コード例 #1
0
ファイル: thellier_magic_redo.py プロジェクト: jholmes/PmagPy
def main():
    """
    NAME
        thellier_magic_redo.py

    DESCRIPTION
        Calculates paleointensity parameters for thellier-thellier type data using bounds
        stored in the "redo" file

    SYNTAX
        thellier_magic_redo [command line options]

    OPTIONS
        -h prints help message
        -usr USER:   identify user, default is ""
        -fcr CRIT, set criteria for grading
        -f IN: specify input file, default is magic_measurements.txt
        -fre REDO: specify redo file, default is "thellier_redo"
        -F OUT: specify output file, default is thellier_specimens.txt
        -leg:  attaches "Recalculated from original measurements; supercedes published results. " to comment field
        -CR PERC TYPE: apply a cooling rate correction.  
            PERC should be a percentage of original (say reduce to 90%)
            TYPE should be one of the following:
               EG (for educated guess); PS (based on pilots); TRM (based on comparison of two TRMs) 
        -Fcr  CRout: specify pmag_specimen format file for cooling rate corrected data
        -ANI: there are anisotropy data to correct thellier results
        -fan ANIFILE: specify rmag_anisotropy format file, default is rmag_anisotropy.txt 
        -Fac  ACout: specify pmag_specimen format file for anisotropy corrected data
                 default is AC_specimens.txt
        -NLT: there are non-linear trm data in the measurements file to correct thellier results
        -fnl NLTFILE: specify magic_measurments format file, default is magic_measurements.txt
        -Fnl NLTout: specify pmag_specimen format file for non-linear trm corrected data
                 default is NLT_specimens.txt
        -z use z component differenences for pTRM calculation
    """
    dir_path='.'
    critout=""
    version_num=pmag.get_version()
    field,first_save=-1,1
    spec,recnum,start,end=0,0,0,0
    frac=0
    NltRecs,PmagSpecs,AniSpecRecs,NltSpecRecs,CRSpecs=[],[],[],[],[]
    meas_file,pmag_file,mk_file="magic_measurements.txt","thellier_specimens.txt","thellier_redo"
    anis_file="rmag_anisotropy.txt"
    anisout,nltout="AC_specimens.txt","NLT_specimens.txt"
    crout="CR_specimens.txt"
    nlt_file=""
    
    comment,user="","unknown"
    anis,nltrm=0,0
    jackknife=0 # maybe in future can do jackknife
    args=sys.argv
    Zdiff=0
    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 "-leg" in args: comment="Recalculated from original measurements; supercedes published results. "
    if "-CR" in args:
        ind=args.index("-CR")
        frac=.01*float(sys.argv[ind+1])
        crtype=sys.argv[ind+2]
    if "-Fcr" in args:
        ind=args.index("-Fcr")
        crout=sys.argv[ind+1]
    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]
    if "-fre" in args:
        ind=args.index("-fre")
        mk_file=args[ind+1]
    #
    #
    if "-ANI" in args:
        anis=1
        ind=args.index("-ANI")
        if "-Fac" in args:
            ind=args.index("-Fac")
            anisout=args[ind+1]
        if "-fan" in args:
            ind=args.index("-fan")
            anis_file=args[ind+1]
    #
    if "-NLT" in args:
        nltrm=1
        if "-Fnl" in args:
            ind=args.index("-Fnl")
            nltout=args[ind+1]
        if "-fnl" in args:
            ind=args.index("-fnl")
            nlt_file=args[ind+1]
    if "-z" in args: Zdiff=1
    if '-fcr' in sys.argv: 
        ind=args.index("-fcr")
        critout=sys.argv[ind+1]
#
#  start reading in data:
#
    meas_file=dir_path+"/"+meas_file
    mk_file=dir_path+"/"+mk_file
    critout=dir_path+"/"+critout
    try:
        open(critout,'rU')
        accept_keys=['specimen_int_ptrm_n','specimen_md','specimen_fvds','specimen_b_beta','specimen_dang','specimen_drats','specimen_Z']
        crit_data,file_type=pmag.magic_read(critout)
        print "Acceptance criteria read in from ", critout
        accept={}
        accept['specimen_int_ptrm_n']=2.0
        for critrec in crit_data:
            if critrec["pmag_criteria_code"]=="IE-SPEC":
                for key in accept_keys:
                    if key not in critrec.keys():
                        accept[key]=-1
                    else:
                        accept[key]=float(critrec[key])
    except:
        critout="" # no acceptance criteria specified
    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()
    try:
        mk_f=open(mk_file,'rU')
    except:
        print "Bad redo file"
        sys.exit()
    mkspec=[]
    speclist=[]
    for line in mk_f.readlines():
        tmp=line.split()
        mkspec.append(tmp)
        speclist.append(tmp[0])
    if anis==1:
        anis_file=dir_path+"/"+anis_file 
        anis_data,file_type=pmag.magic_read(anis_file)
        if file_type != 'rmag_anisotropy':
            print file_type
            print file_type,"This is not a valid rmag_anisotropy file "
            sys.exit()
    if nlt_file=="":
        nlt_data=meas_data  # look for trm acquisition data in the meas_data file
    else:
        nlt_file=dir_path+"/"+nlt_file 
        nlt_data,file_type=pmag.magic_read(nlt_file)
#
# sort the specimen names and step through one by one
#
    sids=pmag.get_specs(meas_data)
# 
    print 'Processing ',len(speclist),' specimens - please wait '
    while spec < len(speclist):
        s=speclist[spec]
        recnum=0
        datablock=[]
        PmagSpecRec={}
        PmagSpecRec["er_analyst_mail_names"]=user
        PmagSpecRec["er_citation_names"]="This study"
        PmagSpecRec["magic_software_packages"]=version_num
        methcodes,inst_code=[],""
    #
    # find the data from the meas_data file for this specimen
    #
        for rec in meas_data:
            if rec["er_specimen_name"].lower()==s.lower(): 
                if "magic_instrument_codes" not in rec.keys():
                    rec["magic_instrument_codes"]="unknown"
                meths=rec["magic_method_codes"]
                for meth in meths:meth.strip()   # get rid of annoying spaces in method codes
                if "LP-PI-TRM" in meths: datablock.append(rec)
    #
    #  collect info for the PmagSpecRec dictionary
    #
        if len(datablock)>0:
            rec=datablock[0]
            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["measurement_step_unit"]="K"
            PmagSpecRec["specimen_correction"]='u'
            if "magic_instrument_codes" not in rec.keys():
                PmagSpecRec["magic_instrument_codes"]="unknown"
            else:
                PmagSpecRec["magic_instrument_codes"]=rec["magic_instrument_codes"]
            if "magic_experiment_name" not in rec.keys():
                rec["magic_experiment_name"]=""
            else:
                PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"]
            meths=rec["magic_experiment_name"].split(":")
            for meth in meths:
                if meth.strip() not in methcodes and "LP-" in meth:methcodes.append(meth.strip())
    #
    # sort out the data into first_Z, first_I, ptrm_check, ptrm_tail
    #
            araiblock,field=pmag.sortarai(datablock,s,Zdiff)
            first_Z=araiblock[0]
            first_I=araiblock[1]
            ptrm_check=araiblock[2]
            ptrm_tail=araiblock[3]
            if len(first_I)<3 or len(first_Z)<4:
                spec+=1
                print 'skipping specimen ', s 
            else:
    #
    # get start, end
    #
                for redospec in mkspec:
                    if redospec[0]==s:
    	                b,e=float(redospec[1]),float(redospec[2])
                        break
                if e > float(first_Z[-1][0]):e=float(first_Z[-1][0])
                for recnum in range(len(first_Z)):
            	    if first_Z[recnum][0]==b:start=recnum
            	    if first_Z[recnum][0]==e:end=recnum
                nsteps=end-start
                if nsteps>2:
                    zijdblock,units=pmag.find_dmag_rec(s,meas_data)
                    pars,errcode=pmag.PintPars(araiblock,zijdblock,start,end)
                    pars['measurement_step_unit']=units
                    pars["specimen_lab_field_dc"]=field
                    pars["specimen_int"]=-1*field*pars["specimen_b"]
                    PmagSpecRec["measurement_step_min"]='%8.3e' % (pars["measurement_step_min"])
                    PmagSpecRec["measurement_step_max"]='%8.3e' % (pars["measurement_step_max"])
                    PmagSpecRec["specimen_int_n"]='%i'%(pars["specimen_int_n"])
                    PmagSpecRec["specimen_lab_field_dc"]='%8.3e'%(pars["specimen_lab_field_dc"])
                    PmagSpecRec["specimen_int"]='%9.4e '%(pars["specimen_int"])
                    PmagSpecRec["specimen_b"]='%5.3f '%(pars["specimen_b"])
                    PmagSpecRec["specimen_q"]='%5.1f '%(pars["specimen_q"])
                    PmagSpecRec["specimen_f"]='%5.3f '%(pars["specimen_f"])
                    PmagSpecRec["specimen_fvds"]='%5.3f'%(pars["specimen_fvds"])
                    PmagSpecRec["specimen_b_beta"]='%5.3f'%(pars["specimen_b_beta"])
                    PmagSpecRec["specimen_int_mad"]='%7.1f'%(pars["specimen_int_mad"])
                    PmagSpecRec["specimen_Z"]='%7.1f'%(pars["specimen_Z"])
                    PmagSpecRec["specimen_gamma"]='%7.1f'%(pars["specimen_gamma"])
                    if pars["method_codes"]!="" and pars["method_codes"] not in methcodes: methcodes.append(pars["method_codes"])
                    PmagSpecRec["specimen_dec"]='%7.1f'%(pars["specimen_dec"])
                    PmagSpecRec["specimen_inc"]='%7.1f'%(pars["specimen_inc"])
                    PmagSpecRec["specimen_tilt_correction"]='-1'
                    PmagSpecRec["specimen_direction_type"]='l'
                    PmagSpecRec["direction_type"]='l' # this is redudant, but helpful - won't be imported
                    PmagSpecRec["specimen_dang"]='%7.1f '%(pars["specimen_dang"])
                    PmagSpecRec["specimen_drats"]='%7.1f '%(pars["specimen_drats"])
                    PmagSpecRec["specimen_int_ptrm_n"]='%i '%(pars["specimen_int_ptrm_n"])
                    PmagSpecRec["specimen_rsc"]='%6.4f '%(pars["specimen_rsc"])
                    PmagSpecRec["specimen_md"]='%i '%(int(pars["specimen_md"]))
                    if PmagSpecRec["specimen_md"]=='-1':PmagSpecRec["specimen_md"]=""
                    PmagSpecRec["specimen_b_sigma"]='%5.3f '%(pars["specimen_b_sigma"])
                    if "IE-TT" not in  methcodes:methcodes.append("IE-TT")
                    methods=""
                    for meth in methcodes:
                        methods=methods+meth+":"
                    PmagSpecRec["magic_method_codes"]=methods[:-1]
                    PmagSpecRec["magic_software_packages"]=version_num
                    PmagSpecRec["specimen_description"]=comment
                    if critout!="":
                        score,kill=pmag.grade(PmagSpecRec,accept)
                        Grade=""
                        if score==len(accept.keys()):Grade='A'
                        if score==len(accept.keys())-1:Grade='B'
                        if score==len(accept.keys())-2:Grade='C'
                        if score==len(accept.keys())-3:Grade='D'
                        if score<=len(accept.keys())-4:Grade='F'
                        PmagSpecRec["specimen_grade"]=Grade
                    else:
                        PmagSpecRec["specimen_grade"]=""
                    if nltrm==0 and anis==0 and frac!=0: # apply cooling rate correction
                        CrSpecRec={}
                        for key in PmagSpecRec.keys():CrSpecRec[key]=PmagSpecRec[key]
                        inten=frac*float(CrSpecRec['specimen_int'])
                        CrSpecRec["specimen_int"]='%9.4e '%(inten) # adjust specimen intensity by cooling rate correction
                        CrSpecRec['magic_method_codes'] = CrSpecRec['magic_method_codes']+':DA-CR-'+crtype
                        CrSpecRec["specimen_correction"]='c'
                        CRSpecs.append(CrSpecRec)
                    PmagSpecs.append(PmagSpecRec)
                    NltSpecRec=""
    #
    # check on non-linear TRM correction
    #
                    if nltrm==1:
    #
    # find the data from the nlt_data list for this specimen
    #
                        TRMs,Bs=[],[]
                        NltSpecRec=""
                        NltRecs=[]
                        for NltRec in nlt_data:
                            if NltRec['er_specimen_name']==PmagSpecRec["er_specimen_name"]:
                                meths=NltRec["magic_method_codes"].split(":")
                                for meth in meths:meth.strip()
                                if "LP-TRM" in meths: NltRecs.append(NltRec)
                        if len(NltRecs) > 2:
                            for NltRec in NltRecs:
                                Bs.append(float(NltRec['treatment_dc_field']))
                                TRMs.append(float(NltRec['measurement_magn_moment']))
                            NLTpars=nlt.NLtrm(Bs,TRMs,float(PmagSpecRec['specimen_int']),float(PmagSpecRec['specimen_lab_field_dc']),0) 
                            if NLTpars['banc']>0:
                                NltSpecRec={}
                                for key in PmagSpecRec.keys():
                                    NltSpecRec[key]=PmagSpecRec[key]
                                NltSpecRec['specimen_int']='%9.4e'%(NLTpars['banc'])  
                                NltSpecRec['magic_method_codes']=PmagSpecRec["magic_method_codes"]+":DA-NL"
                                NltSpecRec["specimen_correction"]='c'
                                NltSpecRec['specimen_grade']=PmagSpecRec['specimen_grade']
                                NltSpecRec["magic_software_packages"]=version_num
                                print NltSpecRec['er_specimen_name'],  ' Banc= ',float(NLTpars['banc'])*1e6
                                if anis==0 and frac!=0:
                                    CrSpecRec={}
                                    for key in NltSpecRec.keys():CrSpecRec[key]=NltSpecRec[key]
                                    inten=frac*float(CrSpecRec['specimen_int'])
                                    CrSpecRec["specimen_int"]='%9.4e '%(inten) # adjust specimen intensity by cooling rate correction
                                    CrSpecRec['magic_method_codes'] = CrSpecRec['magic_method_codes']+':DA-CR-'+crtype
                                    CRSpecs.append(CrSpecRec)
                                NltSpecRecs.append(NltSpecRec)
    #
    # check on anisotropy correction
                        if anis==1:
                            if NltSpecRec!="":  
                                Spc=NltSpecRec
                            else: # find uncorrected data
                                Spc=PmagSpecRec
                            for AniSpec in anis_data:
                                if AniSpec["er_specimen_name"]==PmagSpecRec["er_specimen_name"]:
                                    AniSpecRec=pmag.thellier_anis_corr(Spc,AniSpec)
                                    AniSpecRec['specimen_grade']=PmagSpecRec['specimen_grade']
                                    inst_codes=Spc["magic_instrument_codes"]
                                    if "magic_instrument_codes" in AniSpec.keys():
                                        if inst_codes=="unknown":
                                            inst_codes=AniSpec["magic_instrument_codes"]
                                        else:
                                            inst_codes=inst_codes+":"+AniSpec["magic_instrument_codes"]
                                    AniSpecRec["magic_instrument_codes"]=inst_codes
                                    AniSpecRec["specimen_correction"]='c'
                                    AniSpecRec["magic_software_packages"]=version_num
                                    if frac!=0:
                                        CrSpecRec={}
                                        for key in AniSpecRec.keys():CrSpecRec[key]=AniSpecRec[key]
                                        inten=frac*float(CrSpecRec['specimen_int'])
                                        CrSpecRec["specimen_int"]='%9.4e '%(inten) # adjust specimen intensity by cooling rate correction
                                        CrSpecRec['magic_method_codes'] = CrSpecRec['magic_method_codes']+':DA-CR-'+crtype
                                        CRSpecs.append(CrSpecRec)
                                    AniSpecRecs.append(AniSpecRec) 
                                    break
                    elif anis==1:
                        for AniSpec in anis_data:
                            if AniSpec["er_specimen_name"]==PmagSpecRec["er_specimen_name"]:
                                AniSpecRec=pmag.thellier_anis_corr(PmagSpecRec,AniSpec)
                                AniSpecRec['specimen_grade']=PmagSpecRec['specimen_grade']
                                inst_codes=PmagSpecRec["magic_instrument_codes"]
                                if "magic_instrument_codes" in AniSpec.keys():
                                    if inst_codes=="unknown":
                                        inst_codes=AniSpec["magic_instrument_codes"]
                                    else:
                                        inst_codes=inst_codes+":"+AniSpec["magic_instrument_codes"]
                                AniSpecRec["magic_instrument_codes"]=inst_codes
                                AniSpecRec["specimen_correction"]='c'
                                AniSpecRec["magic_software_packages"]=version_num
                                if frac!=0:
                                    CrSpecRec={}
                                    for key in AniSpecRec.keys():CrSpecRec[key]=AniSpecRec[key]
                                    inten=frac*float(CrSpecRec['specimen_int'])
                                    CrSpecRec["specimen_int"]='%9.4e '%(inten) # adjust specimen intensity by cooling rate correction
                                    CrSpecRec['magic_method_codes'] = CrSpecRec['magic_method_codes']+':DA-CR-'+crtype
                                    CRSpecs.append(CrSpecRec)
                                AniSpecRecs.append(AniSpecRec) 
                                break
                spec +=1
        else:
            print "skipping ",s
            spec+=1
    pmag_file=dir_path+'/'+pmag_file
    pmag.magic_write(pmag_file,PmagSpecs,'pmag_specimens')
    if anis==1:
        anisout=dir_path+'/'+anisout
        pmag.magic_write(anisout,AniSpecRecs,'pmag_specimens')
    if nltrm==1:
        nltout=dir_path+'/'+nltout
        pmag.magic_write(nltout,NltSpecRecs,'pmag_specimens')
    if frac!=0:
        crout=dir_path+'/'+crout
        pmag.magic_write(crout,CRSpecs,'pmag_specimens')
コード例 #2
0
ファイル: zeq_magic_redo.py プロジェクト: jholmes/PmagPy
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
コード例 #3
0
def main():
    """
    NAME
        thellier_magic_redo.py

    DESCRIPTION
        Calculates paleointensity parameters for thellier-thellier type data using bounds
        stored in the "redo" file

    SYNTAX
        thellier_magic_redo [command line options]

    OPTIONS
        -h prints help message
        -usr USER:   identify user, default is ""
        -fcr CRIT, set criteria for grading
        -f IN: specify input file, default is magic_measurements.txt
        -fre REDO: specify redo file, default is "thellier_redo"
        -F OUT: specify output file, default is thellier_specimens.txt
        -leg:  attaches "Recalculated from original measurements; supercedes published results. " to comment field
        -CR PERC TYPE: apply a blanket cooling rate correction if none supplied in the er_samples.txt file 
            PERC should be a percentage of original (say reduce to 90%)
            TYPE should be one of the following:
               EG (for educated guess); PS (based on pilots); TRM (based on comparison of two TRMs) 
        -ANI:  perform anisotropy correction
        -fsa SAMPFILE: er_samples.txt file with cooling rate correction information, default is NO CORRECTION
        -Fcr  CRout: specify pmag_specimen format file for cooling rate corrected data
        -fan ANIFILE: specify rmag_anisotropy format file, default is rmag_anisotropy.txt 
        -Fac  ACout: specify pmag_specimen format file for anisotropy corrected data
                 default is AC_specimens.txt
        -fnl NLTFILE: specify magic_measurments format file, default is magic_measurements.txt
        -Fnl NLTout: specify pmag_specimen format file for non-linear trm corrected data
                 default is NLT_specimens.txt
        -z use z component differenences for pTRM calculation

    INPUT
        a thellier_redo file is Specimen_name Tmin Tmax (where Tmin and Tmax are in Centigrade)
    """
    dir_path = "."
    critout = ""
    version_num = pmag.get_version()
    field, first_save = -1, 1
    spec, recnum, start, end = 0, 0, 0, 0
    crfrac = 0
    NltRecs, PmagSpecs, AniSpecRecs, NltSpecRecs, CRSpecs = [], [], [], [], []
    meas_file, pmag_file, mk_file = "magic_measurements.txt", "thellier_specimens.txt", "thellier_redo"
    anis_file = "rmag_anisotropy.txt"
    anisout, nltout = "AC_specimens.txt", "NLT_specimens.txt"
    crout = "CR_specimens.txt"
    nlt_file = ""
    samp_file = ""
    comment, user = "", "unknown"
    anis, nltrm = 0, 0
    jackknife = 0  # maybe in future can do jackknife
    args = sys.argv
    Zdiff = 0
    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 "-leg" in args:
        comment = "Recalculated from original measurements; supercedes published results. "
    cool = 0
    if "-CR" in args:
        cool = 1
        ind = args.index("-CR")
        crfrac = 0.01 * float(sys.argv[ind + 1])
        crtype = "DA-CR-" + sys.argv[ind + 2]
    if "-Fcr" in args:
        ind = args.index("-Fcr")
        crout = sys.argv[ind + 1]
    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]
    if "-fre" in args:
        ind = args.index("-fre")
        mk_file = args[ind + 1]
    if "-fsa" in args:
        ind = args.index("-fsa")
        samp_file = dir_path + "/" + args[ind + 1]
        Samps, file_type = pmag.magic_read(samp_file)
        SampCRs = pmag.get_dictitem(Samps, "cooling_rate_corr", "", "F")  # get samples cooling rate corrections
        cool = 1
        if file_type != "er_samples":
            print "not a valid er_samples.txt file"
            sys.exit()
    #
    #
    if "-ANI" in args:
        anis = 1
        ind = args.index("-ANI")
        if "-Fac" in args:
            ind = args.index("-Fac")
            anisout = args[ind + 1]
        if "-fan" in args:
            ind = args.index("-fan")
            anis_file = args[ind + 1]
    #
    if "-NLT" in args:
        if "-Fnl" in args:
            ind = args.index("-Fnl")
            nltout = args[ind + 1]
        if "-fnl" in args:
            ind = args.index("-fnl")
            nlt_file = args[ind + 1]
    if "-z" in args:
        Zdiff = 1
    if "-fcr" in sys.argv:
        ind = args.index("-fcr")
        critout = sys.argv[ind + 1]
    #
    #  start reading in data:
    #
    meas_file = dir_path + "/" + meas_file
    mk_file = dir_path + "/" + mk_file
    accept = pmag.default_criteria(1)[0]  # set criteria to none
    if critout != "":
        critout = dir_path + "/" + critout
        crit_data, file_type = pmag.magic_read(critout)
        if file_type != "pmag_criteria":
            print "bad pmag_criteria file, using no acceptance criteria"
        print "Acceptance criteria read in from ", critout
        for critrec in crit_data:
            if "sample_int_sigma_uT" in critrec.keys():  # accommodate Shaar's new criterion
                critrec["sample_int_sigma"] = "%10.3e" % (eval(critrec["sample_int_sigma_uT"]) * 1e-6)
            for key in critrec.keys():
                if key not in accept.keys() and critrec[key] != "":
                    accept[key] = critrec[key]
    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()
    try:
        mk_f = open(mk_file, "rU")
    except:
        print "Bad redo file"
        sys.exit()
    mkspec = []
    speclist = []
    for line in mk_f.readlines():
        tmp = line.split()
        mkspec.append(tmp)
        speclist.append(tmp[0])
    if anis == 1:
        anis_file = dir_path + "/" + anis_file
        anis_data, file_type = pmag.magic_read(anis_file)
        if file_type != "rmag_anisotropy":
            print file_type
            print file_type, "This is not a valid rmag_anisotropy file "
            sys.exit()
    if nlt_file == "":
        nlt_data = pmag.get_dictitem(
            meas_data, "magic_method_codes", "LP-TRM", "has"
        )  # look for trm acquisition data in the meas_data file
    else:
        nlt_file = dir_path + "/" + nlt_file
        nlt_data, file_type = pmag.magic_read(nlt_file)
    if len(nlt_data) > 0:
        nltrm = 1
    #
    # sort the specimen names and step through one by one
    #
    sids = pmag.get_specs(meas_data)
    #
    print "Processing ", len(speclist), " specimens - please wait "
    while spec < len(speclist):
        s = speclist[spec]
        recnum = 0
        datablock = []
        PmagSpecRec = {}
        PmagSpecRec["er_analyst_mail_names"] = user
        PmagSpecRec["er_citation_names"] = "This study"
        PmagSpecRec["magic_software_packages"] = version_num
        methcodes, inst_code = [], ""
        #
        # find the data from the meas_data file for this specimen
        #
        datablock = pmag.get_dictitem(meas_data, "er_specimen_name", s, "T")
        datablock = pmag.get_dictitem(
            datablock, "magic_method_codes", "LP-PI-TRM", "has"
        )  # pick out the thellier experiment data
        if len(datablock) > 0:
            for rec in datablock:
                if "magic_instrument_codes" not in rec.keys():
                    rec["magic_instrument_codes"] = "unknown"
            #
            #  collect info for the PmagSpecRec dictionary
            #
            rec = datablock[0]
            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["measurement_step_unit"] = "K"
            PmagSpecRec["specimen_correction"] = "u"
            if "er_expedition_name" in rec.keys():
                PmagSpecRec["er_expedition_name"] = rec["er_expedition_name"]
            if "magic_instrument_codes" not in rec.keys():
                PmagSpecRec["magic_instrument_codes"] = "unknown"
            else:
                PmagSpecRec["magic_instrument_codes"] = rec["magic_instrument_codes"]
            if "magic_experiment_name" not in rec.keys():
                rec["magic_experiment_name"] = ""
            else:
                PmagSpecRec["magic_experiment_names"] = rec["magic_experiment_name"]
            meths = rec["magic_experiment_name"].split(":")
            for meth in meths:
                if meth.strip() not in methcodes and "LP-" in meth:
                    methcodes.append(meth.strip())
            #
            # sort out the data into first_Z, first_I, ptrm_check, ptrm_tail
            #
            araiblock, field = pmag.sortarai(datablock, s, Zdiff)
            first_Z = araiblock[0]
            first_I = araiblock[1]
            ptrm_check = araiblock[2]
            ptrm_tail = araiblock[3]
            if len(first_I) < 3 or len(first_Z) < 4:
                spec += 1
                print "skipping specimen ", s
            else:
                #
                # get start, end
                #
                for redospec in mkspec:
                    if redospec[0] == s:
                        b, e = float(redospec[1]), float(redospec[2])
                        break
                if e > float(first_Z[-1][0]):
                    e = float(first_Z[-1][0])
                for recnum in range(len(first_Z)):
                    if first_Z[recnum][0] == b:
                        start = recnum
                    if first_Z[recnum][0] == e:
                        end = recnum
                nsteps = end - start
                if nsteps > 2:
                    zijdblock, units = pmag.find_dmag_rec(s, meas_data)
                    pars, errcode = pmag.PintPars(datablock, araiblock, zijdblock, start, end, accept)
                    if "specimen_scat" in pars.keys():
                        PmagSpecRec["specimen_scat"] = pars["specimen_scat"]
                    if "specimen_frac" in pars.keys():
                        PmagSpecRec["specimen_frac"] = "%5.3f" % (pars["specimen_frac"])
                    if "specimen_gmax" in pars.keys():
                        PmagSpecRec["specimen_gmax"] = "%5.3f" % (pars["specimen_gmax"])
                    pars["measurement_step_unit"] = units
                    pars["specimen_lab_field_dc"] = field
                    pars["specimen_int"] = -1 * field * pars["specimen_b"]
                    PmagSpecRec["measurement_step_min"] = "%8.3e" % (pars["measurement_step_min"])
                    PmagSpecRec["measurement_step_max"] = "%8.3e" % (pars["measurement_step_max"])
                    PmagSpecRec["specimen_int_n"] = "%i" % (pars["specimen_int_n"])
                    PmagSpecRec["specimen_lab_field_dc"] = "%8.3e" % (pars["specimen_lab_field_dc"])
                    PmagSpecRec["specimen_int"] = "%9.4e " % (pars["specimen_int"])
                    PmagSpecRec["specimen_b"] = "%5.3f " % (pars["specimen_b"])
                    PmagSpecRec["specimen_q"] = "%5.1f " % (pars["specimen_q"])
                    PmagSpecRec["specimen_f"] = "%5.3f " % (pars["specimen_f"])
                    PmagSpecRec["specimen_fvds"] = "%5.3f" % (pars["specimen_fvds"])
                    PmagSpecRec["specimen_b_beta"] = "%5.3f" % (pars["specimen_b_beta"])
                    PmagSpecRec["specimen_int_mad"] = "%7.1f" % (pars["specimen_int_mad"])
                    PmagSpecRec["specimen_Z"] = "%7.1f" % (pars["specimen_Z"])
                    PmagSpecRec["specimen_gamma"] = "%7.1f" % (pars["specimen_gamma"])
                    if pars["method_codes"] != "" and pars["method_codes"] not in methcodes:
                        methcodes.append(pars["method_codes"])
                    PmagSpecRec["specimen_dec"] = "%7.1f" % (pars["specimen_dec"])
                    PmagSpecRec["specimen_inc"] = "%7.1f" % (pars["specimen_inc"])
                    PmagSpecRec["specimen_tilt_correction"] = "-1"
                    PmagSpecRec["specimen_direction_type"] = "l"
                    PmagSpecRec["direction_type"] = "l"  # this is redudant, but helpful - won't be imported
                    PmagSpecRec["specimen_dang"] = "%7.1f " % (pars["specimen_dang"])
                    PmagSpecRec["specimen_drats"] = "%7.1f " % (pars["specimen_drats"])
                    PmagSpecRec["specimen_drat"] = "%7.1f " % (pars["specimen_drat"])
                    PmagSpecRec["specimen_int_ptrm_n"] = "%i " % (pars["specimen_int_ptrm_n"])
                    PmagSpecRec["specimen_rsc"] = "%6.4f " % (pars["specimen_rsc"])
                    PmagSpecRec["specimen_md"] = "%i " % (int(pars["specimen_md"]))
                    if PmagSpecRec["specimen_md"] == "-1":
                        PmagSpecRec["specimen_md"] = ""
                    PmagSpecRec["specimen_b_sigma"] = "%5.3f " % (pars["specimen_b_sigma"])
                    if "IE-TT" not in methcodes:
                        methcodes.append("IE-TT")
                    methods = ""
                    for meth in methcodes:
                        methods = methods + meth + ":"
                    PmagSpecRec["magic_method_codes"] = methods.strip(":")
                    PmagSpecRec["magic_software_packages"] = version_num
                    PmagSpecRec["specimen_description"] = comment
                    if critout != "":
                        kill = pmag.grade(PmagSpecRec, accept, "specimen_int")
                        if len(kill) > 0:
                            Grade = "F"  # fails
                        else:
                            Grade = "A"  # passes
                        PmagSpecRec["specimen_grade"] = Grade
                    else:
                        PmagSpecRec["specimen_grade"] = ""  # not graded
                    if nltrm == 0 and anis == 0 and cool != 0:  # apply cooling rate correction
                        SCR = pmag.get_dictitem(
                            SampCRs, "er_sample_name", PmagSpecRec["er_sample_name"], "T"
                        )  # get this samples, cooling rate correction
                        CrSpecRec = pmag.cooling_rate(PmagSpecRec, SCR, crfrac, crtype)
                        if CrSpecRec["er_specimen_name"] != "none":
                            CrSpecs.append(CrSpecRec)
                    PmagSpecs.append(PmagSpecRec)
                    NltSpecRec = ""
                    #
                    # check on non-linear TRM correction
                    #
                    if nltrm == 1:
                        #
                        # find the data from the nlt_data list for this specimen
                        #
                        TRMs, Bs = [], []
                        NltSpecRec = ""
                        NltRecs = pmag.get_dictitem(
                            nlt_data, "er_specimen_name", PmagSpecRec["er_specimen_name"], "has"
                        )  # fish out all the NLT data for this specimen
                        if len(NltRecs) > 2:
                            for NltRec in NltRecs:
                                Bs.append(float(NltRec["treatment_dc_field"]))
                                TRMs.append(float(NltRec["measurement_magn_moment"]))
                            NLTpars = nlt.NLtrm(
                                Bs,
                                TRMs,
                                float(PmagSpecRec["specimen_int"]),
                                float(PmagSpecRec["specimen_lab_field_dc"]),
                                0,
                            )
                            if NLTpars["banc"] > 0:
                                NltSpecRec = {}
                                for key in PmagSpecRec.keys():
                                    NltSpecRec[key] = PmagSpecRec[key]
                                NltSpecRec["specimen_int"] = "%9.4e" % (NLTpars["banc"])
                                NltSpecRec["magic_method_codes"] = PmagSpecRec["magic_method_codes"] + ":DA-NL"
                                NltSpecRec["specimen_correction"] = "c"
                                NltSpecRec["specimen_grade"] = PmagSpecRec["specimen_grade"]
                                NltSpecRec["magic_software_packages"] = version_num
                                print NltSpecRec["er_specimen_name"], " Banc= ", float(NLTpars["banc"]) * 1e6
                                if anis == 0 and cool != 0:
                                    SCR = pmag.get_dictitem(
                                        SampCRs, "er_sample_name", NltSpecRec["er_sample_name"], "T"
                                    )  # get this samples, cooling rate correction
                                    CrSpecRec = pmag.cooling_rate(NltSpecRec, SCR, crfrac, crtype)
                                    if CrSpecRec["er_specimen_name"] != "none":
                                        CrSpecs.append(CrSpecRec)
                                NltSpecRecs.append(NltSpecRec)
                        #
                        # check on anisotropy correction
                        if anis == 1:
                            if NltSpecRec != "":
                                Spc = NltSpecRec
                            else:  # find uncorrected data
                                Spc = PmagSpecRec
                            AniSpecs = pmag.get_dictitem(
                                anis_data, "er_specimen_name", PmagSpecRec["er_specimen_name"], "T"
                            )
                            if len(AniSpecs) > 0:
                                AniSpec = AniSpecs[0]
                                AniSpecRec = pmag.doaniscorr(Spc, AniSpec)
                                AniSpecRec["specimen_grade"] = PmagSpecRec["specimen_grade"]
                                AniSpecRec["magic_instrument_codes"] = PmagSpecRec["magic_instrument_codes"]
                                AniSpecRec["specimen_correction"] = "c"
                                AniSpecRec["magic_software_packages"] = version_num
                                if cool != 0:
                                    SCR = pmag.get_dictitem(
                                        SampCRs, "er_sample_name", AniSpecRec["er_sample_name"], "T"
                                    )  # get this samples, cooling rate correction
                                    CrSpecRec = pmag.cooling_rate(AniSpecRec, SCR, crfrac, crtype)
                                    if CrSpecRec["er_specimen_name"] != "none":
                                        CrSpecs.append(CrSpecRec)
                                AniSpecRecs.append(AniSpecRec)
                    elif anis == 1:
                        AniSpecs = pmag.get_dictitem(
                            anis_data, "er_specimen_name", PmagSpecRec["er_specimen_name"], "T"
                        )
                        if len(AniSpecs) > 0:
                            AniSpec = AniSpecs[0]
                            AniSpecRec = pmag.doaniscorr(PmagSpecRec, AniSpec)
                            AniSpecRec["specimen_grade"] = PmagSpecRec["specimen_grade"]
                            AniSpecRec["magic_instrument_codes"] = PmagSpecRec["magic_instrument_codes"]
                            AniSpecRec["specimen_correction"] = "c"
                            AniSpecRec["magic_software_packages"] = version_num
                            if crfrac != 0:
                                CrSpecRec = {}
                                for key in AniSpecRec.keys():
                                    CrSpecRec[key] = AniSpecRec[key]
                                inten = frac * float(CrSpecRec["specimen_int"])
                                CrSpecRec["specimen_int"] = "%9.4e " % (
                                    inten
                                )  # adjust specimen intensity by cooling rate correction
                                CrSpecRec["magic_method_codes"] = CrSpecRec["magic_method_codes"] + ":DA-CR-" + crtype
                                CRSpecs.append(CrSpecRec)
                            AniSpecRecs.append(AniSpecRec)
                spec += 1
        else:
            print "skipping ", s
            spec += 1
    pmag_file = dir_path + "/" + pmag_file
    pmag.magic_write(pmag_file, PmagSpecs, "pmag_specimens")
    print "uncorrected thellier data saved in: ", pmag_file
    if anis == 1 and len(AniSpecRecs) > 0:
        anisout = dir_path + "/" + anisout
        pmag.magic_write(anisout, AniSpecRecs, "pmag_specimens")
        print "anisotropy corrected data saved in: ", anisout
    if nltrm == 1 and len(NltSpecRecs) > 0:
        nltout = dir_path + "/" + nltout
        pmag.magic_write(nltout, NltSpecRecs, "pmag_specimens")
        print "non-linear TRM corrected data saved in: ", nltout
    if crfrac != 0:
        crout = dir_path + "/" + crout
        pmag.magic_write(crout, CRSpecs, "pmag_specimens")
        print "cooling rate corrected data saved in: ", crout
コード例 #4
0
ファイル: thellier_magic.py プロジェクト: ihilburn/PmagPy
def main():
    """
    NAME
        thellier_magic.py
    
    DESCRIPTION
        plots Thellier-Thellier, allowing interactive setting of bounds
        and customizing of selection criteria.  Saves and reads interpretations
        from a pmag_specimen formatted table, default: thellier_specimens.txt

    SYNTAX 
        thellier_magic.py [command line options]

    OPTIONS
        -h prints help message and quits
        -f MEAS, set magic_measurements input file
        -fsp PRIOR, set pmag_specimen prior interpretations file
        -fan ANIS, set rmag_anisotropy file for doing the anisotropy corrections
        -fcr CRIT, set criteria file for grading.  
        -fmt [svg,png,jpg], format for images - default is svg
        -sav,  saves plots with out review (default format)
        -spc SPEC, plots single specimen SPEC, saves plot with specified format
            with optional -b bounds adn quits
        -b BEG END: sets  bounds for calculation
           BEG: starting step for slope calculation
           END: ending step for slope calculation
        -z use only z component difference for pTRM calculation
        
    DEFAULTS
        MEAS: magic_measurements.txt
        REDO: thellier_redo
        CRIT: NONE
        PRIOR: NONE
  
    OUTPUT 
        figures:
            ALL:  numbers refer to temperature steps in command line window
            1) Arai plot:  closed circles are zero-field first/infield
                           open circles are infield first/zero-field
                           triangles are pTRM checks
                           squares are pTRM tail checks
                           VDS is vector difference sum
                           diamonds are bounds for interpretation
            2) Zijderveld plot:  closed (open) symbols are X-Y (X-Z) planes
                                 X rotated to NRM direction
            3) (De/Re)Magnetization diagram:
                           circles are NRM remaining
                           squares are pTRM gained
            4) equal area projections:
 			   green triangles are pTRM gained direction
                           red (purple) circles are lower(upper) hemisphere of ZI step directions 
                           blue (cyan) squares are lower(upper) hemisphere IZ step directions 
            5) Optional:  TRM acquisition
            6) Optional: TDS normalization
        command line window:
            list is: temperature step numbers, temperatures (C), Dec, Inc, Int (units of magic_measuements)
                     list of possible commands: type letter followed by return to select option
                     saving of plots creates .svg format files with specimen_name, plot type as name
    """ 
#
#   initializations
#
    meas_file,critout,inspec="magic_measurements.txt","","thellier_specimens.txt"
    first=1
    inlt=0
    version_num=pmag.get_version()
    TDinit,Tinit,field,first_save=0,0,-1,1
    user,comment,AniSpec,locname="",'',"",""
    ans,specimen,recnum,start,end=0,0,0,0,0
    plots,pmag_out,samp_file,style=0,"","","svg"
    verbose=pmagplotlib.verbose 
    fmt='.'+style
#
# default acceptance criteria
#
    accept=pmag.default_criteria(0)[0] # set the default criteria
#
# parse command line options
#
    Zdiff,anis=0,0
    spc,BEG,END="","",""
    if '-h' in sys.argv:
        print main.__doc__
        sys.exit()
    if '-f' in sys.argv:
        ind=sys.argv.index('-f')
        meas_file=sys.argv[ind+1]
    if '-fsp' in sys.argv:
        ind=sys.argv.index('-fsp')
        inspec=sys.argv[ind+1]
    if '-fan' in sys.argv:
        ind=sys.argv.index('-fan')
        anisfile=sys.argv[ind+1]
        anis=1
        anis_data,file_type=pmag.magic_read(anisfile)
        if verbose: print "Anisotropy data read in from ", anisfile
    if '-fmt' in sys.argv:
        ind=sys.argv.index('-fmt')
        fmt='.'+sys.argv[ind+1]
    if '-sav' in sys.argv: 
        plots=1
        verbose=0
    if '-z' in sys.argv: Zdiff=1
    if '-spc' in sys.argv:
        ind=sys.argv.index('-spc')
        spc=sys.argv[ind+1]
        if '-b' in sys.argv:
            ind=sys.argv.index('-b')
            BEG=int(sys.argv[ind+1])
            END=int(sys.argv[ind+2])
    if '-fcr' in sys.argv:
        ind=sys.argv.index('-fcr')
        critout=sys.argv[ind+1]
        crit_data,file_type=pmag.magic_read(critout)
        if file_type!='pmag_criteria':
            if verbose: print 'bad pmag_criteria file, using no acceptance criteria'
            accept=pmag.default_criteria(1)[0]
        else:
            if verbose: print "Acceptance criteria read in from ", critout
            accept={'pmag_criteria_code':'ACCEPTANCE','er_citation_names':'This study'}
            for critrec in crit_data:
                if 'sample_int_sigma_uT' in critrec.keys(): # accommodate Shaar's new criterion
                    critrec['sample_int_sigma']='%10.3e'%(eval(critrec['sample_int_sigma_uT'])*1e-6)
                for key in critrec.keys():
                    if key not in accept.keys() and critrec[key]!='':
                        accept[key]=critrec[key]
    try:
        open(inspec,'rU')
        PriorRecs,file_type=pmag.magic_read(inspec)
        if file_type != 'pmag_specimens':
            print file_type
            print file_type,inspec," is not a valid pmag_specimens file " 
            sys.exit()
        for rec in PriorRecs:
            if 'magic_software_packages' not in rec.keys():rec['magic_software_packages']=""
    except IOError:
        PriorRecs=[]
        if verbose:print "starting new specimen interpretation file: ",inspec
    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()
    backup=0
    # define figure numbers for arai, zijderveld and 
    #   de-,re-magization diagrams
    AZD={}
    AZD['deremag'], AZD['zijd'],AZD['arai'],AZD['eqarea']=1,2,3,4
    pmagplotlib.plot_init(AZD['arai'],5,5)
    pmagplotlib.plot_init(AZD['zijd'],5,5)
    pmagplotlib.plot_init(AZD['deremag'],5,5)
    pmagplotlib.plot_init(AZD['eqarea'],5,5)
    #
    #
    #
    # get list of unique specimen names
    #
    CurrRec=[]
    sids=pmag.get_specs(meas_data)
    # get plots for specimen s - default is just to step through arai diagrams
    #
    if spc!="": specimen =sids.index(spc)
    while specimen < len(sids):
        methcodes=[]
       
        if verbose:
            print sids[specimen],specimen+1, 'of ', len(sids)
        MeasRecs=[]
        s=sids[specimen]
        datablock,trmblock,tdsrecs=[],[],[]
        PmagSpecRec={}
        if first==0:
           for key in keys:PmagSpecRec[key]="" # make sure all new records have same set of keys
        PmagSpecRec["er_analyst_mail_names"]=user
        PmagSpecRec["specimen_correction"]='u'
    #
    # find the data from the meas_data file for this specimen
    #
        for rec in meas_data:
            if rec["er_specimen_name"]==s:
                MeasRecs.append(rec)
                if "magic_method_codes" not in rec.keys():
                    rec["magic_method_codes"]=""
                methods=rec["magic_method_codes"].split(":")
                meths=[]
                for meth in methods:
                    meths.append(meth.strip()) # take off annoying spaces
                methods=""
                for meth in meths:
                    if meth.strip() not in methcodes and "LP-" in meth:methcodes.append(meth.strip())
                    methods=methods+meth+":"
                methods=methods[:-1]
                rec["magic_method_codes"]=methods 
                if "LP-PI-TRM" in meths: datablock.append(rec)
                if "LP-TRM" in meths: trmblock.append(rec)
                if "LP-TRM-TD" in meths: tdsrecs.append(rec)
        if len(trmblock)>2 and inspec!="":
            if Tinit==0:
                Tinit=1
                AZD['TRM']=5
                pmagplotlib.plot_init(AZD['TRM'],5,5)
        elif Tinit==1: # clear the TRM figure if not needed
            pmagplotlib.clearFIG(AZD['TRM'])
        if len(tdsrecs)>2:
            if TDinit==0:
                TDinit=1
                AZD['TDS']=6
                pmagplotlib.plot_init(AZD['TDS'],5,5)
        elif TDinit==1: # clear the TDS figure if not needed
            pmagplotlib.clearFIG(AZD['TDS'])
        if len(datablock) <4:
           if backup==0:
               specimen+=1
               if verbose:
                   print 'skipping specimen - moving forward ', s
           else:
               specimen-=1
               if verbose:
                   print 'skipping specimen - moving backward ', s
    #
    #  collect info for the PmagSpecRec dictionary
    #
        else:
           rec=datablock[0]
           PmagSpecRec["er_citation_names"]="This study"
           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"]
           locname=rec['er_location_name'].replace('/','-')
           if "er_expedition_name" in rec.keys():PmagSpecRec["er_expedition_name"]=rec["er_expedition_name"]
           if "magic_instrument_codes" not in rec.keys():rec["magic_instrument_codes"]=""
           PmagSpecRec["magic_instrument_codes"]=rec["magic_instrument_codes"]
           PmagSpecRec["measurement_step_unit"]="K"
           if "magic_experiment_name" not in rec.keys():
               rec["magic_experiment_name"]=""
           else:
               PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"]
    
           meths=rec["magic_method_codes"].split()
       # sort data into types
           araiblock,field=pmag.sortarai(datablock,s,Zdiff)
           first_Z=araiblock[0]
           GammaChecks=araiblock[5]
           if len(first_Z)<3:
               if backup==0:
                   specimen+=1
                   if verbose:
                       print 'skipping specimen - moving forward ', s
               else:
                   specimen-=1
                   if verbose:
                       print 'skipping specimen - moving backward ', s
           else:
               backup=0
               zijdblock,units=pmag.find_dmag_rec(s,meas_data)
               recnum=0
               if verbose:
                   print "index step Dec   Inc  Int       Gamma"
                   for plotrec in zijdblock:
                       if GammaChecks!="":
                           gamma=""
                           for g in GammaChecks:
                               if g[0]==plotrec[0]-273:
                                   gamma=g[1]
                                   break
                       if gamma!="":
                           print '%i     %i %7.1f %7.1f %8.3e %7.1f' % (recnum,plotrec[0]-273,plotrec[1],plotrec[2],plotrec[3],gamma)
                       else:
                           print '%i     %i %7.1f %7.1f %8.3e ' % (recnum,plotrec[0]-273,plotrec[1],plotrec[2],plotrec[3])
                       recnum += 1
               pmagplotlib.plotAZ(AZD,araiblock,zijdblock,s,units[0])
               if verbose:pmagplotlib.drawFIGS(AZD)
               if len(tdsrecs)>2: # a TDS experiment
                   tdsblock=[] # make a list for the TDS  data
                   Mkeys=['measurement_magnitude','measurement_magn_moment','measurement_magn_volume','measuruement_magn_mass']
                   mkey,k="",0
                   while mkey=="" and k<len(Mkeys)-1: # find which type of intensity
                       key= Mkeys[k]
                       if key in tdsrecs[0].keys() and tdsrecs[0][key]!="": mkey=key
                       k+=1
                   if mkey=="":break # get outta here
                   Tnorm=""
                   for tdrec in tdsrecs:
                       meths=tdrec['magic_method_codes'].split(":")
                       for meth in meths: meth.replace(" ","") # strip off potential nasty spaces
                       if  'LT-T-I' in meths and Tnorm=="": # found first total TRM 
                           Tnorm=float(tdrec[mkey]) # normalize by total TRM 
                           tdsblock.append([273,zijdblock[0][3]/Tnorm,1.]) # put in the zero step
                       if  'LT-T-Z' in meths and Tnorm!="": # found a LP-TRM-TD demag step, now need complementary LT-T-Z from zijdblock
                           step=float(tdrec['treatment_temp'])
                           Tint=""
                           if mkey!="":
                               Tint=float(tdrec[mkey])
                           if Tint!="":
                               for zrec in zijdblock:
                                   if zrec[0]==step:  # found matching
                                       tdsblock.append([step,zrec[3]/Tnorm,Tint/Tnorm])
                                       break
                   if len(tdsblock)>2: 
                       pmagplotlib.plotTDS(AZD['TDS'],tdsblock,s+':LP-PI-TDS:')
                       if verbose:pmagplotlib(drawFIGS(AZD)) 
                   else: 
                       print "Something wrong here"
               if anis==1:   # look up anisotropy data for this specimen
                   AniSpec=""
                   for aspec in anis_data:
                       if aspec["er_specimen_name"]==PmagSpecRec["er_specimen_name"]:
                           AniSpec=aspec
                           if verbose: print 'Found anisotropy record...'
                           break
               if inspec !="":
                   if verbose: print 'Looking up saved interpretation....'
                   found = 0
                   for k in range(len(PriorRecs)):
                       try:
                         if PriorRecs[k]["er_specimen_name"]==s:
                           found =1
                           CurrRec.append(PriorRecs[k])
                           for j in range(len(zijdblock)):
                               if float(zijdblock[j][0])==float(PriorRecs[k]["measurement_step_min"]):start=j
                               if float(zijdblock[j][0])==float(PriorRecs[k]["measurement_step_max"]):end=j
                           pars,errcode=pmag.PintPars(datablock,araiblock,zijdblock,start,end,accept)
                           pars['measurement_step_unit']="K"
                           pars['experiment_type']='LP-PI-TRM'
                           del PriorRecs[k]  # put in CurrRec, take out of PriorRecs
                           if errcode!=1:
                               pars["specimen_lab_field_dc"]=field
                               pars["specimen_int"]=-1*field*pars["specimen_b"]
                               pars["er_specimen_name"]=s
                               if verbose:
                                   print 'Saved interpretation: '
                               pars,kill=pmag.scoreit(pars,PmagSpecRec,accept,'',verbose)
                               pmagplotlib.plotB(AZD,araiblock,zijdblock,pars)
                               if verbose:pmagplotlib.drawFIGS(AZD)
                               if len(trmblock)>2:
                                   blab=field
                                   best=pars["specimen_int"]
                                   Bs,TRMs=[],[]
                                   for trec in trmblock:
                                       Bs.append(float(trec['treatment_dc_field']))
                                       TRMs.append(float(trec['measurement_magn_moment']))
                                   NLpars=nlt.NLtrm(Bs,TRMs,best,blab,0) # calculate best fit parameters through TRM acquisition data, and get new banc
                                   Mp,Bp=[],[]
                                   for k in  range(int(max(Bs)*1e6)):
                                       Bp.append(float(k)*1e-6)
                                       npred=nlt.TRM(Bp[-1],NLpars['xopt'][0],NLpars['xopt'][1]) # predicted NRM for this field
                                       Mp.append(npred)
                                   pmagplotlib.plotTRM(AZD['TRM'],Bs,TRMs,Bp,Mp,NLpars,trec['magic_experiment_name'])
                                   PmagSpecRec['specimen_int']=NLpars['banc'] 
                                   if verbose:
                                       print 'Banc= ',float(NLpars['banc'])*1e6
                                       pmagplotlib.drawFIGS(AZD)
                               mpars=pmag.domean(araiblock[1],start,end,'DE-BFL')
                               if verbose:
                                       print 'pTRM direction= ','%7.1f'%(mpars['specimen_dec']),' %7.1f'%(mpars['specimen_inc']),' MAD:','%7.1f'%(mpars['specimen_mad'])
                               if AniSpec!="":
                                   CpTRM=pmag.Dir_anis_corr([mpars['specimen_dec'],mpars['specimen_inc']],AniSpec)
                                   AniSpecRec=pmag.doaniscorr(PmagSpecRec,AniSpec)
                                   if verbose:
                                       print 'Anisotropy corrected TRM direction= ','%7.1f'%(CpTRM[0]),' %7.1f'%(CpTRM[1])
                                       print 'Anisotropy corrected intensity= ',float(AniSpecRec['specimen_int'])*1e6
                           else:
                               print 'error on specimen ',s
                       except:
                         pass
                   if verbose and found==0: print  '    None found :(  ' 
               if spc!="":
                   if BEG!="": 
                       pars,errcode=pmag.PintPars(datablock,araiblock,zijdblock,BEG,END,accept)
                       pars['measurement_step_unit']="K"
                       pars["specimen_lab_field_dc"]=field
                       pars["specimen_int"]=-1*field*pars["specimen_b"]
                       pars["er_specimen_name"]=s
                       pars['specimen_grade']='' # ungraded
                       pmagplotlib.plotB(AZD,araiblock,zijdblock,pars)
                       if verbose:pmagplotlib.drawFIGS(AZD)
                       if len(trmblock)>2:
                           if inlt==0:
                               inlt=1
                           blab=field
                           best=pars["specimen_int"]
                           Bs,TRMs=[],[]
                           for trec in trmblock:
                               Bs.append(float(trec['treatment_dc_field']))
                               TRMs.append(float(trec['measurement_magn_moment']))
                           NLpars=nlt.NLtrm(Bs,TRMs,best,blab,0) # calculate best fit parameters through TRM acquisition data, and get new banc
    #
                           Mp,Bp=[],[]
                           for k in  range(int(max(Bs)*1e6)):
                               Bp.append(float(k)*1e-6)
                               npred=nlt.TRM(Bp[-1],NLpars['xopt'][0],NLpars['xopt'][1]) # predicted NRM for this field
                   files={}
                   for key in AZD.keys():
                       files[key]=s+'_'+key+fmt 
                   pmagplotlib.saveP(AZD,files)
                   sys.exit()
               if verbose:
                   ans='b'
                   while ans != "":
                       print """
               s[a]ve plot, set [b]ounds for calculation, [d]elete current interpretation, [p]revious, [s]ample, [q]uit:
               """
                       ans=raw_input('Return for next specimen \n')
                       if ans=="": 
                           specimen +=1
                       if ans=="d": 
                           save_redo(PriorRecs,inspec)
                           CurrRec=[]
                           pmagplotlib.plotAZ(AZD,araiblock,zijdblock,s,units[0])
                           if verbose:pmagplotlib.drawFIGS(AZD)
                       if ans=='a':
                           files={}
                           for key in AZD.keys():
                               files[key]="LO:_"+locname+'_SI:_'+PmagSpecRec['er_site_name']+'_SA:_'+PmagSpecRec['er_sample_name']+'_SP:_'+s+'_CO:_s_TY:_'+key+fmt
                           pmagplotlib.saveP(AZD,files)
                           ans=""
                       if ans=='q':
                           print "Good bye"
                           sys.exit()
                       if ans=='p':
                           specimen =specimen -1
                           backup = 1
                           ans=""
                       if ans=='s':
                           keepon=1
                           spec=raw_input('Enter desired specimen name (or first part there of): ')
                           while keepon==1:
                               try:
                                   specimen =sids.index(spec)
                                   keepon=0
                               except:
                                   tmplist=[]
                                   for qq in range(len(sids)):
                                       if spec in sids[qq]:tmplist.append(sids[qq])
                                   print specimen," not found, but this was: "
                                   print tmplist
                                   spec=raw_input('Select one or try again\n ')
                           ans=""
                       if  ans=='b':
                           if end==0 or end >=len(zijdblock):end=len(zijdblock)-1
                           GoOn=0
                           while GoOn==0:
                               answer=raw_input('Enter index of first point for calculation: ['+str(start)+']  ')
                               try:
                                   start=int(answer)
                                   answer=raw_input('Enter index  of last point for calculation: ['+str(end)+']  ')
                                   end=int(answer)
                                   if start >=0 and start <len(zijdblock)-2 and end >0 and end <len(zijdblock) or start>=end:
                                       GoOn=1
                                   else:
                                       print "Bad endpoints - try again! "
                                       start,end=0,len(zijdblock)
                               except ValueError:
                                   print "Bad endpoints - try again! "
                                   start,end=0,len(zijdblock)
                           s=sids[specimen] 
                           pars,errcode=pmag.PintPars(datablock,araiblock,zijdblock,start,end,accept)
                           pars['measurement_step_unit']="K"
                           pars["specimen_lab_field_dc"]=field
                           pars["specimen_int"]=-1*field*pars["specimen_b"]
                           pars["er_specimen_name"]=s
                           pars,kill=pmag.scoreit(pars,PmagSpecRec,accept,'',0)
                           PmagSpecRec['specimen_scat']=pars['specimen_scat']
                           PmagSpecRec['specimen_frac']='%5.3f'%(pars['specimen_frac'])
                           PmagSpecRec['specimen_gmax']='%5.3f'%(pars['specimen_gmax'])
                           PmagSpecRec["measurement_step_min"]='%8.3e' % (pars["measurement_step_min"])
                           PmagSpecRec["measurement_step_max"]='%8.3e' % (pars["measurement_step_max"])
                           PmagSpecRec["measurement_step_unit"]="K"
                           PmagSpecRec["specimen_int_n"]='%i'%(pars["specimen_int_n"])
                           PmagSpecRec["specimen_lab_field_dc"]='%8.3e'%(pars["specimen_lab_field_dc"])
                           PmagSpecRec["specimen_int"]='%9.4e '%(pars["specimen_int"])
                           PmagSpecRec["specimen_b"]='%5.3f '%(pars["specimen_b"])
                           PmagSpecRec["specimen_q"]='%5.1f '%(pars["specimen_q"])
                           PmagSpecRec["specimen_f"]='%5.3f '%(pars["specimen_f"])
                           PmagSpecRec["specimen_fvds"]='%5.3f'%(pars["specimen_fvds"])
                           PmagSpecRec["specimen_b_beta"]='%5.3f'%(pars["specimen_b_beta"])
                           PmagSpecRec["specimen_int_mad"]='%7.1f'%(pars["specimen_int_mad"])
                           PmagSpecRec["specimen_Z"]='%7.1f'%(pars["specimen_Z"])
                           PmagSpecRec["specimen_gamma"]='%7.1f'%(pars["specimen_gamma"])
                           PmagSpecRec["specimen_grade"]=pars["specimen_grade"]
                           if pars["method_codes"]!="":
                               tmpcodes=pars["method_codes"].split(":")
                               for t in tmpcodes:
                                   if t.strip() not in methcodes:methcodes.append(t.strip())
                           PmagSpecRec["specimen_dec"]='%7.1f'%(pars["specimen_dec"])
                           PmagSpecRec["specimen_inc"]='%7.1f'%(pars["specimen_inc"])
                           PmagSpecRec["specimen_tilt_correction"]='-1'
                           PmagSpecRec["specimen_direction_type"]='l'
                           PmagSpecRec["direction_type"]='l' # this is redundant, but helpful - won't be imported
                           PmagSpecRec["specimen_int_dang"]='%7.1f '%(pars["specimen_int_dang"])
                           PmagSpecRec["specimen_drats"]='%7.1f '%(pars["specimen_drats"])
                           PmagSpecRec["specimen_drat"]='%7.1f '%(pars["specimen_drat"])
                           PmagSpecRec["specimen_int_ptrm_n"]='%i '%(pars["specimen_int_ptrm_n"])
                           PmagSpecRec["specimen_rsc"]='%6.4f '%(pars["specimen_rsc"])
                           PmagSpecRec["specimen_md"]='%i '%(int(pars["specimen_md"]))
                           if PmagSpecRec["specimen_md"]=='-1':PmagSpecRec["specimen_md"]=""
                           PmagSpecRec["specimen_b_sigma"]='%5.3f '%(pars["specimen_b_sigma"])
                           if "IE-TT" not in  methcodes:methcodes.append("IE-TT")
                           methods=""
                           for meth in methcodes:
                               methods=methods+meth+":"
                           PmagSpecRec["magic_method_codes"]=methods[:-1]
                           PmagSpecRec["specimen_description"]=comment
                           PmagSpecRec["magic_software_packages"]=version_num
                           pmagplotlib.plotAZ(AZD,araiblock,zijdblock,s,units[0])
                           pmagplotlib.plotB(AZD,araiblock,zijdblock,pars)
                           if verbose:pmagplotlib.drawFIGS(AZD)
                           if len(trmblock)>2:
                               blab=field
                               best=pars["specimen_int"]
                               Bs,TRMs=[],[]
                               for trec in trmblock:
                                   Bs.append(float(trec['treatment_dc_field']))
                                   TRMs.append(float(trec['measurement_magn_moment']))
                               NLpars=nlt.NLtrm(Bs,TRMs,best,blab,0) # calculate best fit parameters through TRM acquisition data, and get new banc
                               Mp,Bp=[],[]
                               for k in  range(int(max(Bs)*1e6)):
                                   Bp.append(float(k)*1e-6)
                                   npred=nlt.TRM(Bp[-1],NLpars['xopt'][0],NLpars['xopt'][1]) # predicted NRM for this field
                                   Mp.append(npred)
                               pmagplotlib.plotTRM(AZD['TRM'],Bs,TRMs,Bp,Mp,NLpars,trec['magic_experiment_name'])
                               if verbose:
                                   print 'Non-linear TRM corrected intensity= ',float(NLpars['banc'])*1e6
                           if verbose:pmagplotlib.drawFIGS(AZD)
                           pars["specimen_lab_field_dc"]=field
                           pars["specimen_int"]=-1*field*pars["specimen_b"]
                           pars,kill=pmag.scoreit(pars,PmagSpecRec,accept,'',verbose)
                           saveit=raw_input("Save this interpretation? [y]/n \n")
                           if saveit!='n':
                               PriorRecs.append(PmagSpecRec) # put back an interpretation
                               specimen+=1
                               save_redo(PriorRecs,inspec)
                           ans=""
               elif plots==1:
                   specimen+=1
                   if fmt != ".pmag":
                       files={}
                       for key in AZD.keys():
                           files[key]="LO:_"+locname+'_SI:_'+PmagSpecRec['er_site_name']+'_SA:_'+PmagSpecRec['er_sample_name']+'_SP:_'+s+'_CO:_s_TY:_'+key+'_'+fmt
                       if pmagplotlib.isServer:
                           black     = '#000000'
                           purple    = '#800080'
                           titles={}
                           titles['deremag']='DeReMag Plot'
                           titles['zijd']='Zijderveld Plot'
                           titles['arai']='Arai Plot'
                           AZD = pmagplotlib.addBorders(AZD,titles,black,purple)
                       pmagplotlib.saveP(AZD,files)
    #                   pmagplotlib.combineFigs(s,files,3)
                   else:  # save in pmag format 
                       script="grep "+s+" output.mag | thellier -mfsi"
                       script=script+' %8.4e'%(field)
                       min='%i'%((pars["measurement_step_min"]-273))
                       Max='%i'%((pars["measurement_step_max"]-273))
                       script=script+" "+min+" "+Max
                       script=script+" |plotxy;cat mypost >>thellier.ps\n"
                       pltf.write(script)
                       pmag.domagicmag(outf,MeasRecs)
        if len(CurrRec)>0:
            for rec in CurrRec:
                PriorRecs.append(rec)
        CurrRec=[]
    if plots!=1 and verbose:
        ans=raw_input(" Save last plot? 1/[0] ")
        if ans=="1":
            if fmt != ".pmag":
                files={}
                for key in AZD.keys():
                    files[key]=s+'_'+key+fmt
                pmagplotlib.saveP(AZD,files)
        else:
            print "\n Good bye\n"
            sys.exit()
        if len(CurrRec)>0:PriorRecs.append(CurrRec) # put back an interpretation
        if len(PriorRecs)>0:
            save_redo(PriorRecs,inspec)
            print 'Updated interpretations saved in ',inspec
    if verbose:
        print "Good bye"
コード例 #5
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
コード例 #6
0
ファイル: zeq_magic.py プロジェクト: headmetal/PmagPy
def main():
    """
    NAME
        zeq_magic.py

    DESCRIPTION
        reads in magic_measurements formatted file, makes plots of remanence decay
        during demagnetization experiments.  Reads in prior interpretations saved in 
        a pmag_specimens formatted file and  allows re-interpretations of best-fit lines
        and planes and saves (revised or new) interpretations in a pmag_specimens file.  
        interpretations are saved in the coordinate system used. Also allows judicious editting of
        measurements to eliminate "bad" measurements.  These are marked as such in the magic_measurements
        input file.  they are NOT deleted, just ignored. 

    SYNTAX
        zeq_magic.py [command line options]

    OPTIONS
        -h prints help message and quits
        -f  MEASFILE: sets magic_measurements format input file, default: magic_measurements.txt
        -fsp SPECFILE: sets pmag_specimens format file with prior interpreations, default: zeq_specimens.txt
        -Fp PLTFILE: sets filename for saved plot, default is name_type.fmt (where type is zijd, eqarea or decay curve)
        -crd [s,g,t]: sets coordinate system,  g=geographic, t=tilt adjusted, default: specimen coordinate system
        -fsa SAMPFILE: sets er_samples format file with orientation information, default: er_samples.txt
        -spc SPEC  plots single specimen SPEC, saves plot with specified format 
              with optional -dir settings and quits
        -dir [L,P,F][beg][end]: sets calculation type for principal component analysis, default is none
             beg: starting step for PCA calculation
             end: ending step for PCA calculation
             [L,P,F]: calculation type for line, plane or fisher mean
             must be used with -spc option
        -fmt FMT: set format of saved plot [png,svg,jpg]
        -A:  suppresses averaging of  replicate measurements, default is to average
        -sav: saves all plots without review
    SCREEN OUTPUT:
        Specimen, N, a95, StepMin, StepMax, Dec, Inc, calculation type

    """
    # initialize some variables
    doave,e,b=1,0,0 # average replicates, initial end and beginning step
    plots,coord=0,'s'
    noorient=0
    version_num=pmag.get_version()
    verbose=pmagplotlib.verbose
    beg_pca,end_pca,direction_type="","",'l'
    calculation_type,fmt="","svg"
    user,spec_keys,locname="",[],''
    plot_file=""
    sfile=""
    plot_file=""
    PriorRecs=[] # empty list for prior interpretations
    backup=0
    specimen="" # can skip everything and just plot one specimen with bounds e,b
    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]
    else:
        dir_path='.'
    inspec=dir_path+'/'+'zeq_specimens.txt'
    meas_file,geo,tilt,ask,samp_file=dir_path+'/magic_measurements.txt',0,0,0,dir_path+'/er_samples.txt'
    if '-f' in sys.argv:
        ind=sys.argv.index('-f')
        meas_file=dir_path+'/'+sys.argv[ind+1]
    if '-fsp' in sys.argv:
        ind=sys.argv.index('-fsp')
        inspec=dir_path+'/'+sys.argv[ind+1]
    if '-fsa' in sys.argv:
        ind=sys.argv.index('-fsa')
        samp_file=dir_path+'/'+sys.argv[ind+1]
        sfile='ok'
    if '-crd' in sys.argv:
        ind=sys.argv.index('-crd')
        coord=sys.argv[ind+1]
        if coord=='g' or coord=='t':
            samp_data,file_type=pmag.magic_read(samp_file)
            if file_type=='er_samples':sfile='ok'
            geo=1
            if coord=='t':tilt=1
    if '-spc' in sys.argv:
        ind=sys.argv.index('-spc')
        specimen=sys.argv[ind+1]
        if '-dir' in sys.argv:
            ind=sys.argv.index('-dir')
            direction_type=sys.argv[ind+1]
            beg_pca=int(sys.argv[ind+2])
            end_pca=int(sys.argv[ind+3])
            if direction_type=='L':calculation_type='DE-BFL'
            if direction_type=='P':calculation_type='DE-BFP'
            if direction_type=='F':calculation_type='DE-FM'
        if '-Fp' in sys.argv: 
            ind=sys.argv.index('-Fp')
            plot_file=dir_path+'/'+sys.argv[ind+1]
    if '-A' in sys.argv: doave=0
    if '-sav' in sys.argv: 
        plots=1
        verbose=0
    if '-fmt' in sys.argv:
        ind=sys.argv.index('-fmt')
        fmt=sys.argv[ind+1]
    #
    first_save=1
    meas_data,file_type=pmag.magic_read(meas_file)
    changeM,changeS=0,0 # check if data or interpretations have changed
    if file_type != 'magic_measurements':
        print file_type
        print file_type,"This is not a valid magic_measurements file " 
        sys.exit()
    for rec in  meas_data:
        if  "magic_method_codes" not in rec.keys(): rec["magic_method_codes"]=""
        methods=""
        tmp=rec["magic_method_codes"].replace(" ","").split(":")
        for meth in tmp:
            methods=methods+meth+":"
        rec["magic_method_codes"]=methods[:-1]  # get rid of annoying spaces in Anthony's export files 
        if "magic_instrument_codes" not in rec.keys() :rec["magic_instrument_codes"]=""
    PriorSpecs=[]
    PriorRecs,file_type=pmag.magic_read(inspec)
    if len(PriorRecs)==0: 
        if verbose:print "starting new file ",inspec
    for Rec in PriorRecs:
        if 'magic_software_packages' not in Rec.keys():Rec['magic_software_packages']=""
        if Rec['er_specimen_name'] not in PriorSpecs:
            if 'specimen_comp_name' not in Rec.keys():Rec['specimen_comp_name']="A"
            PriorSpecs.append(Rec['er_specimen_name'])
        else:
            if 'specimen_comp_name' not in Rec.keys():Rec['specimen_comp_name']="A"
        if "magic_method_codes" in Rec.keys():
            methods=[]
            tmp=Rec["magic_method_codes"].replace(" ","").split(":")
            for meth in tmp:
                methods.append(meth)
            if 'DE-FM' in methods:
                Rec['calculation_type']='DE-FM' # this won't be imported but helps
            if 'DE-BFL' in methods:
                Rec['calculation_type']='DE-BFL'
            if 'DE-BFL-A' in methods:
                Rec['calculation_type']='DE-BFL-A'
            if 'DE-BFL-O' in methods:
                Rec['calculation_type']='DE-BFL-O'
            if 'DE-BFP' in methods:
                Rec['calculation_type']='DE-BFP'
        else:
            Rec['calculation_type']='DE-BFL' # default is to assume a best-fit line
    #
    # get list of unique specimen names
    #
    sids=pmag.get_specs(meas_data)
    #
    #  set up plots, angle sets X axis to horizontal,  direction_type 'l' is best-fit line
    # direction_type='p' is great circle
    #     
    #
    # draw plots for sample s - default is just to step through zijderveld diagrams
    #
    #
    # define figure numbers for equal area, zijderveld,  
    #  and intensity vs. demagnetiztion step respectively
    ZED={}
    ZED['eqarea'],ZED['zijd'],  ZED['demag']=1,2,3 
    pmagplotlib.plot_init(ZED['eqarea'],5,5)
    pmagplotlib.plot_init(ZED['zijd'],6,5)
    pmagplotlib.plot_init(ZED['demag'],5,5)
    save_pca=0
    if specimen=="":
        k = 0
    else:
        k=sids.index(specimen)
    angle,direction_type="",""
    setangle=0
    CurrRecs=[]
    while k < len(sids):
        CurrRecs=[]
        if setangle==0:angle=""
        method_codes,inst_code=[],""
        s=sids[k]
        PmagSpecRec={}
        PmagSpecRec["er_analyst_mail_names"]=user
        PmagSpecRec['magic_software_packages']=version_num
        PmagSpecRec['specimen_description']=""
        PmagSpecRec['magic_method_codes']=""
        if verbose and  s!="":print s, k , 'out of ',len(sids)
    #
    #  collect info for the PmagSpecRec dictionary
    #
        s_meas=pmag.get_dictitem(meas_data,'er_specimen_name',s,'T') # fish out this specimen
        s_meas=pmag.get_dictitem(s_meas,'magic_method_codes','Z','has') # fish out zero field steps
        if len(s_meas)>0:
          for rec in  s_meas: # fix up a few things for the output record
               PmagSpecRec["magic_instrument_codes"]=rec["magic_instrument_codes"]  # copy over instruments
               PmagSpecRec["er_citation_names"]="This study"
               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"]
               locname=rec['er_location_name']
               if 'er_expedition_name' in rec.keys(): PmagSpecRec["er_expedition_name"]=rec["er_expedition_name"]
               PmagSpecRec["magic_method_codes"]=rec["magic_method_codes"]
               if "magic_experiment_name" not in rec.keys():
                   PmagSpecRec["magic_experiment_names"]=""
               else:    
                   PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"]
               break
    #
    # find the data from the meas_data file for this specimen
    #
          data,units=pmag.find_dmag_rec(s,meas_data)
          PmagSpecRec["measurement_step_unit"]= units
          u=units.split(":")
          if "T" in units:PmagSpecRec["magic_method_codes"]=PmagSpecRec["magic_method_codes"]+":LP-DIR-AF"
          if "K" in units:PmagSpecRec["magic_method_codes"]=PmagSpecRec["magic_method_codes"]+":LP-DIR-T"
          if "J" in units:PmagSpecRec["magic_method_codes"]=PmagSpecRec["magic_method_codes"]+":LP-DIR-M"
    #
    # find prior interpretation
    #
          if len(CurrRecs)==0: # check if already in
            beg_pca,end_pca="",""
            calculation_type=""
            if inspec !="":
              if verbose: print "    looking up previous interpretations..."
              precs=pmag.get_dictitem(PriorRecs,'er_specimen_name',s,'T') # get all the prior recs with this specimen name
              precs=pmag.get_dictitem(precs,'magic_method_codes','LP-DIR','has') # get the directional data
              PriorRecs=pmag.get_dictitem(PriorRecs,'er_specimen_name',s,'F') # take them all out of prior recs
         # get the ones that meet the current coordinate system
              for prec in precs:
                if 'specimen_tilt_correction' not in prec.keys() or prec['specimen_tilt_correction']=='-1':
                    crd='s'
                elif prec['specimen_tilt_correction']=='0':
                    crd='g'
                elif prec['specimen_tilt_correction']=='100':
                    crd='t'
                else:
                    crd='?'
                CurrRec={}
                for key in prec.keys():CurrRec[key]=prec[key]
                CurrRecs.append(CurrRec) # put in CurrRecs
                method_codes= CurrRec["magic_method_codes"].replace(" ","").split(':')
                calculation_type='DE-BFL'
                if 'DE-FM' in method_codes: calculation_type='DE-FM'
                if 'DE-BFP' in method_codes: calculation_type='DE-BFP'
                if 'DE-BFL-A' in method_codes: calculation_type='DE-BFL-A'
                if 'specimen_dang' not in CurrRec.keys():
                    if verbose:print 'Run mk_redo.py and zeq_magic_redo.py to get the specimen_dang values'
                    CurrRec['specimen_dang']=-1
                if calculation_type!='DE-FM' and crd==coord: # not a fisher mean
                    if verbose:print "Specimen  N    MAD    DANG  start     end      dec     inc  type  component coordinates"
                    if units=='K':
                            if verbose:print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f  %s  %s       %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_mad"]),float(CurrRec["specimen_dang"]),float(CurrRec["measurement_step_min"])-273,float(CurrRec["measurement_step_max"])-273,float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,CurrRec['specimen_comp_name'],crd)
                    elif units=='T':
                       if verbose:print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f  %s  %s %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_mad"]),float(CurrRec["specimen_dang"]),float(CurrRec["measurement_step_min"])*1e3,float(CurrRec["measurement_step_max"])*1e3,float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,CurrRec['specimen_comp_name'],crd)
                    elif 'T' in units and 'K' in units:
                            if float(CurrRec['measurement_step_min'])<1.0 :
                                min=float(CurrRec['measurement_step_min'])*1e3
                            else:
                                min=float(CurrRec['measurement_step_min'])-273
                            if float(CurrRec['measurement_step_max'])<1.0 :
                                max=float(CurrRec['measurement_step_max'])*1e3
                            else:
                                max=float(CurrRec['measurement_step_max'])-273
                            if verbose:print '%s %i %7.1f %i %i %7.1f %7.1f %7.1f, %s        %s\n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_mad"]),float(CurrRec['specimen_dang']),min,max,float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,crd)
                    elif 'J' in units:
                       if verbose:print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f  %s  %s       %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_mad"]),float(CurrRec['specimen_dang']),float(CurrRec["measurement_step_min"]),float(CurrRec["measurement_step_max"]),float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,CurrRec['specimen_comp_name'],crd)
                elif calculation_type=='DE-FM' and crd==coord: # fisher mean
                    if verbose:print "Specimen  a95 DANG   start     end      dec     inc  type  component coordinates"
                    if units=='K':
                         if verbose:print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f  %s  %s       %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_alpha95"]),float(CurrRec["measurement_step_min"])-273,float(CurrRec["measurement_step_max"])-273,float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,CurrRec['specimen_comp_name'],crd)
                    elif units=='T':
                          if verbose:print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f  %s  %s       %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_alpha95"]),float(CurrRec["measurement_step_min"])*1e3,float(CurrRec["measurement_step_max"])*1e3,float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,CurrRec['specimen_comp_name'],crd)
                    elif 'T' in units and 'K' in units:
                            if float(CurrRec['measurement_step_min'])<1.0 :
                                min=float(CurrRec['measurement_step_min'])*1e3
                            else:
                                min=float(CurrRec['measurement_step_min'])-273
                            if float(CurrRec['measurement_step_max'])<1.0 :
                                max=float(CurrRec['measurement_step_max'])*1e3
                            else:
                                max=float(CurrRec['measurement_step_max'])-273
                            if verbose:print '%s %i %7.1f %i %i %7.1f %7.1f %s       %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_alpha95"]),min,max,float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,crd)
                    elif 'J' in units:
                       if verbose:print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %s %s       %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_mad"]),float(CurrRec["measurement_step_min"]),float(CurrRec["measurement_step_max"]),float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,CurrRec['specimen_comp_name'],crd)
              if len(CurrRecs)==0:beg_pca,end_pca="",""
          datablock=data
          noskip=1
          if len(datablock) <3: 
            noskip=0
            if backup==0:
                k+=1
            else:
                k-=1
            if len(CurrRecs)>0:
                for rec in CurrRecs:
                    PriorRecs.append(rec)
            CurrRecs=[]
          else:
            backup=0 
          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
                orient,az_type=pmag.get_orient(samp_data,PmagSpecRec["er_sample_name"])
                if az_type=='SO-NO':
                    if verbose: print "no orientation data for ",s 
                    orient["sample_azimuth"]=0
                    orient["sample_dip"]=0
                    noorient=1
                    method_codes.append("SO-NO")
                    orient["sample_azimuth"]=0
                    orient["sample_dip"]=0
                    orient["sample_bed_dip_azimuth"]=0
                    orient["sample_bed_dip"]=0
                    noorient=1
                    method_codes.append("SO-NO")
                else: 
                    noorient=0
        #
        #  if stratigraphic selected,  get stratigraphic correction
        #
                tiltblock,geoblock=[],[]
                for rec in datablock:
                    d_geo,i_geo=pmag.dogeo(rec[1],rec[2],float(orient["sample_azimuth"]),float(orient["sample_dip"]))
                    geoblock.append([rec[0],d_geo,i_geo,rec[3],rec[4],rec[5],rec[6]])
                    if tilt==1 and "sample_bed_dip" in orient.keys() and float(orient['sample_bed_dip'])!=0: 
                        d_tilt,i_tilt=pmag.dotilt(d_geo,i_geo,float(orient["sample_bed_dip_direction"]),float(orient["sample_bed_dip"]))
                        tiltblock.append([rec[0],d_tilt,i_tilt,rec[3],rec[4],rec[5],rec[6]])
                    if tilt==1: plotblock=tiltblock
                    if geo==1 and tilt==0:plotblock=geoblock
            if geo==0 and tilt==0: plotblock=datablock
    #
    # set the end pca point to last point  if not set
            if e==0 or e>len(plotblock)-1: e=len(plotblock)-1
            if angle=="": angle=plotblock[0][1] # rotate to NRM declination
            title=s+'_s'
            if geo==1 and tilt==0 and noorient!=1:title=s+'_g'
            if tilt==1 and noorient!=1:title=s+'_t'
            pmagplotlib.plotZED(ZED,plotblock,angle,title,units)
            if verbose:pmagplotlib.drawFIGS(ZED)
            if len(CurrRecs)!=0:
                for prec in CurrRecs:
                    if 'calculation_type' not in prec.keys():
                        calculation_type=''
                    else:
                        calculation_type=prec["calculation_type"]
                    direction_type=prec["specimen_direction_type"]
                    if calculation_type !="":
                        beg_pca,end_pca="",""
                        for j in range(len(datablock)):
                            if data[j][0]==float(prec["measurement_step_min"]):beg_pca=j
                            if data[j][0]==float(prec["measurement_step_max"]):end_pca=j
                        if beg_pca=="" or end_pca=="":  
                            if verbose:
                                print "something wrong with prior interpretation "
                            break
                    if calculation_type!="":
                        if beg_pca=="":beg_pca=0
                        if end_pca=="":end_pca=len(plotblock)-1
                        if geo==1 and tilt==0:
                            mpars=pmag.domean(geoblock,beg_pca,end_pca,calculation_type)
                            if mpars["specimen_direction_type"]!="Error":
                                pmagplotlib.plotDir(ZED,mpars,geoblock,angle)
                                if verbose:pmagplotlib.drawFIGS(ZED)
                        if geo==1 and tilt==1:
                            mpars=pmag.domean(tiltblock,beg_pca,end_pca,calculation_type)
                            if mpars["specimen_direction_type"]!="Error":
                                pmagplotlib.plotDir(ZED,mpars,tiltblock,angle)
                                if verbose:pmagplotlib.drawFIGS(ZED)
                        if geo==0 and tilt==0: 
                            mpars=pmag.domean(datablock,beg_pca,end_pca,calculation_type)
                        if mpars["specimen_direction_type"]!="Error":
                                pmagplotlib.plotDir(ZED,mpars,plotblock,angle)
                                if verbose:pmagplotlib.drawFIGS(ZED)
    #
    # print out data for this sample to screen
    #
            recnum=0
            for plotrec in plotblock:
                if units=='T' and verbose: print '%s: %i  %7.1f %s  %8.3e %7.1f %7.1f %s' % (plotrec[5], recnum,plotrec[0]*1e3," mT",plotrec[3],plotrec[1],plotrec[2],plotrec[6])
                if units=="K" and verbose: print '%s: %i  %7.1f %s  %8.3e %7.1f %7.1f %s' % (plotrec[5], recnum,plotrec[0]-273,' C',plotrec[3],plotrec[1],plotrec[2],plotrec[6])
                if units=="J" and verbose: print '%s: %i  %7.1f %s  %8.3e %7.1f %7.1f %s' % (plotrec[5], recnum,plotrec[0],' J',plotrec[3],plotrec[1],plotrec[2],plotrec[6])
                if 'K' in units and 'T' in units:
                    if plotrec[0]>=1. and verbose: print '%s: %i  %7.1f %s  %8.3e %7.1f %7.1f %s' % (plotrec[5], recnum,plotrec[0]-273,' C',plotrec[3],plotrec[1],plotrec[2],plotrec[6])
                    if plotrec[0]<1. and  verbose: print '%s: %i  %7.1f %s  %8.3e %7.1f %7.1f %s' % (plotrec[5], recnum,plotrec[0]*1e3," mT",plotrec[3],plotrec[1],plotrec[2],plotrec[6])
                recnum += 1
            if specimen!="":
                if plot_file=="":
                    basename=locname+'_'+s
                else:
                    basename=plot_file
                files={}
                for key in ZED.keys():
                    files[key]=basename+'_'+key+'.'+fmt 
                pmagplotlib.saveP(ZED,files)
                sys.exit()
            else:  # interactive
              if plots==0:
                ans='b'
                k+=1
                changeS=0
                while ans != "":
                    if len(CurrRecs)==0:
                        print """
                g/b: indicates  good/bad measurement.  "bad" measurements excluded from calculation

                set s[a]ve plot, [b]ounds for pca and calculate, [p]revious, [s]pecimen, 
                 change [h]orizontal projection angle,   change [c]oordinate systems, 
                 [e]dit data,  [q]uit: 
                """
                    else:
                        print """
                g/b: indicates  good/bad measurement.  "bad" measurements excluded from calculation

                 set s[a]ve plot, [b]ounds for pca and calculate, [p]revious, [s]pecimen, 
                 change [h]orizontal projection angle,   change [c]oordinate systems, 
                 [d]elete current interpretation(s), [e]dit data,   [q]uit: 
                """
                    ans=raw_input('<Return>  for  next specimen \n')
                    setangle=0
                    if ans=='d': # delete this interpretation
                        CurrRecs=[]
                        k-=1 # replot same specimen
                        ans=""
                        changeS=1
                    if  ans=='q': 
                        if changeM==1:
                            ans=raw_input('Save changes to magic_measurements.txt? y/[n] ')
                            if ans=='y':
                                pmag.magic_write(meas_file,meas_data,'magic_measurements')
                        print "Good bye"
                        sys.exit()
                    if  ans=='a':
                        if plot_file=="":
                            basename=locname+'_'+s+'_'
                        else:
                            basename=plot_file
                        files={}
                        for key in ZED.keys():
                            files[key]=basename+'_'+coord+'_'+key+'.'+fmt 
                        pmagplotlib.saveP(ZED,files)
                        ans=""
                    if  ans=='p':
                        k-=2
                        ans=""
                        backup=1
                    if ans=='c':
                        k-=1 # replot same block
                        if tilt==0 and geo ==1:print "You  are currently viewing geographic  coordinates "
                        if tilt==1 and geo ==1:print "You  are currently viewing stratigraphic  coordinates "
                        if tilt==0 and geo ==0: print "You  are currently viewing sample coordinates "
                        print "\n Which coordinate system do you wish to view? "
                        coord=raw_input(" <Return>  specimen, [g] geographic, [t] tilt corrected ")
                        if coord=="g":geo,tilt=1,0
                        if coord=="t":
                            geo=1
                            tilt=1
                        if coord=="":
                            coord='s'
                            geo=0
                            tilt=0
                        if geo==1 and sfile=="":
                            samp_file=raw_input(" Input er_samples file for sample orientations [er_samples.txt] " )
                            if samp_file=="":samp_file="er_samples.txt"
                            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 - coordinate system not changed" 
                            else:
                               sfile="ok"
                        ans=""
                    if ans=='s':
                        keepon=1
                        sample=raw_input('Enter desired specimen name (or first part there of): ')
                        while keepon==1:
                            try:
                                k =sids.index(sample)
                                keepon=0
                            except:
                                tmplist=[]
                                for qq in range(len(sids)):
                                    if sample in sids[qq]:tmplist.append(sids[qq])
                                print sample," not found, but this was: "
                                print tmplist
                                sample=raw_input('Select one or try again\n ')
                        angle,direction_type="",""
                        setangle=0
                        ans=""
                    if ans=='h':
                        k-=1
                        angle=raw_input("Enter desired  declination for X axis 0-360 ")
                        angle=float(angle)
                        if angle==0:angle=0.001
                        s=sids[k]
                        setangle=1
                        ans=""
                    if  ans=='e':
                        k-=1
                        ans=""
                        recnum=0
                        for plotrec in plotblock:
                            if plotrec[0]<=200 and verbose: print '%s: %i  %7.1f %s  %8.3e %7.1f %7.1f ' % (plotrec[5], recnum,plotrec[0]*1e3," mT",plotrec[3],plotrec[1],plotrec[2])
                            if plotrec[0]>200 and verbose: print '%s: %i  %7.1f %s  %8.3e %7.1f %7.1f ' % (plotrec[5], recnum,plotrec[0]-273,' C',plotrec[3],plotrec[1],plotrec[2])
                            recnum += 1
                        answer=raw_input('Enter index of point to change from bad to good or vice versa:  ')
                        try: 
                                ind=int(answer)
                                meas_data=pmag.mark_dmag_rec(s,ind,meas_data)
                                changeM=1
                        except:
                                'bad entry, try again'
                    if  ans=='b':
                        if end_pca=="":end_pca=len(plotblock)-1
                        if beg_pca=="":beg_pca=0
                        k-=1   # stay on same sample until through
                        GoOn=0
                        while GoOn==0:
                            print 'Enter index of first point for pca: ','[',beg_pca,']'
                            answer=raw_input('return to keep default  ')
                            if answer != "":
                                beg_pca=int(answer)
                            print 'Enter index  of last point for pca: ','[',end_pca,']'
                            answer=raw_input('return to keep default  ')
                            try:
                                end_pca=int(answer) 
                                if plotblock[beg_pca][5]=='b' or plotblock[end_pca][5]=='b': 
                                    print "Can't select 'bad' measurement for PCA bounds -try again"
                                    end_pca=len(plotblock)-1
                                    beg_pca=0
                                elif beg_pca >=0 and beg_pca<=len(plotblock)-2 and end_pca>0 and end_pca<len(plotblock): 
                                    GoOn=1
                                else:
                                    print beg_pca,end_pca, " are bad entry of indices - try again"
                                    end_pca=len(plotblock)-1
                                    beg_pca=0
                            except:
                                print beg_pca,end_pca, " are bad entry of indices - try again"
                                end_pca=len(plotblock)-1
                                beg_pca=0
                        GoOn=0
                        while GoOn==0:
                            if calculation_type!="":
                                print "Prior calculation type = ",calculation_type
                            ct=raw_input('Enter new Calculation Type: best-fit line,  plane or fisher mean [l]/p/f :  ' )
                            if ct=="" or ct=="l": 
                                direction_type="l"
                                calculation_type="DE-BFL"
                                GoOn=1
                            elif ct=='p':
                                direction_type="p"
                                calculation_type="DE-BFP"
                                GoOn=1
                            elif ct=='f':
                                direction_type="l"
                                calculation_type="DE-FM"
                                GoOn=1
                            else: 
                                print "bad entry of calculation type: try again. "
                        pmagplotlib.plotZED(ZED,plotblock,angle,s,units)
                        if verbose:pmagplotlib.drawFIGS(ZED)
                        if geo==1 and tilt==0:
                            mpars=pmag.domean(geoblock,beg_pca,end_pca,calculation_type)
                            if mpars['specimen_direction_type']=='Error':break
                            PmagSpecRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
                            PmagSpecRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
                            if "SO-NO" not in method_codes:
                                PmagSpecRec["specimen_tilt_correction"]='0'
                                method_codes.append("DA-DIR-GEO")
                            else:
                                PmagSpecRec["specimen_tilt_correction"]='-1'
                            pmagplotlib.plotDir(ZED,mpars,geoblock,angle)
                            if verbose:pmagplotlib.drawFIGS(ZED)
                        if geo==1 and  tilt==1:
                            mpars=pmag.domean(tiltblock,beg_pca,end_pca,calculation_type)
                            if mpars['specimen_direction_type']=='Error':break
                            PmagSpecRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
                            PmagSpecRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
                            if "SO-NO" not in method_codes:
                                PmagSpecRec["specimen_tilt_correction"]='100'
                                method_codes.append("DA-DIR-TILT")
                            else:
                                PmagSpecRec["specimen_tilt_correction"]='-1'
                            pmagplotlib.plotDir(ZED,mpars,tiltblock,angle)
                            if verbose:pmagplotlib.drawFIGS(ZED)
                        if geo==0 and tilt==0: 
                            mpars=pmag.domean(datablock,beg_pca,end_pca,calculation_type)
                            if mpars['specimen_direction_type']=='Error':break
                            PmagSpecRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
                            PmagSpecRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
                            PmagSpecRec["specimen_tilt_correction"]='-1'
                            pmagplotlib.plotDir(ZED,mpars,plotblock,angle)
                            if verbose:pmagplotlib.drawFIGS(ZED)
                        PmagSpecRec["measurement_step_min"]='%8.3e ' %(mpars["measurement_step_min"])
                        PmagSpecRec["measurement_step_max"]='%8.3e ' %(mpars["measurement_step_max"])
                        PmagSpecRec["specimen_correction"]='u'
                        PmagSpecRec["specimen_dang"]='%7.1f ' %(mpars['specimen_dang'])
                        print 'DANG: ',PmagSpecRec["specimen_dang"]
                        if calculation_type!='DE-FM':
                            PmagSpecRec["specimen_mad"]='%7.1f ' %(mpars["specimen_mad"])
                            PmagSpecRec["specimen_alpha95"]=""
                        else:
                            PmagSpecRec["specimen_alpha95"]='%7.1f ' %(mpars["specimen_alpha95"])
                            PmagSpecRec["specimen_mad"]=""
                        PmagSpecRec["specimen_n"]='%i ' %(mpars["specimen_n"])
                        PmagSpecRec["specimen_direction_type"]=direction_type
                        PmagSpecRec["calculation_type"]=calculation_type # redundant and won't be imported - just for convenience
                        method_codes=PmagSpecRec["magic_method_codes"].split(':')
                        if len(method_codes) != 0:
                            methstring=""
                            for meth in method_codes:
                                ctype=meth.split('-')
                                if 'DE' not in ctype:methstring=methstring+ ":" +meth # don't include old direction estimation methods
                        methstring=methstring+':'+calculation_type
                        PmagSpecRec["magic_method_codes"]= methstring.strip(':')
                        print 'Method codes: ',PmagSpecRec['magic_method_codes']
                        if calculation_type!='DE-FM':
                            if units=='K': 
                                print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_mad"]),float(PmagSpecRec["specimen_dang"]),float(PmagSpecRec["measurement_step_min"])-273,float(PmagSpecRec["measurement_step_max"])-273,float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
                            elif units== 'T':
                                print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_mad"]),float(PmagSpecRec["specimen_dang"]),float(PmagSpecRec["measurement_step_min"])*1e3,float(PmagSpecRec["measurement_step_max"])*1e3,float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
                            elif 'T' in units and 'K' in units:
                                if float(PmagSpecRec['measurement_step_min'])<1.0 :
                                    min=float(PmagSpecRec['measurement_step_min'])*1e3
                                else:
                                    min=float(PmagSpecRec['measurement_step_min'])-273
                                if float(PmagSpecRec['measurement_step_max'])<1.0 :
                                    max=float(PmagSpecRec['measurement_step_max'])*1e3
                                else:
                                    max=float(PmagSpecRec['measurement_step_max'])-273
                                print '%s %i %7.1f %i %i %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_mad"]),float(PmagSpecRec["specimen_dang"]),min,max,float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
                            else:
                                print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_mad"]),float(PmagSpecRec["specimen_dang"]),float(PmagSpecRec["measurement_step_min"]),float(PmagSpecRec["measurement_step_max"]),float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
                        else:
                            if 'K' in units:
                                print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_alpha95"]),float(PmagSpecRec["specimen_dang"]),float(PmagSpecRec["measurement_step_min"])-273,float(PmagSpecRec["measurement_step_max"])-273,float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
                            elif 'T' in units:
                                print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_alpha95"]),float(PmagSpecRec["specimen_dang"]),float(PmagSpecRec["measurement_step_min"])*1e3,float(PmagSpecRec["measurement_step_max"])*1e3,float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
                            elif 'T' in units and 'K' in units:
                                if float(PmagSpecRec['measurement_step_min'])<1.0 :
                                    min=float(PmagSpecRec['measurement_step_min'])*1e3
                                else:
                                    min=float(PmagSpecRec['measurement_step_min'])-273
                                if float(PmagSpecRec['measurement_step_max'])<1.0 :
                                    max=float(PmagSpecRec['measurement_step_max'])*1e3
                                else:
                                    max=float(PmagSpecRec['measurement_step_max'])-273
                                print '%s %i %7.1f %i %i %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_alpha95"]),min,max,float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
                            else:
                                print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_alpha95"]),float(PmagSpecRec["measurement_step_min"]),float(PmagSpecRec["measurement_step_max"]),float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
                        saveit=raw_input("Save this interpretation? [y]/n \n")
                        if saveit!="n":
                            changeS=1
#
# put in details
#
                            angle,direction_type,setangle="","",0
                            if len(CurrRecs)>0:
                                replace=raw_input(" [0] add new component, or [1] replace existing interpretation(s) [default is replace] ")
                                if replace=="1" or replace=="":
                                    CurrRecs=[]
                                    PmagSpecRec['specimen_comp_name']='A'
                                    CurrRecs.append(PmagSpecRec)
                                else:
                                    print 'These are the current component names for this specimen: '
                                    for trec in CurrRecs:print trec['specimen_comp_name']
                                    compnum=raw_input("Enter new component name: ")
                                    PmagSpecRec['specimen_comp_name']=compnum
                                    print "Adding new component: ",PmagSpecRec['specimen_comp_name']
                                    CurrRecs.append(PmagSpecRec)
                            else:
                                PmagSpecRec['specimen_comp_name']='A'
                                CurrRecs.append(PmagSpecRec)
                            k+=1 
                            ans=""
                        else:
                            ans=""
              else:  # plots=1
                  k+=1
                  files={}
                  locname.replace('/','-')
                  print PmagSpecRec
                  for key in ZED.keys():
                      files[key]="LO:_"+locname+'_SI:_'+PmagSpecRec['er_site_name']+'_SA:_'+PmagSpecRec['er_sample_name']+'_SP:_'+s+'_CO:_'+coord+'_TY:_'+key+'_.'+fmt
                  if pmagplotlib.isServer:
                      black     = '#000000'
                      purple    = '#800080'
                      titles={}
                      titles['demag']='DeMag Plot'
                      titles['zijd']='Zijderveld Plot'
                      titles['eqarea']='Equal Area Plot'
                      ZED = pmagplotlib.addBorders(ZED,titles,black,purple)
                  pmagplotlib.saveP(ZED,files)
            if len(CurrRecs)>0:
                for rec in CurrRecs: PriorRecs.append(rec)
            if changeS==1:
                if len(PriorRecs)>0:
                    save_redo(PriorRecs,inspec)
                else:
                    os.system('rm '+inspec)
            CurrRecs,beg_pca,end_pca=[],"","" # next up
            changeS=0
        else: k+=1 # skip record - not enough data
    if changeM==1:
        pmag.magic_write(meas_file,meas_data,'magic_measurements')
コード例 #7
0
ファイル: microwave_magic.py プロジェクト: headmetal/PmagPy
def main():
    """
    NAME
        microwave_magic.py
    
    DESCRIPTION
        plots microwave paleointensity data, allowing interactive setting of bounds.
        Saves and reads interpretations
        from a pmag_specimen formatted table, default: microwave_specimens.txt

    SYNTAX 
        microwave_magic.py [command line options]

    OPTIONS
        -h prints help message and quits
        -f MEAS, set magic_measurements input file
        -fsp PRIOR, set pmag_specimen prior interpretations file
        -fcr CRIT, set criteria file for grading.  
        -fmt [svg,png,jpg], format for images - default is svg
        -sav,  saves plots with out review (default format)
        -spc SPEC, plots single specimen SPEC, saves plot with specified format
            with optional -b bounds adn quits
        -b BEG END: sets  bounds for calculation
           BEG: starting step for slope calculation
           END: ending step for slope calculation
        
    DEFAULTS
        MEAS: magic_measurements.txt
        CRIT: NONE
        PRIOR: microwave_specimens.txt
  
    OUTPUT 
        figures:
            ALL:  numbers refer to temperature steps in command line window
            1) Arai plot:  closed circles are zero-field first/infield
                           open circles are infield first/zero-field
                           triangles are pTRM checks
                           squares are pTRM tail checks
                           VDS is vector difference sum
                           diamonds are bounds for interpretation
            2) Zijderveld plot:  closed (open) symbols are X-Y (X-Z) planes
                                 X rotated to NRM direction
            3) (De/Re)Magnetization diagram:
                           circles are NRM remaining
                           squares are pTRM gained
        command line window:
            list is: temperature step numbers, power (J), Dec, Inc, Int (units of magic_measuements)
                     list of possible commands: type letter followed by return to select option
                     saving of plots creates .svg format files with specimen_name, plot type as name
    """ 
#
#   initializations
#
    meas_file,critout,inspec="magic_measurements.txt","","microwave_specimens.txt"
    inlt=0
    version_num=pmag.get_version()
    Tinit,DCZ,field,first_save=0,0,-1,1
    user,comment="",''
    ans,specimen,recnum,start,end=0,0,0,0,0
    plots,pmag_out,samp_file,style=0,"","","svg"
    fmt='.'+style
#
# default acceptance criteria
#
    accept_keys=['specimen_int_ptrm_n','specimen_md','specimen_fvds','specimen_b_beta','specimen_dang','specimen_drats','specimen_Z']
    accept={}
    accept['specimen_int_ptrm_n']=2
    accept['specimen_md']=10
    accept['specimen_fvds']=0.35
    accept['specimen_b_beta']=.1
    accept['specimen_int_mad']=7
    accept['specimen_dang']=10
    accept['specimen_drats']=10
    accept['specimen_Z']=10
#
# parse command line options
#
    spc,BEG,END="","",""
    if '-h' in sys.argv:
        print main.__doc__
        sys.exit()
    if '-f' in sys.argv:
        ind=sys.argv.index('-f')
        meas_file=sys.argv[ind+1]
    if '-fsp' in sys.argv:
        ind=sys.argv.index('-fsp')
        inspec=sys.argv[ind+1]
    if '-fcr' in sys.argv:
        ind=sys.argv.index('-fcr')
        critout=sys.argv[ind+1]
    if '-fmt' in sys.argv:
        ind=sys.argv.index('-fmt')
        fmt='.'+sys.argv[ind+1]
    if '-spc' in sys.argv:
        ind=sys.argv.index('-spc')
        spc=sys.argv[ind+1]
        if '-b' in sys.argv:
            ind=sys.argv.index('-b')
            BEG=int(sys.argv[ind+1])
            END=int(sys.argv[ind+2])
    if critout!="":
        crit_data,file_type=pmag.magic_read(critout)
        if pmagplotlib.verbose:
            print "Acceptance criteria read in from ", critout
        accept={}
        accept['specimen_int_ptrm_n']=2.0
        for critrec in crit_data:
            if critrec["pmag_criteria_code"]=="IE-SPEC": 
                for key in accept_keys:
                    if key not in critrec.keys():
                        accept[key]=-1
                    else:
                        accept[key]=float(critrec[key])
    try:
        open(inspec,'rU')
        PriorRecs,file_type=pmag.magic_read(inspec)
        if file_type != 'pmag_specimens':
            print file_type
            print file_type,inspec," is not a valid pmag_specimens file " 
            sys.exit()
        for rec in PriorRecs:
            if 'magic_software_packages' not in rec.keys():rec['magic_software_packages']=""
    except IOError:
        PriorRecs=[]
        if pmagplotlib.verbose:print "starting new specimen interpretation file: ",inspec
    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()
    backup=0
    # define figure numbers for arai, zijderveld and 
    #   de-,re-magization diagrams
    AZD={}
    AZD['deremag'], AZD['zijd'],AZD['arai'],AZD['eqarea']=1,2,3,4
    pmagplotlib.plot_init(AZD['arai'],4,4)
    pmagplotlib.plot_init(AZD['zijd'],4,4)
    pmagplotlib.plot_init(AZD['deremag'],4,4)
    pmagplotlib.plot_init(AZD['eqarea'],4,4)
    #
    #
    #
    # get list of unique specimen names
    #
    CurrRec=[]
    sids=pmag.get_specs(meas_data)
    # get plots for specimen s - default is just to step through arai diagrams
    #
    if spc!="": specimen =sids.index(spc)
    while specimen < len(sids):
        methcodes=[]
        if pmagplotlib.verbose and spc!="":
            print sids[specimen],specimen+1, 'of ', len(sids)
        MeasRecs=[]
        s=sids[specimen]
        datablock,trmblock=[],[]
        PmagSpecRec={}
        PmagSpecRec["er_analyst_mail_names"]=user
        PmagSpecRec["specimen_correction"]='u'
    #
    # find the data from the meas_data file for this specimen
    #
        for rec in meas_data:
            if rec["er_specimen_name"]==s:
                MeasRecs.append(rec)
                methods=rec["magic_method_codes"].split(":")
                meths=[]
                for meth in methods:
                    meths.append(meth.strip()) # take off annoying spaces
                methods=""
                for meth in meths:
                    if meth.strip() not in methcodes and "LP-" in meth:methcodes.append(meth.strip())
                    methods=methods+meth+":"
                methods=methods[:-1]
                rec["magic_method_codes"]=methods 
                if "LP-PI-M" in meths: datablock.append(rec)
                if "LP-MRM" in meths: trmblock.append(rec)
        if len(trmblock)>2 and inspec!="":
            if Tinit==0:
                Tinit=1
                AZD['MRM']=4
                pmagplotlib.plot_init(AZD['MRM'],4,4)
            elif Tinit==1:
                pmagplotlib.clearFIG(AZD['MRM'])
        if len(datablock) <4:
           if backup==0:
               specimen+=1
               if pmagplotlib.verbose:
                   print 'skipping specimen - moving forward ', s
           else:
               specimen-=1
               if pmagplotlib.verbose:
                   print 'skipping specimen - moving backward ', s
    #
    #  collect info for the PmagSpecRec dictionary
    #
        else:
           rec=datablock[0]
           PmagSpecRec["er_citation_names"]="This study"
           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"]
           if "magic_instrument_codes" not in rec.keys():rec["magic_instrument_codes"]=""
           PmagSpecRec["magic_instrument_codes"]=rec["magic_instrument_codes"]
           PmagSpecRec["measurement_step_unit"]="J"
           if "magic_experiment_name" not in rec.keys():
               rec["magic_experiment_name"]=""
           else:
               PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"]
    
           meths=rec["magic_method_codes"].split(':')
       # sort data into types
           if "LP-PI-M-D" in meths: # this is a double heating experiment
               exp_type="LP-PI-M-D"
           elif "LP-PI-M-S" in meths:
               exp_type="LP-PI-M-S"
           else:
               print "experiment type not supported yet "
               break
           araiblock,field=pmag.sortmwarai(datablock,exp_type)
           first_Z=araiblock[0]
           first_I=araiblock[1]
           GammaChecks=araiblock[-3]
           ThetaChecks=araiblock[-2]
           DeltaChecks=araiblock[-1]
           if len(first_Z)<3:
               if backup==0:
                   specimen+=1
                   if pmagplotlib.verbose:
                       print 'skipping specimen - moving forward ', s
               else:
                   specimen-=1
                   if pmagplotlib.verbose:
                       print 'skipping specimen - moving backward ', s
           else:
               backup=0
               zijdblock,units=pmag.find_dmag_rec(s,meas_data)
               if exp_type=="LP-PI-M-D":
                   recnum=0
                   print "ZStep Watts  Dec Inc  Int"
                   for plotrec in zijdblock:
                       if pmagplotlib.verbose:
                           print '%i  %i %7.1f %7.1f %8.3e ' % (recnum,plotrec[0],plotrec[1],plotrec[2],plotrec[3])
                           recnum += 1
                   recnum = 1
                   if GammaChecks!="":
                       print "IStep Watts  Gamma"
                       for gamma in GammaChecks:
                           if pmagplotlib.verbose: print '%i %i %7.1f ' % (recnum, gamma[0],gamma[1])
                           recnum += 1
               if exp_type=="LP-PI-M-S":
                   if pmagplotlib.verbose:
                       print "IStep Watts  Theta"
                       kk=0
                       for theta in ThetaChecks:
                           kk+=1
                           print '%i  %i %7.1f ' % (kk,theta[0],theta[1])
                   if pmagplotlib.verbose:
                       print "Watts  Delta"
                       for delta in DeltaChecks:
                           print '%i %7.1f ' % (delta[0],delta[1])
               pmagplotlib.plotAZ(AZD,araiblock,zijdblock,s,units[0])
               if inspec !="":
                   if pmagplotlib.verbose: print 'Looking up saved interpretation....'
                   found = 0
                   for k in range(len(PriorRecs)):
                       try:
                         if PriorRecs[k]["er_specimen_name"]==s:
                           found =1
                           CurrRec.append(PriorRecs[k])
                           for j in range(len(araiblock[0])):
                               if float(araiblock[0][j][0])==float(PriorRecs[k]["measurement_step_min"]):start=j
                               if float(araiblock[0][j][0])==float(PriorRecs[k]["measurement_step_max"]):end=j
                           pars,errcode=pmag.PintPars(araiblock,zijdblock,start,end)
                           pars['measurement_step_unit']="J"
                           del PriorRecs[k]  # put in CurrRec, take out of PriorRecs
                           if errcode!=1:
                               pars["specimen_lab_field_dc"]=field
                               pars["specimen_int"]=-1*field*pars["specimen_b"]
                               pars["er_specimen_name"]=s
                               if pmagplotlib.verbose:
                                   print 'Saved interpretation: '
                               pars=pmag.scoreit(pars,PmagSpecRec,accept,'',0)
                               pmagplotlib.plotB(AZD,araiblock,zijdblock,pars)
                               if len(trmblock)>2:
                                   blab=field
                                   best=pars["specimen_int"]
                                   Bs,TRMs=[],[]
                                   for trec in trmblock:
                                       Bs.append(float(trec['treatment_dc_field']))
                                       TRMs.append(float(trec['measurement_magn_moment']))
                                   NLpars=nlt.NLtrm(Bs,TRMs,best,blab,0) # calculate best fit parameters through TRM acquisition data, and get new banc
                                   Mp,Bp=[],[]
                                   for k in  range(int(max(Bs)*1e6)):
                                       Bp.append(float(k)*1e-6)
                                       npred=nlt.TRM(Bp[-1],NLpars['xopt'][0],NLpars['xopt'][1]) # predicted NRM for this field
                                       Mp.append(npred)
                                   pmagplotlib.plotTRM(AZD['MRM'],Bs,TRMs,Bp,Mp,NLpars,trec['magic_experiment_name'])
                                   print npred
                                   print 'Banc= ',float(NLpars['banc'])*1e6
                                   if pmagplotlib.verbose:
                                       print 'Banc= ',float(NLpars['banc'])*1e6
                                   pmagplotlib.drawFIGS(AZD)
                           else:
                               print 'error on specimen ',s
                       except:
                         pass
                   if pmagplotlib.verbose and found==0: print  '    None found :(  ' 
               if spc!="":
                   if BEG!="":
                       pars,errcode=pmag.PintPars(araiblock,zijdblock,BEG,END)
                       pars['measurement_step_unit']="J"
                       pars["specimen_lab_field_dc"]=field
                       pars["specimen_int"]=-1*field*pars["specimen_b"]
                       pars["er_specimen_name"]=s
                       pars['specimen_grade']='' # ungraded
                       pmagplotlib.plotB(AZD,araiblock,zijdblock,pars)
                       if len(trmblock)>2:
                           if inlt==0:
                               donlt()
                               inlt=1
                           blab=field
                           best=pars["specimen_int"]
                           Bs,TRMs=[],[]
                           for trec in trmblock:
                               Bs.append(float(trec['treatment_dc_field']))
                               TRMs.append(float(trec['measurement_magn_moment']))
                           NLpars=nlt.NLtrm(Bs,TRMs,best,blab,0) # calculate best fit parameters through TRM acquisition data, and get new banc
    #
                           Mp,Bp=[],[]
                           for k in  range(int(max(Bs)*1e6)):
                               Bp.append(float(k)*1e-6)
                               npred=nlt.TRM(Bp[-1],NLpars['xopt'][0],NLpars['xopt'][1]) # predicted NRM for this field
                   files={}
                   for key in AZD.keys():
                       files[key]=s+'_'+key+fmt 
                   pmagplotlib.saveP(AZD,files)
                   sys.exit()
               if plots==0:
                   ans='b'
                   while ans != "":
                       print """
               s[a]ve plot, set [b]ounds for calculation, [d]elete current interpretation, [p]revious, [s]ample, [q]uit:
               """
                       ans=raw_input('Return for next specimen \n')
                       if ans=="": 
                           specimen +=1
                       if ans=="d": 
                           save_redo(PriorRecs,inspec)
                           CurrRec=[]
                           pmagplotlib.plotAZ(AZD,araiblock,zijdblock,s,units[0])
                           pmagplotlib.drawFIGS(AZD)
                       if ans=='a':
                           files={}
                           for key in AZD.keys():
                               files[key]=s+'_'+key+fmt 
                           pmagplotlib.saveP(AZD,files)
                           ans=""
                       if ans=='q':
                           print "Good bye"
                           sys.exit()
                       if ans=='p':
                           specimen =specimen -1
                           backup = 1
                           ans=""
                       if ans=='s':
                           keepon=1
                           spec=raw_input('Enter desired specimen name (or first part there of): ')
                           while keepon==1:
                               try:
                                   specimen =sids.index(spec)
                                   keepon=0
                               except:
                                   tmplist=[]
                                   for qq in range(len(sids)):
                                       if spec in sids[qq]:tmplist.append(sids[qq])
                                   print specimen," not found, but this was: "
                                   print tmplist
                                   spec=raw_input('Select one or try again\n ')
                           ans=""
                       if  ans=='b':
                           if end==0 or end >=len(araiblock[0]):end=len(araiblock[0])-1
                           GoOn=0
                           while GoOn==0:
                               print 'Enter index of first point for calculation: ','[',start,']'
                               answer=raw_input('return to keep default  ')
                               if answer != "":start=int(answer)
                               print 'Enter index  of last point for calculation: ','[',end,']'
                               answer=raw_input('return to keep default  ')
                               if answer != "":
                                   end=int(answer)
                               if start >=0 and start <len(araiblock[0])-2 and end >0 and end <len(araiblock[0]) and start<end:
                                   GoOn=1
                               else:
                                   print "Bad endpoints - try again! "
                                   start,end=0,len(araiblock)
                           s=sids[specimen]
                           pars,errcode=pmag.PintPars(araiblock,zijdblock,start,end)
                           pars['measurement_step_unit']="J"
                           pars["specimen_lab_field_dc"]=field
                           pars["specimen_int"]=-1*field*pars["specimen_b"]
                           pars["er_specimen_name"]=s
                           pars=pmag.scoreit(pars,PmagSpecRec,accept,'',0)
                           PmagSpecRec["measurement_step_min"]='%8.3e' % (pars["measurement_step_min"])
                           PmagSpecRec["measurement_step_max"]='%8.3e' % (pars["measurement_step_max"])
                           PmagSpecRec["measurement_step_unit"]="J"
                           PmagSpecRec["specimen_int_n"]='%i'%(pars["specimen_int_n"])
                           PmagSpecRec["specimen_lab_field_dc"]='%8.3e'%(pars["specimen_lab_field_dc"])
                           PmagSpecRec["specimen_int"]='%8.3e '%(pars["specimen_int"])
                           PmagSpecRec["specimen_b"]='%5.3f '%(pars["specimen_b"])
                           PmagSpecRec["specimen_q"]='%5.1f '%(pars["specimen_q"])
                           PmagSpecRec["specimen_f"]='%5.3f '%(pars["specimen_f"])
                           PmagSpecRec["specimen_fvds"]='%5.3f'%(pars["specimen_fvds"])
                           PmagSpecRec["specimen_b_beta"]='%5.3f'%(pars["specimen_b_beta"])
                           PmagSpecRec["specimen_int_mad"]='%7.1f'%(pars["specimen_int_mad"])
                           PmagSpecRec["specimen_Z"]='%7.1f'%(pars["specimen_Z"])
                           if pars["method_codes"]!="":
                               tmpcodes=pars["method_codes"].split(":")
                               for t in tmpcodes:
                                   if t.strip() not in methcodes:methcodes.append(t.strip())
                           PmagSpecRec["specimen_dec"]='%7.1f'%(pars["specimen_dec"])
                           PmagSpecRec["specimen_inc"]='%7.1f'%(pars["specimen_inc"])
                           PmagSpecRec["specimen_tilt_correction"]='-1'
                           PmagSpecRec["specimen_direction_type"]='l'
                           PmagSpecRec["direction_type"]='l' # this is redudant, but helpful - won't be imported
                           PmagSpecRec["specimen_dang"]='%7.1f '%(pars["specimen_dang"])
                           PmagSpecRec["specimen_drats"]='%7.1f '%(pars["specimen_drats"])
                           PmagSpecRec["specimen_int_ptrm_n"]='%i '%(pars["specimen_int_ptrm_n"])
                           PmagSpecRec["specimen_rsc"]='%6.4f '%(pars["specimen_rsc"])
                           PmagSpecRec["specimen_md"]='%i '%(int(pars["specimen_md"]))
                           if PmagSpecRec["specimen_md"]=='-1':PmagSpecRec["specimen_md"]=""
                           PmagSpecRec["specimen_b_sigma"]='%5.3f '%(pars["specimen_b_sigma"])
                           if "IE-TT" not in  methcodes:methcodes.append("IE-TT")
                           methods=""
                           for meth in methcodes:
                               methods=methods+meth+":"
                           PmagSpecRec["magic_method_codes"]=methods[:-1]
                           PmagSpecRec["specimen_description"]=comment
                           PmagSpecRec["magic_software_packages"]=version_num
                           pmagplotlib.plotAZ(AZD,araiblock,zijdblock,s,units[0])
                           pmagplotlib.plotB(AZD,araiblock,zijdblock,pars)
                           if len(trmblock)>2:
                               blab=field
                               best=pars["specimen_int"]
                               Bs,TRMs=[],[]
                               for trec in trmblock:
                                   Bs.append(float(trec['treatment_dc_field']))
                                   TRMs.append(float(trec['measurement_magn_moment']))
                               NLpars=nlt.NLtrm(Bs,TRMs,best,blab,0) # calculate best fit parameters through TRM acquisition data, and get new banc
                               Mp,Bp=[],[]
                               for k in  range(int(max(Bs)*1e6)):
                                   Bp.append(float(k)*1e-6)
                                   npred=nlt.TRM(Bp[-1],NLpars['xopt'][0],NLpars['xopt'][1]) # predicted NRM for this field
                                   Mp.append(npred)
                               pmagplotlib.plotTRM(AZD['MRM'],Bs,TRMs,Bp,Mp,NLpars,trec['magic_experiment_name'])
                               print 'Banc= ',float(NLpars['banc'])*1e6
                           pmagplotlib.drawFIGS(AZD)
                           pars["specimen_lab_field_dc"]=field
                           pars["specimen_int"]=-1*field*pars["specimen_b"]
                           saveit=raw_input("Save this interpretation? [y]/n \n")
                           if saveit!='n':
                               specimen+=1
                               PriorRecs.append(PmagSpecRec) # put back an interpretation
                               save_redo(PriorRecs,inspec)
                           ans=""
               else:
                   specimen+=1
                   if fmt != ".pmag":
                       basename=s+'_microwave'+fmt
                       files={}
                       for key in AZD.keys():
                           files[key]=s+'_'+key+fmt 
                       if pmagplotlib.isServer:
                           black     = '#000000'
                           purple    = '#800080'
                           titles={}
                           titles['deremag']='DeReMag Plot'
                           titles['zijd']='Zijderveld Plot'
                           titles['arai']='Arai Plot'
                           AZD = pmagplotlib.addBorders(AZD,titles,black,purple)
                       pmagplotlib.saveP(AZD,files)
    #                   pmagplotlib.combineFigs(s,files,3)
        if len(CurrRec)>0:
            for rec in CurrRec:
                PriorRecs.append(rec)
        CurrRec=[]
    if plots!=1:
        ans=raw_input(" Save last plot? 1/[0] ")
        if ans=="1":
            if fmt != ".pmag":
                files={}
                for key in AZD.keys():
                    files[key]=s+'_'+key+fmt
                pmagplotlib.saveP(AZD,files)
        if len(CurrRec)>0:PriorRecs.append(CurrRec) # put back an interpretation
        if len(PriorRecs)>0:
            save_redo(PriorRecs,inspec)
            print 'Updated interpretations saved in ',inspec
    if pmagplotlib.verbose:
        print "Good bye"