"""

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')