def plot_AMS(sdata,pointsize=50,errors='None',bedding=[],incolor='N',):
"""
adapted from pmagplotlib.plotANIS
set errors to 'h' for hext ellipses, 'b' for bootstrap, 'p' for parametric bootstrap
bootstrap trials currently hard-coded as 1000
for bedding, give as [strike,dip] ;
"""
subplot_net() #set up stereonet
if incolor=='N': colours=['0.4','0.6','0.5'] #specify greyscale colours
else: colours=['lightcoral','lightskyblue','lightgreen']
#if bedding plot bedding plane
if bedding !=[]:
# hard-coded version of pmag.plotC
D_c,I_c=pmag.circ(bedding[0]-90.,90.-bedding[1],90.)
X_c_d,Y_c_d=[],[]
for k in range(len(D_c)):
XY=pmag.dimap(D_c[k],I_c[k])
if I_c[k]>0:
X_c_d.append(XY[0])
Y_c_d.append(XY[1])
plt.plot(X_c_d,Y_c_d,color='grey',dashes=[10,2],linewidth=3,zorder=1)
Vs=[]
#plot individual sample data
for s in sdata:
tau,V=pmag.doseigs(s)
Vs.append(V)
plotEVEC(Vs,pointsize,colours)
#plot mean eigenvectors
nf,sigma,avs=pmag.sbar(sdata)
Vs=[]
mtau,mV=pmag.doseigs(avs)
Vs.append(mV)
plotEVEC(Vs,pointsize*4,['w','w','w'], 'black',7)
#plot confidence limits
hpars=pmag.dohext(nf,sigma,avs)
if errors=='h':
ellpars=[hpars["v1_dec"],hpars["v1_inc"],hpars["e12"],hpars["v2_dec"],hpars["v2_inc"],hpars["e13"],hpars["v3_dec"],hpars["v3_inc"]]
plotELL(ellpars,'black',1,1)
ellpars=[hpars["v2_dec"],hpars["v2_inc"],hpars["e23"],hpars["v3_dec"],hpars["v3_inc"],hpars["e12"],hpars["v1_dec"],hpars["v1_inc"]]
plotELL(ellpars,'black',1,1)
ellpars=[hpars["v3_dec"],hpars["v3_inc"],hpars["e13"],hpars["v1_dec"],hpars["v1_inc"],hpars["e23"],hpars["v2_dec"],hpars["v2_inc"]]
plotELL(ellpars,'black',1,1)
elif errors=='b' or errors=='p':
if errors=='p': ipar=1
else: ipar=0
Tmean,Vmean,Taus,BVs=pmag.s_boot(sdata,ipar,1000) # get eigenvectors of mean tensor
# the problem with the bootstrap is that for fabrics where one or more eigenvectors is close to the horizontal,
# you end up with dipolar data
bpars=pmag.sbootpars(Taus,BVs,Vmean)
bpars['t1']=hpars['t1']
bpars['t2']=hpars['t2']
bpars['t3']=hpars['t3']
#have to pair zeta value with eta dec/inc, and vice-versa, to align error ellipses correctly.
ellpars=[bpars["v1_dec"],bpars["v1_inc"],bpars["v1_eta"],bpars["v1_eta_dec"],bpars["v1_eta_inc"],bpars["v1_zeta"],bpars["v1_zeta_dec"],bpars["v1_zeta_inc"]]
plotELL(ellpars,'black',1,1)
ellpars=[bpars["v2_dec"],bpars["v2_inc"],bpars["v2_eta"],bpars["v2_eta_dec"],bpars["v2_eta_inc"],bpars["v2_zeta"],bpars["v2_zeta_dec"],bpars["v2_zeta_inc"]]
plotELL(ellpars,'black',1,1)
ellpars=[bpars["v3_dec"],bpars["v3_inc"],bpars["v3_eta"],bpars["v3_eta_dec"],bpars["v3_eta_inc"],bpars["v3_zeta"],bpars["v3_zeta_dec"],bpars["v3_zeta_inc"]]
plotELL(ellpars,'black',1,1)
def plot_AMS(
sdata,
pointsize=50,
errors='None',
bedding=[],
incolor='N',
):
"""
adapted from pmagplotlib.plotANIS
set errors to 'h' for hext ellipses, 'b' for bootstrap, 'p' for parametric bootstrap
bootstrap trials currently hard-coded as 1000
for bedding, give as [strike,dip] ;
"""
subplot_net() #set up stereonet
if incolor == 'N':
colours = ['0.4', '0.6', '0.5'] #specify greyscale colours
else:
colours = ['lightcoral', 'lightskyblue', 'lightgreen']
#if bedding plot bedding plane
if bedding != []:
# hard-coded version of pmag.plotC
D_c, I_c = pmag.circ(bedding[0] - 90., 90. - bedding[1], 90.)
X_c_d, Y_c_d = [], []
for k in range(len(D_c)):
XY = pmag.dimap(D_c[k], I_c[k])
if I_c[k] > 0:
X_c_d.append(XY[0])
Y_c_d.append(XY[1])
plt.plot(X_c_d,
Y_c_d,
color='grey',
dashes=[10, 2],
linewidth=3,
zorder=1)
Vs = []
#plot individual sample data
for s in sdata:
tau, V = pmag.doseigs(s)
Vs.append(V)
plotEVEC(Vs, pointsize, colours)
#plot mean eigenvectors
nf, sigma, avs = pmag.sbar(sdata)
Vs = []
mtau, mV = pmag.doseigs(avs)
Vs.append(mV)
plotEVEC(Vs, pointsize * 4, ['w', 'w', 'w'], 'black', 7)
#plot confidence limits
hpars = pmag.dohext(nf, sigma, avs)
if errors == 'h':
ellpars = [
hpars["v1_dec"], hpars["v1_inc"], hpars["e12"], hpars["v2_dec"],
hpars["v2_inc"], hpars["e13"], hpars["v3_dec"], hpars["v3_inc"]
]
plotELL(ellpars, 'black', 1, 1)
ellpars = [
hpars["v2_dec"], hpars["v2_inc"], hpars["e23"], hpars["v3_dec"],
hpars["v3_inc"], hpars["e12"], hpars["v1_dec"], hpars["v1_inc"]
]
plotELL(ellpars, 'black', 1, 1)
ellpars = [
hpars["v3_dec"], hpars["v3_inc"], hpars["e13"], hpars["v1_dec"],
hpars["v1_inc"], hpars["e23"], hpars["v2_dec"], hpars["v2_inc"]
]
plotELL(ellpars, 'black', 1, 1)
elif errors == 'b' or errors == 'p':
if errors == 'p': ipar = 1
else: ipar = 0
Tmean, Vmean, Taus, BVs = pmag.s_boot(
sdata, ipar, 1000) # get eigenvectors of mean tensor
# the problem with the bootstrap is that for fabrics where one or more eigenvectors is close to the horizontal,
# you end up with dipolar data
bpars = pmag.sbootpars(Taus, BVs, Vmean)
bpars['t1'] = hpars['t1']
bpars['t2'] = hpars['t2']
bpars['t3'] = hpars['t3']
#have to pair zeta value with eta dec/inc, and vice-versa, to align error ellipses correctly.
ellpars = [
bpars["v1_dec"], bpars["v1_inc"], bpars["v1_eta"],
bpars["v1_eta_dec"], bpars["v1_eta_inc"], bpars["v1_zeta"],
bpars["v1_zeta_dec"], bpars["v1_zeta_inc"]
]
plotELL(ellpars, 'black', 1, 1)
ellpars = [
bpars["v2_dec"], bpars["v2_inc"], bpars["v2_eta"],
bpars["v2_eta_dec"], bpars["v2_eta_inc"], bpars["v2_zeta"],
bpars["v2_zeta_dec"], bpars["v2_zeta_inc"]
]
plotELL(ellpars, 'black', 1, 1)
ellpars = [
bpars["v3_dec"], bpars["v3_inc"], bpars["v3_eta"],
bpars["v3_eta_dec"], bpars["v3_eta_inc"], bpars["v3_zeta"],
bpars["v3_zeta_dec"], bpars["v3_zeta_inc"]
]
plotELL(ellpars, 'black', 1, 1)
def main():
"""
NAME
k15_magic.py
DESCRIPTION
converts .k15 format data to magic_measurements format.
assums Jelinek Kappabridge measurement scheme
SYNTAX
k15_magic.py [-h] [command line options]
OPTIONS
-h prints help message and quits
-f KFILE: specify .k15 format input file
-F MFILE: specify magic_measurements format output file
-Fsa SFILE, specify er_samples format file for output
-Fa AFILE, specify rmag_anisotropy format file for output
-loc LOC: specify location name for study
-ins INST: specify instrument that measurements were made on
-spc NUM: specify number of digets for specimen ID, default is 0
-ncn NCOM: specify naming convention (default is #1)
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXXYYY: YYY is sample designation with Z characters from site XXX
[5] sample = site
[6] sample, site, location info in er_samples.txt
[7] all others you will have to either customize your
DEFAULTS
MFILE: k15_measurements.txt
SFILE: er_samples.txt
AFILE: rmag_anisotropy.txt
LOC: unknown
INST: unknown
INPUT
name [az,pl,strike,dip], followed by
3 rows of 5 measurements for each specimen
"""
#
# initialize some variables
#
version_num=pmag.get_version()
specnum=0
sampfile, measfile="er_samples.txt","k15_measurements.txt"
anisfile='rmag_anisotropy.txt'
resfile='rmag_results.txt'
syn=0
er_location_name="unknown"
inst="unknown"
itilt,igeo,linecnt,key=0,0,0,""
first_save=1
k15,specnum=[],0
citation='This study'
dir_path='.'
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
# pick off stuff from command line
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index('-f')
k15file=sys.argv[ind+1]
if '-F' in sys.argv:
ind=sys.argv.index('-F')
measfile=sys.argv[ind+1]
if '-Fsa' in sys.argv:
ind=sys.argv.index('-Fsa')
sampfile=sys.argv[ind+1]
if '-Fa' in sys.argv:
ind=sys.argv.index('-Fa')
anisfile=sys.argv[ind+1]
if '-loc' in sys.argv:
ind=sys.argv.index('-loc')
er_location_name=sys.argv[ind+1]
if '-spc' in sys.argv:
ind=sys.argv.index('-spc')
specnum=-int(sys.argv[ind+1])
samp_con,Z="1",""
if "-ncn" in sys.argv:
ind=sys.argv.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
if samp_con=='6':
Samps,filetype=pmag.magic_read(dirpath+'/er_samples.txt')
sampfile, measfile=dir_path+'/'+sampfile,dir_path+'/'+measfile
anisfile=dir_path+'/'+anisfile
resfile=dir_path+'/'+resfile
k15file=dir_path+'/'+k15file
try:
SampRecs,filetype=pmag.magic_read(sampfile) # append new records to existing
samplist=[]
for samp in SampRecs:
if samp['er_sample_name'] not in samplist:samplist.append(samp['er_sample_name'])
except IOError:
SampRecs=[]
# measurement directions for Jelinek 1977 protocol:
Decs=[315,225,180,135,45,90,270,270,270,90,180,180,0,0,0]
Incs=[0,0,0,0,0,-45,-45,0,45,45,45,-45,-90,-45,45]
# some defaults to read in .k15 file format
# list of measurements and default number of characters for specimen ID
# some magic default definitions
#
# read in data
input=open(k15file,'rU')
MeasRecs,SpecRecs,AnisRecs,ResRecs=[],[],[],[]
# read in data
MeasRec,SpecRec,SampRec,SiteRec,AnisRec,ResRec={},{},{},{},{},{}
for line in input.readlines():
linecnt+=1
rec=line.split()
if linecnt==1:
MeasRec["magic_method_codes"]=""
SpecRec["magic_method_codes"]=""
SampRec["magic_method_codes"]=""
AnisRec["magic_method_codes"]=""
SiteRec["magic_method_codes"]=""
ResRec["magic_smethod_codes"]=""
MeasRec["magic_software_packages"]=version_num
SpecRec["magic_software_packages"]=version_num
SampRec["magic_software_packages"]=version_num
AnisRec["magic_software_packages"]=version_num
SiteRec["magic_software_packages"]=version_num
ResRec["magic_software_packages"]=version_num
MeasRec["magic_method_codes"]="LP-X"
MeasRec["measurement_flag"]="g"
MeasRec["measurement_standard"]="u"
MeasRec["er_citation_names"]="This study"
SpecRec["er_citation_names"]="This study"
SampRec["er_citation_names"]="This study"
AnisRec["er_citation_names"]="This study"
ResRec["er_citation_names"]="This study"
MeasRec["er_specimen_name"]=rec[0]
MeasRec["magic_experiment_name"]=rec[0]+":LP-AN-MS"
AnisRec["magic_experiment_names"]=rec[0]+":AMS"
ResRec["magic_experiment_names"]=rec[0]+":AMS"
SpecRec["er_specimen_name"]=rec[0]
AnisRec["er_specimen_name"]=rec[0]
SampRec["er_specimen_name"]=rec[0]
ResRec["rmag_result_name"]=rec[0]
if specnum!=0: MeasRec["er_sample_name"]=rec[0][:specnum]
if specnum==0: MeasRec["er_sample_name"]=rec[0]
SampRec["er_sample_name"]=MeasRec["er_sample_name"]
SpecRec["er_sample_name"]=MeasRec["er_sample_name"]
AnisRec["er_sample_name"]=MeasRec["er_sample_name"]
ResRec["er_sample_names"]=MeasRec["er_sample_name"]
if samp_con=="6":
for samp in Samps:
if samp['er_sample_name']==AnisRec["er_sample_name"]:
sitename=samp['er_site_name']
er_location_name=samp['er_location_name']
elif samp_con!="":
sitename=pmag.parse_site(AnisRec['er_sample_name'],samp_con,Z)
MeasRec["er_site_name"]=sitename
MeasRec["er_location_name"]=er_location_name
SampRec["er_site_name"]=MeasRec["er_site_name"]
SpecRec["er_site_name"]=MeasRec["er_site_name"]
AnisRec["er_site_name"]=MeasRec["er_site_name"]
ResRec["er_site_names"]=MeasRec["er_site_name"]
SampRec["er_location_name"]=MeasRec["er_location_name"]
SpecRec["er_location_name"]=MeasRec["er_location_name"]
AnisRec["er_location_name"]=MeasRec["er_location_name"]
ResRec["er_location_names"]=MeasRec["er_location_name"]
if len(rec)>=3:
SampRec["sample_azimuth"],SampRec["sample_dip"]=rec[1],rec[2]
az,pl,igeo=float(rec[1]),float(rec[2]),1
if len(rec)==5:
SampRec["sample_bed_dip_direction"],SampRec["sample_bed_dip"]= '(%7.1f)'%(90.+float(rec[3])),(rec[4])
bed_az,bed_dip,itilt,igeo=90.+float(rec[3]),float(rec[4]),1,1
else:
for i in range(5):
k15.append(1e-6*float(rec[i])) # assume measurements in micro SI
if linecnt==4:
sbar,sigma,bulk=pmag.dok15_s(k15)
hpars=pmag.dohext(9,sigma,sbar)
MeasRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
for i in range(15):
NewMeas=copy.deepcopy(MeasRec)
NewMeas["measurement_orient_phi"]='%7.1f' %(Decs[i])
NewMeas["measurement_orient_theta"]='%7.1f'% (Incs[i])
NewMeas["measurement_chi_volume"]='%12.10f'% (k15[i])
NewMeas["measurement_number"]='%i'% (i+1)
NewMeas["magic_experiment_name"]=rec[0]+":LP-AN-MS"
MeasRecs.append(NewMeas)
if SampRec['er_sample_name'] not in samplist:
SampRecs.append(SampRec)
samplist.append(SampRec['er_sample_name'])
SpecRecs.append(SpecRec)
AnisRec["anisotropy_type"]="AMS"
ResRec["anisotropy_type"]="AMS"
AnisRec["anisotropy_s1"]='%12.10f'%(sbar[0])
AnisRec["anisotropy_s2"]='%12.10f'%(sbar[1])
AnisRec["anisotropy_s3"]='%12.10f'%(sbar[2])
AnisRec["anisotropy_s4"]='%12.10f'%(sbar[3])
AnisRec["anisotropy_s5"]='%12.10f'%(sbar[4])
AnisRec["anisotropy_s6"]='%12.10f'%(sbar[5])
AnisRec["anisotropy_mean"]='%12.10f'%(bulk)
AnisRec["anisotropy_sigma"]='%12.10f'%(sigma)
AnisRec["anisotropy_unit"]='SI'
AnisRec["anisotropy_n"]='15'
AnisRec["anisotropy_tilt_correction"]='-1'
AnisRec["magic_method_codes"]='LP-X:AE-H:LP-AN-MS'
AnisRecs.append(AnisRec)
ResRec["magic_method_codes"]='LP-X:AE-H:LP-AN-MS'
ResRec["anisotropy_tilt_correction"]='-1'
ResRec["anisotropy_t1"]='%12.10f'%(hpars['t1'])
ResRec["anisotropy_t2"]='%12.10f'%(hpars['t2'])
ResRec["anisotropy_t3"]='%12.10f'%(hpars['t3'])
ResRec["anisotropy_fest"]='%12.10f'%(hpars['F'])
ResRec["anisotropy_ftest12"]='%12.10f'%(hpars['F12'])
ResRec["anisotropy_ftest23"]='%12.10f'%(hpars['F23'])
ResRec["anisotropy_v1_dec"]='%7.1f'%(hpars['v1_dec'])
ResRec["anisotropy_v2_dec"]='%7.1f'%(hpars['v2_dec'])
ResRec["anisotropy_v3_dec"]='%7.1f'%(hpars['v3_dec'])
ResRec["anisotropy_v1_inc"]='%7.1f'%(hpars['v1_inc'])
ResRec["anisotropy_v2_inc"]='%7.1f'%(hpars['v2_inc'])
ResRec["anisotropy_v3_inc"]='%7.1f'%(hpars['v3_inc'])
ResRec['anisotropy_v1_eta_dec']=ResRec['anisotropy_v2_dec']
ResRec['anisotropy_v1_eta_inc']=ResRec['anisotropy_v2_inc']
ResRec['anisotropy_v1_zeta_dec']=ResRec['anisotropy_v3_dec']
ResRec['anisotropy_v1_zeta_inc']=ResRec['anisotropy_v3_inc']
ResRec['anisotropy_v2_eta_dec']=ResRec['anisotropy_v1_dec']
ResRec['anisotropy_v2_eta_inc']=ResRec['anisotropy_v1_inc']
ResRec['anisotropy_v2_zeta_dec']=ResRec['anisotropy_v3_dec']
ResRec['anisotropy_v2_zeta_inc']=ResRec['anisotropy_v3_inc']
ResRec['anisotropy_v3_eta_dec']=ResRec['anisotropy_v1_dec']
ResRec['anisotropy_v3_eta_inc']=ResRec['anisotropy_v1_inc']
ResRec['anisotropy_v3_zeta_dec']=ResRec['anisotropy_v2_dec']
ResRec['anisotropy_v3_zeta_inc']=ResRec['anisotropy_v2_inc']
ResRec["anisotropy_v1_eta_semi_angle"]='%7.1f'%(hpars['e12'])
ResRec["anisotropy_v1_zeta_semi_angle"]='%7.1f'%(hpars['e13'])
ResRec["anisotropy_v2_eta_semi_angle"]='%7.1f'%(hpars['e12'])
ResRec["anisotropy_v2_zeta_semi_angle"]='%7.1f'%(hpars['e23'])
ResRec["anisotropy_v3_eta_semi_angle"]='%7.1f'%(hpars['e13'])
ResRec["anisotropy_v3_zeta_semi_angle"]='%7.1f'%(hpars['e23'])
ResRec["result_description"]='Critical F: '+hpars["F_crit"]+';Critical F12/F13: '+hpars["F12_crit"]
ResRecs.append(ResRec)
if igeo==1:
sbarg=pmag.dosgeo(sbar,az,pl)
hparsg=pmag.dohext(9,sigma,sbarg)
AnisRecG=copy.copy(AnisRec)
ResRecG=copy.copy(ResRec)
AnisRecG["anisotropy_s1"]='%12.10f'%(sbarg[0])
AnisRecG["anisotropy_s2"]='%12.10f'%(sbarg[1])
AnisRecG["anisotropy_s3"]='%12.10f'%(sbarg[2])
AnisRecG["anisotropy_s4"]='%12.10f'%(sbarg[3])
AnisRecG["anisotropy_s5"]='%12.10f'%(sbarg[4])
AnisRecG["anisotropy_s6"]='%12.10f'%(sbarg[5])
AnisRecG["anisotropy_tilt_correction"]='0'
ResRecG["anisotropy_tilt_correction"]='0'
ResRecG["anisotropy_v1_dec"]='%7.1f'%(hparsg['v1_dec'])
ResRecG["anisotropy_v2_dec"]='%7.1f'%(hparsg['v2_dec'])
ResRecG["anisotropy_v3_dec"]='%7.1f'%(hparsg['v3_dec'])
ResRecG["anisotropy_v1_inc"]='%7.1f'%(hparsg['v1_inc'])
ResRecG["anisotropy_v2_inc"]='%7.1f'%(hparsg['v2_inc'])
ResRecG["anisotropy_v3_inc"]='%7.1f'%(hparsg['v3_inc'])
ResRecG['anisotropy_v1_eta_dec']=ResRecG['anisotropy_v2_dec']
ResRecG['anisotropy_v1_eta_inc']=ResRecG['anisotropy_v2_inc']
ResRecG['anisotropy_v1_zeta_dec']=ResRecG['anisotropy_v3_dec']
ResRecG['anisotropy_v1_zeta_inc']=ResRecG['anisotropy_v3_inc']
ResRecG['anisotropy_v2_eta_dec']=ResRecG['anisotropy_v1_dec']
ResRecG['anisotropy_v2_eta_inc']=ResRecG['anisotropy_v1_inc']
ResRecG['anisotropy_v2_zeta_dec']=ResRecG['anisotropy_v3_dec']
ResRecG['anisotropy_v2_zeta_inc']=ResRecG['anisotropy_v3_inc']
ResRecG['anisotropy_v3_eta_dec']=ResRecG['anisotropy_v1_dec']
ResRecG['anisotropy_v3_eta_inc']=ResRecG['anisotropy_v1_inc']
ResRecG['anisotropy_v3_zeta_dec']=ResRecG['anisotropy_v2_dec']
ResRecG['anisotropy_v3_zeta_inc']=ResRecG['anisotropy_v2_inc']
ResRecG["result_description"]='Critical F: '+hpars["F_crit"]+';Critical F12/F13: '+hpars["F12_crit"]
ResRecs.append(ResRecG)
AnisRecs.append(AnisRecG)
if itilt==1:
sbart=pmag.dostilt(sbarg,bed_az,bed_dip)
hparst=pmag.dohext(9,sigma,sbart)
AnisRecT=copy.copy(AnisRec)
ResRecT=copy.copy(ResRec)
AnisRecT["anisotropy_s1"]='%12.10f'%(sbart[0])
AnisRecT["anisotropy_s2"]='%12.10f'%(sbart[1])
AnisRecT["anisotropy_s3"]='%12.10f'%(sbart[2])
AnisRecT["anisotropy_s4"]='%12.10f'%(sbart[3])
AnisRecT["anisotropy_s5"]='%12.10f'%(sbart[4])
AnisRecT["anisotropy_s6"]='%12.10f'%(sbart[5])
AnisRecT["anisotropy_tilt_correction"]='100'
ResRecT["anisotropy_v1_dec"]='%7.1f'%(hparst['v1_dec'])
ResRecT["anisotropy_v2_dec"]='%7.1f'%(hparst['v2_dec'])
ResRecT["anisotropy_v3_dec"]='%7.1f'%(hparst['v3_dec'])
ResRecT["anisotropy_v1_inc"]='%7.1f'%(hparst['v1_inc'])
ResRecT["anisotropy_v2_inc"]='%7.1f'%(hparst['v2_inc'])
ResRecT["anisotropy_v3_inc"]='%7.1f'%(hparst['v3_inc'])
ResRecT['anisotropy_v1_eta_dec']=ResRecT['anisotropy_v2_dec']
ResRecT['anisotropy_v1_eta_inc']=ResRecT['anisotropy_v2_inc']
ResRecT['anisotropy_v1_zeta_dec']=ResRecT['anisotropy_v3_dec']
ResRecT['anisotropy_v1_zeta_inc']=ResRecT['anisotropy_v3_inc']
ResRecT['anisotropy_v2_eta_dec']=ResRecT['anisotropy_v1_dec']
ResRecT['anisotropy_v2_eta_inc']=ResRecT['anisotropy_v1_inc']
ResRecT['anisotropy_v2_zeta_dec']=ResRecT['anisotropy_v3_dec']
ResRecT['anisotropy_v2_zeta_inc']=ResRecT['anisotropy_v3_inc']
ResRecT['anisotropy_v3_eta_dec']=ResRecT['anisotropy_v1_dec']
ResRecT['anisotropy_v3_eta_inc']=ResRecT['anisotropy_v1_inc']
ResRecT['anisotropy_v3_zeta_dec']=ResRecT['anisotropy_v2_dec']
ResRecT['anisotropy_v3_zeta_inc']=ResRecT['anisotropy_v2_inc']
ResRecT["anisotropy_tilt_correction"]='100'
ResRecT["result_description"]='Critical F: '+hpars["F_crit"]+';Critical F12/F13: '+hpars["F12_crit"]
ResRecs.append(ResRecT)
AnisRecs.append(AnisRecT)
k15,linecnt=[],0
MeasRec,SpecRec,SampRec,SiteRec,AnisRec={},{},{},{},{}
pmag.magic_write(sampfile,SampRecs,'er_samples')
pmag.magic_write(anisfile,AnisRecs,'rmag_anisotropy')
pmag.magic_write(resfile,ResRecs,'rmag_results')
pmag.magic_write(measfile,MeasRecs,'magic_measurements')
print "Data saved to: ",sampfile,anisfile,resfile,measfile
def main():
"""
NAME
aniso_magic.py
DESCRIPTION
plots anisotropy data with either bootstrap or hext ellipses
SYNTAX
aniso_magic.py [-h] [command line options]
OPTIONS
-h plots help message and quits
-usr USER: set the user name
-f AFILE, specify rmag_anisotropy formatted file for input
-F RFILE, specify rmag_results formatted file for output
-x Hext [1963] and bootstrap
-B DON'T do bootstrap, do Hext
-par Tauxe [1998] parametric bootstrap
-v plot bootstrap eigenvectors instead of ellipses
-sit plot by site instead of entire file
-crd [s,g,t] coordinate system, default is specimen (g=geographic, t=tilt corrected)
-P don't make any plots - just make rmag_results table
-sav don't make the rmag_results table - just save all the plots
-fmt [svg, jpg, eps] format for output images, pdf default
-gtc DEC INC dec,inc of pole to great circle [down(up) in green (cyan)
-d Vi DEC INC; Vi (1,2,3) to compare to direction DEC INC
-nb N; specifies the number of bootstraps - default is 1000
DEFAULTS
AFILE: rmag_anisotropy.txt
RFILE: rmag_results.txt
plot bootstrap ellipses of Constable & Tauxe [1987]
NOTES
minor axis: circles
major axis: triangles
principal axis: squares
directions are plotted on the lower hemisphere
for bootstrapped eigenvector components: Xs: blue, Ys: red, Zs: black
"""
#
dir_path = "."
version_num = pmag.get_version()
verbose = pmagplotlib.verbose
args = sys.argv
ipar, ihext, ivec, iboot, imeas, isite, iplot, vec = 0, 0, 0, 1, 1, 0, 1, 0
hpars, bpars, PDir = [], [], []
CS, crd = "-1", "s"
nb = 1000
fmt = "pdf"
ResRecs = []
orlist = []
outfile, comp, Dir, gtcirc, PDir = "rmag_results.txt", 0, [], 0, []
infile = "rmag_anisotropy.txt"
if "-h" in args:
print main.__doc__
sys.exit()
if "-WD" in args:
ind = args.index("-WD")
dir_path = args[ind + 1]
if "-nb" in args:
ind = args.index("-nb")
nb = int(args[ind + 1])
if "-usr" in args:
ind = args.index("-usr")
user = args[ind + 1]
else:
user = ""
if "-B" in args:
iboot, ihext = 0, 1
if "-par" in args:
ipar = 1
if "-x" in args:
ihext = 1
if "-v" in args:
ivec = 1
if "-sit" in args:
isite = 1
if "-P" in args:
iplot = 0
if "-f" in args:
ind = args.index("-f")
infile = args[ind + 1]
if "-F" in args:
ind = args.index("-F")
outfile = args[ind + 1]
if "-crd" in sys.argv:
ind = sys.argv.index("-crd")
crd = sys.argv[ind + 1]
if crd == "g":
CS = "0"
if crd == "t":
CS = "100"
if "-fmt" in args:
ind = args.index("-fmt")
fmt = args[ind + 1]
if "-sav" in args:
plots = 1
verbose = 0
else:
plots = 0
if "-gtc" in args:
ind = args.index("-gtc")
d, i = float(args[ind + 1]), float(args[ind + 2])
PDir.append(d)
PDir.append(i)
if "-d" in args:
comp = 1
ind = args.index("-d")
vec = int(args[ind + 1]) - 1
Dir = [float(args[ind + 2]), float(args[ind + 3])]
#
# set up plots
#
if infile[0] != "/":
infile = dir_path + "/" + infile
if outfile[0] != "/":
outfile = dir_path + "/" + outfile
ANIS = {}
initcdf, inittcdf = 0, 0
ANIS["data"], ANIS["conf"] = 1, 2
if iboot == 1:
ANIS["tcdf"] = 3
if iplot == 1:
inittcdf = 1
pmagplotlib.plot_init(ANIS["tcdf"], 5, 5)
if comp == 1 and iplot == 1:
initcdf = 1
ANIS["vxcdf"], ANIS["vycdf"], ANIS["vzcdf"] = 4, 5, 6
pmagplotlib.plot_init(ANIS["vxcdf"], 5, 5)
pmagplotlib.plot_init(ANIS["vycdf"], 5, 5)
pmagplotlib.plot_init(ANIS["vzcdf"], 5, 5)
if iplot == 1:
pmagplotlib.plot_init(ANIS["conf"], 5, 5)
pmagplotlib.plot_init(ANIS["data"], 5, 5)
# read in the data
data, ifiletype = pmag.magic_read(infile)
for rec in data: # find all the orientation systems
if "anisotropy_tilt_correction" not in rec.keys():
rec["anisotropy_tilt_correction"] = "-1"
if rec["anisotropy_tilt_correction"] not in orlist:
orlist.append(rec["anisotropy_tilt_correction"])
if CS not in orlist:
if len(orlist) > 0:
CS = orlist[0]
else:
CS = "-1"
if CS == "-1":
crd = "s"
if CS == "0":
crd = "g"
if CS == "100":
crd = "t"
if verbose:
print "desired coordinate system not available, using available: ", crd
if isite == 1:
sitelist = []
for rec in data:
if rec["er_site_name"] not in sitelist:
sitelist.append(rec["er_site_name"])
sitelist.sort()
plt = len(sitelist)
else:
plt = 1
k = 0
while k < plt:
site = ""
sdata, Ss = [], [] # list of S format data
Locs, Sites, Samples, Specimens, Cits = [], [], [], [], []
if isite == 0:
sdata = data
else:
site = sitelist[k]
for rec in data:
if rec["er_site_name"] == site:
sdata.append(rec)
anitypes = []
csrecs = pmag.get_dictitem(sdata, "anisotropy_tilt_correction", CS, "T")
for rec in csrecs:
if rec["anisotropy_type"] not in anitypes:
anitypes.append(rec["anisotropy_type"])
if rec["er_location_name"] not in Locs:
Locs.append(rec["er_location_name"])
if rec["er_site_name"] not in Sites:
Sites.append(rec["er_site_name"])
if rec["er_sample_name"] not in Samples:
Samples.append(rec["er_sample_name"])
if rec["er_specimen_name"] not in Specimens:
Specimens.append(rec["er_specimen_name"])
if rec["er_citation_names"] not in Cits:
Cits.append(rec["er_citation_names"])
s = []
s.append(float(rec["anisotropy_s1"]))
s.append(float(rec["anisotropy_s2"]))
s.append(float(rec["anisotropy_s3"]))
s.append(float(rec["anisotropy_s4"]))
s.append(float(rec["anisotropy_s5"]))
s.append(float(rec["anisotropy_s6"]))
if s[0] <= 1.0:
Ss.append(s) # protect against crap
# tau,Vdirs=pmag.doseigs(s)
fpars = pmag.dohext(int(rec["anisotropy_n"]) - 6, float(rec["anisotropy_sigma"]), s)
ResRec = {}
ResRec["er_location_names"] = rec["er_location_name"]
ResRec["er_citation_names"] = rec["er_citation_names"]
ResRec["er_site_names"] = rec["er_site_name"]
ResRec["er_sample_names"] = rec["er_sample_name"]
ResRec["er_specimen_names"] = rec["er_specimen_name"]
ResRec["rmag_result_name"] = rec["er_specimen_name"] + ":" + rec["anisotropy_type"]
ResRec["er_analyst_mail_names"] = user
ResRec["tilt_correction"] = CS
ResRec["anisotropy_type"] = rec["anisotropy_type"]
ResRec["anisotropy_v1_dec"] = "%7.1f" % (fpars["v1_dec"])
ResRec["anisotropy_v2_dec"] = "%7.1f" % (fpars["v2_dec"])
ResRec["anisotropy_v3_dec"] = "%7.1f" % (fpars["v3_dec"])
ResRec["anisotropy_v1_inc"] = "%7.1f" % (fpars["v1_inc"])
ResRec["anisotropy_v2_inc"] = "%7.1f" % (fpars["v2_inc"])
ResRec["anisotropy_v3_inc"] = "%7.1f" % (fpars["v3_inc"])
ResRec["anisotropy_t1"] = "%10.8f" % (fpars["t1"])
ResRec["anisotropy_t2"] = "%10.8f" % (fpars["t2"])
ResRec["anisotropy_t3"] = "%10.8f" % (fpars["t3"])
ResRec["anisotropy_ftest"] = "%10.3f" % (fpars["F"])
ResRec["anisotropy_ftest12"] = "%10.3f" % (fpars["F12"])
ResRec["anisotropy_ftest23"] = "%10.3f" % (fpars["F23"])
ResRec["result_description"] = "F_crit: " + fpars["F_crit"] + "; F12,F23_crit: " + fpars["F12_crit"]
ResRec["anisotropy_type"] = pmag.makelist(anitypes)
ResRecs.append(ResRec)
if len(Ss) > 1:
title = "LO:_" + ResRec["er_location_names"] + "_SI:_" + site + "_SA:__SP:__CO:_" + crd
ResRec["er_location_names"] = pmag.makelist(Locs)
bpars, hpars = pmagplotlib.plotANIS(ANIS, Ss, iboot, ihext, ivec, ipar, title, iplot, comp, vec, Dir, nb)
if len(PDir) > 0:
pmagplotlib.plotC(ANIS["data"], PDir, 90.0, "g")
pmagplotlib.plotC(ANIS["conf"], PDir, 90.0, "g")
if verbose and plots == 0:
pmagplotlib.drawFIGS(ANIS)
ResRec["er_location_names"] = pmag.makelist(Locs)
if plots == 1:
save(ANIS, fmt, title)
ResRec = {}
ResRec["er_citation_names"] = pmag.makelist(Cits)
ResRec["er_location_names"] = pmag.makelist(Locs)
ResRec["er_site_names"] = pmag.makelist(Sites)
ResRec["er_sample_names"] = pmag.makelist(Samples)
ResRec["er_specimen_names"] = pmag.makelist(Specimens)
ResRec["rmag_result_name"] = pmag.makelist(Sites) + ":" + pmag.makelist(anitypes)
ResRec["anisotropy_type"] = pmag.makelist(anitypes)
ResRec["er_analyst_mail_names"] = user
ResRec["tilt_correction"] = CS
if isite == "0":
ResRec["result_description"] = "Study average using coordinate system: " + CS
if isite == "1":
ResRec["result_description"] = "Site average using coordinate system: " + CS
if hpars != [] and ihext == 1:
HextRec = {}
for key in ResRec.keys():
HextRec[key] = ResRec[key] # copy over stuff
HextRec["anisotropy_v1_dec"] = "%7.1f" % (hpars["v1_dec"])
HextRec["anisotropy_v2_dec"] = "%7.1f" % (hpars["v2_dec"])
HextRec["anisotropy_v3_dec"] = "%7.1f" % (hpars["v3_dec"])
HextRec["anisotropy_v1_inc"] = "%7.1f" % (hpars["v1_inc"])
HextRec["anisotropy_v2_inc"] = "%7.1f" % (hpars["v2_inc"])
HextRec["anisotropy_v3_inc"] = "%7.1f" % (hpars["v3_inc"])
HextRec["anisotropy_t1"] = "%10.8f" % (hpars["t1"])
HextRec["anisotropy_t2"] = "%10.8f" % (hpars["t2"])
HextRec["anisotropy_t3"] = "%10.8f" % (hpars["t3"])
HextRec["anisotropy_hext_F"] = "%7.1f " % (hpars["F"])
HextRec["anisotropy_hext_F12"] = "%7.1f " % (hpars["F12"])
HextRec["anisotropy_hext_F23"] = "%7.1f " % (hpars["F23"])
HextRec["anisotropy_v1_eta_semi_angle"] = "%7.1f " % (hpars["e12"])
HextRec["anisotropy_v1_eta_dec"] = "%7.1f " % (hpars["v2_dec"])
HextRec["anisotropy_v1_eta_inc"] = "%7.1f " % (hpars["v2_inc"])
HextRec["anisotropy_v1_zeta_semi_angle"] = "%7.1f " % (hpars["e13"])
HextRec["anisotropy_v1_zeta_dec"] = "%7.1f " % (hpars["v3_dec"])
HextRec["anisotropy_v1_zeta_inc"] = "%7.1f " % (hpars["v3_inc"])
HextRec["anisotropy_v2_eta_semi_angle"] = "%7.1f " % (hpars["e12"])
HextRec["anisotropy_v2_eta_dec"] = "%7.1f " % (hpars["v1_dec"])
HextRec["anisotropy_v2_eta_inc"] = "%7.1f " % (hpars["v1_inc"])
HextRec["anisotropy_v2_zeta_semi_angle"] = "%7.1f " % (hpars["e23"])
HextRec["anisotropy_v2_zeta_dec"] = "%7.1f " % (hpars["v3_dec"])
HextRec["anisotropy_v2_zeta_inc"] = "%7.1f " % (hpars["v3_inc"])
HextRec["anisotropy_v3_eta_semi_angle"] = "%7.1f " % (hpars["e12"])
HextRec["anisotropy_v3_eta_dec"] = "%7.1f " % (hpars["v1_dec"])
HextRec["anisotropy_v3_eta_inc"] = "%7.1f " % (hpars["v1_inc"])
HextRec["anisotropy_v3_zeta_semi_angle"] = "%7.1f " % (hpars["e23"])
HextRec["anisotropy_v3_zeta_dec"] = "%7.1f " % (hpars["v2_dec"])
HextRec["anisotropy_v3_zeta_inc"] = "%7.1f " % (hpars["v2_inc"])
HextRec["magic_method_codes"] = "LP-AN:AE-H"
if verbose:
print "Hext Statistics: "
print " tau_i, V_i_D, V_i_I, V_i_zeta, V_i_zeta_D, V_i_zeta_I, V_i_eta, V_i_eta_D, V_i_eta_I"
print HextRec["anisotropy_t1"], HextRec["anisotropy_v1_dec"], HextRec["anisotropy_v1_inc"], HextRec[
"anisotropy_v1_eta_semi_angle"
], HextRec["anisotropy_v1_eta_dec"], HextRec["anisotropy_v1_eta_inc"], HextRec[
"anisotropy_v1_zeta_semi_angle"
], HextRec[
"anisotropy_v1_zeta_dec"
], HextRec[
"anisotropy_v1_zeta_inc"
]
print HextRec["anisotropy_t2"], HextRec["anisotropy_v2_dec"], HextRec["anisotropy_v2_inc"], HextRec[
"anisotropy_v2_eta_semi_angle"
], HextRec["anisotropy_v2_eta_dec"], HextRec["anisotropy_v2_eta_inc"], HextRec[
"anisotropy_v2_zeta_semi_angle"
], HextRec[
"anisotropy_v2_zeta_dec"
], HextRec[
"anisotropy_v2_zeta_inc"
]
print HextRec["anisotropy_t3"], HextRec["anisotropy_v3_dec"], HextRec["anisotropy_v3_inc"], HextRec[
"anisotropy_v3_eta_semi_angle"
], HextRec["anisotropy_v3_eta_dec"], HextRec["anisotropy_v3_eta_inc"], HextRec[
"anisotropy_v3_zeta_semi_angle"
], HextRec[
"anisotropy_v3_zeta_dec"
], HextRec[
"anisotropy_v3_zeta_inc"
]
HextRec["magic_software_packages"] = version_num
ResRecs.append(HextRec)
if bpars != []:
BootRec = {}
for key in ResRec.keys():
BootRec[key] = ResRec[key] # copy over stuff
BootRec["anisotropy_v1_dec"] = "%7.1f" % (bpars["v1_dec"])
BootRec["anisotropy_v2_dec"] = "%7.1f" % (bpars["v2_dec"])
BootRec["anisotropy_v3_dec"] = "%7.1f" % (bpars["v3_dec"])
BootRec["anisotropy_v1_inc"] = "%7.1f" % (bpars["v1_inc"])
BootRec["anisotropy_v2_inc"] = "%7.1f" % (bpars["v2_inc"])
BootRec["anisotropy_v3_inc"] = "%7.1f" % (bpars["v3_inc"])
BootRec["anisotropy_t1"] = "%10.8f" % (bpars["t1"])
BootRec["anisotropy_t2"] = "%10.8f" % (bpars["t2"])
BootRec["anisotropy_t3"] = "%10.8f" % (bpars["t3"])
BootRec["anisotropy_v1_eta_inc"] = "%7.1f " % (bpars["v1_eta_inc"])
BootRec["anisotropy_v1_eta_dec"] = "%7.1f " % (bpars["v1_eta_dec"])
BootRec["anisotropy_v1_eta_semi_angle"] = "%7.1f " % (bpars["v1_eta"])
BootRec["anisotropy_v1_zeta_inc"] = "%7.1f " % (bpars["v1_zeta_inc"])
BootRec["anisotropy_v1_zeta_dec"] = "%7.1f " % (bpars["v1_zeta_dec"])
BootRec["anisotropy_v1_zeta_semi_angle"] = "%7.1f " % (bpars["v1_zeta"])
BootRec["anisotropy_v2_eta_inc"] = "%7.1f " % (bpars["v2_eta_inc"])
BootRec["anisotropy_v2_eta_dec"] = "%7.1f " % (bpars["v2_eta_dec"])
BootRec["anisotropy_v2_eta_semi_angle"] = "%7.1f " % (bpars["v2_eta"])
BootRec["anisotropy_v2_zeta_inc"] = "%7.1f " % (bpars["v2_zeta_inc"])
BootRec["anisotropy_v2_zeta_dec"] = "%7.1f " % (bpars["v2_zeta_dec"])
BootRec["anisotropy_v2_zeta_semi_angle"] = "%7.1f " % (bpars["v2_zeta"])
BootRec["anisotropy_v3_eta_inc"] = "%7.1f " % (bpars["v3_eta_inc"])
BootRec["anisotropy_v3_eta_dec"] = "%7.1f " % (bpars["v3_eta_dec"])
BootRec["anisotropy_v3_eta_semi_angle"] = "%7.1f " % (bpars["v3_eta"])
BootRec["anisotropy_v3_zeta_inc"] = "%7.1f " % (bpars["v3_zeta_inc"])
BootRec["anisotropy_v3_zeta_dec"] = "%7.1f " % (bpars["v3_zeta_dec"])
BootRec["anisotropy_v3_zeta_semi_angle"] = "%7.1f " % (bpars["v3_zeta"])
BootRec["anisotropy_hext_F"] = ""
BootRec["anisotropy_hext_F12"] = ""
BootRec["anisotropy_hext_F23"] = ""
BootRec["magic_method_codes"] = "LP-AN:AE-H:AE-BS" # regular bootstrap
if ipar == 1:
BootRec["magic_method_codes"] = "LP-AN:AE-H:AE-BS-P" # parametric bootstrap
if verbose:
print "Boostrap Statistics: "
print " tau_i, V_i_D, V_i_I, V_i_zeta, V_i_zeta_D, V_i_zeta_I, V_i_eta, V_i_eta_D, V_i_eta_I"
print BootRec["anisotropy_t1"], BootRec["anisotropy_v1_dec"], BootRec["anisotropy_v1_inc"], BootRec[
"anisotropy_v1_eta_semi_angle"
], BootRec["anisotropy_v1_eta_dec"], BootRec["anisotropy_v1_eta_inc"], BootRec[
"anisotropy_v1_zeta_semi_angle"
], BootRec[
"anisotropy_v1_zeta_dec"
], BootRec[
"anisotropy_v1_zeta_inc"
]
print BootRec["anisotropy_t2"], BootRec["anisotropy_v2_dec"], BootRec["anisotropy_v2_inc"], BootRec[
"anisotropy_v2_eta_semi_angle"
], BootRec["anisotropy_v2_eta_dec"], BootRec["anisotropy_v2_eta_inc"], BootRec[
"anisotropy_v2_zeta_semi_angle"
], BootRec[
"anisotropy_v2_zeta_dec"
], BootRec[
"anisotropy_v2_zeta_inc"
]
print BootRec["anisotropy_t3"], BootRec["anisotropy_v3_dec"], BootRec["anisotropy_v3_inc"], BootRec[
"anisotropy_v3_eta_semi_angle"
], BootRec["anisotropy_v3_eta_dec"], BootRec["anisotropy_v3_eta_inc"], BootRec[
"anisotropy_v3_zeta_semi_angle"
], BootRec[
"anisotropy_v3_zeta_dec"
], BootRec[
"anisotropy_v3_zeta_inc"
]
BootRec["magic_software_packages"] = version_num
ResRecs.append(BootRec)
k += 1
goon = 1
while goon == 1 and iplot == 1 and verbose:
if iboot == 1:
print "compare with [d]irection "
print " plot [g]reat circle, change [c]oord. system, change [e]llipse calculation, s[a]ve plots, [q]uit "
if isite == 1:
print " [p]revious, [s]ite, [q]uit, <return> for next "
ans = raw_input("")
if ans == "q":
sys.exit()
if ans == "e":
iboot, ipar, ihext, ivec = 1, 0, 0, 0
e = raw_input("Do Hext Statistics 1/[0]: ")
if e == "1":
ihext = 1
e = raw_input("Suppress bootstrap 1/[0]: ")
if e == "1":
iboot = 0
if iboot == 1:
e = raw_input("Parametric bootstrap 1/[0]: ")
if e == "1":
ipar = 1
e = raw_input("Plot bootstrap eigenvectors: 1/[0]: ")
if e == "1":
ivec = 1
if iplot == 1:
if inittcdf == 0:
ANIS["tcdf"] = 3
pmagplotlib.plot_init(ANIS["tcdf"], 5, 5)
inittcdf = 1
bpars, hpars = pmagplotlib.plotANIS(
ANIS, Ss, iboot, ihext, ivec, ipar, title, iplot, comp, vec, Dir, nb
)
if verbose and plots == 0:
pmagplotlib.drawFIGS(ANIS)
if ans == "c":
print "Current Coordinate system is: "
if CS == "-1":
print " Specimen"
if CS == "0":
print " Geographic"
if CS == "100":
print " Tilt corrected"
key = raw_input(" Enter desired coordinate system: [s]pecimen, [g]eographic, [t]ilt corrected ")
if key == "s":
CS = "-1"
if key == "g":
CS = "0"
if key == "t":
CS = "100"
if CS not in orlist:
if len(orlist) > 0:
CS = orlist[0]
else:
CS = "-1"
if CS == "-1":
crd = "s"
if CS == "0":
crd = "g"
if CS == "100":
crd = "t"
print "desired coordinate system not available, using available: ", crd
k -= 1
goon = 0
if ans == "":
if isite == 1:
goon = 0
else:
print "Good bye "
sys.exit()
if ans == "d":
if initcdf == 0:
initcdf = 1
ANIS["vxcdf"], ANIS["vycdf"], ANIS["vzcdf"] = 4, 5, 6
pmagplotlib.plot_init(ANIS["vxcdf"], 5, 5)
pmagplotlib.plot_init(ANIS["vycdf"], 5, 5)
pmagplotlib.plot_init(ANIS["vzcdf"], 5, 5)
Dir, comp = [], 1
print """
Input: Vi D I to compare eigenvector Vi with direction D/I
where Vi=1: principal
Vi=2: major
Vi=3: minor
D= declination of comparison direction
I= inclination of comparison direction"""
con = 1
while con == 1:
try:
vdi = raw_input("Vi D I: ").split()
vec = int(vdi[0]) - 1
Dir = [float(vdi[1]), float(vdi[2])]
con = 0
except IndexError:
print " Incorrect entry, try again "
bpars, hpars = pmagplotlib.plotANIS(
ANIS, Ss, iboot, ihext, ivec, ipar, title, iplot, comp, vec, Dir, nb
)
Dir, comp = [], 0
if ans == "g":
con, cnt = 1, 0
while con == 1:
try:
print " Input: input pole to great circle ( D I) to plot a great circle: "
di = raw_input(" D I: ").split()
PDir.append(float(di[0]))
PDir.append(float(di[1]))
con = 0
except:
cnt += 1
if cnt < 10:
print " enter the dec and inc of the pole on one line "
else:
print "ummm - you are doing something wrong - i give up"
sys.exit()
pmagplotlib.plotC(ANIS["data"], PDir, 90.0, "g")
pmagplotlib.plotC(ANIS["conf"], PDir, 90.0, "g")
if verbose and plots == 0:
pmagplotlib.drawFIGS(ANIS)
if ans == "p":
k -= 2
goon = 0
if ans == "q":
k = plt
goon = 0
if ans == "s":
keepon = 1
site = raw_input(" print site or part of site desired: ")
while keepon == 1:
try:
k = sitelist.index(site)
keepon = 0
except:
tmplist = []
for qq in range(len(sitelist)):
if site in sitelist[qq]:
tmplist.append(sitelist[qq])
print site, " not found, but this was: "
print tmplist
site = raw_input("Select one or try again\n ")
k = sitelist.index(site)
goon, ans = 0, ""
if ans == "a":
locs = pmag.makelist(Locs)
title = "LO:_" + locs + "_SI:__" + "_SA:__SP:__CO:_" + crd
save(ANIS, fmt, title)
goon = 0
else:
if verbose:
print "skipping plot - not enough data points"
k += 1
# put rmag_results stuff here
if len(ResRecs) > 0:
ResOut, keylist = pmag.fillkeys(ResRecs)
pmag.magic_write(outfile, ResOut, "rmag_results")
if verbose:
print " Good bye "
def main():
"""
NAME
aarm_magic.py
DESCRIPTION
Converts AARM data to best-fit tensor (6 elements plus sigma)
Original program ARMcrunch written to accomodate ARM anisotropy data
collected from 6 axial directions (+X,+Y,+Z,-X,-Y,-Z) using the
off-axis remanence terms to construct the tensor. A better way to
do the anisotropy of ARMs is to use 9,12 or 15 measurements in
the Hext rotational scheme.
SYNTAX
aarm_magic.py [-h][command line options]
OPTIONS
-h prints help message and quits
-usr USER: identify user, default is ""
-f FILE: specify input file, default is aarm_measurements.txt
-Fa FILE: specify anisotropy output file, default is rmag_anisotropy.txt
-Fr FILE: specify results output file, default is rmag_results.txt
INPUT
Input for the present program is a series of baseline, ARM pairs.
The baseline should be the AF demagnetized state (3 axis demag is
preferable) for the following ARM acquisition. The order of the
measurements is:
positions 1,2,3, 6,7,8, 11,12,13 (for 9 positions)
positions 1,2,3,4, 6,7,8,9, 11,12,13,14 (for 12 positions)
positions 1-15 (for 15 positions)
"""
# initialize some parameters
args=sys.argv
user=""
meas_file="aarm_measurements.txt"
rmag_anis="rmag_anisotropy.txt"
rmag_res="rmag_results.txt"
dir_path='.'
#
# get name of file from command line
#
if '-WD' in args:
ind=args.index('-WD')
dir_path=args[ind+1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=sys.argv[ind+1]
if "-f" in args:
ind=args.index("-f")
meas_file=sys.argv[ind+1]
if "-Fa" in args:
ind=args.index("-Fa")
rmag_anis=args[ind+1]
if "-Fr" in args:
ind=args.index("-Fr")
rmag_res=args[ind+1]
meas_file=dir_path+'/'+meas_file
rmag_anis=dir_path+'/'+rmag_anis
rmag_res=dir_path+'/'+rmag_res
# read in data
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
#
ssort=[]
for rec in meas_data:
spec=rec["er_specimen_name"]
ssort.append(spec)
ssort.sort()
bak=ssort[0]
#
# get list of unique specimen names
#
sids=[bak]
for s in ssort:
if s != bak:
sids.append(s)
bak=s
#
# work on each specimen
#
specimen=0
RmagSpecRecs,RmagResRecs=[],[]
while specimen < len(sids):
s=sids[specimen]
data=[]
RmagSpecRec={}
RmagResRec={}
method_codes=[]
#
# find the data from the meas_data file for this sample
#
for rec in meas_data:
if rec["er_specimen_name"]==s:
data.append(rec)
#
# find out the number of measurements (9, 12 or 15)
#
npos=len(data)/2
if npos==9:
print 'Processing: ',s, ' Number of positions: ',npos
#
# get dec, inc, int and convert to x,y,z
#
B,H,tmpH=pmag.designAARM(npos) # B matrix made from design matrix for positions
X=[]
for rec in data:
Dir=[]
Dir.append(float(rec["measurement_dec"]))
Dir.append(float(rec["measurement_inc"]))
Dir.append(float(rec["measurement_magn_moment"]))
X.append(pmag.dir2cart(Dir))
#
# subtract baseline and put in a work array
#
work=numpy.zeros((npos,3),'f')
for i in range(npos):
for j in range(3):
work[i][j]=X[2*i+1][j]-X[2*i][j]
#
# calculate tensor elements
# first put ARM components in w vector
#
w=numpy.zeros((npos*3),'f')
index=0
for i in range(npos):
for j in range(3):
w[index]=work[i][j]
index+=1
s=numpy.zeros((6),'f') # initialize the s matrix
for i in range(6):
for j in range(len(w)):
s[i]+=B[i][j]*w[j]
trace=s[0]+s[1]+s[2] # normalize by the trace
for i in range(6):
s[i]=s[i]/trace
a=pmag.s2a(s)
#------------------------------------------------------------
# Calculating dels is different than in the Kappabridge
# routine. Use trace normalized tensor (a) and the applied
# unit field directions (tmpH) to generate model X,Y,Z
# components. Then compare these with the measured values.
#------------------------------------------------------------
S=0.
comp=numpy.zeros((npos*3),'f')
for i in range(npos):
for j in range(3):
index=i*3+j
compare=a[j][0]*tmpH[i][0]+a[j][1]*tmpH[i][1]+a[j][2]*tmpH[i][2]
comp[index]=compare
for i in range(npos*3):
d=w[i]/trace - comp[i] # del values
S+=d*d
nf=float(npos*3-6) # number of degrees of freedom
if S >0:
sigma=math.sqrt(S/nf)
else: sigma=0
hpars=pmag.dohext(nf,sigma,s)
#
# prepare for output
#
RmagSpecRec["rmag_anisotropy_name"]=data[0]["er_specimen_name"]
RmagSpecRec["er_location_name"]=data[0]["er_location_name"]
RmagSpecRec["er_specimen_name"]=data[0]["er_specimen_name"]
RmagSpecRec["er_sample_name"]=data[0]["er_sample_name"]
RmagSpecRec["er_site_name"]=data[0]["er_site_name"]
RmagSpecRec["magic_experiment_names"]=RmagSpecRec["rmag_anisotropy_name"]+":AARM"
RmagSpecRec["er_citation_names"]="This study"
RmagResRec["rmag_result_name"]=data[0]["er_specimen_name"]
RmagResRec["er_location_names"]=data[0]["er_location_name"]
RmagResRec["er_specimen_names"]=data[0]["er_specimen_name"]
RmagResRec["er_sample_names"]=data[0]["er_sample_name"]
RmagResRec["er_site_names"]=data[0]["er_site_name"]
RmagResRec["magic_experiment_names"]=RmagSpecRec["rmag_anisotropy_name"]+":AARM"
RmagResRec["er_citation_names"]="This study"
if "magic_instrument_codes" in data[0].keys():
RmagSpecRec["magic_instrument_codes"]=data[0]["magic_instrument_codes"]
else:
RmagSpecRec["magic_instrument_codes"]=""
RmagSpecRec["anisotropy_type"]="AARM"
RmagSpecRec["anisotropy_description"]="Hext statistics adapted to AARM"
RmagSpecRec["anisotropy_s1"]='%8.6f'%(s[0])
RmagSpecRec["anisotropy_s2"]='%8.6f'%(s[1])
RmagSpecRec["anisotropy_s3"]='%8.6f'%(s[2])
RmagSpecRec["anisotropy_s4"]='%8.6f'%(s[3])
RmagSpecRec["anisotropy_s5"]='%8.6f'%(s[4])
RmagSpecRec["anisotropy_s6"]='%8.6f'%(s[5])
RmagSpecRec["anisotropy_mean"]='%8.3e'%(trace/3)
RmagSpecRec["anisotropy_sigma"]='%8.6f'%(sigma)
RmagSpecRec["anisotropy_unit"]="Am^2"
RmagSpecRec["anisotropy_n"]='%i'%(npos)
RmagSpecRec["anisotropy_tilt_correction"]='-1'
RmagResRec["anisotropy_t1"]='%8.6f '%(hpars["t1"])
RmagResRec["anisotropy_t2"]='%8.6f '%(hpars["t2"])
RmagResRec["anisotropy_t3"]='%8.6f '%(hpars["t3"])
RmagResRec["anisotropy_v1_dec"]='%7.1f '%(hpars["v1_dec"])
RmagResRec["anisotropy_v2_dec"]='%7.1f '%(hpars["v2_dec"])
RmagResRec["anisotropy_v3_dec"]='%7.1f '%(hpars["v3_dec"])
RmagResRec["anisotropy_v1_inc"]='%7.1f '%(hpars["v1_inc"])
RmagResRec["anisotropy_v2_inc"]='%7.1f '%(hpars["v2_inc"])
RmagResRec["anisotropy_v3_inc"]='%7.1f '%(hpars["v3_inc"])
RmagResRec["anisotropy_ftest"]='%7.1f '%(hpars["F"])
RmagResRec["anisotropy_ftest12"]='%7.1f '%(hpars["F12"])
RmagResRec["anisotropy_ftest23"]='%7.1f '%(hpars["F23"])
if hpars["e12"]>hpars["e13"]:
RmagResRec["anisotropy_v1_zeta_semi_angle"]='%7.1f '%(hpars['e12'])
RmagResRec["anisotropy_v1_zeta_dec"]='%7.1f '%(hpars['v2_dec'])
RmagResRec["anisotropy_v1_zeta_inc"]='%7.1f '%(hpars['v2_inc'])
RmagResRec["anisotropy_v2_zeta_semi_angle"]='%7.1f '%(hpars['e12'])
RmagResRec["anisotropy_v2_zeta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v2_zeta_inc"]='%7.1f '%(hpars['v1_inc'])
RmagResRec["anisotropy_v1_eta_semi_angle"]='%7.1f '%(hpars['e13'])
RmagResRec["anisotropy_v1_eta_dec"]='%7.1f '%(hpars['v3_dec'])
RmagResRec["anisotropy_v1_eta_inc"]='%7.1f '%(hpars['v3_inc'])
RmagResRec["anisotropy_v3_eta_semi_angle"]='%7.1f '%(hpars['e13'])
RmagResRec["anisotropy_v3_eta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v3_eta_inc"]='%7.1f '%(hpars['v1_inc'])
else:
RmagResRec["anisotropy_v1_zeta_semi_angle"]='%7.1f '%(hpars['e13'])
RmagResRec["anisotropy_v1_zeta_dec"]='%7.1f '%(hpars['v3_dec'])
RmagResRec["anisotropy_v1_zeta_inc"]='%7.1f '%(hpars['v3_inc'])
RmagResRec["anisotropy_v3_zeta_semi_angle"]='%7.1f '%(hpars['e13'])
RmagResRec["anisotropy_v3_zeta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v3_zeta_inc"]='%7.1f '%(hpars['v1_inc'])
RmagResRec["anisotropy_v1_eta_semi_angle"]='%7.1f '%(hpars['e12'])
RmagResRec["anisotropy_v1_eta_dec"]='%7.1f '%(hpars['v2_dec'])
RmagResRec["anisotropy_v1_eta_inc"]='%7.1f '%(hpars['v2_inc'])
RmagResRec["anisotropy_v2_eta_semi_angle"]='%7.1f '%(hpars['e12'])
RmagResRec["anisotropy_v2_eta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v2_eta_inc"]='%7.1f '%(hpars['v1_inc'])
if hpars["e23"]>hpars['e12']:
RmagResRec["anisotropy_v2_zeta_semi_angle"]='%7.1f '%(hpars['e23'])
RmagResRec["anisotropy_v2_zeta_dec"]='%7.1f '%(hpars['v3_dec'])
RmagResRec["anisotropy_v2_zeta_inc"]='%7.1f '%(hpars['v3_inc'])
RmagResRec["anisotropy_v3_zeta_semi_angle"]='%7.1f '%(hpars['e23'])
RmagResRec["anisotropy_v3_zeta_dec"]='%7.1f '%(hpars['v2_dec'])
RmagResRec["anisotropy_v3_zeta_inc"]='%7.1f '%(hpars['v2_inc'])
RmagResRec["anisotropy_v3_eta_semi_angle"]='%7.1f '%(hpars['e13'])
RmagResRec["anisotropy_v3_eta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v3_eta_inc"]='%7.1f '%(hpars['v1_inc'])
RmagResRec["anisotropy_v2_eta_semi_angle"]='%7.1f '%(hpars['e12'])
RmagResRec["anisotropy_v2_eta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v2_eta_inc"]='%7.1f '%(hpars['v1_inc'])
else:
RmagResRec["anisotropy_v2_zeta_semi_angle"]='%7.1f '%(hpars['e12'])
RmagResRec["anisotropy_v2_zeta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v2_zeta_inc"]='%7.1f '%(hpars['v1_inc'])
RmagResRec["anisotropy_v3_eta_semi_angle"]='%7.1f '%(hpars['e23'])
RmagResRec["anisotropy_v3_eta_dec"]='%7.1f '%(hpars['v2_dec'])
RmagResRec["anisotropy_v3_eta_inc"]='%7.1f '%(hpars['v2_inc'])
RmagResRec["anisotropy_v3_zeta_semi_angle"]='%7.1f '%(hpars['e13'])
RmagResRec["anisotropy_v3_zeta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v3_zeta_inc"]='%7.1f '%(hpars['v1_inc'])
RmagResRec["anisotropy_v2_eta_semi_angle"]='%7.1f '%(hpars['e23'])
RmagResRec["anisotropy_v2_eta_dec"]='%7.1f '%(hpars['v3_dec'])
RmagResRec["anisotropy_v2_eta_inc"]='%7.1f '%(hpars['v3_inc'])
RmagResRec["tilt_correction"]='-1'
RmagResRec["anisotropy_type"]='AARM'
RmagResRec["magic_method_codes"]='LP-AN-ARM:AE-H'
RmagSpecRec["magic_method_codes"]='LP-AN-ARM:AE-H'
RmagResRec["magic_software_packages"]=pmag.get_version()
RmagSpecRec["magic_software_packages"]=pmag.get_version()
specimen+=1
RmagSpecRecs.append(RmagSpecRec)
RmagResRecs.append(RmagResRec)
else:
print npos
print 'skipping specimen ',s,' only 9 positions supported'
specimen+=1
if rmag_anis=="":rmag_anis="rmag_anisotropy.txt"
pmag.magic_write(rmag_anis,RmagSpecRecs,'rmag_anisotropy')
print "specimen tensor elements stored in ",rmag_anis
if rmag_res=="":rmag_res="rmag_results.txt"
pmag.magic_write(rmag_res,RmagResRecs,'rmag_results')
print "specimen statistics and eigenparameters stored in ",rmag_res
def main():
"""
NAME
aarm_magic.py
DESCRIPTION
Converts AARM data to best-fit tensor (6 elements plus sigma)
Original program ARMcrunch written to accomodate ARM anisotropy data
collected from 6 axial directions (+X,+Y,+Z,-X,-Y,-Z) using the
off-axis remanence terms to construct the tensor. A better way to
do the anisotropy of ARMs is to use 9,12 or 15 measurements in
the Hext rotational scheme.
SYNTAX
aarm_magic.py [-h][command line options]
OPTIONS
-h prints help message and quits
-usr USER: identify user, default is ""
-f FILE: specify input file, default is aarm_measurements.txt
-crd [s,g,t] specify coordinate system, requires er_samples.txt file
-fsa FILE: specify er_samples.txt file, default is er_samples.txt
-Fa FILE: specify anisotropy output file, default is arm_anisotropy.txt
-Fr FILE: specify results output file, default is aarm_results.txt
INPUT
Input for the present program is a series of baseline, ARM pairs.
The baseline should be the AF demagnetized state (3 axis demag is
preferable) for the following ARM acquisition. The order of the
measurements is:
positions 1,2,3, 6,7,8, 11,12,13 (for 9 positions)
positions 1,2,3,4, 6,7,8,9, 11,12,13,14 (for 12 positions)
positions 1-15 (for 15 positions)
"""
# initialize some parameters
args=sys.argv
user=""
meas_file="aarm_measurements.txt"
samp_file="er_samples.txt"
rmag_anis="arm_anisotropy.txt"
rmag_res="aarm_results.txt"
dir_path='.'
#
# get name of file from command line
#
if '-WD' in args:
ind=args.index('-WD')
dir_path=args[ind+1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=sys.argv[ind+1]
if "-f" in args:
ind=args.index("-f")
meas_file=sys.argv[ind+1]
coord='-1'
if "-crd" in sys.argv:
ind=sys.argv.index("-crd")
coord=sys.argv[ind+1]
if coord=='s':coord='-1'
if coord=='g':coord='0'
if coord=='t':coord='100'
if "-fsa" in args:
ind=args.index("-fsa")
samp_file=sys.argv[ind+1]
if "-Fa" in args:
ind=args.index("-Fa")
rmag_anis=args[ind+1]
if "-Fr" in args:
ind=args.index("-Fr")
rmag_res=args[ind+1]
meas_file=dir_path+'/'+meas_file
samp_file=dir_path+'/'+samp_file
rmag_anis=dir_path+'/'+rmag_anis
rmag_res=dir_path+'/'+rmag_res
# read in data
meas_data,file_type=pmag.magic_read(meas_file)
meas_data=pmag.get_dictitem(meas_data,'magic_method_codes','LP-AN-ARM','has')
if file_type != 'magic_measurements':
print file_type
print file_type,"This is not a valid magic_measurements file "
sys.exit()
if coord!='-1': # need to read in sample data
samp_data,file_type=pmag.magic_read(samp_file)
if file_type != 'er_samples':
print file_type
print file_type,"This is not a valid er_samples file "
print "Only specimen coordinates will be calculated"
coord='-1'
#
# sort the specimen names
#
ssort=[]
for rec in meas_data:
spec=rec["er_specimen_name"]
if spec not in ssort: ssort.append(spec)
if len(ssort)>1:
sids=sorted(ssort)
else:
sids=ssort
#
# work on each specimen
#
specimen=0
RmagSpecRecs,RmagResRecs=[],[]
while specimen < len(sids):
s=sids[specimen]
data=[]
RmagSpecRec={}
RmagResRec={}
method_codes=[]
#
# find the data from the meas_data file for this sample
#
data=pmag.get_dictitem(meas_data,'er_specimen_name',s,'T')
#
# find out the number of measurements (9, 12 or 15)
#
npos=len(data)/2
if npos==9:
#
# get dec, inc, int and convert to x,y,z
#
B,H,tmpH=pmag.designAARM(npos) # B matrix made from design matrix for positions
X=[]
for rec in data:
Dir=[]
Dir.append(float(rec["measurement_dec"]))
Dir.append(float(rec["measurement_inc"]))
Dir.append(float(rec["measurement_magn_moment"]))
X.append(pmag.dir2cart(Dir))
#
# subtract baseline and put in a work array
#
work=numpy.zeros((npos,3),'f')
for i in range(npos):
for j in range(3):
work[i][j]=X[2*i+1][j]-X[2*i][j]
#
# calculate tensor elements
# first put ARM components in w vector
#
w=numpy.zeros((npos*3),'f')
index=0
for i in range(npos):
for j in range(3):
w[index]=work[i][j]
index+=1
s=numpy.zeros((6),'f') # initialize the s matrix
for i in range(6):
for j in range(len(w)):
s[i]+=B[i][j]*w[j]
trace=s[0]+s[1]+s[2] # normalize by the trace
for i in range(6):
s[i]=s[i]/trace
a=pmag.s2a(s)
#------------------------------------------------------------
# Calculating dels is different than in the Kappabridge
# routine. Use trace normalized tensor (a) and the applied
# unit field directions (tmpH) to generate model X,Y,Z
# components. Then compare these with the measured values.
#------------------------------------------------------------
S=0.
comp=numpy.zeros((npos*3),'f')
for i in range(npos):
for j in range(3):
index=i*3+j
compare=a[j][0]*tmpH[i][0]+a[j][1]*tmpH[i][1]+a[j][2]*tmpH[i][2]
comp[index]=compare
for i in range(npos*3):
d=w[i]/trace - comp[i] # del values
S+=d*d
nf=float(npos*3-6) # number of degrees of freedom
if S >0:
sigma=numpy.sqrt(S/nf)
else: sigma=0
RmagSpecRec["rmag_anisotropy_name"]=data[0]["er_specimen_name"]
RmagSpecRec["er_location_name"]=data[0]["er_location_name"]
RmagSpecRec["er_specimen_name"]=data[0]["er_specimen_name"]
RmagSpecRec["er_sample_name"]=data[0]["er_sample_name"]
RmagSpecRec["er_site_name"]=data[0]["er_site_name"]
RmagSpecRec["magic_experiment_names"]=RmagSpecRec["rmag_anisotropy_name"]+":AARM"
RmagSpecRec["er_citation_names"]="This study"
RmagResRec["rmag_result_name"]=data[0]["er_specimen_name"]+":AARM"
RmagResRec["er_location_names"]=data[0]["er_location_name"]
RmagResRec["er_specimen_names"]=data[0]["er_specimen_name"]
RmagResRec["er_sample_names"]=data[0]["er_sample_name"]
RmagResRec["er_site_names"]=data[0]["er_site_name"]
RmagResRec["magic_experiment_names"]=RmagSpecRec["rmag_anisotropy_name"]+":AARM"
RmagResRec["er_citation_names"]="This study"
if "magic_instrument_codes" in data[0].keys():
RmagSpecRec["magic_instrument_codes"]=data[0]["magic_instrument_codes"]
else:
RmagSpecRec["magic_instrument_codes"]=""
RmagSpecRec["anisotropy_type"]="AARM"
RmagSpecRec["anisotropy_description"]="Hext statistics adapted to AARM"
if coord!='-1': # need to rotate s
# set orientation priorities
SO_methods=[]
for rec in samp_data:
if "magic_method_codes" not in rec:
rec['magic_method_codes']='SO-NO'
if "magic_method_codes" in rec:
methlist=rec["magic_method_codes"]
for meth in methlist.split(":"):
if "SO" in meth and "SO-POM" not in meth.strip():
if meth.strip() not in SO_methods: SO_methods.append(meth.strip())
SO_priorities=pmag.set_priorities(SO_methods,0)
# continue here
redo,p=1,0
if len(SO_methods)<=1:
az_type=SO_methods[0]
orient=pmag.find_samp_rec(RmagSpecRec["er_sample_name"],samp_data,az_type)
if orient["sample_azimuth"] !="": method_codes.append(az_type)
redo=0
while redo==1:
if p>=len(SO_priorities):
print "no orientation data for ",s
orient["sample_azimuth"]=""
orient["sample_dip"]=""
method_codes.append("SO-NO")
redo=0
else:
az_type=SO_methods[SO_methods.index(SO_priorities[p])]
orient=pmag.find_samp_rec(PmagSpecRec["er_sample_name"],samp_data,az_type)
if orient["sample_azimuth"] !="":
method_codes.append(az_type)
redo=0
p+=1
az,pl=orient['sample_azimuth'],orient['sample_dip']
s=pmag.dosgeo(s,az,pl) # rotate to geographic coordinates
if coord=='100':
sampe_bed_dir,sample_bed_dip=orient['sample_bed_dip_direction'],orient['sample_bed_dip']
s=pmag.dostilt(s,bed_dir,bed_dip) # rotate to geographic coordinates
hpars=pmag.dohext(nf,sigma,s)
#
# prepare for output
#
RmagSpecRec["anisotropy_s1"]='%8.6f'%(s[0])
RmagSpecRec["anisotropy_s2"]='%8.6f'%(s[1])
RmagSpecRec["anisotropy_s3"]='%8.6f'%(s[2])
RmagSpecRec["anisotropy_s4"]='%8.6f'%(s[3])
RmagSpecRec["anisotropy_s5"]='%8.6f'%(s[4])
RmagSpecRec["anisotropy_s6"]='%8.6f'%(s[5])
RmagSpecRec["anisotropy_mean"]='%8.3e'%(trace/3)
RmagSpecRec["anisotropy_sigma"]='%8.6f'%(sigma)
RmagSpecRec["anisotropy_unit"]="Am^2"
RmagSpecRec["anisotropy_n"]='%i'%(npos)
RmagSpecRec["anisotropy_tilt_correction"]=coord
RmagSpecRec["anisotropy_F"]='%7.1f '%(hpars["F"]) # used by thellier_gui - must be taken out for uploading
RmagSpecRec["anisotropy_F_crit"]=hpars["F_crit"] # used by thellier_gui - must be taken out for uploading
RmagResRec["anisotropy_t1"]='%8.6f '%(hpars["t1"])
RmagResRec["anisotropy_t2"]='%8.6f '%(hpars["t2"])
RmagResRec["anisotropy_t3"]='%8.6f '%(hpars["t3"])
RmagResRec["anisotropy_v1_dec"]='%7.1f '%(hpars["v1_dec"])
RmagResRec["anisotropy_v2_dec"]='%7.1f '%(hpars["v2_dec"])
RmagResRec["anisotropy_v3_dec"]='%7.1f '%(hpars["v3_dec"])
RmagResRec["anisotropy_v1_inc"]='%7.1f '%(hpars["v1_inc"])
RmagResRec["anisotropy_v2_inc"]='%7.1f '%(hpars["v2_inc"])
RmagResRec["anisotropy_v3_inc"]='%7.1f '%(hpars["v3_inc"])
RmagResRec["anisotropy_ftest"]='%7.1f '%(hpars["F"])
RmagResRec["anisotropy_ftest12"]='%7.1f '%(hpars["F12"])
RmagResRec["anisotropy_ftest23"]='%7.1f '%(hpars["F23"])
RmagResRec["result_description"]='Critical F: '+hpars["F_crit"]+';Critical F12/F13: '+hpars["F12_crit"]
if hpars["e12"]>hpars["e13"]:
RmagResRec["anisotropy_v1_zeta_semi_angle"]='%7.1f '%(hpars['e12'])
RmagResRec["anisotropy_v1_zeta_dec"]='%7.1f '%(hpars['v2_dec'])
RmagResRec["anisotropy_v1_zeta_inc"]='%7.1f '%(hpars['v2_inc'])
RmagResRec["anisotropy_v2_zeta_semi_angle"]='%7.1f '%(hpars['e12'])
RmagResRec["anisotropy_v2_zeta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v2_zeta_inc"]='%7.1f '%(hpars['v1_inc'])
RmagResRec["anisotropy_v1_eta_semi_angle"]='%7.1f '%(hpars['e13'])
RmagResRec["anisotropy_v1_eta_dec"]='%7.1f '%(hpars['v3_dec'])
RmagResRec["anisotropy_v1_eta_inc"]='%7.1f '%(hpars['v3_inc'])
RmagResRec["anisotropy_v3_eta_semi_angle"]='%7.1f '%(hpars['e13'])
RmagResRec["anisotropy_v3_eta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v3_eta_inc"]='%7.1f '%(hpars['v1_inc'])
else:
RmagResRec["anisotropy_v1_zeta_semi_angle"]='%7.1f '%(hpars['e13'])
RmagResRec["anisotropy_v1_zeta_dec"]='%7.1f '%(hpars['v3_dec'])
RmagResRec["anisotropy_v1_zeta_inc"]='%7.1f '%(hpars['v3_inc'])
RmagResRec["anisotropy_v3_zeta_semi_angle"]='%7.1f '%(hpars['e13'])
RmagResRec["anisotropy_v3_zeta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v3_zeta_inc"]='%7.1f '%(hpars['v1_inc'])
RmagResRec["anisotropy_v1_eta_semi_angle"]='%7.1f '%(hpars['e12'])
RmagResRec["anisotropy_v1_eta_dec"]='%7.1f '%(hpars['v2_dec'])
RmagResRec["anisotropy_v1_eta_inc"]='%7.1f '%(hpars['v2_inc'])
RmagResRec["anisotropy_v2_eta_semi_angle"]='%7.1f '%(hpars['e12'])
RmagResRec["anisotropy_v2_eta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v2_eta_inc"]='%7.1f '%(hpars['v1_inc'])
if hpars["e23"]>hpars['e12']:
RmagResRec["anisotropy_v2_zeta_semi_angle"]='%7.1f '%(hpars['e23'])
RmagResRec["anisotropy_v2_zeta_dec"]='%7.1f '%(hpars['v3_dec'])
RmagResRec["anisotropy_v2_zeta_inc"]='%7.1f '%(hpars['v3_inc'])
RmagResRec["anisotropy_v3_zeta_semi_angle"]='%7.1f '%(hpars['e23'])
RmagResRec["anisotropy_v3_zeta_dec"]='%7.1f '%(hpars['v2_dec'])
RmagResRec["anisotropy_v3_zeta_inc"]='%7.1f '%(hpars['v2_inc'])
RmagResRec["anisotropy_v3_eta_semi_angle"]='%7.1f '%(hpars['e13'])
RmagResRec["anisotropy_v3_eta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v3_eta_inc"]='%7.1f '%(hpars['v1_inc'])
RmagResRec["anisotropy_v2_eta_semi_angle"]='%7.1f '%(hpars['e12'])
RmagResRec["anisotropy_v2_eta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v2_eta_inc"]='%7.1f '%(hpars['v1_inc'])
else:
RmagResRec["anisotropy_v2_zeta_semi_angle"]='%7.1f '%(hpars['e12'])
RmagResRec["anisotropy_v2_zeta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v2_zeta_inc"]='%7.1f '%(hpars['v1_inc'])
RmagResRec["anisotropy_v3_eta_semi_angle"]='%7.1f '%(hpars['e23'])
RmagResRec["anisotropy_v3_eta_dec"]='%7.1f '%(hpars['v2_dec'])
RmagResRec["anisotropy_v3_eta_inc"]='%7.1f '%(hpars['v2_inc'])
RmagResRec["anisotropy_v3_zeta_semi_angle"]='%7.1f '%(hpars['e13'])
RmagResRec["anisotropy_v3_zeta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v3_zeta_inc"]='%7.1f '%(hpars['v1_inc'])
RmagResRec["anisotropy_v2_eta_semi_angle"]='%7.1f '%(hpars['e23'])
RmagResRec["anisotropy_v2_eta_dec"]='%7.1f '%(hpars['v3_dec'])
RmagResRec["anisotropy_v2_eta_inc"]='%7.1f '%(hpars['v3_inc'])
RmagResRec["tilt_correction"]='-1'
RmagResRec["anisotropy_type"]='AARM'
RmagResRec["magic_method_codes"]='LP-AN-ARM:AE-H'
RmagSpecRec["magic_method_codes"]='LP-AN-ARM:AE-H'
RmagResRec["magic_software_packages"]=pmag.get_version()
RmagSpecRec["magic_software_packages"]=pmag.get_version()
specimen+=1
RmagSpecRecs.append(RmagSpecRec)
RmagResRecs.append(RmagResRec)
else:
print 'skipping specimen ',s,' only 9 positions supported','; this has ',npos
specimen+=1
if rmag_anis=="":rmag_anis="rmag_anisotropy.txt"
pmag.magic_write(rmag_anis,RmagSpecRecs,'rmag_anisotropy')
print "specimen tensor elements stored in ",rmag_anis
if rmag_res=="":rmag_res="rmag_results.txt"
pmag.magic_write(rmag_res,RmagResRecs,'rmag_results')
print "specimen statistics and eigenparameters stored in ",rmag_res
def main():
"""
NAME
s_hext.py
DESCRIPTION
calculates Hext statistics for tensor data
SYNTAX
s_hext.py [-h][-i][-f file] [<filename]
OPTIONS
-h prints help message and quits
-f file specifies filename on command line
-l NMEAS do line by line instead of whole file, use number of measurements NMEAS for degrees of freedom
< filename, reads from standard input (Unix like operating systems only)
INPUT
x11,x22,x33,x12,x23,x13,sigma [sigma only if line by line]
OUTPUT
F F12 F23 sigma
and three sets of:
tau dec inc Eij dec inc Eik dec inc
DEFAULT
average whole file
"""
ave=1
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-l' in sys.argv:
ind=sys.argv.index('-l')
npts=int(sys.argv[ind+1])
ave=0
if '-f' in sys.argv:
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
f=open(file,'rU')
data=f.readlines()
f.close()
else:
data=sys.stdin.readlines()
Ss=[]
for line in data:
s=[]
rec=line.split()
for i in range(6):
s.append(float(rec[i]))
if ave==0:
sig=float(rec[6])
hpars=pmag.dohext(npts-6,sig,s)
print '%s %4.2f %s %4.2f %s %4.2f'%('F = ',hpars['F'],'F12 = ',hpars['F12'],'F23 = ',hpars['F23'])
print '%s %i %s %14.12f'%('Nmeas = ',npts,' sigma = ',sig)
print '%7.5f %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f'%(hpars["t1"],hpars["v1_dec"],hpars["v1_inc"],hpars["e12"],hpars["v2_dec"],hpars["v2_inc"],hpars["e13"],hpars["v3_dec"],hpars["v3_inc"] )
print '%7.5f %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f'%(hpars["t2"],hpars["v2_dec"],hpars["v2_inc"],hpars["e23"],hpars["v3_dec"],hpars["v3_inc"],hpars["e12"],hpars["v1_dec"],hpars["v1_inc"] )
print '%7.5f %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f'%(hpars["t3"],hpars["v3_dec"],hpars["v3_inc"],hpars["e13"],hpars["v1_dec"],hpars["v1_inc"],hpars["e23"],hpars["v2_dec"],hpars["v2_inc"] )
else:
Ss.append(s)
if ave==1:
npts=len(Ss)
nf,sigma,avs=pmag.sbar(Ss)
hpars=pmag.dohext(nf,sigma,avs)
print '%s %4.2f %s %4.2f %s %4.2f'%('F = ',hpars['F'],'F12 = ',hpars['F12'],'F23 = ',hpars['F23'])
print '%s %i %s %14.12f'%('N = ',npts,' sigma = ',sigma)
print '%7.5f %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f'%(hpars["t1"],hpars["v1_dec"],hpars["v1_inc"],hpars["e12"],hpars["v2_dec"],hpars["v2_inc"],hpars["e13"],hpars["v3_dec"],hpars["v3_inc"] )
print '%7.5f %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f'%(hpars["t2"],hpars["v2_dec"],hpars["v2_inc"],hpars["e23"],hpars["v3_dec"],hpars["v3_inc"],hpars["e12"],hpars["v1_dec"],hpars["v1_inc"] )
print '%7.5f %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f'%(hpars["t3"],hpars["v3_dec"],hpars["v3_inc"],hpars["e13"],hpars["v1_dec"],hpars["v1_inc"],hpars["e23"],hpars["v2_dec"],hpars["v2_inc"] )
def calculate_aniso_parameters(B,K):
aniso_parameters={}
S_bs=dot(B,K)
# normalize by trace
trace=S_bs[0]+S_bs[1]+S_bs[2]
S_bs=S_bs/trace
s1,s2,s3,s4,s5,s6=S_bs[0],S_bs[1],S_bs[2],S_bs[3],S_bs[4],S_bs[5]
s_matrix=[[s1,s4,s6],[s4,s2,s5],[s6,s5,s3]]
# calculate eigen vector,
t,evectors=eig(s_matrix)
# sort vectors
t=list(t)
t1=max(t)
ix_1=t.index(t1)
t3=min(t)
ix_3=t.index(t3)
for tt in range(3):
if t[tt]!=t1 and t[tt]!=t3:
t2=t[tt]
ix_2=t.index(t2)
v1=[evectors[0][ix_1],evectors[1][ix_1],evectors[2][ix_1]]
v2=[evectors[0][ix_2],evectors[1][ix_2],evectors[2][ix_2]]
v3=[evectors[0][ix_3],evectors[1][ix_3],evectors[2][ix_3]]
DIR_v1=pmag.cart2dir(v1)
DIR_v2=pmag.cart2dir(v2)
DIR_v3=pmag.cart2dir(v3)
aniso_parameters['anisotropy_s1']="%f"%s1
aniso_parameters['anisotropy_s2']="%f"%s2
aniso_parameters['anisotropy_s3']="%f"%s3
aniso_parameters['anisotropy_s4']="%f"%s4
aniso_parameters['anisotropy_s5']="%f"%s5
aniso_parameters['anisotropy_s6']="%f"%s6
aniso_parameters['anisotropy_degree']="%f"%(t1/t3)
aniso_parameters['anisotropy_t1']="%f"%t1
aniso_parameters['anisotropy_t2']="%f"%t2
aniso_parameters['anisotropy_t3']="%f"%t3
aniso_parameters['anisotropy_v1_dec']="%.1f"%DIR_v1[0]
aniso_parameters['anisotropy_v1_inc']="%.1f"%DIR_v1[1]
aniso_parameters['anisotropy_v2_dec']="%.1f"%DIR_v2[0]
aniso_parameters['anisotropy_v2_inc']="%.1f"%DIR_v2[1]
aniso_parameters['anisotropy_v3_dec']="%.1f"%DIR_v3[0]
aniso_parameters['anisotropy_v3_inc']="%.1f"%DIR_v3[1]
# modified from pmagpy:
if len(K)/3==9 or len(K)/3==6 or len(K)/3==15:
n_pos=len(K)/3
tmpH = Matrices[n_pos]['tmpH']
a=s_matrix
S=0.
comp=zeros((n_pos*3),'f')
for i in range(n_pos):
for j in range(3):
index=i*3+j
compare=a[j][0]*tmpH[i][0]+a[j][1]*tmpH[i][1]+a[j][2]*tmpH[i][2]
comp[index]=compare
for i in range(n_pos*3):
d=K[i]/trace - comp[i] # del values
S+=d*d
nf=float(n_pos*3-6) # number of degrees of freedom
if S >0:
sigma=math.sqrt(S/nf)
hpars=pmag.dohext(nf,sigma,[s1,s2,s3,s4,s5,s6])
aniso_parameters['anisotropy_sigma']="%f"%sigma
aniso_parameters['anisotropy_ftest']="%f"%hpars["F"]
aniso_parameters['anisotropy_ftest12']="%f"%hpars["F12"]
aniso_parameters['anisotropy_ftest23']="%f"%hpars["F23"]
aniso_parameters['result_description']="Critical F: %s"%(hpars['F_crit'])
aniso_parameters['anisotropy_F_crit']="%f"%float(hpars['F_crit'])
aniso_parameters['anisotropy_n']=n_pos
return(aniso_parameters)
def main():
"""
NAME
atrm_magic.py
DESCRIPTION
Converts ATRM data to best-fit tensor (6 elements plus sigma)
Original program ARMcrunch written to accomodate ARM anisotropy data
collected from 6 axial directions (+X,+Y,+Z,-X,-Y,-Z) using the
off-axis remanence terms to construct the tensor. A better way to
do the anisotropy of ARMs is to use 9,12 or 15 measurements in
the Hext rotational scheme.
SYNTAX
atrm_magic.py [-h][command line options]
OPTIONS
-h prints help message and quits
-usr USER: identify user, default is ""
-f FILE: specify input file, default is atrm_measurements.txt
-Fa FILE: specify anisotropy output file, default is trm_anisotropy.txt
-Fr FILE: specify results output file, default is atrm_results.txt
INPUT
Input for the present program is a TRM acquisition data with an optional baseline.
The order of the measurements is:
Decs=[0,90,0,180,270,0,0,90,0]
Incs=[0,0,90,0,0,-90,0,0,90]
The last two measurements are optional
"""
# initialize some parameters
args=sys.argv
user=""
meas_file="atrm_measurements.txt"
rmag_anis="trm_anisotropy.txt"
rmag_res="atrm_results.txt"
dir_path='.'
#
# get name of file from command line
#
if '-WD' in args:
ind=args.index('-WD')
dir_path=args[ind+1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=sys.argv[ind+1]
if "-f" in args:
ind=args.index("-f")
meas_file=sys.argv[ind+1]
if "-Fa" in args:
ind=args.index("-Fa")
rmag_anis=args[ind+1]
if "-Fr" in args:
ind=args.index("-Fr")
rmag_res=args[ind+1]
meas_file=dir_path+'/'+meas_file
rmag_anis=dir_path+'/'+rmag_anis
rmag_res=dir_path+'/'+rmag_res
# read in data
meas_data,file_type=pmag.magic_read(meas_file)
meas_data=pmag.get_dictitem(meas_data,'magic_method_codes','LP-AN-TRM','has')
if file_type != 'magic_measurements':
print file_type
print file_type,"This is not a valid magic_measurements file "
sys.exit()
#
#
# get sorted list of unique specimen names
ssort=[]
for rec in meas_data:
spec=rec["er_specimen_name"]
if spec not in ssort:ssort.append(spec)
sids=sorted(ssort)
#
#
# work on each specimen
#
specimen,npos=0,6
RmagSpecRecs,RmagResRecs=[],[]
while specimen < len(sids):
nmeas=0
s=sids[specimen]
RmagSpecRec={}
RmagResRec={}
BX,X=[],[]
method_codes=[]
Spec0=""
#
# find the data from the meas_data file for this sample
# and get dec, inc, int and convert to x,y,z
#
data=pmag.get_dictitem(meas_data,'er_specimen_name',s,'T') # fish out data for this specimen name
if len(data)>5:
RmagSpecRec["rmag_anisotropy_name"]=data[0]["er_specimen_name"]
RmagSpecRec["er_location_name"]=data[0]["er_location_name"]
RmagSpecRec["er_specimen_name"]=data[0]["er_specimen_name"]
RmagSpecRec["er_sample_name"]=data[0]["er_sample_name"]
RmagSpecRec["er_site_name"]=data[0]["er_site_name"]
RmagSpecRec["magic_experiment_names"]=RmagSpecRec["rmag_anisotropy_name"]+":ATRM"
RmagSpecRec["er_citation_names"]="This study"
RmagResRec["rmag_result_name"]=data[0]["er_specimen_name"]+":ATRM"
RmagResRec["er_location_names"]=data[0]["er_location_name"]
RmagResRec["er_specimen_names"]=data[0]["er_specimen_name"]
RmagResRec["er_sample_names"]=data[0]["er_sample_name"]
RmagResRec["er_site_names"]=data[0]["er_site_name"]
RmagResRec["magic_experiment_names"]=RmagSpecRec["rmag_anisotropy_name"]+":ATRM"
RmagResRec["er_citation_names"]="This study"
RmagSpecRec["anisotropy_type"]="ATRM"
if "magic_instrument_codes" in data[0].keys():
RmagSpecRec["magic_instrument_codes"]=data[0]["magic_instrument_codes"]
else:
RmagSpecRec["magic_instrument_codes"]=""
RmagSpecRec["anisotropy_description"]="Hext statistics adapted to ATRM"
for rec in data:
meths=rec['magic_method_codes'].strip().split(':')
Dir=[]
Dir.append(float(rec["measurement_dec"]))
Dir.append(float(rec["measurement_inc"]))
Dir.append(float(rec["measurement_magn_moment"]))
if "LT-T-Z" in meths:
BX.append(pmag.dir2cart(Dir)) # append baseline steps
elif "LT-T-I" in meths:
X.append(pmag.dir2cart(Dir))
nmeas+=1
#
if len(BX)==1:
for i in range(len(X)-1):BX.append(BX[0]) # assume first 0 field step as baseline
elif len(BX)== 0: # assume baseline is zero
for i in range(len(X)):BX.append([0.,0.,0.]) # assume baseline of 0
elif len(BX)!= len(X): # if BX isn't just one measurement or one in between every infield step, just assume it is zero
print 'something odd about the baselines - just assuming zero'
for i in range(len(X)):BX.append([0.,0.,0.]) # assume baseline of 0
if nmeas<6: # must have at least 6 measurements right now -
print 'skipping specimen ',s,' too few measurements'
specimen+=1
else:
B,H,tmpH=pmag.designATRM(npos) # B matrix made from design matrix for positions
#
# subtract optional baseline and put in a work array
#
work=numpy.zeros((nmeas,3),'f')
for i in range(nmeas):
for j in range(3):
work[i][j]=X[i][j]-BX[i][j] # subtract baseline, if available
#
# calculate tensor elements
# first put ARM components in w vector
#
w=numpy.zeros((npos*3),'f')
index=0
for i in range(npos):
for j in range(3):
w[index]=work[i][j]
index+=1
s=numpy.zeros((6),'f') # initialize the s matrix
for i in range(6):
for j in range(len(w)):
s[i]+=B[i][j]*w[j]
trace=s[0]+s[1]+s[2] # normalize by the trace
for i in range(6):
s[i]=s[i]/trace
a=pmag.s2a(s)
#------------------------------------------------------------
# Calculating dels is different than in the Kappabridge
# routine. Use trace normalized tensor (a) and the applied
# unit field directions (tmpH) to generate model X,Y,Z
# components. Then compare these with the measured values.
#------------------------------------------------------------
S=0.
comp=numpy.zeros((npos*3),'f')
for i in range(npos):
for j in range(3):
index=i*3+j
compare=a[j][0]*tmpH[i][0]+a[j][1]*tmpH[i][1]+a[j][2]*tmpH[i][2]
comp[index]=compare
for i in range(npos*3):
d=w[i]/trace - comp[i] # del values
S+=d*d
nf=float(npos*3.-6.) # number of degrees of freedom
if S >0:
sigma=numpy.sqrt(S/nf)
else: sigma=0
hpars=pmag.dohext(nf,sigma,s)
#
# prepare for output
#
RmagSpecRec["anisotropy_s1"]='%8.6f'%(s[0])
RmagSpecRec["anisotropy_s2"]='%8.6f'%(s[1])
RmagSpecRec["anisotropy_s3"]='%8.6f'%(s[2])
RmagSpecRec["anisotropy_s4"]='%8.6f'%(s[3])
RmagSpecRec["anisotropy_s5"]='%8.6f'%(s[4])
RmagSpecRec["anisotropy_s6"]='%8.6f'%(s[5])
RmagSpecRec["anisotropy_mean"]='%8.3e'%(trace/3)
RmagSpecRec["anisotropy_sigma"]='%8.6f'%(sigma)
RmagSpecRec["anisotropy_unit"]="Am^2"
RmagSpecRec["anisotropy_n"]='%i'%(npos)
RmagSpecRec["anisotropy_tilt_correction"]='-1'
RmagSpecRec["anisotropy_F"]='%7.1f '%(hpars["F"]) # used by thellier_gui - must be taken out for uploading
RmagSpecRec["anisotropy_F_crit"]=hpars["F_crit"] # used by thellier_gui - must be taken out for uploading
RmagResRec["anisotropy_t1"]='%8.6f '%(hpars["t1"])
RmagResRec["anisotropy_t2"]='%8.6f '%(hpars["t2"])
RmagResRec["anisotropy_t3"]='%8.6f '%(hpars["t3"])
RmagResRec["anisotropy_v1_dec"]='%7.1f '%(hpars["v1_dec"])
RmagResRec["anisotropy_v2_dec"]='%7.1f '%(hpars["v2_dec"])
RmagResRec["anisotropy_v3_dec"]='%7.1f '%(hpars["v3_dec"])
RmagResRec["anisotropy_v1_inc"]='%7.1f '%(hpars["v1_inc"])
RmagResRec["anisotropy_v2_inc"]='%7.1f '%(hpars["v2_inc"])
RmagResRec["anisotropy_v3_inc"]='%7.1f '%(hpars["v3_inc"])
RmagResRec["anisotropy_ftest"]='%7.1f '%(hpars["F"])
RmagResRec["anisotropy_ftest12"]='%7.1f '%(hpars["F12"])
RmagResRec["anisotropy_ftest23"]='%7.1f '%(hpars["F23"])
RmagResRec["result_description"]='Critical F: '+hpars["F_crit"]+';Critical F12/F13: '+hpars["F12_crit"]
if hpars["e12"]>hpars["e13"]:
RmagResRec["anisotropy_v1_zeta_semi_angle"]='%7.1f '%(hpars['e12'])
RmagResRec["anisotropy_v1_zeta_dec"]='%7.1f '%(hpars['v2_dec'])
RmagResRec["anisotropy_v1_zeta_inc"]='%7.1f '%(hpars['v2_inc'])
RmagResRec["anisotropy_v2_zeta_semi_angle"]='%7.1f '%(hpars['e12'])
RmagResRec["anisotropy_v2_zeta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v2_zeta_inc"]='%7.1f '%(hpars['v1_inc'])
RmagResRec["anisotropy_v1_eta_semi_angle"]='%7.1f '%(hpars['e13'])
RmagResRec["anisotropy_v1_eta_dec"]='%7.1f '%(hpars['v3_dec'])
RmagResRec["anisotropy_v1_eta_inc"]='%7.1f '%(hpars['v3_inc'])
RmagResRec["anisotropy_v3_eta_semi_angle"]='%7.1f '%(hpars['e13'])
RmagResRec["anisotropy_v3_eta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v3_eta_inc"]='%7.1f '%(hpars['v1_inc'])
else:
RmagResRec["anisotropy_v1_zeta_semi_angle"]='%7.1f '%(hpars['e13'])
RmagResRec["anisotropy_v1_zeta_dec"]='%7.1f '%(hpars['v3_dec'])
RmagResRec["anisotropy_v1_zeta_inc"]='%7.1f '%(hpars['v3_inc'])
RmagResRec["anisotropy_v3_zeta_semi_angle"]='%7.1f '%(hpars['e13'])
RmagResRec["anisotropy_v3_zeta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v3_zeta_inc"]='%7.1f '%(hpars['v1_inc'])
RmagResRec["anisotropy_v1_eta_semi_angle"]='%7.1f '%(hpars['e12'])
RmagResRec["anisotropy_v1_eta_dec"]='%7.1f '%(hpars['v2_dec'])
RmagResRec["anisotropy_v1_eta_inc"]='%7.1f '%(hpars['v2_inc'])
RmagResRec["anisotropy_v2_eta_semi_angle"]='%7.1f '%(hpars['e12'])
RmagResRec["anisotropy_v2_eta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v2_eta_inc"]='%7.1f '%(hpars['v1_inc'])
if hpars["e23"]>hpars['e12']:
RmagResRec["anisotropy_v2_zeta_semi_angle"]='%7.1f '%(hpars['e23'])
RmagResRec["anisotropy_v2_zeta_dec"]='%7.1f '%(hpars['v3_dec'])
RmagResRec["anisotropy_v2_zeta_inc"]='%7.1f '%(hpars['v3_inc'])
RmagResRec["anisotropy_v3_zeta_semi_angle"]='%7.1f '%(hpars['e23'])
RmagResRec["anisotropy_v3_zeta_dec"]='%7.1f '%(hpars['v2_dec'])
RmagResRec["anisotropy_v3_zeta_inc"]='%7.1f '%(hpars['v2_inc'])
RmagResRec["anisotropy_v3_eta_semi_angle"]='%7.1f '%(hpars['e13'])
RmagResRec["anisotropy_v3_eta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v3_eta_inc"]='%7.1f '%(hpars['v1_inc'])
RmagResRec["anisotropy_v2_eta_semi_angle"]='%7.1f '%(hpars['e12'])
RmagResRec["anisotropy_v2_eta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v2_eta_inc"]='%7.1f '%(hpars['v1_inc'])
else:
RmagResRec["anisotropy_v2_zeta_semi_angle"]='%7.1f '%(hpars['e12'])
RmagResRec["anisotropy_v2_zeta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v2_zeta_inc"]='%7.1f '%(hpars['v1_inc'])
RmagResRec["anisotropy_v3_eta_semi_angle"]='%7.1f '%(hpars['e23'])
RmagResRec["anisotropy_v3_eta_dec"]='%7.1f '%(hpars['v2_dec'])
RmagResRec["anisotropy_v3_eta_inc"]='%7.1f '%(hpars['v2_inc'])
RmagResRec["anisotropy_v3_zeta_semi_angle"]='%7.1f '%(hpars['e13'])
RmagResRec["anisotropy_v3_zeta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v3_zeta_inc"]='%7.1f '%(hpars['v1_inc'])
RmagResRec["anisotropy_v2_eta_semi_angle"]='%7.1f '%(hpars['e23'])
RmagResRec["anisotropy_v2_eta_dec"]='%7.1f '%(hpars['v3_dec'])
RmagResRec["anisotropy_v2_eta_inc"]='%7.1f '%(hpars['v3_inc'])
RmagResRec["tilt_correction"]='-1'
RmagResRec["anisotropy_type"]='ATRM'
RmagResRec["magic_method_codes"]='LP-AN-TRM:AE-H'
RmagSpecRec["magic_method_codes"]='LP-AN-TRM:AE-H'
RmagResRec["magic_software_packages"]=pmag.get_version()
RmagSpecRec["magic_software_packages"]=pmag.get_version()
RmagSpecRecs.append(RmagSpecRec)
RmagResRecs.append(RmagResRec)
specimen+=1
pmag.magic_write(rmag_anis,RmagSpecRecs,'rmag_anisotropy')
print "specimen tensor elements stored in ",rmag_anis
pmag.magic_write(rmag_res,RmagResRecs,'rmag_results')
print "specimen statistics and eigenparameters stored in ",rmag_res
