,comment= "",1,""
    geo,tilt=0,0
    version_num=pmag.get_version()
    args=sys.argv
    if '-WD' in args:
        ind=args.index('-WD')
        dir_path=args[ind+1]
    meas_file,pmag_file,mk_file= dir_path+"/"+"magic_measurements.txt",dir_path+"/"+"zeq_specimens.txt",dir_path+"/"+"zeq_redo"
    samp_file,coord=dir_path+"/"+"er_samples.txt",""
    if "-h" in args:
        print main.__doc__
        sys.exit()
    if "-usr" in args:
        ind=args.index("-usr")
        user=sys.argv[ind+1]
    if "-A" in args:doave=0
    if "-leg" in args: comment="Recalculated from original measurements; supercedes published results. "
    if "-f" in args:
        ind=args.index("-f")
        meas_file=dir_path+'/'+sys.argv[ind+1]
    if "-F" in args:
        ind=args.index("-F")
        pmag_file=dir_path+'/'+sys.argv[ind+1]
    if "-fre" in args:
        ind=args.index("-fre")
        mk_file=dir_path+"/"+args[ind+1]
    try:
        mk_f=open(mk_file,'rU')
    except:
        print "Bad redo file"
        sys.exit()
    mkspec,skipped=[],[]
    speclist=[]
    for line in mk_f.readlines():
        tmp=line.split()
        mkspec.append(tmp)
        speclist.append(tmp[0])
    if "-fsa" in args:
        ind=args.index("-fsa")
        samp_file=dir_path+'/'+sys.argv[ind+1]
    if "-crd" in args:
        ind=args.index("-crd")
        coord=sys.argv[ind+1]
        if coord=="g":geo,tilt=1,0
        if coord=="t":geo,tilt=1,1
#
# now get down to bidness
    if geo==1:
        samp_data,file_type=pmag.magic_read(samp_file)
        if file_type != 'er_samples':
            print file_type
            print "This is not a valid er_samples file " 
            sys.exit()
    # set orientation priorities
        SO_methods=[]
        for rec in samp_data:
           if "magic_method_codes" in rec:
               methlist=rec["magic_method_codes"]
               for meth in methlist.split(":"):
                   if "SO" in meth and "SO-POM" not in meth.strip():
                       if meth.strip() not in SO_methods: SO_methods.append(meth.strip())
        SO_priorities=pmag.set_priorities(SO_methods,0)
    #
    #
    #

    meas_data,file_type=pmag.magic_read(meas_file)
    if file_type != 'magic_measurements':
        print file_type
        print file_type,"This is not a valid magic_measurements file " 
        sys.exit()
    #
    # sort the specimen names
    #
    k = 0
    print 'Processing ',len(speclist), ' specimens - please wait'
    PmagSpecs=[]
    while k < len(speclist):
        s=speclist[k]
        recnum=0
        PmagSpecRec={}
        method_codes,inst_codes=[],[]
    # find the data from the meas_data file for this sample
    #
    #  collect info for the PmagSpecRec dictionary
    #
        meas_meth=[]
        for rec in  meas_data: # copy of vital stats to PmagSpecRec from first spec record in demag block
           skip=1
           if rec["er_specimen_name"]==s: 
               methods=rec["magic_method_codes"].split(":")
               if len(set(methods) & set(INCL))>0:
                   PmagSpecRec["er_analyst_mail_names"]=user
                   PmagSpecRec["magic_software_packages"]=version_num
                   PmagSpecRec["er_specimen_name"]=s
                   PmagSpecRec["er_sample_name"]=rec["er_sample_name"]
                   PmagSpecRec["er_site_name"]=rec["er_site_name"]
                   PmagSpecRec["er_location_name"]=rec["er_location_name"]
                   PmagSpecRec["er_citation_names"]="This study"
                   if "magic_experiment_name" not in rec.keys(): rec["magic_experiment_name"]=""
                   PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"]
                   if "magic_instrument_codes" not in rec.keys(): rec["magic_instrument_codes"]=""
                   inst=rec['magic_instrument_codes'].split(":")
                   for I in inst:
                       if I not in inst_codes:  # copy over instruments
                           inst_codes.append(I)
                   meths=rec["magic_method_codes"].split(":")
                   for meth in meths:
                       if meth.strip() not in meas_meth:meas_meth.append(meth)
                   if "LP-DIR-AF" in meas_meth or "LT-AF-Z" in meas_meth: 
                       PmagSpecRec["measurement_step_unit"]="T"
                       if "LP-DIR-AF" not in method_codes:method_codes.append("LP-DIR-AF") 
                   if "LP-DIR-T" in meas_meth or "LT-T-Z" in meas_meth: 
                       PmagSpecRec["measurement_step_unit"]="K"
                       if "LP-DIR-T" not in method_codes:method_codes.append("LP-DIR-T") 
                   if "LP-DIR-M" in meas_meth or "LT-M-Z" in meas_meth: 
                       PmagSpecRec["measurement_step_unit"]="J"
                       if "LP-DIR-M" not in method_codes:method_codes.append("LP-DIR-M") 
        if PmagSpecRec=={}:
            print 'no data found for specimen:  ',s
            print 'delete from zeq_redo input file...., then try again'
            sys.exit()
    #
    #
        data,units=pmag.find_dmag_rec(s,meas_data)
    #
        datablock=data
        noskip=1
        if len(datablock) <2 or s not in speclist : 
            noskip=0
            k+=1
#            print 'skipping ', s,len(datablock)
        if noskip:
        #
        # find replicate measurements at given treatment step and average them
        #
#            step_meth,avedata=pmag.vspec(data)
#
#            if len(avedata) != len(datablock):
#                if doave==1: 
#                    method_codes.append("DE-VM")
#                    datablock=avedata
        #
        # do geo or stratigraphic correction now
        #
            if geo==1:
       # find top priority orientation method
                redo,p=1,0
                if len(SO_methods)<=1:
                    az_type=SO_methods[0]
                    orient=pmag.find_samp_rec(PmagSpecRec["er_sample_name"],samp_data,az_type)
                    if orient["sample_azimuth"]  !="": method_codes.append(az_type)
                    redo=0
                while redo==1:
                    if p>=len(SO_priorities):
                        print "no orientation data for ",s
                        orient["sample_azimuth"]=""
                        orient["sample_dip"]=""
                        method_codes.append("SO-NO")
                        redo=0
                    else:
                        az_type=SO_methods[SO_methods.index(SO_priorities[p])]
                        orient=pmag.find_samp_rec(PmagSpecRec["er_sample_name"],samp_data,az_type)
                        if orient["sample_azimuth"]  !="":
                            method_codes.append(az_type)
                            redo=0
                    p+=1
        #
        #  if tilt selected,  get stratigraphic correction
        #
                tiltblock,geoblock=[],[]
                for rec in datablock:
                    if "sample_azimuth" in orient.keys() and orient["sample_azimuth"]!="":
                        d_geo,i_geo=pmag.dogeo(rec[1],rec[2],orient["sample_azimuth"],orient["sample_dip"])
                        geoblock.append([rec[0],d_geo,i_geo,rec[3],rec[4],rec[5]])
                        if tilt==1 and "sample_bed_dip_direction" in orient.keys(): 
                            d_tilt,i_tilt=pmag.dotilt(d_geo,i_geo,orient["sample_bed_dip_direction"],orient["sample_bed_dip"])
                            tiltblock.append([rec[0],d_tilt,i_tilt,rec[3],rec[4],rec[5]])
                        elif tilt==1:
                            if PmagSpecRec["er_sample_name"] not in skipped:
                                print 'no tilt correction for ', PmagSpecRec["er_sample_name"],' skipping....'
                                skipped.append(PmagSpecRec["er_sample_name"])
                    else:
                        if PmagSpecRec["er_sample_name"] not in skipped:
                            print 'no geographic correction for ', PmagSpecRec["er_sample_name"],' skipping....'
                            skipped.append(PmagSpecRec["er_sample_name"])
    #
    #	get beg_pca, end_pca, pca
            if PmagSpecRec['er_sample_name'] not in skipped:
                compnum=-1
                for spec in mkspec:
                    if spec[0]==s:
                        CompRec={}
                        for key in PmagSpecRec.keys():CompRec[key]=PmagSpecRec[key]
                        compnum+=1
                        calculation_type=spec[1]
                        beg=float(spec[2])
                        end=float(spec[3])
                        if len(spec)>4:
                            comp_name=spec[4]
                        else:
                            comp_name=string.uppercase[compnum]
                        CompRec['specimen_comp_name']=comp_name
                        if beg < float(datablock[0][0]):beg=float(datablock[0][0])
                        if end > float(datablock[-1][0]):end=float(datablock[-1][0])
                        for l  in range(len(datablock)):
                            if datablock[l][0]==beg:beg_pca=l
                            if datablock[l][0]==end:end_pca=l
                        if geo==1 and tilt==0:
                            mpars=pmag.domean(geoblock,beg_pca,end_pca,calculation_type)
                            if mpars["specimen_direction_type"]!="Error":
                                CompRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
                                CompRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
                                CompRec["specimen_tilt_correction"]='0'
                        if geo==1 and tilt==1:
                            mpars=pmag.domean(tiltblock,beg_pca,end_pca,calculation_type)
                            if mpars["specimen_direction_type"]!="Error":
                                CompRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
                                CompRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
                                CompRec["specimen_tilt_correction"]='100'
                        if geo==0 and tilt==0: 
                            mpars=pmag.domean(datablock,beg_pca,end_pca,calculation_type)
                            if mpars["specimen_direction_type"]!="Error":
                                CompRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
                                CompRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
                                CompRec["specimen_tilt_correction"]='-1'
                        if mpars["specimen_direction_type"]=="Error": 
                            pass
                        else: 
                            CompRec["measurement_step_min"]='%8.3e '%(datablock[beg_pca][0])
                            try:
                                CompRec["measurement_step_max"]='%8.3e '%(datablock[end_pca][0] )
                            except:
                                print 'error in end_pca ',PmagSpecRec['er_specimen_name']
                            CompRec["specimen_correction"]='u'
                            if calculation_type!='DE-FM':
                                CompRec["specimen_mad"]='%7.1f '%(mpars["specimen_mad"])
                                CompRec["specimen_alpha95"]=""
                            else:
                                CompRec["specimen_mad"]=""
                                CompRec["specimen_alpha95"]='%7.1f '%(mpars["specimen_alpha95"])
                            CompRec["specimen_n"]='%i '%(mpars["specimen_n"])
                            CompMeths=[]
                            for meth in method_codes:
                                if meth not in CompMeths:CompMeths.append(meth)
                            if calculation_type not in CompMeths:CompMeths.append(calculation_type)
                            if geo==1: CompMeths.append("DA-DIR-GEO")
                            if tilt==1: CompMeths.append("DA-DIR-TILT")
                            if "DE-BFP" not in calculation_type:
                                CompRec["specimen_direction_type"]='l'
                            else:
                                CompRec["specimen_direction_type"]='p'
                            CompRec["magic_method_codes"]=""
                            if len(CompMeths) != 0:
                                methstring=""
                                for meth in CompMeths:
                                    methstring=methstring+ ":" +meth
                                CompRec["magic_method_codes"]=methstring.strip(':')
                            CompRec["specimen_description"]=comment
                            if len(inst_codes) != 0:
                                inststring=""
                                for inst in inst_codes:
                                    inststring=inststring+ ":" +inst
                                CompRec["magic_instrument_codes"]=inststring.strip(':')
                            PmagSpecs.append(CompRec)
            k+=1
    pmag.magic_write(pmag_file,PmagSpecs,'pmag_specimens')
    print "Recalculated specimen data stored in ",pmag_file
Пример #2
0
def main():
    """
    NAME
        kly4s_magic.py

    DESCRIPTION
        converts files generated by SIO kly4S labview program to MagIC formated
        files for use with PmagPy plotting software

    SYNTAX
        kly4s_magic.py -h [command line options]

    OPTIONS
        -h: prints the help message and quits
        -i: allows interactive input of input/output filenames
        -f FILE: specify .ams input file name
        -fad AZDIP: specify AZDIP file with orientations, will create er_samples.txt file
        -fsa SFILE: specify existing er_samples.txt file with orientation information
        -fsp SPFILE: specify existing er_specimens.txt file for appending 
        -F MFILE: specify magic_measurements output file
        -Fa AFILE: specify rmag_anisotropy output file
        -ocn ORCON:  specify orientation convention: default is #3 below -only with AZDIP file
        -usr USER: specify who made the measurements
        -loc LOC: specify location name for study 
        -ins INST: specify instrument used
        -spc SPEC: specify number of characters to specify specimen from sample
        -ncn NCON:  specify naming convention: default is #1 below

    DEFAULTS
        MFILE: magic_measurements.txt
        AFILE: rmag_anisotropy.txt
        SPFILE: create new er_specimen.txt file
        USER: ""
        LOC: "unknown" 
        INST: "SIO-KLY4S"
        SPEC: 1  specimen name is same as sample (if SPEC is 1, sample is all but last character)
    NOTES:
        Sample naming convention:
            [1] XXXXY: where XXXX is an arbitrary length site designation and Y
                is the single character sample designation.  e.g., TG001a is the
                first sample from site TG001.    [default]
            [2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length) 
            [3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
            [4-Z] XXXXYYY:  YYY is sample designation with Z characters from site XXX
            [5] all others you will have to either customize your 
                self or e-mail [email protected] for help.  
       Orientation convention:
            [1] Lab arrow azimuth= azimuth; Lab arrow dip=-dip
                i.e., dip is degrees from vertical down - the hade [default]
            [2] Lab arrow azimuth = azimuth-90; Lab arrow dip = -dip
                i.e., azimuth is strike and dip is hade
            [3] Lab arrow azimuth = azimuth; Lab arrow dip = dip-90
                e.g. dip is degrees from horizontal of drill direction
            [4] Lab arrow azimuth = azimuth; Lab arrow dip = dip 
            [5] Lab arrow azimuth = azimuth; Lab arrow dip = 90-dip 
            [6] all others you will have to either customize your
                self or e-mail [email protected] for help.

    """
    citation='This study'
    cont=0
    ask=0
    samp_con,Z="1",1
    or_con="3" # see orientation_magic.py help message
    inst,specnum="SIO-KLY4S",0
    AniRecs,SpecRecs,SampRecs,MeasRecs=[],[],[],[]
    user,locname,specfile="","unknown","er_specimens.txt"
    AppSpec=0
    sampfile,measfile='','magic_measurements.txt'
    anisfile='rmag_anisotropy.txt'
    azdipfile=""
    dir_path='.'
    if '-WD' in sys.argv:
        ind=sys.argv.index('-WD')
        dir_path=sys.argv[ind+1] 
    if '-h' in sys.argv:
        print main.__doc__
        sys.exit()
    if '-usr' in sys.argv:
        ind=sys.argv.index('-usr')
        user=sys.argv[ind+1] 
    if '-ocn' in sys.argv:
        ind=sys.argv.index('-ocn')
        or_con=sys.argv[ind+1] 
    if "-ncn" in sys.argv:
        ind=sys.argv.index("-ncn")
        samp_con=sys.argv[ind+1]
        if "4" in samp_con:
            if "-" not in samp_con:
                print "option [4] must be in form 3-Z where Z is an integer"
                sys.exit()
            else:
                Z=samp_con.split("-")[1]
                samp_con="4"
    if '-f' in sys.argv:
        ind=sys.argv.index('-f')
        amsfile=sys.argv[ind+1] 
    else:
        print main.__doc__
        print 'must specify ascii input file '
        sys.exit()
    if '-F' in sys.argv:
        ind=sys.argv.index('-F')
        measfile=sys.argv[ind+1] 
    if '-Fa' in sys.argv:
        ind=sys.argv.index('-Fa')
        anisfile=sys.argv[ind+1] 
    if '-Fr' in sys.argv:
        ind=sys.argv.index('-Fr')
        routput=sys.argv[ind+1] 
    if '-fsa' in sys.argv:
        ind=sys.argv.index('-fsa')
        sampfile=sys.argv[ind+1] 
    if '-fsp' in sys.argv:
        ind=sys.argv.index('-fsp')
        specfile=sys.argv[ind+1] 
        AppSpec=1
    if '-fad' in sys.argv:
        ind=sys.argv.index('-fad')
        azdipfile=dir_path+"/"+sys.argv[ind+1]
        azfile=open(azdipfile,'rU')
        AzDipDat=azfile.readlines() 
    if '-loc' in sys.argv:
        ind=sys.argv.index('-loc')
        locname=sys.argv[ind+1] 
    if '-spc' in sys.argv:
        ind=sys.argv.index('-spc')
        specnum=-(int(sys.argv[ind+1]))
        #if specnum!=0:specnum=-specnum
    specfile=dir_path+'/'+specfile
    sampfile=dir_path+'/'+sampfile
    measfile=dir_path+'/'+measfile
    anisfile=dir_path+'/'+anisfile
    amsfile=dir_path+'/'+amsfile
    try:
        input=open(amsfile,'rU')
    except:
        print 'Error opening file: ', amsfile
        sys.exit()
    SpecRecs,speclist=[],[]
    if AppSpec==1:
        try:
            SpecRecs,filetype=pmag.magic_read(specfile) # append new records to existing
            if len(SpecRecs)>0:
                for spec in SpecRecs:
                    if spec['er_specimen_name'] not in speclist:speclist.append(spec['er_specimen_name'])
        except IOError:
            print 'trouble opening ',specfile 
    Data=input.readlines()
    samps=[]
    if sampfile!=dir_path+'/': 
        samps,file_type=pmag.magic_read(sampfile)
        SO_methods=[]
        for rec in samps:
           if "magic_method_codes" in rec.keys():
               methlist=rec["magic_method_codes"].replace(" ","").split(":")
               for meth in methlist:
                   if "SO" in meth and "SO-POM" not in meth and "SO-GT5" not in meth and "SO-ASC" not in meth and "SO-BAD" not in meth:
                       if meth not in SO_methods: SO_methods.append(meth)
    #
        SO_priorities=pmag.set_priorities(SO_methods,ask)
    for line in Data:
      rec=line.split()
      if len(rec)>0:
        AniRec,SpecRec,SampRec,SiteRec,MeasRec={},{},{},{},{}
        specname=rec[0]
        if specnum!=0:
            sampname=specname[:specnum]
        else:
            sampname=specname
        site=pmag.parse_site(sampname,samp_con,Z)
        AniRec['er_location_name']=locname
        AniRec['er_citation_names']="This study"
        AniRec['magic_instrument_codes']=inst
        method_codes=['LP-X','AE-H','LP-AN-MS']
        AniRec['magic_experiment_name']=specname+":"+"LP-AN-MS"
        AniRec['er_analyst_mail_names']=user
        AniRec['er_site_name']=site
        AniRec['er_sample_name']=sampname
        AniRec['er_specimen_name']=specname
        labaz,labdip,bed_dip_direction,bed_dip="","","",""
        if azdipfile!="":
            for key in AniRec.keys():SampRec[key]=AniRec[key]
            for oline in AzDipDat: # look for exact match first
                orec=oline.replace('\n','').split()
                if orec[0].upper() in specname.upper(): # we have a match
                   labaz,labdip=pmag.orient(float(orec[1]),float(orec[2]),or_con)  
                   bed_dip_direction=float(orec[3])-90. # assume dip to right of strike
                   bed_dip=float(orec[4])
                   break
            if labaz=="":  # found no exact match - now look at sample level
                for oline in AzDipDat: 
                    orec=oline.split()
                    if orec[0].upper() == sampname.upper(): # we have a match
                       labaz,labdip=pmag.orient(float(orec[1]),float(orec[2]),or_con)  
                       bed_dip_direction=float(orec[3])-90. # assume dip to right of strike
                       bed_dip=float(orec[4])
                       break
            if labaz=="":  # found no exact match - now look at sample level
                print 'found no orientation data - will use specimen coordinates' 
                raw_input("<return> to continue")
            else:
                for key in AniRec.keys():SampRec[key]=AniRec[key]
                SampRec['sample_azimuth']='%7.1f'%(labaz)
                SampRec['sample_dip']='%7.1f'%(labdip)
                SampRec['sample_bed_dip_direction']='%7.1f'%(bed_dip_direction)
                SampRec['sample_bed_dip']='%7.1f'%(bed_dip)
                SampRecs.append(SampRec)
        elif sampfile!=dir_path+'/':
           redo,p=1,0
           orient={}
           if len(SO_methods)==1:
                az_type=SO_methods[0]
                orient=pmag.find_samp_rec(AniRec["er_sample_name"],samps,az_type)
                if orient['sample_azimuth']!="":
                    method_codes.append(az_type)
                else:
                    print "no orientation data for ",AniRec["er_sample_name"],labaz
                    orient["sample_azimuth"]=""
                    orient["sample_dip"]=""
                    orient["sample_bed_dip_direction"]=""
                    orient["sample_bed_dip"]=""
                    noorient=1
                    method_codes.append("SO-NO")
                    redo=0
                redo=0
           while redo==1:
                if p>=len(SO_priorities):
                    print "no orientation data for ",AniRec["er_sample_name"],labaz
                    orient["sample_azimuth"]=""
                    orient["sample_dip"]=""
                    orient["sample_bed_dip_direction"]=""
                    orient["sample_bed_dip"]=""
                    noorient=1
                    method_codes.append("SO-NO")
                    redo=0
                else:
                    az_type=SO_methods[SO_methods.index(SO_priorities[p])]
                    orient=pmag.find_samp_rec(AniRec["er_sample_name"],samps,az_type)
                    if orient["sample_azimuth"]  !="":
                        method_codes.append(az_type)
                        redo=0
                    noorient=0
                p+=1
           if orient['sample_azimuth']!="":labaz=float(orient['sample_azimuth'])
           if orient['sample_dip']!="":labdip=float(orient['sample_dip'])
           if "sample_bed_dip_direction" in orient.keys() and orient['sample_bed_dip_direction']!="": bed_dip_direction=float(orient['sample_bed_dip_direction'])
           if "sample_bed_dip" in orient.keys() and orient['sample_bed_dip']!="": sample_bed_dip=float(orient['sample_bed_dip'])
        for key in AniRec.keys():SpecRec[key]=AniRec[key]
        for key in AniRec.keys():MeasRec[key]=AniRec[key]
        AniRec['anisotropy_type']="AMS"
        AniRec['anisotropy_n']="192"
        AniRec['anisotropy_s1']=rec[1]
        AniRec['anisotropy_s2']=rec[2]
        AniRec['anisotropy_s3']=rec[3]
        AniRec['anisotropy_s4']=rec[4]
        AniRec['anisotropy_s5']=rec[5]
        AniRec['anisotropy_s6']=rec[6]
        AniRec['anisotropy_sigma']=rec[7]
        AniRec['anisotropy_tilt_correction']='-1'
        AniRec['anisotropy_unit']='Normalized by trace'
        SpecRec['specimen_volume']='%8.3e'%(1e-6*float(rec[12])) # volume from cc to m^3
        MeasRec['measurement_flag']='g' # good
        MeasRec['measurement_standard']='u' # unknown
        date=rec[14].split('/')
        if int(date[2])>80:
           date[2]='19'+date[2]
        else: 
           date[2]='20'+date[2]
        datetime=date[2]+':'+date[0]+':'+date[1]+":"
        datetime=datetime+rec[15]
        MeasRec['measurement_number']='1'
        MeasRec['measurement_date']=datetime 
        MeasRec['measurement_lab_field_ac']='%8.3e'%(4*math.pi*1e-7*float(rec[11])) # convert from A/m to T
        MeasRec['measurement_temp']="300" # assumed room T in kelvin
        MeasRec['measurement_chi_volume']=rec[8]
        MeasRec['measurement_description']='Bulk measurement'
        MeasRec['magic_method_codes']='LP-X'
        if SpecRec['er_specimen_name'] not in speclist: # add to list
            speclist.append(SpecRec['er_specimen_name'])
            SpecRecs.append(SpecRec)
        MeasRecs.append(MeasRec)
        methods=""
        for meth in method_codes:
            methods=methods+meth+":"
        AniRec["magic_method_codes"]=methods[:-1]  # get rid of annoying spaces in Anthony's export files
        AniRecs.append(AniRec)
        if labaz!="": # have orientation info
            AniRecG,AniRecT={},{}
            for key in AniRec.keys():AniRecG[key]=AniRec[key]
            for key in AniRec.keys():AniRecT[key]=AniRec[key]
            sbar=[]
            sbar.append(float(AniRec['anisotropy_s1']))
            sbar.append(float(AniRec['anisotropy_s2']))
            sbar.append(float(AniRec['anisotropy_s3']))
            sbar.append(float(AniRec['anisotropy_s4']))
            sbar.append(float(AniRec['anisotropy_s5']))
            sbar.append(float(AniRec['anisotropy_s6']))
            sbarg=pmag.dosgeo(sbar,labaz,labdip)
            AniRecG["anisotropy_s1"]='%12.10f'%(sbarg[0])
            AniRecG["anisotropy_s2"]='%12.10f'%(sbarg[1])
            AniRecG["anisotropy_s3"]='%12.10f'%(sbarg[2])
            AniRecG["anisotropy_s4"]='%12.10f'%(sbarg[3])
            AniRecG["anisotropy_s5"]='%12.10f'%(sbarg[4])
            AniRecG["anisotropy_s6"]='%12.10f'%(sbarg[5])
            AniRecG["anisotropy_tilt_correction"]='0'
            AniRecs.append(AniRecG)
            if bed_dip!="" and bed_dip!=0: # have tilt correction
                sbart=pmag.dostilt(sbarg,bed_dip_direction,bed_dip)
                AniRecT["anisotropy_s1"]='%12.10f'%(sbart[0])
                AniRecT["anisotropy_s2"]='%12.10f'%(sbart[1])
                AniRecT["anisotropy_s3"]='%12.10f'%(sbart[2])
                AniRecT["anisotropy_s4"]='%12.10f'%(sbart[3])
                AniRecT["anisotropy_s5"]='%12.10f'%(sbart[4])
                AniRecT["anisotropy_s6"]='%12.10f'%(sbart[5])
                AniRecT["anisotropy_tilt_correction"]='100'
                AniRecs.append(AniRecT)
    pmag.magic_write(anisfile,AniRecs,'rmag_anisotropy')
    pmag.magic_write(measfile,MeasRecs,'magic_measurements')
    pmag.magic_write(specfile,SpecRecs,'er_specimens')
    print 'anisotropy data saved in ',anisfile
    print 'measurement data saved in ',measfile
    if AppSpec==1:
        print 'new specimen information  added  to ',specfile
    else:
        print 'specimen information  saved in new ',specfile
    if azdipfile!="":
        sampfile='er_samples.txt'
        pmag.magic_write(sampfile,SampRecs,'er_samples')
        print 'sample data saved in ',sampfile
Пример #3
0
def main():
    """
    NAME
        site_edit_magic.py

    DESCRIPTION
       makes equal area projections site by site
         from pmag_specimens.txt file with
         Fisher confidence ellipse using McFadden and McElhinny (1988)
         technique for combining lines and planes
         allows testing and reject specimens for bad orientations

    SYNTAX
        site_edit_magic.py [command line options]

    OPTIONS
       -h: prints help and quits
       -f: specify pmag_specimen format file, default is pmag_specimens.txt
       -fsa: specify er_samples.txt file
       -exc: use existing pmag_criteria.txt file
       -N: reset all sample flags to good
    
    OUPUT
       edited er_samples.txt file

    """
    dir_path='.'
    FIG={} # plot dictionary
    FIG['eqarea']=1 # eqarea is figure 1
    in_file='pmag_specimens.txt'
    sampfile='er_samples.txt'
    out_file=""
    fmt,plot='svg',1
    Crits=""
    M,N=180.,1
    repeat=''
    renew=0
    if '-h' in sys.argv:
        print main.__doc__
        sys.exit()
    if '-WD' in sys.argv:
        ind=sys.argv.index('-WD')
        dir_path=sys.argv[ind+1]
    if '-f' in sys.argv:
        ind=sys.argv.index("-f")
        in_file=sys.argv[ind+1]
    if '-fsa' in sys.argv:
        ind=sys.argv.index("-fsa")
        sampfile=sys.argv[ind+1]
    if '-exc' in sys.argv:
        Crits,file_type=pmag.magic_read(dir_path+'/pmag_criteria.txt')
        for crit in Crits:
            if crit['pmag_criteria_code']=='DE-SPEC':
                M=float(crit['specimen_mad'])
                N=float(crit['specimen_n'])
    if '-fmt' in sys.argv:
        ind=sys.argv.index("-fmt")
        fmt=sys.argv[ind+1]
    if '-N' in sys.argv: renew=1
# 
    if in_file[0]!="/":in_file=dir_path+'/'+in_file
    if sampfile[0]!="/":sampfile=dir_path+'/'+sampfile
    crd='s'
    Specs,file_type=pmag.magic_read(in_file)
    if file_type!='pmag_specimens':
        print ' bad pmag_specimen input file'
        sys.exit()
    Samps,file_type=pmag.magic_read(sampfile)
    if file_type!='er_samples':
        print ' bad er_samples input file'
        sys.exit()
    SO_methods=[]
    for rec in Samps:
       if 'sample_orientation_flag' not in rec.keys(): rec['sample_orientation_flag']='g'
       if 'sample_description' not in rec.keys(): rec['sample_description']=''
       if renew==1:
          rec['sample_orientation_flag']='g'
          description=rec['sample_description']
          if '#' in description:
               newdesc=""
               c=0
               while description[c]!='#' and c<len(description)-1: # look for first pound sign
                   newdesc=newdesc+description[c]
                   c+=1
               while description[c]=='#': 
                   c+=1# skip first set of pound signs
               while description[c]!='#':c+=1 # find second set of pound signs
               while description[c]=='#' and c<len(description)-1:c+=1 # skip second set of pound signs
               while c<len(description)-1: # look for first pound sign
                   newdesc=newdesc+description[c]
                   c+=1
               rec['sample_description']=newdesc # edit out old comment about orientations
       if "magic_method_codes" in rec:
           methlist=rec["magic_method_codes"]
           for meth in methlist.split(":"):
               if "SO" in meth.strip() and "SO-POM" not in meth.strip():
                   if meth.strip() not in SO_methods: SO_methods.append(meth.strip())
    pmag.magic_write(sampfile,Samps,'er_samples')
    SO_priorities=pmag.set_priorities(SO_methods,0)
    sitelist=[]
    for rec in Specs:
        if rec['er_site_name'] not in sitelist: sitelist.append(rec['er_site_name'])
    sitelist.sort()
    EQ={} 
    EQ['eqarea']=1
    pmagplotlib.plot_init(EQ['eqarea'],5,5)
    k=0
    while k<len(sitelist):
        site=sitelist[k]
        print site
        data=[]
        ThisSiteSpecs=pmag.get_dictitem(Specs,'er_site_name',site,'T')
        ThisSiteSpecs=pmag.get_dictitem(ThisSiteSpecs,'specimen_tilt_correction','-1','T') # get all the unoriented data
        for spec in ThisSiteSpecs:
                if spec['specimen_mad']!="" and spec['specimen_n']!="" and float(spec['specimen_mad'])<=M and float(spec['specimen_n'])>=N: 
# good spec, now get orientation....
                    redo,p=1,0
                    if len(SO_methods)<=1:
                        az_type=SO_methods[0]
                        orient=pmag.find_samp_rec(spec["er_sample_name"],Samps,az_type)
                        redo=0
                    while redo==1:
                        if p>=len(SO_priorities):
                            print "no orientation data for ",spec['er_sample_name']
                            orient["sample_azimuth"]=""
                            orient["sample_dip"]=""
                            redo=0
                        else:
                            az_type=SO_methods[SO_methods.index(SO_priorities[p])]
                            orient=pmag.find_samp_rec(spec["er_sample_name"],Samps,az_type)
                            if orient["sample_azimuth"]  !="":
                                redo=0
                        p+=1
                    if orient['sample_azimuth']!="":
                        rec={}
                        for key in spec.keys():rec[key]=spec[key]
                        rec['dec'],rec['inc']=pmag.dogeo(float(spec['specimen_dec']),float(spec['specimen_inc']),float(orient['sample_azimuth']),float(orient['sample_dip']))
                        rec["tilt_correction"]='1'
                        crd='g'
                        rec['sample_azimuth']=orient['sample_azimuth']
                        rec['sample_dip']=orient['sample_dip']
                        data.append(rec)
        if len(data)>2:
            print 'specimen, dec, inc, n_meas/MAD,| method codes '
            for i  in range(len(data)):
                print '%s: %7.1f %7.1f %s / %s | %s' % (data[i]['er_specimen_name'], data[i]['dec'], data[i]['inc'], data[i]['specimen_n'], data[i]['specimen_mad'], data[i]['magic_method_codes'])

            fpars=pmag.dolnp(data,'specimen_direction_type')
            print "\n Site lines planes  kappa   a95   dec   inc"
            print site, fpars["n_lines"], fpars["n_planes"], fpars["K"], fpars["alpha95"], fpars["dec"], fpars["inc"], fpars["R"]
            if out_file!="":
                if float(fpars["alpha95"])<=acutoff and float(fpars["K"])>=kcutoff:
                    out.write('%s %s %s\n'%(fpars["dec"],fpars['inc'],fpars['alpha95']))
            pmagplotlib.plotLNP(EQ['eqarea'],site,data,fpars,'specimen_direction_type')
            pmagplotlib.drawFIGS(EQ)
            if k!=0 and repeat!='y':
                ans=raw_input("s[a]ve plot, [q]uit, [e]dit specimens, [p]revious site, <return> to continue:\n ")
            elif k==0 and repeat!='y':
                ans=raw_input("s[a]ve plot, [q]uit, [e]dit specimens, <return> to continue:\n ")
            if ans=="p": k-=2
            if ans=="a":
                files={}
                files['eqarea']=site+'_'+crd+'_eqarea'+'.'+fmt
                pmagplotlib.saveP(EQ,files)
            if ans=="q": sys.exit()
            if ans=="e" and Samps==[]:
                print "can't edit samples without orientation file, sorry"
            elif ans=="e": 
#                k-=1
                testspec=raw_input("Enter name of specimen to check: ")
                for spec in data:
                    if spec['er_specimen_name']==testspec:
# first test wrong direction of drill arrows (flip drill direction in opposite direction and re-calculate d,i
                        d,i=pmag.dogeo(float(spec['specimen_dec']),float(spec['specimen_inc']),float(spec['sample_azimuth'])-180.,-float(spec['sample_dip']))
                        XY=pmag.dimap(d,i)
                        pmagplotlib.plotXY(EQ['eqarea'],[XY[0]],[XY[1]],sym='g^')
# first test wrong end of compass (take az-180.)
                        d,i=pmag.dogeo(float(spec['specimen_dec']),float(spec['specimen_inc']),float(spec['sample_azimuth'])-180.,float(spec['sample_dip']))
                        XY=pmag.dimap(d,i)
                        pmagplotlib.plotXY(EQ['eqarea'],[XY[0]],[XY[1]],sym='kv')
# did the sample spin in the hole?  
# now spin around specimen's z
                        X_up,Y_up,X_d,Y_d=[],[],[],[]
                        for incr in range(0,360,5):
                            d,i=pmag.dogeo(float(spec['specimen_dec'])+incr,float(spec['specimen_inc']),float(spec['sample_azimuth']),float(spec['sample_dip']))
                            XY=pmag.dimap(d,i)
                            if i>=0:
                                X_d.append(XY[0])
                                Y_d.append(XY[1])
                            else:
                                X_up.append(XY[0])
                                Y_up.append(XY[1])
                        pmagplotlib.plotXY(EQ['eqarea'],X_d,Y_d,sym='b.')
                        pmagplotlib.plotXY(EQ['eqarea'],X_up,Y_up,sym='c.')
                        pmagplotlib.drawFIGS(EQ)
                        break
                print "Triangle: wrong arrow for drill direction."
                print "Delta: wrong end of compass."
                print "Small circle:  wrong mark on sample. [cyan upper hemisphere]"
                deleteme=raw_input("Mark this sample as bad? y/[n]  ")
                if deleteme=='y':
                    reason=raw_input("Reason: [1] broke, [2] wrong drill direction, [3] wrong compass direction, [4] bad mark, [5] displaced block [6] other ")
                    if reason=='1':
                       description=' sample broke while drilling'
                    if reason=='2':
                       description=' wrong drill direction '
                    if reason=='3':
                       description=' wrong compass direction '
                    if reason=='4':
                       description=' bad mark in field'
                    if reason=='5':
                       description=' displaced block'
                    if reason=='6':
                       description=raw_input('Enter brief reason for deletion:   ')
                    for samp in Samps:
                        if samp['er_sample_name']==spec['er_sample_name']:
                            samp['sample_orientation_flag']='b'
                            samp['sample_description']=samp['sample_description']+' ## direction deleted because: '+description+'##' # mark description
                    pmag.magic_write(sampfile,Samps,'er_samples')
                repeat=raw_input("Mark another sample, this site? y/[n]  ")
                if repeat=='y': k-=1
        else:
            print 'skipping site - not enough data with specified coordinate system'
        k+=1 
    print "sample flags stored in ",sampfile
Пример #4
0
def main():
    """
        NAME
            nrm_specimens_magic.py
    
        DESCRIPTION
            converts NRM data in a magic_measurements type file to 
            geographic and tilt corrected data in a pmag_specimens type file
    
        SYNTAX
           nrm_specimens_magic.py [-h][command line options]
        
        OPTIONS:
            -h prints the help message and quits
            -f MFILE: specify input file
            -fsa SFILE: specify er_samples format file [with orientations]
            -F PFILE: specify output file
            -A  do not average replicate measurements
            -crd [g, t]: specify coordinate system ([g]eographic or [t]ilt adjusted)
                 NB: you must have the  SFILE in this directory

        DEFAULTS
            MFILE: magic_measurements.txt
            PFILE: nrm_specimens.txt
            SFILE: er_samples.txt
            coord: specimen
            average replicate measurements?: YES

        
    """
#
#   define some variables
#
    beg,end,pole,geo,tilt,askave,save=0,0,[],0,0,0,0
    samp_file=1
    args=sys.argv
    geo,tilt,orient=0,0,0
    doave=1
    user,comment,doave,coord="","",1,""
    meas_file="magic_measurements.txt"
    pmag_file="nrm_specimens.txt"
    samp_file="er_samples.txt"
    if "-h" in args:
        print main.__doc__
        sys.exit()
    if "-A" in args: doave=0
    if "-f" in args:
        ind=args.index("-f")
        meas_file=sys.argv[ind+1]
    if "-F" in args:
        ind=args.index("-F")
        pmag_file=sys.argv[ind+1]
    speclist=[]
    if "-fsa" in args:
        ind=args.index("-fsa")
        samp_file=sys.argv[ind+1]
    if "-crd" in args:
        ind=args.index("-crd")
        coord=sys.argv[ind+1]
        if coord=="g":
            geo,orient=1,1
        if coord=="t":
            tilt,orient,geo=1,1,1
#
# read in data
    if samp_file!="":
        samp_data,file_type=pmag.magic_read(samp_file)
        if file_type != 'er_samples':
           print file_type
           print "This is not a valid er_samples file " 
           sys.exit()
        else: print samp_file,' read in with ',len(samp_data),' records'
    else:
        print 'no orientations - will create file in specimen coordinates'
        geo,tilt,orient=0,0,0
    #
    #
    meas_data,file_type=pmag.magic_read(meas_file)
    if file_type != 'magic_measurements':
        print file_type
        print file_type,"This is not a valid magic_measurements file " 
        sys.exit()
    #
    if orient==1:
    # set orientation priorities
        SO_methods=[]
        orientation_priorities={'0':'SO-SUN','1':'SO-GPS-DIFF','2':'SO-SIGHT-BACK','3':'SO-CMD-NORTH','4':'SO-MAG'}
        for rec in samp_data:
           if "magic_method_codes" in rec:
               methlist=rec["magic_method_codes"]
               for meth in methlist.split(":"):
                   if "SO" in meth and "SO-POM" not in meth.strip():
                       if meth.strip() not in SO_methods: SO_methods.append(meth.strip())
    #
    # sort the sample names
    #
    sids=pmag.get_specs(meas_data)
    #
    #
    PmagSpecRecs=[]
    for s in sids:
        skip=0
        recnum=0
        PmagSpecRec={}
        PmagSpecRec["er_analyst_mail_names"]=user
        method_codes,inst_code=[],""
    # find the data from the meas_data file for this sample
    #
    #  collect info for the PmagSpecRec dictionary
    #
        meas_meth=[]
        for rec in  meas_data: # copy of vital stats to PmagSpecRec from first spec record
           if rec["er_specimen_name"]==s: 
               PmagSpecRec["er_specimen_name"]=s
               PmagSpecRec["er_sample_name"]=rec["er_sample_name"]
               PmagSpecRec["er_site_name"]=rec["er_site_name"]
               PmagSpecRec["er_location_name"]=rec["er_location_name"]
               PmagSpecRec["er_citation_names"]="This study"
               PmagSpecRec["magic_instrument_codes"]=""
               if "magic_experiment_name" not in rec.keys():
                   rec["magic_experiment_name"]=""
               if "magic_instrument_codes" not in rec.keys():
                   rec["magic_instrument_codes"]=""
               else:
                   PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"]
               if len(rec["magic_instrument_codes"]) > len(inst_code):
                   inst_code=rec["magic_instrument_codes"]
                   PmagSpecRec["magic_instrument_codes"]=inst_code  # copy over instruments
               break
    #
    # now check for correct method labels for all measurements
    #
        nrm_data=[]
        for meas_rec in meas_data:
            if meas_rec['er_specimen_name']==PmagSpecRec['er_specimen_name']:
                meths=meas_rec["magic_method_codes"].split(":")
                for meth in meths:
                    if meth.strip() not in meas_meth:meas_meth.append(meth)
                if "LT-NO" in meas_meth:nrm_data.append(meas_rec)
    #
        data,units=pmag.find_dmag_rec(s,nrm_data)
    #
        datablock=data
        #
        # find replicate measurements at NRM step and average them
        #
        Specs=[]
        if doave==1:
            step_meth,avedata=pmag.vspec(data)
            if len(avedata) != len(datablock):
                method_codes.append("DE-VM")
                SpecRec=avedata[0]
                print 'averaging data '
            else: SpecRec=data[0]
            Specs.append(SpecRec)
        else:
            for spec in data:Specs.append(spec)
        for SpecRec in Specs:
        #
        # do geo or stratigraphic correction now
        #
            if geo==1:
        #
        # find top priority orientation method
                redo,p=1,0
                if len(SO_methods)<=1: 
                    az_type=SO_methods[0] 
                    orient=pmag.find_samp_rec(PmagSpecRec["er_sample_name"],samp_data,az_type)
                    if orient["sample_azimuth"]  !="": method_codes.append(az_type)
                    redo=0
                while redo==1:
                    if p>=len(orientation_priorities):
                        print "no orientation data for ",s 
                        skip,redo=1,0
                        break
                    az_type=orientation_priorities[str(p)]
                    orient=pmag.find_samp_rec(PmagSpecRec["er_sample_name"],samp_data,az_type)
                    if orient["sample_azimuth"]  !="":
                        method_codes.append(az_type.strip())
                        redo=0
                    elif orient["sample_azimuth"]  =="":
                        p+=1
            #
            #  if stratigraphic selected,  get stratigraphic correction
            #
                if skip==0 and orient["sample_azimuth"]!="" and orient["sample_dip"]!="":
                    d_geo,i_geo=pmag.dogeo(SpecRec[1],SpecRec[2],orient["sample_azimuth"],orient["sample_dip"])
                    SpecRec[1]=d_geo
                    SpecRec[2]=i_geo
                    if tilt==1 and "sample_bed_dip" in orient.keys() and orient['sample_bed_dip']!="": 
                        d_tilt,i_tilt=pmag.dotilt(d_geo,i_geo,orient["sample_bed_dip_direction"],orient["sample_bed_dip"])
                        SpecRec[1]=d_tilt
                        SpecRec[2]=i_tilt
            if skip==0:
                PmagSpecRec["specimen_dec"]='%7.1f ' %(SpecRec[1])
                PmagSpecRec["specimen_inc"]='%7.1f ' %(SpecRec[2])
                if geo==1 and tilt==0:PmagSpecRec["specimen_tilt_correction"]='0'
                if geo==1 and tilt==1: PmagSpecRec["specimen_tilt_correction"]='100'
                if geo==0 and tilt==0: PmagSpecRec["specimen_tilt_correction"]='-1'
                PmagSpecRec["specimen_direction_type"]='l'
                PmagSpecRec["magic_method_codes"]="LT-NO"
                if len(method_codes) != 0:
                    methstring=""
                    for meth in method_codes:
                        methstring=methstring+ ":" +meth
                    PmagSpecRec["magic_method_codes"]=methstring[1:]
                PmagSpecRec["specimen_description"]="NRM data"
                PmagSpecRecs.append(PmagSpecRec)
    pmag.magic_write(pmag_file,PmagSpecRecs,'pmag_specimens')
    print "Data saved in ",pmag_file
Пример #5
0
def main():
    """
    NAME
        site_edit_magic.py

    DESCRIPTION
       makes equal area projections site by site
         from zeq_specimens_g.txt file with
         Fisher confidence ellipse using McFadden and McElhinny (1988)
         technique for combining lines and planes
         allows testing and reject specimens for bad orientations

    SYNTAX
        site_edit_magic.py [command line options]

    OPTIONS
       -h: prints help and quits
       -f: specify pmag_specimen format file, default is zeq_specimens_s.txt
       -fsa: specify er_samples.txt file
       -exc: use existing pmag_criteria.txt file
       -N: reset all sample flags to good
    
    OUPUT
       edited er_samples.txt file

    """
    dir_path = "."
    FIG = {}  # plot dictionary
    FIG["eqarea"] = 1  # eqarea is figure 1
    in_file = "zeq_specimens_s.txt"
    sampfile = "er_samples.txt"
    out_file = ""
    fmt, plot = "svg", 1
    Crits = ""
    M, N = 180.0, 1
    repeat = ""
    renew = 0
    if "-h" in sys.argv:
        print main.__doc__
        sys.exit()
    if "-WD" in sys.argv:
        ind = sys.argv.index("-WD")
        dir_path = sys.argv[ind + 1]
    if "-f" in sys.argv:
        ind = sys.argv.index("-f")
        in_file = sys.argv[ind + 1]
    if "-fsa" in sys.argv:
        ind = sys.argv.index("-fsa")
        sampfile = sys.argv[ind + 1]
    if "-exc" in sys.argv:
        Crits, file_type = pmag.magic_read(dir_path + "/pmag_criteria.txt")
        for crit in Crits:
            if crit["pmag_criteria_code"] == "DE-SPEC":
                M = float(crit["specimen_mad"])
                N = float(crit["specimen_n"])
    if "-fmt" in sys.argv:
        ind = sys.argv.index("-fmt")
        fmt = sys.argv[ind + 1]
    if "-N" in sys.argv:
        renew = 1
    #
    in_file = dir_path + "/" + in_file
    sampfile = dir_path + "/" + sampfile
    Specs, file_type = pmag.magic_read(in_file)
    if file_type != "pmag_specimens":
        print " bad pmag_specimen input file"
        sys.exit()
    Samps, file_type = pmag.magic_read(sampfile)
    if file_type != "er_samples":
        print " bad er_samples input file"
        sys.exit()
    SO_methods = []
    for rec in Samps:
        if "sample_orientation_flag" not in rec.keys():
            rec["sample_orientation_flag"] = "g"
        if "sample_description" not in rec.keys():
            rec["sample_description"] = ""
        if renew == 1:
            rec["sample_orientation_flag"] = "g"
            description = rec["sample_description"]
            if "#" in description:
                newdesc = ""
                c = 0
                while description[c] != "#" and c < len(description) - 1:  # look for first pound sign
                    newdesc = newdesc + description[c]
                    c += 1
                while description[c] == "#":
                    c += 1  # skip first set of pound signs
                while description[c] != "#":
                    c += 1  # find second set of pound signs
                while description[c] == "#" and c < len(description) - 1:
                    c += 1  # skip second set of pound signs
                while c < len(description) - 1:  # look for first pound sign
                    newdesc = newdesc + description[c]
                    c += 1
                rec["sample_description"] = newdesc  # edit out old comment about orientations
        if "magic_method_codes" in rec:
            methlist = rec["magic_method_codes"]
            for meth in methlist.split(":"):
                if "SO" in meth.strip() and "SO-POM" not in meth.strip():
                    if meth.strip() not in SO_methods:
                        SO_methods.append(meth.strip())
    pmag.magic_write(sampfile, Samps, "er_samples")
    SO_priorities = pmag.set_priorities(SO_methods, 0)
    sitelist = []
    for rec in Specs:
        if rec["er_site_name"] not in sitelist:
            sitelist.append(rec["er_site_name"])
    sitelist.sort()
    EQ = {}
    EQ["eqarea"] = 1
    pmagplotlib.plot_init(EQ["eqarea"], 5, 5)
    k = 0
    while k < len(sitelist):
        site = sitelist[k]
        print site
        data = []
        for spec in Specs:
            if spec["er_site_name"] == site:
                if (
                    spec["specimen_mad"] != ""
                    and spec["specimen_n"] != ""
                    and float(spec["specimen_mad"]) <= M
                    and float(spec["specimen_n"]) >= N
                ):
                    # good spec, now get orientation....
                    redo, p = 1, 0
                    if len(SO_methods) <= 1:
                        az_type = SO_methods[0]
                        orient = pmag.find_samp_rec(spec["er_sample_name"], Samps, az_type)
                        redo = 0
                    while redo == 1:
                        if p >= len(SO_priorities):
                            print "no orientation data for ", spec["er_sample_name"]
                            orient["sample_azimuth"] = ""
                            orient["sample_dip"] = ""
                            redo = 0
                        else:
                            az_type = SO_methods[SO_methods.index(SO_priorities[p])]
                            orient = pmag.find_samp_rec(spec["er_sample_name"], Samps, az_type)
                            if orient["sample_azimuth"] != "":
                                redo = 0
                        p += 1
                    if orient["sample_azimuth"] != "":
                        rec = {}
                        for key in spec.keys():
                            rec[key] = spec[key]
                        rec["dec"], rec["inc"] = pmag.dogeo(
                            float(spec["specimen_dec"]),
                            float(spec["specimen_inc"]),
                            float(orient["sample_azimuth"]),
                            float(orient["sample_dip"]),
                        )
                        rec["tilt_correction"] = "1"
                        rec["sample_azimuth"] = orient["sample_azimuth"]
                        rec["sample_dip"] = orient["sample_dip"]
                        data.append(rec)
        if len(data) > 2:
            print "specimen, dec, inc, n_meas/MAD,| method codes "
            for i in range(len(data)):
                print "%s: %7.1f %7.1f %s / %s | %s" % (
                    data[i]["er_specimen_name"],
                    data[i]["dec"],
                    data[i]["inc"],
                    data[i]["specimen_n"],
                    data[i]["specimen_mad"],
                    data[i]["magic_method_codes"],
                )

            fpars = pmag.dolnp(data, "specimen_direction_type")
            print "\n Site lines planes  kappa   a95   dec   inc"
            print site, fpars["n_lines"], fpars["n_planes"], fpars["K"], fpars["alpha95"], fpars["dec"], fpars[
                "inc"
            ], fpars["R"]
            if out_file != "":
                if float(fpars["alpha95"]) <= acutoff and float(fpars["K"]) >= kcutoff:
                    out.write("%s %s %s\n" % (fpars["dec"], fpars["inc"], fpars["alpha95"]))
            pmagplotlib.plotLNP(EQ["eqarea"], site, data, fpars, "specimen_direction_type")
            if k != 0 and repeat != "y":
                ans = raw_input("s[a]ve plot, [q]uit, [e]dit specimens, [p]revious site, <return> to continue:\n ")
            elif k == 0 and repeat != "y":
                ans = raw_input("s[a]ve plot, [q]uit, [e]dit specimens, <return> to continue:\n ")
            if ans == "p":
                k -= 2
            if ans == "a":
                files = {}
                files["eqarea"] = site + "_" + crd + "_" + "eqarea" + "." + fmt
                pmagplotlib.saveP(EQ, files)
            if ans == "q":
                sys.exit()
            if ans == "e" and Samps == []:
                print "can't edit samples without orientation file, sorry"
            elif ans == "e":
                #                k-=1
                testspec = raw_input("Enter name of specimen to check: ")
                for spec in data:
                    if spec["er_specimen_name"] == testspec:
                        # first test wrong direction of drill arrows (flip drill direction in opposite direction and re-calculate d,i
                        d, i = pmag.dogeo(
                            float(spec["specimen_dec"]),
                            float(spec["specimen_inc"]),
                            float(spec["sample_azimuth"]) - 180.0,
                            -float(spec["sample_dip"]),
                        )
                        XY = pmag.dimap(d, i)
                        pmagplotlib.plotXY(EQ["eqarea"], [XY[0]], [XY[1]], "g^", "", "", "")
                        # first test wrong end of compass (take az-180.)
                        d, i = pmag.dogeo(
                            float(spec["specimen_dec"]),
                            float(spec["specimen_inc"]),
                            float(spec["sample_azimuth"]) - 180.0,
                            float(spec["sample_dip"]),
                        )
                        XY = pmag.dimap(d, i)
                        pmagplotlib.plotXY(EQ["eqarea"], [XY[0]], [XY[1]], "kv", "", "", "")
                        # did the sample spin in the hole?
                        # now spin around specimen's z
                        X_up, Y_up, X_d, Y_d = [], [], [], []
                        for incr in range(0, 360, 5):
                            d, i = pmag.dogeo(
                                float(spec["specimen_dec"]) + incr,
                                float(spec["specimen_inc"]),
                                float(spec["sample_azimuth"]),
                                float(spec["sample_dip"]),
                            )
                            XY = pmag.dimap(d, i)
                            if i >= 0:
                                X_d.append(XY[0])
                                Y_d.append(XY[1])
                            else:
                                X_up.append(XY[0])
                                Y_up.append(XY[1])
                        pmagplotlib.plotXY(EQ["eqarea"], X_d, Y_d, "b.", "", "", "")
                        pmagplotlib.plotXY(EQ["eqarea"], X_up, Y_up, "c.", "", "", "")
                        pmagplotlib.drawFIGS(EQ)
                        break
                print "Triangle: wrong arrow for drill direction."
                print "Delta: wrong end of compass."
                print "Small circle:  wrong mark on sample. [cyan upper hemisphere]"
                deleteme = raw_input("Mark this sample as bad? y/[n]  ")
                if deleteme == "y":
                    reason = raw_input(
                        "Reason: [1] broke, [2] wrong drill direction, [3] wrong compass direction, [4] bad mark, [5] displaced block [6] other "
                    )
                    if reason == "1":
                        description = " sample broke while drilling"
                    if reason == "2":
                        description = " wrong drill direction "
                    if reason == "3":
                        description = " wrong compass direction "
                    if reason == "4":
                        description = " bad mark in field"
                    if reason == "5":
                        description = " displaced block"
                    if reason == "6":
                        description = raw_input("Enter brief reason for deletion:   ")
                    for samp in Samps:
                        if samp["er_sample_name"] == spec["er_sample_name"]:
                            samp["sample_orientation_flag"] = "b"
                            samp["sample_description"] = (
                                samp["sample_description"] + " ## direction deleted because: " + description + "##"
                            )  # mark description
                    pmag.magic_write(sampfile, Samps, "er_samples")
                repeat = raw_input("Mark another sample, this site? y/[n]  ")
                if repeat == "y":
                    k -= 1
        else:
            print "skipping site - not enough data with specified coordinate system"
        k += 1
    print "sample flags stored in ", sampfile
Пример #6
0
def main():
    """
    NAME
        aarm_magic.py

    DESCRIPTION
        Converts AARM  data to best-fit tensor (6 elements plus sigma)
         Original program ARMcrunch written to accomodate ARM anisotropy data
          collected from 6 axial directions (+X,+Y,+Z,-X,-Y,-Z) using the
          off-axis remanence terms to construct the tensor. A better way to
          do the anisotropy of ARMs is to use 9,12 or 15 measurements in
          the Hext rotational scheme.
    
    SYNTAX 
        aarm_magic.py [-h][command line options]

    OPTIONS
        -h prints help message and quits
        -usr USER:   identify user, default is ""
        -f FILE: specify input file, default is aarm_measurements.txt
        -crd [s,g,t] specify coordinate system, requires er_samples.txt file
        -fsa  FILE: specify er_samples.txt file, default is er_samples.txt
        -Fa FILE: specify anisotropy output file, default is arm_anisotropy.txt
        -Fr FILE: specify results output file, default is aarm_results.txt

    INPUT  
        Input for the present program is a series of baseline, ARM pairs.
      The baseline should be the AF demagnetized state (3 axis demag is
      preferable) for the following ARM acquisition. The order of the
      measurements is:
    
           positions 1,2,3, 6,7,8, 11,12,13 (for 9 positions)
           positions 1,2,3,4, 6,7,8,9, 11,12,13,14 (for 12 positions)
           positions 1-15 (for 15 positions)
    """
    # initialize some parameters
    args=sys.argv
    user=""
    meas_file="aarm_measurements.txt"
    samp_file="er_samples.txt"
    rmag_anis="arm_anisotropy.txt"
    rmag_res="aarm_results.txt"
    dir_path='.'
    #
    # get name of file from command line
    #
    if '-WD' in args:
        ind=args.index('-WD')
        dir_path=args[ind+1]
    if "-h" in args:
        print main.__doc__
        sys.exit()
    if "-usr" in args:
        ind=args.index("-usr")
        user=sys.argv[ind+1]
    if "-f" in args:
        ind=args.index("-f")
        meas_file=sys.argv[ind+1]
    coord='-1'
    if "-crd" in sys.argv:
        ind=sys.argv.index("-crd")
        coord=sys.argv[ind+1]
        if coord=='s':coord='-1'
        if coord=='g':coord='0'
        if coord=='t':coord='100'
        if "-fsa" in args:
            ind=args.index("-fsa")
            samp_file=sys.argv[ind+1]
    if "-Fa" in args:
        ind=args.index("-Fa")
        rmag_anis=args[ind+1]
    if "-Fr" in args:
        ind=args.index("-Fr")
        rmag_res=args[ind+1]
    meas_file=dir_path+'/'+meas_file
    samp_file=dir_path+'/'+samp_file
    rmag_anis=dir_path+'/'+rmag_anis
    rmag_res=dir_path+'/'+rmag_res
    # read in data
    meas_data,file_type=pmag.magic_read(meas_file)
    meas_data=pmag.get_dictitem(meas_data,'magic_method_codes','LP-AN-ARM','has')
    if file_type != 'magic_measurements':
        print file_type
        print file_type,"This is not a valid magic_measurements file " 
        sys.exit()
    if coord!='-1': # need to read in sample data
        samp_data,file_type=pmag.magic_read(samp_file)
        if file_type != 'er_samples':
            print file_type
            print file_type,"This is not a valid er_samples file " 
            print "Only specimen coordinates will be calculated"
            coord='-1'
    #
    # sort the specimen names
    #
    ssort=[]
    for rec in meas_data:
      spec=rec["er_specimen_name"]
      if spec not in ssort: ssort.append(spec)
    if len(ssort)>1:
        sids=sorted(ssort)
    else:
        sids=ssort
    #
    # work on each specimen
    #
    specimen=0
    RmagSpecRecs,RmagResRecs=[],[]
    while specimen < len(sids):
        s=sids[specimen]
        data=[]
        RmagSpecRec={}
        RmagResRec={}
        method_codes=[]
    #
    # find the data from the meas_data file for this sample
    #
        data=pmag.get_dictitem(meas_data,'er_specimen_name',s,'T')
    #
    # find out the number of measurements (9, 12 or 15)
    #
        npos=len(data)/2
        if npos==9:
        #
        # get dec, inc, int and convert to x,y,z
        #
            B,H,tmpH=pmag.designAARM(npos)  # B matrix made from design matrix for positions
            X=[]
            for rec in data:
                Dir=[]
                Dir.append(float(rec["measurement_dec"]))
                Dir.append(float(rec["measurement_inc"]))
                Dir.append(float(rec["measurement_magn_moment"]))
                X.append(pmag.dir2cart(Dir))
        #
        # subtract baseline and put in a work array
        #
            work=numpy.zeros((npos,3),'f')
            for i in range(npos):
                for j in range(3):
                    work[i][j]=X[2*i+1][j]-X[2*i][j]
        #
        # calculate tensor elements
        # first put ARM components in w vector
        #
            w=numpy.zeros((npos*3),'f')
            index=0
            for i in range(npos):
                for j in range(3):
                    w[index]=work[i][j] 
                    index+=1
            s=numpy.zeros((6),'f') # initialize the s matrix
            for i in range(6):
                for j in range(len(w)):
                    s[i]+=B[i][j]*w[j] 
            trace=s[0]+s[1]+s[2]   # normalize by the trace
            for i in range(6):
                s[i]=s[i]/trace
            a=pmag.s2a(s)
        #------------------------------------------------------------
        #  Calculating dels is different than in the Kappabridge
        #  routine. Use trace normalized tensor (a) and the applied
        #  unit field directions (tmpH) to generate model X,Y,Z
        #  components. Then compare these with the measured values.
        #------------------------------------------------------------
            S=0.
            comp=numpy.zeros((npos*3),'f')
            for i in range(npos):
                for j in range(3):
                    index=i*3+j
                    compare=a[j][0]*tmpH[i][0]+a[j][1]*tmpH[i][1]+a[j][2]*tmpH[i][2]
                    comp[index]=compare
            for i in range(npos*3):
                d=w[i]/trace - comp[i] # del values
                S+=d*d
            nf=float(npos*3-6) # number of degrees of freedom
            if S >0: 
                sigma=numpy.sqrt(S/nf)
            else: sigma=0
            RmagSpecRec["rmag_anisotropy_name"]=data[0]["er_specimen_name"]
            RmagSpecRec["er_location_name"]=data[0]["er_location_name"]
            RmagSpecRec["er_specimen_name"]=data[0]["er_specimen_name"]
            RmagSpecRec["er_sample_name"]=data[0]["er_sample_name"]
            RmagSpecRec["er_site_name"]=data[0]["er_site_name"]
            RmagSpecRec["magic_experiment_names"]=RmagSpecRec["rmag_anisotropy_name"]+":AARM"
            RmagSpecRec["er_citation_names"]="This study"
            RmagResRec["rmag_result_name"]=data[0]["er_specimen_name"]+":AARM"
            RmagResRec["er_location_names"]=data[0]["er_location_name"]
            RmagResRec["er_specimen_names"]=data[0]["er_specimen_name"]
            RmagResRec["er_sample_names"]=data[0]["er_sample_name"]
            RmagResRec["er_site_names"]=data[0]["er_site_name"]
            RmagResRec["magic_experiment_names"]=RmagSpecRec["rmag_anisotropy_name"]+":AARM"
            RmagResRec["er_citation_names"]="This study"
            if "magic_instrument_codes" in data[0].keys():
                RmagSpecRec["magic_instrument_codes"]=data[0]["magic_instrument_codes"]
            else:  
                RmagSpecRec["magic_instrument_codes"]=""
            RmagSpecRec["anisotropy_type"]="AARM"
            RmagSpecRec["anisotropy_description"]="Hext statistics adapted to AARM"
            if coord!='-1': # need to rotate s
    # set orientation priorities
                SO_methods=[]
                for rec in samp_data:
                   if "magic_method_codes" not in rec:
                       rec['magic_method_codes']='SO-NO'
                   if "magic_method_codes" in rec:
                       methlist=rec["magic_method_codes"]
                       for meth in methlist.split(":"):
                           if "SO" in meth and "SO-POM" not in meth.strip():
                               if meth.strip() not in SO_methods: SO_methods.append(meth.strip())
                SO_priorities=pmag.set_priorities(SO_methods,0)
# continue here
                redo,p=1,0
                if len(SO_methods)<=1:
                    az_type=SO_methods[0]
                    orient=pmag.find_samp_rec(RmagSpecRec["er_sample_name"],samp_data,az_type)
                    if orient["sample_azimuth"]  !="": method_codes.append(az_type)
                    redo=0
                while redo==1:
                    if p>=len(SO_priorities):
                        print "no orientation data for ",s
                        orient["sample_azimuth"]=""
                        orient["sample_dip"]=""
                        method_codes.append("SO-NO")
                        redo=0
                    else:
                        az_type=SO_methods[SO_methods.index(SO_priorities[p])]
                        orient=pmag.find_samp_rec(PmagSpecRec["er_sample_name"],samp_data,az_type)
                        if orient["sample_azimuth"]  !="":
                            method_codes.append(az_type)
                            redo=0
                    p+=1
                az,pl=orient['sample_azimuth'],orient['sample_dip']
                s=pmag.dosgeo(s,az,pl) # rotate to geographic coordinates
                if coord=='100': 
                    sampe_bed_dir,sample_bed_dip=orient['sample_bed_dip_direction'],orient['sample_bed_dip']
                    s=pmag.dostilt(s,bed_dir,bed_dip) # rotate to geographic coordinates
            hpars=pmag.dohext(nf,sigma,s)
        #
        # prepare for output
        #
            RmagSpecRec["anisotropy_s1"]='%8.6f'%(s[0])
            RmagSpecRec["anisotropy_s2"]='%8.6f'%(s[1])
            RmagSpecRec["anisotropy_s3"]='%8.6f'%(s[2])
            RmagSpecRec["anisotropy_s4"]='%8.6f'%(s[3])
            RmagSpecRec["anisotropy_s5"]='%8.6f'%(s[4])
            RmagSpecRec["anisotropy_s6"]='%8.6f'%(s[5])
            RmagSpecRec["anisotropy_mean"]='%8.3e'%(trace/3)
            RmagSpecRec["anisotropy_sigma"]='%8.6f'%(sigma)
            RmagSpecRec["anisotropy_unit"]="Am^2"
            RmagSpecRec["anisotropy_n"]='%i'%(npos)
            RmagSpecRec["anisotropy_tilt_correction"]=coord
            RmagSpecRec["anisotropy_F"]='%7.1f '%(hpars["F"]) # used by thellier_gui - must be taken out for uploading
            RmagSpecRec["anisotropy_F_crit"]=hpars["F_crit"] # used by thellier_gui - must be taken out for uploading
            RmagResRec["anisotropy_t1"]='%8.6f '%(hpars["t1"])
            RmagResRec["anisotropy_t2"]='%8.6f '%(hpars["t2"])
            RmagResRec["anisotropy_t3"]='%8.6f '%(hpars["t3"])
            RmagResRec["anisotropy_v1_dec"]='%7.1f '%(hpars["v1_dec"])
            RmagResRec["anisotropy_v2_dec"]='%7.1f '%(hpars["v2_dec"])
            RmagResRec["anisotropy_v3_dec"]='%7.1f '%(hpars["v3_dec"])
            RmagResRec["anisotropy_v1_inc"]='%7.1f '%(hpars["v1_inc"])
            RmagResRec["anisotropy_v2_inc"]='%7.1f '%(hpars["v2_inc"])
            RmagResRec["anisotropy_v3_inc"]='%7.1f '%(hpars["v3_inc"])
            RmagResRec["anisotropy_ftest"]='%7.1f '%(hpars["F"])
            RmagResRec["anisotropy_ftest12"]='%7.1f '%(hpars["F12"])
            RmagResRec["anisotropy_ftest23"]='%7.1f '%(hpars["F23"])
            RmagResRec["result_description"]='Critical F: '+hpars["F_crit"]+';Critical F12/F13: '+hpars["F12_crit"]
            if hpars["e12"]>hpars["e13"]:
                RmagResRec["anisotropy_v1_zeta_semi_angle"]='%7.1f '%(hpars['e12'])
                RmagResRec["anisotropy_v1_zeta_dec"]='%7.1f '%(hpars['v2_dec'])
                RmagResRec["anisotropy_v1_zeta_inc"]='%7.1f '%(hpars['v2_inc'])
                RmagResRec["anisotropy_v2_zeta_semi_angle"]='%7.1f '%(hpars['e12'])
                RmagResRec["anisotropy_v2_zeta_dec"]='%7.1f '%(hpars['v1_dec'])
                RmagResRec["anisotropy_v2_zeta_inc"]='%7.1f '%(hpars['v1_inc'])
                RmagResRec["anisotropy_v1_eta_semi_angle"]='%7.1f '%(hpars['e13'])
                RmagResRec["anisotropy_v1_eta_dec"]='%7.1f '%(hpars['v3_dec'])
                RmagResRec["anisotropy_v1_eta_inc"]='%7.1f '%(hpars['v3_inc'])
                RmagResRec["anisotropy_v3_eta_semi_angle"]='%7.1f '%(hpars['e13'])
                RmagResRec["anisotropy_v3_eta_dec"]='%7.1f '%(hpars['v1_dec'])
                RmagResRec["anisotropy_v3_eta_inc"]='%7.1f '%(hpars['v1_inc'])
            else:
                RmagResRec["anisotropy_v1_zeta_semi_angle"]='%7.1f '%(hpars['e13'])
                RmagResRec["anisotropy_v1_zeta_dec"]='%7.1f '%(hpars['v3_dec'])
                RmagResRec["anisotropy_v1_zeta_inc"]='%7.1f '%(hpars['v3_inc'])
                RmagResRec["anisotropy_v3_zeta_semi_angle"]='%7.1f '%(hpars['e13'])
                RmagResRec["anisotropy_v3_zeta_dec"]='%7.1f '%(hpars['v1_dec'])
                RmagResRec["anisotropy_v3_zeta_inc"]='%7.1f '%(hpars['v1_inc'])
                RmagResRec["anisotropy_v1_eta_semi_angle"]='%7.1f '%(hpars['e12'])
                RmagResRec["anisotropy_v1_eta_dec"]='%7.1f '%(hpars['v2_dec'])
                RmagResRec["anisotropy_v1_eta_inc"]='%7.1f '%(hpars['v2_inc'])
                RmagResRec["anisotropy_v2_eta_semi_angle"]='%7.1f '%(hpars['e12'])
                RmagResRec["anisotropy_v2_eta_dec"]='%7.1f '%(hpars['v1_dec'])
                RmagResRec["anisotropy_v2_eta_inc"]='%7.1f '%(hpars['v1_inc'])
            if hpars["e23"]>hpars['e12']:
                RmagResRec["anisotropy_v2_zeta_semi_angle"]='%7.1f '%(hpars['e23'])
                RmagResRec["anisotropy_v2_zeta_dec"]='%7.1f '%(hpars['v3_dec'])
                RmagResRec["anisotropy_v2_zeta_inc"]='%7.1f '%(hpars['v3_inc'])
                RmagResRec["anisotropy_v3_zeta_semi_angle"]='%7.1f '%(hpars['e23'])
                RmagResRec["anisotropy_v3_zeta_dec"]='%7.1f '%(hpars['v2_dec'])
                RmagResRec["anisotropy_v3_zeta_inc"]='%7.1f '%(hpars['v2_inc'])
                RmagResRec["anisotropy_v3_eta_semi_angle"]='%7.1f '%(hpars['e13'])
                RmagResRec["anisotropy_v3_eta_dec"]='%7.1f '%(hpars['v1_dec'])
                RmagResRec["anisotropy_v3_eta_inc"]='%7.1f '%(hpars['v1_inc'])
                RmagResRec["anisotropy_v2_eta_semi_angle"]='%7.1f '%(hpars['e12'])
                RmagResRec["anisotropy_v2_eta_dec"]='%7.1f '%(hpars['v1_dec'])
                RmagResRec["anisotropy_v2_eta_inc"]='%7.1f '%(hpars['v1_inc'])
            else:
                RmagResRec["anisotropy_v2_zeta_semi_angle"]='%7.1f '%(hpars['e12'])
                RmagResRec["anisotropy_v2_zeta_dec"]='%7.1f '%(hpars['v1_dec'])
                RmagResRec["anisotropy_v2_zeta_inc"]='%7.1f '%(hpars['v1_inc'])
                RmagResRec["anisotropy_v3_eta_semi_angle"]='%7.1f '%(hpars['e23'])
                RmagResRec["anisotropy_v3_eta_dec"]='%7.1f '%(hpars['v2_dec'])
                RmagResRec["anisotropy_v3_eta_inc"]='%7.1f '%(hpars['v2_inc'])
                RmagResRec["anisotropy_v3_zeta_semi_angle"]='%7.1f '%(hpars['e13'])
                RmagResRec["anisotropy_v3_zeta_dec"]='%7.1f '%(hpars['v1_dec'])
                RmagResRec["anisotropy_v3_zeta_inc"]='%7.1f '%(hpars['v1_inc'])
                RmagResRec["anisotropy_v2_eta_semi_angle"]='%7.1f '%(hpars['e23'])
                RmagResRec["anisotropy_v2_eta_dec"]='%7.1f '%(hpars['v3_dec'])
                RmagResRec["anisotropy_v2_eta_inc"]='%7.1f '%(hpars['v3_inc'])
            RmagResRec["tilt_correction"]='-1'
            RmagResRec["anisotropy_type"]='AARM'
            RmagResRec["magic_method_codes"]='LP-AN-ARM:AE-H'
            RmagSpecRec["magic_method_codes"]='LP-AN-ARM:AE-H'
            RmagResRec["magic_software_packages"]=pmag.get_version()
            RmagSpecRec["magic_software_packages"]=pmag.get_version()
            specimen+=1
            RmagSpecRecs.append(RmagSpecRec)
            RmagResRecs.append(RmagResRec)
        else:
            print 'skipping specimen ',s,' only 9 positions supported','; this has ',npos
            specimen+=1
    if rmag_anis=="":rmag_anis="rmag_anisotropy.txt"
    pmag.magic_write(rmag_anis,RmagSpecRecs,'rmag_anisotropy')
    print "specimen tensor elements stored in ",rmag_anis
    if rmag_res=="":rmag_res="rmag_results.txt"
    pmag.magic_write(rmag_res,RmagResRecs,'rmag_results')
    print "specimen statistics and eigenparameters stored in ",rmag_res