def main():
"""
NAME
s_tilt.py
DESCRIPTION
rotates .s data into stratigraphic coordinates using strike and dip
SYNTAX
s_tilt.py [-h][-i][-f file][<filename]
OPTIONS
-h prints help message and quits
-i allows interactive entry of file name
-f file specifies filename on command line
< filename, reads from standard input (Unix like operating systems only)
INPUT
x11 x22 x33 x12 x23 x13 strike dip
OUTPUT
x11 x22 x33 x12 x23 x13
"""
if '-h' in sys.argv:
print main.__doc__
sys.exit()
# read in the data
elif '-i' in sys.argv:
file=raw_input("Enter filename for processing: ")
f=open(file,'rU')
data=f.readlines()
f.close()
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()
for line in data:
s=[]
rec=line.split()
for i in range(6):
s.append(float(rec[i]))
bed_az,bed_dip=float(rec[6])+90.,float(rec[7]) #dip direction,dip
#
# get eigenvectors
#
s_rot=pmag.dostilt(s,bed_az,bed_dip)
outstring=""
for s in s_rot:outstring+='%10.8f '%(s)
print outstring
def main():
"""
NAME
kly4s_magic.py
DESCRIPTION
converts files generated by SIO kly4S labview program to MagIC formated
files for use with PmagPy plotting software
SYNTAX
kly4s_magic.py -h [command line options]
OPTIONS
-h: prints the help message and quits
-i: allows interactive input of input/output filenames
-f FILE: specify .ams input file name
-fad AZDIP: specify AZDIP file with orientations, will create er_samples.txt file
-fsa SFILE: specify existing er_samples.txt file with orientation information
-fsp SPFILE: specify existing er_specimens.txt file for appending
-F MFILE: specify magic_measurements output file
-Fa AFILE: specify rmag_anisotropy output file
-ocn ORCON: specify orientation convention: default is #3 below -only with AZDIP file
-usr USER: specify who made the measurements
-loc LOC: specify location name for study
-ins INST: specify instrument used
-spc SPEC: specify number of characters to specify specimen from sample
-ncn NCON: specify naming convention: default is #1 below
DEFAULTS
MFILE: magic_measurements.txt
AFILE: rmag_anisotropy.txt
SPFILE: create new er_specimen.txt file
USER: ""
LOC: "unknown"
INST: "SIO-KLY4S"
SPEC: 1 specimen name is same as sample (if SPEC is 1, sample is all but last character)
NOTES:
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] all others you will have to either customize your
self or e-mail [email protected] for help.
Orientation convention:
[1] Lab arrow azimuth= azimuth; Lab arrow dip=-dip
i.e., dip is degrees from vertical down - the hade [default]
[2] Lab arrow azimuth = azimuth-90; Lab arrow dip = -dip
i.e., azimuth is strike and dip is hade
[3] Lab arrow azimuth = azimuth; Lab arrow dip = dip-90
e.g. dip is degrees from horizontal of drill direction
[4] Lab arrow azimuth = azimuth; Lab arrow dip = dip
[5] Lab arrow azimuth = azimuth; Lab arrow dip = 90-dip
[6] all others you will have to either customize your
self or e-mail [email protected] for help.
"""
citation='This study'
cont=0
ask=0
samp_con,Z="1",1
or_con="3" # see orientation_magic.py help message
inst,specnum="SIO-KLY4S",0
AniRecs,SpecRecs,SampRecs,MeasRecs=[],[],[],[]
user,locname,specfile="","unknown","er_specimens.txt"
AppSpec=0
sampfile,measfile='','magic_measurements.txt'
anisfile='rmag_anisotropy.txt'
azdipfile=""
dir_path='.'
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-usr' in sys.argv:
ind=sys.argv.index('-usr')
user=sys.argv[ind+1]
if '-ocn' in sys.argv:
ind=sys.argv.index('-ocn')
or_con=sys.argv[ind+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 3-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
if '-f' in sys.argv:
ind=sys.argv.index('-f')
amsfile=sys.argv[ind+1]
else:
print main.__doc__
print 'must specify ascii input file '
sys.exit()
if '-F' in sys.argv:
ind=sys.argv.index('-F')
measfile=sys.argv[ind+1]
if '-Fa' in sys.argv:
ind=sys.argv.index('-Fa')
anisfile=sys.argv[ind+1]
if '-Fr' in sys.argv:
ind=sys.argv.index('-Fr')
routput=sys.argv[ind+1]
if '-fsa' in sys.argv:
ind=sys.argv.index('-fsa')
sampfile=sys.argv[ind+1]
if '-fsp' in sys.argv:
ind=sys.argv.index('-fsp')
specfile=sys.argv[ind+1]
AppSpec=1
if '-fad' in sys.argv:
ind=sys.argv.index('-fad')
azdipfile=dir_path+"/"+sys.argv[ind+1]
azfile=open(azdipfile,'rU')
AzDipDat=azfile.readlines()
if '-loc' in sys.argv:
ind=sys.argv.index('-loc')
locname=sys.argv[ind+1]
if '-spc' in sys.argv:
ind=sys.argv.index('-spc')
specnum=-(int(sys.argv[ind+1]))
#if specnum!=0:specnum=-specnum
specfile=dir_path+'/'+specfile
sampfile=dir_path+'/'+sampfile
measfile=dir_path+'/'+measfile
anisfile=dir_path+'/'+anisfile
amsfile=dir_path+'/'+amsfile
try:
input=open(amsfile,'rU')
except:
print 'Error opening file: ', amsfile
sys.exit()
SpecRecs,speclist=[],[]
if AppSpec==1:
try:
SpecRecs,filetype=pmag.magic_read(specfile) # append new records to existing
if len(SpecRecs)>0:
for spec in SpecRecs:
if spec['er_specimen_name'] not in speclist:speclist.append(spec['er_specimen_name'])
except IOError:
print 'trouble opening ',specfile
Data=input.readlines()
samps=[]
if sampfile!=dir_path+'/':
samps,file_type=pmag.magic_read(sampfile)
SO_methods=[]
for rec in samps:
if "magic_method_codes" in rec.keys():
methlist=rec["magic_method_codes"].replace(" ","").split(":")
for meth in methlist:
if "SO" in meth and "SO-POM" not in meth and "SO-GT5" not in meth and "SO-ASC" not in meth and "SO-BAD" not in meth:
if meth not in SO_methods: SO_methods.append(meth)
#
SO_priorities=pmag.set_priorities(SO_methods,ask)
for line in Data:
rec=line.split()
if len(rec)>0:
AniRec,SpecRec,SampRec,SiteRec,MeasRec={},{},{},{},{}
specname=rec[0]
if specnum!=0:
sampname=specname[:specnum]
else:
sampname=specname
site=pmag.parse_site(sampname,samp_con,Z)
AniRec['er_location_name']=locname
AniRec['er_citation_names']="This study"
AniRec['magic_instrument_codes']=inst
method_codes=['LP-X','AE-H','LP-AN-MS']
AniRec['magic_experiment_name']=specname+":"+"LP-AN-MS"
AniRec['er_analyst_mail_names']=user
AniRec['er_site_name']=site
AniRec['er_sample_name']=sampname
AniRec['er_specimen_name']=specname
labaz,labdip,bed_dip_direction,bed_dip="","","",""
if azdipfile!="":
for key in AniRec.keys():SampRec[key]=AniRec[key]
for oline in AzDipDat: # look for exact match first
orec=oline.replace('\n','').split()
if orec[0].upper() in specname.upper(): # we have a match
labaz,labdip=pmag.orient(float(orec[1]),float(orec[2]),or_con)
bed_dip_direction=float(orec[3])-90. # assume dip to right of strike
bed_dip=float(orec[4])
break
if labaz=="": # found no exact match - now look at sample level
for oline in AzDipDat:
orec=oline.split()
if orec[0].upper() == sampname.upper(): # we have a match
labaz,labdip=pmag.orient(float(orec[1]),float(orec[2]),or_con)
bed_dip_direction=float(orec[3])-90. # assume dip to right of strike
bed_dip=float(orec[4])
break
if labaz=="": # found no exact match - now look at sample level
print 'found no orientation data - will use specimen coordinates'
raw_input("<return> to continue")
else:
for key in AniRec.keys():SampRec[key]=AniRec[key]
SampRec['sample_azimuth']='%7.1f'%(labaz)
SampRec['sample_dip']='%7.1f'%(labdip)
SampRec['sample_bed_dip_direction']='%7.1f'%(bed_dip_direction)
SampRec['sample_bed_dip']='%7.1f'%(bed_dip)
SampRecs.append(SampRec)
elif sampfile!=dir_path+'/':
redo,p=1,0
orient={}
if len(SO_methods)==1:
az_type=SO_methods[0]
orient=pmag.find_samp_rec(AniRec["er_sample_name"],samps,az_type)
if orient['sample_azimuth']!="":
method_codes.append(az_type)
else:
print "no orientation data for ",AniRec["er_sample_name"],labaz
orient["sample_azimuth"]=""
orient["sample_dip"]=""
orient["sample_bed_dip_direction"]=""
orient["sample_bed_dip"]=""
noorient=1
method_codes.append("SO-NO")
redo=0
redo=0
while redo==1:
if p>=len(SO_priorities):
print "no orientation data for ",AniRec["er_sample_name"],labaz
orient["sample_azimuth"]=""
orient["sample_dip"]=""
orient["sample_bed_dip_direction"]=""
orient["sample_bed_dip"]=""
noorient=1
method_codes.append("SO-NO")
redo=0
else:
az_type=SO_methods[SO_methods.index(SO_priorities[p])]
orient=pmag.find_samp_rec(AniRec["er_sample_name"],samps,az_type)
if orient["sample_azimuth"] !="":
method_codes.append(az_type)
redo=0
noorient=0
p+=1
if orient['sample_azimuth']!="":labaz=float(orient['sample_azimuth'])
if orient['sample_dip']!="":labdip=float(orient['sample_dip'])
if "sample_bed_dip_direction" in orient.keys() and orient['sample_bed_dip_direction']!="": bed_dip_direction=float(orient['sample_bed_dip_direction'])
if "sample_bed_dip" in orient.keys() and orient['sample_bed_dip']!="": sample_bed_dip=float(orient['sample_bed_dip'])
for key in AniRec.keys():SpecRec[key]=AniRec[key]
for key in AniRec.keys():MeasRec[key]=AniRec[key]
AniRec['anisotropy_type']="AMS"
AniRec['anisotropy_n']="192"
AniRec['anisotropy_s1']=rec[1]
AniRec['anisotropy_s2']=rec[2]
AniRec['anisotropy_s3']=rec[3]
AniRec['anisotropy_s4']=rec[4]
AniRec['anisotropy_s5']=rec[5]
AniRec['anisotropy_s6']=rec[6]
AniRec['anisotropy_sigma']=rec[7]
AniRec['anisotropy_tilt_correction']='-1'
AniRec['anisotropy_unit']='Normalized by trace'
SpecRec['specimen_volume']='%8.3e'%(1e-6*float(rec[12])) # volume from cc to m^3
MeasRec['measurement_flag']='g' # good
MeasRec['measurement_standard']='u' # unknown
date=rec[14].split('/')
if int(date[2])>80:
date[2]='19'+date[2]
else:
date[2]='20'+date[2]
datetime=date[2]+':'+date[0]+':'+date[1]+":"
datetime=datetime+rec[15]
MeasRec['measurement_number']='1'
MeasRec['measurement_date']=datetime
MeasRec['measurement_lab_field_ac']='%8.3e'%(4*math.pi*1e-7*float(rec[11])) # convert from A/m to T
MeasRec['measurement_temp']="300" # assumed room T in kelvin
MeasRec['measurement_chi_volume']=rec[8]
MeasRec['measurement_description']='Bulk measurement'
MeasRec['magic_method_codes']='LP-X'
if SpecRec['er_specimen_name'] not in speclist: # add to list
speclist.append(SpecRec['er_specimen_name'])
SpecRecs.append(SpecRec)
MeasRecs.append(MeasRec)
methods=""
for meth in method_codes:
methods=methods+meth+":"
AniRec["magic_method_codes"]=methods[:-1] # get rid of annoying spaces in Anthony's export files
AniRecs.append(AniRec)
if labaz!="": # have orientation info
AniRecG,AniRecT={},{}
for key in AniRec.keys():AniRecG[key]=AniRec[key]
for key in AniRec.keys():AniRecT[key]=AniRec[key]
sbar=[]
sbar.append(float(AniRec['anisotropy_s1']))
sbar.append(float(AniRec['anisotropy_s2']))
sbar.append(float(AniRec['anisotropy_s3']))
sbar.append(float(AniRec['anisotropy_s4']))
sbar.append(float(AniRec['anisotropy_s5']))
sbar.append(float(AniRec['anisotropy_s6']))
sbarg=pmag.dosgeo(sbar,labaz,labdip)
AniRecG["anisotropy_s1"]='%12.10f'%(sbarg[0])
AniRecG["anisotropy_s2"]='%12.10f'%(sbarg[1])
AniRecG["anisotropy_s3"]='%12.10f'%(sbarg[2])
AniRecG["anisotropy_s4"]='%12.10f'%(sbarg[3])
AniRecG["anisotropy_s5"]='%12.10f'%(sbarg[4])
AniRecG["anisotropy_s6"]='%12.10f'%(sbarg[5])
AniRecG["anisotropy_tilt_correction"]='0'
AniRecs.append(AniRecG)
if bed_dip!="" and bed_dip!=0: # have tilt correction
sbart=pmag.dostilt(sbarg,bed_dip_direction,bed_dip)
AniRecT["anisotropy_s1"]='%12.10f'%(sbart[0])
AniRecT["anisotropy_s2"]='%12.10f'%(sbart[1])
AniRecT["anisotropy_s3"]='%12.10f'%(sbart[2])
AniRecT["anisotropy_s4"]='%12.10f'%(sbart[3])
AniRecT["anisotropy_s5"]='%12.10f'%(sbart[4])
AniRecT["anisotropy_s6"]='%12.10f'%(sbart[5])
AniRecT["anisotropy_tilt_correction"]='100'
AniRecs.append(AniRecT)
pmag.magic_write(anisfile,AniRecs,'rmag_anisotropy')
pmag.magic_write(measfile,MeasRecs,'magic_measurements')
pmag.magic_write(specfile,SpecRecs,'er_specimens')
print 'anisotropy data saved in ',anisfile
print 'measurement data saved in ',measfile
if AppSpec==1:
print 'new specimen information added to ',specfile
else:
print 'specimen information saved in new ',specfile
if azdipfile!="":
sampfile='er_samples.txt'
pmag.magic_write(sampfile,SampRecs,'er_samples')
print 'sample data saved in ',sampfile
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,[]
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
sufar4-asc_magic.py
DESCRIPTION
converts ascii files generated by SUFAR ver.4.0 to MagIC formated
files for use with PmagPy plotting software
SYNTAX
sufar4-asc_magic.py -h [command line options]
OPTIONS
-h: prints the help message and quits
-f FILE: specify .asc input file name
-F MFILE: specify magic_measurements output file
-Fa AFILE: specify rmag_anisotropy output file
-Fr RFILE: specify rmag_results output file
-Fs SFILE: specify er_specimens output file with location, sample, site, etc. information
-usr USER: specify who made the measurements
-loc LOC: specify location name for study
-ins INST: specify instrument used
-spc SPEC: specify number of characters to specify specimen from sample
-ncn NCON: specify naming convention: default is #2 below
-k15 : specify static 15 position mode - default is spinning
-new : replace all existing magic files
DEFAULTS
AFILE: rmag_anisotropy.txt
RFILE: rmag_results.txt
SFILE: default is to create new er_specimen.txt file
USER: ""
LOC: "unknown"
INST: ""
SPEC: 0 sample name is same as site (if SPEC is 1, sample is all but last character)
appends to 'er_specimens.txt, er_samples.txt, er_sites.txt' files
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] This is a synthetic
[9] ODP naming convention
"""
citation = "This study"
cont = 0
samp_con, Z = "1", 1
AniRecSs, AniRecs, SpecRecs, SampRecs, SiteRecs, MeasRecs = [], [], [], [], [], []
user, locname, specfile = "", "unknown", "er_specimens.txt"
isspec, inst, specnum = "0", "", 0
spin, new = 1, 0
dir_path = "."
if "-WD" in sys.argv:
ind = sys.argv.index("-WD")
dir_path = sys.argv[ind + 1]
aoutput, routput, moutput = (
dir_path + "/rmag_anisotropy.txt",
dir_path + "/rmag_results.txt",
dir_path + "/magic_measurements.txt",
)
if "-h" in sys.argv:
print main.__doc__
sys.exit()
if "-usr" in sys.argv:
ind = sys.argv.index("-usr")
user = sys.argv[ind + 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 "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 "-k15" in sys.argv:
spin = 0
if "-ins" in sys.argv:
ind = sys.argv.index("-ins")
inst = sys.argv[ind + 1]
if "-f" in sys.argv:
ind = sys.argv.index("-f")
ascfile = dir_path + "/" + sys.argv[ind + 1]
if "-F" in sys.argv:
ind = sys.argv.index("-F")
moutput = dir_path + "/" + sys.argv[ind + 1]
if "-Fa" in sys.argv:
ind = sys.argv.index("-Fa")
aoutput = dir_path + "/" + sys.argv[ind + 1]
if "-Fr" in sys.argv:
ind = sys.argv.index("-Fr")
routput = dir_path + "/" + sys.argv[ind + 1]
if "-Fs" in sys.argv:
ind = sys.argv.index("-Fs")
specfile = dir_path + "/" + sys.argv[ind + 1]
isspec = "1"
elif "-loc" in sys.argv:
ind = sys.argv.index("-loc")
locname = sys.argv[ind + 1]
if "-spc" in sys.argv:
ind = sys.argv.index("-spc")
specnum = -(int(sys.argv[ind + 1]))
if specnum != 0:
specnum = -specnum
if isspec == "1":
specs, file_type = pmag.magic_read(specfile)
specnames, sampnames, sitenames = [], [], []
if "-new" not in sys.argv: # see if there are already specimen,sample, site files lying around
try:
SpecRecs, file_type = pmag.magic_read(dir_path + "/er_specimens.txt")
for spec in SpecRecs:
if spec["er_specimen_name"] not in specnames:
specnames.append(samp["er_specimen_name"])
except:
SpecRecs, specs = [], []
try:
SampRecs, file_type = pmag.magic_read(dir_path + "/er_samples.txt")
for samp in SampRecs:
if samp["er_sample_name"] not in sampnames:
sampnames.append(samp["er_sample_name"])
except:
sampnames, SampRecs = [], []
try:
SiteRecs, file_type = pmag.magic_read(dir_path + "/er_sites.txt")
for site in SiteRecs:
if site["er_site_names"] not in sitenames:
sitenames.append(site["er_site_name"])
except:
sitenames, SiteRecs = [], []
try:
input = open(ascfile, "rU")
except:
print "Error opening file: ", ascfile
Data = input.readlines()
k = 0
while k < len(Data):
line = Data[k]
words = line.split()
if "ANISOTROPY" in words: # first line of data for the spec
MeasRec, AniRec, SpecRec, SampRec, SiteRec = {}, {}, {}, {}, {}
specname = words[0]
AniRec["er_specimen_name"] = specname
if isspec == "1":
for spec in specs:
if spec["er_specimen_name"] == specname:
AniRec["er_sample_name"] = spec["er_sample_name"]
AniRec["er_site_name"] = spec["er_site_name"]
AniRec["er_location_name"] = spec["er_location_name"]
break
elif isspec == "0":
if specnum != 0:
sampname = specname[:specnum]
else:
sampname = specname
AniRec["er_sample_name"] = sampname
SpecRec["er_specimen_name"] = specname
SpecRec["er_sample_name"] = sampname
SampRec["er_sample_name"] = sampname
SiteRec["er_sample_name"] = sampname
SiteRec["site_description"] = "s"
if samp_con != "9":
AniRec["er_site_name"] = pmag.parse_site(AniRec["er_sample_name"], samp_con, Z)
SpecRec["er_site_name"] = pmag.parse_site(AniRec["er_sample_name"], samp_con, Z)
SampRec["er_site_name"] = pmag.parse_site(AniRec["er_sample_name"], samp_con, Z)
SiteRec["er_site_name"] = pmag.parse_site(AniRec["er_sample_name"], samp_con, Z)
else:
AniRec["er_site_name"] = specname
SpecRec["er_site_name"] = specname
SampRec["er_site_name"] = specname
SiteRec["er_site_name"] = specname
pieces = specname.split("-")
AniRec["er_expedition_name"] = pieces[0]
SpecRec["er_expedition_name"] = pieces[0]
SampRec["er_expedition_name"] = pieces[0]
SiteRec["er_expedition_name"] = pieces[0]
location = pieces[1]
AniRec["er_location_name"] = locname
SpecRec["er_location_name"] = locname
SampRec["er_location_name"] = locname
SiteRec["er_location_name"] = locname
AniRec["er_citation_names"] = "This study"
SpecRec["er_citation_names"] = "This study"
SampRec["er_citation_names"] = "This study"
SiteRec["er_citation_names"] = "This study"
AniRec["er_citation_names"] = "This study"
AniRec["magic_instrument_codes"] = inst
AniRec["magic_method_codes"] = "LP-X:AE-H:LP-AN-MS"
AniRec["magic_experiment_names"] = specname + ":" + "LP-AN-MS"
AniRec["er_analyst_mail_names"] = user
for key in AniRec.keys():
MeasRec[key] = AniRec[key]
MeasRec["measurement_flag"] = "g"
AniRec["anisotropy_flag"] = "g"
MeasRec["measurement_standard"] = "u"
MeasRec["measurement_description"] = "Bulk sucsecptibility measurement"
AniRec["anisotropy_type"] = "AMS"
AniRec["anisotropy_unit"] = "Normalized by trace - bulk in measurements table"
if spin == 1:
AniRec["anisotropy_n"] = "192"
else:
AniRec["anisotropy_n"] = "15"
if "Azi" in words and isspec == "0":
SampRec["sample_azimuth"] = words[1]
labaz = float(words[1])
if "Dip" in words:
SampRec["sample_dip"] = "%7.1f" % (-float(words[1]))
SpecRec["specimen_vol"] = "%8.3e" % (float(words[10]) * 1e-6) # convert actual volume to m^3 from cm^3
labdip = float(words[1])
if "T1" in words and "F1" in words:
k += 2 # read in fourth line down
line = Data[k]
rec = line.split()
dd = rec[1].split("/")
dip_direction = int(dd[0]) + 90
SampRec["sample_bed_dip_direction"] = "%i" % (dip_direction)
SampRec["sample_bed_dip"] = dd[1]
bed_dip = float(dd[1])
if "Mean" in words:
k += 4 # read in fourth line down
line = Data[k]
rec = line.split()
MeasRec["measurement_chi_volume"] = rec[1]
sigma = 0.01 * float(rec[2]) / 3.0
AniRec["anisotropy_sigma"] = "%7.4f" % (sigma)
AniRec["anisotropy_unit"] = "SI"
if "factors" in words:
k += 4 # read in second line down
line = Data[k]
rec = line.split()
if "Specimen" in words: # first part of specimen data
AniRec["anisotropy_s1"] = "%7.4f" % (float(words[5]) / 3.0) # eigenvalues sum to unity - not 3
AniRec["anisotropy_s2"] = "%7.4f" % (float(words[6]) / 3.0)
AniRec["anisotropy_s3"] = "%7.4f" % (float(words[7]) / 3.0)
k += 1
line = Data[k]
rec = line.split()
AniRec["anisotropy_s4"] = "%7.4f" % (float(rec[5]) / 3.0) # eigenvalues sum to unity - not 3
AniRec["anisotropy_s5"] = "%7.4f" % (float(rec[6]) / 3.0)
AniRec["anisotropy_s6"] = "%7.4f" % (float(rec[7]) / 3.0)
AniRec["anisotropy_tilt_correction"] = "-1"
AniRecs.append(AniRec)
AniRecG, AniRecT = {}, {}
for key in AniRec.keys():
AniRecG[key] = AniRec[key]
for key in AniRec.keys():
AniRecT[key] = AniRec[key]
sbar = []
sbar.append(float(AniRec["anisotropy_s1"]))
sbar.append(float(AniRec["anisotropy_s2"]))
sbar.append(float(AniRec["anisotropy_s3"]))
sbar.append(float(AniRec["anisotropy_s4"]))
sbar.append(float(AniRec["anisotropy_s5"]))
sbar.append(float(AniRec["anisotropy_s6"]))
sbarg = pmag.dosgeo(sbar, labaz, labdip)
AniRecG["anisotropy_s1"] = "%12.10f" % (sbarg[0])
AniRecG["anisotropy_s2"] = "%12.10f" % (sbarg[1])
AniRecG["anisotropy_s3"] = "%12.10f" % (sbarg[2])
AniRecG["anisotropy_s4"] = "%12.10f" % (sbarg[3])
AniRecG["anisotropy_s5"] = "%12.10f" % (sbarg[4])
AniRecG["anisotropy_s6"] = "%12.10f" % (sbarg[5])
AniRecG["anisotropy_tilt_correction"] = "0"
AniRecs.append(AniRecG)
if bed_dip != "" and bed_dip != 0: # have tilt correction
sbart = pmag.dostilt(sbarg, dip_direction, bed_dip)
AniRecT["anisotropy_s1"] = "%12.10f" % (sbart[0])
AniRecT["anisotropy_s2"] = "%12.10f" % (sbart[1])
AniRecT["anisotropy_s3"] = "%12.10f" % (sbart[2])
AniRecT["anisotropy_s4"] = "%12.10f" % (sbart[3])
AniRecT["anisotropy_s5"] = "%12.10f" % (sbart[4])
AniRecT["anisotropy_s6"] = "%12.10f" % (sbart[5])
AniRecT["anisotropy_tilt_correction"] = "100"
AniRecs.append(AniRecT)
MeasRecs.append(MeasRec)
if SpecRec["er_specimen_name"] not in specnames:
SpecRecs.append(SpecRec)
specnames.append(SpecRec["er_specimen_name"])
if SampRec["er_sample_name"] not in sampnames:
SampRecs.append(SampRec)
sampnames.append(SampRec["er_sample_name"])
if SiteRec["er_site_name"] not in sitenames:
SiteRecs.append(SiteRec)
sitenames.append(SiteRec["er_site_name"])
k += 1 # skip to next specimen
pmag.magic_write(aoutput, AniRecs, "rmag_anisotropy")
print "anisotropy tensors put in ", aoutput
pmag.magic_write(moutput, MeasRecs, "magic_measurements")
print "bulk measurements put in ", moutput
if isspec == "0":
SpecOut, keys = pmag.fillkeys(SpecRecs)
output = dir_path + "/er_specimens.txt"
pmag.magic_write(output, SpecOut, "er_specimens")
print "specimen info put in ", output
output = dir_path + "/er_samples.txt"
SampOut, keys = pmag.fillkeys(SampRecs)
pmag.magic_write(output, SampOut, "er_samples")
print "sample info put in ", output
output = dir_path + "/er_sites.txt"
SiteOut, keys = pmag.fillkeys(SiteRecs)
pmag.magic_write(output, SiteOut, "er_sites")
print "site info put in ", output
print """"
