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
UB_magic.py
DESCRIPTION
takes University of Barcelona format magnetometer files and converts them to magic_measurements and er_samples.txt
SYNTAX
UB_magic.py [command line options]
OPTIONS
-f FILE: specify master txt file
-fpos FILE: specify stratigraphic position file (.saf format)
-F FILE: specify magic_measurements output file, default is: magic_measurements.txt
-Fsa FILE: specify output file, default is: er_samples.txt
-ncn NCON: specify naming convention: default is #2 below
-ocn OCON: specify orientation convention, default is #5 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
SO-SUN orientation with sun compass
-loc: location name, default="unknown"
-spc NUM : specify number of characters to designate a specimen, default = 0
-ins INST : specify instsrument name
-a: average replicate measurements
INPUT FORMAT
Input files are horrible 2G binary format (who knows why?)
Orientation convention:
[1] Lab arrow azimuth= mag_azimuth; Lab arrow dip=-field_dip
i.e., field_dip is degrees from vertical down - the hade [default]
[2] Lab arrow azimuth = mag_azimuth-90; Lab arrow dip = -field_dip
i.e., mag_azimuth is strike and field_dip is hade
[3] Lab arrow azimuth = mag_azimuth; Lab arrow dip = 90-field_dip
e.g. field_dip is degrees from horizontal of drill direction
[4] lab azimuth and dip are same as mag_azimuth, field_dip
[5] lab azimuth and dip are same as mag_azimuth, field_dip-90
[6] all others you will have to either customize your
self or e-mail [email protected] for help.
Magnetic declination convention:
Az will use supplied declination to correct azimuth
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.
OUTPUT
output saved in magic_measurements.txt & er_samples.txt formatted files
will overwrite any existing files
"""
#
# initialize variables
#
specnum=0
ub_file,samp_file,or_con,corr,meas_file = "","er_samples.txt","3","1","magic_measurements.txt"
pos_file=""
noave=1
args=sys.argv
bed_dip,bed_dip_dir="",""
samp_con,Z,average_bedding="2",1,"0"
meths='FS-FD'
sclass,lithology,type="","",""
user,inst="",""
DecCorr=0.
location_name="unknown"
months=['Jan','Feb','Mar','Apr','May','Jun','Jul','Aug','Sep','Oct','Nov','Dec']
gmeths=""
#
#
dir_path='.'
if '-WD' in args:
ind=args.index("-WD")
dir_path=sys.argv[ind+1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-f" in args:
ind=args.index("-f")
ub_file=sys.argv[ind+1]
if "-fpos" in args:
ind=args.index("-fpos")
pos_file=sys.argv[ind+1]
if "-F" in args:
ind=args.index("-F")
meas_file=sys.argv[ind+1]
if "-Fsa" in args:
ind=args.index("-Fsa")
samp_file=sys.argv[ind+1]
if "-ocn" in args:
ind=args.index("-ocn")
or_con=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 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 "-mcd" in args:
ind=args.index("-mcd")
gmeths=(sys.argv[ind+1])
if "-loc" in args:
ind=args.index("-loc")
location_name=(sys.argv[ind+1])
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if specnum!=0:specnum=-specnum
if "-ins" in args:
ind=args.index("-ins")
inst=args[ind+1]
if "-a" in args:noave=0
#
#
ub_file=dir_path+'/'+ub_file
if pos_file!="":pos_file=dir_path+'/'+pos_file
samp_file=dir_path+'/'+samp_file
meas_file=dir_path+'/'+meas_file
samplist=[]
try:
SampOut,file_type=pmag.magic_read(samp_file)
for rec in SampOut:
if samp['er_sample_name'] not in samplist: samplist.append(samp['er_sample_name'])
except:
SampOut=[]
PosData=[]
if pos_file != "":
p=open(pos_file,'rU')
PosIn=p.readlines()
p.close()
for line in PosIn:
srec=line.split()[0].split(',')
Prec={'er_site_name':srec[0],'sample_height':srec[1]}
PosData.append(Prec)
mastfile=open(ub_file,'rU')
Files=mastfile.readlines()
mastfile.close()
MagRecs,SampRecs=[],[]
for file in Files:
cfile=file.split()[0]
if cfile!='end':
cfile=dir_path+'/'+file.split()[0]+'.dat'
f=open(cfile,'rU')
input=f.read()
f.close()
firstline=1
d=input.split('\xcd')
for line in d:
rec=line.split('\x00')
if firstline==1:
firstline=0
specname,vol="",1
for c in line[15:23]:
if c!='\x00':specname=specname+c
print 'importing ',specname
el=9
while rec[el]!='\x01':el+=1
vcc,date,comment=rec[el-3],rec[el+7],rec[el+8]
el+=10
while rec[el]=="":el+=1
az=float(rec[el])
el+=1
while rec[el]=="":el+=1
pl=float(rec[el])
el+=1
while rec[el]=="":el+=1
bed_dip_dir=float(rec[el])
el+=1
while rec[el]=="":el+=1
bed_dip=float(rec[el])
el+=1
while rec[el]=="":el+=1
if rec[el]=='\x01':
bed_dip=180.-bed_dip
el+=1
while rec[el]=="":el+=1
fold_az=float(rec[el])
el+=1
while rec[el]=="":el+=1
fold_pl=rec[el]
el+=1
while rec[el]=="":el+=1
if rec[el]!="":
deccorr=float(rec[el])
az+=deccorr
bed_dip_dir+=deccorr
fold_az+=deccorr
if bed_dip_dir>=360:bed_dip_dir=bed_dip_dir-360.
if az>=360.:az=az-360.
if fold_az>=360.:fold_az=fold_az-360.
else:
deccorr=0
if specnum!=0:
sample=specname[:specnum]
else:
sample=specname
if sample not in samplist:
samplist.append(sample)
SampRec={}
SampRec["er_sample_name"]=sample
SampRec["er_location_name"]=location_name
SampRec["er_citation_names"]="This study"
labaz,labdip=pmag.orient(az,pl,or_con) # convert to labaz, labpl
#
# parse information common to all orientation methods
#
SampRec["sample_bed_dip"]='%7.1f'%(bed_dip)
SampRec["sample_bed_dip_direction"]='%7.1f'%(bed_dip_dir)
SampRec["sample_dip"]='%7.1f'%(labdip)
SampRec["sample_azimuth"]='%7.1f'%(labaz)
if vcc!="":vol=float(vcc)*1e-6 # convert to m^3 from cc
SampRec["sample_volume"]='%10.3e'%(vol) #
SampRec["sample_class"]=sclass
SampRec["sample_lithology"]=lithology
SampRec["sample_type"]=type
SampRec["sample_declination_correction"]='%7.1f'%(deccorr)
methods=gmeths.split(':')
if deccorr!="0":
if 'SO-MAG' in methods:del methods[methods.index('SO-MAG')]
methods.append('SO-CMD-NORTH')
meths=""
for meth in methods:meths=meths+meth+":"
meths=meths[:-1]
SampRec["magic_method_codes"]=meths
site=pmag.parse_site(SampRec["er_sample_name"],samp_con,Z) # parse out the site name
SampRec["er_site_name"]=site
#
# find position data
#
if PosData!=[]:
SampRec['sample_height']=""
for srec in PosData:
if srec['er_site_name']==site:
SampRec['sample_height']=srec['sample_height']
break
SampOut.append(SampRec)
else:
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"]=specname
MagRec["er_sample_name"]=SampRec['er_sample_name']
MagRec["er_site_name"]=SampRec['er_site_name']
MagRec["er_location_name"]=location_name
el,demag=1,''
treat=rec[el]
if treat[-1]=='C':
demag='T'
elif treat!='NRM':
demag='AF'
el+=1
while rec[el]=="":el+=1
MagRec["measurement_dec"]=rec[el]
cdec=float(rec[el])
el+=1
while rec[el]=="":el+=1
MagRec["measurement_inc"]=rec[el]
cinc=float(rec[el])
el+=1
while rec[el]=="":el+=1
gdec=rec[el]
el+=1
while rec[el]=="":el+=1
ginc=rec[el]
el=skip(2,el,rec) # skip bdec,binc
# el=skip(4,el,rec) # skip gdec,ginc,bdec,binc
# print 'moment emu: ',rec[el]
MagRec["measurement_magn_moment"]='%10.3e'% (float(rec[el])*1e-3) # moment in Am^2 (from emu)
MagRec["measurement_magn_volume"]='%10.3e'% (float(rec[el])*1e-3/vol) # magnetization in A/m
el=skip(2,el,rec) # skip to xsig
MagRec["measurement_sd_x"]='%10.3e'% (float(rec[el])*1e-3) # convert from emu
el=skip(3,el,rec) # skip to ysig
MagRec["measurement_sd_y"]='%10.3e'% (float(rec[el])*1e-3) # convert from emu
el=skip(3,el,rec) # skip to zsig
MagRec["measurement_sd_z"]='%10.3e'% (float(rec[el])*1e-3) # convert from emu
el+=1 # skip to positions
MagRec["measurement_positions"]=rec[el]
el=skip(5,el,rec) # skip to date
date=rec[el].split()
mm=str(months.index(date[0]))
if len(mm)==1:
mm='0'+str(mm)
else:
mm=str(mm)
dstring=date[2]+':'+mm+':'+date[1]+":"+date[3]
MagRec['measurement_date']=dstring
MagRec["magic_instrument_codes"]=inst
MagRec["er_analyst_mail_names"]="unknown"
MagRec["er_citation_names"]="This study"
MagRec["magic_method_codes"]=meas_type
if demag=="AF":
MagRec["treatment_ac_field"]='%8.3e' %(float(treat[:-2])*1e-3) # peak field in tesla
meas_type="LT-AF-Z"
MagRec["treatment_dc_field"]='0'
elif demag=="T":
MagRec["treatment_temp"]='%8.3e' % (float(treat[:-1])+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 "Measurements put in ",meas_file
pmag.magic_write(samp_file,SampOut,"er_samples")
print "Sample orientation info saved in ", samp_file
print "Good bye"
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
2G_bin_magic.py
DESCRIPTION
takes the binary 2G format magnetometer files and converts them to magic_measurements, er_samples.txt and er_sites.txt file
SYNTAX
2G_magic.py [command line options]
OPTIONS
-f FILE: specify input 2G (binary) file
-F FILE: specify magic_measurements output file, default is: magic_measurements.txt
-Fsa FILE: specify output file, default is: er_samples.txt
-Fsi FILE: specify output file, default is: er_sies.txt
-ncn NCON: specify naming convention: default is #2 below
-ocn OCON: specify orientation convention, default is #5 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
SO-SUN orientation with sun compass
-loc: location name, default="unknown"
-spc NUM : specify number of characters to designate a specimen, default = 0
-ins INST : specify instsrument name
-a: average replicate measurements
INPUT FORMAT
Input files are horrible mag binary format (who knows why?)
Orientation convention:
[1] Lab arrow azimuth= mag_azimuth; Lab arrow dip=-field_dip
i.e., field_dip is degrees from vertical down - the hade [default]
[2] Lab arrow azimuth = mag_azimuth-90; Lab arrow dip = -field_dip
i.e., mag_azimuth is strike and field_dip is hade
[3] Lab arrow azimuth = mag_azimuth; Lab arrow dip = 90-field_dip
i.e., lab arrow same as field arrow, but field_dip was a hade.
[4] lab azimuth and dip are same as mag_azimuth, field_dip
[5] lab azimuth is same as mag_azimuth,lab arrow dip=field_dip-90
[6] Lab arrow azimuth = mag_azimuth-90; Lab arrow dip = 90-field_dip
[7] all others you will have to either customize your
self or e-mail [email protected] for help.
Magnetic declination convention:
Az will use supplied declination to correct azimuth
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.
OUTPUT
output saved in magic_measurements.txt & er_samples.txt formatted files
will overwrite any existing files
"""
#
# initialize variables
#
specnum = 0
ub_file, samp_file, or_con, corr, meas_file = "", "er_samples.txt", "3", "1", "magic_measurements.txt"
pos_file, site_file = "", "er_sites.txt"
noave = 1
args = sys.argv
bed_dip, bed_dip_dir = "", ""
samp_con, Z, average_bedding = "2", 1, "0"
meths = "FS-FD"
sclass, lithology, type = "", "", ""
user, inst = "", ""
DecCorr = 0.0
location_name = "unknown"
months = ["Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec"]
gmeths = ""
#
#
dir_path = "."
if "-WD" in args:
ind = args.index("-WD")
dir_path = sys.argv[ind + 1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-f" in args:
ind = args.index("-f")
mag_file = sys.argv[ind + 1]
if "-fpos" in args:
ind = args.index("-fpos")
pos_file = sys.argv[ind + 1]
if "-F" in args:
ind = args.index("-F")
meas_file = sys.argv[ind + 1]
if "-Fsa" in args:
ind = args.index("-Fsa")
samp_file = sys.argv[ind + 1]
if "-Fsi" in args:
ind = args.index("-Fsi")
site_file = sys.argv[ind + 1]
if "-ocn" in args:
ind = args.index("-ocn")
or_con = 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 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 "6" in samp_con:
try:
Samps, file_type = pmag.magic_read(dir_path + "/er_samples.txt")
except:
print "there is no er_samples.txt file available - you can't use naming convention #6"
sys.exit()
if "-mcd" in args:
ind = args.index("-mcd")
gmeths = sys.argv[ind + 1]
if "-loc" in args:
ind = args.index("-loc")
location_name = sys.argv[ind + 1]
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind + 1])
if specnum != 0:
specnum = -specnum
if "-ins" in args:
ind = args.index("-ins")
inst = args[ind + 1]
if "-a" in args:
noave = 0
#
#
mag_file = dir_path + "/" + mag_file
samp_file = dir_path + "/" + samp_file
site_file = dir_path + "/" + site_file
meas_file = dir_path + "/" + meas_file
samplist = []
try:
Samps, file_type = pmag.magic_read(samp_file)
for samp in Samps:
if samp["er_sample_name"] not in samplist:
samplist.append(samp["er_sample_name"])
except:
Samps = []
MagRecs = []
f = open(mag_file, "rU")
input = f.read()
f.close()
firstline, date = 1, ""
d = input.split("\xcd")
for line in d:
rec = line.split("\x00")
if firstline == 1:
firstline = 0
spec, vol = "", 1
for c in line[15:23]:
if c != "\x00":
spec = spec + c
# check for bad sample name
test = spec.split(".")
date = ""
if len(test) > 1:
spec = test[0]
kk = 24
while line[kk] != "\x01" and line[kk] != "\x00":
kk += 1
vcc = line[24:kk]
el = 10
while rec[el].strip() != "":
el += 1
date, comments = rec[el + 7], []
else:
el = 9
while rec[el] != "\x01":
el += 1
vcc, date, comments = rec[el - 3], rec[el + 7], []
specname = spec.lower()
print "importing ", specname
el += 8
while rec[el].isdigit() == False:
comments.append(rec[el])
el += 1
while rec[el] == "":
el += 1
az = float(rec[el])
el += 1
while rec[el] == "":
el += 1
pl = float(rec[el])
el += 1
while rec[el] == "":
el += 1
bed_dip_dir = float(rec[el])
el += 1
while rec[el] == "":
el += 1
bed_dip = float(rec[el])
el += 1
while rec[el] == "":
el += 1
if rec[el] == "\x01":
bed_dip = 180.0 - bed_dip
el += 1
while rec[el] == "":
el += 1
fold_az = float(rec[el])
el += 1
while rec[el] == "":
el += 1
fold_pl = rec[el]
el += 1
while rec[el] == "":
el += 1
if rec[el] != "" and rec[el] != "\x02" and rec[el] != "\x01":
deccorr = float(rec[el])
az += deccorr
bed_dip_dir += deccorr
fold_az += deccorr
if bed_dip_dir >= 360:
bed_dip_dir = bed_dip_dir - 360.0
if az >= 360.0:
az = az - 360.0
if fold_az >= 360.0:
fold_az = fold_az - 360.0
else:
deccorr = 0
if specnum != 0:
sample = specname[:specnum]
else:
sample = specname
SampRec = {}
SampRec["er_sample_name"] = sample
SampRec["er_location_name"] = location_name
SampRec["er_citation_names"] = "This study"
labaz, labdip = pmag.orient(az, pl, or_con) # convert to labaz, labpl
#
# parse information common to all orientation methods
#
SampRec["sample_bed_dip"] = "%7.1f" % (bed_dip)
SampRec["sample_bed_dip_direction"] = "%7.1f" % (bed_dip_dir)
SampRec["sample_dip"] = "%7.1f" % (labdip)
SampRec["sample_azimuth"] = "%7.1f" % (labaz)
if vcc.strip() != "":
vol = float(vcc) * 1e-6 # convert to m^3 from cc
SampRec["sample_volume"] = "%10.3e" % (vol) #
SampRec["sample_class"] = sclass
SampRec["sample_lithology"] = lithology
SampRec["sample_type"] = type
SampRec["sample_declination_correction"] = "%7.1f" % (deccorr)
methods = gmeths.split(":")
if deccorr != "0":
if "SO-MAG" in methods:
del methods[methods.index("SO-MAG")]
methods.append("SO-CMD-NORTH")
meths = ""
for meth in methods:
meths = meths + meth + ":"
meths = meths[:-1]
SampRec["magic_method_codes"] = meths
if int(samp_con) < 6:
site = pmag.parse_site(SampRec["er_sample_name"], samp_con, Z) # parse out the site name
SampRec["er_site_name"] = site
elif len(Samps) > 1:
site, location = "", ""
for samp in Samps:
if samp["er_sample_name"] == SampRec["er_sample_name"]:
site = samp["er_site_name"]
location = samp["er_location_name"]
break
SampRec["er_location_name"] = samp["er_location_name"]
SampRec["er_site_name"] = samp["er_site_name"]
if sample not in samplist:
samplist.append(sample)
Samps.append(SampRec)
else:
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"] = specname
MagRec["er_sample_name"] = SampRec["er_sample_name"]
MagRec["er_site_name"] = SampRec["er_site_name"]
MagRec["er_location_name"] = location_name
el, demag = 1, ""
treat = rec[el]
if treat[-1] == "C":
demag = "T"
elif treat != "NRM":
demag = "AF"
el += 1
while rec[el] == "":
el += 1
MagRec["measurement_dec"] = rec[el]
cdec = float(rec[el])
el += 1
while rec[el] == "":
el += 1
MagRec["measurement_inc"] = rec[el]
cinc = float(rec[el])
el += 1
while rec[el] == "":
el += 1
gdec = rec[el]
el += 1
while rec[el] == "":
el += 1
ginc = rec[el]
el = skip(2, el, rec) # skip bdec,binc
# el=skip(4,el,rec) # skip gdec,ginc,bdec,binc
# print 'moment emu: ',rec[el]
MagRec["measurement_magn_moment"] = "%10.3e" % (float(rec[el]) * 1e-3) # moment in Am^2 (from emu)
MagRec["measurement_magn_volume"] = "%10.3e" % (float(rec[el]) * 1e-3 / vol) # magnetization in A/m
el = skip(2, el, rec) # skip to xsig
MagRec["measurement_sd_x"] = "%10.3e" % (float(rec[el]) * 1e-3) # convert from emu
el = skip(3, el, rec) # skip to ysig
MagRec["measurement_sd_y"] = "%10.3e" % (float(rec[el]) * 1e-3) # convert from emu
el = skip(3, el, rec) # skip to zsig
MagRec["measurement_sd_z"] = "%10.3e" % (float(rec[el]) * 1e-3) # convert from emu
el += 1 # skip to positions
MagRec["measurement_positions"] = rec[el]
# el=skip(5,el,rec) # skip to date
# mm=str(months.index(date[0]))
# if len(mm)==1:
# mm='0'+str(mm)
# else:
# mm=str(mm)
# dstring=date[2]+':'+mm+':'+date[1]+":"+date[3]
# MagRec['measurement_date']=dstring
MagRec["magic_instrument_codes"] = inst
MagRec["er_analyst_mail_names"] = ""
MagRec["er_citation_names"] = "This study"
MagRec["magic_method_codes"] = meas_type
if demag == "AF":
MagRec["treatment_ac_field"] = "%8.3e" % (float(treat[:-2]) * 1e-3) # peak field in tesla
meas_type = "LT-AF-Z"
MagRec["treatment_dc_field"] = "0"
elif demag == "T":
MagRec["treatment_temp"] = "%8.3e" % (float(treat[:-1]) + 273.0) # 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 "Measurements put in ", meas_file
SampsOut, sampkeys = pmag.fillkeys(Samps)
pmag.magic_write(samp_file, SampsOut, "er_samples")
Sites = []
for samp in Samps:
SiteRec = {}
SiteRec["er_site_name"] = samp["er_site_name"]
SiteRec["er_location_name"] = samp["er_location_name"]
SiteRec["site_definition"] = "s"
SiteRec["er_citation_names"] = "This study"
if "sample_class" in samp.keys():
SiteRec["site_class"] = samp["sample_class"]
if "sample_lithology" in samp.keys():
SiteRec["site_lithology"] = samp["sample_lithology"]
if "sample_type" in samp.keys():
SiteRec["site_lithology"] = samp["sample_lithology"]
if "sample_lat" in samp.keys():
SiteRec["site_lat"] = samp["sample_lat"]
else:
SiteRec["site_lat"] = "-999"
if "sample_lon" in samp.keys():
SiteRec["site_lon"] = samp["sample_lon"]
else:
SiteRec["site_lon"] = "-999"
if "sample_height" in samp.keys():
SiteRec["site_height"] = samp["sample_height"]
Sites.append(SiteRec)
pmag.magic_write(site_file, Sites, "er_sites")
def main():
"""
NAME
orientation_magic.py
DESCRIPTION
takes tab delimited field notebook information and converts to MagIC formatted tables
SYNTAX
orientation_magic.py [command line options]
OPTIONS
-f FILE: specify input file, default is: orient.txt
-Fsa FILE: specify output file, default is: er_samples.txt
-Fsi FILE: specify output site location file, default is: er_sites.txt
-app append/update these data in existing er_samples.txt, er_sites.txt files
-ocn OCON: specify orientation convention, default is #1 below
-dcn DCON [DEC]: specify declination convention, default is #1 below
if DCON = 2, you must supply the declination correction
-BCN don't correct bedding_dip_dir for magnetic declination -already corrected
-ncn NCON: specify naming convention: default is #1 below
-a: averages all bedding poles and uses average for all samples: default is NO
-gmt HRS: specify hours to subtract from local time to get GMT: default is 0
-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
INPUT FORMAT
Input files must be tab delimited and have in the first line:
tab location_name
Note: The "location_name" will facilitate searching in the MagIC database. Data from different
"locations" should be put in separate files. The definition of a "location" is rather loose.
Also this is the word 'tab' not a tab, which will be indicated by '\t'.
The second line has the names of the columns (tab delimited), e.g.:
site_name sample_name mag_azimuth field_dip date lat long sample_lithology sample_type sample_class shadow_angle hhmm stratigraphic_height bedding_dip_direction bedding_dip GPS_baseline image_name image_look image_photographer participants method_codes site_description sample_description GPS_Az, sample_igsn, sample_texture, sample_cooling_rate, cooling_rate_corr, cooling_rate_mcd
Notes:
1) column order doesn't matter but the NAMES do.
2) sample_name, sample_lithology, sample_type, sample_class, lat and long are required. all others are optional.
3) If subsequent data are the same (e.g., date, bedding orientation, participants, stratigraphic_height),
you can leave the field blank and the program will fill in the last recorded information. BUT if you really want a blank stratigraphic_height, enter a '-1'. These will not be inherited and must be specified for each entry: image_name, look, photographer or method_codes
4) hhmm must be in the format: hh:mm and the hh must be in 24 hour time.
date must be mm/dd/yy (years < 50 will be converted to 20yy and >50 will be assumed 19yy)
5) image_name, image_look and image_photographer are colon delimited lists of file name (e.g., IMG_001.jpg) image look direction and the name of the photographer respectively. If all images had same look and photographer, just enter info once. The images will be assigned to the site for which they were taken - not at the sample level.
6) participants: Names of who helped take the samples. These must be a colon delimited list.
7) method_codes: Special method codes on a sample level, e.g., SO-GT5 which means the orientation is has an uncertainty of >5 degrees
for example if it broke off before orienting....
8) GPS_Az is the place to put directly determined GPS Azimuths, using, e.g., points along the drill direction.
9) sample_cooling_rate is the cooling rate in K per Ma
10) int_corr_cooling_rate
11) cooling_rate_mcd: data adjustment method code for cooling rate correction; DA-CR-EG is educated guess; DA-CR-PS is percent estimated from pilot samples; DA-CR-TRM is comparison between 2 TRMs acquired with slow and rapid cooling rates.
is the percent cooling rate factor to apply to specimens from this sample, DA-CR-XX is the method code
Orientation convention:
Samples are oriented in the field with a "field arrow" and measured in the laboratory with a "lab arrow". The lab arrow is the positive X direction of the right handed coordinate system of the specimen measurements. The lab and field arrows may not be the same. In the MagIC database, we require the orientation (azimuth and plunge) of the X direction of the measurements (lab arrow). Here are some popular conventions that convert the field arrow azimuth (mag_azimuth in the orient.txt file) and dip (field_dip in orient.txt) to the azimuth and plunge of the laboratory arrow (sample_azimuth and sample_dip in er_samples.txt). The two angles, mag_azimuth and field_dip are explained below.
[1] Standard Pomeroy convention of azimuth and hade (degrees from vertical down)
of the drill direction (field arrow). lab arrow azimuth= sample_azimuth = mag_azimuth;
lab arrow dip = sample_dip =-field_dip. i.e. the lab arrow dip is minus the hade.
[2] Field arrow is the strike of the plane orthogonal to the drill direction,
Field dip is the hade of the drill direction. Lab arrow azimuth = mag_azimuth-90
Lab arrow dip = -field_dip
[3] Lab arrow is the same as the drill direction;
hade was measured in the field.
Lab arrow azimuth = mag_azimuth; Lab arrow dip = 90-field_dip
[4] lab azimuth and dip are same as mag_azimuth, field_dip : use this for unoriented samples too
[5] Same as AZDIP convention explained below -
azimuth and inclination of the drill direction are mag_azimuth and field_dip;
lab arrow is as in [1] above.
lab azimuth is same as mag_azimuth,lab arrow dip=field_dip-90
[6] Lab arrow azimuth = mag_azimuth-90; Lab arrow dip = 90-field_dip
[7] all others you will have to either customize your
self or e-mail [email protected] for help.
Magnetic declination convention:
[1] Use the IGRF value at the lat/long and date supplied [default]
[2] Will supply declination correction
[3] mag_az is already corrected in file
[4] Correct mag_az but not bedding_dip_dir
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 = sample name
[6] site name entered in site_name column in the orient.txt format input file
[7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY
NB: all others you will have to either customize your
self or e-mail [email protected] for help.
OUTPUT
output saved in er_samples.txt and er_sites.txt - will overwrite any existing files
"""
#
# initialize variables
#
stratpos=""
args=sys.argv
date,lat,lon="","","" # date of sampling, latitude (pos North), longitude (pos East)
bed_dip,bed_dip_dir="",""
participantlist=""
Lats,Lons=[],[] # list of latitudes and longitudes
SampOuts,SiteOuts,ImageOuts=[],[],[] # lists of Sample records and Site records
samplelist,sitelist,imagelist=[],[],[]
samp_con,Z,average_bedding,DecCorr="1",1,"0",0.
newbaseline,newbeddir,newbeddip="","",""
meths=''
delta_u="0"
sclass,lithology,type="","",""
newclass,newlith,newtype='','',''
user=""
BPs=[]# bedding pole declinations, bedding pole inclinations
#
#
dir_path,AddTo='.',0
if "-WD" in args:
ind=args.index("-WD")
dir_path=sys.argv[ind+1]
orient_file,samp_file,or_con,corr = dir_path+"/orient.txt",dir_path+"/er_samples.txt","1","1"
site_file=dir_path+"/er_sites.txt"
image_file=dir_path+"/er_images.txt"
SampRecs,SiteRecs,ImageRecs=[],[],[]
if "-h" in args:
print main.__doc__
sys.exit()
if "-f" in args:
ind=args.index("-f")
orient_file=dir_path+'/'+sys.argv[ind+1]
if "-Fsa" in args:
ind=args.index("-Fsa")
samp_file=dir_path+'/'+sys.argv[ind+1]
if "-Fsi" in args:
ind=args.index("-Fsi")
site_file=dir_path+'/'+sys.argv[ind+1]
if '-app' in args:
AddTo=1
try:
SampRecs,file_type=pmag.magic_read(samp_file)
print 'sample data to be appended to: ', samp_file
except:
print 'problem with existing file: ',samp_file, ' will create new.'
try:
SiteRecs,file_type=pmag.magic_read(site_file)
print 'site data to be appended to: ',site_file
except:
print 'problem with existing file: ',site_file,' will create new.'
try:
ImageRecs,file_type=pmag.magic_read(image_file)
print 'image data to be appended to: ',image_file
except:
print 'problem with existing file: ',image_file,' will create new.'
if "-ocn" in args:
ind=args.index("-ocn")
or_con=sys.argv[ind+1]
if "-dcn" in args:
ind=args.index("-dcn")
corr=sys.argv[ind+1]
if corr=="2":
DecCorr=float(sys.argv[ind+2])
elif corr=="3":
DecCorr=0.
if '-BCN' in args:
BedCorr=0
else:
BedCorr=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 "-gmt" in args:
ind=args.index("-gmt")
delta_u=(sys.argv[ind+1])
if "-mcd" in args:
ind=args.index("-mcd")
meths=(sys.argv[ind+1])
if "-a" in args: average_bedding="1"
#
# read in file to convert
#
OrData,location_name=pmag.magic_read(orient_file)
#
# step through the data sample by sample
#
for OrRec in OrData:
if 'mag_azimuth' not in OrRec.keys():OrRec['mag_azimuth']=""
if 'field_dip' not in OrRec.keys():OrRec['field_dip']=""
if OrRec['mag_azimuth']==" ":OrRec["mag_azimuth"]=""
if OrRec['field_dip']==" ":OrRec["field_dip"]=""
if 'sample_description' in OrRec.keys():
sample_description=OrRec['sample_description']
else:
sample_description=""
if 'sample_igsn' in OrRec.keys():
sample_igsn=OrRec['sample_igsn']
else:
sample_igsn=""
if 'sample_texture' in OrRec.keys():
sample_texture=OrRec['sample_texture']
else:
sample_texture=""
if 'sample_cooling_rate' in OrRec.keys():
sample_cooling_rate=OrRec['sample_cooling_rate']
else:
sample_cooling_rate=""
if 'cooling_rate_corr' in OrRec.keys():
cooling_rate_corr=OrRec['cooling_rate_corr']
if 'cooling_rate_mcd' in OrRec.keys():
cooling_rate_mcd=OrRec['cooling_rate_mcd']
else:
cooling_rate_mcd='DA-CR'
else:
cooling_rate_corr=""
cooling_rate_mcd=""
sample_orientation_flag='g'
if 'sample_orientation_flag' in OrRec.keys():
if OrRec['sample_orientation_flag']=='b' or OrRec["mag_azimuth"]=="":
sample_orientation_flag='b'
methcodes=meths # initialize method codes
if meths!='':
if 'method_codes' in OrRec.keys() and OrRec['method_codes'].strip()!="":methcodes=methcodes+":"+OrRec['method_codes'] # add notes
else:
if 'method_codes' in OrRec.keys() and OrRec['method_codes'].strip()!="":methcodes=OrRec['method_codes'] # add notes
codes=methcodes.replace(" ","").split(":")
MagRec={}
MagRec["er_location_name"]=location_name
MagRec["er_citation_names"]="This study"
MagRec['sample_orientation_flag']=sample_orientation_flag
MagRec['sample_igsn']=sample_igsn
MagRec['sample_texture']=sample_texture
MagRec['sample_cooling_rate']=sample_cooling_rate
MagRec['cooling_rate_corr']=cooling_rate_corr
MagRec['cooling_rate_mcd']=cooling_rate_mcd
#
# parse information common to all orientation methods
#
MagRec["er_sample_name"]=OrRec["sample_name"]
if "IGSN" in OrRec.keys():
MagRec["sample_igsn"]=OrRec["IGSN"]
else:
MagRec["sample_igsn"]=""
MagRec["sample_height"],MagRec["sample_bed_dip_direction"],MagRec["sample_bed_dip"]="","",""
if "er_sample_alternatives" in OrRec.keys():MagRec["er_sample_alternatives"]=OrRec["sample_alternatives"]
sample=OrRec["sample_name"]
if OrRec['mag_azimuth']=="" and OrRec['field_dip']!="":
OrRec['mag_azimuth']='999'
if OrRec["mag_azimuth"]!="":
labaz,labdip=pmag.orient(float(OrRec["mag_azimuth"]),float(OrRec["field_dip"]),or_con)
if labaz<0:labaz+=360.
else:
labaz,labdip="",""
if OrRec['mag_azimuth']=='999':labaz=""
if "GPS_baseline" in OrRec.keys() and OrRec['GPS_baseline']!="":newbaseline=OrRec["GPS_baseline"]
if newbaseline!="":baseline=float(newbaseline)
if 'participants' in OrRec.keys() and OrRec['participants']!="" and OrRec['participants']!=participantlist:
participantlist=OrRec['participants']
MagRec['er_scientist_mail_names']=participantlist
newlat=OrRec["lat"]
if newlat!="":lat=float(newlat)
if lat=="":
print "No latitude specified for ! ",sample
sys.exit()
MagRec["sample_lat"]='%11.5f'%(lat)
newlon=OrRec["long"]
if newlon!="":lon=float(newlon)
if lon=="":
print "No longitude specified for ! ",sample
sys.exit()
MagRec["sample_lon"]='%11.5f'%(lon)
if 'bedding_dip_direction' in OrRec.keys(): newbeddir=OrRec["bedding_dip_direction"]
if newbeddir!="":bed_dip_dir=OrRec['bedding_dip_direction']
if 'bedding_dip' in OrRec.keys(): newbeddip=OrRec["bedding_dip"]
if newbeddip!="":bed_dip=OrRec['bedding_dip']
MagRec["sample_bed_dip"]=bed_dip
MagRec["sample_bed_dip_direction"]=bed_dip_dir
if "sample_class" in OrRec.keys():newclass=OrRec["sample_class"]
if newclass!="":sclass=newclass
if sclass=="": sclass="Not Specified"
MagRec["sample_class"]=sclass
if "sample_lithology" in OrRec.keys():newlith=OrRec["sample_lithology"]
if newlith!="":lithology=newlith
if lithology=="": lithology="Not Specified"
MagRec["sample_lithology"]=lithology
if "sample_type" in OrRec.keys():newtype=OrRec["sample_type"]
if newtype!="":type=newtype
if type=="": type="Not Specified"
MagRec["sample_type"]=type
if labdip!="":
MagRec["sample_dip"]='%7.1f'%labdip
else:
MagRec["sample_dip"]=""
if "date" in OrRec.keys():
newdate=OrRec["date"]
if newdate!="":date=newdate
mmddyy=date.split('/')
yy=int(mmddyy[2])
if yy>50:
yy=1900+yy
else:
yy=2000+yy
decimal_year=yy+float(mmddyy[0])/12
sample_date='%i:%s:%s'%(yy,mmddyy[0],mmddyy[1])
MagRec["sample_date"]=sample_date
if labaz!="":
MagRec["sample_azimuth"]='%7.1f'%(labaz)
else:
MagRec["sample_azimuth"]=""
if "stratigraphic_height" in OrRec.keys():
if OrRec["stratigraphic_height"]!="":
MagRec["sample_height"]=OrRec["stratigraphic_height"]
stratpos=OrRec["stratigraphic_height"]
elif OrRec["stratigraphic_height"]=='-1':
MagRec["sample_height"]="" # make empty
else:
MagRec["sample_height"]=stratpos # keep last record if blank
#
if corr=="1" and MagRec['sample_azimuth']!="": # get magnetic declination (corrected with igrf value)
x,y,z,f=pmag.doigrf(lon,lat,0,decimal_year)
Dir=pmag.cart2dir( (x,y,z))
DecCorr=Dir[0]
if "bedding_dip" in OrRec.keys():
if OrRec["bedding_dip"]!="":
MagRec["sample_bed_dip"]=OrRec["bedding_dip"]
bed_dip=OrRec["bedding_dip"]
else:
MagRec["sample_bed_dip"]=bed_dip
else: MagRec["sample_bed_dip"]='0'
if "bedding_dip_direction" in OrRec.keys():
if OrRec["bedding_dip_direction"]!="" and BedCorr==1:
dd=float(OrRec["bedding_dip_direction"])+DecCorr
if dd>360.:dd=dd-360.
MagRec["sample_bed_dip_direction"]='%7.1f'%(dd)
dip_dir=MagRec["sample_bed_dip_direction"]
else:
MagRec["sample_bed_dip_direction"]=OrRec['bedding_dip_direction']
else: MagRec["sample_bed_dip_direction"]='0'
if average_bedding!="0": BPs.append([float(MagRec["sample_bed_dip_direction"]),float(MagRec["sample_bed_dip"])-90.,1.])
if MagRec['sample_azimuth']=="" and MagRec['sample_dip']=="":
MagRec["sample_declination_correction"]=''
methcodes=methcodes+':SO-NO'
MagRec["magic_method_codes"]=methcodes
MagRec['sample_description']=sample_description
#
# work on the site stuff too
if 'site_name' in OrRec.keys():
site=OrRec['site_name']
else:
site=pmag.parse_site(OrRec["sample_name"],samp_con,Z) # parse out the site name
MagRec["er_site_name"]=site
site_description="" # overwrite any prior description
if 'site_description' in OrRec.keys() and OrRec['site_description']!="":
site_description=OrRec['site_description'].replace(",",";")
if "image_name" in OrRec.keys():
images=OrRec["image_name"].split(":")
if "image_look" in OrRec.keys():
looks=OrRec['image_look'].split(":")
else:
looks=[]
if "image_photographer" in OrRec.keys():
photographers=OrRec['image_photographer'].split(":")
else:
photographers=[]
for image in images:
if image !="" and image not in imagelist:
imagelist.append(image)
ImageRec={}
ImageRec['er_image_name']=image
ImageRec['image_type']="outcrop"
ImageRec['image_date']=sample_date
ImageRec['er_citation_names']="This study"
ImageRec['er_location_name']=location_name
ImageRec['er_site_name']=MagRec['er_site_name']
k=images.index(image)
if len(looks)>k:
ImageRec['er_image_description']="Look direction: "+looks[k]
elif len(looks)>=1:
ImageRec['er_image_description']="Look direction: "+looks[-1]
else:
ImageRec['er_image_description']="Look direction: unknown"
if len(photographers)>k:
ImageRec['er_photographer_mail_names']=photographers[k]
elif len(photographers)>=1:
ImageRec['er_photographer_mail_names']=photographers[-1]
else:
ImageRec['er_photographer_mail_names']="unknown"
ImageOuts.append(ImageRec)
if site not in sitelist:
sitelist.append(site) # collect unique site names
SiteRec={}
SiteRec["er_site_name"]=site
SiteRec["site_definition"]="s"
SiteRec["er_location_name"]=location_name
SiteRec["er_citation_names"]="This study"
SiteRec["site_lat"]=MagRec["sample_lat"]
SiteRec["site_lon"]=MagRec["sample_lon"]
SiteRec["site_height"]=MagRec["sample_height"]
SiteRec["site_class"]=MagRec["sample_class"]
SiteRec["site_lithology"]=MagRec["sample_lithology"]
SiteRec["site_type"]=MagRec["sample_type"]
SiteRec["site_description"]=site_description
SiteOuts.append(SiteRec)
if sample not in samplelist:
samplelist.append(sample)
if MagRec['sample_azimuth']!="": # assume magnetic compass only
MagRec['magic_method_codes']=MagRec['magic_method_codes']+':SO-MAG'
MagRec['magic_method_codes']=MagRec['magic_method_codes'].strip(":")
SampOuts.append(MagRec)
if MagRec['sample_azimuth']!="" and corr!='3':
az=labaz+DecCorr
if az>360.:az=az-360.
CMDRec={}
for key in MagRec.keys():
CMDRec[key]=MagRec[key] # make a copy of MagRec
CMDRec["sample_azimuth"]='%7.1f'%(az)
CMDRec["magic_method_codes"]=methcodes+':SO-CMD-NORTH'
CMDRec["magic_method_codes"]=CMDRec['magic_method_codes'].strip(':')
CMDRec["sample_declination_correction"]='%7.1f'%(DecCorr)
if corr=='1':
CMDRec['sample_description']=sample_description+':Declination correction calculated from IGRF'
else:
CMDRec['sample_description']=sample_description+':Declination correction supplied by user'
CMDRec["sample_description"]=CMDRec['sample_description'].strip(':')
SampOuts.append(CMDRec)
if "mag_az_bs" in OrRec.keys() and OrRec["mag_az_bs"] !="" and OrRec["mag_az_bs"]!=" ":
SRec={}
for key in MagRec.keys():
SRec[key]=MagRec[key] # make a copy of MagRec
labaz=float(OrRec["mag_az_bs"])
az=labaz+DecCorr
if az>360.:az=az-360.
SRec["sample_azimuth"]='%7.1f'%(az)
SRec["sample_declination_correction"]='%7.1f'%(DecCorr)
SRec["magic_method_codes"]=methcodes+':SO-SIGHT-BACK:SO-CMD-NORTH'
SampOuts.append(SRec)
#
# check for suncompass data
#
if "shadow_angle" in OrRec.keys() and OrRec["shadow_angle"]!="": # there are sun compass data
if delta_u=="":
delta_u=raw_input("Enter hours to SUBTRACT from time for GMT: [0] ")
if delta_u=="":delta_u="0"
SunRec,sundata={},{}
shad_az=float(OrRec["shadow_angle"])
sundata["date"]='%i:%s:%s:%s'%(yy,mmddyy[0],mmddyy[1],OrRec["hhmm"])
# if eval(delta_u)<0:
# MagRec["sample_time_zone"]='GMT'+delta_u+' hours'
# else:
# MagRec["sample_time_zone"]='GMT+'+delta_u+' hours'
sundata["delta_u"]=delta_u
sundata["lon"]='%7.1f'%(lon)
sundata["lat"]='%7.1f'%(lat)
sundata["shadow_angle"]=OrRec["shadow_angle"]
sundec=pmag.dosundec(sundata)
for key in MagRec.keys():
SunRec[key]=MagRec[key] # make a copy of MagRec
SunRec["sample_azimuth"]='%7.1f'%(sundec)
SunRec["sample_declination_correction"]=''
SunRec["magic_method_codes"]=methcodes+':SO-SUN'
SunRec["magic_method_codes"]=SunRec['magic_method_codes'].strip(':')
SampOuts.append(SunRec)
#
# check for differential GPS data
#
if "prism_angle" in OrRec.keys() and OrRec["prism_angle"]!="": # there are diff GPS data
GPSRec={}
for key in MagRec.keys():
GPSRec[key]=MagRec[key] # make a copy of MagRec
prism_angle=float(OrRec["prism_angle"])
laser_angle=float(OrRec["laser_angle"])
if OrRec["GPS_baseline"]!="": baseline=float(OrRec["GPS_baseline"]) # new baseline
gps_dec=baseline+laser_angle+prism_angle-90.
while gps_dec>360.:
gps_dec=gps_dec-360.
while gps_dec<0:
gps_dec=gps_dec+360.
for key in MagRec.keys():
GPSRec[key]=MagRec[key] # make a copy of MagRec
GPSRec["sample_azimuth"]='%7.1f'%(gps_dec)
GPSRec["sample_declination_correction"]=''
GPSRec["magic_method_codes"]=methcodes+':SO-GPS-DIFF'
SampOuts.append(GPSRec)
if "GPS_Az" in OrRec.keys() and OrRec["GPS_Az"]!="": # there are differential GPS Azimuth data
GPSRec={}
for key in MagRec.keys():
GPSRec[key]=MagRec[key] # make a copy of MagRec
GPSRec["sample_azimuth"]='%7.1f'%(float(OrRec["GPS_Az"]))
GPSRec["sample_declination_correction"]=''
GPSRec["magic_method_codes"]=methcodes+':SO-GPS-DIFF'
SampOuts.append(GPSRec)
if average_bedding!="0":
fpars=pmag.fisher_mean(BPs)
print 'over-writing all bedding with average '
Samps=[]
for rec in SampOuts:
if average_bedding!="0":
rec['sample_bed_dip_direction']='%7.1f'%(fpars['dec'])
rec['sample_bed_dip']='%7.1f'%(fpars['inc']+90.)
Samps.append(rec)
else:
Samps.append(rec)
for rec in SampRecs:
if rec['er_sample_name'] not in samplelist: # overwrite prior for this sample
Samps.append(rec)
for rec in SiteRecs:
if rec['er_site_name'] not in sitelist: # overwrite prior for this sample
SiteOuts.append(rec)
for rec in ImageRecs:
if rec['er_image_name'] not in imagelist: # overwrite prior for this sample
ImageOuts.append(rec)
print 'saving data...'
SampsOut,keys=pmag.fillkeys(Samps)
Sites,keys=pmag.fillkeys(SiteOuts)
pmag.magic_write(samp_file,SampsOut,"er_samples")
pmag.magic_write(site_file,Sites,"er_sites")
print "Data saved in ", samp_file,' and ',site_file
if len(ImageOuts)>0:
Images,keys=pmag.fillkeys(ImageOuts)
pmag.magic_write(image_file,Images,"er_images")
print "Image info saved in ",image_file
def main():
"""
NAME
UU_magic.py
DESCRIPTION
takes Fort Hoofddijk (University of Utrecht) format magnetometer files and converts them to magic_measurements and er_samples.txt
SYNTAX
UU_magic.py [command line options]
OPTIONS
-f FILE: specify input file
-fpos FILE: specify stratigraphic position file (.saf format)
-F FILE: specify magic_measurements output file, default is: magic_measurements.txt
-Fsa FILE: specify output file, default is: er_samples.txt
-ncn NCON: specify naming convention: default is #1 below
-ocn OCON: specify orientation 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
SO-SUN orientation with sun compass
-loc: location name, default="unknown"
-spc NUM : specify number of characters to designate a specimen, default = 0
-ins INST : specify instsrument name
INPUT FORMAT
Input files must be colon delimited:
"file_name", "instrument"
"specimen name","",az,pl,vol(cc),strike,dip
treatment,X,Y,Z,CSD,"yy-mm-dd","hh:mm"
Orientation convention:
[1] Lab arrow azimuth= mag_azimuth; Lab arrow dip=-dip
i.e., dip is degrees from vertical down - the hade [default]
[2] Lab arrow azimuth = mag_azimuth-90; Lab arrow dip = -dip
i.e., mag_azimuth is strike and dip is hade
[3] Lab arrow azimuth = mag_azimuth; Lab arrow dip = dip-90
e.g. dip is degrees from horizontal of drill direction
[4] Lab arrow azimuth = mag_azimuth; Lab arrow dip = dip
[5] Lab arrow azimuth = mag_azimuth; Lab arrow dip = 90-dip
[6] all others you will have to either customize your
self or e-mail [email protected] for help.
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] 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.
OUTPUT
output saved in magic_measurements.txt & er_samples.txt formatted files
will overwrite any existing files
"""
#
# initialize variables
#
uu_file,samp_file,or_con,corr,meas_file = "","er_samples.txt","1","1","magic_measurements.txt"
pos_file=""
specnum=-1
args=sys.argv
bed_dip,bed_dip_dir="",""
samp_con,Z,average_bedding="1",1,"0"
meths='FS-FD:SO-POM'
sclass,lithology,type="","",""
user,inst="",""
or_con='1'
corr=="3"
DecCorr=0.
location_name="unknown"
#
#
dir_path='.'
if '-WD' in args:
ind=args.index("-WD")
dir_path=sys.argv[ind+1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-f" in args:
ind=args.index("-f")
uu_file=sys.argv[ind+1]
d=uu_file.split('.')
if d[1].upper()=="AF":demag="AF"
if d[1].upper()=="TH":demag="T"
if "-fpos" in args:
ind=args.index("-fpos")
pos_file=sys.argv[ind+1]
if "-F" in args:
ind=args.index("-F")
meas_file=sys.argv[ind+1]
if "-Fsa" in args:
ind=args.index("-Fsa")
samp_file=sys.argv[ind+1]
if "-ocn" in args:
ind=args.index("-ocn")
or_con=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 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 "-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 "-spc" in args:
ind=args.index("-spc")
specnum=-int(args[ind+1])
if specnum!=0:specnum=-specnum
if "-ins" in args:
ind=args.index("-ins")
inst=args[ind+1]
#
#
uu_file=dir_path+'/'+uu_file
samp_file=dir_path+'/'+samp_file
meas_file=dir_path+'/'+meas_file
if pos_file!="":pos_file=dir_path+'/'+pos_file
samplist=[]
try:
SampOut,file_type=pmag.magic_read(samp_file)
for rec in SampOut:
if rec['er_sample_name'] not in samplist: samplist.append(rec['er_sample_name'])
except:
SampOut=[]
PosData=[]
if pos_file != "":
p=open(pos_file,'rU')
PosIn=p.readlines()
p.close()
for line in PosIn:
srec=line.split()[0].split(',')
Prec={'er_site_name':srec[0],'sample_height':srec[1]}
PosData.append(Prec)
infile=open(uu_file,'rU')
Data=infile.readlines()
infile.close()
MagRecs=[]
header=Data[0].split(',')
if inst=="":inst=header[1].strip('"')
if inst=='2G DC':
inst=="FH-2GDC" # Dc Squid machine at Fort Hoofddijk
else:
inst=""
newsamp=1
for k in range(1,len(Data)-1): # step through file, skipping header and "END" statement
line=Data[k].split('\n')[0]
rec=line.split(',')
if newsamp==1 and rec[0].lower()!='end':
newsamp=0
specname=rec[0].strip('"') # take off quotation marks
if specnum!=0:
sample=specname[:specnum]
else:
sample=specname
site=pmag.parse_site(sample,samp_con,Z) # parse out the site name
SampRec={}
SampRec["er_sample_name"]=sample
SampRec["er_location_name"]=location_name
SampRec["er_citation_names"]="This study"
labaz,labdip=pmag.orient(float(rec[2]),float(rec[3]),or_con)
bed_dip=float(rec[6])
if bed_dip!=0:
bed_dip_dir=float(rec[5])+90. # assume dip to right of strike
if bed_dip_dir>=360:bed_dip_dir=bed_dip_dir-360.
else:
bed_dip_dir=float(rec[5])
# parse information common to all orientation methods
#
SampRec["sample_bed_dip"]='%7.1f'%(bed_dip)
SampRec["sample_bed_dip_direction"]='%7.1f'%(bed_dip_dir)
SampRec["sample_dip"]='%7.1f'%(labdip)
SampRec["sample_azimuth"]='%7.1f'%(labaz)
vol=float(rec[4])*1e-6
SampRec["sample_volume"]='%10.3e'%(vol) # convert cc into m^3
SampRec["sample_class"]=sclass
SampRec["sample_lithology"]=lithology
SampRec["sample_type"]=type
SampRec["magic_method_codes"]=meths
SampRec["er_site_name"]=site
#
# find position data
#
if PosData!=[]:
for srec in PosData:
if srec['er_site_name']==site:
SampRec['sample_height']=srec['sample_height']
break
if sample not in samplist:
samplist.append(sample)
SampOut.append(SampRec)
elif rec[0]=='9999': # end of this specimen
k=k+1 # move on
newsamp=1
elif rec[0].lower()!='end' and rec[0]!="": # got some data
line=Data[k].split('\n')[0]
rec=line.split(',')
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"]=specname
MagRec["er_sample_name"]=sample
MagRec["er_site_name"]=site
MagRec["er_location_name"]=location_name
MagRec["measurement_csd"]=rec[4]
cart=[]
cart.append(-float(rec[2])) # appending x,y,z from data record
cart.append(float(rec[3]))
cart.append(-float(rec[1]))
Dir=pmag.cart2dir(cart)
MagRec["measurement_magn_volume"]='%10.3e'% (float(Dir[2])*1e-6) # moment in A/m (from 10^-6 A/m)
MagRec["measurement_magn_moment"]='%10.3e'% (float(Dir[2])*vol*1e-6) # moment in Am^2
MagRec["measurement_dec"]='%7.1f'%(Dir[0])
MagRec["measurement_inc"]='%7.1f'%(Dir[1])
MagRec["magic_instrument_codes"]=inst
MagRec["er_analyst_mail_names"]=""
MagRec["er_citation_names"]="This study"
MagRec["magic_method_codes"]=meas_type
if demag=="AF":
MagRec["treatment_ac_field"]='%8.3e' %(float(rec[0])*1e-3) # peak field in tesla
meas_type="LT-AF-Z"
MagRec["treatment_dc_field"]='0'
elif demag=="T":
MagRec["treatment_temp"]='%8.3e' % (float(rec[0])+273.) # temp in kelvin
meas_type="LT-T-Z"
MagRec['magic_method_codes']=meas_type
# date=rec[5].strip('"').split('-')
# time=rec[6].strip('"')
# if int(date[0])<50: # assume this century
# yyyy='20'+date[0]
# else:
# yyyy='19'+date[0] # assume last century
# dstring=yyyy+':'+date[1]+':'+date[2]+":"+time
# MagRec['measurement_date']=dstring
MagRecs.append(MagRec)
MagOuts=pmag.measurements_methods(MagRecs,0)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print "Measurements put in ",meas_file
pmag.magic_write(samp_file,SampOut,"er_samples")
print "Sample orientation info saved in ", samp_file
print "Good bye"
def main():
"""
NAME
azdip_magic.py
DESCRIPTION
takes space delimited AzDip file and converts to MagIC formatted tables
SYNTAX
azdip_magic.py [command line options]
OPTIONS
-f FILE: specify input file
-Fsa FILE: specify output file, default is: er_samples.txt
-ncn NCON: specify naming convention: default is #1 below
-mcd: specify sampling method codes as a colon delimited string: [default is: FS-FD]
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"
-app appends to existing er_samples.txt file, default is to overwrite
INPUT FORMAT
Input files must be space delimited:
Samp Az Dip Strike 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] 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.
OUTPUT
output saved in er_samples.txt will overwrite any existing files
"""
#
# initialize variables
#
DEBUG = 0
version_num = pmag.get_version()
orient_file, samp_file, or_con, corr = "orient.txt", "er_samples.txt", "3", "1"
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"
delta_u = "0"
sclass, lithology, type = "", "", ""
newclass, newlith, newtype = "", "", ""
user = ""
corr == "3"
DecCorr = 0.0
location_name = "unknown"
#
#
if "-h" in args:
print main.__doc__
sys.exit()
if "-f" in args:
ind = args.index("-f")
orient_file = sys.argv[ind + 1]
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 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 "-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 "-app" in args:
try:
SampRecs, file_type = pmag.magic_read(samp_file)
print "sample data to be appended to: ", samp_file
except:
print "problem with existing samp file: ", samp_file, " will create new"
#
# read in file to convert
#
azfile = open(orient_file, "rU")
AzDipDat = azfile.readlines()
azfile.close()
SampOut, samplist = [], []
for line in AzDipDat:
orec = line.split()
if len(orec) > 2:
labaz, labdip = pmag.orient(float(orec[1]), float(orec[2]), or_con)
bed_dip = float(orec[4])
if bed_dip != 0:
bed_dip_dir = float(orec[3]) - 90.0 # assume dip to right of strike
else:
bed_dip_dir = float(orec[3]) # assume dip to right of strike
MagRec = {}
MagRec["er_location_name"] = location_name
MagRec["er_citation_names"] = "This study"
#
# parse information common to all orientation methods
#
MagRec["er_sample_name"] = orec[0]
MagRec["sample_bed_dip"] = "%7.1f" % (bed_dip)
MagRec["sample_bed_dip_direction"] = "%7.1f" % (bed_dip_dir)
MagRec["sample_dip"] = "%7.1f" % (labdip)
MagRec["sample_azimuth"] = "%7.1f" % (labaz)
methods = meths.replace(" ", "").split(":")
OR = 0
for method in methods:
type = method.split("-")
if "SO" in type:
OR = 1
if OR == 0:
meths = meths + ":SO-NO"
MagRec["magic_method_codes"] = meths
site = pmag.parse_site(orec[0], samp_con, Z) # parse out the site name
MagRec["er_site_name"] = site
MagRec["magic_software_packages"] = version_num
SampOut.append(MagRec)
if MagRec["er_sample_name"] not in samplist:
samplist.append(MagRec["er_sample_name"])
for samp in SampRecs:
if samp not in samplist:
SampOut.append(samp)
Samps, keys = pmag.fillkeys(SampOut)
pmag.magic_write(samp_file, Samps, "er_samples")
print "Data saved in ", samp_file
def main(command_line=True, **kwargs):
"""
NAME
2G_bin_magic.py
DESCRIPTION
takes the binary 2G format magnetometer files and converts them to magic_measurements, er_samples.txt and er_sites.txt file
SYNTAX
2G_bin_magic.py [command line options]
OPTIONS
-f FILE: specify input 2G (binary) file
-F FILE: specify magic_measurements output file, default is: magic_measurements.txt
-Fsa FILE: specify output file, default is: er_samples.txt
-Fsi FILE: specify output file, default is: er_sites.txt
-ncn NCON: specify naming convention: default is #2 below
-ocn OCON: specify orientation convention, default is #5 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
SO-SUN orientation with sun compass
-loc: location name, default="unknown"
-spc NUM : specify number of characters to designate a specimen, default = 0
-ins INST : specify instsrument name
-a: average replicate measurements
INPUT FORMAT
Input files are horrible mag binary format (who knows why?)
Orientation convention:
[1] Lab arrow azimuth= mag_azimuth; Lab arrow dip=-field_dip
i.e., field_dip is degrees from vertical down - the hade [default]
[2] Lab arrow azimuth = mag_azimuth-90; Lab arrow dip = -field_dip
i.e., mag_azimuth is strike and field_dip is hade
[3] Lab arrow azimuth = mag_azimuth; Lab arrow dip = 90-field_dip
i.e., lab arrow same as field arrow, but field_dip was a hade.
[4] lab azimuth and dip are same as mag_azimuth, field_dip
[5] lab azimuth is same as mag_azimuth,lab arrow dip=field_dip-90
[6] Lab arrow azimuth = mag_azimuth-90; Lab arrow dip = 90-field_dip
[7] all others you will have to either customize your
self or e-mail [email protected] for help.
Magnetic declination convention:
Az will use supplied declination to correct azimuth
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.
OUTPUT
output saved in magic_measurements.txt & er_samples.txt formatted files
will overwrite any existing files
"""
#
# initialize variables
#
mag_file = ''
specnum=0
ub_file,samp_file,or_con,corr,meas_file = "","er_samples.txt","3","1","magic_measurements.txt"
pos_file,site_file="","er_sites.txt"
noave=1
args=sys.argv
bed_dip,bed_dip_dir="",""
samp_con,Z,average_bedding="2",1,"0"
meths='FS-FD'
sclass,lithology,_type="","",""
user,inst="",""
DecCorr=0.
location_name="unknown"
months=['Jan','Feb','Mar','Apr','May','Jun','Jul','Aug','Sep','Oct','Nov','Dec']
gmeths=""
#
#
dir_path='.'
if command_line:
if '-WD' in args:
ind=args.index("-WD")
dir_path=sys.argv[ind+1]
if "-h" in args:
print main.__doc__
return False
if "-f" in args:
ind=args.index("-f")
mag_file=sys.argv[ind+1]
if "-fpos" in args:
ind=args.index("-fpos")
pos_file=sys.argv[ind+1]
if "-F" in args:
ind=args.index("-F")
meas_file=sys.argv[ind+1]
if "-Fsa" in args:
ind=args.index("-Fsa")
samp_file=sys.argv[ind+1]
if "-Fsi" in args:
ind=args.index("-Fsi")
site_file=sys.argv[ind+1]
if "-ocn" in args:
ind=args.index("-ocn")
or_con=sys.argv[ind+1]
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "-mcd" in args:
ind=args.index("-mcd")
gmeths=(sys.argv[ind+1])
if "-loc" in args:
ind=args.index("-loc")
location_name=(sys.argv[ind+1])
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if "-ins" in args:
ind=args.index("-ins")
inst=args[ind+1]
if "-a" in args:
noave=0
#
ID = False
if '-ID' in args:
ind = args.index('-ID')
ID = args[ind+1]
#
if not command_line:
dir_path = kwargs.get('dir_path', '.')
mag_file = kwargs.get('mag_file', '')
pos_file = kwargs.get('pos_file', '')
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
site_file = kwargs.get('site_file', 'er_sites.txt')
or_con = kwargs.get('or_con', '3')
samp_con = kwargs.get('samp_con', '2')
corr = kwargs.get('corr', '1')
gmeths = kwargs.get('gmeths', '')
location_name = kwargs.get('location_name', '')
specnum = int(kwargs.get('specnum', 0))
inst = kwargs.get('inst', '')
noave = kwargs.get('noave', 1) # default is DO average
ID = kwargs.get('ID', '')
# format and fix variables acquired from command line args or input with **kwargs
if specnum!=0:specnum=-specnum
if ID:
input_dir_path = ID
else:
input_dir_path = dir_path
if samp_con:
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
return False, "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, "option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
if "6" in samp_con:
try:
Samps,file_type=pmag.magic_read(os.path.join(input_dir_path, 'er_samples.txt'))
except:
print "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
return False, "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
if file_type == 'bad_file':
print "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
return False, "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
if not mag_file:
print "mag file is required input"
return False, "mag file is required input"
output_dir_path = dir_path
mag_file = os.path.join(input_dir_path, mag_file)
samp_file = output_dir_path+'/'+samp_file
site_file = output_dir_path+'/'+site_file
meas_file= output_dir_path+'/'+meas_file
samplist=[]
try:
Samps,file_type=pmag.magic_read(samp_file)
for samp in Samps:
if samp['er_sample_name'] not in samplist: samplist.append(samp['er_sample_name'])
except:
Samps=[]
MagRecs=[]
try:
f=open(mag_file,'rU')
input=f.read()
f.close()
except Exception as ex:
print 'ex', ex
print "bad mag file"
return False, "bad mag file"
firstline,date=1,""
d=input.split('\xcd')
for line in d:
rec=line.split('\x00')
if firstline==1:
firstline=0
spec,vol="",1
for c in line[15:23]:
if c!='\x00':spec=spec+c
# check for bad sample name
test=spec.split('.')
date=""
if len(test)>1:
spec=test[0]
kk=24
while line[kk]!='\x01' and line[kk]!='\x00':
kk+=1
vcc=line[24:kk]
el=10
while rec[el].strip()!='':el+=1
date,comments=rec[el+7],[]
else:
el=9
while rec[el]!='\x01':el+=1
vcc,date,comments=rec[el-3],rec[el+7],[]
specname=spec.lower()
print 'importing ',specname
el+=8
while rec[el].isdigit()==False:
comments.append(rec[el])
el+=1
while rec[el]=="":el+=1
az=float(rec[el])
el+=1
while rec[el]=="":el+=1
pl=float(rec[el])
el+=1
while rec[el]=="":el+=1
bed_dip_dir=float(rec[el])
el+=1
while rec[el]=="":el+=1
bed_dip=float(rec[el])
el+=1
while rec[el]=="":el+=1
if rec[el]=='\x01':
bed_dip=180.-bed_dip
el+=1
while rec[el]=="":el+=1
fold_az=float(rec[el])
el+=1
while rec[el]=="":el+=1
fold_pl=rec[el]
el+=1
while rec[el]=="":el+=1
if rec[el]!="" and rec[el]!='\x02' and rec[el]!='\x01':
deccorr=float(rec[el])
az+=deccorr
bed_dip_dir+=deccorr
fold_az+=deccorr
if bed_dip_dir>=360:bed_dip_dir=bed_dip_dir-360.
if az>=360.:az=az-360.
if fold_az>=360.:fold_az=fold_az-360.
else:
deccorr=0
if specnum!=0:
sample=specname[:specnum]
else:
sample=specname
SampRec={}
SampRec["er_sample_name"]=sample
SampRec["er_location_name"]=location_name
SampRec["er_citation_names"]="This study"
labaz,labdip=pmag.orient(az,pl,or_con) # convert to labaz, labpl
#
# parse information common to all orientation methods
#
SampRec["sample_bed_dip"]='%7.1f'%(bed_dip)
SampRec["sample_bed_dip_direction"]='%7.1f'%(bed_dip_dir)
SampRec["sample_dip"]='%7.1f'%(labdip)
SampRec["sample_azimuth"]='%7.1f'%(labaz)
if vcc.strip()!="":vol=float(vcc)*1e-6 # convert to m^3 from cc
SampRec["sample_volume"]='%10.3e'%(vol) #
SampRec["sample_class"]=sclass
SampRec["sample_lithology"]=lithology
SampRec["sample_type"]=_type
SampRec["sample_declination_correction"]='%7.1f'%(deccorr)
methods=gmeths.split(':')
if deccorr!="0":
if 'SO-MAG' in methods:del methods[methods.index('SO-MAG')]
methods.append('SO-CMD-NORTH')
meths=""
for meth in methods:meths=meths+meth+":"
meths=meths[:-1]
SampRec["magic_method_codes"]=meths
if int(samp_con)<6 or int(samp_con) == 7:
site=pmag.parse_site(SampRec["er_sample_name"],samp_con,Z) # parse out the site name
SampRec["er_site_name"]=site
elif len(Samps)>1:
site,location="",""
for samp in Samps:
if samp["er_sample_name"] == SampRec["er_sample_name"]:
site=samp["er_site_name"]
location=samp["er_location_name"]
break
SampRec["er_location_name"]=samp["er_location_name"]
SampRec["er_site_name"]=samp["er_site_name"]
if sample not in samplist:
samplist.append(sample)
Samps.append(SampRec)
else:
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"]=specname
MagRec["er_sample_name"]=SampRec['er_sample_name']
MagRec["er_site_name"]=SampRec['er_site_name']
MagRec["er_location_name"]=location_name
el,demag=1,''
treat=rec[el]
if treat[-1]=='C':
demag='T'
elif treat!='NRM':
demag='AF'
el+=1
while rec[el]=="":el+=1
MagRec["measurement_dec"]=rec[el]
cdec=float(rec[el])
el+=1
while rec[el]=="":el+=1
MagRec["measurement_inc"]=rec[el]
cinc=float(rec[el])
el+=1
while rec[el]=="":el+=1
gdec=rec[el]
el+=1
while rec[el]=="":el+=1
ginc=rec[el]
el=skip(2,el,rec) # skip bdec,binc
# el=skip(4,el,rec) # skip gdec,ginc,bdec,binc
# print 'moment emu: ',rec[el]
MagRec["measurement_magn_moment"]='%10.3e'% (float(rec[el])*1e-3) # moment in Am^2 (from emu)
MagRec["measurement_magn_volume"]='%10.3e'% (float(rec[el])*1e-3/vol) # magnetization in A/m
el=skip(2,el,rec) # skip to xsig
MagRec["measurement_sd_x"]='%10.3e'% (float(rec[el])*1e-3) # convert from emu
el=skip(3,el,rec) # skip to ysig
MagRec["measurement_sd_y"]='%10.3e'% (float(rec[el])*1e-3) # convert from emu
el=skip(3,el,rec) # skip to zsig
MagRec["measurement_sd_z"]='%10.3e'% (float(rec[el])*1e-3) # convert from emu
el+=1 # skip to positions
MagRec["measurement_positions"]=rec[el]
# el=skip(5,el,rec) # skip to date
# mm=str(months.index(date[0]))
# if len(mm)==1:
# mm='0'+str(mm)
# else:
# mm=str(mm)
# dstring=date[2]+':'+mm+':'+date[1]+":"+date[3]
# MagRec['measurement_date']=dstring
MagRec["magic_instrument_codes"]=inst
MagRec["er_analyst_mail_names"]=""
MagRec["er_citation_names"]="This study"
MagRec["magic_method_codes"]=meas_type
if demag=="AF":
MagRec["treatment_ac_field"]='%8.3e' %(float(treat[:-2])*1e-3) # peak field in tesla
meas_type="LT-AF-Z"
MagRec["treatment_dc_field"]='0'
elif demag=="T":
MagRec["treatment_temp"]='%8.3e' % (float(treat[:-1])+273.) # temp in kelvin
meas_type="LT-T-Z"
MagRec['magic_method_codes']=meas_type
MagRecs.append(MagRec)
MagOuts=pmag.measurements_methods(MagRecs,noave)
MagOuts, keylist = pmag.fillkeys(MagOuts)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print "Measurements put in ",meas_file
SampsOut,sampkeys=pmag.fillkeys(Samps)
pmag.magic_write(samp_file,SampsOut,"er_samples")
Sites=[]
for samp in Samps:
SiteRec={}
SiteRec['er_site_name']=samp['er_site_name']
SiteRec['er_location_name']=samp['er_location_name']
SiteRec['site_definition']='s'
SiteRec['er_citation_names']='This study'
if 'sample_class' in samp.keys():SiteRec['site_class']=samp['sample_class']
if 'sample_lithology' in samp.keys():SiteRec['site_lithology']=samp['sample_lithology']
if 'sample_type' in samp.keys():SiteRec['site_lithology']=samp['sample_lithology']
if 'sample_lat' in samp.keys():
SiteRec['site_lat']=samp['sample_lat']
else:
SiteRec['site_lat']="-999"
if 'sample_lon' in samp.keys():
SiteRec['site_lon']=samp['sample_lon']
else:
SiteRec['site_lon']="-999"
if 'sample_height' in samp.keys():SiteRec['site_height']=samp['sample_height']
Sites.append(SiteRec)
pmag.magic_write(site_file,Sites,'er_sites')
return True, meas_file