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
k15_s.py
DESCRIPTION
converts .k15 format data to .s format.
assumes Jelinek Kappabridge measurement scheme
SYNTAX
k15_s.py [-h][-i][command line options][<filename]
OPTIONS
-h prints help message and quits
-i allows interactive entry of options
-f FILE, specifies input file, default: standard input
-F FILE, specifies output file, default: standard output
-crd [g, t] specifies [g]eographic rotation,
or geographic AND tectonic rotation
INPUT
name [az,pl,strike,dip], followed by
3 rows of 5 measurements for each specimen
OUTPUT
least squares matrix elements and sigma:
x11,x22,x33,x12,x23,x13,sigma
"""
firstline,itilt,igeo,linecnt,key=1,0,0,0,""
out=""
data,k15=[],[]
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-i' in sys.argv:
file=raw_input("Input file name [.k15 format]: ")
f=open(file,'rU')
data=f.readlines()
f.close()
file=raw_input("Output file name [.s format]: ")
out=open(file,'w')
print (" [g]eographic, [t]ilt corrected, ")
tg=raw_input(" [return for specimen coordinates]: ")
if tg=='g':
igeo=1
elif tg=='t':
igeo,itilt=1,1
elif '-f' in sys.argv:
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
f=open(file,'rU')
data=f.readlines()
f.close()
else:
data= sys.stdin.readlines()
if len(data)==0:
print main.__doc__
sys.exit()
if '-F' in sys.argv:
ind=sys.argv.index('-F')
file=sys.argv[ind+1]
out=open(file,'w')
if '-crd' in sys.argv:
ind=sys.argv.index('-crd')
tg=sys.argv[ind+1]
if tg=='g':igeo=1
if tg=='t': igeo,itilt=1,1
for line in data:
rec=line.split()
if firstline==1:
firstline=0
nam=rec[0]
if igeo==1: az,pl=float(rec[1]),float(rec[2])
if itilt==1: bed_az,bed_dip=90.+float(rec[3]),float(rec[4])
else:
linecnt+=1
for i in range(5):
k15.append(float(rec[i]))
if linecnt==3:
sbar,sigma,bulk=pmag.dok15_s(k15)
if igeo==1: sbar=pmag.dosgeo(sbar,az,pl)
if itilt==1: sbar=pmag.dostilt(sbar,bed_az,bed_dip)
outstring=""
for s in sbar:outstring+='%10.8f '%(s)
outstring+='%10.8f'%(sigma)
if out=="":
print outstring
else:
out.write(outstring+'\n')
linecnt,firstline,k15=0,1,[]