def main():
"""
NAME
site_edit_magic.py
DESCRIPTION
makes equal area projections site by site
from pmag_specimens.txt file with
Fisher confidence ellipse using McFadden and McElhinny (1988)
technique for combining lines and planes
allows testing and reject specimens for bad orientations
SYNTAX
site_edit_magic.py [command line options]
OPTIONS
-h: prints help and quits
-f: specify pmag_specimen format file, default is pmag_specimens.txt
-fsa: specify er_samples.txt file
-exc: use existing pmag_criteria.txt file
-N: reset all sample flags to good
OUPUT
edited er_samples.txt file
"""
dir_path='.'
FIG={} # plot dictionary
FIG['eqarea']=1 # eqarea is figure 1
in_file='pmag_specimens.txt'
sampfile='er_samples.txt'
out_file=""
fmt,plot='svg',1
Crits=""
M,N=180.,1
repeat=''
renew=0
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-f' in sys.argv:
ind=sys.argv.index("-f")
in_file=sys.argv[ind+1]
if '-fsa' in sys.argv:
ind=sys.argv.index("-fsa")
sampfile=sys.argv[ind+1]
if '-exc' in sys.argv:
Crits,file_type=pmag.magic_read(dir_path+'/pmag_criteria.txt')
for crit in Crits:
if crit['pmag_criteria_code']=='DE-SPEC':
M=float(crit['specimen_mad'])
N=float(crit['specimen_n'])
if '-fmt' in sys.argv:
ind=sys.argv.index("-fmt")
fmt=sys.argv[ind+1]
if '-N' in sys.argv: renew=1
#
if in_file[0]!="/":in_file=dir_path+'/'+in_file
if sampfile[0]!="/":sampfile=dir_path+'/'+sampfile
crd='s'
Specs,file_type=pmag.magic_read(in_file)
if file_type!='pmag_specimens':
print ' bad pmag_specimen input file'
sys.exit()
Samps,file_type=pmag.magic_read(sampfile)
if file_type!='er_samples':
print ' bad er_samples input file'
sys.exit()
SO_methods=[]
for rec in Samps:
if 'sample_orientation_flag' not in rec.keys(): rec['sample_orientation_flag']='g'
if 'sample_description' not in rec.keys(): rec['sample_description']=''
if renew==1:
rec['sample_orientation_flag']='g'
description=rec['sample_description']
if '#' in description:
newdesc=""
c=0
while description[c]!='#' and c<len(description)-1: # look for first pound sign
newdesc=newdesc+description[c]
c+=1
while description[c]=='#':
c+=1# skip first set of pound signs
while description[c]!='#':c+=1 # find second set of pound signs
while description[c]=='#' and c<len(description)-1:c+=1 # skip second set of pound signs
while c<len(description)-1: # look for first pound sign
newdesc=newdesc+description[c]
c+=1
rec['sample_description']=newdesc # edit out old comment about orientations
if "magic_method_codes" in rec:
methlist=rec["magic_method_codes"]
for meth in methlist.split(":"):
if "SO" in meth.strip() and "SO-POM" not in meth.strip():
if meth.strip() not in SO_methods: SO_methods.append(meth.strip())
pmag.magic_write(sampfile,Samps,'er_samples')
SO_priorities=pmag.set_priorities(SO_methods,0)
sitelist=[]
for rec in Specs:
if rec['er_site_name'] not in sitelist: sitelist.append(rec['er_site_name'])
sitelist.sort()
EQ={}
EQ['eqarea']=1
pmagplotlib.plot_init(EQ['eqarea'],5,5)
k=0
while k<len(sitelist):
site=sitelist[k]
print site
data=[]
ThisSiteSpecs=pmag.get_dictitem(Specs,'er_site_name',site,'T')
ThisSiteSpecs=pmag.get_dictitem(ThisSiteSpecs,'specimen_tilt_correction','-1','T') # get all the unoriented data
for spec in ThisSiteSpecs:
if spec['specimen_mad']!="" and spec['specimen_n']!="" and float(spec['specimen_mad'])<=M and float(spec['specimen_n'])>=N:
# good spec, now get orientation....
redo,p=1,0
if len(SO_methods)<=1:
az_type=SO_methods[0]
orient=pmag.find_samp_rec(spec["er_sample_name"],Samps,az_type)
redo=0
while redo==1:
if p>=len(SO_priorities):
print "no orientation data for ",spec['er_sample_name']
orient["sample_azimuth"]=""
orient["sample_dip"]=""
redo=0
else:
az_type=SO_methods[SO_methods.index(SO_priorities[p])]
orient=pmag.find_samp_rec(spec["er_sample_name"],Samps,az_type)
if orient["sample_azimuth"] !="":
redo=0
p+=1
if orient['sample_azimuth']!="":
rec={}
for key in spec.keys():rec[key]=spec[key]
rec['dec'],rec['inc']=pmag.dogeo(float(spec['specimen_dec']),float(spec['specimen_inc']),float(orient['sample_azimuth']),float(orient['sample_dip']))
rec["tilt_correction"]='1'
crd='g'
rec['sample_azimuth']=orient['sample_azimuth']
rec['sample_dip']=orient['sample_dip']
data.append(rec)
if len(data)>2:
print 'specimen, dec, inc, n_meas/MAD,| method codes '
for i in range(len(data)):
print '%s: %7.1f %7.1f %s / %s | %s' % (data[i]['er_specimen_name'], data[i]['dec'], data[i]['inc'], data[i]['specimen_n'], data[i]['specimen_mad'], data[i]['magic_method_codes'])
fpars=pmag.dolnp(data,'specimen_direction_type')
print "\n Site lines planes kappa a95 dec inc"
print site, fpars["n_lines"], fpars["n_planes"], fpars["K"], fpars["alpha95"], fpars["dec"], fpars["inc"], fpars["R"]
if out_file!="":
if float(fpars["alpha95"])<=acutoff and float(fpars["K"])>=kcutoff:
out.write('%s %s %s\n'%(fpars["dec"],fpars['inc'],fpars['alpha95']))
pmagplotlib.plotLNP(EQ['eqarea'],site,data,fpars,'specimen_direction_type')
pmagplotlib.drawFIGS(EQ)
if k!=0 and repeat!='y':
ans=raw_input("s[a]ve plot, [q]uit, [e]dit specimens, [p]revious site, <return> to continue:\n ")
elif k==0 and repeat!='y':
ans=raw_input("s[a]ve plot, [q]uit, [e]dit specimens, <return> to continue:\n ")
if ans=="p": k-=2
if ans=="a":
files={}
files['eqarea']=site+'_'+crd+'_eqarea'+'.'+fmt
pmagplotlib.saveP(EQ,files)
if ans=="q": sys.exit()
if ans=="e" and Samps==[]:
print "can't edit samples without orientation file, sorry"
elif ans=="e":
# k-=1
testspec=raw_input("Enter name of specimen to check: ")
for spec in data:
if spec['er_specimen_name']==testspec:
# first test wrong direction of drill arrows (flip drill direction in opposite direction and re-calculate d,i
d,i=pmag.dogeo(float(spec['specimen_dec']),float(spec['specimen_inc']),float(spec['sample_azimuth'])-180.,-float(spec['sample_dip']))
XY=pmag.dimap(d,i)
pmagplotlib.plotXY(EQ['eqarea'],[XY[0]],[XY[1]],sym='g^')
# first test wrong end of compass (take az-180.)
d,i=pmag.dogeo(float(spec['specimen_dec']),float(spec['specimen_inc']),float(spec['sample_azimuth'])-180.,float(spec['sample_dip']))
XY=pmag.dimap(d,i)
pmagplotlib.plotXY(EQ['eqarea'],[XY[0]],[XY[1]],sym='kv')
# did the sample spin in the hole?
# now spin around specimen's z
X_up,Y_up,X_d,Y_d=[],[],[],[]
for incr in range(0,360,5):
d,i=pmag.dogeo(float(spec['specimen_dec'])+incr,float(spec['specimen_inc']),float(spec['sample_azimuth']),float(spec['sample_dip']))
XY=pmag.dimap(d,i)
if i>=0:
X_d.append(XY[0])
Y_d.append(XY[1])
else:
X_up.append(XY[0])
Y_up.append(XY[1])
pmagplotlib.plotXY(EQ['eqarea'],X_d,Y_d,sym='b.')
pmagplotlib.plotXY(EQ['eqarea'],X_up,Y_up,sym='c.')
pmagplotlib.drawFIGS(EQ)
break
print "Triangle: wrong arrow for drill direction."
print "Delta: wrong end of compass."
print "Small circle: wrong mark on sample. [cyan upper hemisphere]"
deleteme=raw_input("Mark this sample as bad? y/[n] ")
if deleteme=='y':
reason=raw_input("Reason: [1] broke, [2] wrong drill direction, [3] wrong compass direction, [4] bad mark, [5] displaced block [6] other ")
if reason=='1':
description=' sample broke while drilling'
if reason=='2':
description=' wrong drill direction '
if reason=='3':
description=' wrong compass direction '
if reason=='4':
description=' bad mark in field'
if reason=='5':
description=' displaced block'
if reason=='6':
description=raw_input('Enter brief reason for deletion: ')
for samp in Samps:
if samp['er_sample_name']==spec['er_sample_name']:
samp['sample_orientation_flag']='b'
samp['sample_description']=samp['sample_description']+' ## direction deleted because: '+description+'##' # mark description
pmag.magic_write(sampfile,Samps,'er_samples')
repeat=raw_input("Mark another sample, this site? y/[n] ")
if repeat=='y': k-=1
else:
print 'skipping site - not enough data with specified coordinate system'
k+=1
print "sample flags stored in ",sampfile
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
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
def main():
"""
NAME
site_edit_magic.py
DESCRIPTION
makes equal area projections site by site
from pmag_specimens.txt file with
Fisher confidence ellipse using McFadden and McElhinny (1988)
technique for combining lines and planes
allows testing and reject specimens for bad orientations
SYNTAX
site_edit_magic.py [command line options]
OPTIONS
-h: prints help and quits
-f: specify pmag_specimen format file, default is pmag_specimens.txt
-fsa: specify er_samples.txt file
-exc: use existing pmag_criteria.txt file
-N: reset all sample flags to good
OUPUT
edited er_samples.txt file
"""
dir_path = '.'
FIG = {} # plot dictionary
FIG['eqarea'] = 1 # eqarea is figure 1
in_file = 'pmag_specimens.txt'
sampfile = 'er_samples.txt'
out_file = ""
fmt, plot = 'svg', 1
Crits = ""
M, N = 180., 1
repeat = ''
renew = 0
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
if '-f' in sys.argv:
ind = sys.argv.index("-f")
in_file = sys.argv[ind + 1]
if '-fsa' in sys.argv:
ind = sys.argv.index("-fsa")
sampfile = sys.argv[ind + 1]
if '-exc' in sys.argv:
Crits, file_type = pmag.magic_read(dir_path + '/pmag_criteria.txt')
for crit in Crits:
if crit['pmag_criteria_code'] == 'DE-SPEC':
M = float(crit['specimen_mad'])
N = float(crit['specimen_n'])
if '-fmt' in sys.argv:
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
if '-N' in sys.argv: renew = 1
#
if in_file[0] != "/": in_file = dir_path + '/' + in_file
if sampfile[0] != "/": sampfile = dir_path + '/' + sampfile
crd = 's'
Specs, file_type = pmag.magic_read(in_file)
if file_type != 'pmag_specimens':
print(' bad pmag_specimen input file')
sys.exit()
Samps, file_type = pmag.magic_read(sampfile)
if file_type != 'er_samples':
print(' bad er_samples input file')
sys.exit()
SO_methods = []
for rec in Samps:
if 'sample_orientation_flag' not in list(rec.keys()):
rec['sample_orientation_flag'] = 'g'
if 'sample_description' not in list(rec.keys()):
rec['sample_description'] = ''
if renew == 1:
rec['sample_orientation_flag'] = 'g'
description = rec['sample_description']
if '#' in description:
newdesc = ""
c = 0
while description[c] != '#' and c < len(
description) - 1: # look for first pound sign
newdesc = newdesc + description[c]
c += 1
while description[c] == '#':
c += 1 # skip first set of pound signs
while description[c] != '#':
c += 1 # find second set of pound signs
while description[c] == '#' and c < len(description) - 1:
c += 1 # skip second set of pound signs
while c < len(description) - 1: # look for first pound sign
newdesc = newdesc + description[c]
c += 1
rec['sample_description'] = newdesc # edit out old comment about orientations
if "magic_method_codes" in rec:
methlist = rec["magic_method_codes"]
for meth in methlist.split(":"):
if "SO" in meth.strip() and "SO-POM" not in meth.strip():
if meth.strip() not in SO_methods:
SO_methods.append(meth.strip())
pmag.magic_write(sampfile, Samps, 'er_samples')
SO_priorities = pmag.set_priorities(SO_methods, 0)
sitelist = []
for rec in Specs:
if rec['er_site_name'] not in sitelist:
sitelist.append(rec['er_site_name'])
sitelist.sort()
EQ = {}
EQ['eqarea'] = 1
pmagplotlib.plot_init(EQ['eqarea'], 5, 5)
k = 0
while k < len(sitelist):
site = sitelist[k]
print(site)
data = []
ThisSiteSpecs = pmag.get_dictitem(Specs, 'er_site_name', site, 'T')
ThisSiteSpecs = pmag.get_dictitem(ThisSiteSpecs,
'specimen_tilt_correction', '-1',
'T') # get all the unoriented data
for spec in ThisSiteSpecs:
if spec['specimen_mad'] != "" and spec[
'specimen_n'] != "" and float(
spec['specimen_mad']) <= M and float(
spec['specimen_n']) >= N:
# good spec, now get orientation....
redo, p = 1, 0
if len(SO_methods) <= 1:
az_type = SO_methods[0]
orient = pmag.find_samp_rec(spec["er_sample_name"], Samps,
az_type)
redo = 0
while redo == 1:
if p >= len(SO_priorities):
print("no orientation data for ",
spec['er_sample_name'])
orient["sample_azimuth"] = ""
orient["sample_dip"] = ""
redo = 0
else:
az_type = SO_methods[SO_methods.index(
SO_priorities[p])]
orient = pmag.find_samp_rec(spec["er_sample_name"],
Samps, az_type)
if orient["sample_azimuth"] != "":
redo = 0
p += 1
if orient['sample_azimuth'] != "":
rec = {}
for key in list(spec.keys()):
rec[key] = spec[key]
rec['dec'], rec['inc'] = pmag.dogeo(
float(spec['specimen_dec']),
float(spec['specimen_inc']),
float(orient['sample_azimuth']),
float(orient['sample_dip']))
rec["tilt_correction"] = '1'
crd = 'g'
rec['sample_azimuth'] = orient['sample_azimuth']
rec['sample_dip'] = orient['sample_dip']
data.append(rec)
if len(data) > 2:
print('specimen, dec, inc, n_meas/MAD,| method codes ')
for i in range(len(data)):
print('%s: %7.1f %7.1f %s / %s | %s' %
(data[i]['er_specimen_name'], data[i]['dec'],
data[i]['inc'], data[i]['specimen_n'],
data[i]['specimen_mad'], data[i]['magic_method_codes']))
fpars = pmag.dolnp(data, 'specimen_direction_type')
print("\n Site lines planes kappa a95 dec inc")
print(site, fpars["n_lines"], fpars["n_planes"], fpars["K"],
fpars["alpha95"], fpars["dec"], fpars["inc"], fpars["R"])
if out_file != "":
if float(fpars["alpha95"]) <= acutoff and float(
fpars["K"]) >= kcutoff:
out.write('%s %s %s\n' %
(fpars["dec"], fpars['inc'], fpars['alpha95']))
pmagplotlib.plot_lnp(EQ['eqarea'], site, data, fpars,
'specimen_direction_type')
pmagplotlib.draw_figs(EQ)
if k != 0 and repeat != 'y':
ans = input(
"s[a]ve plot, [q]uit, [e]dit specimens, [p]revious site, <return> to continue:\n "
)
elif k == 0 and repeat != 'y':
ans = input(
"s[a]ve plot, [q]uit, [e]dit specimens, <return> to continue:\n "
)
if ans == "p": k -= 2
if ans == "a":
files = {}
files['eqarea'] = site + '_' + crd + '_eqarea' + '.' + fmt
pmagplotlib.save_plots(EQ, files)
if ans == "q": sys.exit()
if ans == "e" and Samps == []:
print("can't edit samples without orientation file, sorry")
elif ans == "e":
# k-=1
testspec = input("Enter name of specimen to check: ")
for spec in data:
if spec['er_specimen_name'] == testspec:
# first test wrong direction of drill arrows (flip drill direction in opposite direction and re-calculate d,i
d, i = pmag.dogeo(float(spec['specimen_dec']),
float(spec['specimen_inc']),
float(spec['sample_azimuth']) - 180.,
-float(spec['sample_dip']))
XY = pmag.dimap(d, i)
pmagplotlib.plot_xy(EQ['eqarea'], [XY[0]], [XY[1]],
sym='g^')
# first test wrong end of compass (take az-180.)
d, i = pmag.dogeo(float(spec['specimen_dec']),
float(spec['specimen_inc']),
float(spec['sample_azimuth']) - 180.,
float(spec['sample_dip']))
XY = pmag.dimap(d, i)
pmagplotlib.plot_xy(EQ['eqarea'], [XY[0]], [XY[1]],
sym='kv')
# did the sample spin in the hole?
# now spin around specimen's z
X_up, Y_up, X_d, Y_d = [], [], [], []
for incr in range(0, 360, 5):
d, i = pmag.dogeo(
float(spec['specimen_dec']) + incr,
float(spec['specimen_inc']),
float(spec['sample_azimuth']),
float(spec['sample_dip']))
XY = pmag.dimap(d, i)
if i >= 0:
X_d.append(XY[0])
Y_d.append(XY[1])
else:
X_up.append(XY[0])
Y_up.append(XY[1])
pmagplotlib.plot_xy(EQ['eqarea'], X_d, Y_d, sym='b.')
pmagplotlib.plot_xy(EQ['eqarea'], X_up, Y_up, sym='c.')
pmagplotlib.draw_figs(EQ)
break
print("Triangle: wrong arrow for drill direction.")
print("Delta: wrong end of compass.")
print(
"Small circle: wrong mark on sample. [cyan upper hemisphere]"
)
deleteme = input("Mark this sample as bad? y/[n] ")
if deleteme == 'y':
reason = input(
"Reason: [1] broke, [2] wrong drill direction, [3] wrong compass direction, [4] bad mark, [5] displaced block [6] other "
)
if reason == '1':
description = ' sample broke while drilling'
if reason == '2':
description = ' wrong drill direction '
if reason == '3':
description = ' wrong compass direction '
if reason == '4':
description = ' bad mark in field'
if reason == '5':
description = ' displaced block'
if reason == '6':
description = input(
'Enter brief reason for deletion: ')
for samp in Samps:
if samp['er_sample_name'] == spec['er_sample_name']:
samp['sample_orientation_flag'] = 'b'
samp['sample_description'] = samp[
'sample_description'] + ' ## direction deleted because: ' + description + '##' # mark description
pmag.magic_write(sampfile, Samps, 'er_samples')
repeat = input("Mark another sample, this site? y/[n] ")
if repeat == 'y': k -= 1
else:
print(
'skipping site - not enough data with specified coordinate system'
)
k += 1
print("sample flags stored in ", sampfile)
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
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