コード例 #1
0
def simulations_GGP(lat,GGPmodel,Nsim,plot=True):
    """ Gerenates four arrays that are directions (dec, inc), x and y equal area coordinates of rotated directions (x,y), 
    rotated directions (dec,inc), x and y equal area coordinates of rotated directions

    input 
    - lat latitude you want generate the directions list
    - GGPmodel: dictionary like GGP_QC96_GAD = {"g10" : -30, "g20" : 0.0, "g30" : 0.0, "sig10" : 3.0, "sig11": 3.0,
            "sig20" : 1.3 , "sig21" : 4.3, "sig22" : 1.3, "alpha": 27.7, "beta": 1.0, "name":'QC96_GAD'}
    - Nsim number of simulations you want

    output:
    lista_sim, lista_xy, lista_r, lista_xyr """
    
    dec_r=180
    pol=-GGPmodel['g10']/abs(GGPmodel['g10'])
    if pol<0:
        dec_r=0
    lista_sim = dii_fromGGPmodels(Nsim,lat,GGPmodel)
    m = psv.m_TAF(GGPmodel, lat)
    Binc = np.rad2deg(np.arctan(m[2]/abs(m[0])))
    lista_r = np.zeros(np.shape(lista_sim))
    
    for j in range(len(lista_sim)):
        lista_r[j,0],lista_r[j,1] = pmag.dotilt(lista_sim[j,0],lista_sim[j,1],dec_r,(90-Binc))
    lista_xyr = np.zeros([len(lista_sim),2])
    lista_xy = np.zeros([len(lista_sim),2])
    for j in range(len(lista_sim)):
        lista_xyr[j,0:2] = pmag.dimap(lista_r[j,0],lista_r[j,1])
        lista_xy[j,0:2] = pmag.dimap(lista_sim[j,0],lista_sim[j,1])
    if plot==True:
        plot_syn_directions(lista_sim, lista_xy, lista_r, lista_xyr,GGPmodel['name'],lat)
    return lista_sim, lista_xy, lista_r, lista_xyr
コード例 #2
0
def main():
    """
    NAME
       di_tilt.py

    DESCRIPTION
       rotates geographic coordinate dec, inc data to stratigraphic
       coordinates using the dip and dip direction (strike+90, dip if dip to right of strike)

    INPUT FORMAT
        declination inclination dip_direction  dip

    SYNTAX
       di_tilt.py [-h][-i][-f FILE] [< filename ]

    OPTIONS
        -h prints help message and quits
        -i for interactive data entry
        -f FILE command line entry of file name
        -F OFILE, specify output file, default is standard output


    OUTPUT:
        declination inclination
 """
    if '-h' in sys.argv:
        print main.__doc__
        sys.exit()
    if '-F' in sys.argv:
        ind = sys.argv.index('-F')
        ofile = sys.argv[ind + 1]
        out = open(ofile, 'w')
        print ofile, ' opened for output'
    else:
        ofile = ""
    if '-i' in sys.argv:  # interactive flag
        while 1:
            try:
                Dec = float(raw_input("Declination: <cntl-D> to quit "))
            except:
                print "\n Good-bye\n"
                sys.exit()
            Inc = float(raw_input("Inclination: "))
            Dip_dir = float(raw_input("Dip direction: "))
            Dip = float(raw_input("Dip: "))
            print '%7.1f %7.1f' % (pmag.dotilt(Dec, Inc, Dip_dir, Dip))
    elif '-f' in sys.argv:
        ind = sys.argv.index('-f')
        file = sys.argv[ind + 1]
        data = numpy.loadtxt(file)
    else:
        data = numpy.loadtxt(
            sys.stdin, dtype=numpy.float)  # read in the data from the datafile
    D, I = pmag.dotilt_V(data)
    for k in range(len(D)):
        if ofile == "":
            print '%7.1f %7.1f' % (D[k], I[k])
        else:
            out.write('%7.1f %7.1f\n' % (D[k], I[k]))
コード例 #3
0
ファイル: di_tilt.py プロジェクト: lfairchild/PmagPy
def main():
    """
    NAME
       di_tilt.py

    DESCRIPTION
       rotates geographic coordinate dec, inc data to stratigraphic
       coordinates using the dip and dip direction (strike+90, dip if dip to right of strike)

    INPUT FORMAT
        declination inclination dip_direction  dip

    SYNTAX
       di_tilt.py [-h][-i][-f FILE] [< filename ]

    OPTIONS
        -h prints help message and quits
        -i for interactive data entry
        -f FILE command line entry of file name
        -F OFILE, specify output file, default is standard output


    OUTPUT:
        declination inclination
 """
    if "-h" in sys.argv:
        print main.__doc__
        sys.exit()
    if "-F" in sys.argv:
        ind = sys.argv.index("-F")
        ofile = sys.argv[ind + 1]
        out = open(ofile, "w")
        print ofile, " opened for output"
    else:
        ofile = ""
    if "-i" in sys.argv:  # interactive flag
        while 1:
            try:
                Dec = float(raw_input("Declination: <cntl-D> to quit "))
            except:
                print "\n Good-bye\n"
                sys.exit()
            Inc = float(raw_input("Inclination: "))
            Dip_dir = float(raw_input("Dip direction: "))
            Dip = float(raw_input("Dip: "))
            print "%7.1f %7.1f" % (pmag.dotilt(Dec, Inc, Dip_dir, Dip))
    elif "-f" in sys.argv:
        ind = sys.argv.index("-f")
        file = sys.argv[ind + 1]
        data = numpy.loadtxt(file)
    else:
        data = numpy.loadtxt(sys.stdin, dtype=numpy.float)  # read in the data from the datafile
    D, I = pmag.dotilt_V(data)
    for k in range(len(D)):
        if ofile == "":
            print "%7.1f %7.1f" % (D[k], I[k])
        else:
            out.write("%7.1f %7.1f\n" % (D[k], I[k]))
コード例 #4
0
ファイル: fishqq.py プロジェクト: CrabGit334/PmagPy
def main():
    """
    NAME
       fishqq.py

    DESCRIPTION
       makes qq plot from dec,inc input data

    INPUT FORMAT
       takes dec/inc pairs in space delimited file

    SYNTAX
       fishqq.py [command line options]

    OPTIONS
        -h help message
        -f FILE, specify file on command line
        -F FILE, specify output file for statistics
        -sav save and quit [saves as input file name plus fmt extension]
        -fmt specify format for output [png, eps, svg, pdf] 

    OUTPUT:
        Dec Inc N Mu Mu_crit Me Me_crit Y/N
     where direction is the principal component and Y/N is Fisherian or not
     separate lines for each mode with N >=10 (N and R)
    """
    fmt,plot='svg',0
    outfile=""
    if '-h' in sys.argv: # check if help is needed
        print(main.__doc__)
        sys.exit() # graceful quit
    elif '-f' in sys.argv: # ask for filename
        ind=sys.argv.index('-f')
        file=sys.argv[ind+1]
        f=open(file,'r')
        data=f.readlines()
    if '-F' in sys.argv:
        ind=sys.argv.index('-F')
        outfile=open(sys.argv[ind+1],'w') # open output file
    if '-sav' in sys.argv: plot=1
    if '-fmt' in sys.argv:
        ind=sys.argv.index('-fmt')
        fmt=sys.argv[ind+1]
    DIs,nDIs,rDIs= [],[],[] # set up list for data
    for line in data:   # read in the data from standard input
        if '\t' in line:
            rec=line.split('\t') # split each line on space to get records
        else:
            rec=line.split() # split each line on space to get records
        DIs.append([float(rec[0]),float(rec[1])]) # append data to Inc
# split into two modes
    ppars=pmag.doprinc(DIs) # get principal directions
    for rec in DIs:
        angle=pmag.angle([rec[0],rec[1]],[ppars['dec'],ppars['inc']])
        if angle>90.:
            rDIs.append(rec)
        else:
            nDIs.append(rec)
    
#
    if len(rDIs) >=10 or len(nDIs) >=10:
        D1,I1=[],[]
        QQ={'unf1':1,'exp1':2}
        pmagplotlib.plot_init(QQ['unf1'],5,5)
        pmagplotlib.plot_init(QQ['exp1'],5,5)
        if len(nDIs) < 10: 
            ppars=pmag.doprinc(rDIs) # get principal directions
            Drbar,Irbar=ppars['dec']-180.,-ppars['inc']
            Nr=len(rDIs)
            for di in rDIs:
                d,irot=pmag.dotilt(di[0],di[1],Drbar-180.,90.-Irbar) # rotate to mean
                drot=d-180.
                if drot<0:drot=drot+360.
                D1.append(drot)           
                I1.append(irot) 
                Dtit='Mode 2 Declinations'
                Itit='Mode 2 Inclinations'
        else:          
            ppars=pmag.doprinc(nDIs) # get principal directions
            Dnbar,Inbar=ppars['dec'],ppars['inc']
            Nn=len(nDIs)
            for di in nDIs:
                d,irot=pmag.dotilt(di[0],di[1],Dnbar-180.,90.-Inbar) # rotate to mean
                drot=d-180.
                if drot<0:drot=drot+360.
                D1.append(drot)
                I1.append(irot)
                Dtit='Mode 1 Declinations'
                Itit='Mode 1 Inclinations'
        Mu_n,Mu_ncr=pmagplotlib.plot_qq_unf(QQ['unf1'],D1,Dtit) # make plot
        Me_n,Me_ncr=pmagplotlib.plot_qq_exp(QQ['exp1'],I1,Itit) # make plot
        #print Mu_n,Mu_ncr,Me_n, Me_ncr
        if outfile!="":
#        Dec Inc N Mu Mu_crit Me Me_crit Y/N
            if Mu_n<=Mu_ncr and Me_n<=Me_ncr:
               F='Y'
            else:
               F='N'
            outstring='%7.1f %7.1f %i %5.3f %5.3f %5.3f %5.3f %s \n'%(Dnbar,Inbar,Nn,Mu_n,Mu_ncr,Me_n,Me_ncr,F)
            outfile.write(outstring)
    else:
        print('you need N> 10 for at least one mode')
        sys.exit()
    if len(rDIs)>10 and len(nDIs)>10:
        D2,I2=[],[]
        QQ['unf2']=3
        QQ['exp2']=4
        pmagplotlib.plot_init(QQ['unf2'],5,5)
        pmagplotlib.plot_init(QQ['exp2'],5,5)
        ppars=pmag.doprinc(rDIs) # get principal directions
        Drbar,Irbar=ppars['dec']-180.,-ppars['inc']
        Nr=len(rDIs)
        for di in rDIs:
            d,irot=pmag.dotilt(di[0],di[1],Drbar-180.,90.-Irbar) # rotate to mean
            drot=d-180.
            if drot<0:drot=drot+360.
            D2.append(drot)           
            I2.append(irot) 
            Dtit='Mode 2 Declinations'
            Itit='Mode 2 Inclinations'
        Mu_r,Mu_rcr=pmagplotlib.plot_qq_unf(QQ['unf2'],D2,Dtit) # make plot
        Me_r,Me_rcr=pmagplotlib.plot_qq_exp(QQ['exp2'],I2,Itit) # make plot
        if outfile!="":
#        Dec Inc N Mu Mu_crit Me Me_crit Y/N
            if Mu_r<=Mu_rcr and Me_r<=Me_rcr:
               F='Y'
            else:
               F='N'
            outstring='%7.1f %7.1f %i %5.3f %5.3f %5.3f %5.3f %s \n'%(Drbar,Irbar,Nr,Mu_r,Mu_rcr,Me_r,Me_rcr,F)
            outfile.write(outstring)
    files={}
    for key in list(QQ.keys()):
        files[key]=file+'_'+key+'.'+fmt 
    if pmagplotlib.isServer:
        black     = '#000000'
        purple    = '#800080'
        titles={}
        titles['eq']='Equal Area Plot'
        EQ = pmagplotlib.add_borders(EQ,titles,black,purple)
        pmagplotlib.save_plots(QQ,files)
    elif plot==1:
        pmagplotlib.save_plots(QQ,files)
    else:
        pmagplotlib.draw_figs(QQ) 
        ans=input(" S[a]ve to save plot, [q]uit without saving:  ")
        if ans=="a": pmagplotlib.save_plots(QQ,files)
コード例 #5
0
def main():
    """
    NAME
        scalc.py

    DESCRIPTION
       calculates Sb from VGP Long,VGP Lat,Directional kappa,Site latitude data

    SYNTAX 
        scalc -h [command line options] [< standard input]
    
    INPUT 
       takes space delimited files with PLong, PLat,[kappa, N_site, slat]
    
    OPTIONS
        -h prints help message and quits
        -f FILE: specify input file
        -c cutoff:  specify VGP colatitude cutoff value
        -k cutoff: specify kappa cutoff
        -v : use the VanDammme criterion 
        -a: use antipodes of reverse data: default is to use only normal
        -C:  use all data without regard to polarity
        -b: do a bootstrap for confidence
        -p: do relative to principle axis
    NOTES
        if kappa, N_site, lat supplied, will consider within site scatter
    OUTPUT
        N Sb  Sb_lower Sb_upper Co-lat. Cutoff
    """
    coord, kappa, cutoff = "0", 0, 90.
    nb, anti, boot = 1000, 0, 0
    all = 0
    n = 0
    v = 0
    spin = 1
    coord_key = 'tilt_correction'
    if '-h' in sys.argv:
        print main.__doc__
        sys.exit()
    if '-f' in sys.argv:
        ind = sys.argv.index("-f")
        in_file = sys.argv[ind + 1]
        f = open(in_file, 'rU')
        lines = f.readlines()
    else:
        lines = sys.stdin.readlines()
    if '-c' in sys.argv:
        ind = sys.argv.index('-c')
        cutoff = float(sys.argv[ind + 1])
    if '-k' in sys.argv:
        ind = sys.argv.index('-k')
        kappa = float(sys.argv[ind + 1])
    if '-n' in sys.argv:
        ind = sys.argv.index('-n')
        n = int(sys.argv[ind + 1])
    if '-a' in sys.argv: anti = 1
    if '-C' in sys.argv: cutoff = 180.  # no cutoff
    if '-b' in sys.argv: boot = 1
    if '-v' in sys.argv: v = 1
    if '-p' in sys.argv: spin = 0
    #
    #
    # find desired vgp lat,lon, kappa,N_site data:
    #
    A, Vgps, slats, Pvgps = 180., [], [], []
    for line in lines:
        if '\t' in line:
            rec = line.replace('\n', '').split(
                '\t')  # split each line on space to get records
        else:
            rec = line.replace(
                '\n', '').split()  # split each line on space to get records
        vgp = {}
        vgp['vgp_lon'], vgp['vgp_lat'] = rec[0], rec[1]
        Pvgps.append([float(rec[0]), float(rec[1])])
        if anti == 1:
            if float(vgp['vgp_lat']) < 0:
                vgp['vgp_lat'] = '%7.1f' % (-1 * float(vgp['vgp_lat']))
                vgp['vgp_lon'] = '%7.1f' % (float(vgp['vgp_lon']) - 180.)
        if len(rec) == 5:
            vgp['average_k'], vgp['average_nn'], vgp['average_lat'] = rec[
                2], rec[3], rec[4]
            slats.append(float(rec[4]))
        else:
            vgp['average_k'], vgp['average_nn'], vgp[
                'average_lat'] = "0", "0", "0"
        if 90. - (float(vgp['vgp_lat'])) <= cutoff and float(
                vgp['average_k']) >= kappa and int(vgp['average_nn']) >= n:
            Vgps.append(vgp)
    if spin == 0:  # do transformation to pole
        ppars = pmag.doprinc(Pvgps)
        for vgp in Vgps:
            vlon, vlat = pmag.dotilt(float(vgp['vgp_lon']),
                                     float(vgp['vgp_lat']),
                                     ppars['dec'] - 180., 90. - ppars['inc'])
            vgp['vgp_lon'] = vlon
            vgp['vgp_lat'] = vlat
            vgp['average_k'] = "0"
    S_B = pmag.get_Sb(Vgps)
    A = cutoff
    if v == 1:
        thetamax, A = 181., 180.
        vVgps, cnt = [], 0
        for vgp in Vgps:
            vVgps.append(vgp)  # make a copy of Vgps
        while thetamax > A:
            thetas = []
            A = 1.8 * S_B + 5
            cnt += 1
            for vgp in vVgps:
                thetas.append(90. - (float(vgp['vgp_lat'])))
            thetas.sort()
            thetamax = thetas[-1]
            if thetamax < A: break
            nVgps = []
            for vgp in vVgps:
                if 90. - (float(vgp['vgp_lat'])) < thetamax: nVgps.append(vgp)
            vVgps = []
            for vgp in nVgps:
                vVgps.append(vgp)
            S_B = pmag.get_Sb(vVgps)
        Vgps = []
        for vgp in vVgps:
            Vgps.append(vgp)  # make a new Vgp list
    SBs, Ns = [], []
    if boot == 1:
        print 'please be patient...   bootstrapping'
        for i in range(nb):  # now do bootstrap
            BVgps = []
            for k in range(len(Vgps)):
                ind = random.randint(0, len(Vgps) - 1)
                random.jumpahead(int(ind * 1000))
                BVgps.append(Vgps[ind])
            SBs.append(pmag.get_Sb(BVgps))
        SBs.sort()
        low = int(.025 * nb)
        high = int(.975 * nb)
        print len(Vgps), '%7.1f %7.1f  %7.1f %7.1f ' % (S_B, SBs[low],
                                                        SBs[high], A)
    else:
        print len(Vgps), '%7.1f  %7.1f ' % (S_B, A)
    if len(slats) > 2:
        stats = pmag.gausspars(slats)
        print 'mean lat = ', '%7.1f' % (stats[0])
コード例 #6
0
ファイル: di_rot.py プロジェクト: dpastorgalan/PmagPy
def main():
    """
    NAME
        di_rot.py

    DESCRIPTION
        rotates set of directions to new coordinate system

    SYNTAX
        di_rot.py [command line options]

    OPTIONS
        -h prints help message and quits
        -f specify input file, default is standard input
        -F specify output file, default is standard output
        -D D specify  Dec of new coordinate system, default is 0
        -I I specify  Inc of new coordinate system, default is 90
    INTPUT/OUTPUT
        dec  inc   [space delimited]  


    """
    D,I=0.,90.
    outfile=""
    infile=""
    if '-h' in sys.argv:
        print main.__doc__
        sys.exit()
    if '-f' in sys.argv:
        ind=sys.argv.index('-f')
        infile=sys.argv[ind+1]
        data=numpy.loadtxt(infile)
    else:
        data=numpy.loadtxt(sys.stdin,dtype=numpy.float)
    if '-F' in sys.argv:
        ind=sys.argv.index('-F')
        outfile=sys.argv[ind+1]
        out=open(outfile,'w')
    if '-D' in sys.argv:
        ind=sys.argv.index('-D')
        D=float(sys.argv[ind+1])
    if '-I' in sys.argv:
        ind=sys.argv.index('-I')
        I=float(sys.argv[ind+1])
    if len(data.shape)>1: # 2-D array
        N=data.shape[0] 
        DipDir,Dip=numpy.ones(N,dtype=numpy.float).transpose()*(D-180.),numpy.ones(N,dtype=numpy.float).transpose()*(90.-I)
        data=data.transpose()
        data=numpy.array([data[0],data[1],DipDir ,Dip]).transpose()
        drot,irot=pmag.dotilt_V(data)
        drot=(drot-180.)%360.  # 
        for k in range(N): 
             if outfile=="":
                print '%7.1f %7.1f ' % (drot[k],irot[k])
             else:
                out.write('%7.1f %7.1f\n' % (drot[k],irot[k]))
    else: 
        d,i=pmag.dotilt(data[0],data[1],(D-180.),90.-I)
        if outfile=="":
            print '%7.1f %7.1f ' % ((d-180.)%360.,i)
        else:
            out.write('%7.1f %7.1f\n' % ((d-180.)%360.,i))
コード例 #7
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,""
    dir_path='.'
    if "-h" in args:
        print main.__doc__
        sys.exit()
    if '-WD' in sys.argv:
        ind=sys.argv.index('-WD')
        dir_path=sys.argv[ind+1]
    meas_file=dir_path+"/magic_measurements.txt"
    pmag_file=dir_path+"/nrm_specimens.txt"
    samp_file=dir_path+"/er_samples.txt"
    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=dir_path+'/'+sys.argv[ind+1]
    speclist=[]
    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,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 #8
0
ファイル: zeq_magic_redo.py プロジェクト: CrabGit334/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,'r')
    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()
    #
    #
    #

    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=[]
        spec=pmag.get_dictitem(meas_data,'er_specimen_name',s,'T')   
        if len(spec)==0:
            print('no data found for specimen:  ',s)
            print('delete from zeq_redo input file...., then try again')
        else: 
          for rec in  spec: # copy of vital stats to PmagSpecRec from first spec record in demag block
           skip=1
           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"]
                   if "er_expedition_name" in list(rec.keys()):PmagSpecRec["er_expedition_name"]=rec["er_expedition_name"]
                   PmagSpecRec["er_citation_names"]="This study"
                   if "magic_experiment_name" not in list(rec.keys()): rec["magic_experiment_name"]=""
                   PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"]
                   if "magic_instrument_codes" not in list(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") 
    #
    #
        datablock,units=pmag.find_dmag_rec(s,spec) # fish out the demag data for this specimen
    #
        if len(datablock) <2 or s not in speclist : 
            k+=1
#            print 'skipping ', s,len(datablock)
        else:
        #
        # 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 or tilt==1:
       # find top priority orientation method
                orient,az_type=pmag.get_orient(samp_data,PmagSpecRec["er_sample_name"])
                if az_type not in method_codes:method_codes.append(az_type)
        #
        #  if tilt selected,  get stratigraphic correction
        #
                tiltblock,geoblock=[],[]
                for rec in datablock:
                    if "sample_azimuth" in list(orient.keys()) and orient["sample_azimuth"]!="":
                        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]])
                        if tilt==1 and "sample_bed_dip_direction" in list(orient.keys()): 
                            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]])
                        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 list(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"])
                            CompRec["specimen_dang"]='%7.1f '%(mpars["specimen_dang"])
                            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 #9
0
ファイル: zeq_magic.py プロジェクト: dpastorgalan/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 #10
0
def main():
    """
    NAME
        scalc_magic.py

    DESCRIPTION
       calculates Sb from pmag_results files

    SYNTAX 
        scalc_magic -h [command line options]
    
    INPUT 
       takes magic formatted pmag_results table
       pmag_result_name must start with "VGP: Site"
       must have average_lat if spin axis is reference
    
    OPTIONS
        -h prints help message and quits
        -f FILE: specify input results file, default is 'pmag_results.txt'
        -c cutoff:  specify VGP colatitude cutoff value
        -k cutoff: specify kappa cutoff
        -crd [s,g,t]: specify coordinate system, default is geographic
        -v : use the VanDammme criterion 
        -a: use antipodes of reverse data: default is to use only normal
        -C: use all data without regard to polarity
        -r:  use reverse data only
        -p: do relative to principle axis
        -b: do bootstrap confidence bounds

     OUTPUT:
         if option -b used: N,  S_B, lower and upper bounds
         otherwise: N,  S_B, cutoff
    """
    in_file = 'pmag_results.txt'
    coord, kappa, cutoff = "0", 1., 90.
    nb, anti, spin, v, boot = 1000, 0, 1, 0, 0
    coord_key = 'tilt_correction'
    rev = 0
    if '-h' in sys.argv:
        print(main.__doc__)
        sys.exit()
    if '-f' in sys.argv:
        ind = sys.argv.index("-f")
        in_file = sys.argv[ind + 1]
    if '-c' in sys.argv:
        ind = sys.argv.index('-c')
        cutoff = float(sys.argv[ind + 1])
    if '-k' in sys.argv:
        ind = sys.argv.index('-k')
        kappa = float(sys.argv[ind + 1])
    if '-crd' in sys.argv:
        ind = sys.argv.index("-crd")
        coord = sys.argv[ind + 1]
        if coord == 's': coord = "-1"
        if coord == 'g': coord = "0"
        if coord == 't': coord = "100"
    if '-a' in sys.argv: anti = 1
    if '-C' in sys.argv: cutoff = 180.  # no cutoff
    if '-r' in sys.argv: rev = 1
    if '-p' in sys.argv: spin = 0
    if '-v' in sys.argv: v = 1
    if '-b' in sys.argv: boot = 1
    data, file_type = pmag.magic_read(in_file)
    #
    #
    # find desired vgp lat,lon, kappa,N_site data:
    #
    #
    #
    A, Vgps, Pvgps = 180., [], []
    VgpRecs = pmag.get_dictitem(data, 'vgp_lat', '',
                                'F')  # get all non-blank vgp latitudes
    VgpRecs = pmag.get_dictitem(VgpRecs, 'vgp_lon', '',
                                'F')  # get all non-blank vgp longitudes
    SiteRecs = pmag.get_dictitem(VgpRecs, 'data_type', 'i',
                                 'T')  # get VGPs (as opposed to averaged)
    SiteRecs = pmag.get_dictitem(SiteRecs, coord_key, coord,
                                 'T')  # get right coordinate system
    for rec in SiteRecs:
        if anti == 1:
            if 90. - abs(float(rec['vgp_lat'])) <= cutoff and float(
                    rec['average_k']) >= kappa:
                if float(rec['vgp_lat']) < 0:
                    rec['vgp_lat'] = '%7.1f' % (-1 * float(rec['vgp_lat']))
                    rec['vgp_lon'] = '%7.1f' % (float(rec['vgp_lon']) - 180.)
                Vgps.append(rec)
                Pvgps.append([float(rec['vgp_lon']), float(rec['vgp_lat'])])
        elif rev == 0:  # exclude normals
            if 90. - (float(rec['vgp_lat'])) <= cutoff and float(
                    rec['average_k']) >= kappa:
                Vgps.append(rec)
                Pvgps.append([float(rec['vgp_lon']), float(rec['vgp_lat'])])
        else:  # include normals
            if 90. - abs(float(rec['vgp_lat'])) <= cutoff and float(
                    rec['average_k']) >= kappa:
                if float(rec['vgp_lat']) < 0:
                    rec['vgp_lat'] = '%7.1f' % (-1 * float(rec['vgp_lat']))
                    rec['vgp_lon'] = '%7.1f' % (float(rec['vgp_lon']) - 180.)
                    Vgps.append(rec)
                    Pvgps.append(
                        [float(rec['vgp_lon']),
                         float(rec['vgp_lat'])])
    if spin == 0:  # do transformation to pole
        ppars = pmag.doprinc(Pvgps)
        for vgp in Vgps:
            vlon, vlat = pmag.dotilt(float(vgp['vgp_lon']),
                                     float(vgp['vgp_lat']),
                                     ppars['dec'] - 180., 90. - ppars['inc'])
            vgp['vgp_lon'] = vlon
            vgp['vgp_lat'] = vlat
            vgp['average_k'] = "0"
    S_B = pmag.get_Sb(Vgps)
    A = cutoff
    if v == 1:
        thetamax, A = 181., 180.
        vVgps, cnt = [], 0
        for vgp in Vgps:
            vVgps.append(vgp)  # make a copy of Vgps
        while thetamax > A:
            thetas = []
            A = 1.8 * S_B + 5
            cnt += 1
            for vgp in vVgps:
                thetas.append(90. - (float(vgp['vgp_lat'])))
            thetas.sort()
            thetamax = thetas[-1]
            if thetamax < A: break
            nVgps = []
            for vgp in vVgps:
                if 90. - (float(vgp['vgp_lat'])) < thetamax: nVgps.append(vgp)
            vVgps = []
            for vgp in nVgps:
                vVgps.append(vgp)
            S_B = pmag.get_Sb(vVgps)
        Vgps = []
        for vgp in vVgps:
            Vgps.append(vgp)  # make a new Vgp list
    SBs = []
    if boot == 1:
        for i in range(nb):  # now do bootstrap
            BVgps = []
            if i % 100 == 0: print(i, ' out of ', nb)
            for k in range(len(Vgps)):
                random.seed()
                ind = random.randint(0, len(Vgps) - 1)
                BVgps.append(Vgps[ind])
            SBs.append(pmag.get_Sb(BVgps))
        SBs.sort()
        low = int(.025 * nb)
        high = int(.975 * nb)
        print(len(Vgps),
              '%7.1f _ %7.1f ^ %7.1f %7.1f' % (S_B, SBs[low], SBs[high], A))
    else:
        print(len(Vgps), '%7.1f  %7.1f ' % (S_B, A))
コード例 #11
0
def main():
    """
    NAME
        zeq_magic_redo.py
   
    DESCRIPTION
        Calculate principal components through demagnetization data using bounds and calculation type stored in "redo" file
  
    SYNTAX
        zeq_magic_redo.py [command line options]

    OPTIONS
        -h prints help message
        -usr USER:   identify user, default is ""
        -f: specify input file, default is magic_measurements.txt
        -F: specify output file, default is zeq_specimens.txt
        -fre  REDO: specify redo file, default is "zeq_redo"
        -fsa  SAMPFILE: specify er_samples format file, default is "er_samples.txt"
        -A : don't average replicate measurements, default is yes
        -crd [s,g,t] : 
             specify coordinate system [s,g,t]  [default is specimen coordinates]
                 are specimen, geographic, and tilt corrected respectively
             NB: you must have a SAMPFILE in this directory to rotate from specimen coordinates
        -leg:  attaches "Recalculated from original measurements; supercedes published results. " to comment field
    INPUTS
        zeq_redo format file is:
        specimen_name calculation_type[DE-BFL,DE-BFL-A,DE-BFL-O,DE-BFP,DE-FM]  step_min step_max component_name[A,B,C]
    """
    dir_path = '.'
    INCL = ["LT-NO", "LT-AF-Z", "LT-T-Z", "LT-M-Z"]  # looking for demag data
    beg, end, pole, geo, tilt, askave, save = 0, 0, [], 0, 0, 0, 0
    user, doave, comment = "", 1, ""
    geo, tilt = 0, 0
    version_num = pmag.get_version()
    args = sys.argv
    if '-WD' in args:
        ind = args.index('-WD')
        dir_path = args[ind + 1]
    meas_file, pmag_file, mk_file = dir_path + "/" + "magic_measurements.txt", dir_path + "/" + "zeq_specimens.txt", dir_path + "/" + "zeq_redo"
    samp_file, coord = dir_path + "/" + "er_samples.txt", ""
    if "-h" in args:
        print(main.__doc__)
        sys.exit()
    if "-usr" in args:
        ind = args.index("-usr")
        user = sys.argv[ind + 1]
    if "-A" in args: doave = 0
    if "-leg" in args:
        comment = "Recalculated from original measurements; supercedes published results. "
    if "-f" in args:
        ind = args.index("-f")
        meas_file = dir_path + '/' + sys.argv[ind + 1]
    if "-F" in args:
        ind = args.index("-F")
        pmag_file = dir_path + '/' + sys.argv[ind + 1]
    if "-fre" in args:
        ind = args.index("-fre")
        mk_file = dir_path + "/" + args[ind + 1]
    try:
        mk_f = open(mk_file, 'r')
    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()
    #
    #
    #

    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 = []
        spec = pmag.get_dictitem(meas_data, 'er_specimen_name', s, 'T')
        if len(spec) == 0:
            print('no data found for specimen:  ', s)
            print('delete from zeq_redo input file...., then try again')
        else:
            for rec in spec:  # copy of vital stats to PmagSpecRec from first spec record in demag block
                skip = 1
                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"]
                    if "er_expedition_name" in list(rec.keys()):
                        PmagSpecRec["er_expedition_name"] = rec[
                            "er_expedition_name"]
                    PmagSpecRec["er_citation_names"] = "This study"
                    if "magic_experiment_name" not in list(rec.keys()):
                        rec["magic_experiment_name"] = ""
                    PmagSpecRec["magic_experiment_names"] = rec[
                        "magic_experiment_name"]
                    if "magic_instrument_codes" not in list(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")
    #
    #
        datablock, units = pmag.find_dmag_rec(
            s, spec)  # fish out the demag data for this specimen
        #
        if len(datablock) < 2 or s not in speclist:
            k += 1


#            print 'skipping ', s,len(datablock)
        else:
            #
            # 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 or tilt == 1:
                # find top priority orientation method
                orient, az_type = pmag.get_orient(
                    samp_data, PmagSpecRec["er_sample_name"])
                if az_type not in method_codes: method_codes.append(az_type)
                #
                #  if tilt selected,  get stratigraphic correction
                #
                tiltblock, geoblock = [], []
                for rec in datablock:
                    if "sample_azimuth" in list(
                            orient.keys()) and orient["sample_azimuth"] != "":
                        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]])
                        if tilt == 1 and "sample_bed_dip_direction" in list(
                                orient.keys()):
                            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]
                            ])
                        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 list(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"])
                            CompRec["specimen_dang"] = '%7.1f ' % (
                                mpars["specimen_dang"])
                            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 #12
0
def main():
    """
    NAME
       fishqq.py

    DESCRIPTION
       makes qq plot from dec,inc input data

    INPUT FORMAT
       takes dec/inc pairs in space delimited file

    SYNTAX
       fishqq.py [command line options]

    OPTIONS
        -h help message
        -f FILE, specify file on command line
        -F FILE, specify output file for statistics
        -sav save and quit [saves as input file name plus fmt extension]
        -fmt specify format for output [png, eps, svg, pdf] 

    OUTPUT:
        Dec Inc N Mu Mu_crit Me Me_crit Y/N
     where direction is the principal component and Y/N is Fisherian or not
     separate lines for each mode with N >=10 (N and R)
    """
    fmt,plot='svg',0
    outfile=""
    if '-h' in sys.argv: # check if help is needed
        print main.__doc__
        sys.exit() # graceful quit
    elif '-f' in sys.argv: # ask for filename
        ind=sys.argv.index('-f')
        file=sys.argv[ind+1]
        f=open(file,'rU')
        data=f.readlines()
    if '-F' in sys.argv:
        ind=sys.argv.index('-F')
        outfile=open(sys.argv[ind+1],'w') # open output file
    if '-sav' in sys.argv: plot=1
    if '-fmt' in sys.argv:
        ind=sys.argv.index('-fmt')
        fmt=sys.argv[ind+1]
    DIs,nDIs,rDIs= [],[],[] # set up list for data
    for line in data:   # read in the data from standard input
        if '\t' in line:
            rec=line.split('\t') # split each line on space to get records
        else:
            rec=line.split() # split each line on space to get records
        DIs.append([float(rec[0]),float(rec[1])]) # append data to Inc
# split into two modes
    ppars=pmag.doprinc(DIs) # get principal directions
    for rec in DIs:
        angle=pmag.angle([rec[0],rec[1]],[ppars['dec'],ppars['inc']])
        if angle>90.:
            rDIs.append(rec)
        else:
            nDIs.append(rec)
    
#
    if len(rDIs) >=10 or len(nDIs) >=10:
        D1,I1=[],[]
        QQ={'unf1':1,'exp1':2}
        pmagplotlib.plot_init(QQ['unf1'],5,5)
        pmagplotlib.plot_init(QQ['exp1'],5,5)
        if len(nDIs) < 10: 
            ppars=pmag.doprinc(rDIs) # get principal directions
            Drbar,Irbar=ppars['dec']-180.,-ppars['inc']
            Nr=len(rDIs)
            for di in rDIs:
                d,irot=pmag.dotilt(di[0],di[1],Drbar-180.,90.-Irbar) # rotate to mean
                drot=d-180.
                if drot<0:drot=drot+360.
                D1.append(drot)           
                I1.append(irot) 
                Dtit='Mode 2 Declinations'
                Itit='Mode 2 Inclinations'
        else:          
            ppars=pmag.doprinc(nDIs) # get principal directions
            Dnbar,Inbar=ppars['dec'],ppars['inc']
            Nn=len(nDIs)
            for di in nDIs:
                d,irot=pmag.dotilt(di[0],di[1],Dnbar-180.,90.-Inbar) # rotate to mean
                drot=d-180.
                if drot<0:drot=drot+360.
                D1.append(drot)
                I1.append(irot)
                Dtit='Mode 1 Declinations'
                Itit='Mode 1 Inclinations'
        Mu_n,Mu_ncr=pmagplotlib.plotQQunf(QQ['unf1'],D1,Dtit) # make plot
        Me_n,Me_ncr=pmagplotlib.plotQQexp(QQ['exp1'],I1,Itit) # make plot
        #print Mu_n,Mu_ncr,Me_n, Me_ncr
        if outfile!="":
#        Dec Inc N Mu Mu_crit Me Me_crit Y/N
            if Mu_n<=Mu_ncr and Me_n<=Me_ncr:
               F='Y'
            else:
               F='N'
            outstring='%7.1f %7.1f %i %5.3f %5.3f %5.3f %5.3f %s \n'%(Dnbar,Inbar,Nn,Mu_n,Mu_ncr,Me_n,Me_ncr,F)
            outfile.write(outstring)
    else:
        print 'you need N> 10 for at least one mode'
        sys.exit()
    if len(rDIs)>10 and len(nDIs)>10:
        D2,I2=[],[]
        QQ['unf2']=3
        QQ['exp2']=4
        pmagplotlib.plot_init(QQ['unf2'],5,5)
        pmagplotlib.plot_init(QQ['exp2'],5,5)
        ppars=pmag.doprinc(rDIs) # get principal directions
        Drbar,Irbar=ppars['dec']-180.,-ppars['inc']
        Nr=len(rDIs)
        for di in rDIs:
            d,irot=pmag.dotilt(di[0],di[1],Drbar-180.,90.-Irbar) # rotate to mean
            drot=d-180.
            if drot<0:drot=drot+360.
            D2.append(drot)           
            I2.append(irot) 
            Dtit='Mode 2 Declinations'
            Itit='Mode 2 Inclinations'
        Mu_r,Mu_rcr=pmagplotlib.plotQQunf(QQ['unf2'],D2,Dtit) # make plot
        Me_r,Me_rcr=pmagplotlib.plotQQexp(QQ['exp2'],I2,Itit) # make plot
        if outfile!="":
#        Dec Inc N Mu Mu_crit Me Me_crit Y/N
            if Mu_r<=Mu_rcr and Me_r<=Me_rcr:
               F='Y'
            else:
               F='N'
            outstring='%7.1f %7.1f %i %5.3f %5.3f %5.3f %5.3f %s \n'%(Drbar,Irbar,Nr,Mu_r,Mu_rcr,Me_r,Me_rcr,F)
            outfile.write(outstring)
    files={}
    for key in QQ.keys():
        files[key]=file+'_'+key+'.'+fmt 
    if pmagplotlib.isServer:
        black     = '#000000'
        purple    = '#800080'
        titles={}
        titles['eq']='Equal Area Plot'
        EQ = pmagplotlib.addBorders(EQ,titles,black,purple)
        pmagplotlib.saveP(QQ,files)
    elif plot==1:
        pmagplotlib.saveP(QQ,files)
    else:
        pmagplotlib.drawFIGS(QQ) 
        ans=raw_input(" S[a]ve to save plot, [q]uit without saving:  ")
        if ans=="a": pmagplotlib.saveP(QQ,files)
コード例 #13
0
ファイル: scalc.py プロジェクト: dpastorgalan/PmagPy
def main():
    """
    NAME
        scalc.py

    DESCRIPTION
       calculates Sb from VGP Long,VGP Lat,Directional kappa,Site latitude data

    SYNTAX 
        scalc -h [command line options] [< standard input]
    
    INPUT 
       takes space delimited files with PLong, PLat,[kappa, N_site, slat]
    
    OPTIONS
        -h prints help message and quits
        -f FILE: specify input file
        -c cutoff:  specify VGP colatitude cutoff value
        -k cutoff: specify kappa cutoff
        -v : use the VanDammme criterion 
        -a: use antipodes of reverse data: default is to use only normal
        -C:  use all data without regard to polarity
        -b: do a bootstrap for confidence
        -p: do relative to principle axis
    NOTES
        if kappa, N_site, lat supplied, will consider within site scatter
    OUTPUT
        N Sb  Sb_lower Sb_upper Co-lat. Cutoff
    """
    coord,kappa,cutoff="0",0,90.
    nb,anti,boot=1000,0,0
    all=0
    n=0
    v=0
    spin=1
    coord_key='tilt_correction'
    if '-h' in sys.argv:
        print main.__doc__
        sys.exit()
    if '-f' in sys.argv:
        ind=sys.argv.index("-f")
        in_file=sys.argv[ind+1]
        f=open(in_file,'rU')
        lines=f.readlines()
    else:
        lines=sys.stdin.readlines()
    if '-c' in sys.argv:
        ind=sys.argv.index('-c')
        cutoff=float(sys.argv[ind+1])
    if '-k' in sys.argv:
        ind=sys.argv.index('-k')
        kappa=float(sys.argv[ind+1])
    if '-n' in sys.argv:
        ind=sys.argv.index('-n')
        n=int(sys.argv[ind+1])
    if '-a' in sys.argv: anti=1
    if '-C' in sys.argv: cutoff=180. # no cutoff
    if '-b' in sys.argv: boot=1
    if '-v' in sys.argv: v=1
    if '-p' in sys.argv: spin=0
    #
    #
    # find desired vgp lat,lon, kappa,N_site data:
    #
    A,Vgps,slats,Pvgps=180.,[],[],[]
    for line in lines:
        if '\t' in line:
            rec=line.replace('\n','').split('\t') # split each line on space to get records
        else:
            rec=line.replace('\n','').split() # split each line on space to get records
        vgp={}
        vgp['vgp_lon'],vgp['vgp_lat']=rec[0],rec[1]
        Pvgps.append([float(rec[0]),float(rec[1])])
        if anti==1:
            if float(vgp['vgp_lat'])<0:
                vgp['vgp_lat']='%7.1f'%(-1*float(vgp['vgp_lat']))
                vgp['vgp_lon']='%7.1f'%(float(vgp['vgp_lon'])-180.)
        if len(rec)==5:
            vgp['average_k'],vgp['average_nn'],vgp['average_lat']=rec[2],rec[3],rec[4]
            slats.append(float(rec[4]))
        else: 
            vgp['average_k'],vgp['average_nn'],vgp['average_lat']="0","0","0"
        if 90.-(float(vgp['vgp_lat']))<=cutoff and float(vgp['average_k'])>=kappa and int(vgp['average_nn'])>=n: Vgps.append(vgp) 
    if spin==0: # do transformation to pole
        ppars=pmag.doprinc(Pvgps)
        for vgp in Vgps:
	    vlon,vlat=pmag.dotilt(float(vgp['vgp_lon']),float(vgp['vgp_lat']),ppars['dec']-180.,90.-ppars['inc'])
            vgp['vgp_lon']=vlon  
            vgp['vgp_lat']=vlat  
            vgp['average_k']="0"
    S_B= pmag.get_Sb(Vgps)
    A=cutoff
    if v==1:
        thetamax,A=181.,180.
        vVgps,cnt=[],0
        for vgp in Vgps:vVgps.append(vgp) # make a copy of Vgps
        while thetamax>A:
            thetas=[]
            A=1.8*S_B+5
            cnt+=1
            for vgp in vVgps:thetas.append(90.-(float(vgp['vgp_lat'])))
            thetas.sort()
            thetamax=thetas[-1]
            if thetamax<A:break
            nVgps=[]
            for  vgp in vVgps:
                if 90.-(float(vgp['vgp_lat']))<thetamax:nVgps.append(vgp)
            vVgps=[]
            for vgp in nVgps:vVgps.append(vgp) 
            S_B= pmag.get_Sb(vVgps)
        Vgps=[]
        for vgp in vVgps:Vgps.append(vgp) # make a new Vgp list
    SBs,Ns=[],[]
    if boot==1:
      print 'please be patient...   bootstrapping'
      for i in range(nb): # now do bootstrap 
        BVgps=[]
        for k in range(len(Vgps)):
            ind=random.randint(0,len(Vgps)-1)
            random.jumpahead(int(ind*1000))
            BVgps.append(Vgps[ind])
        SBs.append(pmag.get_Sb(BVgps))
      SBs.sort()
      low=int(.025*nb)
      high=int(.975*nb)
      print len(Vgps),'%7.1f %7.1f  %7.1f %7.1f '%(S_B,SBs[low],SBs[high],A)
    else:
      print len(Vgps),'%7.1f  %7.1f '%(S_B,A)
    if  len(slats)>2:
        stats= pmag.gausspars(slats)
        print 'mean lat = ','%7.1f'%(stats[0])
コード例 #14
0
ファイル: scalc_magic.py プロジェクト: allochthonous/PmagPy
def main():
    """
    NAME
        scalc_magic.py

    DESCRIPTION
       calculates Sb from pmag_results files

    SYNTAX 
        scalc_magic -h [command line options]
    
    INPUT 
       takes magic formatted pmag_results table
       pmag_result_name must start with "VGP: Site"
       must have average_lat if spin axis is reference
    
    OPTIONS
        -h prints help message and quits
        -f FILE: specify input results file, default is 'pmag_results.txt'
        -c cutoff:  specify VGP colatitude cutoff value
        -k cutoff: specify kappa cutoff
        -crd [s,g,t]: specify coordinate system, default is geographic
        -v : use the VanDammme criterion 
        -a: use antipodes of reverse data: default is to use only normal
        -C: use all data without regard to polarity
        -r:  use reverse data only
        -p: do relative to principle axis
        -b: do bootstrap confidence bounds

     OUTPUT:
         if option -b used: N,  S_B, lower and upper bounds
         otherwise: N,  S_B, cutoff
    """
    in_file='pmag_results.txt'
    coord,kappa,cutoff="0",1.,90.
    nb,anti,spin,v,boot=1000,0,1,0,0
    coord_key='tilt_correction'
    rev=0
    if '-h' in sys.argv:
        print(main.__doc__)
        sys.exit()
    if '-f' in sys.argv:
        ind=sys.argv.index("-f")
        in_file=sys.argv[ind+1]
    if '-c' in sys.argv:
        ind=sys.argv.index('-c')
        cutoff=float(sys.argv[ind+1])
    if '-k' in sys.argv:
        ind=sys.argv.index('-k')
        kappa=float(sys.argv[ind+1])
    if '-crd' in sys.argv:
        ind=sys.argv.index("-crd")
        coord=sys.argv[ind+1]
        if coord=='s':coord="-1"
        if coord=='g':coord="0"
        if coord=='t':coord="100"
    if '-a' in sys.argv: anti=1
    if '-C' in sys.argv: cutoff=180. # no cutoff
    if '-r' in sys.argv: rev=1
    if '-p' in sys.argv: spin=0
    if '-v' in sys.argv: v=1
    if '-b' in sys.argv: boot=1
    data,file_type=pmag.magic_read(in_file)
    #
    #
    # find desired vgp lat,lon, kappa,N_site data:
    #
    #
    #
    A,Vgps,Pvgps=180.,[],[]
    VgpRecs=pmag.get_dictitem(data,'vgp_lat','','F') # get all non-blank vgp latitudes
    VgpRecs=pmag.get_dictitem(VgpRecs,'vgp_lon','','F') # get all non-blank vgp longitudes
    SiteRecs=pmag.get_dictitem(VgpRecs,'data_type','i','T') # get VGPs (as opposed to averaged)
    SiteRecs=pmag.get_dictitem(SiteRecs,coord_key,coord,'T') # get right coordinate system
    for rec in SiteRecs:
        if anti==1:
            if 90.-abs(float(rec['vgp_lat']))<=cutoff and float(rec['average_k'])>=kappa: 
                if float(rec['vgp_lat'])<0:
                    rec['vgp_lat']='%7.1f'%(-1*float(rec['vgp_lat']))
                    rec['vgp_lon']='%7.1f'%(float(rec['vgp_lon'])-180.)
                Vgps.append(rec)
                Pvgps.append([float(rec['vgp_lon']),float(rec['vgp_lat'])])
        elif rev==0: # exclude normals
            if 90.-(float(rec['vgp_lat']))<=cutoff and float(rec['average_k'])>=kappa: 
                Vgps.append(rec)
                Pvgps.append([float(rec['vgp_lon']),float(rec['vgp_lat'])])
        else: # include normals
            if 90.-abs(float(rec['vgp_lat']))<=cutoff and float(rec['average_k'])>=kappa: 
                if float(rec['vgp_lat'])<0:
                    rec['vgp_lat']='%7.1f'%(-1*float(rec['vgp_lat']))
                    rec['vgp_lon']='%7.1f'%(float(rec['vgp_lon'])-180.)
                    Vgps.append(rec)
                    Pvgps.append([float(rec['vgp_lon']),float(rec['vgp_lat'])])
    if spin==0: # do transformation to pole
        ppars=pmag.doprinc(Pvgps)
        for vgp in Vgps:
            vlon,vlat=pmag.dotilt(float(vgp['vgp_lon']),float(vgp['vgp_lat']),ppars['dec']-180.,90.-ppars['inc'])
            vgp['vgp_lon']=vlon
            vgp['vgp_lat']=vlat
            vgp['average_k']="0"
    S_B= pmag.get_Sb(Vgps)
    A=cutoff
    if v==1:
        thetamax,A=181.,180.
        vVgps,cnt=[],0
        for vgp in Vgps:vVgps.append(vgp) # make a copy of Vgps
        while thetamax>A:
            thetas=[]
            A=1.8*S_B+5
            cnt+=1
            for vgp in vVgps:thetas.append(90.-(float(vgp['vgp_lat'])))
            thetas.sort()
            thetamax=thetas[-1]
            if thetamax<A:break
            nVgps=[]
            for  vgp in vVgps:
                if 90.-(float(vgp['vgp_lat']))<thetamax:nVgps.append(vgp)
            vVgps=[]
            for vgp in nVgps:vVgps.append(vgp)
            S_B= pmag.get_Sb(vVgps)
        Vgps=[]
        for vgp in vVgps:Vgps.append(vgp) # make a new Vgp list
    SBs=[]
    if boot==1:
        for i in range(nb): # now do bootstrap 
            BVgps=[]
            if i%100==0: print(i,' out of ',nb)
            for k in range(len(Vgps)):
                random.seed()
                ind=random.randint(0,len(Vgps)-1)
                BVgps.append(Vgps[ind])
            SBs.append(pmag.get_Sb(BVgps))
        SBs.sort()
        low=int(.025*nb)
        high=int(.975*nb)
        print(len(Vgps),'%7.1f _ %7.1f ^ %7.1f %7.1f'%(S_B,SBs[low],SBs[high],A))
    else:
        print(len(Vgps),'%7.1f  %7.1f '%(S_B,A))
コード例 #15
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, ""
    dir_path = "."
    if "-h" in args:
        print main.__doc__
        sys.exit()
    if "-WD" in sys.argv:
        ind = sys.argv.index("-WD")
        dir_path = sys.argv[ind + 1]
    meas_file = dir_path + "/magic_measurements.txt"
    pmag_file = dir_path + "/nrm_specimens.txt"
    samp_file = dir_path + "/er_samples.txt"
    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 = dir_path + "/" + sys.argv[ind + 1]
    speclist = []
    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, 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 #16
0
ファイル: di_rot.py プロジェクト: jbowles100/PmagPy
def main():
    """
    NAME
        di_rot.py

    DESCRIPTION
        rotates set of directions to new coordinate system

    SYNTAX
        di_rot.py [command line options]

    OPTIONS
        -h prints help message and quits
        -f specify input file, default is standard input
        -F specify output file, default is standard output
        -D D specify  Dec of new coordinate system, default is 0
        -I I specify  Inc of new coordinate system, default is 90
    INTPUT/OUTPUT
        dec  inc   [space delimited]  


    """
    D, I = 0., 90.
    outfile = ""
    infile = ""
    if '-h' in sys.argv:
        print main.__doc__
        sys.exit()
    if '-f' in sys.argv:
        ind = sys.argv.index('-f')
        infile = sys.argv[ind + 1]
        data = numpy.loadtxt(infile)
    else:
        data = numpy.loadtxt(sys.stdin, dtype=numpy.float)
    if '-F' in sys.argv:
        ind = sys.argv.index('-F')
        outfile = sys.argv[ind + 1]
        out = open(outfile, 'w')
    if '-D' in sys.argv:
        ind = sys.argv.index('-D')
        D = float(sys.argv[ind + 1])
    if '-I' in sys.argv:
        ind = sys.argv.index('-I')
        I = float(sys.argv[ind + 1])
    if len(data.shape) > 1:  # 2-D array
        N = data.shape[0]
        DipDir, Dip = numpy.ones(N, dtype=numpy.float).transpose() * (
            D - 180.), numpy.ones(N, dtype=numpy.float).transpose() * (90. - I)
        data = data.transpose()
        data = numpy.array([data[0], data[1], DipDir, Dip]).transpose()
        drot, irot = pmag.dotilt_V(data)
        drot = (drot - 180.) % 360.  #
        for k in range(N):
            if outfile == "":
                print '%7.1f %7.1f ' % (drot[k], irot[k])
            else:
                out.write('%7.1f %7.1f\n' % (drot[k], irot[k]))
    else:
        d, i = pmag.dotilt(data[0], data[1], (D - 180.), 90. - I)
        if outfile == "":
            print '%7.1f %7.1f ' % ((d - 180.) % 360., i)
        else:
            out.write('%7.1f %7.1f\n' % ((d - 180.) % 360., i))