def __init__(self, WD=None, name='Main Frame'):
try:
version= pmag.get_version()
except:
version = ""
title = "MakeMagIC version: %s"%version
wx.Frame.__init__(self, None, wx.ID_ANY, title, name=name)
#
self.grid_frame = None
self.panel = wx.Panel(self, size=wx.GetDisplaySize(), name='main panel')
print '-I- Fetching working directory'
self.WD = os.path.realpath(WD) or os.getcwd()
print '-I- Initializing magic data object'
self.data_model = validate_upload.get_data_model()
self.er_magic = builder.ErMagicBuilder(self.WD, self.data_model)
self.edited = False
self.validation_mode = False
# initialize magic data object
# attempt to read magic_measurements.txt, and all er_* and pmag_* files
print '-I- Read in any available data from working directory'
self.er_magic.get_all_magic_info()
# POSSIBLY RELOCATE THIS EVENTUALLY:
print '-I- Initializing headers'
self.er_magic.init_default_headers()
self.er_magic.init_actual_headers()
#
print '-I- Initializing interface'
self.InitUI()
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
core_depthplot.py
DESCRIPTION
plots various measurements versus core_depth or age. plots data flagged as 'FS-SS-C' as discrete samples.
SYNTAX
core_depthplot.py [command line optins]
OPTIONS
-h prints help message and quits
-f FILE: specify input magic_measurments format file from magi
-fsum FILE: specify input LIMS database (IODP) core summary csv file
-fwig FILE: specify input depth,wiggle to plot, in magic format with sample_core_depth key for depth
-fsa FILE: specify input er_samples format file from magic for depth
-fa FILE: specify input er_ages format file from magic for age
NB: must have either -fsa OR -fa (not both)
-fsp FILE sym size: specify input zeq_specimen format file from magic, sym and size
NB: PCAs will have specified color, while fisher means will be white with specified color as the edgecolor
-fres FILE specify input pmag_results file from magic, sym and size
-LP [AF,T,ARM,IRM, X] step [in mT,C,mT,mT, mass/vol] to plot
-S do not plot blanket treatment data (if this is set, you don't need the -LP)
-sym SYM SIZE, symbol, size for continuous points (e.g., ro 5, bs 10, g^ 10 for red dot, blue square, green triangle), default is blue dot at 5 pt
-D do not plot declination
-M do not plot magnetization
-log plot magnetization on a log scale
-L do not connect dots with a line
-I do not plot inclination
-d min max [in m] depth range to plot
-n normalize by weight in er_specimen table
-Iex: plot the expected inc at lat - only available for results with lat info in file
-ts TS amin amax: plot the GPTS for the time interval between amin and amax (numbers in Ma)
TS: [ck95, gts04, gts12]
-ds [mbsf,mcd] specify depth scale, mbsf default
-fmt [svg, eps, pdf, png] specify output format for plot (default: svg)
-sav save plot silently
DEFAULTS:
Measurements file: magic_measurements.txt
Samples file: er_samples.txt
NRM step
Summary file: none
"""
meas_file='magic_measurements.txt'
intlist=['measurement_magnitude','measurement_magn_moment','measurement_magn_volume','measurement_magn_mass']
samp_file='er_samples.txt'
depth_scale='sample_core_depth'
wt_file=''
verbose=pmagplotlib.verbose
width=10
sym,size='bo',5
Ssym,Ssize='cs',5
method,fmt="LT-NO",'.svg'
step=0
pcol=3
pel=3
pltD,pltI,pltM,pltL,pltS=1,1,1,1,1
logit=0
maxInt=-1000
minInt=1e10
maxSuc=-1000
minSuc=10000
plotexp,pTS=0,0
dir_path="."
sum_file=""
suc_file=""
age_file=""
spc_file=""
res_file=""
ngr_file=""
wig_file=""
title,location="",""
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
norm=0
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-L' in sys.argv:
pltL=0
if '-S' in sys.argv: pltS=0 # don't plot the bulk measurements at all
if '-D' in sys.argv:
pltD=0
pcol-=1
pel-=1
width-=2
if '-I' in sys.argv:
pltI=0
pcol-=1
pel-=1
width-=2
if '-M' in sys.argv:
pltM=0
pcol-=1
pel-=1
width-=2
if '-log' in sys.argv:logit=1
if '-ds' in sys.argv and 'mcd' in sys.argv:depth_scale='sample_composite_depth'
if '-sym' in sys.argv:
ind=sys.argv.index('-sym')
sym=sys.argv[ind+1]
size=float(sys.argv[ind+2])
if '-f' in sys.argv:
ind=sys.argv.index('-f')
meas_file=sys.argv[ind+1]
if '-fsa' in sys.argv:
ind=sys.argv.index('-fsa')
samp_file=sys.argv[ind+1]
if '-fa' in sys.argv:
print(main.__doc__)
print('only -fsa OR -fa - not both')
sys.exit()
elif '-fa' in sys.argv:
ind=sys.argv.index('-fa')
age_file=sys.argv[ind+1]
if '-fsp' in sys.argv:
ind=sys.argv.index('-fsp')
spc_file=dir_path+'/'+sys.argv[ind+1]
spc_sym=sys.argv[ind+2]
spc_size=float(sys.argv[ind+3])
if '-fres' in sys.argv:
ind=sys.argv.index('-fres')
res_file=dir_path+'/'+sys.argv[ind+1]
res_sym=sys.argv[ind+2]
res_size=float(sys.argv[ind+3])
if '-fwig' in sys.argv:
ind=sys.argv.index('-fwig')
wig_file=dir_path+'/'+sys.argv[ind+1]
pcol+=1
width+=2
if '-fsum' in sys.argv:
ind=sys.argv.index('-fsum')
sum_file=dir_path+'/'+sys.argv[ind+1]
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt='.'+sys.argv[ind+1]
if '-sav' in sys.argv:
plots=1
verbose=0
if '-LP' in sys.argv:
ind=sys.argv.index('-LP')
meth=sys.argv[ind+1]
if meth=="AF":
step=round(float(sys.argv[ind+2])*1e-3,6)
method='LT-AF-Z'
elif meth== 'T':
step=round(float(sys.argv[ind+2])+273,6)
method='LT-T-Z'
elif meth== 'ARM':
method='LT-AF-I'
step=round(float(sys.argv[ind+2])*1e-3,6)
elif meth== 'IRM':
method='LT-IRM'
step=round(float(sys.argv[ind+2])*1e-3,6)
elif meth== 'X':
method='LP-X'
pcol+=1
if sys.argv[ind+2]=='mass':
suc_key='measurement_chi_mass'
elif sys.argv[ind+2]=='vol':
suc_key='measurement_chi_volume'
else:
print('error in susceptibility units')
sys.exit()
else:
print('method not supported')
sys.exit()
if '-n' in sys.argv:
ind=sys.argv.index('-n')
wt_file=dir_path+'/'+sys.argv[ind+1]
norm=1
dmin,dmax=-1,-1
if '-d' in sys.argv:
ind=sys.argv.index('-d')
dmin=float(sys.argv[ind+1])
dmax=float(sys.argv[ind+2])
if '-ts' in sys.argv:
ind=sys.argv.index('-ts')
ts=sys.argv[ind+1]
amin=float(sys.argv[ind+2])
amax=float(sys.argv[ind+3])
pTS=1
pcol+=1
width+=2
#
#
# get data read in
meas_file=dir_path+'/'+meas_file
if age_file=="":
samp_file=dir_path+'/'+samp_file
Samps,file_type=pmag.magic_read(samp_file)
else:
depth_scale='age'
age_file=dir_path+'/'+age_file
Samps,file_type=pmag.magic_read(age_file)
age_unit=""
if spc_file!="":Specs,file_type=pmag.magic_read(spc_file)
if res_file!="":Results,file_type=pmag.magic_read(res_file)
if norm==1:
ErSpecs,file_type=pmag.magic_read(wt_file)
print(len(ErSpecs), ' specimens read in from ',wt_file)
Cores=[]
core_depth_key="Top depth cored CSF (m)"
if sum_file!="":
input=open(sum_file,'r').readlines()
if "Core Summary" in input[0]:
headline=1
else:
headline=0
keys=input[headline].replace('\n','').split(',')
if "Core Top (m)" in keys:core_depth_key="Core Top (m)"
if "Core Label" in keys:core_label_key="Core Label"
if "Core label" in keys:core_label_key="Core label"
for line in input[2:]:
if 'TOTALS' not in line:
CoreRec={}
for k in range(len(keys)):CoreRec[keys[k]]=line.split(',')[k]
Cores.append(CoreRec)
if len(Cores)==0:
print('no Core depth information available: import core summary file')
sum_file=""
Data=[]
if depth_scale=='sample_core_depth':
ylab="Depth (mbsf)"
elif depth_scale=='age':
ylab="Age"
else:
ylab="Depth (mcd)"
# collect the data for plotting declination
Depths,Decs,Incs,Ints=[],[],[],[]
SDepths,SDecs,SIncs,SInts=[],[],[],[]
SSucs=[]
samples=[]
methods,steps,m2=[],[],[]
if pltS: # plot the bulk measurement data
Meas,file_type=pmag.magic_read(meas_file)
meas_key='measurement_magn_moment'
print(len(Meas), ' measurements read in from ',meas_file)
for m in intlist: # find the intensity key with data
meas_data=pmag.get_dictitem(Meas,m,'','F') # get all non-blank data for this specimen
if len(meas_data)>0:
meas_key=m
break
m1=pmag.get_dictitem(Meas,'magic_method_codes',method,'has') # fish out the desired method code
if method=='LT-T-Z':
m2=pmag.get_dictitem(m1,'treatment_temp',str(step),'eval') # fish out the desired step
elif 'LT-AF' in method:
m2=pmag.get_dictitem(m1,'treatment_ac_field',str(step),'eval')
elif 'LT-IRM' in method:
m2=pmag.get_dictitem(m1,'treatment_dc_field',str(step),'eval')
elif 'LT-X' in method:
m2=pmag.get_dictitem(m1,suc_key,'','F')
if len(m2)>0:
for rec in m2: # fish out depths and weights
D=pmag.get_dictitem(Samps,'er_sample_name',rec['er_sample_name'],'T')
if not D: # if using an age_file, you may need to sort by site
D=pmag.get_dictitem(Samps,'er_site_name',rec['er_site_name'],'T')
depth=pmag.get_dictitem(D,depth_scale,'','F')
if len(depth)>0:
if ylab=='Age': ylab=ylab+' ('+depth[0]['age_unit']+')' # get units of ages - assume they are all the same!
rec['core_depth'] = float(depth[0][depth_scale])
rec['magic_method_codes'] = rec['magic_method_codes']+':'+depth[0]['magic_method_codes']
if norm==1:
specrecs=pmag.get_dictitem(ErSpecs,'er_specimen_name',rec['er_specimen_name'],'T')
specwts=pmag.get_dictitem(specrecs,'specimen_weight',"",'F')
if len(specwts)>0:
rec['specimen_weight'] = specwts[0]['specimen_weight']
Data.append(rec) # fish out data with core_depth and (if needed) weights
else:
Data.append(rec) # fish out data with core_depth and (if needed) weights
if title=="":
pieces=rec['er_sample_name'].split('-')
location=rec['er_location_name']
title=location
SData=pmag.sort_diclist(Data,'core_depth')
for rec in SData: # fish out bulk measurement data from desired depths
if dmax==-1 or float(rec['core_depth'])<dmax and float(rec['core_depth'])>dmin:
Depths.append((rec['core_depth']))
if method=="LP-X":
SSucs.append(float(rec[suc_key]))
else:
if pltD==1:Decs.append(float(rec['measurement_dec']))
if pltI==1:Incs.append(float(rec['measurement_inc']))
if norm==0 and pltM==1:Ints.append(float(rec[meas_key]))
if norm==1 and pltM==1:Ints.append(old_div(float(rec[meas_key]),float(rec['specimen_weight'])))
if len(SSucs)>0:
maxSuc=max(SSucs)
minSuc=min(SSucs)
if len(Ints)>1:
maxInt=max(Ints)
minInt=min(Ints)
if len(Depths)==0:
print('no bulk measurement data matched your request')
SpecDepths,SpecDecs,SpecIncs=[],[],[]
FDepths,FDecs,FIncs=[],[],[]
if spc_file!="": # add depths to spec data
print('spec file found')
BFLs=pmag.get_dictitem(Specs,'magic_method_codes','DE-BFL','has') # get all the discrete data with best fit lines
for spec in BFLs:
if location=="":
location=spec['er_location_name']
samp=pmag.get_dictitem(Samps,'er_sample_name',spec['er_sample_name'],'T')
if len(samp)>0 and depth_scale in list(samp[0].keys()) and samp[0][depth_scale]!="":
if ylab=='Age': ylab=ylab+' ('+samp[0]['age_unit']+')' # get units of ages - assume they are all the same!
if dmax==-1 or float(samp[0][depth_scale])<dmax and float(samp[0][depth_scale])>dmin: # filter for depth
SpecDepths.append(float(samp[0][depth_scale])) # fish out data with core_depth
SpecDecs.append(float(spec['specimen_dec'])) # fish out data with core_depth
SpecIncs.append(float(spec['specimen_inc'])) # fish out data with core_depth
else:
print('no core_depth found for: ',spec['er_specimen_name'])
FMs=pmag.get_dictitem(Specs,'magic_method_codes','DE-FM','has') # get all the discrete data with best fit lines
for spec in FMs:
if location=="":
location=spec['er_location_name']
samp=pmag.get_dictitem(Samps,'er_sample_name',spec['er_sample_name'],'T')
if len(samp)>0 and depth_scale in list(samp[0].keys()) and samp[0][depth_scale]!="":
if ylab=='Age': ylab=ylab+' ('+samp[0]['age_unit']+')' # get units of ages - assume they are all the same!
if dmax==-1 or float(samp[0][depth_scale])<dmax and float(samp[0][depth_scale])>dmin: # filter for depth
FDepths.append(float(samp[0][depth_scale]))# fish out data with core_depth
FDecs.append(float(spec['specimen_dec'])) # fish out data with core_depth
FIncs.append(float(spec['specimen_inc'])) # fish out data with core_depth
else:
print('no core_depth found for: ',spec['er_specimen_name'])
ResDepths,ResDecs,ResIncs=[],[],[]
if 'age' in depth_scale: # set y-key
res_scale='average_age'
else:
res_scale='average_height'
if res_file!="": #creates lists of Result Data
for res in Results:
meths=res['magic_method_codes'].split(":")
if 'DE-FM' in meths:
if dmax==-1 or float(res[res_scale])<dmax and float(res[res_scale])>dmin: # filter for depth
ResDepths.append(float(res[res_scale])) # fish out data with core_depth
ResDecs.append(float(res['average_dec'])) # fish out data with core_depth
ResIncs.append(float(res['average_inc'])) # fish out data with core_depth
Susc,Sus_depths=[],[]
if dmin==-1:
if len(Depths)>0: dmin,dmax=Depths[0],Depths[-1]
if len(FDepths)>0: dmin,dmax=Depths[0],Depths[-1]
if pltS==1 and len(SDepths)>0:
if SDepths[0]<dmin:dmin=SDepths[0]
if SDepths[-1]>dmax:dmax=SDepths[-1]
if len(SpecDepths)>0:
if min(SpecDepths)<dmin:dmin=min(SpecDepths)
if max(SpecDepths)>dmax:dmax=max(SpecDepths)
if len(ResDepths)>0:
if min(ResDepths)<dmin:dmin=min(ResDepths)
if max(ResDepths)>dmax:dmax=max(ResDepths)
if suc_file!="":
sucdat=open(suc_file,'r').readlines()
keys=sucdat[0].replace('\n','').split(',') # splits on underscores
for line in sucdat[1:]:
SucRec={}
for k in range(len(keys)):SucRec[keys[k]]=line.split(',')[k]
if float(SucRec['Top Depth (m)'])<dmax and float(SucRec['Top Depth (m)'])>dmin and SucRec['Magnetic Susceptibility (80 mm)']!="":
Susc.append(float(SucRec['Magnetic Susceptibility (80 mm)']))
if Susc[-1]>maxSuc:maxSuc=Susc[-1]
if Susc[-1]<minSuc:minSuc=Susc[-1]
Sus_depths.append(float(SucRec['Top Depth (m)']))
WIG,WIG_depths=[],[]
if wig_file!="":
wigdat,file_type=pmag.magic_read(wig_file)
swigdat=pmag.sort_diclist(wigdat,depth_scale)
keys=list(wigdat[0].keys())
for key in keys:
if key!=depth_scale:
plt_key=key
break
for wig in swigdat:
if float(wig[depth_scale])<dmax and float(wig[depth_scale])>dmin:
WIG.append(float(wig[plt_key]))
WIG_depths.append(float(wig[depth_scale]))
tint=4.5
plt=1
if len(Decs)>0 and len(Depths)>0 or (len(SpecDecs)>0 and len(SpecDepths)>0) or (len(ResDecs)>0 and len(ResDepths)>0) or (len(SDecs)>0 and len(SDepths)>0) or (len(SInts)>0 and len(SDepths)>0) or (len(SIncs)>0 and len(SDepths)>0):
pylab.figure(1,figsize=(width,8))
version_num=pmag.get_version()
pylab.figtext(.02,.01,version_num)
if pltD==1:
ax=pylab.subplot(1,pcol,plt)
if pltL==1:
pylab.plot(Decs,Depths,'k')
if len(Decs)>0:
pylab.plot(Decs,Depths,sym,markersize=size)
if len(Decs)==0 and pltL==1 and len(SDecs)>0:
pylab.plot(SDecs,SDepths,'k')
if len(SDecs)>0:
pylab.plot(SDecs,SDepths,Ssym,markersize=Ssize)
if spc_file!="":
pylab.plot(SpecDecs,SpecDepths,spc_sym,markersize=spc_size)
if spc_file!="" and len(FDepths)>0:
pylab.scatter(FDecs,FDepths,marker=spc_sym[-1],edgecolor=spc_sym[0],facecolor='white',s=spc_size**2)
if res_file!="":
pylab.plot(ResDecs,ResDepths,res_sym,markersize=res_size)
if sum_file!="":
for core in Cores:
depth=float(core[core_depth_key])
if depth>dmin and depth<dmax:
pylab.plot([0,360.],[depth,depth],'b--')
if pel==plt:pylab.text(360,depth+tint,core[core_label_key])
if pel==plt:
pylab.axis([0,400,dmax,dmin])
else:
pylab.axis([0,360.,dmax,dmin])
pylab.xlabel('Declination')
pylab.ylabel(ylab)
plt+=1
pmagplotlib.delticks(ax) # dec xticks are too crowded otherwise
if pltI==1:
pylab.subplot(1,pcol,plt)
if pltL==1:pylab.plot(Incs,Depths,'k')
if len(Incs)>0:pylab.plot(Incs,Depths,sym,markersize=size)
if len(Incs)==0 and pltL==1 and len(SIncs)>0:pylab.plot(SIncs,SDepths,'k')
if len(SIncs)>0:pylab.plot(SIncs,SDepths,Ssym,markersize=Ssize)
if spc_file!="" and len(SpecDepths)>0:pylab.plot(SpecIncs,SpecDepths,spc_sym,markersize=spc_size)
if spc_file!="" and len(FDepths)>0:
pylab.scatter(FIncs,FDepths,marker=spc_sym[-1],edgecolor=spc_sym[0],facecolor='white',s=spc_size**2)
if res_file!="":pylab.plot(ResIncs,ResDepths,res_sym,markersize=res_size)
if sum_file!="":
for core in Cores:
depth=float(core[core_depth_key])
if depth>dmin and depth<dmax:
if pel==plt:pylab.text(90,depth+tint,core[core_label_key])
pylab.plot([-90,90],[depth,depth],'b--')
pylab.plot([0,0],[dmax,dmin],'k-')
if pel==plt:
pylab.axis([-90,110,dmax,dmin])
else:
pylab.axis([-90,90,dmax,dmin])
pylab.xlabel('Inclination')
pylab.ylabel('')
plt+=1
if pltM==1 and len(Ints)>0 or len(SInts)>0:
pylab.subplot(1,pcol,plt)
for pow in range(-10,10):
if maxInt*10**pow>1:break
if logit==0:
for k in range(len(Ints)):
Ints[k]=Ints[k]*10**pow
for k in range(len(SInts)):
SInts[k]=SInts[k]*10**pow
if pltL==1 and len(Ints)>0: pylab.plot(Ints,Depths,'k')
if len(Ints)>0:pylab.plot(Ints,Depths,sym,markersize=size)
if len(Ints)==0 and pltL==1 and len(SInts)>0:pylab.plot(SInts,SDepths,'k-')
if len(SInts)>0:pylab.plot(SInts,SDepths,Ssym,markersize=Ssize)
if sum_file!="":
for core in Cores:
depth=float(core[core_depth_key])
pylab.plot([0,maxInt*10**pow+.1],[depth,depth],'b--')
if depth>dmin and depth<dmax:pylab.text(maxInt*10**pow-.2*maxInt*10**pow,depth+tint,core[core_label_key])
pylab.axis([0,maxInt*10**pow+.1,dmax,dmin])
if norm==0:
pylab.xlabel('%s %i %s'%('Intensity (10^-',pow,' Am^2)'))
else:
pylab.xlabel('%s %i %s'%('Intensity (10^-',pow,' Am^2/kg)'))
else:
if pltL==1: pylab.semilogx(Ints,Depths,'k')
if len(Ints)>0:pylab.semilogx(Ints,Depths,sym,markersize=size)
if len(Ints)==0 and pltL==1 and len(SInts)>0:pylab.semilogx(SInts,SDepths,'k')
if len(Ints)==0 and pltL==1 and len(SInts)>0:pylab.semilogx(SInts,SDepths,'k')
if len(SInts)>0:pylab.semilogx(SInts,SDepths,Ssym,markersize=Ssize)
if sum_file!="":
for core in Cores:
depth=float(core[core_depth_key])
pylab.semilogx([minInt,maxInt],[depth,depth],'b--')
if depth>dmin and depth<dmax:pylab.text(maxInt-.2*maxInt,depth+tint,core[core_label_key])
pylab.axis([0,maxInt,dmax,dmin])
if norm==0:
pylab.xlabel('Intensity (Am^2)')
else:
pylab.xlabel('Intensity (Am^2/kg)')
plt+=1
if suc_file!="" or len(SSucs)>0:
pylab.subplot(1,pcol,plt)
if len(Susc)>0:
if pltL==1:pylab.plot(Susc,Sus_depths,'k')
if logit==0:pylab.plot(Susc,Sus_depths,sym,markersize=size)
if logit==1:pylab.semilogx(Susc,Sus_depths,sym,markersize=size)
if len(SSucs)>0:
if logit==0:pylab.plot(SSucs,SDepths,sym,markersize=size)
if logit==1:pylab.semilogx(SSucs,SDepths,sym,markersize=size)
if sum_file!="":
for core in Cores:
depth=float(core[core_depth_key])
if logit==0:pylab.plot([minSuc,maxSuc],[depth,depth],'b--')
if logit==1:pylab.semilogx([minSuc,maxSuc],[depth,depth],'b--')
pylab.axis([minSuc,maxSuc,dmax,dmin])
pylab.xlabel('Susceptibility')
plt+=1
if wig_file!="":
pylab.subplot(1,pcol,plt)
pylab.plot(WIG,WIG_depths,'k')
if sum_file!="":
for core in Cores:
depth=float(core[core_depth_key])
pylab.plot([WIG[0],WIG[-1]],[depth,depth],'b--')
pylab.axis([min(WIG),max(WIG),dmax,dmin])
pylab.xlabel(plt_key)
plt+=1
if pTS==1:
ax1=pylab.subplot(1,pcol,plt)
ax1.axis([-.25,1.5,amax,amin])
plt+=1
TS,Chrons=pmag.get_ts(ts)
X,Y,Y2=[0,1],[],[]
cnt=0
if amin<TS[1]: # in the Brunhes
Y=[amin,amin] # minimum age
Y1=[TS[1],TS[1]] # age of the B/M boundary
ax1.fill_between(X,Y,Y1,facecolor='black') # color in Brunhes, black
for d in TS[1:]:
pol=cnt%2
cnt+=1
if d<=amax and d>=amin:
ind=TS.index(d)
Y=[TS[ind],TS[ind]]
Y1=[TS[ind+1],TS[ind+1]]
if pol: ax1.fill_between(X,Y,Y1,facecolor='black') # fill in every other time
ax1.plot([0,1,1,0,0],[amin,amin,amax,amax,amin],'k-')
ax2=ax1.twinx()
pylab.ylabel("Age (Ma): "+ts)
for k in range(len(Chrons)-1):
c=Chrons[k]
cnext=Chrons[k+1]
d=cnext[1]-old_div((cnext[1]-c[1]),3.)
if d>=amin and d<amax:
ax2.plot([1,1.5],[c[1],c[1]],'k-') # make the Chron boundary tick
ax2.text(1.05,d,c[0]) #
ax2.axis([-.25,1.5,amax,amin])
figname=location+'_m:_'+method+'_core-depthplot'+fmt
pylab.title(location)
if verbose:
pylab.draw()
ans=input("S[a]ve plot? ")
if ans=='a':
pylab.savefig(figname)
print('Plot saved as ',figname)
elif plots:
pylab.savefig(figname)
print('Plot saved as ',figname)
sys.exit()
def main():
"""
NAME
thellier_magic_redo.py
DESCRIPTION
Calculates paleointensity parameters for thellier-thellier type data using bounds
stored in the "redo" file
SYNTAX
thellier_magic_redo [command line options]
OPTIONS
-h prints help message
-usr USER: identify user, default is ""
-fcr CRIT, set criteria for grading
-f IN: specify input file, default is magic_measurements.txt
-fre REDO: specify redo file, default is "thellier_redo"
-F OUT: specify output file, default is thellier_specimens.txt
-leg: attaches "Recalculated from original measurements; supercedes published results. " to comment field
-CR PERC TYPE: apply a cooling rate correction.
PERC should be a percentage of original (say reduce to 90%)
TYPE should be one of the following:
EG (for educated guess); PS (based on pilots); TRM (based on comparison of two TRMs)
-Fcr CRout: specify pmag_specimen format file for cooling rate corrected data
-ANI: there are anisotropy data to correct thellier results
-fan ANIFILE: specify rmag_anisotropy format file, default is rmag_anisotropy.txt
-Fac ACout: specify pmag_specimen format file for anisotropy corrected data
default is AC_specimens.txt
-NLT: there are non-linear trm data in the measurements file to correct thellier results
-fnl NLTFILE: specify magic_measurments format file, default is magic_measurements.txt
-Fnl NLTout: specify pmag_specimen format file for non-linear trm corrected data
default is NLT_specimens.txt
-z use z component differenences for pTRM calculation
"""
dir_path='.'
critout=""
version_num=pmag.get_version()
field,first_save=-1,1
spec,recnum,start,end=0,0,0,0
frac=0
NltRecs,PmagSpecs,AniSpecRecs,NltSpecRecs,CRSpecs=[],[],[],[],[]
meas_file,pmag_file,mk_file="magic_measurements.txt","thellier_specimens.txt","thellier_redo"
anis_file="rmag_anisotropy.txt"
anisout,nltout="AC_specimens.txt","NLT_specimens.txt"
crout="CR_specimens.txt"
nlt_file=""
comment,user="","unknown"
anis,nltrm=0,0
jackknife=0 # maybe in future can do jackknife
args=sys.argv
Zdiff=0
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 "-leg" in args: comment="Recalculated from original measurements; supercedes published results. "
if "-CR" in args:
ind=args.index("-CR")
frac=.01*float(sys.argv[ind+1])
crtype=sys.argv[ind+2]
if "-Fcr" in args:
ind=args.index("-Fcr")
crout=sys.argv[ind+1]
if "-f" in args:
ind=args.index("-f")
meas_file=sys.argv[ind+1]
if "-F" in args:
ind=args.index("-F")
pmag_file=sys.argv[ind+1]
if "-fre" in args:
ind=args.index("-fre")
mk_file=args[ind+1]
#
#
if "-ANI" in args:
anis=1
ind=args.index("-ANI")
if "-Fac" in args:
ind=args.index("-Fac")
anisout=args[ind+1]
if "-fan" in args:
ind=args.index("-fan")
anis_file=args[ind+1]
#
if "-NLT" in args:
nltrm=1
if "-Fnl" in args:
ind=args.index("-Fnl")
nltout=args[ind+1]
if "-fnl" in args:
ind=args.index("-fnl")
nlt_file=args[ind+1]
if "-z" in args: Zdiff=1
if '-fcr' in sys.argv:
ind=args.index("-fcr")
critout=sys.argv[ind+1]
#
# start reading in data:
#
meas_file=dir_path+"/"+meas_file
mk_file=dir_path+"/"+mk_file
critout=dir_path+"/"+critout
try:
open(critout,'rU')
accept_keys=['specimen_int_ptrm_n','specimen_md','specimen_fvds','specimen_b_beta','specimen_dang','specimen_drats','specimen_Z']
crit_data,file_type=pmag.magic_read(critout)
print "Acceptance criteria read in from ", critout
accept={}
accept['specimen_int_ptrm_n']=2.0
for critrec in crit_data:
if critrec["pmag_criteria_code"]=="IE-SPEC":
for key in accept_keys:
if key not in critrec.keys():
accept[key]=-1
else:
accept[key]=float(critrec[key])
except:
critout="" # no acceptance criteria specified
meas_data,file_type=pmag.magic_read(meas_file)
if file_type != 'magic_measurements':
print file_type
print file_type,"This is not a valid magic_measurements file "
sys.exit()
try:
mk_f=open(mk_file,'rU')
except:
print "Bad redo file"
sys.exit()
mkspec=[]
speclist=[]
for line in mk_f.readlines():
tmp=line.split()
mkspec.append(tmp)
speclist.append(tmp[0])
if anis==1:
anis_file=dir_path+"/"+anis_file
anis_data,file_type=pmag.magic_read(anis_file)
if file_type != 'rmag_anisotropy':
print file_type
print file_type,"This is not a valid rmag_anisotropy file "
sys.exit()
if nlt_file=="":
nlt_data=meas_data # look for trm acquisition data in the meas_data file
else:
nlt_file=dir_path+"/"+nlt_file
nlt_data,file_type=pmag.magic_read(nlt_file)
#
# sort the specimen names and step through one by one
#
sids=pmag.get_specs(meas_data)
#
print 'Processing ',len(speclist),' specimens - please wait '
while spec < len(speclist):
s=speclist[spec]
recnum=0
datablock=[]
PmagSpecRec={}
PmagSpecRec["er_analyst_mail_names"]=user
PmagSpecRec["er_citation_names"]="This study"
PmagSpecRec["magic_software_packages"]=version_num
methcodes,inst_code=[],""
#
# find the data from the meas_data file for this specimen
#
for rec in meas_data:
if rec["er_specimen_name"].lower()==s.lower():
if "magic_instrument_codes" not in rec.keys():
rec["magic_instrument_codes"]="unknown"
meths=rec["magic_method_codes"]
for meth in meths:meth.strip() # get rid of annoying spaces in method codes
if "LP-PI-TRM" in meths: datablock.append(rec)
#
# collect info for the PmagSpecRec dictionary
#
if len(datablock)>0:
rec=datablock[0]
PmagSpecRec["er_specimen_name"]=s
PmagSpecRec["er_sample_name"]=rec["er_sample_name"]
PmagSpecRec["er_site_name"]=rec["er_site_name"]
PmagSpecRec["er_location_name"]=rec["er_location_name"]
PmagSpecRec["measurement_step_unit"]="K"
PmagSpecRec["specimen_correction"]='u'
if "magic_instrument_codes" not in rec.keys():
PmagSpecRec["magic_instrument_codes"]="unknown"
else:
PmagSpecRec["magic_instrument_codes"]=rec["magic_instrument_codes"]
if "magic_experiment_name" not in rec.keys():
rec["magic_experiment_name"]=""
else:
PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"]
meths=rec["magic_experiment_name"].split(":")
for meth in meths:
if meth.strip() not in methcodes and "LP-" in meth:methcodes.append(meth.strip())
#
# sort out the data into first_Z, first_I, ptrm_check, ptrm_tail
#
araiblock,field=pmag.sortarai(datablock,s,Zdiff)
first_Z=araiblock[0]
first_I=araiblock[1]
ptrm_check=araiblock[2]
ptrm_tail=araiblock[3]
if len(first_I)<3 or len(first_Z)<4:
spec+=1
print 'skipping specimen ', s
else:
#
# get start, end
#
for redospec in mkspec:
if redospec[0]==s:
b,e=float(redospec[1]),float(redospec[2])
break
if e > float(first_Z[-1][0]):e=float(first_Z[-1][0])
for recnum in range(len(first_Z)):
if first_Z[recnum][0]==b:start=recnum
if first_Z[recnum][0]==e:end=recnum
nsteps=end-start
if nsteps>2:
zijdblock,units=pmag.find_dmag_rec(s,meas_data)
pars,errcode=pmag.PintPars(araiblock,zijdblock,start,end)
pars['measurement_step_unit']=units
pars["specimen_lab_field_dc"]=field
pars["specimen_int"]=-1*field*pars["specimen_b"]
PmagSpecRec["measurement_step_min"]='%8.3e' % (pars["measurement_step_min"])
PmagSpecRec["measurement_step_max"]='%8.3e' % (pars["measurement_step_max"])
PmagSpecRec["specimen_int_n"]='%i'%(pars["specimen_int_n"])
PmagSpecRec["specimen_lab_field_dc"]='%8.3e'%(pars["specimen_lab_field_dc"])
PmagSpecRec["specimen_int"]='%9.4e '%(pars["specimen_int"])
PmagSpecRec["specimen_b"]='%5.3f '%(pars["specimen_b"])
PmagSpecRec["specimen_q"]='%5.1f '%(pars["specimen_q"])
PmagSpecRec["specimen_f"]='%5.3f '%(pars["specimen_f"])
PmagSpecRec["specimen_fvds"]='%5.3f'%(pars["specimen_fvds"])
PmagSpecRec["specimen_b_beta"]='%5.3f'%(pars["specimen_b_beta"])
PmagSpecRec["specimen_int_mad"]='%7.1f'%(pars["specimen_int_mad"])
PmagSpecRec["specimen_Z"]='%7.1f'%(pars["specimen_Z"])
PmagSpecRec["specimen_gamma"]='%7.1f'%(pars["specimen_gamma"])
if pars["method_codes"]!="" and pars["method_codes"] not in methcodes: methcodes.append(pars["method_codes"])
PmagSpecRec["specimen_dec"]='%7.1f'%(pars["specimen_dec"])
PmagSpecRec["specimen_inc"]='%7.1f'%(pars["specimen_inc"])
PmagSpecRec["specimen_tilt_correction"]='-1'
PmagSpecRec["specimen_direction_type"]='l'
PmagSpecRec["direction_type"]='l' # this is redudant, but helpful - won't be imported
PmagSpecRec["specimen_dang"]='%7.1f '%(pars["specimen_dang"])
PmagSpecRec["specimen_drats"]='%7.1f '%(pars["specimen_drats"])
PmagSpecRec["specimen_int_ptrm_n"]='%i '%(pars["specimen_int_ptrm_n"])
PmagSpecRec["specimen_rsc"]='%6.4f '%(pars["specimen_rsc"])
PmagSpecRec["specimen_md"]='%i '%(int(pars["specimen_md"]))
if PmagSpecRec["specimen_md"]=='-1':PmagSpecRec["specimen_md"]=""
PmagSpecRec["specimen_b_sigma"]='%5.3f '%(pars["specimen_b_sigma"])
if "IE-TT" not in methcodes:methcodes.append("IE-TT")
methods=""
for meth in methcodes:
methods=methods+meth+":"
PmagSpecRec["magic_method_codes"]=methods[:-1]
PmagSpecRec["magic_software_packages"]=version_num
PmagSpecRec["specimen_description"]=comment
if critout!="":
score,kill=pmag.grade(PmagSpecRec,accept)
Grade=""
if score==len(accept.keys()):Grade='A'
if score==len(accept.keys())-1:Grade='B'
if score==len(accept.keys())-2:Grade='C'
if score==len(accept.keys())-3:Grade='D'
if score<=len(accept.keys())-4:Grade='F'
PmagSpecRec["specimen_grade"]=Grade
else:
PmagSpecRec["specimen_grade"]=""
if nltrm==0 and anis==0 and frac!=0: # apply cooling rate correction
CrSpecRec={}
for key in PmagSpecRec.keys():CrSpecRec[key]=PmagSpecRec[key]
inten=frac*float(CrSpecRec['specimen_int'])
CrSpecRec["specimen_int"]='%9.4e '%(inten) # adjust specimen intensity by cooling rate correction
CrSpecRec['magic_method_codes'] = CrSpecRec['magic_method_codes']+':DA-CR-'+crtype
CrSpecRec["specimen_correction"]='c'
CRSpecs.append(CrSpecRec)
PmagSpecs.append(PmagSpecRec)
NltSpecRec=""
#
# check on non-linear TRM correction
#
if nltrm==1:
#
# find the data from the nlt_data list for this specimen
#
TRMs,Bs=[],[]
NltSpecRec=""
NltRecs=[]
for NltRec in nlt_data:
if NltRec['er_specimen_name']==PmagSpecRec["er_specimen_name"]:
meths=NltRec["magic_method_codes"].split(":")
for meth in meths:meth.strip()
if "LP-TRM" in meths: NltRecs.append(NltRec)
if len(NltRecs) > 2:
for NltRec in NltRecs:
Bs.append(float(NltRec['treatment_dc_field']))
TRMs.append(float(NltRec['measurement_magn_moment']))
NLTpars=nlt.NLtrm(Bs,TRMs,float(PmagSpecRec['specimen_int']),float(PmagSpecRec['specimen_lab_field_dc']),0)
if NLTpars['banc']>0:
NltSpecRec={}
for key in PmagSpecRec.keys():
NltSpecRec[key]=PmagSpecRec[key]
NltSpecRec['specimen_int']='%9.4e'%(NLTpars['banc'])
NltSpecRec['magic_method_codes']=PmagSpecRec["magic_method_codes"]+":DA-NL"
NltSpecRec["specimen_correction"]='c'
NltSpecRec['specimen_grade']=PmagSpecRec['specimen_grade']
NltSpecRec["magic_software_packages"]=version_num
print NltSpecRec['er_specimen_name'], ' Banc= ',float(NLTpars['banc'])*1e6
if anis==0 and frac!=0:
CrSpecRec={}
for key in NltSpecRec.keys():CrSpecRec[key]=NltSpecRec[key]
inten=frac*float(CrSpecRec['specimen_int'])
CrSpecRec["specimen_int"]='%9.4e '%(inten) # adjust specimen intensity by cooling rate correction
CrSpecRec['magic_method_codes'] = CrSpecRec['magic_method_codes']+':DA-CR-'+crtype
CRSpecs.append(CrSpecRec)
NltSpecRecs.append(NltSpecRec)
#
# check on anisotropy correction
if anis==1:
if NltSpecRec!="":
Spc=NltSpecRec
else: # find uncorrected data
Spc=PmagSpecRec
for AniSpec in anis_data:
if AniSpec["er_specimen_name"]==PmagSpecRec["er_specimen_name"]:
AniSpecRec=pmag.thellier_anis_corr(Spc,AniSpec)
AniSpecRec['specimen_grade']=PmagSpecRec['specimen_grade']
inst_codes=Spc["magic_instrument_codes"]
if "magic_instrument_codes" in AniSpec.keys():
if inst_codes=="unknown":
inst_codes=AniSpec["magic_instrument_codes"]
else:
inst_codes=inst_codes+":"+AniSpec["magic_instrument_codes"]
AniSpecRec["magic_instrument_codes"]=inst_codes
AniSpecRec["specimen_correction"]='c'
AniSpecRec["magic_software_packages"]=version_num
if frac!=0:
CrSpecRec={}
for key in AniSpecRec.keys():CrSpecRec[key]=AniSpecRec[key]
inten=frac*float(CrSpecRec['specimen_int'])
CrSpecRec["specimen_int"]='%9.4e '%(inten) # adjust specimen intensity by cooling rate correction
CrSpecRec['magic_method_codes'] = CrSpecRec['magic_method_codes']+':DA-CR-'+crtype
CRSpecs.append(CrSpecRec)
AniSpecRecs.append(AniSpecRec)
break
elif anis==1:
for AniSpec in anis_data:
if AniSpec["er_specimen_name"]==PmagSpecRec["er_specimen_name"]:
AniSpecRec=pmag.thellier_anis_corr(PmagSpecRec,AniSpec)
AniSpecRec['specimen_grade']=PmagSpecRec['specimen_grade']
inst_codes=PmagSpecRec["magic_instrument_codes"]
if "magic_instrument_codes" in AniSpec.keys():
if inst_codes=="unknown":
inst_codes=AniSpec["magic_instrument_codes"]
else:
inst_codes=inst_codes+":"+AniSpec["magic_instrument_codes"]
AniSpecRec["magic_instrument_codes"]=inst_codes
AniSpecRec["specimen_correction"]='c'
AniSpecRec["magic_software_packages"]=version_num
if frac!=0:
CrSpecRec={}
for key in AniSpecRec.keys():CrSpecRec[key]=AniSpecRec[key]
inten=frac*float(CrSpecRec['specimen_int'])
CrSpecRec["specimen_int"]='%9.4e '%(inten) # adjust specimen intensity by cooling rate correction
CrSpecRec['magic_method_codes'] = CrSpecRec['magic_method_codes']+':DA-CR-'+crtype
CRSpecs.append(CrSpecRec)
AniSpecRecs.append(AniSpecRec)
break
spec +=1
else:
print "skipping ",s
spec+=1
pmag_file=dir_path+'/'+pmag_file
pmag.magic_write(pmag_file,PmagSpecs,'pmag_specimens')
if anis==1:
anisout=dir_path+'/'+anisout
pmag.magic_write(anisout,AniSpecRecs,'pmag_specimens')
if nltrm==1:
nltout=dir_path+'/'+nltout
pmag.magic_write(nltout,NltSpecRecs,'pmag_specimens')
if frac!=0:
crout=dir_path+'/'+crout
pmag.magic_write(crout,CRSpecs,'pmag_specimens')
def main():
"""
NAME
HUJI_magic.py
DESCRIPTION
converts HUJI format files to magic_measurements format files
SYNTAX
HUJI_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify input file, required
-F FILE: specify output file, default is magic_measurements.txt
-LP [colon delimited list of protocols, include all that apply]
AF: af demag
T: thermal including thellier but not trm acquisition
N: NRM only
TRM: trm acquisition
ANI: anisotropy experiment
CR: cooling rate experiment.
The treatment coding of the measurement file should be: XXX.00,XXX.10, XXX.20 ...XX.70 etc. (XXX.00 is optional)
where XXX in the temperature and .10,.20... are running numbers of the cooling rates steps.
XXX.00 is optional zerofield baseline. XXX.70 is alteration check.
syntax in sio_magic is: -LP CR xxx,yyy,zzz,.....xx
where xx, yyy,zzz...xxx are cooling time in [K/minutes], seperated by comma, ordered at the same order as XXX.10,XXX.20 ...XX.70
if you use a zerofield step then no need to specify the cooling rate for the zerofield
-spc NUM : specify number of characters to designate a specimen, default = 0
-loc LOCNAME : specify location/study name, must have either LOCNAME or SAMPFILE or be a synthetic
-dc B PHI THETA: dc lab field (in micro tesla) and phi,theta, default is none
NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment
# to do! -ac B : peak AF field (in mT) for ARM acquisition, default is none
-ncn NCON: specify naming convention: default is #1 below
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
[8] synthetic - has no site name
[9] ODP naming convention
INPUT
separate experiments ( AF, thermal, thellier, trm aquisition) should be seperate files
(eg. af.txt, thermal.txt, etc.)
HUJI masurement file format (space delimited text):
Spec lab-running-numbe-code Date Hour Treatment-type(T/N/A) Treatment(XXX.XX) dec(geo) inc(geo) dec(tilt) inc(tilt)
---------
conventions:
Spec: specimen name
Treat: treatment step
XXX T in Centigrade
XXX AF in mT
for special experiments:
Thellier:
XXX.0 first zero field step
XXX.1 first in field step [XXX.0 and XXX.1 can be done in any order]
XXX.2 second in-field step at lower temperature (pTRM check)
ATRM:
X.00 optional baseline
X.1 ATRM step (+X)
X.2 ATRM step (+Y)
X.3 ATRM step (+Z)
X.4 ATRM step (-X)
X.5 ATRM step (-Y)
X.6 ATRM step (-Z)
X.7 optional alteration check (+X)
TRM:
XXX.YYY XXX is temperature step of total TRM
YYY is dc field in microtesla
Intensity assumed to be total moment in 10^3 Am^2 (emu)
Declination: Declination in specimen coordinate system
Inclination: Inclination in specimen coordinate system
Optional metatdata string: mm/dd/yy;hh:mm;[dC,mT];xx.xx;UNITS;USER;INST;NMEAS
hh in 24 hours.
dC or mT units of treatment XXX (see Treat above) for thermal or AF respectively
xx.xxx DC field
UNITS of DC field (microT, mT)
INST: instrument code, number of axes, number of positions (e.g., G34 is 2G, three axes,
measured in four positions)
NMEAS: number of measurements in a single position (1,3,200...)
"""
args=sys.argv
meas_file="magic_measurements.txt"
user=""
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
else:
user=""
if '-F' in args:
ind=args.index("-F")
meas_file=args[ind+1]
if '-f' in args:
ind=args.index("-f")
magfile=args[ind+1]
try:
input=open(magfile,'rU')
except:
print "bad mag file name"
sys.exit()
else:
print "mag_file field is required option"
print main.__doc__
sys.exit()
if "-dc" in args:
ind=args.index("-dc")
labfield=float(args[ind+1])*1e-6
phi=float(args[ind+2])
theta=float(args[ind+3])
if "-ac" in args:
ind=args.index("-ac")
peakfield=float(args[ind+1])*1e-3
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if specnum!=0:specnum=-specnum
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4-" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z=int(samp_con.split("-")[1])
samp_con="4"
if "7-" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z=int(samp_con.split("-")[1])
samp_con="7"
# lab process:
if '-LP' in args:
ind=args.index("-LP")
codelist=args[ind+1]
codes=codelist.split(':')
if "AF" in codes:
demag='AF'
LPcode="LP-DIR-AF"
if "T" in codes:
demag="T"
if '-dc' not in args: LPcode="LP-DIR-T"
if '-dc' in args: LPcode="LP-PI-TRM"
if "ANI" in codes:
if '-dc' not in args:
print "missing option -dc exiting"
exit()
LPcode="LP-AN-TRM"
if "TRM" in codes:
demag="T"
LPcode="LP-TRM"
#trm=1
if "CR" in codes:
demag="T"
# dc should be in the code
if '-dc' not in args:
print "missing option -dc exiting"
exit()
LPcode="LP-TRM-CR" # TRM in different cooling rates
ind=args.index("-LP")
CR_cooling_times=args[ind+2].split(",")
#print CR_cooling_time ,"CR_cooling_time"
version_num=pmag.get_version()
MagRecs=[]
#--------------------------------------
# Read the file
# Assumption:
# 1. different lab protocolsa are in different files
# 2. measurements are in the correct order
#--------------------------------------
Data={}
line_no=0
for line in input.readlines():
line_no+=1
this_line_data={}
line_no+=1
instcode=""
if len(line)<2:
continue
if line[0]=="#": #HUJI way of marking bad data points
continue
rec=line.strip('\n').split()
specimen=rec[0]
date=rec[2].split("/")
hour=rec[3].split(":")
treatment_type=rec[4]
treatment=rec[5].split(".")
dec=rec[6]
inc=rec[7]
dec_tilted=rec[8]
inc_tilted=rec[9]
moment_emu=float(rec[10])
if specimen not in Data.keys():
Data[specimen]=[]
# check duplicate treatments:
# if yes, delete the first and use the second
if len(Data[specimen])>0:
if treatment==Data[specimen][-1]['treatment']:
del(Data[specimen][-1])
print "-W- Identical treatimens in file %s magfile line %i: specimen %s, treatment %s deleting the first. " %(magfile, line_no, specimen,".".join(treatment))
this_line_data={}
this_line_data['specimen']=specimen
this_line_data['date']=date
this_line_data['hour']=hour
this_line_data['treatment_type']=treatment_type
this_line_data['treatment']=treatment
this_line_data['dec']=dec
this_line_data['inc']=inc
this_line_data['dec_tilted']=dec_tilted
this_line_data['inc_tilted']=inc_tilted
this_line_data['moment_emu']=moment_emu
Data[specimen].append(this_line_data)
print "-I- done reading file %s"%magfile
#--------------------------------------
# Convert to MagIC
#--------------------------------------
specimens_list=Data.keys()
specimens_list.sort()
MagRecs=[]
for specimen in specimens_list:
for i in range(len(Data[specimen])):
#print LPcode
this_line_data=Data[specimen][i]
methcode=""
MagRec={}
MagRec["er_specimen_name"]=this_line_data['specimen']
if specnum!=0:
MagRec["er_sample_name"]=this_line_data['specimen'][:specnum]
else:
MagRec["er_sample_name"]=this_line_data['specimen']
if samp_con=="1":
MagRec["er_site_name"]=MagRec["er_sample_name"][:-1]
elif samp_con=="2":
parts=MagRec["er_sample_name"].split('-')
MagRec["er_site_name"]= parts[0]
elif samp_con=="3":
parts=MagRec["er_sample_name"].split('.')
MagRec["er_site_name"]= parts[0]
elif samp_con=='4':
MagRec["er_site_name"]=MagRec["er_sample_name"][0:-Z]
elif samp_con=='5':
MagRec["er_site_name"]=MagRec["er_sample_name"]
elif samp_con=='7':
MagRec["er_site_name"]=MagRec["er_sample_name"][0:Z]
else:
MagRec["er_site_name"]=MagRec["er_sample_name"] # site=sample by default
if "-loc" in args:
MagRec['er_location_name']=er_location_name
else:
MagRec['er_location_name']=MagRec["er_site_name"]
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_magn_moment"]='%10.3e'% (float(this_line_data['moment_emu'])*1e-3) # moment in Am^2 (from emu)
MagRec["measurement_dec"]=this_line_data['dec']
MagRec["measurement_inc"]=this_line_data['inc']
date=this_line_data['date']
hour=this_line_data['hour']
if float(date[2])>80:
yyyy="19"+date[2]
else:
yyyy="20"+date[2]
if len (date[0])==1:
date[0]="0"+date[0]
if len (date[1])==1:
date[1]="0"+date[1]
MagRec["measurement_date"]=":".join([yyyy,date[0],date[1],hour[0],hour[1],"00.00"])
#print MagRec["measurement_date"]," Ron check please"
MagRec["measurement_time_zone"]='JER'
MagRec['er_analyst_mail_names'] =user
MagRec["er_citation_names"]="This study"
MagRec["magic_instrument_codes"]="HUJI-2G"
MagRec["measurement_flag"]="g"
MagRec["measurement_positions"]="1"
MagRec["measurement_positions"]="1"
MagRec["measurement_standard"]="u"
MagRec["measurement_description"]=""
MagRec["treatment_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
#----------------------------------------
# AF demag
# do not support AARM yet
#----------------------------------------
if demag=="AF":
# demag in zero field
if LPcode != "LP-AN-ARM":
MagRec["treatment_ac_field"]='%8.3e' %(float(this_line_data['treatment'][0])*1e-3) # peak field in tesla
MagRec["treatment_dc_field"]='0'
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
if treatment_type=="N":
methcode="LP-DIR-AF:LT-NO"
elif treatment_type=="A":
methcode="LP-DIR-AF:LT-AF-Z"
else:
print "ERROR in treatment field line %i... exiting until you fix the problem" %line_no
exit()
# AARM experiment
else:
print "Dont supprot AARM in HUJI format yet. sorry... do be DONE"
MagRec["magic_method_codes"]=methcode
MagRec["magic_experiment_name"]=specimen+ ":" + LPcode
MagRec["measurement_number"]="%i"%i
MagRec["measurement_description"]=""
MagRecs.append(MagRec)
#continue
#----------------------------------------
# Thermal:
# Thellier experiment: "IZ", "ZI", "IZZI", pTRM checks
# Thermal demag
# Thermal cooling rate experiment
# Thermal NLT
#----------------------------------------
if demag=="T":
treatment=this_line_data['treatment']
treatment_type=this_line_data['treatment_type']
#----------------------------------------
# Thellier experimet
#----------------------------------------
if LPcode == "LP-PI-TRM" : # Thelllier experiment
MagRec["magic_experiment_name"]=specimen+ ":" + LPcode
methcode=LPcode
if treatment_type=="N" or ( (treatment[1]=='0' or treatment[1]=='00') and float(treatment[0])==0):
LT_code="LT-NO"
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
MagRec["treatment_dc_field"]='0'
MagRec["treatment_temp"]='273.'
elif treatment[1]=='0' or treatment[1]=='00':
LT_code="LT-T-Z"
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
MagRec["treatment_dc_field"]='%8.3e'%(0)
MagRec["treatment_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
# check if this is ZI or IZ:
# check if the same temperature already measured:
methcode="LP-PI-TRM:LP-PI-TRM-ZI"
for j in range (0,i):
if Data[specimen][j]['treatment'][0] == treatment[0]:
if Data[specimen][j]['treatment'][1] == '1' or Data[specimen][j]['treatment'][1] == '10':
methcode="LP-PI-TRM:LP-PI-TRM-IZ"
else:
methcode="LP-PI-TRM:LP-PI-TRM-ZI"
elif treatment[1]=='1' or treatment[1]=='10':
LT_code="LT-T-I"
MagRec["treatment_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MagRec["treatment_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MagRec["treatment_dc_field_theta"]='%7.1f' % (theta) # labfield theta
MagRec["treatment_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
# check if this is ZI or IZ:
# check if the same temperature already measured:
methcode="LP-PI-TRM:LP-PI-TRM-IZ"
for j in range (0,i):
if Data[specimen][j]['treatment'][0] == treatment[0]:
if Data[specimen][j]['treatment'][1] == '0' or Data[specimen][j]['treatment'][1] == '00':
methcode="LP-PI-TRM:LP-PI-TRM-ZI"
else:
methcode="LP-PI-TRM:LP-PI-TRM-IZ"
elif treatment[1]=='2' or treatment[1]=='20':
LT_code="LT-PTRM-I"
MagRec["treatment_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MagRec["treatment_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MagRec["treatment_dc_field_theta"]='%7.1f' % (theta) # labfield theta
MagRec["treatment_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
methcode="LP-PI-TRM:LP-PI-TRM-IZ"
else:
print "ERROR in treatment field line %i... exiting until you fix the problem" %line_no
exit()
MagRec["magic_method_codes"]=LT_code+":"+methcode
MagRec["measurement_number"]="%i"%i
MagRec["measurement_description"]=""
MagRecs.append(MagRec)
#continue
#----------------------------------------
# demag experimet
#----------------------------------------
if LPcode == "LP-DIR-T" :
MagRec["magic_experiment_name"]=specimen+ ":" + LPcode
methcode=LPcode
if treatment_type=="N":
LT_code="LT-NO"
else:
LT_code="LT-T-Z"
methcode=LPcode+":"+"LT-T-Z"
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
MagRec["treatment_dc_field"]='%8.3e'%(0)
MagRec["treatment_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
MagRec["magic_method_codes"]=LT_code+":"+methcode
MagRec["measurement_number"]="%i"%i
MagRec["measurement_description"]=""
MagRecs.append(MagRec)
#continue
#----------------------------------------
# ATRM measurements
# The direction of the magnetization is used to determine the
# direction of the lab field.
#----------------------------------------
if LPcode =="LP-AN-TRM" :
MagRec["magic_experiment_name"]=specimen+ ":" + LPcode
methcode=LPcode
if float(treatment[1])==0:
MagRec["magic_method_codes"]="LP-AN-TRM:LT-T-Z"
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
MagRec["treatment_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
MagRec["treatment_dc_field"]='0'
else:
if float(treatment[1])==7:
# alteration check
methcode="LP-AN-TRM:LT-PTRM-I"
MagRec["measurement_number"]='7'# -z
else:
MagRec["magic_method_codes"]="LP-AN-TRM:LT-T-I"
inc=float(MagRec["measurement_inc"]);dec=float(MagRec["measurement_dec"])
if abs(inc)<45 and (dec<45 or dec>315): # +x
tdec,tinc=0,0
MagRec["measurement_number"]='1'
if abs(inc)<45 and (dec<135 and dec>45):
tdec,tinc=90,0
MagRec["measurement_number"]='2' # +y
if inc>45 :
tdec,tinc=0,90
MagRec["measurement_number"]='3' # +z
if abs(inc)<45 and (dec<225 and dec>135):
tdec,tinc=180,0
MagRec["measurement_number"]='4' # -x
if abs(inc)<45 and (dec<315 and dec>225):
tdec,tinc=270,0
MagRec["measurement_number"]='5'# -y
if inc<-45 :
tdec,tinc=0,-90
MagRec["measurement_number"]='6'# -z
MagRec["treatment_dc_field_phi"]='%7.1f' %(tdec)
MagRec["treatment_dc_field_theta"]='%7.1f'% (tinc)
MagRec["treatment_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
MagRec["treatment_dc_field"]='%8.3e'%(labfield)
MagRec["measurement_description"]=""
MagRecs.append(MagRec)
#continue
#----------------------------------------
# NLT measurements
# or TRM acquisistion experiment
#----------------------------------------
if LPcode == "LP-TRM" :
MagRec["magic_experiment_name"]=specimen+ ":" + LPcode
MagRec["magic_method_codes"]="LP-TRM:LT-T-I"
if float(treatment[1])==0:
labfield=0
else:
labfield=float(float(treatment[1]))*1e-6
MagRec["treatment_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
MagRec["treatment_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MagRec["treatment_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MagRec["treatment_dc_field_theta"]='%7.1f' % (theta) # labfield theta
MagRec["measurement_number"]="%i"%i
MagRec["measurement_description"]=""
MagRecs.append(MagRec)
#continue
#----------------------------------------
# Cooling rate experiments
#----------------------------------------
if LPcode =="LP-TRM-CR":
index=int(treatment[1][0])
#print index,"index"
#print CR_cooling_times,"CR_cooling_times"
#print CR_cooling_times[index-1]
#print CR_cooling_times[0:index-1]
CR_cooling_time=CR_cooling_times[index-1]
if CR_cooling_time in CR_cooling_times[0:index-1]:
MagRec["magic_method_codes"]="LP-TRM-CR"+":" +"LT-PTRM-I"
else:
MagRec["magic_method_codes"]="LP-TRM-CR"
MagRec["magic_experiment_name"]=specimen+ ":" + LPcode
MagRec["treatment_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
MagRec["treatment_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MagRec["treatment_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MagRec["treatment_dc_field_theta"]='%7.1f' % (theta) # labfield theta
MagRec["measurement_number"]="%i"%index
MagRec["measurement_description"]="%i minutes cooling time"%int(CR_cooling_time)
MagRecs.append(MagRec)
#continue
pmag.magic_write(meas_file,MagRecs,'magic_measurements')
print "-I- results put in ",meas_file
def main():
"""
NAME
thellier_magic.py
DESCRIPTION
plots Thellier-Thellier, allowing interactive setting of bounds
and customizing of selection criteria. Saves and reads interpretations
from a pmag_specimen formatted table, default: thellier_specimens.txt
SYNTAX
thellier_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f MEAS, set magic_measurements input file
-fsp PRIOR, set pmag_specimen prior interpretations file
-fan ANIS, set rmag_anisotropy file for doing the anisotropy corrections
-fcr CRIT, set criteria file for grading.
-fmt [svg,png,jpg], format for images - default is svg
-sav, saves plots with out review (default format)
-spc SPEC, plots single specimen SPEC, saves plot with specified format
with optional -b bounds adn quits
-b BEG END: sets bounds for calculation
BEG: starting step for slope calculation
END: ending step for slope calculation
-z use only z component difference for pTRM calculation
DEFAULTS
MEAS: magic_measurements.txt
REDO: thellier_redo
CRIT: NONE
PRIOR: NONE
OUTPUT
figures:
ALL: numbers refer to temperature steps in command line window
1) Arai plot: closed circles are zero-field first/infield
open circles are infield first/zero-field
triangles are pTRM checks
squares are pTRM tail checks
VDS is vector difference sum
diamonds are bounds for interpretation
2) Zijderveld plot: closed (open) symbols are X-Y (X-Z) planes
X rotated to NRM direction
3) (De/Re)Magnetization diagram:
circles are NRM remaining
squares are pTRM gained
4) equal area projections:
green triangles are pTRM gained direction
red (purple) circles are lower(upper) hemisphere of ZI step directions
blue (cyan) squares are lower(upper) hemisphere IZ step directions
5) Optional: TRM acquisition
6) Optional: TDS normalization
command line window:
list is: temperature step numbers, temperatures (C), Dec, Inc, Int (units of magic_measuements)
list of possible commands: type letter followed by return to select option
saving of plots creates .svg format files with specimen_name, plot type as name
"""
#
# initializations
#
meas_file,critout,inspec="magic_measurements.txt","","thellier_specimens.txt"
first=1
inlt=0
version_num=pmag.get_version()
TDinit,Tinit,field,first_save=0,0,-1,1
user,comment,AniSpec,locname="",'',"",""
ans,specimen,recnum,start,end=0,0,0,0,0
plots,pmag_out,samp_file,style=0,"","","svg"
verbose=pmagplotlib.verbose
fmt='.'+style
#
# default acceptance criteria
#
accept=pmag.default_criteria(0)[0] # set the default criteria
#
# parse command line options
#
Zdiff,anis=0,0
spc,BEG,END="","",""
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index('-f')
meas_file=sys.argv[ind+1]
if '-fsp' in sys.argv:
ind=sys.argv.index('-fsp')
inspec=sys.argv[ind+1]
if '-fan' in sys.argv:
ind=sys.argv.index('-fan')
anisfile=sys.argv[ind+1]
anis=1
anis_data,file_type=pmag.magic_read(anisfile)
if verbose: print "Anisotropy data read in from ", anisfile
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt='.'+sys.argv[ind+1]
if '-sav' in sys.argv:
plots=1
verbose=0
if '-z' in sys.argv: Zdiff=1
if '-spc' in sys.argv:
ind=sys.argv.index('-spc')
spc=sys.argv[ind+1]
if '-b' in sys.argv:
ind=sys.argv.index('-b')
BEG=int(sys.argv[ind+1])
END=int(sys.argv[ind+2])
if '-fcr' in sys.argv:
ind=sys.argv.index('-fcr')
critout=sys.argv[ind+1]
crit_data,file_type=pmag.magic_read(critout)
if file_type!='pmag_criteria':
if verbose: print 'bad pmag_criteria file, using no acceptance criteria'
accept=pmag.default_criteria(1)[0]
else:
if verbose: print "Acceptance criteria read in from ", critout
accept={'pmag_criteria_code':'ACCEPTANCE','er_citation_names':'This study'}
for critrec in crit_data:
if 'sample_int_sigma_uT' in critrec.keys(): # accommodate Shaar's new criterion
critrec['sample_int_sigma']='%10.3e'%(eval(critrec['sample_int_sigma_uT'])*1e-6)
for key in critrec.keys():
if key not in accept.keys() and critrec[key]!='':
accept[key]=critrec[key]
try:
open(inspec,'rU')
PriorRecs,file_type=pmag.magic_read(inspec)
if file_type != 'pmag_specimens':
print file_type
print file_type,inspec," is not a valid pmag_specimens file "
sys.exit()
for rec in PriorRecs:
if 'magic_software_packages' not in rec.keys():rec['magic_software_packages']=""
except IOError:
PriorRecs=[]
if verbose:print "starting new specimen interpretation file: ",inspec
meas_data,file_type=pmag.magic_read(meas_file)
if file_type != 'magic_measurements':
print file_type
print file_type,"This is not a valid magic_measurements file "
sys.exit()
backup=0
# define figure numbers for arai, zijderveld and
# de-,re-magization diagrams
AZD={}
AZD['deremag'], AZD['zijd'],AZD['arai'],AZD['eqarea']=1,2,3,4
pmagplotlib.plot_init(AZD['arai'],5,5)
pmagplotlib.plot_init(AZD['zijd'],5,5)
pmagplotlib.plot_init(AZD['deremag'],5,5)
pmagplotlib.plot_init(AZD['eqarea'],5,5)
#
#
#
# get list of unique specimen names
#
CurrRec=[]
sids=pmag.get_specs(meas_data)
# get plots for specimen s - default is just to step through arai diagrams
#
if spc!="": specimen =sids.index(spc)
while specimen < len(sids):
methcodes=[]
if verbose:
print sids[specimen],specimen+1, 'of ', len(sids)
MeasRecs=[]
s=sids[specimen]
datablock,trmblock,tdsrecs=[],[],[]
PmagSpecRec={}
if first==0:
for key in keys:PmagSpecRec[key]="" # make sure all new records have same set of keys
PmagSpecRec["er_analyst_mail_names"]=user
PmagSpecRec["specimen_correction"]='u'
#
# find the data from the meas_data file for this specimen
#
for rec in meas_data:
if rec["er_specimen_name"]==s:
MeasRecs.append(rec)
if "magic_method_codes" not in rec.keys():
rec["magic_method_codes"]=""
methods=rec["magic_method_codes"].split(":")
meths=[]
for meth in methods:
meths.append(meth.strip()) # take off annoying spaces
methods=""
for meth in meths:
if meth.strip() not in methcodes and "LP-" in meth:methcodes.append(meth.strip())
methods=methods+meth+":"
methods=methods[:-1]
rec["magic_method_codes"]=methods
if "LP-PI-TRM" in meths: datablock.append(rec)
if "LP-TRM" in meths: trmblock.append(rec)
if "LP-TRM-TD" in meths: tdsrecs.append(rec)
if len(trmblock)>2 and inspec!="":
if Tinit==0:
Tinit=1
AZD['TRM']=5
pmagplotlib.plot_init(AZD['TRM'],5,5)
elif Tinit==1: # clear the TRM figure if not needed
pmagplotlib.clearFIG(AZD['TRM'])
if len(tdsrecs)>2:
if TDinit==0:
TDinit=1
AZD['TDS']=6
pmagplotlib.plot_init(AZD['TDS'],5,5)
elif TDinit==1: # clear the TDS figure if not needed
pmagplotlib.clearFIG(AZD['TDS'])
if len(datablock) <4:
if backup==0:
specimen+=1
if verbose:
print 'skipping specimen - moving forward ', s
else:
specimen-=1
if verbose:
print 'skipping specimen - moving backward ', s
#
# collect info for the PmagSpecRec dictionary
#
else:
rec=datablock[0]
PmagSpecRec["er_citation_names"]="This study"
PmagSpecRec["er_specimen_name"]=s
PmagSpecRec["er_sample_name"]=rec["er_sample_name"]
PmagSpecRec["er_site_name"]=rec["er_site_name"]
PmagSpecRec["er_location_name"]=rec["er_location_name"]
locname=rec['er_location_name'].replace('/','-')
if "er_expedition_name" in rec.keys():PmagSpecRec["er_expedition_name"]=rec["er_expedition_name"]
if "magic_instrument_codes" not in rec.keys():rec["magic_instrument_codes"]=""
PmagSpecRec["magic_instrument_codes"]=rec["magic_instrument_codes"]
PmagSpecRec["measurement_step_unit"]="K"
if "magic_experiment_name" not in rec.keys():
rec["magic_experiment_name"]=""
else:
PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"]
meths=rec["magic_method_codes"].split()
# sort data into types
araiblock,field=pmag.sortarai(datablock,s,Zdiff)
first_Z=araiblock[0]
GammaChecks=araiblock[5]
if len(first_Z)<3:
if backup==0:
specimen+=1
if verbose:
print 'skipping specimen - moving forward ', s
else:
specimen-=1
if verbose:
print 'skipping specimen - moving backward ', s
else:
backup=0
zijdblock,units=pmag.find_dmag_rec(s,meas_data)
recnum=0
if verbose:
print "index step Dec Inc Int Gamma"
for plotrec in zijdblock:
if GammaChecks!="":
gamma=""
for g in GammaChecks:
if g[0]==plotrec[0]-273:
gamma=g[1]
break
if gamma!="":
print '%i %i %7.1f %7.1f %8.3e %7.1f' % (recnum,plotrec[0]-273,plotrec[1],plotrec[2],plotrec[3],gamma)
else:
print '%i %i %7.1f %7.1f %8.3e ' % (recnum,plotrec[0]-273,plotrec[1],plotrec[2],plotrec[3])
recnum += 1
pmagplotlib.plotAZ(AZD,araiblock,zijdblock,s,units[0])
if verbose:pmagplotlib.drawFIGS(AZD)
if len(tdsrecs)>2: # a TDS experiment
tdsblock=[] # make a list for the TDS data
Mkeys=['measurement_magnitude','measurement_magn_moment','measurement_magn_volume','measuruement_magn_mass']
mkey,k="",0
while mkey=="" and k<len(Mkeys)-1: # find which type of intensity
key= Mkeys[k]
if key in tdsrecs[0].keys() and tdsrecs[0][key]!="": mkey=key
k+=1
if mkey=="":break # get outta here
Tnorm=""
for tdrec in tdsrecs:
meths=tdrec['magic_method_codes'].split(":")
for meth in meths: meth.replace(" ","") # strip off potential nasty spaces
if 'LT-T-I' in meths and Tnorm=="": # found first total TRM
Tnorm=float(tdrec[mkey]) # normalize by total TRM
tdsblock.append([273,zijdblock[0][3]/Tnorm,1.]) # put in the zero step
if 'LT-T-Z' in meths and Tnorm!="": # found a LP-TRM-TD demag step, now need complementary LT-T-Z from zijdblock
step=float(tdrec['treatment_temp'])
Tint=""
if mkey!="":
Tint=float(tdrec[mkey])
if Tint!="":
for zrec in zijdblock:
if zrec[0]==step: # found matching
tdsblock.append([step,zrec[3]/Tnorm,Tint/Tnorm])
break
if len(tdsblock)>2:
pmagplotlib.plotTDS(AZD['TDS'],tdsblock,s+':LP-PI-TDS:')
if verbose:pmagplotlib(drawFIGS(AZD))
else:
print "Something wrong here"
if anis==1: # look up anisotropy data for this specimen
AniSpec=""
for aspec in anis_data:
if aspec["er_specimen_name"]==PmagSpecRec["er_specimen_name"]:
AniSpec=aspec
if verbose: print 'Found anisotropy record...'
break
if inspec !="":
if verbose: print 'Looking up saved interpretation....'
found = 0
for k in range(len(PriorRecs)):
try:
if PriorRecs[k]["er_specimen_name"]==s:
found =1
CurrRec.append(PriorRecs[k])
for j in range(len(zijdblock)):
if float(zijdblock[j][0])==float(PriorRecs[k]["measurement_step_min"]):start=j
if float(zijdblock[j][0])==float(PriorRecs[k]["measurement_step_max"]):end=j
pars,errcode=pmag.PintPars(datablock,araiblock,zijdblock,start,end,accept)
pars['measurement_step_unit']="K"
pars['experiment_type']='LP-PI-TRM'
del PriorRecs[k] # put in CurrRec, take out of PriorRecs
if errcode!=1:
pars["specimen_lab_field_dc"]=field
pars["specimen_int"]=-1*field*pars["specimen_b"]
pars["er_specimen_name"]=s
if verbose:
print 'Saved interpretation: '
pars,kill=pmag.scoreit(pars,PmagSpecRec,accept,'',verbose)
pmagplotlib.plotB(AZD,araiblock,zijdblock,pars)
if verbose:pmagplotlib.drawFIGS(AZD)
if len(trmblock)>2:
blab=field
best=pars["specimen_int"]
Bs,TRMs=[],[]
for trec in trmblock:
Bs.append(float(trec['treatment_dc_field']))
TRMs.append(float(trec['measurement_magn_moment']))
NLpars=nlt.NLtrm(Bs,TRMs,best,blab,0) # calculate best fit parameters through TRM acquisition data, and get new banc
Mp,Bp=[],[]
for k in range(int(max(Bs)*1e6)):
Bp.append(float(k)*1e-6)
npred=nlt.TRM(Bp[-1],NLpars['xopt'][0],NLpars['xopt'][1]) # predicted NRM for this field
Mp.append(npred)
pmagplotlib.plotTRM(AZD['TRM'],Bs,TRMs,Bp,Mp,NLpars,trec['magic_experiment_name'])
PmagSpecRec['specimen_int']=NLpars['banc']
if verbose:
print 'Banc= ',float(NLpars['banc'])*1e6
pmagplotlib.drawFIGS(AZD)
mpars=pmag.domean(araiblock[1],start,end,'DE-BFL')
if verbose:
print 'pTRM direction= ','%7.1f'%(mpars['specimen_dec']),' %7.1f'%(mpars['specimen_inc']),' MAD:','%7.1f'%(mpars['specimen_mad'])
if AniSpec!="":
CpTRM=pmag.Dir_anis_corr([mpars['specimen_dec'],mpars['specimen_inc']],AniSpec)
AniSpecRec=pmag.doaniscorr(PmagSpecRec,AniSpec)
if verbose:
print 'Anisotropy corrected TRM direction= ','%7.1f'%(CpTRM[0]),' %7.1f'%(CpTRM[1])
print 'Anisotropy corrected intensity= ',float(AniSpecRec['specimen_int'])*1e6
else:
print 'error on specimen ',s
except:
pass
if verbose and found==0: print ' None found :( '
if spc!="":
if BEG!="":
pars,errcode=pmag.PintPars(datablock,araiblock,zijdblock,BEG,END,accept)
pars['measurement_step_unit']="K"
pars["specimen_lab_field_dc"]=field
pars["specimen_int"]=-1*field*pars["specimen_b"]
pars["er_specimen_name"]=s
pars['specimen_grade']='' # ungraded
pmagplotlib.plotB(AZD,araiblock,zijdblock,pars)
if verbose:pmagplotlib.drawFIGS(AZD)
if len(trmblock)>2:
if inlt==0:
inlt=1
blab=field
best=pars["specimen_int"]
Bs,TRMs=[],[]
for trec in trmblock:
Bs.append(float(trec['treatment_dc_field']))
TRMs.append(float(trec['measurement_magn_moment']))
NLpars=nlt.NLtrm(Bs,TRMs,best,blab,0) # calculate best fit parameters through TRM acquisition data, and get new banc
#
Mp,Bp=[],[]
for k in range(int(max(Bs)*1e6)):
Bp.append(float(k)*1e-6)
npred=nlt.TRM(Bp[-1],NLpars['xopt'][0],NLpars['xopt'][1]) # predicted NRM for this field
files={}
for key in AZD.keys():
files[key]=s+'_'+key+fmt
pmagplotlib.saveP(AZD,files)
sys.exit()
if verbose:
ans='b'
while ans != "":
print """
s[a]ve plot, set [b]ounds for calculation, [d]elete current interpretation, [p]revious, [s]ample, [q]uit:
"""
ans=raw_input('Return for next specimen \n')
if ans=="":
specimen +=1
if ans=="d":
save_redo(PriorRecs,inspec)
CurrRec=[]
pmagplotlib.plotAZ(AZD,araiblock,zijdblock,s,units[0])
if verbose:pmagplotlib.drawFIGS(AZD)
if ans=='a':
files={}
for key in AZD.keys():
files[key]="LO:_"+locname+'_SI:_'+PmagSpecRec['er_site_name']+'_SA:_'+PmagSpecRec['er_sample_name']+'_SP:_'+s+'_CO:_s_TY:_'+key+fmt
pmagplotlib.saveP(AZD,files)
ans=""
if ans=='q':
print "Good bye"
sys.exit()
if ans=='p':
specimen =specimen -1
backup = 1
ans=""
if ans=='s':
keepon=1
spec=raw_input('Enter desired specimen name (or first part there of): ')
while keepon==1:
try:
specimen =sids.index(spec)
keepon=0
except:
tmplist=[]
for qq in range(len(sids)):
if spec in sids[qq]:tmplist.append(sids[qq])
print specimen," not found, but this was: "
print tmplist
spec=raw_input('Select one or try again\n ')
ans=""
if ans=='b':
if end==0 or end >=len(zijdblock):end=len(zijdblock)-1
GoOn=0
while GoOn==0:
answer=raw_input('Enter index of first point for calculation: ['+str(start)+'] ')
try:
start=int(answer)
answer=raw_input('Enter index of last point for calculation: ['+str(end)+'] ')
end=int(answer)
if start >=0 and start <len(zijdblock)-2 and end >0 and end <len(zijdblock) or start>=end:
GoOn=1
else:
print "Bad endpoints - try again! "
start,end=0,len(zijdblock)
except ValueError:
print "Bad endpoints - try again! "
start,end=0,len(zijdblock)
s=sids[specimen]
pars,errcode=pmag.PintPars(datablock,araiblock,zijdblock,start,end,accept)
pars['measurement_step_unit']="K"
pars["specimen_lab_field_dc"]=field
pars["specimen_int"]=-1*field*pars["specimen_b"]
pars["er_specimen_name"]=s
pars,kill=pmag.scoreit(pars,PmagSpecRec,accept,'',0)
PmagSpecRec['specimen_scat']=pars['specimen_scat']
PmagSpecRec['specimen_frac']='%5.3f'%(pars['specimen_frac'])
PmagSpecRec['specimen_gmax']='%5.3f'%(pars['specimen_gmax'])
PmagSpecRec["measurement_step_min"]='%8.3e' % (pars["measurement_step_min"])
PmagSpecRec["measurement_step_max"]='%8.3e' % (pars["measurement_step_max"])
PmagSpecRec["measurement_step_unit"]="K"
PmagSpecRec["specimen_int_n"]='%i'%(pars["specimen_int_n"])
PmagSpecRec["specimen_lab_field_dc"]='%8.3e'%(pars["specimen_lab_field_dc"])
PmagSpecRec["specimen_int"]='%9.4e '%(pars["specimen_int"])
PmagSpecRec["specimen_b"]='%5.3f '%(pars["specimen_b"])
PmagSpecRec["specimen_q"]='%5.1f '%(pars["specimen_q"])
PmagSpecRec["specimen_f"]='%5.3f '%(pars["specimen_f"])
PmagSpecRec["specimen_fvds"]='%5.3f'%(pars["specimen_fvds"])
PmagSpecRec["specimen_b_beta"]='%5.3f'%(pars["specimen_b_beta"])
PmagSpecRec["specimen_int_mad"]='%7.1f'%(pars["specimen_int_mad"])
PmagSpecRec["specimen_Z"]='%7.1f'%(pars["specimen_Z"])
PmagSpecRec["specimen_gamma"]='%7.1f'%(pars["specimen_gamma"])
PmagSpecRec["specimen_grade"]=pars["specimen_grade"]
if pars["method_codes"]!="":
tmpcodes=pars["method_codes"].split(":")
for t in tmpcodes:
if t.strip() not in methcodes:methcodes.append(t.strip())
PmagSpecRec["specimen_dec"]='%7.1f'%(pars["specimen_dec"])
PmagSpecRec["specimen_inc"]='%7.1f'%(pars["specimen_inc"])
PmagSpecRec["specimen_tilt_correction"]='-1'
PmagSpecRec["specimen_direction_type"]='l'
PmagSpecRec["direction_type"]='l' # this is redundant, but helpful - won't be imported
PmagSpecRec["specimen_int_dang"]='%7.1f '%(pars["specimen_int_dang"])
PmagSpecRec["specimen_drats"]='%7.1f '%(pars["specimen_drats"])
PmagSpecRec["specimen_drat"]='%7.1f '%(pars["specimen_drat"])
PmagSpecRec["specimen_int_ptrm_n"]='%i '%(pars["specimen_int_ptrm_n"])
PmagSpecRec["specimen_rsc"]='%6.4f '%(pars["specimen_rsc"])
PmagSpecRec["specimen_md"]='%i '%(int(pars["specimen_md"]))
if PmagSpecRec["specimen_md"]=='-1':PmagSpecRec["specimen_md"]=""
PmagSpecRec["specimen_b_sigma"]='%5.3f '%(pars["specimen_b_sigma"])
if "IE-TT" not in methcodes:methcodes.append("IE-TT")
methods=""
for meth in methcodes:
methods=methods+meth+":"
PmagSpecRec["magic_method_codes"]=methods[:-1]
PmagSpecRec["specimen_description"]=comment
PmagSpecRec["magic_software_packages"]=version_num
pmagplotlib.plotAZ(AZD,araiblock,zijdblock,s,units[0])
pmagplotlib.plotB(AZD,araiblock,zijdblock,pars)
if verbose:pmagplotlib.drawFIGS(AZD)
if len(trmblock)>2:
blab=field
best=pars["specimen_int"]
Bs,TRMs=[],[]
for trec in trmblock:
Bs.append(float(trec['treatment_dc_field']))
TRMs.append(float(trec['measurement_magn_moment']))
NLpars=nlt.NLtrm(Bs,TRMs,best,blab,0) # calculate best fit parameters through TRM acquisition data, and get new banc
Mp,Bp=[],[]
for k in range(int(max(Bs)*1e6)):
Bp.append(float(k)*1e-6)
npred=nlt.TRM(Bp[-1],NLpars['xopt'][0],NLpars['xopt'][1]) # predicted NRM for this field
Mp.append(npred)
pmagplotlib.plotTRM(AZD['TRM'],Bs,TRMs,Bp,Mp,NLpars,trec['magic_experiment_name'])
if verbose:
print 'Non-linear TRM corrected intensity= ',float(NLpars['banc'])*1e6
if verbose:pmagplotlib.drawFIGS(AZD)
pars["specimen_lab_field_dc"]=field
pars["specimen_int"]=-1*field*pars["specimen_b"]
pars,kill=pmag.scoreit(pars,PmagSpecRec,accept,'',verbose)
saveit=raw_input("Save this interpretation? [y]/n \n")
if saveit!='n':
PriorRecs.append(PmagSpecRec) # put back an interpretation
specimen+=1
save_redo(PriorRecs,inspec)
ans=""
elif plots==1:
specimen+=1
if fmt != ".pmag":
files={}
for key in AZD.keys():
files[key]="LO:_"+locname+'_SI:_'+PmagSpecRec['er_site_name']+'_SA:_'+PmagSpecRec['er_sample_name']+'_SP:_'+s+'_CO:_s_TY:_'+key+'_'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['deremag']='DeReMag Plot'
titles['zijd']='Zijderveld Plot'
titles['arai']='Arai Plot'
AZD = pmagplotlib.addBorders(AZD,titles,black,purple)
pmagplotlib.saveP(AZD,files)
# pmagplotlib.combineFigs(s,files,3)
else: # save in pmag format
script="grep "+s+" output.mag | thellier -mfsi"
script=script+' %8.4e'%(field)
min='%i'%((pars["measurement_step_min"]-273))
Max='%i'%((pars["measurement_step_max"]-273))
script=script+" "+min+" "+Max
script=script+" |plotxy;cat mypost >>thellier.ps\n"
pltf.write(script)
pmag.domagicmag(outf,MeasRecs)
if len(CurrRec)>0:
for rec in CurrRec:
PriorRecs.append(rec)
CurrRec=[]
if plots!=1 and verbose:
ans=raw_input(" Save last plot? 1/[0] ")
if ans=="1":
if fmt != ".pmag":
files={}
for key in AZD.keys():
files[key]=s+'_'+key+fmt
pmagplotlib.saveP(AZD,files)
else:
print "\n Good bye\n"
sys.exit()
if len(CurrRec)>0:PriorRecs.append(CurrRec) # put back an interpretation
if len(PriorRecs)>0:
save_redo(PriorRecs,inspec)
print 'Updated interpretations saved in ',inspec
if verbose:
print "Good bye"
def main():
"""
NAME
LIVMW_magic.py
DESCRIPTION
converts Liverpool microwave format files to magic_measurements format files
SYNTAX
LIVMW_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify liverpool format input file, required
-usr USER: identify user, default is ""
-ins INST: identify instrument, e.g., LIV-TRISTAN, LIV-OLD14GHZ, default is ""
-loc LOCNAME : specify location/study name, required
-F FILE: specify output file, default is magic_measurements.txt
-Fsa FILE: specify er_samples formatted file for appending, default is new er_samples.txt
-spc NUM : specify number of characters to designate a specimen, default = 1
-sit Site_name : specify site name for this specimen
-unc measurement units are uncalibrated (default is uAm^2)
-B PHI THETA: dc lab field phi, theta, default is 0, 90
-ncn NCON: specify naming convention - required if -sit not specified
Sample naming convention:
do not use if -sit option used!
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
"""
# initialize some stuff
version_num = pmag.get_version()
noave = 0
methcode, instcode = "", ""
phi, theta, peakfield, labfield = 0, 0, 0, 0
pMRM, MD, samp_con, Z, site = 0, 0, "6", "", ""
er_location_name = ""
citation = "This study"
args = sys.argv
methcode = "LP-NO" # NRM
specnum, measnum = 1, 1
powt_max = 0
ErSamps, Samps = [], []
#
# get command line arguments
#
dirpath = "."
meas_file, samp_file = dirpath + "/magic_measurements.txt", dirpath + "/er_samples.txt"
user = ""
unc = 0
if "-WD" in args:
ind = args.index("-WD")
dirpath = args[ind + 1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind = args.index("-usr")
user = args[ind + 1]
if "-ins" in args:
ind = args.index("-ins")
instcode = args[ind + 1]
if "-F" in args:
ind = args.index("-F")
meas_file = dirpath + "/" + args[ind + 1]
if "-Fsa" in args:
ind = args.index("-Fsa")
samp_file = args[ind + 1]
samp_file = dirpath + "/" + samp_file
try:
open(samp_file, "rU")
ErSamps, file_type = pmag.magic_read(samp_file)
print "sample information will be appended to new er_samples.txt file"
except:
print "er_samples.txt file does not exist"
print "sample information will be stored in new er_samples.txt file"
if "-f" in args:
ind = args.index("-f")
magfile = args[ind + 1]
magfile = dirpath + "/" + magfile
try:
input = open(magfile, "rU")
except:
print "bad mag file name"
sys.exit()
else:
print "mag_file field is required option"
print main.__doc__
sys.exit()
if "-B" in args:
ind = args.index("-B")
phi = args[ind + 1]
theta = args[ind + 2]
else:
phi, theta = "0.", "90."
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind + 1])
if specnum != 0:
specnum = -specnum
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if "-unc" in args:
unc = 1
if "-sit" in args:
ind = args.index("-sit")
site = args[ind + 1]
if "-ncn" in args:
ind = args.index("-ncn")
samp_con = sys.argv[ind + 1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "7"
if samp_con == "6" and site == "":
print "you must either specify a naming convention, or a site name"
print main.__doc__
sys.exit()
MagRecs = []
if len(ErSamps) > 1:
for samp in ErSamps:
if samp["er_sample_name"] not in Samps:
Samps.append(samp["er_sample_name"])
Data = input.readlines()
if 1: # never mind
for line in Data:
if len(line) > 1:
rec = line.split(",")
MagRec = {}
MagRec["er_citation_names"] = "This study"
MagRec["er_location_name"] = er_location_name
MagRec["magic_software_packages"] = version_num
MagRec["treatment_temp"] = "%8.3e" % (273) # room temp in kelvin
MagRec["measurement_temp"] = "%8.3e" % (273) # room temp in kelvin
MagRec["treatment_ac_field"] = "0"
MagRec["treatment_dc_field"] = "0"
MagRec["treatment_dc_field_phi"] = ""
MagRec["treatment_dc_field_theta"] = ""
MagRec["treatment_mw_integral"] = ""
meas_type = "LT-NO"
MagRec["er_specimen_name"] = rec[0][1:-1]
MagRec["er_location_name"] = er_location_name
if specnum != 0:
MagRec["er_sample_name"] = rec[0][1:-1][:specnum]
else:
MagRec["er_sample_name"] = rec[0][1:-1]
if site == "":
site = pmag.parse_site(MagRec["er_sample_name"], samp_con, Z)
MagRec["er_site_name"] = site
MagRec["treatment_mw_power"] = rec[2]
MagRec["treatment_mw_time"] = rec[3]
powt = int(float(MagRec["treatment_mw_power"]) * (float(MagRec["treatment_mw_time"])))
MagRec["treatment_mw_energy"] = "%7.1f" % (powt)
if powt > powt_max:
powt_max = powt
treat = rec[1].strip('"').upper()
if treat == "Z": # in zero field
meas_type = "LT-M-Z" # as opposed to LT-MV-Z
if powt < powt_max:
meas_type = "LT-PMRM-Z"
elif treat == "A": # in zero field
meas_type = "LT-M-I" # as opposed to LT-MV-I
labfield = float(rec[10]) * 1e-6 # assuming uT, convert to T
MagRec["treatment_dc_field"] = "%8.3e" % (labfield) # labfield in tesla (convert from microT)
MagRec["treatment_dc_field_phi"] = phi # labfield phi
MagRec["treatment_dc_field_theta"] = theta # labfield theta
if powt < powt_max:
meas_type = "LT-PMRM-I"
if len(rec) > 10:
MagRec["treatment_mw_integral"] = rec[10]
if unc == 0:
MagRec["measurement_magn_moment"] = "%10.3e" % (float(rec[4]) * 1e-6) # moment in Am^2 (from uAm^2)
if unc == 1:
MagRec["measurement_magnitude"] = rec[4] # uncalibrated moment
cart = []
cart.append(float(rec[7]))
cart.append(float(rec[8]))
cart.append(float(rec[9]))
dir = pmag.cart2dir(cart)
MagRec["measurement_dec"] = "%9.3f" % (dir[0])
MagRec["measurement_inc"] = "%9.3f" % (dir[1])
MagRec["magic_instrument_codes"] = instcode
MagRec["magic_method_codes"] = meas_type
MagRec["measurement_flag"] = "g"
MagRec["measurement_standard"] = "u"
MagRec["measurement_number"] = "%i" % (measnum)
MagRec["magic_experiment_name"] = MagRec["er_specimen_name"] + ":" + methcode
measnum += 1
MagRecs.append(MagRec)
if MagRec["er_sample_name"] not in Samps: # add this puppy to the list in er_samples.txt
Samps.append(MagRec["er_sample_name"])
ErSamp = {}
ErSamp["er_sample_name"] = Samps[-1]
ErSamp["er_location_name"] = MagRec["er_location_name"]
ErSamp["er_site_name"] = site
ErSamp["er_citation_names"] = "This study"
gdec = float(rec[5])
ginc = float(rec[6])
az, pl = pmag.get_azpl(dir[0], dir[1], gdec, ginc)
ErSamp["sample_azimuth"] = "%7.1f" % az
ErSamp["sample_dip"] = "%7.1f" % pl
ErSamps.append(ErSamp)
MagOuts = pmag.mw_measurements_methods(MagRecs)
pmag.magic_write(meas_file, MagOuts, "magic_measurements")
print "measurements put in ", meas_file
pmag.magic_write(samp_file, ErSamps, "er_samples")
print "sample names put in ", samp_file
def main():
"""
NAME
aniso_magic.py
DESCRIPTION
plots anisotropy data with either bootstrap or hext ellipses
SYNTAX
aniso_magic.py [-h] [command line options]
OPTIONS
-h plots help message and quits
-usr USER: set the user name
-f AFILE, specify rmag_anisotropy formatted file for input
-F RFILE, specify rmag_results formatted file for output
-x Hext [1963] and bootstrap
-B DON'T do bootstrap, do Hext
-par Tauxe [1998] parametric bootstrap
-v plot bootstrap eigenvectors instead of ellipses
-sit plot by site instead of entire file
-crd [s,g,t] coordinate system, default is specimen (g=geographic, t=tilt corrected)
-P don't make any plots - just make rmag_results table
-sav don't make the rmag_results table - just save all the plots
-fmt [svg, jpg, eps] format for output images, pdf default
-gtc DEC INC dec,inc of pole to great circle [down(up) in green (cyan)
-d Vi DEC INC; Vi (1,2,3) to compare to direction DEC INC
-nb N; specifies the number of bootstraps - default is 1000
DEFAULTS
AFILE: rmag_anisotropy.txt
RFILE: rmag_results.txt
plot bootstrap ellipses of Constable & Tauxe [1987]
NOTES
minor axis: circles
major axis: triangles
principal axis: squares
directions are plotted on the lower hemisphere
for bootstrapped eigenvector components: Xs: blue, Ys: red, Zs: black
"""
#
dir_path = "."
version_num = pmag.get_version()
verbose = pmagplotlib.verbose
args = sys.argv
ipar, ihext, ivec, iboot, imeas, isite, iplot, vec = 0, 0, 0, 1, 1, 0, 1, 0
hpars, bpars, PDir = [], [], []
CS, crd = "-1", "s"
nb = 1000
fmt = "pdf"
ResRecs = []
orlist = []
outfile, comp, Dir, gtcirc, PDir = "rmag_results.txt", 0, [], 0, []
infile = "rmag_anisotropy.txt"
if "-h" in args:
print main.__doc__
sys.exit()
if "-WD" in args:
ind = args.index("-WD")
dir_path = args[ind + 1]
if "-nb" in args:
ind = args.index("-nb")
nb = int(args[ind + 1])
if "-usr" in args:
ind = args.index("-usr")
user = args[ind + 1]
else:
user = ""
if "-B" in args:
iboot, ihext = 0, 1
if "-par" in args:
ipar = 1
if "-x" in args:
ihext = 1
if "-v" in args:
ivec = 1
if "-sit" in args:
isite = 1
if "-P" in args:
iplot = 0
if "-f" in args:
ind = args.index("-f")
infile = args[ind + 1]
if "-F" in args:
ind = args.index("-F")
outfile = args[ind + 1]
if "-crd" in sys.argv:
ind = sys.argv.index("-crd")
crd = sys.argv[ind + 1]
if crd == "g":
CS = "0"
if crd == "t":
CS = "100"
if "-fmt" in args:
ind = args.index("-fmt")
fmt = args[ind + 1]
if "-sav" in args:
plots = 1
verbose = 0
else:
plots = 0
if "-gtc" in args:
ind = args.index("-gtc")
d, i = float(args[ind + 1]), float(args[ind + 2])
PDir.append(d)
PDir.append(i)
if "-d" in args:
comp = 1
ind = args.index("-d")
vec = int(args[ind + 1]) - 1
Dir = [float(args[ind + 2]), float(args[ind + 3])]
#
# set up plots
#
if infile[0] != "/":
infile = dir_path + "/" + infile
if outfile[0] != "/":
outfile = dir_path + "/" + outfile
ANIS = {}
initcdf, inittcdf = 0, 0
ANIS["data"], ANIS["conf"] = 1, 2
if iboot == 1:
ANIS["tcdf"] = 3
if iplot == 1:
inittcdf = 1
pmagplotlib.plot_init(ANIS["tcdf"], 5, 5)
if comp == 1 and iplot == 1:
initcdf = 1
ANIS["vxcdf"], ANIS["vycdf"], ANIS["vzcdf"] = 4, 5, 6
pmagplotlib.plot_init(ANIS["vxcdf"], 5, 5)
pmagplotlib.plot_init(ANIS["vycdf"], 5, 5)
pmagplotlib.plot_init(ANIS["vzcdf"], 5, 5)
if iplot == 1:
pmagplotlib.plot_init(ANIS["conf"], 5, 5)
pmagplotlib.plot_init(ANIS["data"], 5, 5)
# read in the data
data, ifiletype = pmag.magic_read(infile)
for rec in data: # find all the orientation systems
if "anisotropy_tilt_correction" not in rec.keys():
rec["anisotropy_tilt_correction"] = "-1"
if rec["anisotropy_tilt_correction"] not in orlist:
orlist.append(rec["anisotropy_tilt_correction"])
if CS not in orlist:
if len(orlist) > 0:
CS = orlist[0]
else:
CS = "-1"
if CS == "-1":
crd = "s"
if CS == "0":
crd = "g"
if CS == "100":
crd = "t"
if verbose:
print "desired coordinate system not available, using available: ", crd
if isite == 1:
sitelist = []
for rec in data:
if rec["er_site_name"] not in sitelist:
sitelist.append(rec["er_site_name"])
sitelist.sort()
plt = len(sitelist)
else:
plt = 1
k = 0
while k < plt:
site = ""
sdata, Ss = [], [] # list of S format data
Locs, Sites, Samples, Specimens, Cits = [], [], [], [], []
if isite == 0:
sdata = data
else:
site = sitelist[k]
for rec in data:
if rec["er_site_name"] == site:
sdata.append(rec)
anitypes = []
csrecs = pmag.get_dictitem(sdata, "anisotropy_tilt_correction", CS, "T")
for rec in csrecs:
if rec["anisotropy_type"] not in anitypes:
anitypes.append(rec["anisotropy_type"])
if rec["er_location_name"] not in Locs:
Locs.append(rec["er_location_name"])
if rec["er_site_name"] not in Sites:
Sites.append(rec["er_site_name"])
if rec["er_sample_name"] not in Samples:
Samples.append(rec["er_sample_name"])
if rec["er_specimen_name"] not in Specimens:
Specimens.append(rec["er_specimen_name"])
if rec["er_citation_names"] not in Cits:
Cits.append(rec["er_citation_names"])
s = []
s.append(float(rec["anisotropy_s1"]))
s.append(float(rec["anisotropy_s2"]))
s.append(float(rec["anisotropy_s3"]))
s.append(float(rec["anisotropy_s4"]))
s.append(float(rec["anisotropy_s5"]))
s.append(float(rec["anisotropy_s6"]))
if s[0] <= 1.0:
Ss.append(s) # protect against crap
# tau,Vdirs=pmag.doseigs(s)
fpars = pmag.dohext(int(rec["anisotropy_n"]) - 6, float(rec["anisotropy_sigma"]), s)
ResRec = {}
ResRec["er_location_names"] = rec["er_location_name"]
ResRec["er_citation_names"] = rec["er_citation_names"]
ResRec["er_site_names"] = rec["er_site_name"]
ResRec["er_sample_names"] = rec["er_sample_name"]
ResRec["er_specimen_names"] = rec["er_specimen_name"]
ResRec["rmag_result_name"] = rec["er_specimen_name"] + ":" + rec["anisotropy_type"]
ResRec["er_analyst_mail_names"] = user
ResRec["tilt_correction"] = CS
ResRec["anisotropy_type"] = rec["anisotropy_type"]
ResRec["anisotropy_v1_dec"] = "%7.1f" % (fpars["v1_dec"])
ResRec["anisotropy_v2_dec"] = "%7.1f" % (fpars["v2_dec"])
ResRec["anisotropy_v3_dec"] = "%7.1f" % (fpars["v3_dec"])
ResRec["anisotropy_v1_inc"] = "%7.1f" % (fpars["v1_inc"])
ResRec["anisotropy_v2_inc"] = "%7.1f" % (fpars["v2_inc"])
ResRec["anisotropy_v3_inc"] = "%7.1f" % (fpars["v3_inc"])
ResRec["anisotropy_t1"] = "%10.8f" % (fpars["t1"])
ResRec["anisotropy_t2"] = "%10.8f" % (fpars["t2"])
ResRec["anisotropy_t3"] = "%10.8f" % (fpars["t3"])
ResRec["anisotropy_ftest"] = "%10.3f" % (fpars["F"])
ResRec["anisotropy_ftest12"] = "%10.3f" % (fpars["F12"])
ResRec["anisotropy_ftest23"] = "%10.3f" % (fpars["F23"])
ResRec["result_description"] = "F_crit: " + fpars["F_crit"] + "; F12,F23_crit: " + fpars["F12_crit"]
ResRec["anisotropy_type"] = pmag.makelist(anitypes)
ResRecs.append(ResRec)
if len(Ss) > 1:
title = "LO:_" + ResRec["er_location_names"] + "_SI:_" + site + "_SA:__SP:__CO:_" + crd
ResRec["er_location_names"] = pmag.makelist(Locs)
bpars, hpars = pmagplotlib.plotANIS(ANIS, Ss, iboot, ihext, ivec, ipar, title, iplot, comp, vec, Dir, nb)
if len(PDir) > 0:
pmagplotlib.plotC(ANIS["data"], PDir, 90.0, "g")
pmagplotlib.plotC(ANIS["conf"], PDir, 90.0, "g")
if verbose and plots == 0:
pmagplotlib.drawFIGS(ANIS)
ResRec["er_location_names"] = pmag.makelist(Locs)
if plots == 1:
save(ANIS, fmt, title)
ResRec = {}
ResRec["er_citation_names"] = pmag.makelist(Cits)
ResRec["er_location_names"] = pmag.makelist(Locs)
ResRec["er_site_names"] = pmag.makelist(Sites)
ResRec["er_sample_names"] = pmag.makelist(Samples)
ResRec["er_specimen_names"] = pmag.makelist(Specimens)
ResRec["rmag_result_name"] = pmag.makelist(Sites) + ":" + pmag.makelist(anitypes)
ResRec["anisotropy_type"] = pmag.makelist(anitypes)
ResRec["er_analyst_mail_names"] = user
ResRec["tilt_correction"] = CS
if isite == "0":
ResRec["result_description"] = "Study average using coordinate system: " + CS
if isite == "1":
ResRec["result_description"] = "Site average using coordinate system: " + CS
if hpars != [] and ihext == 1:
HextRec = {}
for key in ResRec.keys():
HextRec[key] = ResRec[key] # copy over stuff
HextRec["anisotropy_v1_dec"] = "%7.1f" % (hpars["v1_dec"])
HextRec["anisotropy_v2_dec"] = "%7.1f" % (hpars["v2_dec"])
HextRec["anisotropy_v3_dec"] = "%7.1f" % (hpars["v3_dec"])
HextRec["anisotropy_v1_inc"] = "%7.1f" % (hpars["v1_inc"])
HextRec["anisotropy_v2_inc"] = "%7.1f" % (hpars["v2_inc"])
HextRec["anisotropy_v3_inc"] = "%7.1f" % (hpars["v3_inc"])
HextRec["anisotropy_t1"] = "%10.8f" % (hpars["t1"])
HextRec["anisotropy_t2"] = "%10.8f" % (hpars["t2"])
HextRec["anisotropy_t3"] = "%10.8f" % (hpars["t3"])
HextRec["anisotropy_hext_F"] = "%7.1f " % (hpars["F"])
HextRec["anisotropy_hext_F12"] = "%7.1f " % (hpars["F12"])
HextRec["anisotropy_hext_F23"] = "%7.1f " % (hpars["F23"])
HextRec["anisotropy_v1_eta_semi_angle"] = "%7.1f " % (hpars["e12"])
HextRec["anisotropy_v1_eta_dec"] = "%7.1f " % (hpars["v2_dec"])
HextRec["anisotropy_v1_eta_inc"] = "%7.1f " % (hpars["v2_inc"])
HextRec["anisotropy_v1_zeta_semi_angle"] = "%7.1f " % (hpars["e13"])
HextRec["anisotropy_v1_zeta_dec"] = "%7.1f " % (hpars["v3_dec"])
HextRec["anisotropy_v1_zeta_inc"] = "%7.1f " % (hpars["v3_inc"])
HextRec["anisotropy_v2_eta_semi_angle"] = "%7.1f " % (hpars["e12"])
HextRec["anisotropy_v2_eta_dec"] = "%7.1f " % (hpars["v1_dec"])
HextRec["anisotropy_v2_eta_inc"] = "%7.1f " % (hpars["v1_inc"])
HextRec["anisotropy_v2_zeta_semi_angle"] = "%7.1f " % (hpars["e23"])
HextRec["anisotropy_v2_zeta_dec"] = "%7.1f " % (hpars["v3_dec"])
HextRec["anisotropy_v2_zeta_inc"] = "%7.1f " % (hpars["v3_inc"])
HextRec["anisotropy_v3_eta_semi_angle"] = "%7.1f " % (hpars["e12"])
HextRec["anisotropy_v3_eta_dec"] = "%7.1f " % (hpars["v1_dec"])
HextRec["anisotropy_v3_eta_inc"] = "%7.1f " % (hpars["v1_inc"])
HextRec["anisotropy_v3_zeta_semi_angle"] = "%7.1f " % (hpars["e23"])
HextRec["anisotropy_v3_zeta_dec"] = "%7.1f " % (hpars["v2_dec"])
HextRec["anisotropy_v3_zeta_inc"] = "%7.1f " % (hpars["v2_inc"])
HextRec["magic_method_codes"] = "LP-AN:AE-H"
if verbose:
print "Hext Statistics: "
print " tau_i, V_i_D, V_i_I, V_i_zeta, V_i_zeta_D, V_i_zeta_I, V_i_eta, V_i_eta_D, V_i_eta_I"
print HextRec["anisotropy_t1"], HextRec["anisotropy_v1_dec"], HextRec["anisotropy_v1_inc"], HextRec[
"anisotropy_v1_eta_semi_angle"
], HextRec["anisotropy_v1_eta_dec"], HextRec["anisotropy_v1_eta_inc"], HextRec[
"anisotropy_v1_zeta_semi_angle"
], HextRec[
"anisotropy_v1_zeta_dec"
], HextRec[
"anisotropy_v1_zeta_inc"
]
print HextRec["anisotropy_t2"], HextRec["anisotropy_v2_dec"], HextRec["anisotropy_v2_inc"], HextRec[
"anisotropy_v2_eta_semi_angle"
], HextRec["anisotropy_v2_eta_dec"], HextRec["anisotropy_v2_eta_inc"], HextRec[
"anisotropy_v2_zeta_semi_angle"
], HextRec[
"anisotropy_v2_zeta_dec"
], HextRec[
"anisotropy_v2_zeta_inc"
]
print HextRec["anisotropy_t3"], HextRec["anisotropy_v3_dec"], HextRec["anisotropy_v3_inc"], HextRec[
"anisotropy_v3_eta_semi_angle"
], HextRec["anisotropy_v3_eta_dec"], HextRec["anisotropy_v3_eta_inc"], HextRec[
"anisotropy_v3_zeta_semi_angle"
], HextRec[
"anisotropy_v3_zeta_dec"
], HextRec[
"anisotropy_v3_zeta_inc"
]
HextRec["magic_software_packages"] = version_num
ResRecs.append(HextRec)
if bpars != []:
BootRec = {}
for key in ResRec.keys():
BootRec[key] = ResRec[key] # copy over stuff
BootRec["anisotropy_v1_dec"] = "%7.1f" % (bpars["v1_dec"])
BootRec["anisotropy_v2_dec"] = "%7.1f" % (bpars["v2_dec"])
BootRec["anisotropy_v3_dec"] = "%7.1f" % (bpars["v3_dec"])
BootRec["anisotropy_v1_inc"] = "%7.1f" % (bpars["v1_inc"])
BootRec["anisotropy_v2_inc"] = "%7.1f" % (bpars["v2_inc"])
BootRec["anisotropy_v3_inc"] = "%7.1f" % (bpars["v3_inc"])
BootRec["anisotropy_t1"] = "%10.8f" % (bpars["t1"])
BootRec["anisotropy_t2"] = "%10.8f" % (bpars["t2"])
BootRec["anisotropy_t3"] = "%10.8f" % (bpars["t3"])
BootRec["anisotropy_v1_eta_inc"] = "%7.1f " % (bpars["v1_eta_inc"])
BootRec["anisotropy_v1_eta_dec"] = "%7.1f " % (bpars["v1_eta_dec"])
BootRec["anisotropy_v1_eta_semi_angle"] = "%7.1f " % (bpars["v1_eta"])
BootRec["anisotropy_v1_zeta_inc"] = "%7.1f " % (bpars["v1_zeta_inc"])
BootRec["anisotropy_v1_zeta_dec"] = "%7.1f " % (bpars["v1_zeta_dec"])
BootRec["anisotropy_v1_zeta_semi_angle"] = "%7.1f " % (bpars["v1_zeta"])
BootRec["anisotropy_v2_eta_inc"] = "%7.1f " % (bpars["v2_eta_inc"])
BootRec["anisotropy_v2_eta_dec"] = "%7.1f " % (bpars["v2_eta_dec"])
BootRec["anisotropy_v2_eta_semi_angle"] = "%7.1f " % (bpars["v2_eta"])
BootRec["anisotropy_v2_zeta_inc"] = "%7.1f " % (bpars["v2_zeta_inc"])
BootRec["anisotropy_v2_zeta_dec"] = "%7.1f " % (bpars["v2_zeta_dec"])
BootRec["anisotropy_v2_zeta_semi_angle"] = "%7.1f " % (bpars["v2_zeta"])
BootRec["anisotropy_v3_eta_inc"] = "%7.1f " % (bpars["v3_eta_inc"])
BootRec["anisotropy_v3_eta_dec"] = "%7.1f " % (bpars["v3_eta_dec"])
BootRec["anisotropy_v3_eta_semi_angle"] = "%7.1f " % (bpars["v3_eta"])
BootRec["anisotropy_v3_zeta_inc"] = "%7.1f " % (bpars["v3_zeta_inc"])
BootRec["anisotropy_v3_zeta_dec"] = "%7.1f " % (bpars["v3_zeta_dec"])
BootRec["anisotropy_v3_zeta_semi_angle"] = "%7.1f " % (bpars["v3_zeta"])
BootRec["anisotropy_hext_F"] = ""
BootRec["anisotropy_hext_F12"] = ""
BootRec["anisotropy_hext_F23"] = ""
BootRec["magic_method_codes"] = "LP-AN:AE-H:AE-BS" # regular bootstrap
if ipar == 1:
BootRec["magic_method_codes"] = "LP-AN:AE-H:AE-BS-P" # parametric bootstrap
if verbose:
print "Boostrap Statistics: "
print " tau_i, V_i_D, V_i_I, V_i_zeta, V_i_zeta_D, V_i_zeta_I, V_i_eta, V_i_eta_D, V_i_eta_I"
print BootRec["anisotropy_t1"], BootRec["anisotropy_v1_dec"], BootRec["anisotropy_v1_inc"], BootRec[
"anisotropy_v1_eta_semi_angle"
], BootRec["anisotropy_v1_eta_dec"], BootRec["anisotropy_v1_eta_inc"], BootRec[
"anisotropy_v1_zeta_semi_angle"
], BootRec[
"anisotropy_v1_zeta_dec"
], BootRec[
"anisotropy_v1_zeta_inc"
]
print BootRec["anisotropy_t2"], BootRec["anisotropy_v2_dec"], BootRec["anisotropy_v2_inc"], BootRec[
"anisotropy_v2_eta_semi_angle"
], BootRec["anisotropy_v2_eta_dec"], BootRec["anisotropy_v2_eta_inc"], BootRec[
"anisotropy_v2_zeta_semi_angle"
], BootRec[
"anisotropy_v2_zeta_dec"
], BootRec[
"anisotropy_v2_zeta_inc"
]
print BootRec["anisotropy_t3"], BootRec["anisotropy_v3_dec"], BootRec["anisotropy_v3_inc"], BootRec[
"anisotropy_v3_eta_semi_angle"
], BootRec["anisotropy_v3_eta_dec"], BootRec["anisotropy_v3_eta_inc"], BootRec[
"anisotropy_v3_zeta_semi_angle"
], BootRec[
"anisotropy_v3_zeta_dec"
], BootRec[
"anisotropy_v3_zeta_inc"
]
BootRec["magic_software_packages"] = version_num
ResRecs.append(BootRec)
k += 1
goon = 1
while goon == 1 and iplot == 1 and verbose:
if iboot == 1:
print "compare with [d]irection "
print " plot [g]reat circle, change [c]oord. system, change [e]llipse calculation, s[a]ve plots, [q]uit "
if isite == 1:
print " [p]revious, [s]ite, [q]uit, <return> for next "
ans = raw_input("")
if ans == "q":
sys.exit()
if ans == "e":
iboot, ipar, ihext, ivec = 1, 0, 0, 0
e = raw_input("Do Hext Statistics 1/[0]: ")
if e == "1":
ihext = 1
e = raw_input("Suppress bootstrap 1/[0]: ")
if e == "1":
iboot = 0
if iboot == 1:
e = raw_input("Parametric bootstrap 1/[0]: ")
if e == "1":
ipar = 1
e = raw_input("Plot bootstrap eigenvectors: 1/[0]: ")
if e == "1":
ivec = 1
if iplot == 1:
if inittcdf == 0:
ANIS["tcdf"] = 3
pmagplotlib.plot_init(ANIS["tcdf"], 5, 5)
inittcdf = 1
bpars, hpars = pmagplotlib.plotANIS(
ANIS, Ss, iboot, ihext, ivec, ipar, title, iplot, comp, vec, Dir, nb
)
if verbose and plots == 0:
pmagplotlib.drawFIGS(ANIS)
if ans == "c":
print "Current Coordinate system is: "
if CS == "-1":
print " Specimen"
if CS == "0":
print " Geographic"
if CS == "100":
print " Tilt corrected"
key = raw_input(" Enter desired coordinate system: [s]pecimen, [g]eographic, [t]ilt corrected ")
if key == "s":
CS = "-1"
if key == "g":
CS = "0"
if key == "t":
CS = "100"
if CS not in orlist:
if len(orlist) > 0:
CS = orlist[0]
else:
CS = "-1"
if CS == "-1":
crd = "s"
if CS == "0":
crd = "g"
if CS == "100":
crd = "t"
print "desired coordinate system not available, using available: ", crd
k -= 1
goon = 0
if ans == "":
if isite == 1:
goon = 0
else:
print "Good bye "
sys.exit()
if ans == "d":
if initcdf == 0:
initcdf = 1
ANIS["vxcdf"], ANIS["vycdf"], ANIS["vzcdf"] = 4, 5, 6
pmagplotlib.plot_init(ANIS["vxcdf"], 5, 5)
pmagplotlib.plot_init(ANIS["vycdf"], 5, 5)
pmagplotlib.plot_init(ANIS["vzcdf"], 5, 5)
Dir, comp = [], 1
print """
Input: Vi D I to compare eigenvector Vi with direction D/I
where Vi=1: principal
Vi=2: major
Vi=3: minor
D= declination of comparison direction
I= inclination of comparison direction"""
con = 1
while con == 1:
try:
vdi = raw_input("Vi D I: ").split()
vec = int(vdi[0]) - 1
Dir = [float(vdi[1]), float(vdi[2])]
con = 0
except IndexError:
print " Incorrect entry, try again "
bpars, hpars = pmagplotlib.plotANIS(
ANIS, Ss, iboot, ihext, ivec, ipar, title, iplot, comp, vec, Dir, nb
)
Dir, comp = [], 0
if ans == "g":
con, cnt = 1, 0
while con == 1:
try:
print " Input: input pole to great circle ( D I) to plot a great circle: "
di = raw_input(" D I: ").split()
PDir.append(float(di[0]))
PDir.append(float(di[1]))
con = 0
except:
cnt += 1
if cnt < 10:
print " enter the dec and inc of the pole on one line "
else:
print "ummm - you are doing something wrong - i give up"
sys.exit()
pmagplotlib.plotC(ANIS["data"], PDir, 90.0, "g")
pmagplotlib.plotC(ANIS["conf"], PDir, 90.0, "g")
if verbose and plots == 0:
pmagplotlib.drawFIGS(ANIS)
if ans == "p":
k -= 2
goon = 0
if ans == "q":
k = plt
goon = 0
if ans == "s":
keepon = 1
site = raw_input(" print site or part of site desired: ")
while keepon == 1:
try:
k = sitelist.index(site)
keepon = 0
except:
tmplist = []
for qq in range(len(sitelist)):
if site in sitelist[qq]:
tmplist.append(sitelist[qq])
print site, " not found, but this was: "
print tmplist
site = raw_input("Select one or try again\n ")
k = sitelist.index(site)
goon, ans = 0, ""
if ans == "a":
locs = pmag.makelist(Locs)
title = "LO:_" + locs + "_SI:__" + "_SA:__SP:__CO:_" + crd
save(ANIS, fmt, title)
goon = 0
else:
if verbose:
print "skipping plot - not enough data points"
k += 1
# put rmag_results stuff here
if len(ResRecs) > 0:
ResOut, keylist = pmag.fillkeys(ResRecs)
pmag.magic_write(outfile, ResOut, "rmag_results")
if verbose:
print " Good bye "
def main():
"""
NAME
ODP_dcs_magic.py
DESCRIPTION
converts ODP discrete sample format files to magic_measurements format files
SYNTAX
ODP_dsc_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsp FILE: specify output er_specimens.txt file, default is er_specimens.txt
-Fsa FILE: specify output er_samples.txt file for appending, default is er_samples.txt
-Fsi FILE: specify output er_sites.txt file, default is er_sites.txt
-dc B PHI THETA: dc lab field (in micro tesla) and phi,theta, default is none
NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment
-ac B : peak AF field (in mT) for ARM acquisition, default is none
-A : don't average replicate measurements
INPUT
Put data from separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.) in separate directory
"""
#
#
version_num=pmag.get_version()
meas_file='magic_measurements.txt'
spec_file='er_specimens.txt'
samp_file='er_samples.txt'
site_file='er_sites.txt'
ErSpecs,ErSamps,ErSites,ErLocs,ErCits=[],[],[],[],[]
MagRecs=[]
citation="This study"
dir_path,demag='.','NRM'
args=sys.argv
noave=0
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-A" in args: noave=1
if '-F' in args:
ind=args.index("-F")
meas_file=args[ind+1]
if '-Fsp' in args:
ind=args.index("-Fsp")
spec_file=args[ind+1]
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file=dir_path+'/'+args[ind+1]
ErSamps,file_type=pmag.magic_read(samp_file)
else:
samp_file=dir_path+'/'+samp_file
if '-LP' in args:
ind=args.index("-LP")
codelist=args[ind+1]
codes=codelist.split(':')
if "AF" in codes:
demag='AF'
if'-dc' not in args: methcode="LT-AF-Z"
if'-dc' in args: methcode="LT-AF-I"
if "T" in codes:
demag="T"
if '-dc' not in args: methcode="LT-T-Z"
if '-dc' in args: methcode="LT-T-I"
if "I" in codes:
methcode="LP-IRM"
if "S" in codes:
demag="S"
methcode="LP-PI-TRM:LP-PI-ALT-AFARM"
trm_labfield=labfield
ans=raw_input("DC lab field for ARM step: [50uT] ")
if ans=="":
arm_labfield=50e-6
else:
arm_labfield=float(ans)*1e-6
ans=raw_input("temperature for total trm step: [600 C] ")
if ans=="":
trm_peakT=600+273 # convert to kelvin
else:
trm_peakT=float(ans)+273 # convert to kelvin
if "G" in codes: methcode="LT-AF-G"
if "D" in codes: methcode="LT-AF-D"
if "TRM" in codes:
demag="T"
trm=1
if demag=="T" and "ANI" in codes:
methcode="LP-AN-TRM"
if demag=="AF" and "ANI" in codes:
methcode="LP-AN-ARM"
if labfield==0: labfield=50e-6
if peakfield==0: peakfield=.180
spec_file=dir_path+'/'+spec_file
site_file=dir_path+'/'+site_file
meas_file=dir_path+'/'+meas_file
filelist=os.listdir(dir_path) # read in list of files to import
specimens,samples,sites=[],[],[]
MagRecs,SpecRecs,SampRecs=[],[],[]
for samp in ErSamps:
if samp['er_sample_name'] not in samples:
samples.append(samp['er_sample_name'])
SampRecs.append(samp)
for file in filelist: # parse each file
if file[-3:].lower()=='dsc':
print 'processing: ',file
MagRec,SpecRec,SampRec={},{},{}
treatment_type,treatment_value,user="","",""
inst="ODP-SRM"
input=open(dir_path+'/'+file,'rU').readlines()
IDs=file.split('_') # splits on underscores
pieces=IDs[0].split('-')
expedition=pieces[0]
location=pieces[1]
if file[0]!='_':
while len(pieces[2])<4:pieces[2]='0'+pieces[2] # pad core to be 3 characters
specimen=""
else:
specimen="test"
for piece in pieces:
specimen=specimen+piece+'-'
specimen=specimen[:-1]
alt_spec=IDs[1] # alternate specimen is second field in field name
# set up specimen record for Er_specimens table
SpecRec['er_expedition_name']=expedition
SpecRec['er_location_name']=location
SpecRec['er_site_name']=specimen
SpecRec['er_sample_name']=specimen
SpecRec['er_citation_names']=citation
for key in SpecRec.keys():SampRec[key]=SpecRec[key]
SampRec['sample_azimuth']='0'
SampRec['sample_dip']='0'
SampRec['magic_method_codes']='FS-C-DRILL-IODP:FS-SS-C:SO-V'
SpecRec['er_specimen_name']=specimen
for key in SpecRec.keys():MagRec[key]=SpecRec[key]
# set up measurement record - default is NRM
MagRec['er_analyst_mail_names']=user
MagRec['magic_method_codes']='LT-NO'
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["treatment_ac_field"]=0.
MagRec["treatment_dc_field"]='0'
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
MagRec["measurement_flag"]='g' # assume all data are "good"
MagRec["measurement_standard"]='u' # assume all data are "good"
MagRec["measurement_csd"]='' # set csd to blank
SpecRec['er_specimen_alternatives']=alt_spec
vol=7e-6 # assume 7 cc samples
datestamp=input[1].split() # date time is second line of file
mmddyy=datestamp[0].split('/') # break into month day year
date=mmddyy[2]+':'+mmddyy[0]+":"+mmddyy[1] +':' +datestamp[1]
MagRec["measurement_date"]=date
for k in range(len(input)):
fields= input[k].split("=")
if 'treatment_type' in fields[0]:
if "Alternating Frequency Demagnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst=inst+':ODP-DTECH' # measured on shipboard AF DTECH D2000
treatment_type="AF"
if "Anhysteretic Remanent Magnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-AF-I'
inst=inst+':ODP-DTECH' # measured on shipboard AF DTECH D2000
treatment_type="ARM"
if "Isothermal Remanent Magnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-IRM'
inst=inst+':ODP-IMP' # measured on shipboard ASC IMPULSE magnetizer
treatment_type="IRM"
if "treatment_value" in fields[0]:
values=fields[1].split(',')
value=values[0]
if value!=" \n":
if treatment_type=="AF":
treatment_value=float(value)*1e-3
MagRec["treatment_ac_field"]=treatment_value # AF demag in treat mT => T
elif treatment_type=="IRM":
treatment_value=float(value)*1e-3
MagRec["treatment_dc_field"]='%8.3e'%(treatment_value) # IRM treat mT => T
if treatment_type=="ARM":
treatment_value=float(value)*1e-3
dc_value=float(values[1])*1e-3
MagRec["treatment_ac_field"]=treatment_value # AF demag in treat mT => T
MagRec["treatment_dc_field"]='%8.3e'%(dc_value) # DC mT => T
if 'user' in fields[0]:
user=fields[-1]
MagRec["er_analyst_mail_names"]=user
if 'sample_orientation' in fields[0]:
MagRec["measurement_description"]=fields[-1]
MagRec["measurement_standard"]='u' # assume all data are "good"
if 'sample_area' in fields[0]: vol=float(fields[1])*1e-6 # takes volume (cc) and converts to m^3
if 'run_number' in fields[0]:
MagRec['external_database_ids']=fields[1] # run number is the LIMS measurement number
MagRec['external_database_names']='LIMS'
if input[k][0:7]=='<MULTI>':
rec=input[k+1].split(',') # list of data
for item in rec:
items=item.split('=')
if items[0].strip()=='demag_level' and treatment_value=="" :
treat= float(items[1])
if treat!=0:
MagRec['magic_method_codes']='LT-AF-Z'
inst=inst+':ODP-SRM-AF'
MagRec["treatment_ac_field"]=treat*1e-3 # AF demag in treat mT => T
if items[0].strip()=='inclination_w_tray_w_bkgrd': MagRec['measurement_inc']=items[1]
if items[0].strip()=='declination_w_tray_w_bkgrd': MagRec['measurement_dec']=items[1]
if items[0].strip()=='intensity_w_tray_w_bkgrd': MagRec['measurement_magn_moment']='%8.3e'%(float(items[1])*vol) # convert intensity from A/m to Am^2 using vol
if items[0].strip()=='x_stdev':MagRec['measurement_x_sd']=items[1]
if items[0].strip()=='y_stdev':MagRec['measurement_y_sd']=items[1]
if items[0].strip()=='z_stdev':MagRec['measurement_z_sd']=items[1]
MagRec['magic_instrument_codes']=inst
MagRec['measurement_number']='1'
MagRecs.append(MagRec)
if specimen not in specimens:
specimens.append(specimen)
SpecRecs.append(SpecRec)
if MagRec['er_sample_name'] not in samples:
samples.append(MagRec['er_sample_name'])
SampRecs.append(SampRec)
MagOuts=pmag.sort_diclist(MagRecs,'treatment_ac_field')
for MagRec in MagOuts:
MagRec["treatment_ac_field"]='%8.3e'%(MagRec["treatment_ac_field"]) # convert to string
pmag.magic_write(spec_file,SpecRecs,'er_specimens')
if len(SampRecs)>0:
SampOut,keys=pmag.fillkeys(SampRecs)
pmag.magic_write(samp_file,SampOut,'er_samples')
print 'samples stored in ',samp_file
pmag.magic_write(samp_file,SampRecs,'er_samples')
print 'specimens stored in ',spec_file
Fixed=pmag.measurements_methods(MagOuts,noave)
pmag.magic_write(meas_file,Fixed,'magic_measurements')
print 'data stored in ',meas_file
def main():
"""
NAME
convert_samples.py
DESCRIPTION
takes an er_samples.txt file and creates an orient.txt file
SYNTAX
convert_samples.py [command line options]
OPTIONS
-f FILE: specify input file, default is er_samples.txt
-F FILE: specify output file, default is: location_orient.txt
INPUT FORMAT
er_samples.txt formatted file
OUTPUT
orient.txt formatted file
"""
#
# initialize variables
#
version_num=pmag.get_version()
orient_file,samp_file = "orient","er_samples.txt"
args=sys.argv
dir_path='.'
#
#
if '-WD' in args:
ind=args.index('-WD')
dir_path=args[ind+1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-F" in args:
ind=args.index("-F")
opath=sys.argv[ind+1]
pathlist=opath.split('/')
opath=""
for p in pathlist[:-1]:opath=opath+p+"/"
orient_file=pathlist[-1]
if "-f" in args:
ind=args.index("-f")
samp_file=dir_path+'/'+sys.argv[ind+1]
#
# read in file to convert
#
Samps,file_type=pmag.magic_read(samp_file)
Locs=[]
OrKeys=['sample_name','mag_azimuth','field_dip','sample_class','sample_type','sample_lithology','lat','long','stratigraphic_height','method_codes','site_name','site_description']
SampKeys=['er_sample_name','sample_azimuth','sample_dip','sample_class','sample_type','sample_lithology','sample_lat','sample_lon','sample_height','magic_method_codes','er_site_name','er_sample_description']
for samp in Samps:
if samp['er_location_name'] not in Locs:Locs.append(samp['er_location_name']) # get all the location names
for location_name in Locs:
OrOut=[]
for samp in Samps:
if samp['er_location_name']==location_name:
OrRec={}
if 'sample_date' in samp.keys() and samp['sample_date'].strip()!="":
date=samp['sample_date'].split(':')
OrRec['date']=date[1]+'/'+date[2]+'/'+date[0][2:4]
for i in range(len(SampKeys)):
if SampKeys[i] in samp.keys():OrRec[OrKeys[i]]=samp[SampKeys[i]]
OrOut.append(OrRec)
loc=location_name.replace(" ","_")
outfile=opath+orient_file+'_'+loc+'.txt'
pmag.magic_write(outfile,OrOut,location_name)
print "Data saved in: ", outfile
def main():
"""
NAME
LDGO_magic.py
DESCRIPTION
converts LDGO format files to magic_measurements format files
SYNTAX
LDGO_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify .ldgo format input file, required
-fsa SAMPFILE : specify er_samples.txt file relating samples, site and locations names,default is none
-F FILE: specify output file, default is magic_measurements.txt
-Fsy: specify er_synthetics file, default is er_sythetics.txt
-Fsa: specify output er_samples file, default is NONE (only for LDGO formatted files)
-LP [colon delimited list of protocols, include all that apply]
AF: af demag
T: thermal including thellier but not trm acquisition
S: Shaw method
I: IRM (acquisition)
N: NRM only
TRM: trm acquisition
ANI: anisotropy experiment
D: double AF demag
G: triple AF demag (GRM protocol)
-V [1,2,3] units of IRM field in volts using ASC coil #1,2 or 3
-spc NUM : specify number of characters to designate a specimen, default = 0
-loc LOCNAME : specify location/study name, must have either LOCNAME or SAMPFILE or be a synthetic
-syn INST TYPE: sets these specimens as synthetics created at institution INST and of type TYPE
-ins INST : specify which demag instrument was used (e.g, SIO-Suzy or SIO-Odette),default is ""
-dc B PHI THETA: dc lab field (in micro tesla) and phi,theta, default is none
NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment
-ac B : peak AF field (in mT) for ARM acquisition, default is none
-ncn NCON: specify naming convention: default is #1 below
-A: don't average replicate measurements
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
[8] synthetic - has no site name
INPUT
Best to put separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.) in
seperate .mag files (eg. af.mag, thermal.mag, etc.)
Format of LDEO files:
isaf2.fix
LAT: .00 LON: .00
ID TREAT I CD J CDECL CINCL GDECL GINCL BDECL BINCL SUSC M/V
________________________________________________________________________________
is031c2 .0 SD 0 461.600 163.9 17.5 337.1 74.5 319.1 74.4 .0 .0
ID: specimen name
TREAT: treatment step
I: Instrument
CD: Circular standard devation
J: intensity. assumed to be total moment in 10^-4 (emu)
CDECL: Declination in specimen coordinate system
CINCL: Declination in specimen coordinate system
GDECL: Declination in geographic coordinate system
GINCL: Declination in geographic coordinate system
BDECL: Declination in bedding adjusted coordinate system
BINCL: Declination in bedding adjusted coordinate system
SUSC: magnetic susceptibility (in micro SI)a
M/V: mass or volume for nomalizing (0 won't normalize)
"""
# initialize some stuff
noave = 0
methcode, inst = "LP-NO", ""
phi, theta, peakfield, labfield = 0, 0, 0, 0
pTRM, MD, samp_con, Z = 0, 0, '1', 1
dec = [315, 225, 180, 135, 45, 90, 270, 270, 270, 90, 180, 180, 0, 0, 0]
inc = [0, 0, 0, 0, 0, -45, -45, 0, 45, 45, 45, -45, -90, -45, 45]
tdec = [0, 90, 0, 180, 270, 0, 0, 90, 0]
tinc = [0, 0, 90, 0, 0, -90, 0, 0, 90]
missing = 1
demag = "N"
er_location_name = ""
citation = 'This study'
args = sys.argv
fmt = 'old'
syn = 0
synfile = 'er_synthetics.txt'
samp_file, ErSamps = '', []
trm = 0
irm = 0
specnum = 0
coil = ""
#
# get command line arguments
#
meas_file = "magic_measurements.txt"
user = ""
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind = args.index("-usr")
user = args[ind + 1]
if '-F' in args:
ind = args.index("-F")
meas_file = args[ind + 1]
if '-Fsy' in args:
ind = args.index("-Fsy")
synfile = args[ind + 1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = args[ind + 1]
try:
open(samp_file, 'rU')
ErSamps, file_type = pmag.magic_read(samp_file)
print 'sample information will be appended to new er_samples.txt file'
except:
print 'sample information will be stored in new er_samples.txt file'
if '-f' in args:
ind = args.index("-f")
magfile = args[ind + 1]
try:
input = open(magfile, 'rU')
except:
print "bad mag file name"
sys.exit()
else:
print "mag_file field is required option"
print main.__doc__
sys.exit()
if "-dc" in args:
ind = args.index("-dc")
labfield = float(args[ind + 1]) * 1e-6
phi = float(args[ind + 2])
theta = float(args[ind + 3])
if "-ac" in args:
ind = args.index("-ac")
peakfield = float(args[ind + 1]) * 1e-3
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind + 1])
if specnum != 0: specnum = -specnum
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if "-fsa" in args:
ind = args.index("-fsa")
Samps, file_type = pmag.magic_read(args[ind + 1])
if '-syn' in args:
syn = 1
ind = args.index("-syn")
institution = args[ind + 1]
syntype = args[ind + 2]
if '-fsy' in args:
ind = args.index("-fsy")
synfile = args[ind + 1]
if "-ins" in args:
ind = args.index("-ins")
inst = args[ind + 1]
if "-A" in args: noave = 1
if "-ncn" in args:
ind = args.index("-ncn")
samp_con = sys.argv[ind + 1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "4"
if '-LP' in args:
ind = args.index("-LP")
codelist = args[ind + 1]
codes = codelist.split(':')
if "AF" in codes:
demag = 'AF'
if '-dc' not in args: methcode = "LT-AF-Z"
if '-dc' in args: methcode = "LT-AF-I"
if "T" in codes:
demag = "T"
if '-dc' not in args: methcode = "LT-T-Z"
if '-dc' in args: methcode = "LT-T-I"
if "I" in codes:
methcode = "LP-IRM"
irmunits = "mT"
if "S" in codes:
demag = "S"
methcode = "LP-PI-TRM:LP-PI-ALT-AFARM"
trm_labfield = labfield
ans = raw_input("DC lab field for ARM step: [50uT] ")
if ans == "":
arm_labfield = 50e-6
else:
arm_labfield = float(ans) * 1e-6
ans = raw_input("temperature for total trm step: [600 C] ")
if ans == "":
trm_peakT = 600 + 273 # convert to kelvin
else:
trm_peakT = float(ans) + 273 # convert to kelvin
if "G" in codes: methcode = "LT-AF-G"
if "D" in codes: methcode = "LT-AF-D"
if "TRM" in codes:
demag = "T"
trm = 1
if "-V" in args:
methcode = "LP-IRM"
ind = args.index("-V")
irmunits = "V"
coil = args[ind + 1]
if coil not in ["1", "2", "3"]:
print main.__doc__
print 'not a valid coil specification'
sys.exit()
if demag == "T" and "ANI" in codes:
methcode = "LP-AN-TRM"
if demag == "AF" and "ANI" in codes:
methcode = "LP-AN-ARM"
if labfield == 0: labfield = 50e-6
if peakfield == 0: peakfield = .180
SynRecs, MagRecs = [], []
version_num = pmag.get_version()
if 1: # ldgo file format
#
# find start of data:
#
Samps = [] # keeps track of sample orientations
DIspec = []
Data, k = input.readlines(), 0
for k in range(len(Data)):
rec = Data[k].split()
if rec[0][0] == "_" or rec[0][0:2] == "!_":
break
start = k + 1
for k in range(start, len(Data)):
rec = Data[k].split()
if len(rec) > 0:
MagRec = {}
MagRec["treatment_temp"] = '%8.3e' % (273
) # room temp in kelvin
MagRec["measurement_temp"] = '%8.3e' % (
273) # room temp in kelvin
MagRec["treatment_ac_field"] = '0'
MagRec["treatment_dc_field"] = '0'
MagRec["treatment_dc_field_phi"] = '0'
MagRec["treatment_dc_field_theta"] = '0'
meas_type = "LT-NO"
MagRec["measurement_flag"] = 'g'
MagRec["measurement_standard"] = 'u'
MagRec["measurement_number"] = '1'
MagRec["er_specimen_name"] = rec[0]
if specnum != 0:
MagRec["er_sample_name"] = rec[0][:specnum]
else:
MagRec["er_sample_name"] = rec[0]
site = pmag.parse_site(MagRec['er_sample_name'], samp_con, Z)
MagRec["er_site_name"] = site
MagRec["er_location_name"] = er_location_name
MagRec["measurement_csd"] = rec[3]
MagRec["measurement_magn_moment"] = '%10.3e' % (
float(rec[4]) * 1e-7) # moment in Am^2 (from 10^-4 emu)
#
#if samp_file!="" and MagRec["er_sample_name"] not in Samps: # create er_samples.txt file with these data
# cdec,cinc=float(rec[5]),float(rec[6])
# gdec,ginc=float(rec[7]),float(rec[8])
# az,pl=pmag.get_azpl(cdec,cinc,gdec,ginc)
# bdec,binc=float(rec[9]),float(rec[10])
# if rec[7]!=rec[9] and rec[6]!=rec[8]:
# dipdir,dip=pmag.get_tilt(gdec,ginc,bdec,binc)
# else:
# dipdir,dip=0,0
# ErSampRec={}
# ErSampRec['er_location_name']=MagRec['er_location_name']
# ErSampRec['er_sample_name']=MagRec['er_sample_name']
# ErSampRec['er_site_name']=MagRec['er_site_name']
# ErSampRec['sample_azimuth']='%7.1f'%(az)
# ErSampRec['sample_dip']='%7.1f'%(pl)
# ErSampRec['sample_bed_dip_direction']='%7.1f'%(dipdir)
# ErSampRec['sample_bed_dip']='%7.1f'%(dip)
# ErSampRec['sample_description']='az,pl,dip_dir and dip recalculated from [c,g,b][dec,inc] in ldeo file'
# ErSampRec['magic_method_codes']='SO-REC'
# ErSamps.append(ErSampRec)
# Samps.append(ErSampRec['er_sample_name'])
MagRec["measurement_dec"] = rec[5]
MagRec["measurement_inc"] = rec[6]
MagRec["measurement_chi"] = '%10.3e' % (
float(rec[11]) * 1e-5
) #convert to SI (assume Bartington, 10-5 SI)
#MagRec["magic_instrument_codes"]=rec[2]
#MagRec["er_analyst_mail_names"]=""
MagRec["er_citation_names"] = "This study"
MagRec["magic_method_codes"] = meas_type
if demag == "AF":
if methcode != "LP-AN-ARM":
MagRec["treatment_ac_field"] = '%8.3e' % (
float(rec[1]) * 1e-3) # peak field in tesla
meas_type = "LT-AF-Z"
MagRec["treatment_dc_field"] = '0'
else: # AARM experiment
if treat[1][0] == '0':
meas_type = "LT-AF-Z"
MagRec["treatment_ac_field"] = '%8.3e' % (
peakfield) # peak field in tesla
else:
meas_type = "LT-AF-I"
ipos = int(treat[0]) - 1
MagRec["treatment_dc_field_phi"] = '%7.1f' % (
dec[ipos])
MagRec["treatment_dc_field_theta"] = '%7.1f' % (
inc[ipos])
MagRec["treatment_dc_field"] = '%8.3e' % (labfield)
MagRec["treatment_ac_field"] = '%8.3e' % (
peakfield) # peak field in tesla
elif demag == "T":
if rec[1][0] == ".": rec[1] = "0" + rec[1]
treat = rec[1].split('.')
if len(treat) == 1: treat.append('0')
MagRec["treatment_temp"] = '%8.3e' % (float(rec[1]) + 273.
) # temp in kelvin
meas_type = "LT-T-Z"
MagRec["treatment_temp"] = '%8.3e' % (
float(treat[0]) + 273.) # temp in kelvin
if trm == 0: # demag=T and not trmaq
if treat[1][0] == '0':
meas_type = "LT-T-Z"
else:
MagRec["treatment_dc_field"] = '%8.3e' % (
labfield
) # labfield in tesla (convert from microT)
MagRec["treatment_dc_field_phi"] = '%7.1f' % (
phi) # labfield phi
MagRec["treatment_dc_field_theta"] = '%7.1f' % (
theta) # labfield theta
if treat[1][0] == '1':
meas_type = "LT-T-I" # in-field thermal step
if treat[1][0] == '2':
meas_type = "LT-PTRM-I" # pTRM check
pTRM = 1
if treat[1][0] == '3':
MagRec[
"treatment_dc_field"] = '0' # this is a zero field step
meas_type = "LT-PTRM-MD" # pTRM tail check
else:
meas_type = "LT-T-I" # trm acquisition experiment
MagRec['magic_method_codes'] = meas_type
MagRecs.append(MagRec)
MagOuts = pmag.measurements_methods(MagRecs, noave)
pmag.magic_write(meas_file, MagOuts, 'magic_measurements')
print "results put in ", meas_file
if samp_file != "":
pmag.magic_write(samp_file, ErSamps, 'er_samples')
print "sample orientations put in ", samp_file
if len(SynRecs) > 0:
pmag.magic_write(synfile, SynRecs, 'er_synthetics')
print "synthetics put in ", synfile
def main():
"""
NAME
IODP_csv_magic.py
DESCRIPTION
converts ODP LIMS sample format files to magic_measurements format files
SYNTAX
IODP_csv_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input .csv file, default is all in directory
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsp FILE: specify output er_specimens.txt file, default is er_specimens.txt
-Fsa FILE: specify output er_samples.txt file, default is er_samples.txt
-Fsi FILE: specify output er_sites.txt file, default is er_sites.txt
-A : don't average replicate measurements
INPUTS
IODP .csv file format exported from LIMS database
"""
#
#
version_num=pmag.get_version()
meas_file='magic_measurements.txt'
spec_file='er_specimens.txt'
samp_file='er_samples.txt'
site_file='er_sites.txt'
csv_file=''
ErSpecs,ErSamps,ErSites,ErLocs,ErCits=[],[],[],[],[]
MagRecs=[]
citation="This study"
dir_path,demag='.','NRM'
args=sys.argv
noave=0
depth_method='a'
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
print "dir_path", dir_path
if "-h" in args:
print main.__doc__
sys.exit()
if "-A" in args: noave=1
if '-f' in args:
ind=args.index("-f")
# csv_file=args[ind+1] # original
csv_file=dir_path + '/' + args[ind+1] # LJ
if '-F' in args:
ind=args.index("-F")
meas_file=args[ind+1]
if '-Fsp' in args:
ind=args.index("-Fsp")
spec_file=dir_path+'/'+args[ind+1]
Specs,file_type=pmag.magic_read(spec_file)
else:
spec_file=dir_path+'/'+spec_file
if '-Fsi' in args:
ind=args.index("-Fsi")
site_file=args[ind+1]
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file=dir_path+'/'+args[ind+1]
ErSamps,file_type=pmag.magic_read(samp_file)
else:
samp_file=dir_path+'/'+samp_file
site_file=dir_path+'/'+site_file
meas_file=dir_path+'/'+meas_file
if csv_file=="":
filelist=os.listdir(dir_path) # read in list of files to import
else:
filelist=[csv_file]
specimens,samples,sites=[],[],[]
MagRecs,SpecRecs,SampRecs,SiteRecs=[],[],[],[]
for samp in ErSamps:
if samp['er_sample_name'] not in samples:
samples.append(samp['er_sample_name'])
SampRecs.append(samp)
print "filelist", filelist # LJ
for file in filelist: # parse each file
if file[-3:].lower()=='csv':
print 'processing: ',file
input=open(file,'rU').readlines()
keys=input[0].replace('\n','').split(',') # splits on underscores
if "Interval Top (cm) on SHLF" in keys:interval_key="Interval Top (cm) on SHLF"
if " Interval Bot (cm) on SECT" in keys:interval_key=" Interval Bot (cm) on SECT"
if "Top Depth (m)" in keys:depth_key="Top Depth (m)"
if "CSF-A Top (m)" in keys:depth_key="CSF-A Top (m)"
if "CSF-B Top (m)" in keys:
comp_depth_key="CSF-B Top (m)" # use this model if available
else:
comp_depth_key=""
if "Demag level (mT)" in keys:demag_key="Demag level (mT)"
if "Demag Level (mT)" in keys: demag_key="Demag Level (mT)"
if "Inclination (Tray- and Bkgrd-Corrected) (deg)" in keys:inc_key="Inclination (Tray- and Bkgrd-Corrected) (deg)"
if "Inclination background + tray corrected (deg)" in keys:inc_key="Inclination background + tray corrected (deg)"
if "Inclination background + tray corrected (\xc2\xb0)" in keys:inc_key="Inclination background + tray corrected (\xc2\xb0)"
if "Declination (Tray- and Bkgrd-Corrected) (deg)" in keys:dec_key="Declination (Tray- and Bkgrd-Corrected) (deg)"
if "Declination background + tray corrected (deg)" in keys:dec_key="Declination background + tray corrected (deg)"
if "Declination background + tray corrected (\xc2\xb0)" in keys:dec_key="Declination background + tray corrected (\xc2\xb0)"
if "Intensity (Tray- and Bkgrd-Corrected) (A/m)" in keys:int_key="Intensity (Tray- and Bkgrd-Corrected) (A/m)"
if "Intensity background + tray corrected (A/m)" in keys:int_key="Intensity background + tray corrected (A/m)"
if "Core Type" in keys:
type="Core Type"
else: type="Type"
for line in input[1:]:
InRec={}
for k in range(len(keys)):InRec[keys[k]]=line.split(',')[k]
try:
run_number=""
inst="ODP-SRM"
volume='15.59' # set default volume to this
MagRec,SpecRec,SampRec,SiteRec={},{},{},{}
expedition=InRec['Exp']
location=InRec['Site']+InRec['Hole']
# Maintain backward compatibility for the ever-changing LIMS format (Argh!)
while len(InRec['Core'])<3:
InRec['Core']='0'+InRec['Core']
if "Last Tray Measurment" in InRec.keys() and "Discrete" in InRec['Last Tray Measurement'] or 'dscr' in csv_file : # assume discrete sample
specimen=expedition+'-'+location+'-'+InRec['Core']+InRec[type]+"-"+InRec['Section']+'-'+InRec['Section Half']+'-'+InRec[interval_key]
else: # mark as continuous measurements
specimen=expedition+'-'+location+'-'+InRec['Core']+InRec[type]+"_"+InRec['Section']+InRec['Section Half']+'-'+InRec[interval_key]
SpecRec['er_expedition_name']=expedition
SpecRec['er_location_name']=location
SpecRec['er_site_name']=specimen
SpecRec['er_citation_names']=citation
for key in SpecRec.keys():SampRec[key]=SpecRec[key]
for key in SpecRec.keys():SiteRec[key]=SpecRec[key]
SampRec['sample_azimuth']='0'
SampRec['sample_dip']='0'
SampRec['sample_core_depth']=InRec[depth_key]
if comp_depth_key!='':
SampRec['sample_composite_depth']=InRec[comp_depth_key]
if "Discrete" in InRec['Last Tray Measurement']:
SampRec['magic_method_codes']='FS-C-DRILL-IODP:SP-SS-C:SO-V'
else:
SampRec['magic_method_codes']='FS-C-DRILL-IODP:SO-V'
SpecRec['er_specimen_name']=specimen
SpecRec['er_sample_name']=specimen
SampRec['er_sample_name']=specimen
SampRec['er_specimen_names']=specimen
SiteRec['er_specimen_names']=specimen
for key in SpecRec.keys():MagRec[key]=SpecRec[key]
# set up measurement record - default is NRM
MagRec['er_analyst_mail_names']=InRec['Test Entered By']
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["treatment_ac_field"]=0
MagRec["treatment_dc_field"]='0'
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
MagRec["measurement_flag"]='g' # assume all data are "good"
MagRec["measurement_standard"]='u' # assume all data are "good"
SpecRec['er_specimen_alternatives']=InRec['Text Id']
if 'Sample Area (cm?)' in InRec.keys() and InRec['Sample Area (cm?)']!= "": volume=InRec['Sample Area (cm?)']
if InRec['Run Number']!= "": run_number=InRec['Run Number']
datestamp=InRec['Test Changed On'].split() # date time is second line of file
mmddyy=datestamp[0].split('/') # break into month day year
if len(mmddyy[0])==1: mmddyy[0]='0'+mmddyy[0] # make 2 characters
if len(mmddyy[1])==1: mmddyy[1]='0'+mmddyy[1] # make 2 characters
if len(datestamp[1])==1: datestamp[1]='0'+datestamp[1] # make 2 characters
date='20'+mmddyy[2]+':'+mmddyy[0]+":"+mmddyy[1] +':' +datestamp[1]+":00.00"
MagRec["measurement_date"]=date
MagRec["magic_method_codes"]='LT-NO'
if InRec[demag_key]!="0":
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst=inst+':ODP-SRM-AF' # measured on shipboard in-line 2G AF
treatment_value=float(InRec[demag_key].strip('"'))*1e-3 # convert mT => T
MagRec["treatment_ac_field"]=treatment_value # AF demag in treat mT => T
if InRec['Treatment Type']!="":
if 'Alternating Frequency' in InRec['Treatment Type']:
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst=inst+':ODP-DTECH' # measured on shipboard Dtech D2000
treatment_value=float(InRec['Treatment Value'])*1e-3 # convert mT => T
MagRec["treatment_ac_field"]=treatment_value # AF demag in treat mT => T
elif 'Thermal' in InRec['Treatment Type']:
MagRec['magic_method_codes'] = 'LT-T-Z'
inst=inst+':ODP-TDS' # measured on shipboard Schonstedt thermal demagnetizer
treatment_value=float(InRec['Treatment Value'])+273 # convert C => K
MagRec["treatment_temp"]='%8.3e'%(treatment_value) #
MagRec["measurement_standard"]='u' # assume all data are "good"
vol=float(volume)*1e-6 # convert from cc to m^3
if run_number!="":
MagRec['external_database_ids']=run_number
MagRec['external_database_names']='LIMS'
else:
MagRec['external_database_ids']=""
MagRec['external_database_names']=''
MagRec['measurement_inc']=InRec[inc_key].strip('"')
MagRec['measurement_dec']=InRec[dec_key].strip('"')
intens= InRec[int_key].strip('"')
MagRec['measurement_magn_moment']='%8.3e'%(float(intens)*vol) # convert intensity from A/m to Am^2 using vol
MagRec['magic_instrument_codes']=inst
MagRec['measurement_number']='1'
MagRec['measurement_csd']=''
MagRec['measurement_positions']=''
MagRecs.append(MagRec)
if specimen not in specimens:
specimens.append(specimen)
SpecRecs.append(SpecRec)
if MagRec['er_sample_name'] not in samples:
samples.append(MagRec['er_sample_name'])
SampRecs.append(SampRec)
if MagRec['er_site_name'] not in sites:
sites.append(MagRec['er_site_name'])
SiteRecs.append(SiteRec)
except:
pass
if len(SpecRecs)>0:
pmag.magic_write(spec_file,SpecRecs,'er_specimens')
print 'specimens stored in ',spec_file
if len(SampRecs)>0:
SampOut,keys=pmag.fillkeys(SampRecs)
pmag.magic_write(samp_file,SampOut,'er_samples')
print 'samples stored in ',samp_file
if len(SiteRecs)>0:
pmag.magic_write(site_file,SiteRecs,'er_sites')
print 'sites stored in ',site_file
MagSort=pmag.sortbykeys(MagRecs,["er_specimen_name","treatment_ac_field"])
MagOuts=[]
for MagRec in MagSort:
MagRec["treatment_ac_field"]='%8.3e'%(MagRec['treatment_ac_field']) # convert to string
MagOuts.append(MagRec)
Fixed=pmag.measurements_methods(MagOuts,noave)
pmag.magic_write(meas_file,Fixed,'magic_measurements')
print 'data stored in ',meas_file
def main():
"""
NAME
specimens_results_magic.py
DESCRIPTION
combines pmag_specimens.txt file with age, location, acceptance criteria and
outputs pmag_results table along with other MagIC tables necessary for uploading to the database
SYNTAX
specimens_results_magic.py [command line options]
OPTIONS
-h prints help message and quits
-usr USER: identify user, default is ""
-f: specimen input magic_measurements format file, default is "magic_measurements.txt"
-fsp: specimen input pmag_specimens format file, default is "pmag_specimens.txt"
-fsm: sample input er_samples format file, default is "er_samples.txt"
-fsi: specimen input er_sites format file, default is "er_sites.txt"
-fla: specify a file with paleolatitudes for calculating VADMs, default is not to calculate VADMS
format is: site_name paleolatitude (space delimited file)
-fa AGES: specify er_ages format file with age information
-crd [s,g,t,b]: specify coordinate system
(s, specimen, g geographic, t, tilt corrected, b, geographic and tilt corrected)
Default is to assume geographic
NB: only the tilt corrected data will appear on the results table, if both g and t are selected.
-cor [AC:CR:NL]: colon delimited list of required data adjustments for all specimens
included in intensity calculations (anisotropy, cooling rate, non-linear TRM)
unless specified, corrections will not be applied
-pri [TRM:ARM] colon delimited list of priorities for anisotropy correction (-cor must also be set to include AC). default is TRM, then ARM
-age MIN MAX UNITS: specify age boundaries and units
-exc: use exiting selection criteria (in pmag_criteria.txt file), default is default criteria
-C: no acceptance criteria
-aD: average directions per sample, default is NOT
-aI: average multiple specimen intensities per sample, default is by site
-aC: average all components together, default is NOT
-pol: calculate polarity averages
-sam: save sample level vgps and v[a]dms, default is by site
-xSi: skip the site level intensity calculation
-p: plot directions and look at intensities by site, default is NOT
-fmt: specify output for saved images, default is svg (only if -p set)
-lat: use present latitude for calculating VADMs, default is not to calculate VADMs
-xD: skip directions
-xI: skip intensities
OUPUT
writes pmag_samples, pmag_sites, pmag_results tables
"""
# set defaults
Comps=[] # list of components
version_num=pmag.get_version()
args=sys.argv
DefaultAge=["none"]
skipdirs,coord,excrit,custom,vgps,average,Iaverage,plotsites,opt=1,0,0,0,0,0,0,0,0
get_model_lat=0 # this skips VADM calculation altogether, when get_model_lat=1, uses present day
fmt='svg'
dir_path="."
model_lat_file=""
Caverage=0
infile='pmag_specimens.txt'
measfile="magic_measurements.txt"
sampfile="er_samples.txt"
sitefile="er_sites.txt"
agefile="er_ages.txt"
specout="er_specimens.txt"
sampout="pmag_samples.txt"
siteout="pmag_sites.txt"
resout="pmag_results.txt"
critout="pmag_criteria.txt"
instout="magic_instruments.txt"
sigcutoff,OBJ="",""
noDir,noInt=0,0
polarity=0
coords=['0']
Dcrit,Icrit,nocrit=0,0,0
corrections=[]
nocorrection=['DA-NL','DA-AC','DA-CR']
priorities=['DA-AC-ARM','DA-AC-TRM'] # priorities for anisotropy correction
# get command line stuff
if "-h" in args:
print main.__doc__
sys.exit()
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if '-cor' in args:
ind=args.index('-cor')
cors=args[ind+1].split(':') # list of required data adjustments
for cor in cors:
nocorrection.remove('DA-'+cor)
corrections.append('DA-'+cor)
if '-pri' in args:
ind=args.index('-pri')
priorities=args[ind+1].split(':') # list of required data adjustments
for p in priorities:
p='DA-AC-'+p
if '-f' in args:
ind=args.index("-f")
measfile=args[ind+1]
if '-fsp' in args:
ind=args.index("-fsp")
infile=args[ind+1]
if '-fsi' in args:
ind=args.index("-fsi")
sitefile=args[ind+1]
if "-crd" in args:
ind=args.index("-crd")
coord=args[ind+1]
if coord=='s':coords=['-1']
if coord=='g':coords=['0']
if coord=='t':coords=['100']
if coord=='b':coords=['0','100']
if "-usr" in args:
ind=args.index("-usr")
user=sys.argv[ind+1]
else: user=""
if "-C" in args: Dcrit,Icrit,nocrit=1,1,1 # no selection criteria
if "-sam" in args: vgps=1 # save sample level VGPS/VADMs
if "-xSi" in args:
nositeints=1 # skip site level intensity
else:
nositeints=0
if "-age" in args:
ind=args.index("-age")
DefaultAge[0]=args[ind+1]
DefaultAge.append(args[ind+2])
DefaultAge.append(args[ind+3])
Daverage,Iaverage,Caverage=0,0,0
if "-aD" in args: Daverage=1 # average by sample directions
if "-aI" in args: Iaverage=1 # average by sample intensities
if "-aC" in args: Caverage=1 # average all components together ??? why???
if "-pol" in args: polarity=1 # calculate averages by polarity
if '-xD' in args:noDir=1
if '-xI' in args:
noInt=1
elif "-fla" in args:
if '-lat' in args:
print "you should set a paleolatitude file OR use present day lat - not both"
sys.exit()
ind=args.index("-fla")
model_lat_file=dir_path+'/'+args[ind+1]
get_model_lat=2
mlat=open(model_lat_file,'rU')
ModelLats=[]
for line in mlat.readlines():
ModelLat={}
tmp=line.split()
ModelLat["er_site_name"]=tmp[0]
ModelLat["site_model_lat"]=tmp[1]
ModelLat["er_sample_name"]=tmp[0]
ModelLat["sample_lat"]=tmp[1]
ModelLats.append(ModelLat)
get_model_lat=2
elif '-lat' in args:
get_model_lat=1
if "-p" in args:
plotsites=1
if "-fmt" in args:
ind=args.index("-fmt")
fmt=args[ind+1]
if noDir==0: # plot by site - set up plot window
import pmagplotlib
EQ={}
EQ['eqarea']=1
pmagplotlib.plot_init(EQ['eqarea'],5,5) # define figure 1 as equal area projection
pmagplotlib.plotNET(EQ['eqarea']) # I don't know why this has to be here, but otherwise the first plot never plots...
pmagplotlib.drawFIGS(EQ)
if '-WD' in args:
infile=dir_path+'/'+infile
measfile=dir_path+'/'+measfile
instout=dir_path+'/'+instout
sampfile=dir_path+'/'+sampfile
sitefile=dir_path+'/'+sitefile
agefile=dir_path+'/'+agefile
specout=dir_path+'/'+specout
sampout=dir_path+'/'+sampout
siteout=dir_path+'/'+siteout
resout=dir_path+'/'+resout
critout=dir_path+'/'+critout
if "-exc" in args: # use existing pmag_criteria file
if "-C" in args:
print 'you can not use both existing and no criteria - choose either -exc OR -C OR neither (for default)'
sys.exit()
crit_data,file_type=pmag.magic_read(critout)
print "Acceptance criteria read in from ", critout
else : # use default criteria (if nocrit set, then get really loose criteria as default)
crit_data=pmag.default_criteria(nocrit)
if nocrit==0:
print "Acceptance criteria are defaults"
else:
print "No acceptance criteria used "
accept={}
for critrec in crit_data:
for key in critrec.keys():
if 'sample_int_sigma_uT' in critrec.keys():
critrec['sample_int_sigma']='%10.3e'%(eval(critrec['sample_int_sigma_uT'])*1e-6)
if key not in accept.keys() and critrec[key]!='':
accept[key]=critrec[key]
#
#
if "-exc" not in args and "-C" not in args:
print "args",args
pmag.magic_write(critout,[accept],'pmag_criteria')
print "\n Pmag Criteria stored in ",critout,'\n'
#
# now we're done slow dancing
#
SiteNFO,file_type=pmag.magic_read(sitefile) # read in site data - has the lats and lons
SampNFO,file_type=pmag.magic_read(sampfile) # read in site data - has the lats and lons
height_nfo=pmag.get_dictitem(SiteNFO,'site_height','','F') # find all the sites with height info.
if agefile !="":AgeNFO,file_type=pmag.magic_read(agefile) # read in the age information
Data,file_type=pmag.magic_read(infile) # read in specimen interpretations
IntData=pmag.get_dictitem(Data,'specimen_int','','F') # retrieve specimens with intensity data
comment,orient="",[]
samples,sites=[],[]
for rec in Data: # run through the data filling in missing keys and finding all components, coordinates available
# fill in missing fields, collect unique sample and site names
if 'er_sample_name' not in rec.keys():
rec['er_sample_name']=""
elif rec['er_sample_name'] not in samples:
samples.append(rec['er_sample_name'])
if 'er_site_name' not in rec.keys():
rec['er_site_name']=""
elif rec['er_site_name'] not in sites:
sites.append(rec['er_site_name'])
if 'specimen_int' not in rec.keys():rec['specimen_int']=''
if 'specimen_comp_name' not in rec.keys() or rec['specimen_comp_name']=="":rec['specimen_comp_name']='A'
if rec['specimen_comp_name'] not in Comps:Comps.append(rec['specimen_comp_name'])
rec['specimen_tilt_correction']=rec['specimen_tilt_correction'].strip('\n')
if "specimen_tilt_correction" not in rec.keys(): rec["specimen_tilt_correction"]="-1" # assume sample coordinates
if rec["specimen_tilt_correction"] not in orient: orient.append(rec["specimen_tilt_correction"]) # collect available coordinate systems
if "specimen_direction_type" not in rec.keys(): rec["specimen_direction_type"]='l' # assume direction is line - not plane
if "specimen_dec" not in rec.keys(): rec["specimen_direction_type"]='' # if no declination, set direction type to blank
if "specimen_n" not in rec.keys(): rec["specimen_n"]='' # put in n
if "specimen_alpha95" not in rec.keys(): rec["specimen_alpha95"]='' # put in alpha95
if "magic_method_codes" not in rec.keys(): rec["magic_method_codes"]=''
#
# start parsing data into SpecDirs, SpecPlanes, SpecInts
SpecInts,SpecDirs,SpecPlanes=[],[],[]
samples.sort() # get sorted list of samples and sites
sites.sort()
if noInt==0: # don't skip intensities
IntData=pmag.get_dictitem(Data,'specimen_int','','F') # retrieve specimens with intensity data
if nocrit==0: # use selection criteria
for rec in IntData: # do selection criteria
kill=pmag.grade(rec,accept,'specimen_int')
if len(kill)==0: SpecInts.append(rec) # intensity record to be included in sample, site calculations
else:
SpecInts=IntData[:] # take everything - no selection criteria
# check for required data adjustments
if len(corrections)>0 and len(SpecInts)>0:
for cor in corrections:
SpecInts=pmag.get_dictitem(SpecInts,'magic_method_codes',cor,'has') # only take specimens with the required corrections
if len(nocorrection)>0 and len(SpecInts)>0:
for cor in nocorrection:
SpecInts=pmag.get_dictitem(SpecInts,'magic_method_codes',cor,'not') # exclude the corrections not specified for inclusion
# take top priority specimen of its name in remaining specimens (only one per customer)
PrioritySpecInts=[]
specimens=pmag.get_specs(SpecInts) # get list of uniq specimen names
for spec in specimens:
ThisSpecRecs=pmag.get_dictitem(SpecInts,'er_specimen_name',spec,'T') # all the records for this specimen
if len(ThisSpecRecs)==1:
PrioritySpecInts.append(ThisSpecRecs[0])
elif len(ThisSpecRecs)>1: # more than one
prec=[]
for p in priorities:
ThisSpecRecs=pmag.get_dictitem(SpecInts,'magic_method_codes',p,'has') # all the records for this specimen
if len(ThisSpecRecs)>0:prec.append(ThisSpecRecs[0])
PrioritySpecInts.append(prec[0]) # take the best one
SpecInts=PrioritySpecInts # this has the first specimen record
if noDir==0: # don't skip directions
AllDirs=pmag.get_dictitem(Data,'specimen_direction_type','','F') # retrieve specimens with directed lines and planes
Ns=pmag.get_dictitem(AllDirs,'specimen_n','','F') # get all specimens with specimen_n information
if nocrit!=1: # use selection criteria
for rec in Ns: # look through everything with specimen_n for "good" data
kill=pmag.grade(rec,accept,'specimen_dir')
if len(kill)==0: # nothing killed it
SpecDirs.append(rec)
else: # no criteria
SpecDirs=AllDirs[:] # take them all
# SpecDirs is now the list of all specimen directions (lines and planes) that pass muster
#
PmagSamps,SampDirs=[],[] # list of all sample data and list of those that pass the DE-SAMP criteria
PmagSites,PmagResults=[],[] # list of all site data and selected results
SampInts=[]
for samp in samples: # run through the sample names
if Daverage==1: # average by sample if desired
SampDir=pmag.get_dictitem(SpecDirs,'er_sample_name',samp,'T') # get all the directional data for this sample
if len(SampDir)>0: # there are some directions
for coord in coords: # step through desired coordinate systems
CoordDir=pmag.get_dictitem(SampDir,'specimen_tilt_correction',coord,'T') # get all the directions for this sample
if len(CoordDir)>0: # there are some with this coordinate system
if Caverage==0: # look component by component
for comp in Comps:
CompDir=pmag.get_dictitem(CoordDir,'specimen_comp_name',comp,'T') # get all directions from this component
if len(CompDir)>0: # there are some
PmagSampRec=pmag.lnpbykey(CompDir,'sample','specimen') # get a sample average from all specimens
PmagSampRec["er_location_name"]=CompDir[0]['er_location_name'] # decorate the sample record
PmagSampRec["er_site_name"]=CompDir[0]['er_site_name']
PmagSampRec["er_sample_name"]=samp
PmagSampRec["er_citation_names"]="This study"
PmagSampRec["er_analyst_mail_names"]=user
PmagSampRec['magic_software_packages']=version_num
if nocrit!=1:PmagSampRec['pmag_criteria_codes']="ACCEPT"
if agefile != "": PmagSampRec= pmag.get_age(PmagSampRec,"er_site_name","sample_inferred_",AgeNFO,DefaultAge)
site_height=pmag.get_dictitem(height_nfo,'er_site_name',PmagSampRec['er_site_name'],'T')
if len(site_height)>0:PmagSampRec["sample_height"]=site_height[0]['site_height'] # add in height if available
PmagSampRec['sample_comp_name']=comp
PmagSampRec['sample_tilt_correction']=coord
PmagSampRec['er_specimen_names']= pmag.get_list(CompDir,'er_specimen_name') # get a list of the specimen names used
PmagSampRec['magic_method_codes']= pmag.get_list(CompDir,'magic_method_codes') # get a list of the methods used
if nocrit!=1: # apply selection criteria
kill=pmag.grade(PmagSampRec,accept,'sample_dir')
else:
kill=[]
if len(kill)==0:
SampDirs.append(PmagSampRec)
if vgps==1: # if sample level VGP info desired, do that now
PmagResRec=pmag.getsampVGP(PmagSampRec,SiteNFO)
if PmagResRec!="":PmagResults.append(PmagResRec)
PmagSamps.append(PmagSampRec)
if Caverage==1: # average all components together basically same as above
PmagSampRec=pmag.lnpbykey(CoordDir,'sample','specimen')
PmagSampRec["er_location_name"]=CoordDir[0]['er_location_name']
PmagSampRec["er_site_name"]=CoordDir[0]['er_site_name']
PmagSampRec["er_sample_name"]=samp
PmagSampRec["er_citation_names"]="This study"
PmagSampRec["er_analyst_mail_names"]=user
PmagSampRec['magic_software_packages']=version_num
if nocrit!=1:PmagSampRec['pmag_criteria_codes']=""
if agefile != "": PmagSampRec= pmag.get_age(PmagSampRec,"er_site_name","sample_inferred_",AgeNFO,DefaultAge)
site_height=pmag.get_dictitem(height_nfo,'er_site_name',site,'T')
if len(site_height)>0:PmagSampRec["sample_height"]=site_height[0]['site_height'] # add in height if available
PmagSampRec['sample_tilt_correction']=coord
PmagSampRec['sample_comp_name']= pmag.get_list(CoordDir,'specimen_comp_name') # get components used
PmagSampRec['er_specimen_names']= pmag.get_list(CoordDir,'er_specimen_name') # get specimne names averaged
PmagSampRec['magic_method_codes']= pmag.get_list(CoordDir,'magic_method_codes') # assemble method codes
if nocrit!=1: # apply selection criteria
kill=pmag.grade(PmagSampRec,accept,'sample_dir')
if len(kill)==0: # passes the mustard
SampDirs.append(PmagSampRec)
if vgps==1:
PmagResRec=pmag.getsampVGP(PmagSampRec,SiteNFO)
if PmagResRec!="":PmagResults.append(PmagResRec)
else: # take everything
SampDirs.append(PmagSampRec)
if vgps==1:
PmagResRec=pmag.getsampVGP(PmagSampRec,SiteNFO)
if PmagResRec!="":PmagResults.append(PmagResRec)
PmagSamps.append(PmagSampRec)
if Iaverage==1: # average by sample if desired
SampI=pmag.get_dictitem(SpecInts,'er_sample_name',samp,'T') # get all the intensity data for this sample
if len(SampI)>0: # there are some
PmagSampRec=pmag.average_int(SampI,'specimen','sample') # get average intensity stuff
PmagSampRec["sample_description"]="sample intensity" # decorate sample record
PmagSampRec["sample_direction_type"]=""
PmagSampRec['er_site_name']=SampI[0]["er_site_name"]
PmagSampRec['er_sample_name']=samp
PmagSampRec['er_location_name']=SampI[0]["er_location_name"]
PmagSampRec["er_citation_names"]="This study"
PmagSampRec["er_analyst_mail_names"]=user
if agefile != "": PmagSampRec=pmag.get_age(PmagSampRec,"er_site_name","sample_inferred_", AgeNFO,DefaultAge)
site_height=pmag.get_dictitem(height_nfo,'er_site_name',PmagSampRec['er_site_name'],'T')
if len(site_height)>0:PmagSampRec["sample_height"]=site_height[0]['site_height'] # add in height if available
PmagSampRec['er_specimen_names']= pmag.get_list(SampI,'er_specimen_name')
PmagSampRec['magic_method_codes']= pmag.get_list(SampI,'magic_method_codes')
if nocrit!=1: # apply criteria!
kill=pmag.grade(PmagSampRec,accept,'sample_int')
if len(kill)==0:
PmagSampRec['pmag_criteria_codes']="ACCEPT"
SampInts.append(PmagSampRec)
PmagSamps.append(PmagSampRec)
else:PmagSampRec={} # sample rejected
else: # no criteria
SampInts.append(PmagSampRec)
PmagSamps.append(PmagSampRec)
PmagSampRec['pmag_criteria_codes']=""
if vgps==1 and get_model_lat!=0 and PmagSampRec!={}: #
if get_model_lat==1: # use sample latitude
PmagResRec=pmag.getsampVDM(PmagSampRec,SampNFO)
del(PmagResRec['model_lat']) # get rid of the model lat key
elif get_model_lat==2: # use model latitude
PmagResRec=pmag.getsampVDM(PmagSampRec,ModelLats)
if PmagResRec!={}:PmagResRec['magic_method_codes']=PmagResRec['magic_method_codes']+":IE-MLAT"
if PmagResRec!={}:
PmagResRec['er_specimen_names']=PmagSampRec['er_specimen_names']
PmagResRec['er_sample_names']=PmagSampRec['er_sample_name']
PmagResRec['pmag_criteria_codes']='ACCEPT'
PmagResRec['average_int_sigma_perc']=PmagSampRec['sample_int_sigma_perc']
PmagResRec['average_int_sigma']=PmagSampRec['sample_int_sigma']
PmagResRec['average_int_n']=PmagSampRec['sample_int_n']
PmagResRec['vadm_n']=PmagSampRec['sample_int_n']
PmagResRec['data_type']='i'
PmagResults.append(PmagResRec)
if len(PmagSamps)>0:
TmpSamps,keylist=pmag.fillkeys(PmagSamps) # fill in missing keys from different types of records
pmag.magic_write(sampout,TmpSamps,'pmag_samples') # save in sample output file
print ' sample averages written to ',sampout
#
#create site averages from specimens or samples as specified
#
for site in sites:
if Daverage==0: key,dirlist='specimen',SpecDirs # if specimen averages at site level desired
if Daverage==1: key,dirlist='sample',SampDirs # if sample averages at site level desired
tmp=pmag.get_dictitem(dirlist,'er_site_name',site,'T') # get all the sites with directions
tmp1=pmag.get_dictitem(tmp,key+'_tilt_correction',coords[-1],'T') # use only the last coordinate if Caverage==0
sd=pmag.get_dictitem(SiteNFO,'er_site_name',site,'T') # fish out site information (lat/lon, etc.)
if len(sd)>0:
sitedat=sd[0]
if Caverage==0: # do component wise averaging
for comp in Comps:
siteD=pmag.get_dictitem(tmp1,key+'_comp_name',comp,'T') # get all components comp
if len(siteD)>0: # there are some for this site and component name
PmagSiteRec=pmag.lnpbykey(siteD,'site',key) # get an average for this site
PmagSiteRec['site_comp_name']=comp # decorate the site record
PmagSiteRec["er_location_name"]=siteD[0]['er_location_name']
PmagSiteRec["er_site_name"]=siteD[0]['er_site_name']
PmagSiteRec['site_tilt_correction']=coords[-1]
PmagSiteRec['site_comp_name']= pmag.get_list(siteD,key+'_comp_name')
if Daverage==1:
PmagSiteRec['er_sample_names']= pmag.get_list(siteD,'er_sample_name')
else:
PmagSiteRec['er_specimen_names']= pmag.get_list(siteD,'er_specimen_name')
# determine the demagnetization code (DC3,4 or 5) for this site
AFnum=len(pmag.get_dictitem(siteD,'magic_method_codes','LP-DIR-AF','has'))
Tnum=len(pmag.get_dictitem(siteD,'magic_method_codes','LP-DIR-T','has'))
DC=3
if AFnum>0:DC+=1
if Tnum>0:DC+=1
PmagSiteRec['magic_method_codes']= pmag.get_list(siteD,'magic_method_codes')+':'+ 'LP-DC'+str(DC)
PmagSiteRec['magic_method_codes'].strip(":")
if plotsites==1:
print PmagSiteRec['er_site_name']
pmagplotlib.plotSITE(EQ['eqarea'],PmagSiteRec,siteD,key) # plot and list the data
pmagplotlib.drawFIGS(EQ)
PmagSites.append(PmagSiteRec)
else: # last component only
siteD=tmp1[:] # get the last orientation system specified
if len(siteD)>0: # there are some
PmagSiteRec=pmag.lnpbykey(siteD,'site',key) # get the average for this site
PmagSiteRec["er_location_name"]=siteD[0]['er_location_name'] # decorate the record
PmagSiteRec["er_site_name"]=siteD[0]['er_site_name']
PmagSiteRec['site_comp_name']=comp
PmagSiteRec['site_tilt_correction']=coords[-1]
PmagSiteRec['site_comp_name']= pmag.get_list(siteD,key+'_comp_name')
PmagSiteRec['er_specimen_names']= pmag.get_list(siteD,'er_specimen_name')
PmagSiteRec['er_sample_names']= pmag.get_list(siteD,'er_sample_name')
AFnum=len(pmag.get_dictitem(siteD,'magic_method_codes','LP-DIR-AF','has'))
Tnum=len(pmag.get_dictitem(siteD,'magic_method_codes','LP-DIR-T','has'))
DC=3
if AFnum>0:DC+=1
if Tnum>0:DC+=1
PmagSiteRec['magic_method_codes']= pmag.get_list(siteD,'magic_method_codes')+':'+ 'LP-DC'+str(DC)
PmagSiteRec['magic_method_codes'].strip(":")
if Daverage==0:PmagSiteRec['site_comp_name']= pmag.get_list(siteD,key+'_comp_name')
if plotsites==1:
pmagplotlib.plotSITE(EQ['eqarea'],PmagSiteRec,siteD,key)
pmagplotlib.drawFIGS(EQ)
PmagSites.append(PmagSiteRec)
else:
print 'site information not found in er_sites for site, ',site,' site will be skipped'
for PmagSiteRec in PmagSites: # now decorate each dictionary some more, and calculate VGPs etc. for results table
PmagSiteRec["er_citation_names"]="This study"
PmagSiteRec["er_analyst_mail_names"]=user
PmagSiteRec['magic_software_packages']=version_num
if agefile != "": PmagSiteRec= pmag.get_age(PmagSiteRec,"er_site_name","site_inferred_",AgeNFO,DefaultAge)
PmagSiteRec['pmag_criteria_codes']='ACCEPT'
if 'site_n_lines' in PmagSiteRec.keys() and 'site_n_planes' in PmagSiteRec.keys() and PmagSiteRec['site_n_lines']!="" and PmagSiteRec['site_n_planes']!="":
if int(PmagSiteRec["site_n_planes"])>0:
PmagSiteRec["magic_method_codes"]=PmagSiteRec['magic_method_codes']+":DE-FM-LP"
elif int(PmagSiteRec["site_n_lines"])>2:
PmagSiteRec["magic_method_codes"]=PmagSiteRec['magic_method_codes']+":DE-FM"
kill=pmag.grade(PmagSiteRec,accept,'site_dir')
if len(kill)==0:
PmagResRec={} # set up dictionary for the pmag_results table entry
PmagResRec['data_type']='i' # decorate it a bit
PmagResRec['magic_software_packages']=version_num
PmagSiteRec['site_description']='Site direction included in results table'
PmagResRec['pmag_criteria_codes']='ACCEPT'
dec=float(PmagSiteRec["site_dec"])
inc=float(PmagSiteRec["site_inc"])
if 'site_alpha95' in PmagSiteRec.keys() and PmagSiteRec['site_alpha95']!="":
a95=float(PmagSiteRec["site_alpha95"])
else:a95=180.
sitedat=pmag.get_dictitem(SiteNFO,'er_site_name',PmagSiteRec['er_site_name'],'T')[0] # fish out site information (lat/lon, etc.)
lat=float(sitedat['site_lat'])
lon=float(sitedat['site_lon'])
plong,plat,dp,dm=pmag.dia_vgp(dec,inc,a95,lat,lon) # get the VGP for this site
if PmagSiteRec['site_tilt_correction']=='-1':C=' (spec coord) '
if PmagSiteRec['site_tilt_correction']=='0':C=' (geog. coord) '
if PmagSiteRec['site_tilt_correction']=='100':C=' (strat. coord) '
PmagResRec["pmag_result_name"]="VGP Site: "+PmagSiteRec["er_site_name"] # decorate some more
PmagResRec["result_description"]="Site VGP, coord system = "+str(coord)+' component: '+comp
PmagResRec['er_site_names']=PmagSiteRec['er_site_name']
PmagResRec['pmag_criteria_codes']='ACCEPT'
PmagResRec['er_citation_names']='This study'
PmagResRec['er_analyst_mail_names']=user
PmagResRec["er_location_names"]=PmagSiteRec["er_location_name"]
if Daverage==1:
PmagResRec["er_sample_names"]=PmagSiteRec["er_sample_names"]
else:
PmagResRec["er_specimen_names"]=PmagSiteRec["er_specimen_names"]
PmagResRec["tilt_correction"]=PmagSiteRec['site_tilt_correction']
PmagResRec["pole_comp_name"]=PmagSiteRec['site_comp_name']
PmagResRec["average_dec"]=PmagSiteRec["site_dec"]
PmagResRec["average_inc"]=PmagSiteRec["site_inc"]
PmagResRec["average_alpha95"]=PmagSiteRec["site_alpha95"]
PmagResRec["average_n"]=PmagSiteRec["site_n"]
PmagResRec["average_n_lines"]=PmagSiteRec["site_n_lines"]
PmagResRec["average_n_planes"]=PmagSiteRec["site_n_planes"]
PmagResRec["vgp_n"]=PmagSiteRec["site_n"]
PmagResRec["average_k"]=PmagSiteRec["site_k"]
PmagResRec["average_r"]=PmagSiteRec["site_r"]
PmagResRec["average_lat"]='%10.4f ' %(lat)
PmagResRec["average_lon"]='%10.4f ' %(lon)
if agefile != "": PmagResRec= pmag.get_age(PmagResRec,"er_site_names","average_",AgeNFO,DefaultAge)
site_height=pmag.get_dictitem(height_nfo,'er_site_name',site,'T')
if len(site_height)>0:PmagResRec["average_height"]=site_height[0]['site_height']
PmagResRec["vgp_lat"]='%7.1f ' % (plat)
PmagResRec["vgp_lon"]='%7.1f ' % (plong)
PmagResRec["vgp_dp"]='%7.1f ' % (dp)
PmagResRec["vgp_dm"]='%7.1f ' % (dm)
PmagResRec["magic_method_codes"]= PmagSiteRec["magic_method_codes"]
if PmagSiteRec['site_tilt_correction']=='0':PmagSiteRec['magic_method_codes']=PmagSiteRec['magic_method_codes']+":DA-DIR-GEO"
if PmagSiteRec['site_tilt_correction']=='100':PmagSiteRec['magic_method_codes']=PmagSiteRec['magic_method_codes']+":DA-DIR-TILT"
PmagSiteRec['site_polarity']=""
if polarity==1: # assign polarity based on angle of pole lat to spin axis - may want to re-think this sometime
angle=pmag.angle([0,0],[0,(90-plat)])
if angle <= 55.: PmagSiteRec["site_polarity"]='n'
if angle > 55. and angle < 125.: PmagSiteRec["site_polarity"]='t'
if angle >= 125.: PmagSiteRec["site_polarity"]='r'
PmagResults.append(PmagResRec)
if noInt!=1 and nositeints!=1:
for site in sites: # now do intensities for each site
if plotsites==1:print site
if Iaverage==0: key,intlist='specimen',SpecInts # if using specimen level data
if Iaverage==1: key,intlist='sample',PmagSamps # if using sample level data
Ints=pmag.get_dictitem(intlist,'er_site_name',site,'T') # get all the intensities for this site
if len(Ints)>0: # there are some
PmagSiteRec=pmag.average_int(Ints,key,'site') # get average intensity stuff for site table
PmagResRec=pmag.average_int(Ints,key,'average') # get average intensity stuff for results table
if plotsites==1: # if site by site examination requested - print this site out to the screen
for rec in Ints:print rec['er_'+key+'_name'],' %7.1f'%(1e6*float(rec[key+'_int']))
if len(Ints)>1:
print 'Average: ','%7.1f'%(1e6*float(PmagResRec['average_int'])),'N: ',len(Ints)
print 'Sigma: ','%7.1f'%(1e6*float(PmagResRec['average_int_sigma'])),'Sigma %: ',PmagResRec['average_int_sigma_perc']
raw_input('Press any key to continue\n')
er_location_name=Ints[0]["er_location_name"]
PmagSiteRec["er_location_name"]=er_location_name # decorate the records
PmagSiteRec["er_citation_names"]="This study"
PmagResRec["er_location_names"]=er_location_name
PmagResRec["er_citation_names"]="This study"
PmagSiteRec["er_analyst_mail_names"]=user
PmagResRec["er_analyst_mail_names"]=user
PmagResRec["data_type"]='i'
if Iaverage==0:
PmagSiteRec['er_specimen_names']= pmag.get_list(Ints,'er_specimen_name') # list of all specimens used
PmagResRec['er_specimen_names']= pmag.get_list(Ints,'er_specimen_name')
PmagSiteRec['er_sample_names']= pmag.get_list(Ints,'er_sample_name') # list of all samples used
PmagResRec['er_sample_names']= pmag.get_list(Ints,'er_sample_name')
PmagSiteRec['er_site_name']= site
PmagResRec['er_site_names']= site
PmagSiteRec['magic_method_codes']= pmag.get_list(Ints,'magic_method_codes')
PmagResRec['magic_method_codes']= pmag.get_list(Ints,'magic_method_codes')
kill=pmag.grade(PmagSiteRec,accept,'site_int')
if nocrit==1 or len(kill)==0:
b,sig=float(PmagResRec['average_int']),""
if(PmagResRec['average_int_sigma'])!="":sig=float(PmagResRec['average_int_sigma'])
sdir=pmag.get_dictitem(PmagResults,'er_site_names',site,'T') # fish out site direction
if len(sdir)>0 and sdir[-1]['average_inc']!="": # get the VDM for this record using last average inclination (hope it is the right one!)
inc=float(sdir[0]['average_inc']) #
mlat=pmag.magnetic_lat(inc) # get magnetic latitude using dipole formula
PmagResRec["vdm"]='%8.3e '% (pmag.b_vdm(b,mlat)) # get VDM with magnetic latitude
PmagResRec["vdm_n"]=PmagResRec['average_int_n']
if 'average_int_sigma' in PmagResRec.keys() and PmagResRec['average_int_sigma']!="":
vdm_sig=pmag.b_vdm(float(PmagResRec['average_int_sigma']),mlat)
PmagResRec["vdm_sigma"]='%8.3e '% (vdm_sig)
else:
PmagResRec["vdm_sigma"]=""
mlat="" # define a model latitude
if get_model_lat==1: # use present site latitude
mlats=pmag.get_dictitem(SiteNFO,'er_site_name',site,'T')
if len(mlats)>0: mlat=mlats[0]['site_lat']
elif get_model_lat==2: # use a model latitude from some plate reconstruction model (or something)
mlats=pmag.get_dictitem(ModelLats,'er_site_name',site,'T')
if len(mlats)>0: PmagResRec['model_lat']=mlats[0]['site_model_lat']
mlat=PmagResRec['model_lat']
if mlat!="":
PmagResRec["vadm"]='%8.3e '% (pmag.b_vdm(b,float(mlat))) # get the VADM using the desired latitude
if sig!="":
vdm_sig=pmag.b_vdm(float(PmagResRec['average_int_sigma']),float(mlat))
PmagResRec["vadm_sigma"]='%8.3e '% (vdm_sig)
PmagResRec["vadm_n"]=PmagResRec['average_int_n']
else:
PmagResRec["vadm_sigma"]=""
sitedat=pmag.get_dictitem(SiteNFO,'er_site_name',PmagSiteRec['er_site_name'],'T') # fish out site information (lat/lon, etc.)
if len(sitedat)>0:
sitedat=sitedat[0]
PmagResRec['average_lat']=sitedat['site_lat']
PmagResRec['average_lon']=sitedat['site_lon']
else:
PmagResRec['average_lon']='UNKNOWN'
PmagResRec['average_lon']='UNKNOWN'
PmagResRec['magic_software_packages']=version_num
PmagResRec["pmag_result_name"]="V[A]DM: Site "+site
PmagResRec["result_description"]="V[A]DM of site"
PmagResRec["pmag_criteria_codes"]="ACCEPT"
if agefile != "": PmagResRec= pmag.get_age(PmagResRec,"er_site_names","average_",AgeNFO,DefaultAge)
site_height=pmag.get_dictitem(height_nfo,'er_site_name',site,'T')
if len(site_height)>0:PmagResRec["average_height"]=site_height[0]['site_height']
PmagSites.append(PmagSiteRec)
PmagResults.append(PmagResRec)
if len(PmagSites)>0:
Tmp,keylist=pmag.fillkeys(PmagSites)
pmag.magic_write(siteout,Tmp,'pmag_sites')
print ' sites written to ',siteout
else: print "No Site level table"
if len(PmagResults)>0:
TmpRes,keylist=pmag.fillkeys(PmagResults)
pmag.magic_write(resout,TmpRes,'pmag_results')
print ' results written to ',resout
else: print "No Results level table"
def main(command_line=True, **kwargs):
"""
NAME
PMD_magic.py
DESCRIPTION
converts PMD (Enkin) format files to magic_measurements format files
SYNTAX
PMD_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt
-spc NUM : specify number of characters to designate a specimen, default = 1
-loc LOCNAME : specify location/study name
-A: don't average replicate measurements
-ncn NCON: specify naming convention
-mcd [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
INPUT
PMD format files
"""
# initialize some stuff
noave=0
inst=""
samp_con,Z='1',""
missing=1
demag="N"
er_location_name="unknown"
citation='This study'
args=sys.argv
meth_code="LP-NO"
specnum=-1
MagRecs=[]
version_num=pmag.get_version()
Samps=[] # keeps track of sample orientations
DIspec=[]
MagFiles=[]
user=""
mag_file=""
dir_path='.'
ErSamps=[]
SampOuts=[]
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print main.__doc__
return False
if '-F' in args:
ind=args.index("-F")
meas_file = args[ind+1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = args[ind+1]
#try:
# open(samp_file,'rU')
# ErSamps,file_type=pmag.magic_read(samp_file)
# print 'sample information will be appended to ', samp_file
#except:
# print samp_file,' not found: sample information will be stored in new er_samples.txt file'
# samp_file = output_dir_path+'/er_samples.txt'
if '-f' in args:
ind = args.index("-f")
mag_file= args[ind+1]
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind+1])
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-A" in args: noave=1
if "-mcd" in args:
ind=args.index("-mcd")
meth_code=args[ind+1]
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
specnum = kwargs.get('specnum', 0)
samp_con = kwargs.get('samp_con', '1')
er_location_name = kwargs.get('er_location_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
print samp_con
# format variables
mag_file = input_dir_path+"/" + mag_file
meas_file = output_dir_path+"/" + meas_file
samp_file = output_dir_path+"/" + samp_file
if specnum!=0:specnum=-specnum
if "4" in samp_con:
if "-" not in samp_con:
print "naming convention option [4] must be in form 4-Z where Z is an integer"
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
# parse data
data=open(mag_file,'rU').readlines() # read in data from file
comment=data[0]
line=data[1].strip()
line=line.replace("=","= ") # make finding orientations easier
rec=line.split() # read in sample orientation, etc.
er_specimen_name=rec[0]
ErSampRec,ErSiteRec={},{} # make a sample record
if specnum!=0:
er_sample_name=rec[0][:specnum]
else:
er_sample_name=rec[0]
if len(ErSamps)>0: # need to copy existing
for samp in ErSamps:
if samp['er_sample_name']==er_sample_name:
ErSampRec=samp # we'll ammend this one
else:
SampOuts.append(samp) # keep all the others
if int(samp_con)<6:
er_site_name=pmag.parse_site(er_sample_name,samp_con,Z)
else:
if 'er_site_name' in ErSampRec.keys():er_site_name=ErSampREc['er_site_name']
if 'er_location_name' in ErSampRec.keys():er_location_name=ErSampREc['er_location_name']
az_ind=rec.index('a=')+1
ErSampRec['er_sample_name']=er_sample_name
ErSampRec['er_sample_description']=comment
ErSampRec['sample_azimuth']=rec[az_ind]
dip_ind=rec.index('b=')+1
dip=-float(rec[dip_ind])
ErSampRec['sample_dip']='%7.1f'%(dip)
strike_ind=rec.index('s=')+1
ErSampRec['sample_bed_dip_direction']='%7.1f'%(float(rec[strike_ind])+90.)
bd_ind=rec.index('d=')+1
ErSampRec['sample_bed_dip']=rec[bd_ind]
v_ind=rec.index('v=')+1
vol=rec[v_ind][:-3]
date=rec[-2]
time=rec[-1]
ErSampRec['magic_method_codes']=meth_code
if 'er_location_name' not in ErSampRec.keys():ErSampRec['er_location_name']=er_location_name
if 'er_site_name' not in ErSampRec.keys():ErSampRec['er_site_name']=er_site_name
if 'er_citation_names' not in ErSampRec.keys():ErSampRec['er_citation_names']='This study'
if 'magic_method_codes' not in ErSampRec.keys():ErSampRec['magic_method_codes']='SO-NO'
SampOuts.append(ErSampRec)
for k in range(3,len(data)): # read in data
line=data[k]
rec=line.split()
if len(rec)>1: # skip blank lines at bottom
MagRec={}
MagRec['measurement_description']='Date: '+date+' '+time
MagRec["er_citation_names"]="This study"
MagRec['er_location_name']=er_location_name
MagRec['er_site_name']=er_site_name
MagRec['er_sample_name']=er_sample_name
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["er_specimen_name"]=er_specimen_name
if rec[0]=='NRM':
meas_type="LT-NO"
elif rec[0][0]=='M' or rec[0][0]=='H':
meas_type="LT-AF-Z"
elif rec[0][0]=='T':
meas_type="LT-T-Z"
else:
print "measurement type unknown"
return False, "measurement type unknown"
X=[float(rec[1]),float(rec[2]),float(rec[3])]
Vec=pmag.cart2dir(X)
MagRec["measurement_magn_moment"]='%10.3e'% (Vec[2]) # Am^2
MagRec["measurement_magn_volume"]=rec[4] # A/m
MagRec["measurement_dec"]='%7.1f'%(Vec[0])
MagRec["measurement_inc"]='%7.1f'%(Vec[1])
MagRec["treatment_ac_field"]='0'
if meas_type!='LT-NO':
treat=float(rec[0][1:])
else:
treat=0
if meas_type=="LT-AF-Z":
MagRec["treatment_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
elif meas_type=="LT-T-Z":
MagRec["treatment_temp"]='%8.3e' % (treat+273.) # temp in kelvin
MagRec['magic_method_codes']=meas_type
MagRecs.append(MagRec)
MagOuts=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print "results put in ",meas_file
pmag.magic_write(samp_file,SampOuts,'er_samples')
print "sample orientations put in ",samp_file
return True, meas_file
def main():
"""
NAME
aarm_magic.py
DESCRIPTION
Converts AARM data to best-fit tensor (6 elements plus sigma)
Original program ARMcrunch written to accomodate ARM anisotropy data
collected from 6 axial directions (+X,+Y,+Z,-X,-Y,-Z) using the
off-axis remanence terms to construct the tensor. A better way to
do the anisotropy of ARMs is to use 9,12 or 15 measurements in
the Hext rotational scheme.
SYNTAX
aarm_magic.py [-h][command line options]
OPTIONS
-h prints help message and quits
-usr USER: identify user, default is ""
-f FILE: specify input file, default is aarm_measurements.txt
-Fa FILE: specify anisotropy output file, default is rmag_anisotropy.txt
-Fr FILE: specify results output file, default is rmag_results.txt
INPUT
Input for the present program is a series of baseline, ARM pairs.
The baseline should be the AF demagnetized state (3 axis demag is
preferable) for the following ARM acquisition. The order of the
measurements is:
positions 1,2,3, 6,7,8, 11,12,13 (for 9 positions)
positions 1,2,3,4, 6,7,8,9, 11,12,13,14 (for 12 positions)
positions 1-15 (for 15 positions)
"""
# initialize some parameters
args=sys.argv
user=""
meas_file="aarm_measurements.txt"
rmag_anis="rmag_anisotropy.txt"
rmag_res="rmag_results.txt"
dir_path='.'
#
# get name of file from command line
#
if '-WD' in args:
ind=args.index('-WD')
dir_path=args[ind+1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=sys.argv[ind+1]
if "-f" in args:
ind=args.index("-f")
meas_file=sys.argv[ind+1]
if "-Fa" in args:
ind=args.index("-Fa")
rmag_anis=args[ind+1]
if "-Fr" in args:
ind=args.index("-Fr")
rmag_res=args[ind+1]
meas_file=dir_path+'/'+meas_file
rmag_anis=dir_path+'/'+rmag_anis
rmag_res=dir_path+'/'+rmag_res
# read in data
meas_data,file_type=pmag.magic_read(meas_file)
if file_type != 'magic_measurements':
print file_type
print file_type,"This is not a valid magic_measurements file "
sys.exit()
#
# sort the specimen names
#
ssort=[]
for rec in meas_data:
spec=rec["er_specimen_name"]
ssort.append(spec)
ssort.sort()
bak=ssort[0]
#
# get list of unique specimen names
#
sids=[bak]
for s in ssort:
if s != bak:
sids.append(s)
bak=s
#
# work on each specimen
#
specimen=0
RmagSpecRecs,RmagResRecs=[],[]
while specimen < len(sids):
s=sids[specimen]
data=[]
RmagSpecRec={}
RmagResRec={}
method_codes=[]
#
# find the data from the meas_data file for this sample
#
for rec in meas_data:
if rec["er_specimen_name"]==s:
data.append(rec)
#
# find out the number of measurements (9, 12 or 15)
#
npos=len(data)/2
if npos==9:
print 'Processing: ',s, ' Number of positions: ',npos
#
# get dec, inc, int and convert to x,y,z
#
B,H,tmpH=pmag.designAARM(npos) # B matrix made from design matrix for positions
X=[]
for rec in data:
Dir=[]
Dir.append(float(rec["measurement_dec"]))
Dir.append(float(rec["measurement_inc"]))
Dir.append(float(rec["measurement_magn_moment"]))
X.append(pmag.dir2cart(Dir))
#
# subtract baseline and put in a work array
#
work=numpy.zeros((npos,3),'f')
for i in range(npos):
for j in range(3):
work[i][j]=X[2*i+1][j]-X[2*i][j]
#
# calculate tensor elements
# first put ARM components in w vector
#
w=numpy.zeros((npos*3),'f')
index=0
for i in range(npos):
for j in range(3):
w[index]=work[i][j]
index+=1
s=numpy.zeros((6),'f') # initialize the s matrix
for i in range(6):
for j in range(len(w)):
s[i]+=B[i][j]*w[j]
trace=s[0]+s[1]+s[2] # normalize by the trace
for i in range(6):
s[i]=s[i]/trace
a=pmag.s2a(s)
#------------------------------------------------------------
# Calculating dels is different than in the Kappabridge
# routine. Use trace normalized tensor (a) and the applied
# unit field directions (tmpH) to generate model X,Y,Z
# components. Then compare these with the measured values.
#------------------------------------------------------------
S=0.
comp=numpy.zeros((npos*3),'f')
for i in range(npos):
for j in range(3):
index=i*3+j
compare=a[j][0]*tmpH[i][0]+a[j][1]*tmpH[i][1]+a[j][2]*tmpH[i][2]
comp[index]=compare
for i in range(npos*3):
d=w[i]/trace - comp[i] # del values
S+=d*d
nf=float(npos*3-6) # number of degrees of freedom
if S >0:
sigma=math.sqrt(S/nf)
else: sigma=0
hpars=pmag.dohext(nf,sigma,s)
#
# prepare for output
#
RmagSpecRec["rmag_anisotropy_name"]=data[0]["er_specimen_name"]
RmagSpecRec["er_location_name"]=data[0]["er_location_name"]
RmagSpecRec["er_specimen_name"]=data[0]["er_specimen_name"]
RmagSpecRec["er_sample_name"]=data[0]["er_sample_name"]
RmagSpecRec["er_site_name"]=data[0]["er_site_name"]
RmagSpecRec["magic_experiment_names"]=RmagSpecRec["rmag_anisotropy_name"]+":AARM"
RmagSpecRec["er_citation_names"]="This study"
RmagResRec["rmag_result_name"]=data[0]["er_specimen_name"]
RmagResRec["er_location_names"]=data[0]["er_location_name"]
RmagResRec["er_specimen_names"]=data[0]["er_specimen_name"]
RmagResRec["er_sample_names"]=data[0]["er_sample_name"]
RmagResRec["er_site_names"]=data[0]["er_site_name"]
RmagResRec["magic_experiment_names"]=RmagSpecRec["rmag_anisotropy_name"]+":AARM"
RmagResRec["er_citation_names"]="This study"
if "magic_instrument_codes" in data[0].keys():
RmagSpecRec["magic_instrument_codes"]=data[0]["magic_instrument_codes"]
else:
RmagSpecRec["magic_instrument_codes"]=""
RmagSpecRec["anisotropy_type"]="AARM"
RmagSpecRec["anisotropy_description"]="Hext statistics adapted to AARM"
RmagSpecRec["anisotropy_s1"]='%8.6f'%(s[0])
RmagSpecRec["anisotropy_s2"]='%8.6f'%(s[1])
RmagSpecRec["anisotropy_s3"]='%8.6f'%(s[2])
RmagSpecRec["anisotropy_s4"]='%8.6f'%(s[3])
RmagSpecRec["anisotropy_s5"]='%8.6f'%(s[4])
RmagSpecRec["anisotropy_s6"]='%8.6f'%(s[5])
RmagSpecRec["anisotropy_mean"]='%8.3e'%(trace/3)
RmagSpecRec["anisotropy_sigma"]='%8.6f'%(sigma)
RmagSpecRec["anisotropy_unit"]="Am^2"
RmagSpecRec["anisotropy_n"]='%i'%(npos)
RmagSpecRec["anisotropy_tilt_correction"]='-1'
RmagResRec["anisotropy_t1"]='%8.6f '%(hpars["t1"])
RmagResRec["anisotropy_t2"]='%8.6f '%(hpars["t2"])
RmagResRec["anisotropy_t3"]='%8.6f '%(hpars["t3"])
RmagResRec["anisotropy_v1_dec"]='%7.1f '%(hpars["v1_dec"])
RmagResRec["anisotropy_v2_dec"]='%7.1f '%(hpars["v2_dec"])
RmagResRec["anisotropy_v3_dec"]='%7.1f '%(hpars["v3_dec"])
RmagResRec["anisotropy_v1_inc"]='%7.1f '%(hpars["v1_inc"])
RmagResRec["anisotropy_v2_inc"]='%7.1f '%(hpars["v2_inc"])
RmagResRec["anisotropy_v3_inc"]='%7.1f '%(hpars["v3_inc"])
RmagResRec["anisotropy_ftest"]='%7.1f '%(hpars["F"])
RmagResRec["anisotropy_ftest12"]='%7.1f '%(hpars["F12"])
RmagResRec["anisotropy_ftest23"]='%7.1f '%(hpars["F23"])
if hpars["e12"]>hpars["e13"]:
RmagResRec["anisotropy_v1_zeta_semi_angle"]='%7.1f '%(hpars['e12'])
RmagResRec["anisotropy_v1_zeta_dec"]='%7.1f '%(hpars['v2_dec'])
RmagResRec["anisotropy_v1_zeta_inc"]='%7.1f '%(hpars['v2_inc'])
RmagResRec["anisotropy_v2_zeta_semi_angle"]='%7.1f '%(hpars['e12'])
RmagResRec["anisotropy_v2_zeta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v2_zeta_inc"]='%7.1f '%(hpars['v1_inc'])
RmagResRec["anisotropy_v1_eta_semi_angle"]='%7.1f '%(hpars['e13'])
RmagResRec["anisotropy_v1_eta_dec"]='%7.1f '%(hpars['v3_dec'])
RmagResRec["anisotropy_v1_eta_inc"]='%7.1f '%(hpars['v3_inc'])
RmagResRec["anisotropy_v3_eta_semi_angle"]='%7.1f '%(hpars['e13'])
RmagResRec["anisotropy_v3_eta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v3_eta_inc"]='%7.1f '%(hpars['v1_inc'])
else:
RmagResRec["anisotropy_v1_zeta_semi_angle"]='%7.1f '%(hpars['e13'])
RmagResRec["anisotropy_v1_zeta_dec"]='%7.1f '%(hpars['v3_dec'])
RmagResRec["anisotropy_v1_zeta_inc"]='%7.1f '%(hpars['v3_inc'])
RmagResRec["anisotropy_v3_zeta_semi_angle"]='%7.1f '%(hpars['e13'])
RmagResRec["anisotropy_v3_zeta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v3_zeta_inc"]='%7.1f '%(hpars['v1_inc'])
RmagResRec["anisotropy_v1_eta_semi_angle"]='%7.1f '%(hpars['e12'])
RmagResRec["anisotropy_v1_eta_dec"]='%7.1f '%(hpars['v2_dec'])
RmagResRec["anisotropy_v1_eta_inc"]='%7.1f '%(hpars['v2_inc'])
RmagResRec["anisotropy_v2_eta_semi_angle"]='%7.1f '%(hpars['e12'])
RmagResRec["anisotropy_v2_eta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v2_eta_inc"]='%7.1f '%(hpars['v1_inc'])
if hpars["e23"]>hpars['e12']:
RmagResRec["anisotropy_v2_zeta_semi_angle"]='%7.1f '%(hpars['e23'])
RmagResRec["anisotropy_v2_zeta_dec"]='%7.1f '%(hpars['v3_dec'])
RmagResRec["anisotropy_v2_zeta_inc"]='%7.1f '%(hpars['v3_inc'])
RmagResRec["anisotropy_v3_zeta_semi_angle"]='%7.1f '%(hpars['e23'])
RmagResRec["anisotropy_v3_zeta_dec"]='%7.1f '%(hpars['v2_dec'])
RmagResRec["anisotropy_v3_zeta_inc"]='%7.1f '%(hpars['v2_inc'])
RmagResRec["anisotropy_v3_eta_semi_angle"]='%7.1f '%(hpars['e13'])
RmagResRec["anisotropy_v3_eta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v3_eta_inc"]='%7.1f '%(hpars['v1_inc'])
RmagResRec["anisotropy_v2_eta_semi_angle"]='%7.1f '%(hpars['e12'])
RmagResRec["anisotropy_v2_eta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v2_eta_inc"]='%7.1f '%(hpars['v1_inc'])
else:
RmagResRec["anisotropy_v2_zeta_semi_angle"]='%7.1f '%(hpars['e12'])
RmagResRec["anisotropy_v2_zeta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v2_zeta_inc"]='%7.1f '%(hpars['v1_inc'])
RmagResRec["anisotropy_v3_eta_semi_angle"]='%7.1f '%(hpars['e23'])
RmagResRec["anisotropy_v3_eta_dec"]='%7.1f '%(hpars['v2_dec'])
RmagResRec["anisotropy_v3_eta_inc"]='%7.1f '%(hpars['v2_inc'])
RmagResRec["anisotropy_v3_zeta_semi_angle"]='%7.1f '%(hpars['e13'])
RmagResRec["anisotropy_v3_zeta_dec"]='%7.1f '%(hpars['v1_dec'])
RmagResRec["anisotropy_v3_zeta_inc"]='%7.1f '%(hpars['v1_inc'])
RmagResRec["anisotropy_v2_eta_semi_angle"]='%7.1f '%(hpars['e23'])
RmagResRec["anisotropy_v2_eta_dec"]='%7.1f '%(hpars['v3_dec'])
RmagResRec["anisotropy_v2_eta_inc"]='%7.1f '%(hpars['v3_inc'])
RmagResRec["tilt_correction"]='-1'
RmagResRec["anisotropy_type"]='AARM'
RmagResRec["magic_method_codes"]='LP-AN-ARM:AE-H'
RmagSpecRec["magic_method_codes"]='LP-AN-ARM:AE-H'
RmagResRec["magic_software_packages"]=pmag.get_version()
RmagSpecRec["magic_software_packages"]=pmag.get_version()
specimen+=1
RmagSpecRecs.append(RmagSpecRec)
RmagResRecs.append(RmagResRec)
else:
print npos
print 'skipping specimen ',s,' only 9 positions supported'
specimen+=1
if rmag_anis=="":rmag_anis="rmag_anisotropy.txt"
pmag.magic_write(rmag_anis,RmagSpecRecs,'rmag_anisotropy')
print "specimen tensor elements stored in ",rmag_anis
if rmag_res=="":rmag_res="rmag_results.txt"
pmag.magic_write(rmag_res,RmagResRecs,'rmag_results')
print "specimen statistics and eigenparameters stored in ",rmag_res
def main():
"""
NAME
TDT_magic.py
DESCRIPTION
converts ThellierTool format files to magic_measurements format files
SYNTAX
TDT_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify .tdt format input file, required
-F FILE: specify output file, default is magic_measurements.txt
-spc NUM : specify number of characters to designate a specimen, default = 0
-loc LOCNAME : specify location/study name, must have either LOCNAME or SAMPFILE or be a synthetic
-ncn NCON: specify naming convention: default is #1 below
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
INPUT
Format of ThellierTool files:
2 line header:
Thellier-tdt
XX.0 (field in microtesla)
Data:
Spec Treat Intensity Declination Inclination
Spec: specimen name
Treat: treatment step
XXX.00 first zero field step
XXX.11 (or .1) first in field step [XXX.0 and XXX.1 can be done in any order]
XXX.12 (or .2)second in-field step at lower temperature (pTRM check)
XXX.13 (or .3) second zero-field step after infield (pTRM check step)
XXX.13 MUST be done in this order [XXX.00, XXX.11 [optional XXX.12] XXX.13]
Intensity assumed to be total moment in 10^3 Am^2 (emu)
Declination: Declination in specimen coordinate system
Inclination: Declination in specimen coordinate system
"""
# initialize some stuff
noave=0
methcode,inst="",""
phi,theta,labfield=0,90,0
pTRM,MD,samp_con,Z=0,0,'1',1
demag="N"
er_location_name=""
citation='This study'
args=sys.argv
methcode="LP-NO"
specnum=0
#
# get command line arguments
#
dir_path='.'
meas_file,samp_file="magic_measurements.txt","er_samples.txt"
user=""
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=args[ind+1]
if '-F' in args:
ind=args.index("-F")
meas_file=dir_path+'/'+args[ind+1]
if '-f' in args:
ind=args.index("-f")
magfile=dir_path+'/'+args[ind+1]
try:
input=open(magfile,'rU')
except:
print "bad mag file name"
sys.exit()
else:
print "mag_file field is required option"
print main.__doc__
sys.exit()
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if specnum!=0:specnum=-specnum
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
MagRecs=[]
demag="T"
version_num=pmag.get_version()
data=input.readlines()
rec=data[1].split()
labfield=float(rec[0])*1e-6
for line in data[2:]:
rec=line.split()
if len(rec)>2:
MagRec={}
MagRec['er_location_name']=er_location_name
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["treatment_ac_field"]='0'
MagRec["treatment_dc_field"]='0'
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
meas_type="LT-NO"
MagRec["er_specimen_name"]=rec[0]
MagRec["er_synthetic_name"]=""
MagRec["er_site_name"]=""
if specnum!=0:
MagRec["er_sample_name"]=rec[0][:specnum]
else:
MagRec["er_sample_name"]=rec[0]
if "-fsa" in args:
for samp in Samps:
if samp["er_sample_name"] == MagRec["er_sample_name"]:
MagRec["er_location_name"]=samp["er_location_name"]
MagRec["er_site_name"]=samp["er_site_name"]
break
elif int(samp_con)!=6:
site=pmag.parse_site(MagRec['er_sample_name'],samp_con,Z)
MagRec["er_site_name"]=site
if MagRec['er_site_name']=="":
print 'No site name found for: ',MagRec['er_specimen_name'],MagRec['er_sample_name']
if MagRec["er_location_name"]=="":
print 'no location name for: ',MagRec["er_specimen_name"]
if rec[1]==".00":rec[1]="0.00"
treat=rec[1].split('.')
if float(rec[1])==0:
pass
if len(treat)==1:treat.append('0')
MagRec["treatment_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
if treat[1][0]=='0':
meas_type="LT-T-Z"
else:
MagRec["treatment_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MagRec["treatment_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MagRec["treatment_dc_field_theta"]='%7.1f' % (theta) # labfield theta
if treat[1][-1]=='1':meas_type="LT-T-I" # in-field thermal step
if treat[1][-1]=='2':
meas_type="LT-PTRM-I" # pTRM check
pTRM=1
if treat[1][-1]=='3':
MagRec["treatment_dc_field"]='0' # this is a zero field step
meas_type="LT-PTRM-MD" # pTRM tail check
MagRec["measurement_magn_moment"]='%10.3e'% (float(rec[2])*1e-3) # moment in Am^2 (from emu)
MagRec["measurement_dec"]=rec[3]
MagRec["measurement_inc"]=rec[4]
MagRec["er_analyst_mail_names"]=user
MagRec["er_citation_names"]=citation
MagRec["magic_method_codes"]=meas_type
MagRec["measurement_flag"]='g'
MagRec["er_specimen_name"]=rec[0]
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRecs.append(MagRec)
MagOuts=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print "results put in ",meas_file
def main(command_line=True, **kwargs):
"""
NAME
BGC_magic.py
DESCRIPTION
converts Berkeley Geochronology Center (BGC) format files to magic_measurements format files
SYNTAX
BGC_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt (Not working yet)
-loc LOCNAME : specify location/study name
-site SITENAME : specify site name
-A: don't average replicate measurements
-mcd [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
-v NUM : specify the volume in cc of the sample, default 2.5^3cc. Will use vol in data file if volume!=0 in file.
INPUT
BGC paleomag format file
"""
# initialize some stuff
noave = 0
volume = 0.025 ** 3 # default volume is a 2.5cm cube
# inst=""
# samp_con,Z='1',""
# missing=1
# demag="N"
er_location_name = "unknown"
er_site_name = "unknown"
# citation='This study'
args = sys.argv
meth_code = "LP-NO"
# specnum=1
version_num = pmag.get_version()
mag_file = ""
dir_path = "."
MagRecs = []
SampOuts = []
samp_file = "er_samples.txt"
meas_file = "magic_measurements.txt"
meth_code = ""
#
# get command line arguments
#
if command_line:
if "-WD" in sys.argv:
ind = sys.argv.index("-WD")
dir_path = sys.argv[ind + 1]
if "-ID" in sys.argv:
ind = sys.argv.index("-ID")
input_dir_path = sys.argv[ind + 1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print main.__doc__
return False
if "-F" in args:
ind = args.index("-F")
meas_file = args[ind + 1]
if "-Fsa" in args:
ind = args.index("-Fsa")
samp_file = args[ind + 1]
# try:
# open(samp_file,'rU')
# ErSamps,file_type=pmag.magic_read(samp_file)
# print 'sample information will be appended to ', samp_file
# except:
# print samp_file,' not found: sample information will be stored in new er_samples.txt file'
# samp_file = output_dir_path+'/er_samples.txt'
if "-f" in args:
ind = args.index("-f")
mag_file = args[ind + 1]
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if "-site" in args:
ind = args.index("-site")
er_site_name = args[ind + 1]
if "-A" in args:
noave = 1
if "-mcd" in args:
ind = args.index("-mcd")
meth_code = args[ind + 1]
# samp_con='5'
if "-v" in args:
ind = args.index("-v")
volume = float(args[ind + 1]) * 1e-6 # enter volume in cc, convert to m^3
if not command_line:
dir_path = kwargs.get("dir_path", ".")
input_dir_path = kwargs.get("input_dir_path", dir_path)
output_dir_path = dir_path
meas_file = kwargs.get("meas_file", "magic_measurements.txt")
mag_file = kwargs.get("mag_file")
samp_file = kwargs.get("samp_file", "er_samples.txt")
er_location_name = kwargs.get("er_location_name", "")
er_site_name = kwargs.get("er_site_name", "")
noave = kwargs.get("noave", 0) # default (0) means DO average
meth_code = kwargs.get("meth_code", "LP-NO")
volume = float(kwargs.get("volume", 0))
if not volume:
volume = 0.025 ** 3 # default volume is a 2.5 cm cube, translated to meters cubed
else:
# convert cm^3 to m^3
volume *= 1e-6
# format variables
if not mag_file:
return False, "You must provide a BCG format file"
mag_file = os.path.join(input_dir_path, mag_file)
meas_file = os.path.join(output_dir_path, meas_file)
samp_file = os.path.join(output_dir_path, samp_file)
ErSampRec = {}
# parse data
# Open up the BGC file and read the header information
print "mag_file in BGC_magic", mag_file
pre_data = open(mag_file, "rU")
line = pre_data.readline()
line_items = line.split(" ")
sample_name = line_items[2]
sample_name = sample_name.replace("\n", "")
line = pre_data.readline()
line = pre_data.readline()
line_items = line.split("\t")
sample_azimuth = float(line_items[1])
sample_dip = 90.0 - float(line_items[2])
sample_bed_dip = line_items[3]
sample_bed_azimuth = line_items[4]
sample_lon = line_items[5]
sample_lat = line_items[6]
tmp_volume = line_items[7]
if tmp_volume != 0.0:
volume = float(tmp_volume) * 1e-6
pre_data.close()
data = pd.read_csv(mag_file, sep="\t", header=3, index_col=False)
# print "\ndata\n", data
cart = np.array([data["X"], data["Y"], data["Z"]]).transpose()
direction = pmag.cart2dir(cart).transpose()
data["measurement_dec"] = direction[0]
data["measurement_inc"] = direction[1]
data["measurement_magn_moment"] = direction[2] * 1000 * volume # the data are in EMU - this converts to Am^2
data["measurement_magn_volume"] = direction[2] * 1000 # EMU - data converted to A/m
# DGEOs, IGEOs = [], []
# print "len(data)=",len(data)
# for ind in range(len(data)):
# dgeo,igeo=pmag.dogeo(data.ix[ind]['measurement_dec'],data.ix[ind]['measurement_inc'],90-sample_azimuth,sample_dip)
# DGEOs.append(dgeo)
# IGEOs.append(igeo)
# data['specimen_dec']=DGEOs
# data['specimen_inc']=IGEOs
# data['specimen_tilt']='1'
# print "data specimn_dec=",DGEOs
# print "data specimn_inc=",IGEOs
# Configure the er_sample table
ErSampRec["er_sample_name"] = sample_name
ErSampRec["sample_azimuth"] = sample_azimuth
ErSampRec["sample_dip"] = sample_dip
ErSampRec["sample_bed_dip_direction"] = sample_bed_azimuth
ErSampRec["sample_bed_dip"] = sample_bed_dip
ErSampRec["sample_lat"] = sample_lat
ErSampRec["sample_lon"] = sample_lon
ErSampRec["magic_method_codes"] = meth_code
ErSampRec["er_location_name"] = er_location_name
ErSampRec["er_site_name"] = er_site_name
ErSampRec["er_citation_names"] = "This study"
SampOuts.append(ErSampRec.copy())
# Configure the magic_measurements table
for rowNum, row in data.iterrows():
MagRec = {}
MagRec["measurement_description"] = "Date: " + str(row["Date"]) + " Time: " + str(row["Time"])
MagRec["er_citation_names"] = "This study"
MagRec["er_location_name"] = er_location_name
MagRec["er_site_name"] = er_site_name
MagRec["er_sample_name"] = sample_name
MagRec["magic_software_packages"] = version_num
MagRec["treatment_temp"] = "%8.3e" % (273) # room temp in kelvin
MagRec["measurement_temp"] = "%8.3e" % (273) # room temp in kelvin
MagRec["measurement_flag"] = "g"
MagRec["measurement_standard"] = "u"
MagRec["measurement_number"] = "1"
MagRec["er_specimen_name"] = sample_name
MagRec["treatment_ac_field"] = "0"
if row["DM Val"] == "0":
meas_type = "LT-NO"
elif int(row["DM Type"]) > 0.0:
meas_type = "LT-AF-Z"
treat = float(row["DM Val"])
MagRec["treatment_ac_field"] = "%8.3e" % (treat * 1e-3) # convert from mT to tesla
elif int(row["DM Type"]) == -1:
meas_type = "LT-T-Z"
treat = float(row["DM Val"])
MagRec["treatment_temp"] = "%8.3e" % (treat + 273.0) # temp in kelvin
else:
print "measurement type unknown:", row["DM Type"], " in row ", rowNum
MagRec["measurement_magn_moment"] = str(row["measurement_magn_moment"])
MagRec["measurement_magn_volume"] = str(row["measurement_magn_volume"])
MagRec["measurement_dec"] = str(row["measurement_dec"])
MagRec["measurement_inc"] = str(row["measurement_inc"])
MagRec["magic_method_codes"] = meas_type
MagRec["measurement_csd"] = "0.0" # added due to magic.write error
MagRec["measurement_positions"] = "1" # added due to magic.write error
MagRecs.append(MagRec.copy())
pmag.magic_write(samp_file, SampOuts, "er_samples")
print "sample orientations put in ", samp_file
MagOuts = pmag.measurements_methods(MagRecs, noave)
pmag.magic_write(meas_file, MagOuts, "magic_measurements")
print "results put in ", meas_file
print "exit!"
return True, meas_file
def main():
"""
NAME
IPG_magic.py
DESCRIPTION
converts PMD (IPG - PaleoMac) format files to magic_measurements format files
SYNTAX
IPG_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt
-spc NUM : specify number of characters to designate a specimen, default = 1
-loc LOCNAME : specify location/study name
-A: don't average replicate measurements
-ncn NCON: specify naming convention
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
INPUT
IPG-PMD format files
"""
# initialize some stuff
noave = 0
methcode, inst = "", ""
samp_con, Z = "1", ""
missing = 1
demag = "N"
er_location_name = "unknown"
citation = "This study"
args = sys.argv
methcode = "LP-NO"
specnum = -1
MagRecs = []
version_num = pmag.get_version()
Samps = [] # keeps track of sample orientations
DIspec = []
MagFiles = []
#
# get command line arguments
#
user = ""
mag_file = ""
dir_path = "."
ErSamps = []
SampOuts = []
if "-WD" in sys.argv:
ind = sys.argv.index("-WD")
dir_path = sys.argv[ind + 1]
samp_file = dir_path + "/er_samples.txt"
meas_file = dir_path + "/magic_measurements.txt"
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind = args.index("-usr")
user = args[ind + 1]
if "-F" in args:
ind = args.index("-F")
meas_file = dir_path + "/" + args[ind + 1]
if "-Fsa" in args:
ind = args.index("-Fsa")
samp_file = dir_path + "/" + args[ind + 1]
try:
open(samp_file, "rU")
ErSamps, file_type = pmag.magic_read(samp_file)
print "sample information will be appended to ", samp_file
except:
print samp_file, " not found: sample information will be stored in new er_samples.txt file"
samp_file = dir_path + "/er_samples.txt"
if "-f" in args:
ind = args.index("-f")
mag_file = dir_path + "/" + args[ind + 1]
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind + 1])
if specnum != 0:
specnum = -specnum
if "-ncn" in args:
ind = args.index("-ncn")
samp_con = sys.argv[ind + 1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "7"
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if "-A" in args:
noave = 1
data = open(mag_file, "rU").readlines() # read in data from file
for line in data:
rec = line.split()
if "E-" not in rec[1] and "E+" not in rec[1]: # new specimen
er_specimen_name = rec[0]
ErSampRec, ErSiteRec = {}, {} # make a sample record
if specnum != 0:
er_sample_name = rec[0][:specnum]
else:
er_sample_name = rec[0]
if len(ErSamps) > 0: # need to copy existing
for samp in ErSamps:
if samp["er_sample_name"] == er_sample_name:
ErSampRec = samp # we'll ammend this one
else:
SampOuts.append(samp) # keep all the others
if int(samp_con) < 6:
er_site_name = pmag.parse_site(er_sample_name, samp_con, Z)
else:
if "er_site_name" in ErSampRec.keys():
er_site_name = ErSampREc["er_site_name"]
if "er_location_name" in ErSampRec.keys():
er_location_name = ErSampREc["er_location_name"]
ErSampRec["er_sample_name"] = er_sample_name
ErSampRec["sample_azimuth"] = rec[1]
dip = -float(rec[2])
ErSampRec["sample_dip"] = "%7.1f" % (dip)
ErSampRec["sample_bed_dip_direction"] = "%7.1f" % (float(rec[3]) + 90.0)
ErSampRec["sample_bed_dip"] = rec[4]
if "er_location_name" not in ErSampRec.keys():
ErSampRec["er_location_name"] = er_location_name
if "er_site_name" not in ErSampRec.keys():
ErSampRec["er_site_name"] = er_site_name
if "er_citation_names" not in ErSampRec.keys():
ErSampRec["er_citation_names"] = "This study"
if "magic_method_codes" not in ErSampRec.keys():
ErSampRec["magic_method_codes"] = "SO-NO"
SampOuts.append(ErSampRec)
elif rec[0][0] == "N" or rec[0][0] == "T" or rec[0][0] == "M":
if len(rec) > 1: # skip blank lines at bottom
MagRec = {}
# MagRec['measurement_date']=measdate
MagRec["er_citation_names"] = "This study"
MagRec["er_location_name"] = er_location_name
MagRec["er_site_name"] = er_site_name
MagRec["er_sample_name"] = er_sample_name
MagRec["magic_software_packages"] = version_num
MagRec["treatment_temp"] = "%8.3e" % (273) # room temp in kelvin
MagRec["measurement_temp"] = "%8.3e" % (273) # room temp in kelvin
MagRec["measurement_flag"] = "g"
MagRec["measurement_standard"] = "u"
MagRec["measurement_number"] = "1"
MagRec["er_specimen_name"] = er_specimen_name
if rec[0] == "NRM":
meas_type = "LT-NO"
elif rec[0][0] == "M":
meas_type = "LT-AF-Z"
elif rec[0][0] == "T":
meas_type = "LT-T-Z"
else:
print "measurement type unknown"
sys.exit()
X = [float(rec[1]), float(rec[2]), float(rec[3])]
Vec = pmag.cart2dir(X)
MagRec["measurement_magn_moment"] = "%10.3e" % (Vec[2]) # Am^2
# MagRec["measurement_magn_volume"]=rec[4] # A/m
MagRec["measurement_dec"] = "%7.1f" % (Vec[0])
MagRec["measurement_inc"] = "%7.1f" % (Vec[1])
MagRec["treatment_ac_field"] = "0"
if meas_type != "LT-NO":
treat = float(rec[0][1:])
else:
treat = 0
if meas_type == "LT-AF-Z":
MagRec["treatment_ac_field"] = "%8.3e" % (treat * 1e-3) # convert from mT to tesla
elif meas_type == "LT-T-Z":
MagRec["treatment_temp"] = "%8.3e" % (treat + 273.0) # temp in kelvin
MagRec["magic_method_codes"] = meas_type
MagRecs.append(MagRec)
MagOuts = pmag.measurements_methods(MagRecs, noave)
pmag.magic_write(meas_file, MagOuts, "magic_measurements")
print "results put in ", meas_file
pmag.magic_write(samp_file, SampOuts, "er_samples")
print "sample orientations put in ", samp_file
def main(command_line=True, **kwargs):
"""
NAME
IODP_jr6_magic.py
DESCRIPTION
converts shipboard .jr6 format files to magic_measurements format files
SYNTAX
IODP_jr6_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-fsa FILE: specify er_samples.txt file for sample name lookup ,
default is 'er_samples.txt'
-loc HOLE : specify hole name (U1456A)
-A: don't average replicate measurements
INPUT
JR6 .jr6 format file
"""
def fix_separation(filename, new_filename):
old_file = open(filename, 'rU')
data = old_file.readlines()
new_data = []
for line in data:
new_line = line.replace('-', ' -')
new_line = new_line.replace(' ', ' ')
new_data.append(new_line)
new_file = open(new_filename, 'w')
for s in new_data:
new_file.write(s)
old_file.close()
new_file.close()
return new_filename
def old_fix_separation(filename, new_filename):
old_file = open(filename, 'rU')
data = old_file.readlines()
new_data = []
for line in data:
new_line = []
for i in line.split():
if '-' in i[1:]:
lead_char = '-' if i[0] == '-' else ''
if lead_char:
v = i[1:].split('-')
else:
v = i.split('-')
new_line.append(lead_char + v[0])
new_line.append('-' + v[1])
else:
new_line.append(i)
new_line = (' '.join(new_line)) + '\n'
new_data.append(new_line)
new_file = open(new_filename, 'w')
for s in new_data:
new_file.write(s)
new_file.close()
old_file.close()
return new_filename
# initialize some stuff
noave=0
volume=2.5**3 #default volume is a 2.5cm cube
inst=""
samp_con,Z='5',""
missing=1
demag="N"
er_location_name="unknown"
citation='This study'
args=sys.argv
meth_code="LP-NO"
version_num=pmag.get_version()
dir_path='.'
MagRecs=[]
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
mag_file = ''
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print main.__doc__
return False
if '-F' in args:
ind=args.index("-F")
meas_file = args[ind+1]
if '-fsa' in args:
ind = args.index("-fsa")
samp_file = args[ind+1]
if samp_file[0]!='/':
samp_file = os.path.join(input_dir_path, samp_file)
try:
open(samp_file,'rU')
ErSamps,file_type=pmag.magic_read(samp_file)
except:
print samp_file,' not found: '
print ' download csv file and import to MagIC with IODP_samples_magic.py'
if '-f' in args:
ind = args.index("-f")
mag_file= args[ind+1]
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-A" in args:
noave=1
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file', '')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
specnum = kwargs.get('specnum', 1)
samp_con = kwargs.get('samp_con', '1')
if len(str(samp_con)) > 1:
samp_con, Z = samp_con.split('-')
else:
Z = ''
er_location_name = kwargs.get('er_location_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
# format variables
meth_code=meth_code+":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code=meth_code.strip(":")
if mag_file:
mag_file = os.path.join(input_dir_path, mag_file)
samp_file = os.path.join(input_dir_path, samp_file)
meas_file = os.path.join(output_dir_path, meas_file)
# validate variables
if not mag_file:
print "You must provide an IODP_jr6 format file"
return False, "You must provide an IODP_jr6 format file"
if not os.path.exists(mag_file):
print 'The input file you provided: {} does not exist.\nMake sure you have specified the correct filename AND correct input directory name.'.format(os.path.join(input_dir_path, mag_file))
return False, 'The input file you provided: {} does not exist.\nMake sure you have specified the correct filename AND correct input directory name.'.format(magfile)
if not os.path.exists(samp_file):
print 'samp_file', samp_file
print "Your input directory:\n{}\nmust contain an er_samples.txt file, or you must explicitly provide one".format(input_dir_path)
return False, "Your input directory:\n{}\nmust contain an er_samples.txt file, or you must explicitly provide one".format(input_dir_path)
# parse data
temp = os.path.join(output_dir_path, 'temp.txt')
fix_separation(mag_file, temp)
#os.rename('temp.txt', mag_file)
#data = open(mag_file, 'rU').readlines()
data=pd.read_csv(temp, delim_whitespace=True,header=None)
os.remove(temp)
samples,filetype = pmag.magic_read(samp_file)
data.columns=['specname','step','negz','y','x','expon','sample_azimuth','sample_dip','sample_bed_dip_direction','sample_bed_dip','bed_dip_dir2','bed_dip2','param1','param2','param3','param4','measurement_csd']
cart=np.array([data['x'],data['y'],-data['negz']]).transpose()
dir= pmag.cart2dir(cart).transpose()
data['measurement_dec']=dir[0]
data['measurement_inc']=dir[1]
data['measurement_magn_volume']=dir[2]*(10.0**data['expon']) # A/m - data in A/m
data['measurement_flag']='g'
data['measurement_standard']='u'
data['measurement_number']='1'
data['measurement_temp']='273'
data['er_location_name']=er_location_name
for rowNum, row in data.iterrows():
MagRec={}
spec_text_id=row['specname'].split('_')[1]
SampRecs=pmag.get_dictitem(samples,'er_sample_alternatives',spec_text_id,'has') # retrieve sample record for this specimen
if len(SampRecs)>0: # found one
MagRec['er_specimen_name']=SampRecs[0]['er_sample_name']
MagRec['er_sample_name']=MagRec['er_specimen_name']
MagRec['er_site_name']=MagRec['er_specimen_name']
MagRec["er_citation_names"]="This study"
MagRec['er_location_name']=er_location_name
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["treatment_ac_field"]='0'
volume=float(SampRecs[0]['sample_volume'])
moment=row['measurement_magn_volume'] * volume
MagRec["measurement_magn_moment"]=str(moment)
MagRec["measurement_magn_volume"]=str(row['measurement_magn_volume'])
MagRec["measurement_dec"]='%7.1f'%(row['measurement_dec'])
MagRec["measurement_inc"]='%7.1f'%(row['measurement_inc'])
if row['step'] == 'NRM':
meas_type="LT-NO"
elif row['step'][0:2] == 'AD':
meas_type="LT-AF-Z"
treat=float(row['step'][2:])
MagRec["treatment_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
elif row['step'][0] == 'TD':
meas_type="LT-T-Z"
treat=float(row['step'][2:])
MagRec["treatment_temp"]='%8.3e' % (treat+273.) # temp in kelvin
elif row['step'][0:3]=='ARM': #
meas_type="LT-AF-I"
treat=float(row['step'][3:])
MagRec["treatment_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
MagRec["treatment_dc_field"]='%8.3e' %(50e-6) # assume 50uT DC field
MagRec["measurement_description"]='Assumed DC field - actual unknown'
elif row['step'][0:3]=='IRM': #
meas_type="LT-IRM"
treat=float(row['step'][3:])
MagRec["treatment_dc_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
else:
print 'unknown treatment type for ',row
return False, 'unknown treatment type for ',row
MagRec['magic_method_codes']=meas_type
MagRecs.append(MagRec.copy())
else:
print 'sample name not found: ',row['specname']
MagOuts=pmag.measurements_methods(MagRecs,noave)
file_created, error_message = pmag.magic_write(meas_file,MagOuts,'magic_measurements')
if file_created:
return True, meas_file
else:
return False, 'Results not written to file'
def main(command_line=True, **kwargs):
"""
NAME
IODP_dscr_magic.py
DESCRIPTION
converts ODP LIMS discrete sample format files to magic_measurements format files
SYNTAX
IODP_descr_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input .csv file, default is all in directory
-F FILE: specify output measurements file, default is magic_measurements.txt
-A : don't average replicate measurements
INPUTS
IODP discrete sample .csv file format exported from LIMS database
"""
#
# initialize defaults
version_num = pmag.get_version()
meas_file = "magic_measurements.txt"
csv_file = ""
MagRecs, Specs = [], []
citation = "This study"
dir_path, demag = ".", "NRM"
args = sys.argv
noave = 0
# get command line args
if command_line:
if "-WD" in args:
ind = args.index("-WD")
dir_path = args[ind + 1]
if "-ID" in args:
ind = args.index("-ID")
input_dir_path = args[ind + 1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print main.__doc__
return False
if "-A" in args:
noave = 1
if "-f" in args:
ind = args.index("-f")
csv_file = args[ind + 1]
if "-F" in args:
ind = args.index("-F")
meas_file = args[ind + 1]
if not command_line:
dir_path = kwargs.get("dir_path", ".")
input_dir_path = kwargs.get("input_dir_path", dir_path)
output_dir_path = dir_path # rename dir_path after input_dir_path is set
noave = kwargs.get("noave", 0) # default (0) is DO average
csv_file = kwargs.get("csv_file", "")
meas_file = kwargs.get("meas_file", "magic_measurements.txt")
# format variables
meas_file = os.path.join(output_dir_path, meas_file)
if csv_file == "":
filelist = os.listdir(input_dir_path) # read in list of files to import
else:
csv_file = os.path.join(input_dir_path, csv_file)
filelist = [csv_file]
# parsing the data
file_found = False
for file in filelist: # parse each file
if file[-3:].lower() == "csv":
file_found = True
print "processing: ", file
input = open(file, "rU").readlines()
keys = input[0].replace("\n", "").split(",") # splits on underscores
interval_key = "Offset (cm)"
demag_key = "Demag level (mT)"
offline_demag_key = "Treatment Value (mT or °C)"
offline_treatment_type = "Treatment type"
run_key = "Test No."
if "Inclination background + tray corrected (deg)" in keys:
inc_key = "Inclination background + tray corrected (deg)"
if "Inclination background & tray corrected (deg)" in keys:
inc_key = "Inclination background & tray corrected (deg)"
if "Declination background + tray corrected (deg)" in keys:
dec_key = "Declination background + tray corrected (deg)"
if "Declination background & tray corrected (deg)" in keys:
dec_key = "Declination background & tray corrected (deg)"
if "Intensity background + tray corrected (A/m)" in keys:
int_key = "Intensity background + tray corrected (A/m)"
if "Intensity background & tray corrected (A/m)" in keys:
int_key = "Intensity background & tray corrected (A/m)"
type = "Type"
sect_key = "Sect"
half_key = "A/W"
# need to add volume_key to LORE format!
if "Sample volume (cm^3)" in keys:
volume_key = "Sample volume (cm^3)"
if "Sample volume (cc)" in keys:
volume_key = "Sample volume (cc)"
if "Sample volume (cm³)" in keys:
volume_key = "Sample volume (cm³)"
for line in input[1:]:
InRec = {}
for k in range(len(keys)):
InRec[keys[k]] = line.split(",")[k]
inst = "IODP-SRM"
MagRec = {}
expedition = InRec["Exp"]
location = InRec["Site"] + InRec["Hole"]
offsets = InRec[interval_key].split(
"."
) # maintain consistency with er_samples convention of using top interval
if len(offsets) == 1:
offset = int(offsets[0])
else:
offset = int(offsets[0]) - 1
# interval=str(offset+1)# maintain consistency with er_samples convention of using top interval
interval = str(offset) # maintain consistency with er_samples convention of using top interval
specimen = (
expedition
+ "-"
+ location
+ "-"
+ InRec["Core"]
+ InRec[type]
+ "-"
+ InRec[sect_key]
+ "_"
+ InRec[half_key]
+ "_"
+ interval
)
if specimen not in Specs:
Specs.append(specimen)
MagRec["er_expedition_name"] = expedition
MagRec["er_location_name"] = location
MagRec["er_site_name"] = specimen
MagRec["er_citation_names"] = citation
MagRec["er_specimen_name"] = specimen
MagRec["er_sample_name"] = specimen
MagRec["er_site_name"] = specimen
# set up measurement record - default is NRM
MagRec["magic_software_packages"] = version_num
MagRec["treatment_temp"] = "%8.3e" % (273) # room temp in kelvin
MagRec["measurement_temp"] = "%8.3e" % (273) # room temp in kelvin
MagRec["treatment_ac_field"] = "0"
MagRec["treatment_dc_field"] = "0"
MagRec["treatment_dc_field_phi"] = "0"
MagRec["treatment_dc_field_theta"] = "0"
MagRec["measurement_flag"] = "g" # assume all data are "good"
MagRec["measurement_standard"] = "u" # assume all data are "good"
MagRec["measurement_csd"] = "0" # assume all data are "good"
volume = InRec[volume_key]
MagRec["magic_method_codes"] = "LT-NO"
sort_by = "treatment_ac_field" # set default to AF demag
if InRec[demag_key] != "0":
MagRec["magic_method_codes"] = "LT-AF-Z"
inst = inst + ":IODP-SRM-AF" # measured on shipboard in-line 2G AF
treatment_value = float(InRec[demag_key].strip('"')) * 1e-3 # convert mT => T
if sort_by == "treatment_ac_field":
MagRec["treatment_ac_field"] = treatment_value # AF demag in treat mT => T
else:
MagRec["treatment_ac_field"] = str(treatment_value) # AF demag in treat mT => T
elif offline_treatment_type in InRec.keys() and InRec[offline_treatment_type] != "":
if "Lowrie" in InRec["Comments"]:
MagRec["magic_method_codes"] = "LP-IRM-3D"
treatment_value = float(InRec[offline_demag_key].strip('"')) + 273.0 # convert C => K
MagRec["treatment_temp"] = treatment_value
MagRec["treatment_ac_field"] = "0"
sort_by = "treatment_temp"
elif "Isothermal" in InRec[offline_treatment_type]:
MagRec["magic_method_codes"] = "LT-IRM"
treatment_value = float(InRec[offline_demag_key].strip('"')) * 1e-3 # convert mT => T
MagRec["treatment_dc_field"] = treatment_value
MagRec["treatment_ac_field"] = "0"
sort_by = "treatment_dc_field"
MagRec["measurement_standard"] = "u" # assume all data are "good"
vol = float(volume) * 1e-6 # convert from cc to m^3
if run_key in InRec.keys():
run_number = InRec[run_key]
MagRec["external_database_ids"] = run_number
MagRec["external_database_names"] = "LIMS"
else:
MagRec["external_database_ids"] = ""
MagRec["external_database_names"] = ""
MagRec["measurement_description"] = "sample orientation: " + InRec["Sample orientation"]
MagRec["measurement_inc"] = InRec[inc_key].strip('"')
MagRec["measurement_dec"] = InRec[dec_key].strip('"')
intens = InRec[int_key].strip('"')
MagRec["measurement_magn_moment"] = "%8.3e" % (
float(intens) * vol
) # convert intensity from A/m to Am^2 using vol
MagRec["magic_instrument_codes"] = inst
MagRec["measurement_number"] = "1"
MagRec["measurement_positions"] = ""
MagRecs.append(MagRec)
if not file_found:
print "No .csv files were found"
return False, "No .csv files were found"
MagOuts = []
for spec in Specs:
Speclist = pmag.get_dictitem(MagRecs, "er_specimen_name", spec, "T")
sorted = pmag.sort_diclist(Speclist, sort_by)
for rec in sorted:
for key in rec.keys():
rec[key] = str(rec[key])
MagOuts.append(rec)
Fixed = pmag.measurements_methods(MagOuts, noave)
Out, keys = pmag.fillkeys(Fixed)
if pmag.magic_write(meas_file, Out, "magic_measurements"):
print "data stored in ", meas_file
return True, meas_file
else:
print "no data found. bad magfile?"
return False, "no data found. bad magfile?"
def main():
"""
NAME
MsT_magic.py
DESCRIPTION
converts MsT data (T,M) to magic_measurements format files
SYNTAX
MsT_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify T,M format input file, required
-fsa SFILE: name with sample, site, location information
-F FILE: specify output file, default is MsT_measurements.txt
-dc H: specify applied field during measurement, default is 0.5 T
-syn : This is a synthetic specimen and has no sample/site/location information
-spn SPEC: specimen name
-spc NUM : specify number of characters to designate a specimen, default = 0
-loc LOCNAME : specify location/study name, must have either LOCNAME or SAMPFILE or be a synthetic
-ncn NCON: specify naming convention: default is #1 below
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
INPUT files:
T M: T is in Centigrade and M is uncalibrated magnitude
"""
# initialize some stuff
samp_con,Z="1","0"
dir_path='.'
citation='This study'
args=sys.argv
specnum,measnum=0,1
#
# get command line arguments
#
user=""
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
meas_file=dir_path+"/MsT_measurements.txt"
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
labfield='0.5'
if "-dc" in args:
ind=args.index("-dc")
labfield=args[ind+1]
if '-F' in args:
ind=args.index("-F")
meas_file=dir_path+'/'+args[ind+1]
if "-fsa" in args:
ind=args.index("-fsa")
samp_file=dir_path+'/'+args[ind+1]
Samps,file_type=pmag.magic_read(samp_file)
if '-f' in args:
ind=args.index("-f")
infile=dir_path+'/'+args[ind+1]
try:
input=open(infile,'rU')
except:
print "bad mag file name"
sys.exit()
else:
print main.__doc__
print "-f is required option"
sys.exit()
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if specnum!=0:specnum=-specnum
er_location_name,syn,specimen_name='unknown',0,'unknown'
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-spn" in args:
ind=args.index("-spn")
specimen_name=args[ind+1]
else:
print main.__doc__
print "-spn is required option"
sys.exit()
if "-syn" in args: syn=1
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
samp_con=sys.argv[ind+1]
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="7"
MagRecs,specs=[],[]
version_num=pmag.get_version()
data=input.readlines()
T0=float(data[0].split()[0])
for line in data:
instcode=""
if len(line)>1:
MagRec={}
if syn==0: MagRec['er_location_name']=er_location_name
MagRec['magic_software_packages']=version_num
MagRec["treatment_dc_field"]=labfield
rec=line.split()
T=float(rec[0])
MagRec["measurment_temp"]='%8.3e' % (float(rec[0])+273.) # temp in kelvin
if T>T0:
MagRec["magic_method_codes"]='LP-MW-I'
elif T<T0:
MagRec["magic_method_codes"]='LP-MC-I'
T0=T
else:
print 'skipping repeated temperature step'
MagRec["magic_method_codes"]=''
T0=T
MagRec["measurement_magnitude"]='%10.3e'% (float(rec[1])) # uncalibrated magnitude
if syn==0:
MagRec["er_specimen_name"]=specimen_name
MagRec["er_site_name"]=""
if specnum!=0:
MagRec["er_sample_name"]=specimen_name[:specnum]
else:
MagRec["er_sample_name"]=specimen_name
if "-fsa" in args:
for samp in Samps:
if samp["er_sample_name"] == MagRec["er_sample_name"]:
MagRec["er_location_name"]=samp["er_location_name"]
MagRec["er_site_name"]=samp["er_site_name"]
break
elif int(samp_con)!=6:
site=pmag.parse_site(MagRec['er_sample_name'],samp_con,Z)
MagRec["er_site_name"]=site
if MagRec['er_site_name']=="":
print 'No site name found for: ',MagRec['er_specimen_name'],MagRec['er_sample_name']
if MagRec["er_location_name"]=="":
print 'no location name for: ',MagRec["er_specimen_name"]
else:
MagRec["er_synthetic_name"]=specimen_name
MagRec["er_location_name"]=""
MagRec["er_sample_name"]=""
MagRec["er_site_name"]=""
MagRec["er_specimen_name"]=""
MagRec["magic_instrument_codes"]=instcode
MagRec["er_analyst_mail_names"]=user
MagRec["er_citation_names"]=citation
MagRec["measurement_flag"]='g'
MagRec["measurement_number"]=str(measnum)
measnum+=1
MagRecs.append(MagRec)
for rec in MagRecs: # sort out the measurements by experiment type
rec['magic_experiment_name']=specimen_name
if rec['magic_method_codes']=='LP-MW-I':
rec["magic_experiment_name"]=specimen_name+':LP-MW-I:Curie'
elif rec['magic_method_codes']=='LP-MC-I':
rec["magic_experiment_name"]=specimen_name+':LP-MC-I'
pmag.magic_write(meas_file,MagRecs,'magic_measurements')
print "results put in ",meas_file
def main(command_line=True, **kwargs):
"""
NAME
IODP_jr6_magic.py
DESCRIPTION
converts shipboard .jr6 format files to magic_measurements format files
SYNTAX
IODP_jr6_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-fsa FILE: specify er_samples.txt file for sample name lookup ,
default is 'er_samples.txt'
-loc HOLE : specify hole name (U1456A)
-A: don't average replicate measurements
INPUT
JR6 .jr6 format file
"""
def fix_separation(filename, new_filename):
old_file = open(filename, "rU")
data = old_file.readlines()
new_data = []
for line in data:
new_line = line.replace("-", " -")
new_line = new_line.replace(" ", " ")
new_data.append(new_line)
new_file = open(new_filename, "w")
for s in new_data:
new_file.write(s)
old_file.close()
new_file.close()
return new_filename
def old_fix_separation(filename, new_filename):
old_file = open(filename, "rU")
data = old_file.readlines()
new_data = []
for line in data:
new_line = []
for i in line.split():
if "-" in i[1:]:
lead_char = "-" if i[0] == "-" else ""
if lead_char:
v = i[1:].split("-")
else:
v = i.split("-")
new_line.append(lead_char + v[0])
new_line.append("-" + v[1])
else:
new_line.append(i)
new_line = (" ".join(new_line)) + "\n"
new_data.append(new_line)
new_file = open(new_filename, "w")
for s in new_data:
new_file.write(s)
new_file.close()
old_file.close()
return new_filename
# initialize some stuff
noave = 0
volume = 2.5 ** 3 # default volume is a 2.5cm cube
inst = ""
samp_con, Z = "5", ""
missing = 1
demag = "N"
er_location_name = "unknown"
citation = "This study"
args = sys.argv
meth_code = "LP-NO"
version_num = pmag.get_version()
dir_path = "."
MagRecs = []
samp_file = "er_samples.txt"
meas_file = "magic_measurements.txt"
mag_file = ""
#
# get command line arguments
#
if command_line:
if "-WD" in sys.argv:
ind = sys.argv.index("-WD")
dir_path = sys.argv[ind + 1]
if "-ID" in sys.argv:
ind = sys.argv.index("-ID")
input_dir_path = sys.argv[ind + 1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print main.__doc__
return False
if "-F" in args:
ind = args.index("-F")
meas_file = args[ind + 1]
if "-fsa" in args:
ind = args.index("-fsa")
samp_file = args[ind + 1]
if samp_file[0] != "/":
samp_file = os.path.join(input_dir_path, samp_file)
try:
open(samp_file, "rU")
ErSamps, file_type = pmag.magic_read(samp_file)
except:
print samp_file, " not found: "
print " download csv file and import to MagIC with IODP_samples_magic.py"
if "-f" in args:
ind = args.index("-f")
mag_file = args[ind + 1]
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if "-A" in args:
noave = 1
if not command_line:
dir_path = kwargs.get("dir_path", ".")
input_dir_path = kwargs.get("input_dir_path", dir_path)
output_dir_path = dir_path
meas_file = kwargs.get("meas_file", "magic_measurements.txt")
mag_file = kwargs.get("mag_file", "")
samp_file = kwargs.get("samp_file", "er_samples.txt")
specnum = kwargs.get("specnum", 1)
samp_con = kwargs.get("samp_con", "1")
if len(str(samp_con)) > 1:
samp_con, Z = samp_con.split("-")
else:
Z = ""
er_location_name = kwargs.get("er_location_name", "")
noave = kwargs.get("noave", 0) # default (0) means DO average
meth_code = kwargs.get("meth_code", "LP-NO")
# format variables
meth_code = meth_code + ":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code = meth_code.strip(":")
if mag_file:
mag_file = os.path.join(input_dir_path, mag_file)
samp_file = os.path.join(input_dir_path, samp_file)
meas_file = os.path.join(output_dir_path, meas_file)
# validate variables
if not mag_file:
print "You must provide an IODP_jr6 format file"
return False, "You must provide an IODP_jr6 format file"
if not os.path.exists(mag_file):
print "The input file you provided: {} does not exist.\nMake sure you have specified the correct filename AND correct input directory name.".format(
mag_file
)
return (
False,
"The input file you provided: {} does not exist.\nMake sure you have specified the correct filename AND correct input directory name.".format(
mag_file
),
)
if not os.path.exists(samp_file):
print "Your input directory:\n{}\nmust contain an er_samples.txt file, or you must explicitly provide one".format(
input_dir_path
)
return (
False,
"Your input directory:\n{}\nmust contain an er_samples.txt file, or you must explicitly provide one".format(
input_dir_path
),
)
# parse data
temp = os.path.join(output_dir_path, "temp.txt")
fix_separation(mag_file, temp)
samples, filetype = pmag.magic_read(samp_file)
lines = open(temp, "rU").readlines()
os.remove(temp)
for line in lines:
MagRec = {}
line = line.split()
spec_text_id = line[0].split("_")[1]
SampRecs = pmag.get_dictitem(samples, "er_sample_alternatives", spec_text_id, "has")
if len(SampRecs) > 0: # found one
MagRec["er_specimen_name"] = SampRecs[0]["er_sample_name"]
MagRec["er_sample_name"] = MagRec["er_specimen_name"]
MagRec["er_site_name"] = MagRec["er_specimen_name"]
MagRec["er_citation_names"] = "This study"
MagRec["er_location_name"] = er_location_name
MagRec["magic_software_packages"] = version_num
MagRec["treatment_temp"] = "%8.3e" % (273) # room temp in kelvin
MagRec["measurement_temp"] = "%8.3e" % (273) # room temp in kelvin
MagRec["measurement_flag"] = "g"
MagRec["measurement_standard"] = "u"
MagRec["measurement_number"] = "1"
MagRec["treatment_ac_field"] = "0"
volume = float(SampRecs[0]["sample_volume"])
x = float(line[4])
y = float(line[3])
negz = float(line[2])
cart = np.array([x, y, -negz]).transpose()
direction = pmag.cart2dir(cart).transpose()
expon = float(line[5])
magn_volume = direction[2] * (10.0 ** expon)
moment = magn_volume * volume
MagRec["measurement_magn_moment"] = str(moment)
MagRec["measurement_magn_volume"] = str(magn_volume) # str(direction[2] * (10.0 ** expon))
MagRec["measurement_dec"] = "%7.1f" % (direction[0])
MagRec["measurement_inc"] = "%7.1f" % (direction[1])
step = line[1]
if step == "NRM":
meas_type = "LT-NO"
elif step[0:2] == "AD":
meas_type = "LT-AF-Z"
treat = float(step[2:])
MagRec["treatment_ac_field"] = "%8.3e" % (treat * 1e-3) # convert from mT to tesla
elif step[0:2] == "TD":
meas_type = "LT-T-Z"
treat = float(step[2:])
MagRec["treatment_temp"] = "%8.3e" % (treat + 273.0) # temp in kelvin
elif step[0:3] == "ARM": #
meas_type = "LT-AF-I"
treat = float(row["step"][3:])
MagRec["treatment_ac_field"] = "%8.3e" % (treat * 1e-3) # convert from mT to tesla
MagRec["treatment_dc_field"] = "%8.3e" % (50e-6) # assume 50uT DC field
MagRec["measurement_description"] = "Assumed DC field - actual unknown"
elif step[0:3] == "IRM": #
meas_type = "LT-IRM"
treat = float(step[3:])
MagRec["treatment_dc_field"] = "%8.3e" % (treat * 1e-3) # convert from mT to tesla
else:
print "unknown treatment type for ", row
return False, "unknown treatment type for ", row
MagRec["magic_method_codes"] = meas_type
MagRecs.append(MagRec.copy())
else:
print "sample name not found: ", row["specname"]
MagOuts = pmag.measurements_methods(MagRecs, noave)
file_created, error_message = pmag.magic_write(meas_file, MagOuts, "magic_measurements")
if file_created:
return True, meas_file
else:
return False, "Results not written to file"
def main():
"""
NAME
UCSC_leg_magic.py
DESCRIPTION
converts UCSC legacy format files to magic_measurements format files
SYNTAX
UCSC_leg_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify input file, or
-fin INDEX: specify index file for reading whole directory: default is index.txt
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt
-spc NUM : specify number of characters to designate a specimen, default = 1
-loc LOCNAME : specify location/study name
-A: don't average replicate measurements
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXXYYY: YYY is sample designation with Z characters from site XXX
[5] sample = site
[6] all others you will have to either customize your
self or e-mail [email protected] for help.
INPUT
Format of UCSC legacy files:
Spec Treat CDec CInc GDec GInc SDec SInc Int [optional A95]
Treat is HX where X is AF field in Oe, TX where X is T in C, or NRM
Intensity assumed to be total moment in (emu/cc) with a 10cc specimen volume
CDec: Declination in specimen coordinate system
CInc: Declination in specimen coordinate system
GDec: Declination in geographic coordinate system
GInc: Declination in geographic coordinate system
SDec: Declination in stratigraphic coordinate system
SInc: Declination in stratigraphic coordinate system
index file: must be formatted:
FILENAME SITE
"""
# initialize some stuff
noave=0
methcode,inst="",""
samp_con,Z='4',3
missing=1
demag="N"
er_location_name=""
citation='This study'
args=sys.argv
methcode="LP-NO"
specnum=-1
MagRecs=[]
version_num=pmag.get_version()
Samps=[] # keeps track of sample orientations
DIspec=[]
MagFiles=[]
#
# get command line arguments
#
user=""
mag_file=""
ind_file=""
dir_path='.'
ErSamps,ErSites=[],[]
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
samp_file=dir_path+'/er_samples.txt'
site_file=dir_path+'/er_sites.txt'
meas_file=dir_path+"/magic_measurements.txt"
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
if '-F' in args:
ind=args.index("-F")
meas_file=dir_path+'/'+args[ind+1]
if '-Fsi' in args:
ind=args.index("-Fsi")
site_file=dirpath+'.'+args[ind+1]
try:
open(site_file,'rU')
ErSites,file_type=pmag.magic_read(site_file)
print 'site information will be appended to ', site_file
except:
print site_file,' not found: site information will be stored in new er_sites.txt file'
site_file=dir_path+'/er_sites.txt'
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file=dirpath+'/'+args[ind+1]
try:
open(samp_file,'rU')
ErSamps,file_type=pmag.magic_read(samp_file)
print 'sample information will be appended to ', samp_file
except:
print samp_file,' not found: sample information will be stored in new er_samples.txt file'
samp_file=dir_path+'/er_samples.txt'
if '-f' in args:
ind=args.index("-f")
mag_file=args[ind+1]
site=mag_file.split('.')[0]
magfile=dir_path+'/'+mag_file
try:
input=open(magfile,'rU')
MagFiles.append([magfile,site])
except:
print "bad input file name"
sys.exit()
elif '-fin' in args:
ind=args.index("-fin")
ind_file=args[ind+1]
ind_file=dir_path+'/'+ind_file
try:
index_file=open(ind_file,'rU')
except:
print "bad index file name"
sys.exit()
elif '-fin' not in args:
ind_file=dir_path+'/index.txt'
try:
index_file=open(ind_file,'rU')
except:
print "bad index file name"
sys.exit()
if ind_file!="":
Files=index_file.readlines()
for file in Files:
rec=file.split()
MagFiles.append(rec)
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if specnum!=0:specnum=-specnum
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
else:
print "-loc is required option"
print main.__doc__
sys.exit()
if "-A" in args: noave=1
Sites=[]
for file in MagFiles:
site=file[1] # attach site name either from file name or from index file
if site not in Sites:
Sites.append(site)
ErSiteRec={'er_location_name': er_location_name,'er_site_name':site,'er_citation_names':citation,'site_definition':'s','site_lat':'','site_lon':"",'site_class':"",'site_lithology':"",'site_type':""}
ErSites.append(ErSiteRec)
print 'processing file: ',file[0],' for site: ',site
data=open(dir_path+'/'+file[0],'rU').readlines() # read in data from file
firstrec=data[0].split()
if firstrec[0]=='FILE': # this file has a header, must look for start of data
for k in range(len(data)):
if data[k][0]=='-': break
else:
k=-1
while k<len(data)-1:
k+=1
line=data[k]
if len(line)>2: # skip stupid terminal lines
line=line.replace(' T ',' T') # make columns consistent
line=line.replace(' H ',' H') # make columns consistent
line=line.replace(' T ',' T') # make columns consistent
line=line.replace(' H ',' H') # make columns consistent
rec=line.split()
if len(rec)<2: break # skip junk
MagRec={}
MagRec['er_location_name']=er_location_name
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["treatment_ac_field"]='0'
meas_type="LT-NO"
MagRec["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["er_specimen_name"]=rec[0]
if specnum!=0:
MagRec["er_sample_name"]=rec[0][:specnum]
else:
MagRec["er_sample_name"]=rec[0]
# site=pmag.parse_site(MagRec['er_sample_name'],samp_con,Z)
MagRec["er_site_name"]=site
MagRec["measurement_magn_moment"]='%10.3e'% (float(rec[8])*1e-4) # # int is in emu/cc; assuming 10cc, this converts to Am^2
#
if samp_file!="" and MagRec["er_sample_name"] not in Samps: # create er_samples.txt file with these data
cdec,cinc=float(rec[2]),float(rec[3])
gdec,ginc=float(rec[4]),float(rec[5])
az,pl=pmag.get_azpl(cdec,cinc,gdec,ginc)
bdec,binc=float(rec[6]),float(rec[7])
if rec[4]!=rec[6] and rec[5]!=rec[7]:
dipdir,dip=pmag.get_tilt(gdec,ginc,bdec,binc)
else:
dipdir,dip=0,0
ErSampRec={}
ErSampRec['er_citation_names']='This study'
ErSampRec['er_location_name']=MagRec['er_location_name']
ErSampRec['er_site_name']=MagRec['er_site_name']
ErSampRec['er_sample_name']=MagRec['er_sample_name']
ErSampRec['sample_azimuth']='%7.1f'%(az)
ErSampRec['sample_dip']='%7.1f'%(pl)
ErSampRec['sample_bed_dip_direction']='%7.1f'%(dipdir)
ErSampRec['sample_bed_dip']='%7.1f'%(dip)
ErSampRec['sample_description']='az,pl,dip_dir and dip recalculated from [c,g,b][dec,inc] in UCSC legacy file'
ErSampRec['magic_method_codes']='SO-NO'
ErSamps.append(ErSampRec)
Samps.append(ErSampRec['er_sample_name'])
MagRec["measurement_dec"]=rec[2]
MagRec["measurement_inc"]=rec[3]
MagRec["er_analyst_mail_names"]=""
MagRec["er_citation_names"]="This study"
demag=rec[1][0]
if demag!='N':
treat=float(rec[1][1:])
else:
treat=0
if demag=="H":
MagRec["treatment_ac_field"]='%8.3e' %(treat*1e-4) # convert from oe to tesla
meas_type="LT-AF-Z"
elif demag=="T":
MagRec["treatment_temp"]='%8.3e' % (treat+273.) # temp in kelvin
meas_type="LT-T-Z"
MagRec['magic_method_codes']=meas_type
MagRecs.append(MagRec)
MagOuts=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print "results put in ",meas_file
pmag.magic_write(samp_file,ErSamps,'er_samples')
print "sample orientations put in ",samp_file
pmag.magic_write(site_file,ErSites,'er_sites')
print "site names put in ",site_file
def main():
"""
NAME
sio_magic.py
DESCRIPTION
converts SIO .mag format files to magic_measurements format files
SYNTAX
sio_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify .mag format input file, required
-fsa SAMPFILE : specify er_samples.txt file relating samples, site and locations names,default is none
-F FILE: specify output file, default is magic_measurements.txt
-Fsy: specify er_synthetics file, default is er_sythetics.txt
-Fsa: specify output er_samples file, default is NONE (only for LDGO formatted files)
-LP [colon delimited list of protocols, include all that apply]
AF: af demag
T: thermal including thellier but not trm acquisition
S: Shaw method
I: IRM (acquisition)
I3d: 3D IRM experiment
N: NRM only
TRM: trm acquisition
ANI: anisotropy experiment
D: double AF demag
G: triple AF demag (GRM protocol)
CR: cooling rate experiment.
The treatment coding of the measurement file should be: XXX.00,XXX.10, XXX.20 ...XX.70 etc. (XXX.00 is optional)
where XXX in the temperature and .10,.20... are running numbers of the cooling rates steps.
XXX.00 is optional zerofield baseline. XXX.70 is alteration check.
syntax in sio_magic is: -LP CR xxx,yyy,zzz,.....xx -A
where xx, yyy,zzz...xxx are cooling time in [K/minutes], seperated by comma, ordered at the same order as XXX.10,XXX.20 ...XX.70
if you use a zerofield step then no need to specify the cooling rate for the zerofield
It is important to add to the command line the -A option so the measurements will not be evraged.
But users need to make sure that there are no duplicate meaurements in the file
-V [1,2,3] units of IRM field in volts using ASC coil #1,2 or 3
-spc NUM : specify number of characters to designate a specimen, default = 0
-loc LOCNAME : specify location/study name, must have either LOCNAME or SAMPFILE or be a synthetic
-syn INST TYPE: sets these specimens as synthetics created at institution INST and of type TYPE
-ins INST : specify which demag instrument was used (e.g, SIO-Suzy or SIO-Odette),default is ""
-dc B PHI THETA: dc lab field (in micro tesla) and phi,theta, default is none
NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment
-ac B : peak AF field (in mT) for ARM acquisition, default is none
-ncn NCON: specify naming convention: default is #1 below
-A: don't average replicate measurements
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
[8] synthetic - has no site name
[9] ODP naming convention
INPUT
Best to put separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.) in
seperate .mag files (eg. af.mag, thermal.mag, etc.)
Format of SIO .mag files:
Spec Treat CSD Intensity Declination Inclination [optional metadata string]
Spec: specimen name
Treat: treatment step
XXX T in Centigrade
XXX AF in mT
for special experiments:
Thellier:
XXX.0 first zero field step
XXX.1 first in field step [XXX.0 and XXX.1 can be done in any order]
XXX.2 second in-field step at lower temperature (pTRM check)
XXX.3 second zero-field step after infield (pTRM check step)
XXX.3 MUST be done in this order [XXX.0, XXX.1 [optional XXX.2] XXX.3]
AARM:
X.00 baseline step (AF in zero bias field - high peak field)
X.1 ARM step (in field step) where
X is the step number in the 15 position scheme
(see Appendix to Lecture 13 - http://magician.ucsd.edu/Essentials_2)
ATRM:
X.00 optional baseline
X.1 ATRM step (+X)
X.2 ATRM step (+Y)
X.3 ATRM step (+Z)
X.4 ATRM step (-X)
X.5 ATRM step (-Y)
X.6 ATRM step (-Z)
X.7 optional alteration check (+X)
TRM:
XXX.YYY XXX is temperature step of total TRM
YYY is dc field in microtesla
Intensity assumed to be total moment in 10^3 Am^2 (emu)
Declination: Declination in specimen coordinate system
Inclination: Declination in specimen coordinate system
Optional metatdata string: mm/dd/yy;hh:mm;[dC,mT];xx.xx;UNITS;USER;INST;NMEAS
hh in 24 hours.
dC or mT units of treatment XXX (see Treat above) for thermal or AF respectively
xx.xxx DC field
UNITS of DC field (microT, mT)
INST: instrument code, number of axes, number of positions (e.g., G34 is 2G, three axes,
measured in four positions)
NMEAS: number of measurements in a single position (1,3,200...)
"""
# initialize some stuff
infile_type="mag"
noave=0
methcode,inst="LP-NO",""
phi,theta,peakfield,labfield=0,0,0,0
pTRM,MD,samp_con,Z=0,0,'1',1
dec=[315,225,180,135,45,90,270,270,270,90,180,180,0,0,0]
inc=[0,0,0,0,0,-45,-45,0,45,45,45,-45,-90,-45,45]
tdec=[0,90,0,180,270,0,0,90,0]
tinc=[0,0,90,0,0,-90,0,0,90]
missing=1
demag="N"
er_location_name=""
citation='This study'
args=sys.argv
fmt='old'
syn=0
synfile='er_synthetics.txt'
samp_file,ErSamps='',[]
trm=0
irm=0
specnum=0
coil=""
#
# get command line arguments
#
meas_file="magic_measurements.txt"
user=""
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
if '-F' in args:
ind=args.index("-F")
meas_file=args[ind+1]
if '-Fsy' in args:
ind=args.index("-Fsy")
synfile=args[ind+1]
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file=args[ind+1]
try:
open(samp_file,'rU')
ErSamps,file_type=pmag.magic_read(samp_file)
print 'sample information will be appended to new er_samples.txt file'
except:
print 'sample information will be stored in new er_samples.txt file'
if '-f' in args:
ind=args.index("-f")
magfile=args[ind+1]
try:
input=open(magfile,'rU')
except:
print "bad mag file name"
sys.exit()
else:
print "mag_file field is required option"
print main.__doc__
sys.exit()
if "-dc" in args:
ind=args.index("-dc")
labfield=float(args[ind+1])*1e-6
phi=float(args[ind+2])
theta=float(args[ind+3])
if "-ac" in args:
ind=args.index("-ac")
peakfield=float(args[ind+1])*1e-3
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if specnum!=0:specnum=-specnum
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-fsa" in args:
ind=args.index("-fsa")
Samps,file_type=pmag.magic_read(args[ind+1])
if '-syn' in args:
syn=1
ind=args.index("-syn")
institution=args[ind+1]
syntype=args[ind+2]
if '-fsy' in args:
ind=args.index("-fsy")
synfile=args[ind+1]
if "-ins" in args:
ind=args.index("-ins")
inst=args[ind+1]
if "-A" in args: noave=1
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4-" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7-" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="7"
if '-LP' in args:
ind=args.index("-LP")
codelist=args[ind+1]
codes=codelist.split(':')
if "AF" in codes:
demag='AF'
if'-dc' not in args: methcode="LT-AF-Z"
if'-dc' in args: methcode="LT-AF-I"
if "T" in codes:
demag="T"
if '-dc' not in args: methcode="LT-T-Z"
if '-dc' in args: methcode="LT-T-I"
if "I" in codes:
methcode="LP-IRM"
irmunits="mT"
if "I3d" in codes:
methcode="LT-T-Z:LP-IRM-3D"
if "S" in codes:
demag="S"
methcode="LP-PI-TRM:LP-PI-ALT-AFARM"
trm_labfield=labfield
ans=raw_input("DC lab field for ARM step: [50uT] ")
if ans=="":
arm_labfield=50e-6
else:
arm_labfield=float(ans)*1e-6
ans=raw_input("temperature for total trm step: [600 C] ")
if ans=="":
trm_peakT=600+273 # convert to kelvin
else:
trm_peakT=float(ans)+273 # convert to kelvin
if "G" in codes: methcode="LT-AF-G"
if "D" in codes: methcode="LT-AF-D"
if "TRM" in codes:
demag="T"
trm=1
if "CR" in codes:
demag="T"
cooling_rate_experiment=1
ind=args.index("CR")
coolling_times=args[ind+1]
coolling_times_list=coolling_times.split(',')
if "-V" in args:
methcode="LP-IRM"
ind=args.index("-V")
irmunits="V"
coil=args[ind+1]
if coil not in ["1","2","3"]:
print main.__doc__
print 'not a valid coil specification'
sys.exit()
if demag=="T" and "ANI" in codes:
methcode="LP-AN-TRM"
if demag=="T" and "CR" in codes:
methcode="LP-CR-TRM"
if demag=="AF" and "ANI" in codes:
methcode="LP-AN-ARM"
if labfield==0: labfield=50e-6
if peakfield==0: peakfield=.180
SynRecs,MagRecs=[],[]
version_num=pmag.get_version()
if 1:
#if infile_type=="SIO format":
for line in input.readlines():
instcode=""
if len(line)>2:
SynRec={}
MagRec={}
MagRec['er_location_name']=er_location_name
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["treatment_ac_field"]='0'
MagRec["treatment_dc_field"]='0'
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
meas_type="LT-NO"
rec=line.split()
if rec[1]==".00":rec[1]="0.00"
treat=rec[1].split('.')
if methcode=="LP-IRM":
if irmunits=='mT':
labfield=float(treat[0])*1e-3
else:
labfield=pmag.getfield(irmunits,coil,treat[0])
if rec[1][0]!="-":
phi,theta=0.,90.
else:
phi,theta=0.,-90.
meas_type="LT-IRM"
MagRec["treatment_dc_field"]='%8.3e'%(labfield)
MagRec["treatment_dc_field_phi"]='%7.1f'%(phi)
MagRec["treatment_dc_field_theta"]='%7.1f'%(theta)
if len(rec)>6:
code1=rec[6].split(';') # break e.g., 10/15/02;7:45 indo date and time
if len(code1)==2: # old format with AM/PM
missing=0
code2=code1[0].split('/') # break date into mon/day/year
code3=rec[7].split(';') # break e.g., AM;C34;200 into time;instr/axes/measuring pos;number of measurements
yy=int(code2[2])
if yy <90:
yyyy=str(2000+yy)
else: yyyy=str(1900+yy)
mm=int(code2[0])
if mm<10:
mm="0"+str(mm)
else: mm=str(mm)
dd=int(code2[1])
if dd<10:
dd="0"+str(dd)
else: dd=str(dd)
time=code1[1].split(':')
hh=int(time[0])
if code3[0]=="PM":hh=hh+12
if hh<10:
hh="0"+str(hh)
else: hh=str(hh)
min=int(time[1])
if min<10:
min= "0"+str(min)
else: min=str(min)
MagRec["measurement_date"]=yyyy+":"+mm+":"+dd+":"+hh+":"+min+":00.00"
MagRec["measurement_time_zone"]='SAN'
if inst=="":
if code3[1][0]=='C':instcode='SIO-bubba'
if code3[1][0]=='G':instcode='SIO-flo'
else:
instcode=''
MagRec["measurement_positions"]=code3[1][2]
elif len(code1)>2: # newest format (cryo7 or later)
if "LP-AN-ARM" not in methcode:labfield=0
fmt='new'
date=code1[0].split('/') # break date into mon/day/year
yy=int(date[2])
if yy <90:
yyyy=str(2000+yy)
else: yyyy=str(1900+yy)
mm=int(date[0])
if mm<10:
mm="0"+str(mm)
else: mm=str(mm)
dd=int(date[1])
if dd<10:
dd="0"+str(dd)
else: dd=str(dd)
time=code1[1].split(':')
hh=int(time[0])
if hh<10:
hh="0"+str(hh)
else: hh=str(hh)
min=int(time[1])
if min<10:
min= "0"+str(min)
else: min=str(min)
MagRec["measurement_date"]=yyyy+":"+mm+":"+dd+":"+hh+":"+min+":00.00"
MagRec["measurement_time_zone"]='SAN'
if inst=="":
if code1[6][0]=='C':instcode='SIO-bubba'
if code1[6][0]=='G':instcode='SIO-flo'
else:
instcode=''
if len(code1)>1:
MagRec["measurement_positions"]=code1[6][2]
else:
MagRec["measurement_positions"]=code1[7] # takes care of awkward format with bubba and flo being different
if user=="":user=code1[5]
if code1[2][-1]=='C':
demag="T"
if code1[4]=='microT' and float(code1[3])!=0. and "LP-AN-ARM" not in methcode: labfield=float(code1[3])*1e-6
if code1[2]=='mT' and methcode!="LP-IRM":
demag="AF"
if code1[4]=='microT' and float(code1[3])!=0.: labfield=float(code1[3])*1e-6
if code1[4]=='microT' and labfield!=0. and meas_type!="LT-IRM":
phi,theta=0.,-90.
if demag=="T": meas_type="LT-T-I"
if demag=="AF": meas_type="LT-AF-I"
MagRec["treatment_dc_field"]='%8.3e'%(labfield)
MagRec["treatment_dc_field_phi"]='%7.1f'%(phi)
MagRec["treatment_dc_field_theta"]='%7.1f'%(theta)
if code1[4]=='' or labfield==0. and meas_type!="LT-IRM":
if demag=='T':meas_type="LT-T-Z"
if demag=="AF":meas_type="LT-AF-Z"
MagRec["treatment_dc_field"]='0'
if syn==0:
MagRec["er_specimen_name"]=rec[0]
MagRec["er_synthetic_name"]=""
MagRec["er_site_name"]=""
if specnum!=0:
MagRec["er_sample_name"]=rec[0][:specnum]
else:
MagRec["er_sample_name"]=rec[0]
if "-fsa" in args:
samp=pmag.get_dictitem(Samps,'er_sample_name',MagRec['er_sample_name'],'T')
if len(samp)>0:
MagRec["er_location_name"]=samp[0]["er_location_name"]
MagRec["er_site_name"]=samp[0]["er_site_name"]
else:
MagRec['er_location_name']=''
MagRec["er_site_name"]=''
elif int(samp_con)!=6:
site=pmag.parse_site(MagRec['er_sample_name'],samp_con,Z)
MagRec["er_site_name"]=site
if MagRec['er_site_name']=="":
print 'No site name found for: ',MagRec['er_specimen_name'],MagRec['er_sample_name']
if MagRec["er_location_name"]=="":
print 'no location name for: ',MagRec["er_specimen_name"]
else:
if specnum!=0:
MagRec["er_sample_name"]=rec[0][:specnum]
else:
MagRec["er_sample_name"]=rec[0]
MagRec["er_site_name"]=""
MagRec["er_synthetic_name"]=MagRec["er_specimen_name"]
SynRec["er_synthetic_name"]=MagRec["er_specimen_name"]
site=pmag.parse_site(MagRec['er_sample_name'],samp_con,Z)
SynRec["synthetic_parent_sample"]=site
SynRec["er_citation_names"]="This study"
SynRec["synthetic_institution"]=institution
SynRec["synthetic_type"]=syntype
SynRecs.append(SynRec)
if float(rec[1])==0:
pass
elif demag=="AF":
if methcode != "LP-AN-ARM":
MagRec["treatment_ac_field"]='%8.3e' %(float(rec[1])*1e-3) # peak field in tesla
if meas_type=="LT-AF-Z": MagRec["treatment_dc_field"]='0'
else: # AARM experiment
if treat[1][0]=='0':
meas_type="LT-AF-Z:LP-AN-ARM:"
MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
MagRec["treatment_dc_field"]='%8.3e'%(0)
if labfield!=0 and methcode!="LP-AN-ARM": print "Warning - inconsistency in mag file with lab field - overriding file with 0"
else:
meas_type="LT-AF-I:LP-AN-ARM"
ipos=int(treat[0])-1
MagRec["treatment_dc_field_phi"]='%7.1f' %(dec[ipos])
MagRec["treatment_dc_field_theta"]='%7.1f'% (inc[ipos])
MagRec["treatment_dc_field"]='%8.3e'%(labfield)
MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
elif demag=="T" and methcode == "LP-AN-TRM":
MagRec["treatment_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
if treat[1][0]=='0':
meas_type="LT-T-Z:LP-AN-TRM"
MagRec["treatment_dc_field"]='%8.3e'%(0)
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
else:
MagRec["treatment_dc_field"]='%8.3e'%(labfield)
if treat[1][0]=='7': # alteration check as final measurement
meas_type="LT-PTRM-I:LP-AN-TRM"
else:
meas_type="LT-T-I:LP-AN-TRM"
# find the direction of the lab field in two ways:
# (1) using the treatment coding (XX.1=+x, XX.2=+y, XX.3=+z, XX.4=-x, XX.5=-y, XX.6=-z)
ipos_code=int(treat[1][0])-1
# (2) using the magnetization
DEC=float(rec[4])
INC=float(rec[5])
if INC < 45 and INC > -45:
if DEC>315 or DEC<45: ipos_guess=0
if DEC>45 and DEC<135: ipos_guess=1
if DEC>135 and DEC<225: ipos_guess=3
if DEC>225 and DEC<315: ipos_guess=4
else:
if INC >45: ipos_guess=2
if INC <-45: ipos_guess=5
# prefer the guess over the code
ipos=ipos_guess
MagRec["treatment_dc_field_phi"]='%7.1f' %(tdec[ipos])
MagRec["treatment_dc_field_theta"]='%7.1f'% (tinc[ipos])
# check it
if ipos_guess!=ipos_code and treat[1][0]!='7':
print "-E- ERROR: check specimen %s step %s, ATRM measurements, coding does not match the direction of the lab field!"%(rec[0],".".join(list(treat)))
elif demag=="S": # Shaw experiment
if treat[1][1]=='0':
if int(treat[0])!=0:
MagRec["treatment_ac_field"]='%8.3e' % (float(treat[0])*1e-3) # AF field in tesla
MagRec["treatment_dc_field"]='0'
meas_type="LT-AF-Z" # first AF
else:
meas_type="LT-NO"
MagRec["treatment_ac_field"]='0'
MagRec["treatment_dc_field"]='0'
elif treat[1][1]=='1':
if int(treat[0])==0:
MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
MagRec["treatment_dc_field"]='%8.3e'%(arm_labfield)
MagRec["treatment_dc_field_phi"]='%7.1f'%(phi)
MagRec["treatment_dc_field_theta"]='%7.1f'%(theta)
meas_type="LT-AF-I"
else:
MagRec["treatment_ac_field"]='%8.3e' % ( float(treat[0])*1e-3) # AF field in tesla
MagRec["treatment_dc_field"]='0'
meas_type="LT-AF-Z"
elif treat[1][1]=='2':
if int(treat[0])==0:
MagRec["treatment_ac_field"]='0'
MagRec["treatment_dc_field"]='%8.3e'%(trm_labfield)
MagRec["treatment_dc_field_phi"]='%7.1f'%(phi)
MagRec["treatment_dc_field_theta"]='%7.1f'%(theta)
MagRec["treatment_temp"]='%8.3e' % (trm_peakT)
meas_type="LT-T-I"
else:
MagRec["treatment_ac_field"]='%8.3e' % ( float(treat[0])*1e-3) # AF field in tesla
MagRec["treatment_dc_field"]='0'
meas_type="LT-AF-Z"
elif treat[1][1]=='3':
if int(treat[0])==0:
MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
MagRec["treatment_dc_field"]='%8.3e'%(arm_labfield)
MagRec["treatment_dc_field_phi"]='%7.1f'%(phi)
MagRec["treatment_dc_field_theta"]='%7.1f'%(theta)
meas_type="LT-AF-I"
else:
MagRec["treatment_ac_field"]='%8.3e' % ( float(treat[0])*1e-3) # AF field in tesla
MagRec["treatment_dc_field"]='0'
meas_type="LT-AF-Z"
# Cooling rate experient # added by rshaar
elif demag=="T" and methcode == "LP-CR-TRM":
MagRec["treatment_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
if treat[1][0]=='0':
meas_type="LT-T-Z:LP-CR-TRM"
MagRec["treatment_dc_field"]='%8.3e'%(0)
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
else:
MagRec["treatment_dc_field"]='%8.3e'%(labfield)
if treat[1][0]=='7': # alteration check as final measurement
meas_type="LT-PTRM-I:LP-CR-TRM"
else:
meas_type="LT-T-I:LP-CR-TRM"
MagRec["treatment_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MagRec["treatment_dc_field_theta"]='%7.1f' % (theta) # labfield theta
indx=int(treat[1][0])-1
# alteration check matjed as 0.7 in the measurement file
if indx==6:
cooling_time= coolling_times_list[-1]
else:
cooling_time=coolling_times_list[indx]
MagRec["measurement_description"]="cooling_rate"+":"+cooling_time+":"+"K/min"
elif demag!='N':
if len(treat)==1:treat.append('0')
MagRec["treatment_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
if trm==0: # demag=T and not trmaq
if treat[1][0]=='0':
meas_type="LT-T-Z"
else:
MagRec["treatment_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MagRec["treatment_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MagRec["treatment_dc_field_theta"]='%7.1f' % (theta) # labfield theta
if treat[1][0]=='1':meas_type="LT-T-I" # in-field thermal step
if treat[1][0]=='2':
meas_type="LT-PTRM-I" # pTRM check
pTRM=1
if treat[1][0]=='3':
MagRec["treatment_dc_field"]='0' # this is a zero field step
meas_type="LT-PTRM-MD" # pTRM tail check
else:
labfield=float(treat[1])*1e-6
MagRec["treatment_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MagRec["treatment_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MagRec["treatment_dc_field_theta"]='%7.1f' % (theta) # labfield theta
meas_type="LT-T-I:LP-TRM" # trm acquisition experiment
MagRec["measurement_csd"]=rec[2]
MagRec["measurement_magn_moment"]='%10.3e'% (float(rec[3])*1e-3) # moment in Am^2 (from emu)
MagRec["measurement_dec"]=rec[4]
MagRec["measurement_inc"]=rec[5]
MagRec["magic_instrument_codes"]=instcode
MagRec["er_analyst_mail_names"]=user
MagRec["er_citation_names"]=citation
if "LP-IRM-3D" in methcode : meas_type=methcode
#MagRec["magic_method_codes"]=methcode.strip(':')
MagRec["magic_method_codes"]=meas_type
MagRec["measurement_flag"]='g'
MagRec["er_specimen_name"]=rec[0]
if 'std' in rec[0]:
MagRec["measurement_standard"]='s'
else:
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
#print MagRec['treatment_temp']
MagRecs.append(MagRec)
MagOuts=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print "results put in ",meas_file
if samp_file!="":
pmag.magic_write(samp_file,ErSamps,'er_samples')
print "sample orientations put in ",samp_file
if len(SynRecs)>0:
pmag.magic_write(synfile,SynRecs,'er_synthetics')
print "synthetics put in ",synfile
def main():
"""
NAME
thellier_magic_redo.py
DESCRIPTION
Calculates paleointensity parameters for thellier-thellier type data using bounds
stored in the "redo" file
SYNTAX
thellier_magic_redo [command line options]
OPTIONS
-h prints help message
-usr USER: identify user, default is ""
-fcr CRIT, set criteria for grading
-f IN: specify input file, default is magic_measurements.txt
-fre REDO: specify redo file, default is "thellier_redo"
-F OUT: specify output file, default is thellier_specimens.txt
-leg: attaches "Recalculated from original measurements; supercedes published results. " to comment field
-CR PERC TYPE: apply a blanket cooling rate correction if none supplied in the er_samples.txt file
PERC should be a percentage of original (say reduce to 90%)
TYPE should be one of the following:
EG (for educated guess); PS (based on pilots); TRM (based on comparison of two TRMs)
-ANI: perform anisotropy correction
-fsa SAMPFILE: er_samples.txt file with cooling rate correction information, default is NO CORRECTION
-Fcr CRout: specify pmag_specimen format file for cooling rate corrected data
-fan ANIFILE: specify rmag_anisotropy format file, default is rmag_anisotropy.txt
-Fac ACout: specify pmag_specimen format file for anisotropy corrected data
default is AC_specimens.txt
-fnl NLTFILE: specify magic_measurments format file, default is magic_measurements.txt
-Fnl NLTout: specify pmag_specimen format file for non-linear trm corrected data
default is NLT_specimens.txt
-z use z component differenences for pTRM calculation
INPUT
a thellier_redo file is Specimen_name Tmin Tmax (where Tmin and Tmax are in Centigrade)
"""
dir_path = "."
critout = ""
version_num = pmag.get_version()
field, first_save = -1, 1
spec, recnum, start, end = 0, 0, 0, 0
crfrac = 0
NltRecs, PmagSpecs, AniSpecRecs, NltSpecRecs, CRSpecs = [], [], [], [], []
meas_file, pmag_file, mk_file = "magic_measurements.txt", "thellier_specimens.txt", "thellier_redo"
anis_file = "rmag_anisotropy.txt"
anisout, nltout = "AC_specimens.txt", "NLT_specimens.txt"
crout = "CR_specimens.txt"
nlt_file = ""
samp_file = ""
comment, user = "", "unknown"
anis, nltrm = 0, 0
jackknife = 0 # maybe in future can do jackknife
args = sys.argv
Zdiff = 0
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 "-leg" in args:
comment = "Recalculated from original measurements; supercedes published results. "
cool = 0
if "-CR" in args:
cool = 1
ind = args.index("-CR")
crfrac = 0.01 * float(sys.argv[ind + 1])
crtype = "DA-CR-" + sys.argv[ind + 2]
if "-Fcr" in args:
ind = args.index("-Fcr")
crout = sys.argv[ind + 1]
if "-f" in args:
ind = args.index("-f")
meas_file = sys.argv[ind + 1]
if "-F" in args:
ind = args.index("-F")
pmag_file = sys.argv[ind + 1]
if "-fre" in args:
ind = args.index("-fre")
mk_file = args[ind + 1]
if "-fsa" in args:
ind = args.index("-fsa")
samp_file = dir_path + "/" + args[ind + 1]
Samps, file_type = pmag.magic_read(samp_file)
SampCRs = pmag.get_dictitem(Samps, "cooling_rate_corr", "", "F") # get samples cooling rate corrections
cool = 1
if file_type != "er_samples":
print "not a valid er_samples.txt file"
sys.exit()
#
#
if "-ANI" in args:
anis = 1
ind = args.index("-ANI")
if "-Fac" in args:
ind = args.index("-Fac")
anisout = args[ind + 1]
if "-fan" in args:
ind = args.index("-fan")
anis_file = args[ind + 1]
#
if "-NLT" in args:
if "-Fnl" in args:
ind = args.index("-Fnl")
nltout = args[ind + 1]
if "-fnl" in args:
ind = args.index("-fnl")
nlt_file = args[ind + 1]
if "-z" in args:
Zdiff = 1
if "-fcr" in sys.argv:
ind = args.index("-fcr")
critout = sys.argv[ind + 1]
#
# start reading in data:
#
meas_file = dir_path + "/" + meas_file
mk_file = dir_path + "/" + mk_file
accept = pmag.default_criteria(1)[0] # set criteria to none
if critout != "":
critout = dir_path + "/" + critout
crit_data, file_type = pmag.magic_read(critout)
if file_type != "pmag_criteria":
print "bad pmag_criteria file, using no acceptance criteria"
print "Acceptance criteria read in from ", critout
for critrec in crit_data:
if "sample_int_sigma_uT" in critrec.keys(): # accommodate Shaar's new criterion
critrec["sample_int_sigma"] = "%10.3e" % (eval(critrec["sample_int_sigma_uT"]) * 1e-6)
for key in critrec.keys():
if key not in accept.keys() and critrec[key] != "":
accept[key] = critrec[key]
meas_data, file_type = pmag.magic_read(meas_file)
if file_type != "magic_measurements":
print file_type
print file_type, "This is not a valid magic_measurements file "
sys.exit()
try:
mk_f = open(mk_file, "rU")
except:
print "Bad redo file"
sys.exit()
mkspec = []
speclist = []
for line in mk_f.readlines():
tmp = line.split()
mkspec.append(tmp)
speclist.append(tmp[0])
if anis == 1:
anis_file = dir_path + "/" + anis_file
anis_data, file_type = pmag.magic_read(anis_file)
if file_type != "rmag_anisotropy":
print file_type
print file_type, "This is not a valid rmag_anisotropy file "
sys.exit()
if nlt_file == "":
nlt_data = pmag.get_dictitem(
meas_data, "magic_method_codes", "LP-TRM", "has"
) # look for trm acquisition data in the meas_data file
else:
nlt_file = dir_path + "/" + nlt_file
nlt_data, file_type = pmag.magic_read(nlt_file)
if len(nlt_data) > 0:
nltrm = 1
#
# sort the specimen names and step through one by one
#
sids = pmag.get_specs(meas_data)
#
print "Processing ", len(speclist), " specimens - please wait "
while spec < len(speclist):
s = speclist[spec]
recnum = 0
datablock = []
PmagSpecRec = {}
PmagSpecRec["er_analyst_mail_names"] = user
PmagSpecRec["er_citation_names"] = "This study"
PmagSpecRec["magic_software_packages"] = version_num
methcodes, inst_code = [], ""
#
# find the data from the meas_data file for this specimen
#
datablock = pmag.get_dictitem(meas_data, "er_specimen_name", s, "T")
datablock = pmag.get_dictitem(
datablock, "magic_method_codes", "LP-PI-TRM", "has"
) # pick out the thellier experiment data
if len(datablock) > 0:
for rec in datablock:
if "magic_instrument_codes" not in rec.keys():
rec["magic_instrument_codes"] = "unknown"
#
# collect info for the PmagSpecRec dictionary
#
rec = datablock[0]
PmagSpecRec["er_specimen_name"] = s
PmagSpecRec["er_sample_name"] = rec["er_sample_name"]
PmagSpecRec["er_site_name"] = rec["er_site_name"]
PmagSpecRec["er_location_name"] = rec["er_location_name"]
PmagSpecRec["measurement_step_unit"] = "K"
PmagSpecRec["specimen_correction"] = "u"
if "er_expedition_name" in rec.keys():
PmagSpecRec["er_expedition_name"] = rec["er_expedition_name"]
if "magic_instrument_codes" not in rec.keys():
PmagSpecRec["magic_instrument_codes"] = "unknown"
else:
PmagSpecRec["magic_instrument_codes"] = rec["magic_instrument_codes"]
if "magic_experiment_name" not in rec.keys():
rec["magic_experiment_name"] = ""
else:
PmagSpecRec["magic_experiment_names"] = rec["magic_experiment_name"]
meths = rec["magic_experiment_name"].split(":")
for meth in meths:
if meth.strip() not in methcodes and "LP-" in meth:
methcodes.append(meth.strip())
#
# sort out the data into first_Z, first_I, ptrm_check, ptrm_tail
#
araiblock, field = pmag.sortarai(datablock, s, Zdiff)
first_Z = araiblock[0]
first_I = araiblock[1]
ptrm_check = araiblock[2]
ptrm_tail = araiblock[3]
if len(first_I) < 3 or len(first_Z) < 4:
spec += 1
print "skipping specimen ", s
else:
#
# get start, end
#
for redospec in mkspec:
if redospec[0] == s:
b, e = float(redospec[1]), float(redospec[2])
break
if e > float(first_Z[-1][0]):
e = float(first_Z[-1][0])
for recnum in range(len(first_Z)):
if first_Z[recnum][0] == b:
start = recnum
if first_Z[recnum][0] == e:
end = recnum
nsteps = end - start
if nsteps > 2:
zijdblock, units = pmag.find_dmag_rec(s, meas_data)
pars, errcode = pmag.PintPars(datablock, araiblock, zijdblock, start, end, accept)
if "specimen_scat" in pars.keys():
PmagSpecRec["specimen_scat"] = pars["specimen_scat"]
if "specimen_frac" in pars.keys():
PmagSpecRec["specimen_frac"] = "%5.3f" % (pars["specimen_frac"])
if "specimen_gmax" in pars.keys():
PmagSpecRec["specimen_gmax"] = "%5.3f" % (pars["specimen_gmax"])
pars["measurement_step_unit"] = units
pars["specimen_lab_field_dc"] = field
pars["specimen_int"] = -1 * field * pars["specimen_b"]
PmagSpecRec["measurement_step_min"] = "%8.3e" % (pars["measurement_step_min"])
PmagSpecRec["measurement_step_max"] = "%8.3e" % (pars["measurement_step_max"])
PmagSpecRec["specimen_int_n"] = "%i" % (pars["specimen_int_n"])
PmagSpecRec["specimen_lab_field_dc"] = "%8.3e" % (pars["specimen_lab_field_dc"])
PmagSpecRec["specimen_int"] = "%9.4e " % (pars["specimen_int"])
PmagSpecRec["specimen_b"] = "%5.3f " % (pars["specimen_b"])
PmagSpecRec["specimen_q"] = "%5.1f " % (pars["specimen_q"])
PmagSpecRec["specimen_f"] = "%5.3f " % (pars["specimen_f"])
PmagSpecRec["specimen_fvds"] = "%5.3f" % (pars["specimen_fvds"])
PmagSpecRec["specimen_b_beta"] = "%5.3f" % (pars["specimen_b_beta"])
PmagSpecRec["specimen_int_mad"] = "%7.1f" % (pars["specimen_int_mad"])
PmagSpecRec["specimen_Z"] = "%7.1f" % (pars["specimen_Z"])
PmagSpecRec["specimen_gamma"] = "%7.1f" % (pars["specimen_gamma"])
if pars["method_codes"] != "" and pars["method_codes"] not in methcodes:
methcodes.append(pars["method_codes"])
PmagSpecRec["specimen_dec"] = "%7.1f" % (pars["specimen_dec"])
PmagSpecRec["specimen_inc"] = "%7.1f" % (pars["specimen_inc"])
PmagSpecRec["specimen_tilt_correction"] = "-1"
PmagSpecRec["specimen_direction_type"] = "l"
PmagSpecRec["direction_type"] = "l" # this is redudant, but helpful - won't be imported
PmagSpecRec["specimen_dang"] = "%7.1f " % (pars["specimen_dang"])
PmagSpecRec["specimen_drats"] = "%7.1f " % (pars["specimen_drats"])
PmagSpecRec["specimen_drat"] = "%7.1f " % (pars["specimen_drat"])
PmagSpecRec["specimen_int_ptrm_n"] = "%i " % (pars["specimen_int_ptrm_n"])
PmagSpecRec["specimen_rsc"] = "%6.4f " % (pars["specimen_rsc"])
PmagSpecRec["specimen_md"] = "%i " % (int(pars["specimen_md"]))
if PmagSpecRec["specimen_md"] == "-1":
PmagSpecRec["specimen_md"] = ""
PmagSpecRec["specimen_b_sigma"] = "%5.3f " % (pars["specimen_b_sigma"])
if "IE-TT" not in methcodes:
methcodes.append("IE-TT")
methods = ""
for meth in methcodes:
methods = methods + meth + ":"
PmagSpecRec["magic_method_codes"] = methods.strip(":")
PmagSpecRec["magic_software_packages"] = version_num
PmagSpecRec["specimen_description"] = comment
if critout != "":
kill = pmag.grade(PmagSpecRec, accept, "specimen_int")
if len(kill) > 0:
Grade = "F" # fails
else:
Grade = "A" # passes
PmagSpecRec["specimen_grade"] = Grade
else:
PmagSpecRec["specimen_grade"] = "" # not graded
if nltrm == 0 and anis == 0 and cool != 0: # apply cooling rate correction
SCR = pmag.get_dictitem(
SampCRs, "er_sample_name", PmagSpecRec["er_sample_name"], "T"
) # get this samples, cooling rate correction
CrSpecRec = pmag.cooling_rate(PmagSpecRec, SCR, crfrac, crtype)
if CrSpecRec["er_specimen_name"] != "none":
CrSpecs.append(CrSpecRec)
PmagSpecs.append(PmagSpecRec)
NltSpecRec = ""
#
# check on non-linear TRM correction
#
if nltrm == 1:
#
# find the data from the nlt_data list for this specimen
#
TRMs, Bs = [], []
NltSpecRec = ""
NltRecs = pmag.get_dictitem(
nlt_data, "er_specimen_name", PmagSpecRec["er_specimen_name"], "has"
) # fish out all the NLT data for this specimen
if len(NltRecs) > 2:
for NltRec in NltRecs:
Bs.append(float(NltRec["treatment_dc_field"]))
TRMs.append(float(NltRec["measurement_magn_moment"]))
NLTpars = nlt.NLtrm(
Bs,
TRMs,
float(PmagSpecRec["specimen_int"]),
float(PmagSpecRec["specimen_lab_field_dc"]),
0,
)
if NLTpars["banc"] > 0:
NltSpecRec = {}
for key in PmagSpecRec.keys():
NltSpecRec[key] = PmagSpecRec[key]
NltSpecRec["specimen_int"] = "%9.4e" % (NLTpars["banc"])
NltSpecRec["magic_method_codes"] = PmagSpecRec["magic_method_codes"] + ":DA-NL"
NltSpecRec["specimen_correction"] = "c"
NltSpecRec["specimen_grade"] = PmagSpecRec["specimen_grade"]
NltSpecRec["magic_software_packages"] = version_num
print NltSpecRec["er_specimen_name"], " Banc= ", float(NLTpars["banc"]) * 1e6
if anis == 0 and cool != 0:
SCR = pmag.get_dictitem(
SampCRs, "er_sample_name", NltSpecRec["er_sample_name"], "T"
) # get this samples, cooling rate correction
CrSpecRec = pmag.cooling_rate(NltSpecRec, SCR, crfrac, crtype)
if CrSpecRec["er_specimen_name"] != "none":
CrSpecs.append(CrSpecRec)
NltSpecRecs.append(NltSpecRec)
#
# check on anisotropy correction
if anis == 1:
if NltSpecRec != "":
Spc = NltSpecRec
else: # find uncorrected data
Spc = PmagSpecRec
AniSpecs = pmag.get_dictitem(
anis_data, "er_specimen_name", PmagSpecRec["er_specimen_name"], "T"
)
if len(AniSpecs) > 0:
AniSpec = AniSpecs[0]
AniSpecRec = pmag.doaniscorr(Spc, AniSpec)
AniSpecRec["specimen_grade"] = PmagSpecRec["specimen_grade"]
AniSpecRec["magic_instrument_codes"] = PmagSpecRec["magic_instrument_codes"]
AniSpecRec["specimen_correction"] = "c"
AniSpecRec["magic_software_packages"] = version_num
if cool != 0:
SCR = pmag.get_dictitem(
SampCRs, "er_sample_name", AniSpecRec["er_sample_name"], "T"
) # get this samples, cooling rate correction
CrSpecRec = pmag.cooling_rate(AniSpecRec, SCR, crfrac, crtype)
if CrSpecRec["er_specimen_name"] != "none":
CrSpecs.append(CrSpecRec)
AniSpecRecs.append(AniSpecRec)
elif anis == 1:
AniSpecs = pmag.get_dictitem(
anis_data, "er_specimen_name", PmagSpecRec["er_specimen_name"], "T"
)
if len(AniSpecs) > 0:
AniSpec = AniSpecs[0]
AniSpecRec = pmag.doaniscorr(PmagSpecRec, AniSpec)
AniSpecRec["specimen_grade"] = PmagSpecRec["specimen_grade"]
AniSpecRec["magic_instrument_codes"] = PmagSpecRec["magic_instrument_codes"]
AniSpecRec["specimen_correction"] = "c"
AniSpecRec["magic_software_packages"] = version_num
if crfrac != 0:
CrSpecRec = {}
for key in AniSpecRec.keys():
CrSpecRec[key] = AniSpecRec[key]
inten = frac * float(CrSpecRec["specimen_int"])
CrSpecRec["specimen_int"] = "%9.4e " % (
inten
) # adjust specimen intensity by cooling rate correction
CrSpecRec["magic_method_codes"] = CrSpecRec["magic_method_codes"] + ":DA-CR-" + crtype
CRSpecs.append(CrSpecRec)
AniSpecRecs.append(AniSpecRec)
spec += 1
else:
print "skipping ", s
spec += 1
pmag_file = dir_path + "/" + pmag_file
pmag.magic_write(pmag_file, PmagSpecs, "pmag_specimens")
print "uncorrected thellier data saved in: ", pmag_file
if anis == 1 and len(AniSpecRecs) > 0:
anisout = dir_path + "/" + anisout
pmag.magic_write(anisout, AniSpecRecs, "pmag_specimens")
print "anisotropy corrected data saved in: ", anisout
if nltrm == 1 and len(NltSpecRecs) > 0:
nltout = dir_path + "/" + nltout
pmag.magic_write(nltout, NltSpecRecs, "pmag_specimens")
print "non-linear TRM corrected data saved in: ", nltout
if crfrac != 0:
crout = dir_path + "/" + crout
pmag.magic_write(crout, CRSpecs, "pmag_specimens")
print "cooling rate corrected data saved in: ", crout
def main():
"""
NAME
HUJI_sample_magic.py
DESCRIPTION
takes tab delimited Hebrew University sample file and converts to MagIC formatted tables
SYNTAX
HUJI_sample_magic.py [command line options]
OPTIONS
-f FILE: specify input file
-Fsa FILE: specify sample output file, default is: er_samples.txt
-Fsi FILE: specify site output file, default is: er_sites.txt
-Iso: import sample orientation info - default is to set sample_az/dip to 0,0
-ncn NCON: specify naming convention: default is #1 below
-mcd: specify sampling method codes as a colon delimited string: [default is: FS-FD:SO-POM]
FS-FD field sampling done with a drill
FS-H field sampling done with hand samples
FS-LOC-GPS field location done with GPS
FS-LOC-MAP field location done with map
SO-POM a Pomeroy orientation device was used
SO-ASC an ASC orientation device was used
SO-MAG orientation with magnetic compass
-loc: location name, default="unknown"
INPUT FORMAT
Input files must be tab delimited:
Samp Az Dip Dip_dir Dip
Orientation convention:
Lab arrow azimuth = mag_azimuth; Lab arrow dip = 90-field_dip
e.g. field_dip is degrees from horizontal of drill direction
Magnetic declination convention:
Az is already corrected in file
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXXYYY: YYY is sample designation with Z characters from site XXX
[5] sample = site
[5] all others you will have to either customize your
self or e-mail [email protected] for help.
OUTPUT
output saved in er_samples.txt will overwrite any existing files
"""
#
# initialize variables
#
version_num=pmag.get_version()
samp_file,or_con,corr = "er_samples.txt","1","1"
site_file='er_sites.txt'
args=sys.argv
date,lat,lon="","","" # date of sampling, latitude (pos North), longitude (pos East)
bed_dip,bed_dip_dir="",""
participantlist=""
sites=[] # list of site names
Lats,Lons=[],[] # list of latitudes and longitudes
SampRecs,SiteRecs,ImageRecs,imagelist=[],[],[],[] # lists of Sample records and Site records
samp_con,Z,average_bedding="1",1,"0"
newbaseline,newbeddir,newbeddip="","",""
meths='FS-FD:SO-POM:SO-SUN'
delta_u="0"
sclass,lithology,type="","",""
newclass,newlith,newtype='','',''
user=""
or_con='3'
corr=="3"
DecCorr=0.
location_name="unknown"
ignore=1
#
#
if "-h" in args:
print main.__doc__
sys.exit()
if "-f" in args:
ind=args.index("-f")
orient_file=sys.argv[ind+1]
else:
"Must have orientation file name"
sys.exit()
if "-Fsa" in args:
ind=args.index("-Fsa")
samp_file=sys.argv[ind+1]
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 3-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
print samp_con, Z
if "-mcd" in args:
ind=args.index("-mcd")
meths=(sys.argv[ind+1])
if "-loc" in args:
ind=args.index("-loc")
location_name=(sys.argv[ind+1])
if "-Iso" in args: ignore=0
#
# read in file to convert
#
azfile=open(orient_file,'rU')
AzDipDat=azfile.readlines()
azfile.close()
SampOut=[]
SiteOut=[]
for line in AzDipDat[1:]:
orec=line.split()
if len(orec)>1:
labaz,labdip=pmag.orient(float(orec[1]),float(orec[2]),or_con)
bed_dip_dir=(orec[3])
bed_dip=(orec[4])
SampRec={}
SiteRec={}
SampRec["er_location_name"]=location_name
SampRec["er_citation_names"]="This study"
SiteRec["er_location_name"]=location_name
SiteRec["er_citation_names"]="This study"
SiteRec["site_class"]=""
SiteRec["site_lithology"]=""
SiteRec["site_type"]=""
SiteRec["site_definition"]="s"
SiteRec["er_citation_names"]="This study"
#
# parse information common to all orientation methods
#
SampRec["er_sample_name"]=orec[0]
SampRec["sample_bed_dip_direction"]=orec[3]
SampRec["sample_bed_dip"]=orec[4]
SiteRec["site_bed_dip_direction"]=orec[3]
SiteRec["site_bed_dip"]=orec[4]
if ignore==0:
SampRec["sample_dip"]='%7.1f'%(labdip)
SampRec["sample_azimuth"]='%7.1f'%(labaz)
else:
SampRec["sample_dip"]='0'
SampRec["sample_azimuth"]='0'
SampRec["sample_lat"]=orec[5]
SampRec["sample_lon"]=orec[6]
SiteRec["site_lat"]=orec[5]
SiteRec["site_lon"]=orec[6]
methods=meths.split(":")
SampRec["magic_method_codes"]=meths
site=pmag.parse_site(orec[0],samp_con,Z) # parse out the site name
SampRec["er_site_name"]=site
SampRec['magic_software_packages']=version_num
SiteRec["er_site_name"]=site
SiteRec['magic_software_packages']=version_num
SampOut.append(SampRec)
SiteOut.append(SiteRec)
pmag.magic_write(samp_file,SampOut,"er_samples")
print "Sample info saved in ", samp_file
pmag.magic_write(site_file,SiteOut,"er_sites")
print "Site info saved in ", site_file
def main():
"""
NAME
zeq_magic_redo.py
DESCRIPTION
Calculate principal components through demagnetization data using bounds and calculation type stored in "redo" file
SYNTAX
zeq_magic_redo.py [command line options]
OPTIONS
-h prints help message
-usr USER: identify user, default is ""
-f: specify input file, default is magic_measurements.txt
-F: specify output file, default is zeq_specimens.txt
-fre REDO: specify redo file, default is "zeq_redo"
-fsa SAMPFILE: specify er_samples format file, default is "er_samples.txt"
-A : don't average replicate measurements, default is yes
-crd [s,g,t] :
specify coordinate system [s,g,t] [default is specimen coordinates]
are specimen, geographic, and tilt corrected respectively
NB: you must have a SAMPFILE in this directory to rotate from specimen coordinates
-leg: attaches "Recalculated from original measurements; supercedes published results. " to comment field
INPUTS
zeq_redo format file is:
specimen_name calculation_type[DE-BFL,DE-BFL-A,DE-BFL-O,DE-BFP,DE-FM] step_min step_max component_name[A,B,C]
"""
dir_path='.'
INCL=["LT-NO","LT-AF-Z","LT-T-Z","LT-M-Z"] # looking for demag data
beg,end,pole,geo,tilt,askave,save=0,0,[],0,0,0,0
user,doave,comment= "",1,""
geo,tilt=0,0
version_num=pmag.get_version()
args=sys.argv
if '-WD' in args:
ind=args.index('-WD')
dir_path=args[ind+1]
meas_file,pmag_file,mk_file= dir_path+"/"+"magic_measurements.txt",dir_path+"/"+"zeq_specimens.txt",dir_path+"/"+"zeq_redo"
samp_file,coord=dir_path+"/"+"er_samples.txt",""
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=sys.argv[ind+1]
if "-A" in args:doave=0
if "-leg" in args: comment="Recalculated from original measurements; supercedes published results. "
if "-f" in args:
ind=args.index("-f")
meas_file=dir_path+'/'+sys.argv[ind+1]
if "-F" in args:
ind=args.index("-F")
pmag_file=dir_path+'/'+sys.argv[ind+1]
if "-fre" in args:
ind=args.index("-fre")
mk_file=dir_path+"/"+args[ind+1]
try:
mk_f=open(mk_file,'rU')
except:
print "Bad redo file"
sys.exit()
mkspec,skipped=[],[]
speclist=[]
for line in mk_f.readlines():
tmp=line.split()
mkspec.append(tmp)
speclist.append(tmp[0])
if "-fsa" in args:
ind=args.index("-fsa")
samp_file=dir_path+'/'+sys.argv[ind+1]
if "-crd" in args:
ind=args.index("-crd")
coord=sys.argv[ind+1]
if coord=="g":geo,tilt=1,0
if coord=="t":geo,tilt=1,1
#
# now get down to bidness
if geo==1:
samp_data,file_type=pmag.magic_read(samp_file)
if file_type != 'er_samples':
print file_type
print "This is not a valid er_samples file "
sys.exit()
# set orientation priorities
SO_methods=[]
for rec in samp_data:
if "magic_method_codes" in rec:
methlist=rec["magic_method_codes"]
for meth in methlist.split(":"):
if "SO" in meth and "SO-POM" not in meth.strip():
if meth.strip() not in SO_methods: SO_methods.append(meth.strip())
SO_priorities=pmag.set_priorities(SO_methods,0)
#
#
#
meas_data,file_type=pmag.magic_read(meas_file)
if file_type != 'magic_measurements':
print file_type
print file_type,"This is not a valid magic_measurements file "
sys.exit()
#
# sort the specimen names
#
k = 0
print 'Processing ',len(speclist), ' specimens - please wait'
PmagSpecs=[]
while k < len(speclist):
s=speclist[k]
recnum=0
PmagSpecRec={}
method_codes,inst_codes=[],[]
# find the data from the meas_data file for this sample
#
# collect info for the PmagSpecRec dictionary
#
meas_meth=[]
for rec in meas_data: # copy of vital stats to PmagSpecRec from first spec record in demag block
skip=1
if rec["er_specimen_name"]==s:
methods=rec["magic_method_codes"].split(":")
if len(set(methods) & set(INCL))>0:
PmagSpecRec["er_analyst_mail_names"]=user
PmagSpecRec["magic_software_packages"]=version_num
PmagSpecRec["er_specimen_name"]=s
PmagSpecRec["er_sample_name"]=rec["er_sample_name"]
PmagSpecRec["er_site_name"]=rec["er_site_name"]
PmagSpecRec["er_location_name"]=rec["er_location_name"]
PmagSpecRec["er_citation_names"]="This study"
if "magic_experiment_name" not in rec.keys(): rec["magic_experiment_name"]=""
PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"]
if "magic_instrument_codes" not in rec.keys(): rec["magic_instrument_codes"]=""
inst=rec['magic_instrument_codes'].split(":")
for I in inst:
if I not in inst_codes: # copy over instruments
inst_codes.append(I)
meths=rec["magic_method_codes"].split(":")
for meth in meths:
if meth.strip() not in meas_meth:meas_meth.append(meth)
if "LP-DIR-AF" in meas_meth or "LT-AF-Z" in meas_meth:
PmagSpecRec["measurement_step_unit"]="T"
if "LP-DIR-AF" not in method_codes:method_codes.append("LP-DIR-AF")
if "LP-DIR-T" in meas_meth or "LT-T-Z" in meas_meth:
PmagSpecRec["measurement_step_unit"]="K"
if "LP-DIR-T" not in method_codes:method_codes.append("LP-DIR-T")
if "LP-DIR-M" in meas_meth or "LT-M-Z" in meas_meth:
PmagSpecRec["measurement_step_unit"]="J"
if "LP-DIR-M" not in method_codes:method_codes.append("LP-DIR-M")
if PmagSpecRec=={}:
print 'no data found for specimen: ',s
print 'delete from zeq_redo input file...., then try again'
sys.exit()
#
#
data,units=pmag.find_dmag_rec(s,meas_data)
#
datablock=data
noskip=1
if len(datablock) <2 or s not in speclist :
noskip=0
k+=1
# print 'skipping ', s,len(datablock)
if noskip:
#
# find replicate measurements at given treatment step and average them
#
# step_meth,avedata=pmag.vspec(data)
#
# if len(avedata) != len(datablock):
# if doave==1:
# method_codes.append("DE-VM")
# datablock=avedata
#
# do geo or stratigraphic correction now
#
if geo==1:
# find top priority orientation method
redo,p=1,0
if len(SO_methods)<=1:
az_type=SO_methods[0]
orient=pmag.find_samp_rec(PmagSpecRec["er_sample_name"],samp_data,az_type)
if orient["sample_azimuth"] !="": method_codes.append(az_type)
redo=0
while redo==1:
if p>=len(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
#
# if tilt selected, get stratigraphic correction
#
tiltblock,geoblock=[],[]
for rec in datablock:
if "sample_azimuth" in orient.keys() and orient["sample_azimuth"]!="":
d_geo,i_geo=pmag.dogeo(rec[1],rec[2],orient["sample_azimuth"],orient["sample_dip"])
geoblock.append([rec[0],d_geo,i_geo,rec[3],rec[4],rec[5]])
if tilt==1 and "sample_bed_dip_direction" in orient.keys():
d_tilt,i_tilt=pmag.dotilt(d_geo,i_geo,orient["sample_bed_dip_direction"],orient["sample_bed_dip"])
tiltblock.append([rec[0],d_tilt,i_tilt,rec[3],rec[4],rec[5]])
elif tilt==1:
if PmagSpecRec["er_sample_name"] not in skipped:
print 'no tilt correction for ', PmagSpecRec["er_sample_name"],' skipping....'
skipped.append(PmagSpecRec["er_sample_name"])
else:
if PmagSpecRec["er_sample_name"] not in skipped:
print 'no geographic correction for ', PmagSpecRec["er_sample_name"],' skipping....'
skipped.append(PmagSpecRec["er_sample_name"])
#
# get beg_pca, end_pca, pca
if PmagSpecRec['er_sample_name'] not in skipped:
compnum=-1
for spec in mkspec:
if spec[0]==s:
CompRec={}
for key in PmagSpecRec.keys():CompRec[key]=PmagSpecRec[key]
compnum+=1
calculation_type=spec[1]
beg=float(spec[2])
end=float(spec[3])
if len(spec)>4:
comp_name=spec[4]
else:
comp_name=string.uppercase[compnum]
CompRec['specimen_comp_name']=comp_name
if beg < float(datablock[0][0]):beg=float(datablock[0][0])
if end > float(datablock[-1][0]):end=float(datablock[-1][0])
for l in range(len(datablock)):
if datablock[l][0]==beg:beg_pca=l
if datablock[l][0]==end:end_pca=l
if geo==1 and tilt==0:
mpars=pmag.domean(geoblock,beg_pca,end_pca,calculation_type)
if mpars["specimen_direction_type"]!="Error":
CompRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
CompRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
CompRec["specimen_tilt_correction"]='0'
if geo==1 and tilt==1:
mpars=pmag.domean(tiltblock,beg_pca,end_pca,calculation_type)
if mpars["specimen_direction_type"]!="Error":
CompRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
CompRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
CompRec["specimen_tilt_correction"]='100'
if geo==0 and tilt==0:
mpars=pmag.domean(datablock,beg_pca,end_pca,calculation_type)
if mpars["specimen_direction_type"]!="Error":
CompRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
CompRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
CompRec["specimen_tilt_correction"]='-1'
if mpars["specimen_direction_type"]=="Error":
pass
else:
CompRec["measurement_step_min"]='%8.3e '%(datablock[beg_pca][0])
try:
CompRec["measurement_step_max"]='%8.3e '%(datablock[end_pca][0] )
except:
print 'error in end_pca ',PmagSpecRec['er_specimen_name']
CompRec["specimen_correction"]='u'
if calculation_type!='DE-FM':
CompRec["specimen_mad"]='%7.1f '%(mpars["specimen_mad"])
CompRec["specimen_alpha95"]=""
else:
CompRec["specimen_mad"]=""
CompRec["specimen_alpha95"]='%7.1f '%(mpars["specimen_alpha95"])
CompRec["specimen_n"]='%i '%(mpars["specimen_n"])
CompMeths=[]
for meth in method_codes:
if meth not in CompMeths:CompMeths.append(meth)
if calculation_type not in CompMeths:CompMeths.append(calculation_type)
if geo==1: CompMeths.append("DA-DIR-GEO")
if tilt==1: CompMeths.append("DA-DIR-TILT")
if "DE-BFP" not in calculation_type:
CompRec["specimen_direction_type"]='l'
else:
CompRec["specimen_direction_type"]='p'
CompRec["magic_method_codes"]=""
if len(CompMeths) != 0:
methstring=""
for meth in CompMeths:
methstring=methstring+ ":" +meth
CompRec["magic_method_codes"]=methstring.strip(':')
CompRec["specimen_description"]=comment
if len(inst_codes) != 0:
inststring=""
for inst in inst_codes:
inststring=inststring+ ":" +inst
CompRec["magic_instrument_codes"]=inststring.strip(':')
PmagSpecs.append(CompRec)
k+=1
pmag.magic_write(pmag_file,PmagSpecs,'pmag_specimens')
print "Recalculated specimen data stored in ",pmag_file
def main():
"""
NAME
k15_magic.py
DESCRIPTION
converts .k15 format data to magic_measurements format.
assums Jelinek Kappabridge measurement scheme
SYNTAX
k15_magic.py [-h] [command line options]
OPTIONS
-h prints help message and quits
-f KFILE: specify .k15 format input file
-F MFILE: specify magic_measurements format output file
-Fsa SFILE, specify er_samples format file for output
-Fa AFILE, specify rmag_anisotropy format file for output
-loc LOC: specify location name for study
-ins INST: specify instrument that measurements were made on
-spc NUM: specify number of digets for specimen ID, default is 0
-ncn NCOM: specify naming convention (default is #1)
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXXYYY: YYY is sample designation with Z characters from site XXX
[5] sample = site
[6] sample, site, location info in er_samples.txt
[7] all others you will have to either customize your
DEFAULTS
MFILE: k15_measurements.txt
SFILE: er_samples.txt
AFILE: rmag_anisotropy.txt
LOC: unknown
INST: unknown
INPUT
name [az,pl,strike,dip], followed by
3 rows of 5 measurements for each specimen
"""
#
# initialize some variables
#
version_num=pmag.get_version()
specnum=0
sampfile, measfile="er_samples.txt","k15_measurements.txt"
anisfile='rmag_anisotropy.txt'
resfile='rmag_results.txt'
syn=0
er_location_name="unknown"
inst="unknown"
itilt,igeo,linecnt,key=0,0,0,""
first_save=1
k15,specnum=[],0
citation='This study'
dir_path='.'
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
# pick off stuff from command line
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index('-f')
k15file=sys.argv[ind+1]
if '-F' in sys.argv:
ind=sys.argv.index('-F')
measfile=sys.argv[ind+1]
if '-Fsa' in sys.argv:
ind=sys.argv.index('-Fsa')
sampfile=sys.argv[ind+1]
if '-Fa' in sys.argv:
ind=sys.argv.index('-Fa')
anisfile=sys.argv[ind+1]
if '-loc' in sys.argv:
ind=sys.argv.index('-loc')
er_location_name=sys.argv[ind+1]
if '-spc' in sys.argv:
ind=sys.argv.index('-spc')
specnum=-int(sys.argv[ind+1])
samp_con,Z="1",""
if "-ncn" in sys.argv:
ind=sys.argv.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
if samp_con=='6':
Samps,filetype=pmag.magic_read(dirpath+'/er_samples.txt')
sampfile, measfile=dir_path+'/'+sampfile,dir_path+'/'+measfile
anisfile=dir_path+'/'+anisfile
resfile=dir_path+'/'+resfile
k15file=dir_path+'/'+k15file
try:
SampRecs,filetype=pmag.magic_read(sampfile) # append new records to existing
samplist=[]
for samp in SampRecs:
if samp['er_sample_name'] not in samplist:samplist.append(samp['er_sample_name'])
except IOError:
SampRecs=[]
# measurement directions for Jelinek 1977 protocol:
Decs=[315,225,180,135,45,90,270,270,270,90,180,180,0,0,0]
Incs=[0,0,0,0,0,-45,-45,0,45,45,45,-45,-90,-45,45]
# some defaults to read in .k15 file format
# list of measurements and default number of characters for specimen ID
# some magic default definitions
#
# read in data
input=open(k15file,'rU')
MeasRecs,SpecRecs,AnisRecs,ResRecs=[],[],[],[]
# read in data
MeasRec,SpecRec,SampRec,SiteRec,AnisRec,ResRec={},{},{},{},{},{}
for line in input.readlines():
linecnt+=1
rec=line.split()
if linecnt==1:
MeasRec["magic_method_codes"]=""
SpecRec["magic_method_codes"]=""
SampRec["magic_method_codes"]=""
AnisRec["magic_method_codes"]=""
SiteRec["magic_method_codes"]=""
ResRec["magic_smethod_codes"]=""
MeasRec["magic_software_packages"]=version_num
SpecRec["magic_software_packages"]=version_num
SampRec["magic_software_packages"]=version_num
AnisRec["magic_software_packages"]=version_num
SiteRec["magic_software_packages"]=version_num
ResRec["magic_software_packages"]=version_num
MeasRec["magic_method_codes"]="LP-X"
MeasRec["measurement_flag"]="g"
MeasRec["measurement_standard"]="u"
MeasRec["er_citation_names"]="This study"
SpecRec["er_citation_names"]="This study"
SampRec["er_citation_names"]="This study"
AnisRec["er_citation_names"]="This study"
ResRec["er_citation_names"]="This study"
MeasRec["er_specimen_name"]=rec[0]
MeasRec["magic_experiment_name"]=rec[0]+":LP-AN-MS"
AnisRec["magic_experiment_names"]=rec[0]+":AMS"
ResRec["magic_experiment_names"]=rec[0]+":AMS"
SpecRec["er_specimen_name"]=rec[0]
AnisRec["er_specimen_name"]=rec[0]
SampRec["er_specimen_name"]=rec[0]
ResRec["rmag_result_name"]=rec[0]
if specnum!=0: MeasRec["er_sample_name"]=rec[0][:specnum]
if specnum==0: MeasRec["er_sample_name"]=rec[0]
SampRec["er_sample_name"]=MeasRec["er_sample_name"]
SpecRec["er_sample_name"]=MeasRec["er_sample_name"]
AnisRec["er_sample_name"]=MeasRec["er_sample_name"]
ResRec["er_sample_names"]=MeasRec["er_sample_name"]
if samp_con=="6":
for samp in Samps:
if samp['er_sample_name']==AnisRec["er_sample_name"]:
sitename=samp['er_site_name']
er_location_name=samp['er_location_name']
elif samp_con!="":
sitename=pmag.parse_site(AnisRec['er_sample_name'],samp_con,Z)
MeasRec["er_site_name"]=sitename
MeasRec["er_location_name"]=er_location_name
SampRec["er_site_name"]=MeasRec["er_site_name"]
SpecRec["er_site_name"]=MeasRec["er_site_name"]
AnisRec["er_site_name"]=MeasRec["er_site_name"]
ResRec["er_site_names"]=MeasRec["er_site_name"]
SampRec["er_location_name"]=MeasRec["er_location_name"]
SpecRec["er_location_name"]=MeasRec["er_location_name"]
AnisRec["er_location_name"]=MeasRec["er_location_name"]
ResRec["er_location_names"]=MeasRec["er_location_name"]
if len(rec)>=3:
SampRec["sample_azimuth"],SampRec["sample_dip"]=rec[1],rec[2]
az,pl,igeo=float(rec[1]),float(rec[2]),1
if len(rec)==5:
SampRec["sample_bed_dip_direction"],SampRec["sample_bed_dip"]= '(%7.1f)'%(90.+float(rec[3])),(rec[4])
bed_az,bed_dip,itilt,igeo=90.+float(rec[3]),float(rec[4]),1,1
else:
for i in range(5):
k15.append(1e-6*float(rec[i])) # assume measurements in micro SI
if linecnt==4:
sbar,sigma,bulk=pmag.dok15_s(k15)
hpars=pmag.dohext(9,sigma,sbar)
MeasRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MeasRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
for i in range(15):
NewMeas=copy.deepcopy(MeasRec)
NewMeas["measurement_orient_phi"]='%7.1f' %(Decs[i])
NewMeas["measurement_orient_theta"]='%7.1f'% (Incs[i])
NewMeas["measurement_chi_volume"]='%12.10f'% (k15[i])
NewMeas["measurement_number"]='%i'% (i+1)
NewMeas["magic_experiment_name"]=rec[0]+":LP-AN-MS"
MeasRecs.append(NewMeas)
if SampRec['er_sample_name'] not in samplist:
SampRecs.append(SampRec)
samplist.append(SampRec['er_sample_name'])
SpecRecs.append(SpecRec)
AnisRec["anisotropy_type"]="AMS"
ResRec["anisotropy_type"]="AMS"
AnisRec["anisotropy_s1"]='%12.10f'%(sbar[0])
AnisRec["anisotropy_s2"]='%12.10f'%(sbar[1])
AnisRec["anisotropy_s3"]='%12.10f'%(sbar[2])
AnisRec["anisotropy_s4"]='%12.10f'%(sbar[3])
AnisRec["anisotropy_s5"]='%12.10f'%(sbar[4])
AnisRec["anisotropy_s6"]='%12.10f'%(sbar[5])
AnisRec["anisotropy_mean"]='%12.10f'%(bulk)
AnisRec["anisotropy_sigma"]='%12.10f'%(sigma)
AnisRec["anisotropy_unit"]='SI'
AnisRec["anisotropy_n"]='15'
AnisRec["anisotropy_tilt_correction"]='-1'
AnisRec["magic_method_codes"]='LP-X:AE-H:LP-AN-MS'
AnisRecs.append(AnisRec)
ResRec["magic_method_codes"]='LP-X:AE-H:LP-AN-MS'
ResRec["anisotropy_tilt_correction"]='-1'
ResRec["anisotropy_t1"]='%12.10f'%(hpars['t1'])
ResRec["anisotropy_t2"]='%12.10f'%(hpars['t2'])
ResRec["anisotropy_t3"]='%12.10f'%(hpars['t3'])
ResRec["anisotropy_fest"]='%12.10f'%(hpars['F'])
ResRec["anisotropy_ftest12"]='%12.10f'%(hpars['F12'])
ResRec["anisotropy_ftest23"]='%12.10f'%(hpars['F23'])
ResRec["anisotropy_v1_dec"]='%7.1f'%(hpars['v1_dec'])
ResRec["anisotropy_v2_dec"]='%7.1f'%(hpars['v2_dec'])
ResRec["anisotropy_v3_dec"]='%7.1f'%(hpars['v3_dec'])
ResRec["anisotropy_v1_inc"]='%7.1f'%(hpars['v1_inc'])
ResRec["anisotropy_v2_inc"]='%7.1f'%(hpars['v2_inc'])
ResRec["anisotropy_v3_inc"]='%7.1f'%(hpars['v3_inc'])
ResRec['anisotropy_v1_eta_dec']=ResRec['anisotropy_v2_dec']
ResRec['anisotropy_v1_eta_inc']=ResRec['anisotropy_v2_inc']
ResRec['anisotropy_v1_zeta_dec']=ResRec['anisotropy_v3_dec']
ResRec['anisotropy_v1_zeta_inc']=ResRec['anisotropy_v3_inc']
ResRec['anisotropy_v2_eta_dec']=ResRec['anisotropy_v1_dec']
ResRec['anisotropy_v2_eta_inc']=ResRec['anisotropy_v1_inc']
ResRec['anisotropy_v2_zeta_dec']=ResRec['anisotropy_v3_dec']
ResRec['anisotropy_v2_zeta_inc']=ResRec['anisotropy_v3_inc']
ResRec['anisotropy_v3_eta_dec']=ResRec['anisotropy_v1_dec']
ResRec['anisotropy_v3_eta_inc']=ResRec['anisotropy_v1_inc']
ResRec['anisotropy_v3_zeta_dec']=ResRec['anisotropy_v2_dec']
ResRec['anisotropy_v3_zeta_inc']=ResRec['anisotropy_v2_inc']
ResRec["anisotropy_v1_eta_semi_angle"]='%7.1f'%(hpars['e12'])
ResRec["anisotropy_v1_zeta_semi_angle"]='%7.1f'%(hpars['e13'])
ResRec["anisotropy_v2_eta_semi_angle"]='%7.1f'%(hpars['e12'])
ResRec["anisotropy_v2_zeta_semi_angle"]='%7.1f'%(hpars['e23'])
ResRec["anisotropy_v3_eta_semi_angle"]='%7.1f'%(hpars['e13'])
ResRec["anisotropy_v3_zeta_semi_angle"]='%7.1f'%(hpars['e23'])
ResRec["result_description"]='Critical F: '+hpars["F_crit"]+';Critical F12/F13: '+hpars["F12_crit"]
ResRecs.append(ResRec)
if igeo==1:
sbarg=pmag.dosgeo(sbar,az,pl)
hparsg=pmag.dohext(9,sigma,sbarg)
AnisRecG=copy.copy(AnisRec)
ResRecG=copy.copy(ResRec)
AnisRecG["anisotropy_s1"]='%12.10f'%(sbarg[0])
AnisRecG["anisotropy_s2"]='%12.10f'%(sbarg[1])
AnisRecG["anisotropy_s3"]='%12.10f'%(sbarg[2])
AnisRecG["anisotropy_s4"]='%12.10f'%(sbarg[3])
AnisRecG["anisotropy_s5"]='%12.10f'%(sbarg[4])
AnisRecG["anisotropy_s6"]='%12.10f'%(sbarg[5])
AnisRecG["anisotropy_tilt_correction"]='0'
ResRecG["anisotropy_tilt_correction"]='0'
ResRecG["anisotropy_v1_dec"]='%7.1f'%(hparsg['v1_dec'])
ResRecG["anisotropy_v2_dec"]='%7.1f'%(hparsg['v2_dec'])
ResRecG["anisotropy_v3_dec"]='%7.1f'%(hparsg['v3_dec'])
ResRecG["anisotropy_v1_inc"]='%7.1f'%(hparsg['v1_inc'])
ResRecG["anisotropy_v2_inc"]='%7.1f'%(hparsg['v2_inc'])
ResRecG["anisotropy_v3_inc"]='%7.1f'%(hparsg['v3_inc'])
ResRecG['anisotropy_v1_eta_dec']=ResRecG['anisotropy_v2_dec']
ResRecG['anisotropy_v1_eta_inc']=ResRecG['anisotropy_v2_inc']
ResRecG['anisotropy_v1_zeta_dec']=ResRecG['anisotropy_v3_dec']
ResRecG['anisotropy_v1_zeta_inc']=ResRecG['anisotropy_v3_inc']
ResRecG['anisotropy_v2_eta_dec']=ResRecG['anisotropy_v1_dec']
ResRecG['anisotropy_v2_eta_inc']=ResRecG['anisotropy_v1_inc']
ResRecG['anisotropy_v2_zeta_dec']=ResRecG['anisotropy_v3_dec']
ResRecG['anisotropy_v2_zeta_inc']=ResRecG['anisotropy_v3_inc']
ResRecG['anisotropy_v3_eta_dec']=ResRecG['anisotropy_v1_dec']
ResRecG['anisotropy_v3_eta_inc']=ResRecG['anisotropy_v1_inc']
ResRecG['anisotropy_v3_zeta_dec']=ResRecG['anisotropy_v2_dec']
ResRecG['anisotropy_v3_zeta_inc']=ResRecG['anisotropy_v2_inc']
ResRecG["result_description"]='Critical F: '+hpars["F_crit"]+';Critical F12/F13: '+hpars["F12_crit"]
ResRecs.append(ResRecG)
AnisRecs.append(AnisRecG)
if itilt==1:
sbart=pmag.dostilt(sbarg,bed_az,bed_dip)
hparst=pmag.dohext(9,sigma,sbart)
AnisRecT=copy.copy(AnisRec)
ResRecT=copy.copy(ResRec)
AnisRecT["anisotropy_s1"]='%12.10f'%(sbart[0])
AnisRecT["anisotropy_s2"]='%12.10f'%(sbart[1])
AnisRecT["anisotropy_s3"]='%12.10f'%(sbart[2])
AnisRecT["anisotropy_s4"]='%12.10f'%(sbart[3])
AnisRecT["anisotropy_s5"]='%12.10f'%(sbart[4])
AnisRecT["anisotropy_s6"]='%12.10f'%(sbart[5])
AnisRecT["anisotropy_tilt_correction"]='100'
ResRecT["anisotropy_v1_dec"]='%7.1f'%(hparst['v1_dec'])
ResRecT["anisotropy_v2_dec"]='%7.1f'%(hparst['v2_dec'])
ResRecT["anisotropy_v3_dec"]='%7.1f'%(hparst['v3_dec'])
ResRecT["anisotropy_v1_inc"]='%7.1f'%(hparst['v1_inc'])
ResRecT["anisotropy_v2_inc"]='%7.1f'%(hparst['v2_inc'])
ResRecT["anisotropy_v3_inc"]='%7.1f'%(hparst['v3_inc'])
ResRecT['anisotropy_v1_eta_dec']=ResRecT['anisotropy_v2_dec']
ResRecT['anisotropy_v1_eta_inc']=ResRecT['anisotropy_v2_inc']
ResRecT['anisotropy_v1_zeta_dec']=ResRecT['anisotropy_v3_dec']
ResRecT['anisotropy_v1_zeta_inc']=ResRecT['anisotropy_v3_inc']
ResRecT['anisotropy_v2_eta_dec']=ResRecT['anisotropy_v1_dec']
ResRecT['anisotropy_v2_eta_inc']=ResRecT['anisotropy_v1_inc']
ResRecT['anisotropy_v2_zeta_dec']=ResRecT['anisotropy_v3_dec']
ResRecT['anisotropy_v2_zeta_inc']=ResRecT['anisotropy_v3_inc']
ResRecT['anisotropy_v3_eta_dec']=ResRecT['anisotropy_v1_dec']
ResRecT['anisotropy_v3_eta_inc']=ResRecT['anisotropy_v1_inc']
ResRecT['anisotropy_v3_zeta_dec']=ResRecT['anisotropy_v2_dec']
ResRecT['anisotropy_v3_zeta_inc']=ResRecT['anisotropy_v2_inc']
ResRecT["anisotropy_tilt_correction"]='100'
ResRecT["result_description"]='Critical F: '+hpars["F_crit"]+';Critical F12/F13: '+hpars["F12_crit"]
ResRecs.append(ResRecT)
AnisRecs.append(AnisRecT)
k15,linecnt=[],0
MeasRec,SpecRec,SampRec,SiteRec,AnisRec={},{},{},{},{}
pmag.magic_write(sampfile,SampRecs,'er_samples')
pmag.magic_write(anisfile,AnisRecs,'rmag_anisotropy')
pmag.magic_write(resfile,ResRecs,'rmag_results')
pmag.magic_write(measfile,MeasRecs,'magic_measurements')
print "Data saved to: ",sampfile,anisfile,resfile,measfile
def main():
"""
NAME
ODP_srm_magic.py
DESCRIPTION
converts ODP measurement format files to magic_measurements format files
SYNTAX
ODP_srm_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsa FILE: specify output er_sample.txt file, default is er_sample.txt
-A : don't average replicate measurements
INPUT
put data from a single core into a directory. depths will be below core top
"""
#
#
version_num=pmag.get_version()
meas_file='magic_measurements.txt'
samp_file='er_samples.txt'
ErSpecs,ErSamps,ErSites,ErLocs,ErCits=[],[],[],[],[]
MagRecs=[]
citation="This study"
dir_path,demag='.','NRM'
args=sys.argv
noave=0,
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-A" in args: noave=1
if '-F' in args:
ind=args.index("-F")
meas_file=args[ind+1]
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file=args[ind+1]
if '-LP' in args:
ind=args.index("-LP")
codelist=args[ind+1]
codes=codelist.split(':')
if "AF" in codes:
demag='AF'
if'-dc' not in args: methcode="LT-AF-Z"
if'-dc' in args: methcode="LT-AF-I"
if "T" in codes:
demag="T"
if '-dc' not in args: methcode="LT-T-Z"
if '-dc' in args: methcode="LT-T-I"
if "I" in codes:
methcode="LP-IRM"
if "S" in codes:
demag="S"
methcode="LP-PI-TRM:LP-PI-ALT-AFARM"
trm_labfield=labfield
ans=raw_input("DC lab field for ARM step: [50uT] ")
if ans=="":
arm_labfield=50e-6
else:
arm_labfield=float(ans)*1e-6
ans=raw_input("temperature for total trm step: [600 C] ")
if ans=="":
trm_peakT=600+273 # convert to kelvin
else:
trm_peakT=float(ans)+273 # convert to kelvin
if "G" in codes: methcode="LT-AF-G"
if "D" in codes: methcode="LT-AF-D"
if "TRM" in codes:
demag="T"
trm=1
if demag=="T" and "ANI" in codes:
methcode="LP-AN-TRM"
if demag=="AF" and "ANI" in codes:
methcode="LP-AN-ARM"
if labfield==0: labfield=50e-6
if peakfield==0: peakfield=.180
samp_file=dir_path+'/'+samp_file
meas_file=dir_path+'/'+meas_file
filelist=os.listdir(dir_path) # read in list of files to import
specimens,samples,sites=[],[],[]
MagRecs,SpecRecs,SampRecs=[],[],[]
for file in filelist: # parse each file
if file[-3:].lower()=='srm':
print 'processing: ',file
Nfo=file.split('_')[0].split('-')
try:
sect=int(Nfo[3][:-1])
except:
sect=1
input=open(file,'rU').readlines()
MagRec,SpecRec,SampRec={},{},{}
alt_spec,treatment_type,treatment_value,user="","","",""
inst="ODP-SRM"
SampRec['sample_azimuth']='0'
SampRec['sample_dip']='0'
SampRec['magic_method_code']='FS-C-DRILL-IODP:SP-SS-C'
MagRec['er_analyst_mail_names']=user
MagRec['magic_method_codes']='LT-NO'
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["treatment_ac_field"]='0'
MagRec["treatment_dc_field"]='0'
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
MagRec["measurement_flag"]='g' # assume all data are "good"
MagRec["measurement_standard"]='u' # assume all data are "good"
MagRec["measurement_csd"]='' # set csd to blank
SpecRec['er_specimen_alternatives']=alt_spec
vol=7e-6 # assume 7 cc samples
datestamp=input[1].split() # date time is second line of file
mmddyy=datestamp[0].split('/') # break into month day year
date=mmddyy[2]+':'+mmddyy[0]+":"+mmddyy[1] +':' +datestamp[1]
MagRec["measurement_date"]=date
treatment_value,inst="","ODP-SRM"
k=0
while 1:
fields= input[k].replace('\n','').split("=")
if 'treatment_type' in fields[0]:
if "Alternating Frequency Demagnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst=inst+':ODP-DTECH' # measured on shipboard AF DTECH D2000
if "treatment_value" in fields[0]:
value=fields[1]
if value!=" ":
treatment_value=float(value)*1e-3
MagRec["treatment_ac_field"]='%8.3e'%(treatment_value) # AF demag in treat mT => T
if 'user' in fields[0]:
user=fields[-1]
MagRec["er_analyst_mail_names"]=user
MagRec["measurement_standard"]='u' # assume all data are "good"
if 'sample_area' in fields[0]: vol=float(fields[1])*1e-6 # takes volume (cc) and converts to m^3
if 'run_number' in fields[0]:
MagRec['external_database_ids']=fields[1] # run number is the LIMS measurement number
MagRec['external_database_names']='LIMS'
k+=1
if input[k][0:7]=='<MULTI>':
break
while 1:
k+=1
line = input[k]
if line[0:5]=='<RAW>':
break
treatment_value=""
rec=line.replace('\n','').split(',') # list of data
if len(rec)>2:
MeasRec,SampRec={},{'core_depth':'0','er_sample_name':'0','er_site_name':'0','er_location_name':'location'}
for key in MagRec.keys():MeasRec[key]=MagRec[key]
for item in rec:
items=item.split('=')
if 'demag_level' in items[0]:
treat= float(items[1])
if treat!=0:
MeasRec['magic_method_codes']='LT-AF-Z'
inst=inst+':ODP-SRM-AF'
MeasRec["treatment_ac_field"]='%8.3e'%(treat*1e-3) # AF demag in treat mT => T
if 'inclination_w_tray_w_bkgrd' in items[0]: MeasRec['measurement_inc']=items[1]
if 'declination_w_tray_w_bkgrd' in items[0]: MeasRec['measurement_dec']=items[1]
if 'intensity_w_tray_w_bkgrd' in items[0]: MeasRec['measurement_magn_moment']='%8.3e'%(float(items[1])*vol) # convert intensity from A/m to Am^2 using vol
MeasRec['magic_instrument_codes']=inst
if 'offset' in items[0]:
depth='%7.3f'%(float(sect-1)*1.5+float(items[1]))
SampRec['core_depth']=depth
MeasRec['er_specimen_name']=depth
MeasRec['er_sample_name']=depth
MeasRec['er_site_name']=depth
MeasRec['er_location_name']='location'
SampRec['er_sample_name']=depth
SampRec['er_site_name']=depth
SampRec['er_location_name']='location'
MeasRec['measurement_number']='1'
SampRecs.append(SampRec)
MagRecs.append(MeasRec)
pmag.magic_write(samp_file,SampRecs,'er_samples')
print 'samples stored in ',samp_file
Fixed=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(meas_file,Fixed,'magic_measurements')
print 'data stored in ',meas_file
def main():
"""
NAME
UMICH_magic.py
DESCRIPTION
converts UMICH .mag format files to magic_measurements format files
SYNTAX
UMICH_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify .mag format input file, required
-fsa SAMPFILE : specify er_samples.txt file relating samples, site and locations names,default is none
-F FILE: specify output file, default is magic_measurements.txt
-spc NUM : specify number of characters to designate a specimen, default = 0
-loc LOCNAME : specify location/study name, must have either LOCNAME or SAMPFILE or be a synthetic
-ncn NCON: specify naming convention: default is #1 below
-A: don't average replicate measurements
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
Format of UMICH .mag files:
Spec Treat CSD Intensity Declination Inclination metadata string
Spec: specimen name
Treat: treatment step
XXX T in Centigrade
XXX AF in mT
Intensity assumed to be total moment in 10^3 Am^2 (emu)
Declination: Declination in specimen coordinate system
Inclination: Declination in specimen coordinate system
metatdata string: mm/dd/yy;hh:mm;[dC,mT];xx.xx;UNITS;USER;INST;NMEAS
hh in 24 hours.
dC or mT units of treatment XXX (see Treat above) for thermal or AF respectively
xx.xxx DC field
UNITS of DC field (microT, mT)
INST: instrument code, number of axes, number of positions (e.g., G34 is 2G, three axes,
measured in four positions)
NMEAS: number of measurements in a single position (1,3,200...)
"""
# initialize some stuff
dir_path='.'
infile_type="mag"
noave=0
methcode,inst="",""
phi,theta,peakfield,labfield=0,0,0,0
pTRM,MD,samp_con,Z=0,0,'1',1
missing=1
demag="N"
er_location_name=""
citation='This study'
args=sys.argv
methcode="LP-NO"
samp_file,ErSamps='',[]
specnum=0
#
# get command line arguments
#
meas_file="magic_measurements.txt"
user=""
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=args[ind+1]
if '-F' in args:
ind=args.index("-F")
meas_file=dir_path+'/'+args[ind+1]
if '-f' in args:
ind=args.index("-f")
magfile=dir_path+'/'+args[ind+1]
try:
input=open(magfile,'rU')
except:
print "bad mag file name"
sys.exit()
else:
print "mag_file field is required option"
print main.__doc__
sys.exit()
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if specnum!=0:specnum=-specnum
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-fsa" in args:
ind=args.index("-fsa")
samp_file=dir_path+'/'+args[ind+1]
Samps,file_type=pmag.magic_read(samp_file)
if "-A" in args: noave=1
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
samp_con=sys.argv[ind+1]
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="7"
MagRecs,specs=[],[]
version_num=pmag.get_version()
if infile_type=="mag":
for line in input.readlines():
instcode=""
if len(line)>2:
MagRec={}
MagRec['er_location_name']=er_location_name
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["treatment_ac_field"]='0'
MagRec["treatment_dc_field"]='0'
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
meas_type="LT-NO"
rec=line.split()
labfield=0
code1=rec[6].split(';')
date=code1[0].split('/') # break date into mon/day/year
yy=int(date[2])
if yy <90:
yyyy=str(2000+yy)
else: yyyy=str(1900+yy)
mm=int(date[0])
if mm<10:
mm="0"+str(mm)
else: mm=str(mm)
dd=int(date[1])
if dd<10:
dd="0"+str(dd)
else: dd=str(dd)
time=code1[1].split(':')
hh=int(time[0])
if hh<10:
hh="0"+str(hh)
else: hh=str(hh)
min=int(time[1])
if min<10:
min= "0"+str(min)
else: min=str(min)
MagRec["measurement_date"]=yyyy+":"+mm+":"+dd+":"+hh+":"+min+":00.00"
MagRec["measurement_time_zone"]=''
instcode=''
if len(code1)>1:
MagRec["measurement_positions"]=code1[6][2]
else:
MagRec["measurement_positions"]=code1[7] # takes care of awkward format with bubba and flo being different
if user=="":user=code1[5]
if code1[2][-1]=='C': demag="T"
if code1[2]=='mT': demag="AF"
treat=rec[1].split('.')
if len(treat)==1:treat.append('0')
if demag=='T' and treat!=0:
meas_type="LT-T-Z"
MagRec["treatment_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
if demag=="AF":
meas_type="LT-AF-Z"
MagRec["treatment_ac_field"]='%8.3e' % (float(treat[0])*1e-3) # Af field in T
MagRec["treatment_dc_field"]='0'
MagRec["er_specimen_name"]=rec[0]
if rec[0] not in specs:specs.append(rec[0]) # get a list of specimen names
experiment=rec[0]+":"
MagRec["er_site_name"]=""
if specnum!=0:
MagRec["er_sample_name"]=rec[0][:specnum]
else:
MagRec["er_sample_name"]=rec[0]
if "-fsa" in args:
for samp in Samps:
if samp["er_sample_name"] == MagRec["er_sample_name"]:
MagRec["er_location_name"]=samp["er_location_name"]
MagRec["er_site_name"]=samp["er_site_name"]
break
elif int(samp_con)!=6:
site=pmag.parse_site(MagRec['er_sample_name'],samp_con,Z)
MagRec["er_site_name"]=site
if MagRec['er_site_name']=="":
print 'No site name found for: ',MagRec['er_specimen_name'],MagRec['er_sample_name']
if MagRec["er_location_name"]=="":
print 'no location name for: ',MagRec["er_specimen_name"]
if rec[1]==".00":rec[1]="0.00"
MagRec["measurement_csd"]=rec[2]
MagRec["measurement_magn_moment"]='%10.3e'% (float(rec[3])*1e-3) # moment in Am^2 (from emu)
MagRec["measurement_dec"]=rec[4]
MagRec["measurement_inc"]=rec[5]
MagRec["magic_instrument_codes"]=instcode
MagRec["er_analyst_mail_names"]=user
MagRec["er_citation_names"]=citation
MagRec["magic_method_codes"]=meas_type
MagRec["measurement_flag"]='g'
MagRec["er_specimen_name"]=rec[0]
MagRec["measurement_number"]='1'
MagRecs.append(MagRec)
MagOuts=[]
for spec in specs: # gather all demag types for this specimen
SpecRecs,meths,measnum=[],[],1
for rec in MagRecs:
if rec['er_specimen_name']==spec:
rec['measurement_number']=str(measnum)
measnum+=1
if rec['magic_method_codes'] not in meths:meths.append(rec['magic_method_codes'])
SpecRecs.append(rec)
expname=spec
if "LT-AF-Z" in meths:expname=expname+ ':LP-DIR-AF'
if "LT-T-Z" in meths:expname=expname+ ':LP-DIR-T'
for rec in SpecRecs:
rec['magic_experiment_name']=expname
MagOuts.append(rec)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print "results put in ",meas_file
