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
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
-n 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 '-n' in args:
ind = args.index('-n')
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)
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']
if "anisotropy_n" not in rec.keys():
rec["anisotropy_n"] = "6"
if "anisotropy_sigma" not in rec.keys():
rec["anisotropy_sigma"] = "0"
fpars = pmag.dohext(
int(rec["anisotropy_n"])-6, float(rec["anisotropy_sigma"]), s)
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:
if pmagplotlib.isServer:
title = "LO:_"+ResRec['er_location_names'] + \
'_SI:_'+site+'_SA:__SP:__CO:_'+crd
else:
title = ResRec['er_location_names']
if site:
title += "_{}".format(site)
title += '_{}'.format(crd)
ResRec['er_location_names'] = pmag.makelist(Locs)
bpars, hpars = pmagplotlib.plot_anis(
ANIS, Ss, iboot, ihext, ivec, ipar, title, iplot, comp, vec, Dir, nb)
if len(PDir) > 0:
pmagplotlib.plot_circ(ANIS['data'], PDir, 90., 'g')
pmagplotlib.plot_circ(ANIS['conf'], PDir, 90., 'g')
if verbose and plots == 0:
pmagplotlib.draw_figs(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"] = ''
# regular bootstrap
BootRec["magic_method_codes"] = 'LP-AN:AE-H:AE-BS'
if ipar == 1:
# parametric bootstrap
BootRec["magic_method_codes"] = 'LP-AN:AE-H:AE-BS-P'
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 = input("")
if ans == "q":
sys.exit()
if ans == "e":
iboot, ipar, ihext, ivec = 1, 0, 0, 0
e = input("Do Hext Statistics 1/[0]: ")
if e == "1":
ihext = 1
e = input("Suppress bootstrap 1/[0]: ")
if e == "1":
iboot = 0
if iboot == 1:
e = input("Parametric bootstrap 1/[0]: ")
if e == "1":
ipar = 1
e = 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.plot_anis(
ANIS, Ss, iboot, ihext, ivec, ipar, title, iplot, comp, vec, Dir, nb)
if verbose and plots == 0:
pmagplotlib.draw_figs(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 = 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 = 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.plot_anis(
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 = 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.plot_circ(ANIS['data'], PDir, 90., 'g')
pmagplotlib.plot_circ(ANIS['conf'], PDir, 90., 'g')
if verbose and plots == 0:
pmagplotlib.draw_figs(ANIS)
if ans == "p":
k -= 2
goon = 0
if ans == "q":
k = plt
goon = 0
if ans == "s":
keepon = 1
site = 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 = input('Select one or try again\n ')
k = sitelist.index(site)
goon, ans = 0, ""
if ans == "a":
locs = pmag.makelist(Locs)
if pmagplotlib.isServer: # use server plot naming convention
title = "LO:_"+locs+'_SI:__'+'_SA:__SP:__CO:_'+crd
else: # use more readable plot naming convention
title = "{}_{}".format(locs, 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
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)
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']
if "anisotropy_n" not in rec.keys(): rec["anisotropy_n"] = "6"
if "anisotropy_sigma" not in rec.keys():
rec["anisotropy_sigma"] = "0"
fpars = pmag.dohext(
int(rec["anisotropy_n"]) - 6, float(rec["anisotropy_sigma"]),
s)
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:
if pmagplotlib.isServer:
title = "LO:_" + ResRec[
'er_location_names'] + '_SI:_' + site + '_SA:__SP:__CO:_' + crd
else:
title = ResRec['er_location_names']
if site:
title += "_{}".format(site)
title += '_{}'.format(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., 'g')
pmagplotlib.plotC(ANIS['conf'], PDir, 90., '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 = input("")
if ans == "q":
sys.exit()
if ans == "e":
iboot, ipar, ihext, ivec = 1, 0, 0, 0
e = input("Do Hext Statistics 1/[0]: ")
if e == "1": ihext = 1
e = input("Suppress bootstrap 1/[0]: ")
if e == "1": iboot = 0
if iboot == 1:
e = input("Parametric bootstrap 1/[0]: ")
if e == "1": ipar = 1
e = 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 = 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 = 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 = 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., 'g')
pmagplotlib.plotC(ANIS['conf'], PDir, 90., '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 = 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 = input('Select one or try again\n ')
k = sitelist.index(site)
goon, ans = 0, ""
if ans == "a":
locs = pmag.makelist(Locs)
if pmagplotlib.isServer: # use server plot naming convention
title = "LO:_" + locs + '_SI:__' + '_SA:__SP:__CO:_' + crd
else: # use more readable plot naming convention
title = "{}_{}".format(locs, 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
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 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 list(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] = old_div(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 = old_div(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(old_div(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' % (old_div(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)
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 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
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"] )
