def main():
"""
NAME
HUJI_magic.py
DESCRIPTION
converts Hebrew University, Jerusalem format files to magic_measurements format files
SYNTAX
HUJI_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify HUJI format input file, required
-F FILE: specify output file, default is magic_measurements.txt
-LP [colon delimited list of protocols, include all that apply]
AF: af demag
T: thermal including thellier but not trm acquisition
N: NRM only
TRM: trm acquisition
ANI: anisotropy experiment
G: triple AF demag (GRM protocol)
-spc NUM : specify number of characters to designate a specimen, default = 0
-loc LOCNAME : specify location/study name, must have either LOCNAME
-dc B PHI THETA: dc lab field (in micro tesla) and phi,theta, default is none
NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment
-ac B : peak AF field (in mT) for ARM acquisition, default is none
-ncn NCON: specify naming convention: default is #1 below
-A: don't average replicate measurements
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
[8] this is a synthetic sample with no site name
NB: all others you will have to customize your self
or e-mail [email protected] for help.
INPUT
Best to put separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.) in
seperate files (eg. af.txt, thermal.txt, etc.)
Spec: specimen name
Treat: treatment step
XXX T in Centigrade
XXX AF in mT
for special experiments:
Thellier:
XXX.0 first zero field step
XXX.1 first in field step [XXX.0 and XXX.1 can be done in any order]
XXX.2 second in-field step at lower temperature (pTRM check)
XXX.3 second zero-field step after infield (pTRM check step)
XXX.3 MUST be done in this order [XXX.0, XXX.1 [optional XXX.2] XXX.3]
AARM:
X.00 baseline step (AF in zero bias field - high peak field)
X.1 ARM step (in field step) where
X is the step number in the 15 position scheme
(see Appendix to Lecture 13 - Lectures in Paleomagnetism, 2007)
TRM:
XXX.YYY XXX is temperature step of total TRM
YYY is dc field in microtesla
Intensity assumed to be total moment in 10^3 Am^2 (emu)
Declination: Declination in geographic coordinate system
Inclination: Declination in geographic coordinate system
"""
# initialize some stuff
WD="."
version_num=pmag.get_version()
noave=0
methcode,inst="",""
phi,theta,peakfield,labfield=0,0,0,0
pTRM,MD,samp_con,Z=0,0,'1',1
dec=[315,225,180,135,45,90,270,270,270,90,180,180,0,0,0] # applied field for remanence anisotropy directions
inc=[0,0,0,0,0,-45,-45,0,45,45,45,-45,-90,-45,45]
demag="N"
er_location_name=""
citation='This study'
args=sys.argv
methcode="LP-NO" # NRM
syn=0
synfile='er_synthetics.txt'
samp_file,site_file,ErSamps='er_samples.txt','er_sites.txt',[]
samp_file_in=""
meas_file="magic_measurements.txt"
trm=0
irm=0
specnum=-1
#
# get command line arguments
#
user=""
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
if '-F' in args:
ind=args.index("-F")
meas_file=args[ind+1]
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file=args[ind+1]
try:
open(samp_file,'rU')
ErSamps,file_type=pmag.magic_read(samp_file)
print 'sample information will be appended to new er_samples.txt file'
except:
print 'sample information will be stored in new er_samples.txt file'
if '-f' in args:
ind=args.index("-f")
magfile=args[ind+1]
try:
input=open(magfile,'rU')
except:
print "bad input file name"
sys.exit()
else:
print "mag_file field is required option"
print main.__doc__
sys.exit()
if "-dc" in args:
ind=args.index("-dc")
labfield=float(args[ind+1])*1e-6
phi=float(args[ind+2])
theta=float(args[ind+3])
if "-ac" in args:
ind=args.index("-ac")
peakfield=float(args[ind+1])*1e-3
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if specnum!=0:specnum=-specnum
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if '-syn' in args:
syn=1
ind=args.index("-syn")
institution=args[ind+1]
syntype=args[ind+2]
if '-fsy' in args:
ind=args.index("-fsy")
synfile=args[ind+1]
if "-A" in args: noave=1
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="7"
if '-LP' in args:
ind=args.index("-LP")
codelist=args[ind+1]
codes=codelist.split(':')
if "AF" in codes:
demag='AF'
if'-dc' not in args: methcode="LT-AF-Z"
if'-dc' in args: methcode="LT-AF-I"
if "T" in codes:
demag="T"
if '-dc' not in args: methcode="LT-T-Z"
if '-dc' in args: methcode="LT-T-I"
if "I" in codes:
methcode="LP-IRM"
if "G" in codes: methcode="LT-AF-G"
if "TRM" in codes:
trm=1
noave=1
if demag=="T" and "ANI" in codes:
methcode="LP-AN-TRM"
if demag=="AF" and "ANI" in codes:
methcode="LP-AN-ARM"
if labfield==0: labfield=50e-6
if peakfield==0: peakfield=180
SynRecs,MagRecs=[],[]
Data=input.readlines()
for line in Data:
instcode="HUJI-2G"
if len(line)>1:
rec=line.split()
if rec[0][0]!='#': # HUJI way of marking bad data points
SynRec={}
MagRec={}
MagRec['er_location_name']=er_location_name
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["treatment_ac_field"]='0'
MagRec["treatment_dc_field"]='0'
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
meas_type="LT-NO"
mmddyy=rec[2].split('/') # break date into mon/day/year
hhmm=rec[3]
yyyy=mmddyy[2]
mm=int(mmddyy[0])
if mm<10:
mm="0"+str(mm)
else:
mm=str(mm)
dd=int(mmddyy[1])
if dd<10:
dd="0"+str(dd)
else:
dd=str(dd)
time=mmddyy[1].split(':')
MagRec["measurement_date"]=yyyy+":"+mm+":"+dd+":"+hhmm+":00.00"
MagRec["measurement_time_zone"]='30'
MagRec["measurement_positions"]='1'
if rec[4]=='T': demag="T"
if rec[4]=='A': demag="AF"
MagRec["er_specimen_name"]=rec[0]
if specnum!=0:
MagRec["er_sample_name"]=rec[0][:specnum]
else:
MagRec["er_sample_name"]=rec[0]
if samp_con!='8':
site=pmag.parse_site(MagRec['er_sample_name'],samp_con,Z)
MagRec["er_site_name"]=site
MagRec["er_location_name"]=er_location_name
else:
MagRec["er_site_name"]=""
MagRec["er_location_name"]=""
MagRec["er_synthetic_name"]=rec[0]
treat=rec[5].split('.')
if len(treat)==1:treat.append('.0')
if demag=="AF":
if methcode != "LP-AN-ARM":
MagRec["treatment_ac_field"]='%8.3e' %(float(treat[0])*1e-3) # peak field in tesla
meas_type="LT-AF-Z"
MagRec["treatment_dc_field"]='0'
else: # AARM experiment
if treat[1][0]=='0':
meas_type="LT-AF-Z"
MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
MagRec["treatment_dc_field"]='%8.3e'%(0)
if labfield!=0: print "inconsistency in mag file with lab field"
else:
meas_type="LT-AF-I"
ipos=int(treat[0])-1
MagRec["treatment_dc_field_phi"]='%7.1f' %(dec[ipos])
MagRec["treatment_dc_field_theta"]='%7.1f'% (inc[ipos])
MagRec["treatment_dc_field"]='%8.3e'%(labfield)
MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
else: # thermal treatment
MagRec["treatment_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
if trm==0: # demag=T and not trmaq
if treat[1][0]=='0':
meas_type="LT-T-Z"
else:
MagRec["treatment_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MagRec["treatment_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MagRec["treatment_dc_field_theta"]='%7.1f' % (theta) # labfield theta
if treat[1][0]=='1':meas_type="LT-T-I" # in-field thermal step
if treat[1][0]=='2':
meas_type="LT-PTRM-I" # pTRM check
pTRM=1
if treat[1][0]=='3':
MagRec["treatment_dc_field"]='0' # this is a zero field step
meas_type="LT-PTRM-MD" # pTRM tail check
else:
meas_type="LT-T-I" # trm acquisition experiment
MagRec["treatment_dc_field"]='%8.3e' % (float(treat[1])*1e-6) # labfield in tesla (convert from microT)
MagRec["measurement_magn_moment"]='%10.3e'% (float(rec[10])*1e-3) # moment in Am^2 (from emu)
MagRec["measurement_dec"]=rec[6]
MagRec["measurement_inc"]=rec[7]
MagRec["magic_instrument_codes"]=instcode
MagRec["er_citation_names"]=citation
MagRec["magic_method_codes"]=meas_type
MagRec["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRecs.append(MagRec)
else:
print 'skipping: ',rec[0]
MagOuts=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print "results put in ",meas_file
def main():
"""
NAME
LIVMW_magic.py
DESCRIPTION
converts Liverpool microwave format files to magic_measurements format files
SYNTAX
LIVMW_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify liverpool format input file, required
-usr USER: identify user, default is ""
-ins INST: identify instrument, e.g., LIV-TRISTAN, LIV-OLD14GHZ, default is ""
-loc LOCNAME : specify location/study name, required
-F FILE: specify output file, default is magic_measurements.txt
-Fsa FILE: specify er_samples formatted file for appending, default is new er_samples.txt
-spc NUM : specify number of characters to designate a specimen, default = 1
-sit Site_name : specify site name for this specimen
-unc measurement units are uncalibrated (default is uAm^2)
-B PHI THETA: dc lab field phi, theta, default is 0, 90
-ncn NCON: specify naming convention - required if -sit not specified
Sample naming convention:
do not use if -sit option used!
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
"""
# initialize some stuff
version_num = pmag.get_version()
noave = 0
methcode, instcode = "", ""
phi, theta, peakfield, labfield = 0, 0, 0, 0
pMRM, MD, samp_con, Z, site = 0, 0, "6", "", ""
er_location_name = ""
citation = "This study"
args = sys.argv
methcode = "LP-NO" # NRM
specnum, measnum = 1, 1
powt_max = 0
ErSamps, Samps = [], []
#
# get command line arguments
#
dirpath = "."
meas_file, samp_file = dirpath + "/magic_measurements.txt", dirpath + "/er_samples.txt"
user = ""
unc = 0
if "-WD" in args:
ind = args.index("-WD")
dirpath = args[ind + 1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind = args.index("-usr")
user = args[ind + 1]
if "-ins" in args:
ind = args.index("-ins")
instcode = args[ind + 1]
if "-F" in args:
ind = args.index("-F")
meas_file = dirpath + "/" + args[ind + 1]
if "-Fsa" in args:
ind = args.index("-Fsa")
samp_file = args[ind + 1]
samp_file = dirpath + "/" + samp_file
try:
open(samp_file, "rU")
ErSamps, file_type = pmag.magic_read(samp_file)
print "sample information will be appended to new er_samples.txt file"
except:
print "er_samples.txt file does not exist"
print "sample information will be stored in new er_samples.txt file"
if "-f" in args:
ind = args.index("-f")
magfile = args[ind + 1]
magfile = dirpath + "/" + magfile
try:
input = open(magfile, "rU")
except:
print "bad mag file name"
sys.exit()
else:
print "mag_file field is required option"
print main.__doc__
sys.exit()
if "-B" in args:
ind = args.index("-B")
phi = args[ind + 1]
theta = args[ind + 2]
else:
phi, theta = "0.", "90."
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind + 1])
if specnum != 0:
specnum = -specnum
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if "-unc" in args:
unc = 1
if "-sit" in args:
ind = args.index("-sit")
site = args[ind + 1]
if "-ncn" in args:
ind = args.index("-ncn")
samp_con = sys.argv[ind + 1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "7"
if samp_con == "6" and site == "":
print "you must either specify a naming convention, or a site name"
print main.__doc__
sys.exit()
MagRecs = []
if len(ErSamps) > 1:
for samp in ErSamps:
if samp["er_sample_name"] not in Samps:
Samps.append(samp["er_sample_name"])
Data = input.readlines()
if 1: # never mind
for line in Data:
if len(line) > 1:
rec = line.split(",")
MagRec = {}
MagRec["er_citation_names"] = "This study"
MagRec["er_location_name"] = er_location_name
MagRec["magic_software_packages"] = version_num
MagRec["treatment_temp"] = "%8.3e" % (273) # room temp in kelvin
MagRec["measurement_temp"] = "%8.3e" % (273) # room temp in kelvin
MagRec["treatment_ac_field"] = "0"
MagRec["treatment_dc_field"] = "0"
MagRec["treatment_dc_field_phi"] = ""
MagRec["treatment_dc_field_theta"] = ""
MagRec["treatment_mw_integral"] = ""
meas_type = "LT-NO"
MagRec["er_specimen_name"] = rec[0][1:-1]
MagRec["er_location_name"] = er_location_name
if specnum != 0:
MagRec["er_sample_name"] = rec[0][1:-1][:specnum]
else:
MagRec["er_sample_name"] = rec[0][1:-1]
if site == "":
site = pmag.parse_site(MagRec["er_sample_name"], samp_con, Z)
MagRec["er_site_name"] = site
MagRec["treatment_mw_power"] = rec[2]
MagRec["treatment_mw_time"] = rec[3]
powt = int(float(MagRec["treatment_mw_power"]) * (float(MagRec["treatment_mw_time"])))
MagRec["treatment_mw_energy"] = "%7.1f" % (powt)
if powt > powt_max:
powt_max = powt
treat = rec[1].strip('"').upper()
if treat == "Z": # in zero field
meas_type = "LT-M-Z" # as opposed to LT-MV-Z
if powt < powt_max:
meas_type = "LT-PMRM-Z"
elif treat == "A": # in zero field
meas_type = "LT-M-I" # as opposed to LT-MV-I
labfield = float(rec[10]) * 1e-6 # assuming uT, convert to T
MagRec["treatment_dc_field"] = "%8.3e" % (labfield) # labfield in tesla (convert from microT)
MagRec["treatment_dc_field_phi"] = phi # labfield phi
MagRec["treatment_dc_field_theta"] = theta # labfield theta
if powt < powt_max:
meas_type = "LT-PMRM-I"
if len(rec) > 10:
MagRec["treatment_mw_integral"] = rec[10]
if unc == 0:
MagRec["measurement_magn_moment"] = "%10.3e" % (float(rec[4]) * 1e-6) # moment in Am^2 (from uAm^2)
if unc == 1:
MagRec["measurement_magnitude"] = rec[4] # uncalibrated moment
cart = []
cart.append(float(rec[7]))
cart.append(float(rec[8]))
cart.append(float(rec[9]))
dir = pmag.cart2dir(cart)
MagRec["measurement_dec"] = "%9.3f" % (dir[0])
MagRec["measurement_inc"] = "%9.3f" % (dir[1])
MagRec["magic_instrument_codes"] = instcode
MagRec["magic_method_codes"] = meas_type
MagRec["measurement_flag"] = "g"
MagRec["measurement_standard"] = "u"
MagRec["measurement_number"] = "%i" % (measnum)
MagRec["magic_experiment_name"] = MagRec["er_specimen_name"] + ":" + methcode
measnum += 1
MagRecs.append(MagRec)
if MagRec["er_sample_name"] not in Samps: # add this puppy to the list in er_samples.txt
Samps.append(MagRec["er_sample_name"])
ErSamp = {}
ErSamp["er_sample_name"] = Samps[-1]
ErSamp["er_location_name"] = MagRec["er_location_name"]
ErSamp["er_site_name"] = site
ErSamp["er_citation_names"] = "This study"
gdec = float(rec[5])
ginc = float(rec[6])
az, pl = pmag.get_azpl(dir[0], dir[1], gdec, ginc)
ErSamp["sample_azimuth"] = "%7.1f" % az
ErSamp["sample_dip"] = "%7.1f" % pl
ErSamps.append(ErSamp)
MagOuts = pmag.mw_measurements_methods(MagRecs)
pmag.magic_write(meas_file, MagOuts, "magic_measurements")
print "measurements put in ", meas_file
pmag.magic_write(samp_file, ErSamps, "er_samples")
print "sample names put in ", samp_file
def main():
"""
NAME
MsT_magic.py
DESCRIPTION
converts MsT data (T,M) to magic_measurements format files
SYNTAX
MsT_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify T,M format input file, required
-fsa SFILE: name with sample, site, location information
-F FILE: specify output file, default is MsT_measurements.txt
-dc H: specify applied field during measurement, default is 0.5 T
-syn : This is a synthetic specimen and has no sample/site/location information
-spn SPEC: specimen name
-spc NUM : specify number of characters to designate a specimen, default = 0
-loc LOCNAME : specify location/study name, must have either LOCNAME or SAMPFILE or be a synthetic
-ncn NCON: specify naming convention: default is #1 below
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
INPUT files:
T M: T is in Centigrade and M is uncalibrated magnitude
"""
# initialize some stuff
samp_con,Z="1","0"
dir_path='.'
citation='This study'
args=sys.argv
specnum,measnum=0,1
#
# get command line arguments
#
user=""
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
meas_file=dir_path+"/MsT_measurements.txt"
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
labfield='0.5'
if "-dc" in args:
ind=args.index("-dc")
labfield=args[ind+1]
if '-F' in args:
ind=args.index("-F")
meas_file=dir_path+'/'+args[ind+1]
if "-fsa" in args:
ind=args.index("-fsa")
samp_file=dir_path+'/'+args[ind+1]
Samps,file_type=pmag.magic_read(samp_file)
if '-f' in args:
ind=args.index("-f")
infile=dir_path+'/'+args[ind+1]
try:
input=open(infile,'rU')
except:
print "bad mag file name"
sys.exit()
else:
print main.__doc__
print "-f is required option"
sys.exit()
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if specnum!=0:specnum=-specnum
er_location_name,syn,specimen_name='unknown',0,'unknown'
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-spn" in args:
ind=args.index("-spn")
specimen_name=args[ind+1]
else:
print main.__doc__
print "-spn is required option"
sys.exit()
if "-syn" in args: syn=1
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
samp_con=sys.argv[ind+1]
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="7"
MagRecs,specs=[],[]
version_num=pmag.get_version()
data=input.readlines()
T0=float(data[0].split()[0])
for line in data:
instcode=""
if len(line)>1:
MagRec={}
if syn==0: MagRec['er_location_name']=er_location_name
MagRec['magic_software_packages']=version_num
MagRec["treatment_dc_field"]=labfield
rec=line.split()
T=float(rec[0])
MagRec["measurment_temp"]='%8.3e' % (float(rec[0])+273.) # temp in kelvin
if T>T0:
MagRec["magic_method_codes"]='LP-MW-I'
elif T<T0:
MagRec["magic_method_codes"]='LP-MC-I'
T0=T
else:
print 'skipping repeated temperature step'
MagRec["magic_method_codes"]=''
T0=T
MagRec["measurement_magnitude"]='%10.3e'% (float(rec[1])) # uncalibrated magnitude
if syn==0:
MagRec["er_specimen_name"]=specimen_name
MagRec["er_site_name"]=""
if specnum!=0:
MagRec["er_sample_name"]=specimen_name[:specnum]
else:
MagRec["er_sample_name"]=specimen_name
if "-fsa" in args:
for samp in Samps:
if samp["er_sample_name"] == MagRec["er_sample_name"]:
MagRec["er_location_name"]=samp["er_location_name"]
MagRec["er_site_name"]=samp["er_site_name"]
break
elif int(samp_con)!=6:
site=pmag.parse_site(MagRec['er_sample_name'],samp_con,Z)
MagRec["er_site_name"]=site
if MagRec['er_site_name']=="":
print 'No site name found for: ',MagRec['er_specimen_name'],MagRec['er_sample_name']
if MagRec["er_location_name"]=="":
print 'no location name for: ',MagRec["er_specimen_name"]
else:
MagRec["er_synthetic_name"]=specimen_name
MagRec["er_location_name"]=""
MagRec["er_sample_name"]=""
MagRec["er_site_name"]=""
MagRec["er_specimen_name"]=""
MagRec["magic_instrument_codes"]=instcode
MagRec["er_analyst_mail_names"]=user
MagRec["er_citation_names"]=citation
MagRec["measurement_flag"]='g'
MagRec["measurement_number"]=str(measnum)
measnum+=1
MagRecs.append(MagRec)
for rec in MagRecs: # sort out the measurements by experiment type
rec['magic_experiment_name']=specimen_name
if rec['magic_method_codes']=='LP-MW-I':
rec["magic_experiment_name"]=specimen_name+':LP-MW-I:Curie'
elif rec['magic_method_codes']=='LP-MC-I':
rec["magic_experiment_name"]=specimen_name+':LP-MC-I'
pmag.magic_write(meas_file,MagRecs,'magic_measurements')
print "results put in ",meas_file
def main():
"""
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
TDT_magic.py
DESCRIPTION
converts ThellierTool format files to magic_measurements format files
SYNTAX
TDT_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify .tdt format input file, required
-F FILE: specify output file, default is magic_measurements.txt
-spc NUM : specify number of characters to designate a specimen, default = 0
-loc LOCNAME : specify location/study name, must have either LOCNAME or SAMPFILE or be a synthetic
-ncn NCON: specify naming convention: default is #1 below
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
INPUT
Format of ThellierTool files:
2 line header:
Thellier-tdt
XX.0 (field in microtesla)
Data:
Spec Treat Intensity Declination Inclination
Spec: specimen name
Treat: treatment step
XXX.00 first zero field step
XXX.11 (or .1) first in field step [XXX.0 and XXX.1 can be done in any order]
XXX.12 (or .2)second in-field step at lower temperature (pTRM check)
XXX.13 (or .3) second zero-field step after infield (pTRM check step)
XXX.13 MUST be done in this order [XXX.00, XXX.11 [optional XXX.12] XXX.13]
Intensity assumed to be total moment in 10^3 Am^2 (emu)
Declination: Declination in specimen coordinate system
Inclination: Declination in specimen coordinate system
"""
# initialize some stuff
noave=0
methcode,inst="",""
phi,theta,labfield=0,90,0
pTRM,MD,samp_con,Z=0,0,'1',1
demag="N"
er_location_name=""
citation='This study'
args=sys.argv
methcode="LP-NO"
specnum=0
#
# get command line arguments
#
dir_path='.'
meas_file,samp_file="magic_measurements.txt","er_samples.txt"
user=""
if "-WD" in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
if '-F' in args:
ind=args.index("-F")
meas_file=dir_path+'/'+args[ind+1]
if '-f' in args:
ind=args.index("-f")
magfile=dir_path+'/'+args[ind+1]
try:
input=open(magfile,'rU')
except:
print "bad mag file name"
sys.exit()
else:
print "mag_file field is required option"
print main.__doc__
sys.exit()
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if specnum!=0:specnum=-specnum
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
MagRecs=[]
demag="T"
version_num=pmag.get_version()
data=input.readlines()
rec=data[1].split()
labfield=float(rec[0])*1e-6
for line in data[2:]:
rec=line.split()
if len(rec)>2:
MagRec={}
MagRec['er_location_name']=er_location_name
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["treatment_ac_field"]='0'
MagRec["treatment_dc_field"]='0'
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
meas_type="LT-NO"
MagRec["er_specimen_name"]=rec[0]
MagRec["er_synthetic_name"]=""
MagRec["er_site_name"]=""
if specnum!=0:
MagRec["er_sample_name"]=rec[0][:specnum]
else:
MagRec["er_sample_name"]=rec[0]
if "-fsa" in args:
for samp in Samps:
if samp["er_sample_name"] == MagRec["er_sample_name"]:
MagRec["er_location_name"]=samp["er_location_name"]
MagRec["er_site_name"]=samp["er_site_name"]
break
elif int(samp_con)!=6:
site=pmag.parse_site(MagRec['er_sample_name'],samp_con,Z)
MagRec["er_site_name"]=site
if MagRec['er_site_name']=="":
print 'No site name found for: ',MagRec['er_specimen_name'],MagRec['er_sample_name']
if MagRec["er_location_name"]=="":
print 'no location name for: ',MagRec["er_specimen_name"]
if rec[1]==".00":rec[1]="0.00"
treat=rec[1].split('.')
if float(rec[1])==0:
pass
if len(treat)==1:treat.append('0')
MagRec["treatment_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
if treat[1][0]=='0':
meas_type="LT-T-Z"
else:
MagRec["treatment_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MagRec["treatment_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MagRec["treatment_dc_field_theta"]='%7.1f' % (theta) # labfield theta
if treat[1][-1]=='1':meas_type="LT-T-I" # in-field thermal step
if treat[1][-1]=='2':
meas_type="LT-PTRM-I" # pTRM check
pTRM=1
if treat[1][-1]=='3':
MagRec["treatment_dc_field"]='0' # this is a zero field step
meas_type="LT-PTRM-MD" # pTRM tail check
MagRec["measurement_magn_moment"]='%10.3e'% (float(rec[2])*1e-3) # moment in Am^2 (from emu)
MagRec["measurement_dec"]=rec[3]
MagRec["measurement_inc"]=rec[4]
MagRec["er_analyst_mail_names"]=user
MagRec["er_citation_names"]=citation
MagRec["magic_method_codes"]=meas_type
MagRec["measurement_flag"]='g'
MagRec["er_specimen_name"]=rec[0]
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRecs.append(MagRec)
MagOuts=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print "results put in ",meas_file
def main():
"""
NAME
s_magic.py
DESCRIPTION
converts .s format data to magic_measurements format.
SYNTAX
s_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f SFILE specifies the .s file name
-sig last column has sigma
-typ Anisotropy type: AMS,AARM,ATRM (default is AMS)
-F RFILE specifies the rmag_anisotropy file name
-usr USER specify username
-loc location specify location/study name
-spc NUM : specify number of characters to
designate a specimen, default = 0
-spn SPECNAME, this specimen has the name SPECNAME
-n first column has specimen name
-crd [s,g,t], specify coordinate system of data
s=specimen,g=geographic,t=tilt adjusted, default is 's'
-ncn NCON: naming conventionconvention NCON
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
DEFAULT
RFILE: rmag_anisotropy.txt
INPUT
X11,X22,X33,X12,X23,X13 (.s format file)
X11,X22,X33,X12,X23,X13,sigma (.s format file with -sig option)
SID, X11,X22,X33,X12,X23,X13 (.s format file with -n option)
OUTPUT
rmag_anisotropy.txt format file
NOTE
because .s files do not have specimen names or location information, the output MagIC files
will have to be changed prior to importing to data base.
"""
sfile,anisfile="","rmag_anisotropy.txt"
location='unknown'
user=""
sitename,specnum='unknown',0
samp_con,Z="",1
user=""
dir_path='.'
name,sigma,spec=0,0,'unknown'
type='AMS'
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 "-spc" in sys.argv:
ind=sys.argv.index("-spc")
specnum=int(sys.argv[ind+1])
if specnum!=0:specnum=-specnum
if "-spn" in sys.argv:
ind=sys.argv.index("-spn")
spec=sys.argv[ind+1]
if '-f' in sys.argv:
ind=sys.argv.index('-f')
sfile = sys.argv[ind+1]
if '-sig' in sys.argv: sigma=1
if '-typ' in sys.argv:
ind=sys.argv.index('-typ')
type = sys.argv[ind+1]
if '-F' in sys.argv:
ind=sys.argv.index('-F')
anisfile = sys.argv[ind+1]
if '-usr' in sys.argv:
ind=sys.argv.index('-usr')
user = sys.argv[ind+1]
if '-loc' in sys.argv:
ind=sys.argv.index('-loc')
location = sys.argv[ind+1]
if "-n" in sys.argv:
name=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 "-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')
#
# get down to bidness
sfile=dir_path+'/'+sfile
anisfile=dir_path+'/'+anisfile
input=open(sfile,'rU')
AnisRecs=[]
linecnt=0
citation="This study"
# read in data
for line in input.readlines():
AnisRec={}
rec=line.split()
if name==1:
k=1
spec=rec[0]
else:
k=0
trace=float(rec[k])+float(rec[k+1])+float(rec[k+2])
s1='%10.9e'%(float(rec[k])/trace)
s2='%10.9e'%(float(rec[k+1])/trace)
s3='%10.9e'%(float(rec[k+2])/trace)
s4='%10.9e'%(float(rec[k+3])/trace)
s5='%10.9e'%(float(rec[k+4])/trace)
s6='%10.9e'%(float(rec[k+5])/trace)
AnisRec["er_citation_names"]=citation
AnisRec["er_specimen_name"]=spec
if specnum!=0:
AnisRec["er_sample_name"]=spec[:specnum]
else:
AnisRec["er_sample_name"]=spec
if samp_con=="6":
for samp in Samps:
if samp['er_sample_name']==AnisRec["er_sample_name"]:
sitename=samp['er_site_name']
location=samp['er_location_name']
elif samp_con!="":
sitename=pmag.parse_site(AnisRec['er_sample_name'],samp_con,Z)
AnisRec["er_location_name"]=location
AnisRec["er_site_name"]=sitename
AnisRec["er_anylist_mail_names"]=user
if type=='AMS':
AnisRec["anisotropy_type"]="AMS"
AnisRec["magic_experiment_names"]=spec+":LP-X"
else:
AnisRec["anisotropy_type"]=type
AnisRec["magic_experiment_names"]=spec+":LP-"+type
AnisRec["anisotropy_s1"]=s1
AnisRec["anisotropy_s2"]=s2
AnisRec["anisotropy_s3"]=s3
AnisRec["anisotropy_s4"]=s4
AnisRec["anisotropy_s5"]=s5
AnisRec["anisotropy_s6"]=s6
if sigma==1:AnisRec["anisotropy_sigma"]='%10.8e'%(float(rec[k+6])/trace)
AnisRec["anisotropy_unit"]='SI'
AnisRec["anisotropy_tilt_correction"]=coord
AnisRec["magic_method_codes"]='LP-'+type
AnisRecs.append(AnisRec)
pmag.magic_write(anisfile,AnisRecs,'rmag_anisotropy')
print 'data saved in ',anisfile
def main():
"""
NAME
sio_magic.py
DESCRIPTION
converts SIO .mag format files to magic_measurements format files
SYNTAX
sio_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify .mag format input file, required
-fsa SAMPFILE : specify er_samples.txt file relating samples, site and locations names,default is none
-F FILE: specify output file, default is magic_measurements.txt
-Fsy: specify er_synthetics file, default is er_sythetics.txt
-Fsa: specify output er_samples file, default is NONE (only for LDGO formatted files)
-LP [colon delimited list of protocols, include all that apply]
AF: af demag
T: thermal including thellier but not trm acquisition
S: Shaw method
I: IRM (acquisition)
I3d: 3D IRM experiment
N: NRM only
TRM: trm acquisition
ANI: anisotropy experiment
D: double AF demag
G: triple AF demag (GRM protocol)
CR: cooling rate experiment.
The treatment coding of the measurement file should be: XXX.00,XXX.10, XXX.20 ...XX.70 etc. (XXX.00 is optional)
where XXX in the temperature and .10,.20... are running numbers of the cooling rates steps.
XXX.00 is optional zerofield baseline. XXX.70 is alteration check.
syntax in sio_magic is: -LP CR xxx,yyy,zzz,.....xx -A
where xx, yyy,zzz...xxx are cooling time in [K/minutes], seperated by comma, ordered at the same order as XXX.10,XXX.20 ...XX.70
if you use a zerofield step then no need to specify the cooling rate for the zerofield
It is important to add to the command line the -A option so the measurements will not be evraged.
But users need to make sure that there are no duplicate meaurements in the file
-V [1,2,3] units of IRM field in volts using ASC coil #1,2 or 3
-spc NUM : specify number of characters to designate a specimen, default = 0
-loc LOCNAME : specify location/study name, must have either LOCNAME or SAMPFILE or be a synthetic
-syn INST TYPE: sets these specimens as synthetics created at institution INST and of type TYPE
-ins INST : specify which demag instrument was used (e.g, SIO-Suzy or SIO-Odette),default is ""
-dc B PHI THETA: dc lab field (in micro tesla) and phi,theta, default is none
NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment
-ac B : peak AF field (in mT) for ARM acquisition, default is none
-ncn NCON: specify naming convention: default is #1 below
-A: don't average replicate measurements
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
[8] synthetic - has no site name
[9] ODP naming convention
INPUT
Best to put separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.) in
seperate .mag files (eg. af.mag, thermal.mag, etc.)
Format of SIO .mag files:
Spec Treat CSD Intensity Declination Inclination [optional metadata string]
Spec: specimen name
Treat: treatment step
XXX T in Centigrade
XXX AF in mT
for special experiments:
Thellier:
XXX.0 first zero field step
XXX.1 first in field step [XXX.0 and XXX.1 can be done in any order]
XXX.2 second in-field step at lower temperature (pTRM check)
XXX.3 second zero-field step after infield (pTRM check step)
XXX.3 MUST be done in this order [XXX.0, XXX.1 [optional XXX.2] XXX.3]
AARM:
X.00 baseline step (AF in zero bias field - high peak field)
X.1 ARM step (in field step) where
X is the step number in the 15 position scheme
(see Appendix to Lecture 13 - http://magician.ucsd.edu/Essentials_2)
ATRM:
X.00 optional baseline
X.1 ATRM step (+X)
X.2 ATRM step (+Y)
X.3 ATRM step (+Z)
X.4 ATRM step (-X)
X.5 ATRM step (-Y)
X.6 ATRM step (-Z)
X.7 optional alteration check (+X)
TRM:
XXX.YYY XXX is temperature step of total TRM
YYY is dc field in microtesla
Intensity assumed to be total moment in 10^3 Am^2 (emu)
Declination: Declination in specimen coordinate system
Inclination: Declination in specimen coordinate system
Optional metatdata string: mm/dd/yy;hh:mm;[dC,mT];xx.xx;UNITS;USER;INST;NMEAS
hh in 24 hours.
dC or mT units of treatment XXX (see Treat above) for thermal or AF respectively
xx.xxx DC field
UNITS of DC field (microT, mT)
INST: instrument code, number of axes, number of positions (e.g., G34 is 2G, three axes,
measured in four positions)
NMEAS: number of measurements in a single position (1,3,200...)
"""
# initialize some stuff
infile_type="mag"
noave=0
methcode,inst="LP-NO",""
phi,theta,peakfield,labfield=0,0,0,0
pTRM,MD,samp_con,Z=0,0,'1',1
dec=[315,225,180,135,45,90,270,270,270,90,180,180,0,0,0]
inc=[0,0,0,0,0,-45,-45,0,45,45,45,-45,-90,-45,45]
tdec=[0,90,0,180,270,0,0,90,0]
tinc=[0,0,90,0,0,-90,0,0,90]
missing=1
demag="N"
er_location_name=""
citation='This study'
args=sys.argv
fmt='old'
syn=0
synfile='er_synthetics.txt'
samp_file,ErSamps='',[]
trm=0
irm=0
specnum=0
coil=""
#
# get command line arguments
#
meas_file="magic_measurements.txt"
user=""
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
if '-F' in args:
ind=args.index("-F")
meas_file=args[ind+1]
if '-Fsy' in args:
ind=args.index("-Fsy")
synfile=args[ind+1]
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file=args[ind+1]
try:
open(samp_file,'rU')
ErSamps,file_type=pmag.magic_read(samp_file)
print 'sample information will be appended to new er_samples.txt file'
except:
print 'sample information will be stored in new er_samples.txt file'
if '-f' in args:
ind=args.index("-f")
magfile=args[ind+1]
try:
input=open(magfile,'rU')
except:
print "bad mag file name"
sys.exit()
else:
print "mag_file field is required option"
print main.__doc__
sys.exit()
if "-dc" in args:
ind=args.index("-dc")
labfield=float(args[ind+1])*1e-6
phi=float(args[ind+2])
theta=float(args[ind+3])
if "-ac" in args:
ind=args.index("-ac")
peakfield=float(args[ind+1])*1e-3
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if specnum!=0:specnum=-specnum
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-fsa" in args:
ind=args.index("-fsa")
Samps,file_type=pmag.magic_read(args[ind+1])
if '-syn' in args:
syn=1
ind=args.index("-syn")
institution=args[ind+1]
syntype=args[ind+2]
if '-fsy' in args:
ind=args.index("-fsy")
synfile=args[ind+1]
if "-ins" in args:
ind=args.index("-ins")
inst=args[ind+1]
if "-A" in args: noave=1
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4-" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7-" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="7"
if '-LP' in args:
ind=args.index("-LP")
codelist=args[ind+1]
codes=codelist.split(':')
if "AF" in codes:
demag='AF'
if'-dc' not in args: methcode="LT-AF-Z"
if'-dc' in args: methcode="LT-AF-I"
if "T" in codes:
demag="T"
if '-dc' not in args: methcode="LT-T-Z"
if '-dc' in args: methcode="LT-T-I"
if "I" in codes:
methcode="LP-IRM"
irmunits="mT"
if "I3d" in codes:
methcode="LT-T-Z:LP-IRM-3D"
if "S" in codes:
demag="S"
methcode="LP-PI-TRM:LP-PI-ALT-AFARM"
trm_labfield=labfield
ans=raw_input("DC lab field for ARM step: [50uT] ")
if ans=="":
arm_labfield=50e-6
else:
arm_labfield=float(ans)*1e-6
ans=raw_input("temperature for total trm step: [600 C] ")
if ans=="":
trm_peakT=600+273 # convert to kelvin
else:
trm_peakT=float(ans)+273 # convert to kelvin
if "G" in codes: methcode="LT-AF-G"
if "D" in codes: methcode="LT-AF-D"
if "TRM" in codes:
demag="T"
trm=1
if "CR" in codes:
demag="T"
cooling_rate_experiment=1
ind=args.index("CR")
coolling_times=args[ind+1]
coolling_times_list=coolling_times.split(',')
if "-V" in args:
methcode="LP-IRM"
ind=args.index("-V")
irmunits="V"
coil=args[ind+1]
if coil not in ["1","2","3"]:
print main.__doc__
print 'not a valid coil specification'
sys.exit()
if demag=="T" and "ANI" in codes:
methcode="LP-AN-TRM"
if demag=="T" and "CR" in codes:
methcode="LP-CR-TRM"
if demag=="AF" and "ANI" in codes:
methcode="LP-AN-ARM"
if labfield==0: labfield=50e-6
if peakfield==0: peakfield=.180
SynRecs,MagRecs=[],[]
version_num=pmag.get_version()
if 1:
#if infile_type=="SIO format":
for line in input.readlines():
instcode=""
if len(line)>2:
SynRec={}
MagRec={}
MagRec['er_location_name']=er_location_name
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["treatment_ac_field"]='0'
MagRec["treatment_dc_field"]='0'
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
meas_type="LT-NO"
rec=line.split()
if rec[1]==".00":rec[1]="0.00"
treat=rec[1].split('.')
if methcode=="LP-IRM":
if irmunits=='mT':
labfield=float(treat[0])*1e-3
else:
labfield=pmag.getfield(irmunits,coil,treat[0])
if rec[1][0]!="-":
phi,theta=0.,90.
else:
phi,theta=0.,-90.
meas_type="LT-IRM"
MagRec["treatment_dc_field"]='%8.3e'%(labfield)
MagRec["treatment_dc_field_phi"]='%7.1f'%(phi)
MagRec["treatment_dc_field_theta"]='%7.1f'%(theta)
if len(rec)>6:
code1=rec[6].split(';') # break e.g., 10/15/02;7:45 indo date and time
if len(code1)==2: # old format with AM/PM
missing=0
code2=code1[0].split('/') # break date into mon/day/year
code3=rec[7].split(';') # break e.g., AM;C34;200 into time;instr/axes/measuring pos;number of measurements
yy=int(code2[2])
if yy <90:
yyyy=str(2000+yy)
else: yyyy=str(1900+yy)
mm=int(code2[0])
if mm<10:
mm="0"+str(mm)
else: mm=str(mm)
dd=int(code2[1])
if dd<10:
dd="0"+str(dd)
else: dd=str(dd)
time=code1[1].split(':')
hh=int(time[0])
if code3[0]=="PM":hh=hh+12
if hh<10:
hh="0"+str(hh)
else: hh=str(hh)
min=int(time[1])
if min<10:
min= "0"+str(min)
else: min=str(min)
MagRec["measurement_date"]=yyyy+":"+mm+":"+dd+":"+hh+":"+min+":00.00"
MagRec["measurement_time_zone"]='SAN'
if inst=="":
if code3[1][0]=='C':instcode='SIO-bubba'
if code3[1][0]=='G':instcode='SIO-flo'
else:
instcode=''
MagRec["measurement_positions"]=code3[1][2]
elif len(code1)>2: # newest format (cryo7 or later)
if "LP-AN-ARM" not in methcode:labfield=0
fmt='new'
date=code1[0].split('/') # break date into mon/day/year
yy=int(date[2])
if yy <90:
yyyy=str(2000+yy)
else: yyyy=str(1900+yy)
mm=int(date[0])
if mm<10:
mm="0"+str(mm)
else: mm=str(mm)
dd=int(date[1])
if dd<10:
dd="0"+str(dd)
else: dd=str(dd)
time=code1[1].split(':')
hh=int(time[0])
if hh<10:
hh="0"+str(hh)
else: hh=str(hh)
min=int(time[1])
if min<10:
min= "0"+str(min)
else: min=str(min)
MagRec["measurement_date"]=yyyy+":"+mm+":"+dd+":"+hh+":"+min+":00.00"
MagRec["measurement_time_zone"]='SAN'
if inst=="":
if code1[6][0]=='C':instcode='SIO-bubba'
if code1[6][0]=='G':instcode='SIO-flo'
else:
instcode=''
if len(code1)>1:
MagRec["measurement_positions"]=code1[6][2]
else:
MagRec["measurement_positions"]=code1[7] # takes care of awkward format with bubba and flo being different
if user=="":user=code1[5]
if code1[2][-1]=='C':
demag="T"
if code1[4]=='microT' and float(code1[3])!=0. and "LP-AN-ARM" not in methcode: labfield=float(code1[3])*1e-6
if code1[2]=='mT' and methcode!="LP-IRM":
demag="AF"
if code1[4]=='microT' and float(code1[3])!=0.: labfield=float(code1[3])*1e-6
if code1[4]=='microT' and labfield!=0. and meas_type!="LT-IRM":
phi,theta=0.,-90.
if demag=="T": meas_type="LT-T-I"
if demag=="AF": meas_type="LT-AF-I"
MagRec["treatment_dc_field"]='%8.3e'%(labfield)
MagRec["treatment_dc_field_phi"]='%7.1f'%(phi)
MagRec["treatment_dc_field_theta"]='%7.1f'%(theta)
if code1[4]=='' or labfield==0. and meas_type!="LT-IRM":
if demag=='T':meas_type="LT-T-Z"
if demag=="AF":meas_type="LT-AF-Z"
MagRec["treatment_dc_field"]='0'
if syn==0:
MagRec["er_specimen_name"]=rec[0]
MagRec["er_synthetic_name"]=""
MagRec["er_site_name"]=""
if specnum!=0:
MagRec["er_sample_name"]=rec[0][:specnum]
else:
MagRec["er_sample_name"]=rec[0]
if "-fsa" in args:
samp=pmag.get_dictitem(Samps,'er_sample_name',MagRec['er_sample_name'],'T')
if len(samp)>0:
MagRec["er_location_name"]=samp[0]["er_location_name"]
MagRec["er_site_name"]=samp[0]["er_site_name"]
else:
MagRec['er_location_name']=''
MagRec["er_site_name"]=''
elif int(samp_con)!=6:
site=pmag.parse_site(MagRec['er_sample_name'],samp_con,Z)
MagRec["er_site_name"]=site
if MagRec['er_site_name']=="":
print 'No site name found for: ',MagRec['er_specimen_name'],MagRec['er_sample_name']
if MagRec["er_location_name"]=="":
print 'no location name for: ',MagRec["er_specimen_name"]
else:
if specnum!=0:
MagRec["er_sample_name"]=rec[0][:specnum]
else:
MagRec["er_sample_name"]=rec[0]
MagRec["er_site_name"]=""
MagRec["er_synthetic_name"]=MagRec["er_specimen_name"]
SynRec["er_synthetic_name"]=MagRec["er_specimen_name"]
site=pmag.parse_site(MagRec['er_sample_name'],samp_con,Z)
SynRec["synthetic_parent_sample"]=site
SynRec["er_citation_names"]="This study"
SynRec["synthetic_institution"]=institution
SynRec["synthetic_type"]=syntype
SynRecs.append(SynRec)
if float(rec[1])==0:
pass
elif demag=="AF":
if methcode != "LP-AN-ARM":
MagRec["treatment_ac_field"]='%8.3e' %(float(rec[1])*1e-3) # peak field in tesla
if meas_type=="LT-AF-Z": MagRec["treatment_dc_field"]='0'
else: # AARM experiment
if treat[1][0]=='0':
meas_type="LT-AF-Z:LP-AN-ARM:"
MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
MagRec["treatment_dc_field"]='%8.3e'%(0)
if labfield!=0 and methcode!="LP-AN-ARM": print "Warning - inconsistency in mag file with lab field - overriding file with 0"
else:
meas_type="LT-AF-I:LP-AN-ARM"
ipos=int(treat[0])-1
MagRec["treatment_dc_field_phi"]='%7.1f' %(dec[ipos])
MagRec["treatment_dc_field_theta"]='%7.1f'% (inc[ipos])
MagRec["treatment_dc_field"]='%8.3e'%(labfield)
MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
elif demag=="T" and methcode == "LP-AN-TRM":
MagRec["treatment_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
if treat[1][0]=='0':
meas_type="LT-T-Z:LP-AN-TRM"
MagRec["treatment_dc_field"]='%8.3e'%(0)
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
else:
MagRec["treatment_dc_field"]='%8.3e'%(labfield)
if treat[1][0]=='7': # alteration check as final measurement
meas_type="LT-PTRM-I:LP-AN-TRM"
else:
meas_type="LT-T-I:LP-AN-TRM"
# find the direction of the lab field in two ways:
# (1) using the treatment coding (XX.1=+x, XX.2=+y, XX.3=+z, XX.4=-x, XX.5=-y, XX.6=-z)
ipos_code=int(treat[1][0])-1
# (2) using the magnetization
DEC=float(rec[4])
INC=float(rec[5])
if INC < 45 and INC > -45:
if DEC>315 or DEC<45: ipos_guess=0
if DEC>45 and DEC<135: ipos_guess=1
if DEC>135 and DEC<225: ipos_guess=3
if DEC>225 and DEC<315: ipos_guess=4
else:
if INC >45: ipos_guess=2
if INC <-45: ipos_guess=5
# prefer the guess over the code
ipos=ipos_guess
MagRec["treatment_dc_field_phi"]='%7.1f' %(tdec[ipos])
MagRec["treatment_dc_field_theta"]='%7.1f'% (tinc[ipos])
# check it
if ipos_guess!=ipos_code and treat[1][0]!='7':
print "-E- ERROR: check specimen %s step %s, ATRM measurements, coding does not match the direction of the lab field!"%(rec[0],".".join(list(treat)))
elif demag=="S": # Shaw experiment
if treat[1][1]=='0':
if int(treat[0])!=0:
MagRec["treatment_ac_field"]='%8.3e' % (float(treat[0])*1e-3) # AF field in tesla
MagRec["treatment_dc_field"]='0'
meas_type="LT-AF-Z" # first AF
else:
meas_type="LT-NO"
MagRec["treatment_ac_field"]='0'
MagRec["treatment_dc_field"]='0'
elif treat[1][1]=='1':
if int(treat[0])==0:
MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
MagRec["treatment_dc_field"]='%8.3e'%(arm_labfield)
MagRec["treatment_dc_field_phi"]='%7.1f'%(phi)
MagRec["treatment_dc_field_theta"]='%7.1f'%(theta)
meas_type="LT-AF-I"
else:
MagRec["treatment_ac_field"]='%8.3e' % ( float(treat[0])*1e-3) # AF field in tesla
MagRec["treatment_dc_field"]='0'
meas_type="LT-AF-Z"
elif treat[1][1]=='2':
if int(treat[0])==0:
MagRec["treatment_ac_field"]='0'
MagRec["treatment_dc_field"]='%8.3e'%(trm_labfield)
MagRec["treatment_dc_field_phi"]='%7.1f'%(phi)
MagRec["treatment_dc_field_theta"]='%7.1f'%(theta)
MagRec["treatment_temp"]='%8.3e' % (trm_peakT)
meas_type="LT-T-I"
else:
MagRec["treatment_ac_field"]='%8.3e' % ( float(treat[0])*1e-3) # AF field in tesla
MagRec["treatment_dc_field"]='0'
meas_type="LT-AF-Z"
elif treat[1][1]=='3':
if int(treat[0])==0:
MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
MagRec["treatment_dc_field"]='%8.3e'%(arm_labfield)
MagRec["treatment_dc_field_phi"]='%7.1f'%(phi)
MagRec["treatment_dc_field_theta"]='%7.1f'%(theta)
meas_type="LT-AF-I"
else:
MagRec["treatment_ac_field"]='%8.3e' % ( float(treat[0])*1e-3) # AF field in tesla
MagRec["treatment_dc_field"]='0'
meas_type="LT-AF-Z"
# Cooling rate experient # added by rshaar
elif demag=="T" and methcode == "LP-CR-TRM":
MagRec["treatment_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
if treat[1][0]=='0':
meas_type="LT-T-Z:LP-CR-TRM"
MagRec["treatment_dc_field"]='%8.3e'%(0)
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
else:
MagRec["treatment_dc_field"]='%8.3e'%(labfield)
if treat[1][0]=='7': # alteration check as final measurement
meas_type="LT-PTRM-I:LP-CR-TRM"
else:
meas_type="LT-T-I:LP-CR-TRM"
MagRec["treatment_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MagRec["treatment_dc_field_theta"]='%7.1f' % (theta) # labfield theta
indx=int(treat[1][0])-1
# alteration check matjed as 0.7 in the measurement file
if indx==6:
cooling_time= coolling_times_list[-1]
else:
cooling_time=coolling_times_list[indx]
MagRec["measurement_description"]="cooling_rate"+":"+cooling_time+":"+"K/min"
elif demag!='N':
if len(treat)==1:treat.append('0')
MagRec["treatment_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
if trm==0: # demag=T and not trmaq
if treat[1][0]=='0':
meas_type="LT-T-Z"
else:
MagRec["treatment_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MagRec["treatment_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MagRec["treatment_dc_field_theta"]='%7.1f' % (theta) # labfield theta
if treat[1][0]=='1':meas_type="LT-T-I" # in-field thermal step
if treat[1][0]=='2':
meas_type="LT-PTRM-I" # pTRM check
pTRM=1
if treat[1][0]=='3':
MagRec["treatment_dc_field"]='0' # this is a zero field step
meas_type="LT-PTRM-MD" # pTRM tail check
else:
labfield=float(treat[1])*1e-6
MagRec["treatment_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MagRec["treatment_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MagRec["treatment_dc_field_theta"]='%7.1f' % (theta) # labfield theta
meas_type="LT-T-I:LP-TRM" # trm acquisition experiment
MagRec["measurement_csd"]=rec[2]
MagRec["measurement_magn_moment"]='%10.3e'% (float(rec[3])*1e-3) # moment in Am^2 (from emu)
MagRec["measurement_dec"]=rec[4]
MagRec["measurement_inc"]=rec[5]
MagRec["magic_instrument_codes"]=instcode
MagRec["er_analyst_mail_names"]=user
MagRec["er_citation_names"]=citation
if "LP-IRM-3D" in methcode : meas_type=methcode
#MagRec["magic_method_codes"]=methcode.strip(':')
MagRec["magic_method_codes"]=meas_type
MagRec["measurement_flag"]='g'
MagRec["er_specimen_name"]=rec[0]
if 'std' in rec[0]:
MagRec["measurement_standard"]='s'
else:
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
#print MagRec['treatment_temp']
MagRecs.append(MagRec)
MagOuts=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print "results put in ",meas_file
if samp_file!="":
pmag.magic_write(samp_file,ErSamps,'er_samples')
print "sample orientations put in ",samp_file
if len(SynRecs)>0:
pmag.magic_write(synfile,SynRecs,'er_synthetics')
print "synthetics put in ",synfile
def main():
"""
NAME
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 """"
def main():
"""
NAME
CIT_magic.py
DESCRIPTION
converts CIT and .sam format files to magic_measurements format files
SYNTAX
CIT_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify .sam format input file, required
-fsi SITEFILE : specify file with site names and locations [tab delimited magic file]
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsp FILE: specify output er_specimens.txt file, default is er_specimens.txt
-Fsi FILE: specify output er_sites.txt file, default is er_sites.txt
-Fsa FILE: specify output er_samples.txt file, default is er_samples.txt # LORI
-n [gm,kg,cc,m3]: specify normalization
-A: don't average replicate measurements
-spc NUM : specify number of characters to designate a specimen, default = 0
-ncn NCON: specify naming convention
-loc LOCNAME : specify location/study name, must have either LOCNAME or SITEFILE or be a synthetic
-mcd [FS-FD:SO-MAG,.....] colon delimited list for method codes applied to all specimens in .sam file
-dc B PHI THETA: dc lab field (in micro tesla) and phi,theta, default is none
NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment
-ac B : peak AF field (in mT) for ARM acquisition, default is none
INPUT
Best to put separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.)
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) [default]
[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.
"""
#
#
norm = 'cc'
samp_con, Z = '3', 1
meas_file = 'magic_measurements.txt'
spec_file = 'er_specimens.txt'
samp_file = 'er_samples.txt'
site_file = 'er_sites.txt'
ErSpecs, ErSamps, ErSites, ErLocs, ErCits = [], [], [], [], []
MeasRecs = []
specnum, units, locname = 0, "1", "unknown"
citation = "This study"
dir_path = '.'
args = sys.argv
if '-WD' in args:
ind = args.index("-WD")
dir_path = args[ind + 1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind = args.index("-usr")
user = args[ind + 1]
if '-F' in args:
ind = args.index("-F")
meas_file = args[ind + 1]
if '-Fsp' in args:
ind = args.index("-Fsp")
spec_file = args[ind + 1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = args[ind + 1]
if '-Fsi' in args: # LORI addition
ind = args.index("-Fsi")
site_file = args[ind + 1]
if '-loc' in args:
ind = args.index("-loc")
locname = args[ind + 1]
if '-mcd' in args:
ind = args.index("-mcd")
methods = args[ind + 1]
else:
methods = 'SO-MAG'
if '-spc' in args:
ind = args.index("-spc")
specnum = -int(args[ind + 1])
if '-n' in args:
ind = args.index("-n")
norm = args[ind + 1]
if "-A" in args:
avg = 1
else:
avg = 0
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"
if '-f' in args:
ind = args.index("-f")
magfile = args[ind + 1]
# LJ
if '-ID' in args:
ind = args.index('-ID')
input_dir_path = args[ind + 1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
# LJ
magfile = input_dir_path + '/' + magfile
spec_file = output_dir_path + '/' + spec_file
samp_file = output_dir_path + '/' + samp_file
site_file = output_dir_path + '/' + site_file
meas_file = output_dir_path + '/' + meas_file
try:
input = open(magfile, 'r')
except Exception as ex:
print "bad sam file name"
sys.exit()
File = input.readlines()
sids, ln, format = [], 0, 'CIT'
formats = ['CIT', '2G', 'APP', 'JRA']
ErLocRec = {}
ErLocRec["er_location_name"] = locname
ErLocRec["er_citation_name"] = citation
comment = File[ln]
if comment == 'CIT':
format = comment
ln += 1
comment = File[ln]
print comment
ln += 1
specimens, samples, sites = [], [], []
if format == 'CIT':
line = File[ln].split()
site_lat = line[0]
site_lon = line[1]
ErLocRec["location_begin_lat"] = site_lat
ErLocRec["location_begin_lon"] = site_lon
ErLocRec["location_end_lat"] = site_lat
ErLocRec["location_end_lon"] = site_lon
ErLocs.append(ErLocRec)
Cdec = float(line[2])
for k in range(ln + 1, len(File)):
line = File[k]
rec = line.split()
specimen = rec[0]
specimens.append(specimen)
for specimen in specimens:
ErSpecRec, ErSampRec, ErSiteRec = {}, {}, {}
if specnum != 0:
sample = specimen[:specnum]
else:
sample = specimen
site = pmag.parse_site(sample, samp_con, Z)
ErSpecRec['er_specimen_name'] = specimen
ErSpecRec['er_sample_name'] = sample
ErSpecRec['er_site_name'] = site
ErSpecRec['er_location_name'] = locname
ErSpecRec['er_citation_name'] = citation
ErSampRec['er_sample_name'] = sample
ErSampRec['er_site_name'] = site
ErSampRec['er_location_name'] = locname
ErSampRec['er_citation_name'] = citation
ErSampRec['magic_method_codes'] = methods
ErSampRec['sample_declination_correction'] = '%7.1f' % (Cdec)
ErSiteRec['er_site_name'] = site
ErSiteRec['er_location_name'] = locname
ErSiteRec['er_citation_name'] = citation
ErSiteRec['site_lat'] = site_lat
ErSiteRec['site_lon'] = site_lon
f = open(input_dir_path + '/' + specimen, 'rU')
Lines = f.readlines()
comment = ""
line = Lines[0].split()
if len(line) > 2: comment = line[2]
info = Lines[1].split()
vol = float(info[-1])
if vol != 1.0:
if norm == 'cc': units = "1"
if norm == 'm3': units = "2"
ErSampRec['specimen_weight'] = ""
if units == "1" or "":
ErSampRec['specimen_volume'] = '%10.3e' % (vol * 1e-6)
else:
ErSampRec['specimen_volume'] = '%10.3e' % (vol)
else:
if norm == 'cc': units = "1"
if norm == 'm3': units = "2"
ErSampRec['specimen_volume'] = ""
if units == "1" or "":
ErSampRec['specimen_weight'] = '%10.3e' % (vol * 1e-3)
else:
ErSampRec['specimen_weight'] = '%10.3e' % (vol)
dip = float(info[-2])
dip_direction = float(info[-3]) + Cdec + 90.
sample_dip = -float(info[-4])
sample_azimuth = float(info[-5]) + Cdec - 90.
if len(info) > 5:
ErSampRec['sample_height'] = info[-6]
else:
ErSampRec['sample_height'] = '0'
ErSampRec['sample_azimuth'] = '%7.1f' % (sample_azimuth)
ErSampRec['sample_dip'] = '%7.1f' % (sample_dip)
ErSampRec['sample_bed_dip'] = '%7.1f' % (dip)
ErSampRec['sample_bed_dip_direction'] = '%7.1f' % (dip_direction)
ErSampRec['sample_class'] = ''
ErSampRec['sample_type'] = ''
ErSampRec['sample_lithology'] = ''
if Cdec != 0 or Cdec != "":
ErSampRec['magic_method_codes'] = 'SO-CMD-NORTH'
else:
ErSampRec['magic_method_codes'] = 'SO-MAG'
for line in Lines[2:len(Lines) - 1]:
MeasRec = ErSpecRec.copy()
treat_type = line[0:3]
treat = line[3:6]
if treat_type.strip(
) == 'NRM' or treat == ' ': # reverting back. otherwise breaks examples.
MeasRec['magic_method_codes'] = 'LT-NO'
MeasRec['measurement_temp'] = '273'
MeasRec['treatment_temp'] = '273'
MeasRec['treatment_dc_field'] = '0'
MeasRec['treatment_ac_field'] = '0'
elif treat_type.strip() == 'AF':
MeasRec['magic_method_codes'] = 'LT-AF-Z'
MeasRec['measurement_temp'] = '273'
MeasRec['treatment_temp'] = '273'
MeasRec['treatment_dc_field'] = '0'
MeasRec['treatment_ac_field'] = '%10.3e' % (float(treat) *
1e-3)
elif treat_type.strip() == 'TT':
MeasRec['magic_method_codes'] = 'LT-T-Z'
MeasRec['measurement_temp'] = '273'
MeasRec['treatment_temp'] = '%7.1f' % (float(treat) + 273)
MeasRec['treatment_dc_field'] = '0'
MeasRec['treatment_ac_field'] = '0'
elif treat_type.strip() == 'LT' or treat_type.strip() == 'LN2':
MeasRec['magic_method_codes'] = 'LT-LT-Z'
MeasRec['measurement_temp'] = '273'
MeasRec['treatment_temp'] = '77'
MeasRec['treatment_dc_field'] = '0'
MeasRec['treatment_ac_field'] = '0'
else:
print "trouble with your treatment steps"
MeasRec['measurement_dec'] = line[46:51]
MeasRec['measurement_inc'] = line[52:58]
M = '%8.2e' % (float(line[31:39]) * vol * 1e-3) # convert to Am2
MeasRec['measurement_magn_moment'] = M
MeasRec['measurement_x_sd'] = '%8.2e' % (
float(line[58:67]) * 1e-8) #(convert e-5emu to Am2)
MeasRec['measurement_y_sd'] = '%8.2e' % (float(line[67:76]) * 1e-8)
MeasRec['measurement_z_sd'] = '%8.2e' % (float(line[76:85]) * 1e-8)
MeasRec['measurement_csd'] = '%7.1f' % (eval(line[41:46]))
MeasRec['magic_instrument_codes'] = line[85:]
MeasRec["measurement_positions"] = '1'
MeasRecs.append(MeasRec)
ErSpecs.append(ErSpecRec)
if sample not in samples:
samples.append(sample)
ErSamps.append(ErSampRec)
site = pmag.parse_site(sample, samp_con, Z)
if site not in sites:
sites.append(site)
ErSites.append(ErSiteRec)
pmag.magic_write(spec_file, ErSpecs, 'er_specimens')
print 'specimens stored in ', spec_file
pmag.magic_write(samp_file, ErSamps, 'er_samples')
print 'samples stored in ', samp_file
pmag.magic_write(site_file, ErSites, 'er_sites')
print 'sites stored in ', site_file
Fixed = pmag.measurements_methods(MeasRecs, avg)
pmag.magic_write(meas_file, Fixed, 'magic_measurements')
print 'data stored in ', meas_file
def main():
"""
NAME
kly-asc_magic.py
DESCRIPTION
converts ascii files generated by SUFAR ver.1.2 to MagIC formated
files for use with PmagPy plotting software
SYNTAX
kly-asc_magic.py -h [command line options]
OPTIONS
-h: prints the help message and quits
-f FILE: specify .asc input file name
-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
DEFAULTS
AFILE: rmag_anisotropy.txt
RFILE: rmag_results.txt
SFILE: default is to create new er_specimen.txt file
USER: ""
LOC: "unknown"
INST: "PGL-KLY3"
SPEC: 0 sample name is same as site (if SPEC is 1, sample is all but last character)
creates new 'er_specimens.txt' 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] all others you will have to either customize your
self or e-mail [email protected] for help.
"""
citation = "This study"
cont = 0
samp_con, Z = "1", 1
ResRecs, SucRecs, SpecRecs, SampRecs, SiteRecs = [], [], [], [], []
user, locname, specfile = "", "locname", "er_specimens.txt"
isspec, inst, specnum = "0", "PGL-KLY3", 0
aoutput, routput = "rmag_anisotropy.txt", "rmag_results.txt"
dir_path = "."
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 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")
ascfile = sys.argv[ind + 1]
elif "-i" not in sys.argv:
print "must specify ascii input file or use interactive option [-i]\n\n "
print main.__doc__
sys.exit()
if "-Fa" in sys.argv:
ind = sys.argv.index("-Fa")
aoutput = sys.argv[ind + 1]
if "-Fr" in sys.argv:
ind = sys.argv.index("-Fr")
routput = sys.argv[ind + 1]
if "-Fs" in sys.argv:
ind = sys.argv.index("-Fs")
specfile = sys.argv[ind + 1]
isspec = "1"
elif "-loc" in sys.argv:
ind = sys.argv.index("-loc")
locname = sys.argv[ind + 1]
samp_con, Z = pmag.get_samp_con()
if "-spc" in sys.argv:
ind = sys.argv.index("-spc")
specnum = -(int(sys.argv[ind + 1]))
if "-i" in sys.argv:
user = raw_input("Who made these measurements? \n Use the earthref mailname please, [] \n")
if user == "":
user = ""
isspec = raw_input(
" Is there an existing er_specimen file [1] or do you wish to create one? [0] <return> to skip "
)
if isspec == "1":
specfile = raw_input("Enter er_specimen file name: [er_specimens.txt] ")
if specfile == "":
specfile = "er_specimens.txt"
elif isspec == "0":
locname = raw_input("Enter location name for this study ")
samp_con, Z = pmag.get_samp_con()
ans = raw_input("How many characters to specify specimen [1] ")
if ans == "":
specnum = -1
else:
specnum = -int(ans)
aoutput = raw_input("Filename for output [rmag_anisotropy.txt] ")
if aoutput == "":
aoutput = "rmag_anisotropy.txt"
routput = raw_input("Filename for results output [rmag_results.txt] ")
if routput == "":
routput = "rmag_results.txt"
ascfile = raw_input("Enter asc file for processing ")
if isspec == "1":
specs, file_type = pmag.magic_read(specfile)
try:
input = open(ascfile, "rU")
except:
print "Error opening file: ", ascfile
sys.exit()
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
SucRec, SpecRec, SampRec, SiteRec, ResRec = {}, {}, {}, {}, {}
specname = words[0]
SucRec["er_specimen_name"] = specname
if isspec == "1":
for spec in specs:
if spec["er_specimen_name"] == specname:
SucRec["er_sample_name"] = spec["er_sample_name"]
SucRec["er_site_name"] = spec["er_site_name"]
SucRec["er_location_name"] = spec["er_location_name"]
break
elif isspec == "0":
SucRec["er_sample_name"] = specname[:specnum]
SpecRec["er_sample_name"] = specname[:specnum]
SiteRec["er_sample_name"] = specname[:specnum]
SucRec["er_site_name"] = pmag.parse_site(SucRec["er_sample_name"], samp_con, Z)
SpecRec["er_site_name"] = pmag.parse_site(SucRec["er_sample_name"], samp_con, Z)
SampRec["er_site_name"] = pmag.parse_site(SucRec["er_sample_name"], samp_con, Z)
SiteRec["er_site_name"] = pmag.parse_site(SucRec["er_sample_name"], samp_con, Z)
SucRec["er_location_name"] = locname
SpecRec["er_location_name"] = locname
SampRec["er_location_name"] = locname
SiteRec["er_location_name"] = locname
SpecRec["er_citation_names"] = "This study"
SampRec["er_citation_names"] = "This study"
SiteRec["er_citation_names"] = "This study"
ResRec["er_sample_names"] = SucRec["er_sample_name"]
ResRec["er_site_names"] = SucRec["er_site_name"]
SucRec["er_citation_names"] = "This study"
SucRec["magic_instrument_codes"] = inst
SucRec["magic_method_codes"] = "LP-X:AE-H:LP-AN-MS"
SucRec["magic_experiment_names"] = specname + ":" + "LP-AN-MS"
SucRec["er_analyst_mail_names"] = user
SucRec["anisotropy_type"] = "AMS"
SucRec["anisotropy_n"] = "15"
ResRec["rmag_result_name"] = SucRec["er_specimen_name"] + "Specimen Coordinates"
ResRec["er_specimen_names"] = SucRec["er_specimen_name"]
ResRec["magic_experiment_names"] = SucRec["magic_experiment_names"]
ResRec["anisotropy_type"] = SucRec["anisotropy_type"]
if "Azi" in words and isspec == "0":
SampRec["sample_azimuth"] = words[1]
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
if "[A/m]" in words:
k += 2 # read in second line down
line = Data[k]
words = line.split()
SucRec["anisotropy_mean"] = words[1]
SucRec["anisotropy_sigma"] = words[2]
SucRec["anisotropy_unit"] = "SI"
ResRec["anisotropy_ftest"] = words[3]
ResRec["anisotropy_ftest12"] = words[4]
ResRec["anisotropy_ftest23"] = words[5]
if "susceptibilities" in words:
k += 2 # read in second line down
line = Data[k]
words = line.split()
ResRec["anisotropy_t1"] = "%6.4f" % (float(words[0]) / 3.0)
ResRec["anisotropy_t2"] = "%6.4f" % (float(words[1]) / 3.0)
ResRec["anisotropy_t3"] = "%6.4f" % (float(words[2]) / 3.0)
ResRec["anisotropy_v1_eta_semi_angle"] = words[3]
ResRec["anisotropy_v2_eta_semi_angle"] = words[4]
ResRec["anisotropy_v3_eta_semi_angle"] = words[5]
k += 2 # read in second line down
line = Data[k]
words = line.split()
ResRec["anisotropy_v1_zeta_semi_angle"] = words[4]
ResRec["anisotropy_v2_zeta_semi_angle"] = words[5]
ResRec["anisotropy_v3_zeta_semi_angle"] = words[6]
if "factors" in words:
k += 4 # read in second line down
line = Data[k]
words = line.split()
ResRec["anisotropy_l"] = words[0]
ResRec["anisotropy_f"] = words[1]
ResRec["anisotropy_p"] = words[2]
ResRec["anisotropy_pp"] = words[3]
ResRec["anisotropy_t"] = words[4]
if "Specimen" in words: # first part of specimen data
ResRec["anisotropy_v1_dec"] = words[2]
ResRec["anisotropy_v2_dec"] = words[3]
ResRec["anisotropy_v3_dec"] = words[4]
SucRec["anisotropy_s1"] = "%6.4f" % (float(words[5]) / 3.0) # eigenvalues sum to unity - not 3
SucRec["anisotropy_s2"] = "%6.4f" % (float(words[6]) / 3.0)
SucRec["anisotropy_s3"] = "%6.4f" % (float(words[7]) / 3.0)
k += 1
line = Data[k]
words = line.split()
ResRec["anisotropy_v1_inc"] = words[2]
ResRec["anisotropy_v2_inc"] = words[3]
ResRec["anisotropy_v3_inc"] = words[4]
SucRec["anisotropy_s4"] = "%6.4f" % (float(words[5]) / 3.0) # eigenvalues sum to unity - not 3
SucRec["anisotropy_s5"] = "%6.4f" % (float(words[6]) / 3.0)
SucRec["anisotropy_s6"] = "%6.4f" % (float(words[7]) / 3.0)
SucRec["anisotropy_tilt_correction"] = "-1"
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_tilt_correction"] = "-1"
k += 2
line = Data[k]
words = line.split()
SucRecs.append(SucRec)
ResRecs.append(ResRec)
ResRecG = copy.copy(ResRec)
SucRecG = copy.copy(SucRec)
ResRecG["rmag_result_name"] = SucRec["er_specimen_name"] + "Geographic Coordinates"
ResRecG["anisotropy_v1_dec"] = words[2]
ResRecG["anisotropy_v2_dec"] = words[3]
ResRecG["anisotropy_v3_dec"] = words[4]
SucRecG["anisotropy_s1"] = "%6.4f" % (float(words[5]) / 3.0) # eigenvalues sum to unity - not 3
SucRecG["anisotropy_s2"] = "%6.4f" % (float(words[6]) / 3.0)
SucRecG["anisotropy_s3"] = "%6.4f" % (float(words[7]) / 3.0)
k += 1
line = Data[k]
words = line.split()
ResRecG["anisotropy_v1_inc"] = words[2]
ResRecG["anisotropy_v2_inc"] = words[3]
ResRecG["anisotropy_v3_inc"] = words[4]
SucRecG["anisotropy_s4"] = "%6.4f" % (float(words[5]) / 3.0) # eigenvalues sum to unity - not 3
SucRecG["anisotropy_s5"] = "%6.4f" % (float(words[6]) / 3.0)
SucRecG["anisotropy_s6"] = "%6.4f" % (float(words[7]) / 3.0)
SucRecG["anisotropy_tilt_correction"] = "0"
ResRecG["anisotropy_tilt_correction"] = "0"
Dgeo, Igeo = float(ResRecG["anisotropy_v1_dec"]), float(ResRecG["anisotropy_v1_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"]
k += 2
line = Data[k]
words = line.split()
ResRecs.append(ResRecG)
SucRecs.append(SucRecG)
SucRecT = copy.copy(SucRecG)
ResRecT = copy.copy(ResRecG)
ResRecT["anisotropy_v1_dec"] = words[3]
ResRecT["anisotropy_v2_dec"] = words[4]
ResRecT["anisotropy_v3_dec"] = words[5]
SucRecT["anisotropy_s1"] = "%6.4f" % (float(words[6]) / 3.0) # eigenvalues sum to unity - not 3
SucRecT["anisotropy_s2"] = "%6.4f" % (float(words[7]) / 3.0)
SucRecT["anisotropy_s3"] = "%6.4f" % (float(words[8]) / 3.0)
k += 1 # skip down 1
line = Data[k]
words = line.split()
ResRecT["anisotropy_v1_inc"] = words[2]
ResRecT["anisotropy_v2_inc"] = words[3]
ResRecT["anisotropy_v3_inc"] = words[4]
Dtilt, Itilt = float(ResRecT["anisotropy_v1_dec"]), float(ResRecT["anisotropy_v1_inc"])
DipDir, Dip = pmag.get_tilt(Dgeo, Igeo, Dtilt, Itilt)
SampRec["sample_bed_dip_direction"] = "%7.1f" % (DipDir)
SampRec["sample_bed_dip"] = "%7.1f" % (Dip)
SucRecT["anisotropy_s4"] = "%6.4f" % (float(words[5]) / 3.0) # eigenvalues sum to unity - not 3
SucRecT["anisotropy_s5"] = "%6.4f" % (float(words[6]) / 3.0)
SucRecT["anisotropy_s6"] = "%6.4f" % (float(words[7]) / 3.0)
SucRecT["anisotropy_tilt_correction"] = "100"
ResRecT["anisotropy_tilt_correction"] = "100"
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"]
SucRecs.append(SucRecT)
ResRecs.append(ResRecT)
SpecRecs.append(SpecRec)
SampRecs.append(SampRec)
SiteRecs.append(SiteRec)
k += 1
pmag.magic_write(aoutput, SucRecs, "rmag_anisotropy")
print "anisotropy tensors put in ", aoutput
pmag.magic_write(routput, ResRecs, "rmag_results")
print "anisotropy results put in ", routput
if isspec == "0":
output = "er_specimens.txt"
pmag.magic_write(output, SpecRecs, "er_specimens")
print "specimen info put in ", output
output = "er_samples.txt"
pmag.magic_write(output, SampRecs, "er_samples")
print "sample info put in ", output
output = "er_sites.txt"
pmag.magic_write(output, SiteRecs, "er_sites")
print "site info put in ", output
print """"
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():
"""
NAME
UR_jr6_magic.py
DESCRIPTION
converts University of Rome JR6 format files to magic_measurements format files
SYNTAX
UR_jr6_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsa FILE: specify output er_samples.txt file for appending, default is er_samples.txt
-dc B PHI THETA: dc lab field (in micro tesla) and phi,theta, default is none
NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment
-ac B : peak AF field (in mT) for ARM acquisition, default is none
-A : don't average replicate measurements
-spc NUM : specify number of characters to designate a specimen, default = 0
-loc LOCNAME : specify location/study name, must have either LOCNAME or SAMPFILE or be a synthetic
-mcd: specify sampling method codes as a colon delimited string: [default is: FS-FD:SO-POM:SO-SUN]
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-SUN orientations are from a sun compass
SO-MAG orientations are from a magnetic compass
SO-MAG-CMD orientations declination corrected magnetic compass
-ncn NCON: specify naming convention: default is #1 below
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
[8] synthetic - has no site name
[9] ODP naming convention
INPUT
Put data from separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.) in separate directory
"""
#
#
version_num=pmag.get_version()
er_location_name=""
ErSpecs,ErSamps,ErSites,ErLocs,ErCits=[],[],[],[],[]
MagRecs=[]
citation="This study"
dir_path,demag='.','NRM'
args=sys.argv
noave=0
specnum=0
sampmeths='FS-FD:SO-POM:SO-SUN'
samp_con,Z="4","2"
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
meas_file=dir_path+'/'+'magic_measurements.txt'
samp_file=dir_path+'/'+'er_samples.txt'
if "-h" in args:
print main.__doc__
sys.exit()
if "-A" in args: noave=1
if '-F' in args:
ind=args.index("-F")
meas_file=dir_path+'/'+args[ind+1]
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file=dir_path+'/'+args[ind+1]
ErSamps,file_type=pmag.magic_read(samp_file)
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "-mcd" in args:
ind=args.index("-mcd")
sampmeths=(sys.argv[ind+1])
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if specnum!=0:specnum=-specnum
if '-LP' in args:
ind=args.index("-LP")
codelist=args[ind+1]
codes=codelist.split(':')
if "AF" in codes:
demag='AF'
if'-dc' not in args: methcode="LT-AF-Z"
if'-dc' in args: methcode="LT-AF-I"
if "T" in codes:
demag="T"
if '-dc' not in args: methcode="LT-T-Z"
if '-dc' in args: methcode="LT-T-I"
if "I" in codes:
methcode="LP-IRM"
if "S" in codes:
demag="S"
methcode="LP-PI-TRM:LP-PI-ALT-AFARM"
trm_labfield=labfield
ans=raw_input("DC lab field for ARM step: [50uT] ")
if ans=="":
arm_labfield=50e-6
else:
arm_labfield=float(ans)*1e-6
ans=raw_input("temperature for total trm step: [600 C] ")
if ans=="":
trm_peakT=600+273 # convert to kelvin
else:
trm_peakT=float(ans)+273 # convert to kelvin
if "G" in codes: methcode="LT-AF-G"
if "D" in codes: methcode="LT-AF-D"
if "TRM" in codes:
demag="T"
trm=1
if demag=="T" and "ANI" in codes:
methcode="LP-AN-TRM"
if demag=="AF" and "ANI" in codes:
methcode="LP-AN-ARM"
if labfield==0: labfield=50e-6
if peakfield==0: peakfield=.180
filelist=os.listdir(dir_path) # read in list of files to import
samples=[]
MagRecs,SampRecs=[],[]
for samp in ErSamps:
if samp['er_sample_name'] not in samples:
samples.append(samp['er_sample_name'])
SampRecs.append(samp)
for file in filelist: # parse each file
parts=file.split('.')
if parts[1].upper()=='JR6':
print 'processing: ',file
treatment_type,treatment_value,user="","",""
inst="UR-JR6"
input=open(dir_path+'/'+file,'rU').readlines()
for line in input:
newline=line.replace('-',' -')
rec=newline.split()
MagRec,SampRec={},{}
specimen=rec[0]
if specnum!=0:
SampRec['er_sample_name']=specimen[:specnum]
else:
SampRec['er_sample_name']=specimen
er_site_name=pmag.parse_site(SampRec['er_sample_name'],samp_con,Z)
SampRec['er_site_name']=er_site_name
SampRec['er_location_name']=er_location_name
for key in SampRec.keys():MagRec[key]=SampRec[key]
SampRec['sample_azimuth']=rec[7]
SampRec['sample_dip']='-'+rec[8]
SampRec['sample_bed_dip_direction']=rec[9]
SampRec['sample_bed_dip']=rec[10]
SampRec['magic_method_codes']=sampmeths
MagRec['er_specimen_name']=specimen
MagRec['er_analyst_mail_names']=user
MagRec['magic_software_packages']=version_num
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["treatment_ac_field"]='0'
MagRec["treatment_dc_field"]='0'
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
MagRec["measurement_flag"]='g' # assume all data are "good"
MagRec["measurement_standard"]='u' # assume all data are "good"
MagRec["measurement_csd"]='' # set csd to blank
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec['magic_method_codes']='LT-NO'
if rec[2]=='C':
temp=float(rec[1])+273.
if temp>298:
MagRec["treatment_temp"]='%8.3e' % (temp) # room temp in kelvin
MagRec['magic_method_codes']='LT-T-Z'
else: # measurement is in oe
AC=float(rec[1])*1e-4 # convert to tesla
if AC!=0.:
MagRec["treatment_ac_field"]='%8.3e' %(AC)
MagRec['magic_method_codes']='LT-AF-Z'
vol=10.8*1e-6 # standard Roma lab volume
MagRec['magic_instrument_codes']=inst
MagRec['measurement_number']='1'
mexp=10**(float(rec[6]))
x,y,z=mexp*float(rec[3]),mexp*float(rec[4]),mexp*float(rec[5])
Cart=[x,y,z]
Dir=pmag.cart2dir(Cart)
MagRec['measurement_dec']='%7.1f'%(Dir[0])
MagRec['measurement_inc']='%7.1f'%(Dir[1])
MagRec['measurement_magn_volume']='%8.3e'%(Dir[2])
MagRec['measurement_magn_moment']='%8.3e'%(Dir[2]*vol)
MagRec['measurement_description']='converted A/m to Am^2 using volume of '+str(vol)+' m^3'
MagRecs.append(MagRec)
if MagRec['er_sample_name'] not in samples:
samples.append(MagRec['er_sample_name'])
SampRecs.append(SampRec)
if len(SampRecs)>0:
SampOut,keys=pmag.fillkeys(SampRecs)
pmag.magic_write(samp_file,SampOut,'er_samples')
print 'samples stored in ',samp_file
Fixed=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(meas_file,Fixed,'magic_measurements')
print 'data stored in ',meas_file
def main(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
def main():
"""
NAME
FIN_magic.py
DESCRIPTION
converts FINNISH format files to magic_measurements format files
SYNTAX
FIN_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify index file with list of files for importing [default is index.txt]
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsp FILE: specify output er_specimens.txt file, default is er_specimens.txt
-Fsi FILE: specify output er_sites.txt file, default is er_sites.txt
-n [gm,kg,cc,m3]: specify normalization
-spc NUM : specify number of characters to designate a specimen, default = 1
-ncn NCON: specify naming convention [default is #2 below]
-loc LOCNAME : specify location/study name, must have either LOCNAME or SITEFILE or be a synthetic
-dc B PHI THETA: dc lab field (in micro tesla) and phi,theta, default is none
NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment
-ac B : peak AF field (in mT) for ARM acquisition, default is none
INPUT
Best to put separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.)
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] 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.
"""
#
#
norm='cc'
samp_con,Z='2',1
meas_file='magic_measurements.txt'
spec_file='er_specimens.txt'
samp_file='er_samples.txt'
site_file='er_sites.txt'
magfile='index.txt'
ErSpecs,ErSamps,ErSites,ErLocs,ErCits=[],[],[],[],[]
MeasRecs=[]
specnum,unis,locname=-1,"1","unknown"
citation="This study"
dir_path='.'
args=sys.argv
labfield,phi,theta="","",""
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
if '-F' in args:
ind=args.index("-F")
meas_file=args[ind+1]
if '-Fsp' in args:
ind=args.index("-Fsp")
spec_file=args[ind+1]
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file=args[ind+1]
if '-loc' in args:
ind=args.index("-loc")
locname=args[ind+1]
if '-spc' in args:
ind=args.index("-spc")
specnum=-int(args[ind+1])
if '-dc' in args:
ind=args.index("-dc")
labfield=float(args[ind+1])*1e-6
phi=args[ind+2]
theta=args[ind+3]
if '-n' in args:
ind=args.index("-n")
norm=args[ind+1]
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="7"
if '-f' in args:
ind=args.index("-f")
magfile=args[ind+1]
magfile=dir_path+'/'+magfile
spec_file=dir_path+'/'+spec_file
samp_file=dir_path+'/'+samp_file
site_file=dir_path+'/'+site_file
meas_file=dir_path+'/'+meas_file
try:
input=open(magfile,'rU')
except:
print "bad sam file name"
sys.exit()
Files=input.readlines()
sids,ln=[],0
specimens,samples,sites=[],[],[]
for file in Files:
Zsteps,Isteps=[],[]
print 'processing ',file.split()[0]
data=open(file.split()[0],'rU').readlines()
# parse out header info
line= data[0]
k=6
while k<len(line) and line[k]==' ':k+=1
inst=line[k:]
line= data[1]
rec=line.split(':')
specimen=rec[1].split()[0].lower()
if specnum!=0:
sample=specimen[:specnum]
else: sample=specimen
site=pmag.parse_site(sample,samp_con,Z)
line= data[2]
rec=line.split(':')
lithology=rec[1]
line=data[7]
rec=line.split()
site_lat=rec[0]
site_lon=rec[1]
# sample_azimuth=(float(rec[2])-90.)
# if sample_azimuth<0:sample_azimuth+=360.
## sample_dip=(90.-float(rec[3]))
dip=float(rec[5])
if dip!=0:
dip_direction=(float(rec[4])-90.)
else:
dip_direction=0
if dip_direction<0:dip_direction+=360.
sample_azimuth=0
sample_dip=0
## the data are in geographic coordinates already
vol=float(rec[6])
weight=float(rec[7])
line= data[8]
treat_type=line[:2]
ErSpecRec,ErSampRec,ErSiteRec={},{},{}
ErSpecRec['er_specimen_name']=specimen
ErSpecRec['er_sample_name']=sample
ErSpecRec['er_site_name']=site
ErSpecRec['er_location_name']=locname
ErSpecRec['er_citation_name']=citation
ErSampRec['er_sample_name']=sample
ErSampRec['er_site_name']=site
ErSampRec['er_location_name']=locname
ErSampRec['er_citation_name']=citation
ErSiteRec['sample_lat']=site_lat
ErSiteRec['sample_lon']=site_lon
ErSiteRec['er_site_name']=site
ErSiteRec['er_location_name']=locname
ErSiteRec['er_citation_name']=citation
ErSiteRec['site_lat']=site_lat
ErSiteRec['site_lon']=site_lon
if weight!=0:
ErSpecRec['specimen_weight']='%10.3e'%(weight*1e-3) # convert to kg
else:
ErSpecRec['specimen_weight']=""
if vol!=0:
if norm=='cc':units="1"
if norm=='m3':units="2"
if units=="1" or "":
ErSpecRec['specimen_volume']='%10.3e'%(vol*1e-6)
else:
ErSpecRec['specimen_volume']='%10.3e'%(vol)
else:
ErSpecRec['specimen_volume']=""
ErSampRec['sample_azimuth']='%7.1f'%(sample_azimuth)
ErSampRec['sample_dip']='%7.1f'%(sample_dip)
ErSampRec['sample_bed_dip']='%7.1f'%(dip)
ErSampRec['sample_bed_dip_direction']='%7.1f'%(dip_direction)
ErSampRec['sample_class']=''
ErSampRec['sample_type']=''
ErSampRec['sample_lithology']=lithology
ErSampRec['magic_method_codes']="SO-CMD-NORTH"
lastrec=data[-1]
while len(lastrec.split())<2: # stripping off blanks at end
del data[-1]
lastrec=data[-1]
for line in data[9:]:
MeasRec=ErSpecRec.copy()
MeasRec['measurement_standard']='u'
MeasRec['measurement_temp']='273'
rec=line.split()
if len(rec)==1:
rec=line.split('\t')
treat=rec[0].strip()
if treat=="0":
MeasRec['magic_method_codes']='LT-NO'
MeasRec['treatment_temp']='273'
MeasRec['treatment_dc_field']='0'
MeasRec['treatment_dc_field_phi']=''
MeasRec['treatment_dc_field_theta']=''
MeasRec['treatment_ac_field']='0'
else:
if treat_type.strip()=='AF':
MeasRec['magic_method_codes']='LT-AF-Z'
MeasRec['treatment_temp']='273'
MeasRec['treatment_dc_field']='0'
MeasRec['treatment_dc_field_phi']=''
MeasRec['treatment_dc_field_theta']=''
MeasRec['treatment_ac_field']='%10.3e'%(float(treat)*1e-4) # convert from Oe
elif treat_type.strip()=='TH':
if labfield=="":
MeasRec['magic_method_codes']='LT-T-Z'
MeasRec['treatment_temp']='%7.1f'%(float(treat)+273)
MeasRec['treatment_dc_field']='0'
MeasRec['treatment_dc_field_phi']=''
MeasRec['treatment_dc_field_theta']=''
MeasRec['treatment_ac_field']='0'
else:
if treat not in Zsteps:
print 'first Z: ',treat
Zsteps.append(treat)
MeasRec['magic_method_codes']='LT-T-Z'
MeasRec['treatment_temp']='%7.1f'%(float(treat)+273)
MeasRec['treatment_dc_field']='0'
MeasRec['treatment_dc_field_phi']=''
MeasRec['treatment_dc_field_theta']=''
MeasRec['treatment_ac_field']='0'
elif treat not in Isteps:
print 'first I: ',treat
Isteps.append(treat)
MeasRec['magic_method_codes']='LT-T-I'
MeasRec['treatment_temp']='%7.1f'%(float(treat)+273)
MeasRec['treatment_dc_field']='%10.3e'%(labfield)
MeasRec['treatment_dc_field_phi']=phi
MeasRec['treatment_dc_field_theta']=theta
MeasRec['treatment_ac_field']='0'
elif treat in Isteps:
if float(treat)<float(Zsteps[-1]):
print 'pTRM ',treat
MeasRec['magic_method_codes']='LT-PTRM-Z'
MeasRec['treatment_temp']='%7.1f'%(float(treat)+273)
MeasRec['treatment_dc_field']=''
MeasRec['treatment_dc_field_phi']=''
MeasRec['treatment_dc_field_theta']=''
MeasRec['treatment_ac_field']='0'
else:
print 'pTRM tail ',treat
MeasRec['magic_method_codes']='LT-PTRM-MD'
MeasRec['treatment_temp']='%7.1f'%(float(treat)+273)
MeasRec['treatment_dc_field']=''
MeasRec['treatment_dc_field_phi']=''
MeasRec['treatment_dc_field_theta']=''
MeasRec['treatment_ac_field']='0'
MeasRec['measurement_dec']=rec[1]
MeasRec['measurement_inc']=rec[2]
intens='%8.2e'%(float(rec[3])*1e-3) # convert to A/m
MeasRec['measurement_magn_volume']=intens
MeasRec['measurement_csd']='%7.1f'%(eval(rec[5]))
MeasRec['magic_instrument_codes']=inst
MeasRecs.append(MeasRec)
ErSpecs.append(ErSpecRec)
if sample not in samples:
samples.append(sample)
ErSamps.append(ErSampRec)
if site not in sites:
sites.append(site)
ErSites.append(ErSiteRec)
pmag.magic_write(spec_file,ErSpecs,'er_specimens')
print 'specimens stored in ',spec_file
pmag.magic_write(samp_file,ErSamps,'er_samples')
print 'samples stored in ',samp_file
pmag.magic_write(site_file,ErSites,'er_sites')
Fixed=pmag.measurements_methods(MeasRecs,1)
pmag.magic_write(meas_file,Fixed,'magic_measurements')
print 'data stored in ',meas_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
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
IPG_magic.py
DESCRIPTION
converts PMD (IPG - PaleoMac) format files to magic_measurements format files
SYNTAX
IPG_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt
-spc NUM : specify number of characters to designate a specimen, default = 1
-loc LOCNAME : specify location/study name
-A: don't average replicate measurements
-ncn NCON: specify naming convention
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
INPUT
IPG-PMD format files
"""
# initialize some stuff
noave = 0
methcode, inst = "", ""
samp_con, Z = "1", ""
missing = 1
demag = "N"
er_location_name = "unknown"
citation = "This study"
args = sys.argv
methcode = "LP-NO"
specnum = -1
MagRecs = []
version_num = pmag.get_version()
Samps = [] # keeps track of sample orientations
DIspec = []
MagFiles = []
#
# get command line arguments
#
user = ""
mag_file = ""
dir_path = "."
ErSamps = []
SampOuts = []
if "-WD" in sys.argv:
ind = sys.argv.index("-WD")
dir_path = sys.argv[ind + 1]
samp_file = dir_path + "/er_samples.txt"
meas_file = dir_path + "/magic_measurements.txt"
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind = args.index("-usr")
user = args[ind + 1]
if "-F" in args:
ind = args.index("-F")
meas_file = dir_path + "/" + args[ind + 1]
if "-Fsa" in args:
ind = args.index("-Fsa")
samp_file = dir_path + "/" + args[ind + 1]
try:
open(samp_file, "rU")
ErSamps, file_type = pmag.magic_read(samp_file)
print "sample information will be appended to ", samp_file
except:
print samp_file, " not found: sample information will be stored in new er_samples.txt file"
samp_file = dir_path + "/er_samples.txt"
if "-f" in args:
ind = args.index("-f")
mag_file = dir_path + "/" + args[ind + 1]
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind + 1])
if specnum != 0:
specnum = -specnum
if "-ncn" in args:
ind = args.index("-ncn")
samp_con = sys.argv[ind + 1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "7"
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if "-A" in args:
noave = 1
data = open(mag_file, "rU").readlines() # read in data from file
for line in data:
rec = line.split()
if "E-" not in rec[1] and "E+" not in rec[1]: # new specimen
er_specimen_name = rec[0]
ErSampRec, ErSiteRec = {}, {} # make a sample record
if specnum != 0:
er_sample_name = rec[0][:specnum]
else:
er_sample_name = rec[0]
if len(ErSamps) > 0: # need to copy existing
for samp in ErSamps:
if samp["er_sample_name"] == er_sample_name:
ErSampRec = samp # we'll ammend this one
else:
SampOuts.append(samp) # keep all the others
if int(samp_con) < 6:
er_site_name = pmag.parse_site(er_sample_name, samp_con, Z)
else:
if "er_site_name" in ErSampRec.keys():
er_site_name = ErSampREc["er_site_name"]
if "er_location_name" in ErSampRec.keys():
er_location_name = ErSampREc["er_location_name"]
ErSampRec["er_sample_name"] = er_sample_name
ErSampRec["sample_azimuth"] = rec[1]
dip = -float(rec[2])
ErSampRec["sample_dip"] = "%7.1f" % (dip)
ErSampRec["sample_bed_dip_direction"] = "%7.1f" % (float(rec[3]) + 90.0)
ErSampRec["sample_bed_dip"] = rec[4]
if "er_location_name" not in ErSampRec.keys():
ErSampRec["er_location_name"] = er_location_name
if "er_site_name" not in ErSampRec.keys():
ErSampRec["er_site_name"] = er_site_name
if "er_citation_names" not in ErSampRec.keys():
ErSampRec["er_citation_names"] = "This study"
if "magic_method_codes" not in ErSampRec.keys():
ErSampRec["magic_method_codes"] = "SO-NO"
SampOuts.append(ErSampRec)
elif rec[0][0] == "N" or rec[0][0] == "T" or rec[0][0] == "M":
if len(rec) > 1: # skip blank lines at bottom
MagRec = {}
# MagRec['measurement_date']=measdate
MagRec["er_citation_names"] = "This study"
MagRec["er_location_name"] = er_location_name
MagRec["er_site_name"] = er_site_name
MagRec["er_sample_name"] = er_sample_name
MagRec["magic_software_packages"] = version_num
MagRec["treatment_temp"] = "%8.3e" % (273) # room temp in kelvin
MagRec["measurement_temp"] = "%8.3e" % (273) # room temp in kelvin
MagRec["measurement_flag"] = "g"
MagRec["measurement_standard"] = "u"
MagRec["measurement_number"] = "1"
MagRec["er_specimen_name"] = er_specimen_name
if rec[0] == "NRM":
meas_type = "LT-NO"
elif rec[0][0] == "M":
meas_type = "LT-AF-Z"
elif rec[0][0] == "T":
meas_type = "LT-T-Z"
else:
print "measurement type unknown"
sys.exit()
X = [float(rec[1]), float(rec[2]), float(rec[3])]
Vec = pmag.cart2dir(X)
MagRec["measurement_magn_moment"] = "%10.3e" % (Vec[2]) # Am^2
# MagRec["measurement_magn_volume"]=rec[4] # A/m
MagRec["measurement_dec"] = "%7.1f" % (Vec[0])
MagRec["measurement_inc"] = "%7.1f" % (Vec[1])
MagRec["treatment_ac_field"] = "0"
if meas_type != "LT-NO":
treat = float(rec[0][1:])
else:
treat = 0
if meas_type == "LT-AF-Z":
MagRec["treatment_ac_field"] = "%8.3e" % (treat * 1e-3) # convert from mT to tesla
elif meas_type == "LT-T-Z":
MagRec["treatment_temp"] = "%8.3e" % (treat + 273.0) # temp in kelvin
MagRec["magic_method_codes"] = meas_type
MagRecs.append(MagRec)
MagOuts = pmag.measurements_methods(MagRecs, noave)
pmag.magic_write(meas_file, MagOuts, "magic_measurements")
print "results put in ", meas_file
pmag.magic_write(samp_file, SampOuts, "er_samples")
print "sample orientations put in ", samp_file
def main():
"""
NAME
agm_magic.py
DESCRIPTION
converts Micromag agm files to magic format
SYNTAX
agm_magic.py [-h] [command line options]
OPTIONS
-usr USER: identify user, default is "" - put in quotation marks!
-bak: this is a IRM backfield curve
-f FILE, specify input file, required
-fsa SAMPFILE, specify er_samples.txt file relating samples, site and locations names,default is none
-F MFILE, specify magic measurements formatted output file, default is agm_measurements.txt
-spn SPEC, specimen name, default is base of input file name, e.g. SPECNAME.agm
-spc NUM, specify number of characters to designate a specimen, default = 0
-Fsp SPECFILE : name of er_specimens.txt file for appending data to
[default: er_specimens.txt]
-ncn NCON,: specify naming convention: default is #1 below
-syn SYN, synthetic specimen name
-loc LOCNAME : specify location/study name,
should have either LOCNAME or SAMPFILE (unless synthetic)
-ins INST : specify which instrument was used (e.g, SIO-Maud), default is ""
-u units: [cgs,SI], default is cgs
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
[8] specimen is a synthetic - it has no sample, site, location information
NB: all others you will have to customize your self
or e-mail [email protected] for help.
OUTPUT
MagIC format files: magic_measurements, er_specimens, er_sample, er_site
"""
citation='This study'
MeasRecs=[]
units='cgs'
meth="LP-HYS"
version_num=pmag.get_version()
args=sys.argv
fmt='old'
er_sample_name,er_site_name,er_location_name="","",""
inst=""
er_location_name="unknown"
er_synthetic_name=""
user=""
er_site_name=""
dir_path='.'
if "-WD" in args:
ind=args.index("-WD")
dir_path=args[ind+1]
specfile=dir_path+'/er_specimens.txt'
output=dir_path+"/agm_measurements.txt"
if "-h" in args:
print main.__doc__
sys.exit()
if "-bak" in args:
meth="LP-IRM-DCD"
output=dir_path+"/irm_measurements.txt"
if "-new" in args: fmt='new'
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
if '-F' in args:
ind=args.index("-F")
output=dir_path+'/'+args[ind+1]
if '-f' in args:
ind=args.index("-f")
agm_file=dir_path+'/'+args[ind+1]
er_specimen_name=args[ind+1].split('.')[0]
else:
print "agm_file field is required option"
print main.__doc__
sys.exit()
if '-Fsp' in args:
ind=args.index("-Fsp")
specfile=dir_path+'/'+args[ind+1]
specnum,samp_con,Z=0,'1',1
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if specnum!=0:specnum=-specnum
if "-spn" in args:
ind=args.index("-spn")
er_specimen_name=args[ind+1]
elif "-syn" not in args:
print "you must specify a specimen name"
sys.exit()
if "-syn" in args:
ind=args.index("-syn")
er_synthetic_name=args[ind+1]
er_specimen_name=""
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-fsa" in args:
ind=args.index("-fsa")
sampfile=dir_path+'/'+args[ind+1]
Samps,file_type=pmag.magic_read(sampfile)
print 'sample_file successfully read in'
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 "-ins" in args:
ind=args.index("-ins")
inst=args[ind+1]
if "-u" in args:
ind=args.index("-u")
units=args[ind+1]
ErSpecRecs,filetype=pmag.magic_read(specfile)
ErSpecRec,MeasRec={},{}
ErSpecRec['er_citation_names']="This study"
ErSpecRec['er_specimen_name']=er_specimen_name
ErSpecRec['er_synthetic_name']=er_synthetic_name
if specnum!=0:
ErSpecRec["er_sample_name"]=er_specimen_name[:specnum]
else:
ErSpecRec["er_sample_name"]=er_specimen_name
if "-fsa" in args and er_synthetic_name=="":
for samp in Samps:
if samp["er_sample_name"] == ErSpecRec["er_sample_name"]:
ErSpecRec["er_location_name"]=samp["er_location_name"]
ErSpecRec["er_site_name"]=samp["er_site_name"]
break
elif int(samp_con)!=6 and int(samp_con)!=8:
site=pmag.parse_site(ErSpecRec['er_sample_name'],samp_con,Z)
ErSpecRec["er_site_name"]=site
ErSpecRec["er_location_name"]=er_location_name
ErSpecRec['er_scientist_mail_names']=user.strip()
insert=1
for rec in ErSpecRecs:
if rec['er_specimen_name']==er_specimen_name:
insert=0
break
if insert==1:
ErSpecRecs.append(ErSpecRec)
ErSpecRecs,keylist=pmag.fillkeys(ErSpecRecs)
pmag.magic_write(specfile,ErSpecRecs,'er_specimens')
print "specimen name put in ",specfile
f=open(agm_file,'rU')
Data=f.readlines()
if "ASCII" not in Data[0]:fmt='new'
measnum,start=1,""
if fmt=='new': # new Micromag formatted file
end=2
for skip in range(len(Data)):
line=Data[skip]
rec=line.split()
if 'Units' in line:units=rec[-1]
if "Raw" in rec:
start=skip+2
if "Field" in rec and "Moment" in rec and start=="":
start=skip+2
break
else:
start = 2
end=1
for i in range(start,len(Data)-end): # skip header stuff
MeasRec={}
for key in ErSpecRec.keys():
MeasRec[key]=ErSpecRec[key]
MeasRec['magic_instrument_codes']=inst
MeasRec['magic_method_codes']=meth
if 'er_synthetic_name' in MeasRec.keys() and MeasRec['er_synthetic_name']!="":
MeasRec['magic_experiment_name']=er_synthetic_name+':'+meth
else:
MeasRec['magic_experiment_name']=er_specimen_name+':'+meth
line=Data[i]
rec=line.split(',') # data comma delimited
if rec[0]!='\n':
if units=='cgs':
field =float(rec[0])*1e-4 # convert from oe to tesla
else:
field =float(rec[0]) # field in tesla
if meth=="LP-HYS":
MeasRec['measurement_lab_field_dc']='%10.3e'%(field)
MeasRec['treatment_dc_field']=''
else:
MeasRec['measurement_lab_field_dc']=''
MeasRec['treatment_dc_field']='%10.3e'%(field)
if units=='cgs':
MeasRec['measurement_magn_moment']='%10.3e'%(float(rec[1])*1e-3) # convert from emu to Am^2
else:
MeasRec['measurement_magn_moment']='%10.3e'%(float(rec[1])) # Am^2
MeasRec['treatment_temp']='273' # temp in kelvin
MeasRec['measurement_temp']='273' # temp in kelvin
MeasRec['measurement_flag']='g'
MeasRec['measurement_standard']='u'
MeasRec['measurement_number']='%i'%(measnum)
measnum+=1
MeasRec['magic_software_packages']=version_num
MeasRecs.append(MeasRec)
# now we have to relabel LP-HYS method codes. initial loop is LP-IMT, minor loops are LP-M - do this in measurements_methods function
if meth=='LP-HYS':
recnum=0
while float(MeasRecs[recnum]['measurement_lab_field_dc'])<float(MeasRecs[recnum+1]['measurement_lab_field_dc']) and recnum+1<len(MeasRecs): # this is LP-IMAG
MeasRecs[recnum]['magic_method_codes']='LP-IMAG'
MeasRecs[recnum]['magic_experiment_name']=MeasRecs[recnum]['er_specimen_name']+":"+'LP-IMAG'
recnum+=1
#
pmag.magic_write(output,MeasRecs,'magic_measurements')
print "results put in ",output
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(command_line=True, **kwargs):
"""
NAME
JR6_txt_magic.py
DESCRIPTION
converts JR6 .txt format files to magic_measurements format files
SYNTAX
JR6_txt_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt (Not working yet)
-spc NUM : specify number of characters to designate a specimen, default = 1
-loc LOCNAME : specify location/study name
-A: don't average replicate measurements
-ncn NCON: specify sample naming convention (6 and 7 not yet implemented)
-mcd [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
-v NUM : specify the volume of the sample, default 2.5cm^3.
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
INPUT
JR6 .txt format file
"""
# initialize some stuff
noave=0
volume = 2.5 * 1e-6 # default volume is 2.5 cm^3 (2.5 * 1e-6 meters^3)
inst=""
samp_con,Z='1',""
missing=1
demag="N"
er_location_name="unknown"
citation='This study'
args=sys.argv
meth_code="LP-NO"
specnum=-1
MagRecs=[]
version_num=pmag.get_version()
Samps=[] # keeps track of sample orientations
user=""
mag_file=""
dir_path='.'
ErSamps=[]
SampOuts=[]
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print main.__doc__
return False
if '-F' in args:
ind=args.index("-F")
meas_file = args[ind+1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = args[ind+1]
#try:
# open(samp_file,'rU')
# ErSamps,file_type=pmag.magic_read(samp_file)
# print 'sample information will be appended to ', samp_file
#except:
# print samp_file,' not found: sample information will be stored in new er_samples.txt file'
# samp_file = output_dir_path+'/er_samples.txt'
if '-f' in args:
ind = args.index("-f")
mag_file= args[ind+1]
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind+1])
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-A" in args: noave=1
if "-mcd" in args:
ind=args.index("-mcd")
meth_code=args[ind+1]
if "-v" in args:
ind=args.index("-v")
volume=float(args[ind+1]) * 1e-6
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
specnum = kwargs.get('specnum', 1)
samp_con = kwargs.get('samp_con', '1')
er_location_name = kwargs.get('er_location_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
volume = float(kwargs.get('volume', 0))
if not volume:
volume = 2.5 * 1e-6 #default volume is a 2.5 cm cube, translated to meters cubed
else:
#convert cm^3 to m^3
volume *= 1e-6
# format variables
mag_file = input_dir_path+"/" + mag_file
meas_file = output_dir_path+"/" + meas_file
samp_file = output_dir_path+"/" + samp_file
if specnum!=0:
specnum=-specnum
if "4" in samp_con:
if "-" not in samp_con:
print "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"
ErSampRec,ErSiteRec={},{}
# parse data
data=open(mag_file,'rU')
line=data.readline()
line=data.readline()
line=data.readline()
while line !='':
parsedLine=line.split()
sampleName=parsedLine[0]
demagLevel=parsedLine[2]
date=parsedLine[3]
line=data.readline()
line=data.readline()
line=data.readline()
line=data.readline()
parsedLine=line.split()
specimenAngleDec=parsedLine[1]
specimenAngleInc=parsedLine[2]
while parsedLine[0] != 'MEAN' :
line=data.readline()
parsedLine=line.split()
if len(parsedLine) == 0:
parsedLine=["Hello"]
Mx=parsedLine[1]
My=parsedLine[2]
Mz=parsedLine[3]
line=data.readline()
line=data.readline()
parsedLine=line.split()
splitExp = parsedLine[2].split('A')
intensityVolStr=parsedLine[1] + splitExp[0]
intensityVol = float(intensityVolStr)
# check and see if Prec is too big and messes with the parcing.
precisionStr=''
if len(parsedLine) == 6: #normal line
precisionStr=parsedLine[5][0:-1]
else:
precisionStr=parsedLine[4][0:-1]
precisionPer = float(precisionStr)
precision=intensityVol*precisionPer/100
while parsedLine[0] != 'SPEC.' :
line=data.readline()
parsedLine=line.split()
if len(parsedLine) == 0:
parsedLine=["Hello"]
specimenDec=parsedLine[2]
specimenInc=parsedLine[3]
line=data.readline()
line=data.readline()
parsedLine=line.split()
geographicDec=parsedLine[1]
geographicInc=parsedLine[2]
# Add data to various MagIC data tables.
er_specimen_name = sampleName
if specnum!=0:
er_sample_name=er_specimen_name[:specnum]
else:
er_sample_name=er_specimen_name
if int(samp_con)<6:
er_site_name=pmag.parse_site(er_sample_name,samp_con,Z)
# else:
# if 'er_site_name' in ErSampRec.keys():er_site_name=ErSampRec['er_site_name']
# if 'er_location_name' in ErSampRec.keys():er_location_name=ErSampRec['er_location_name']
# check sample list(SampOuts) to see if sample already exists in list before adding new sample info
sampleFlag=0
for sampRec in SampOuts:
if sampRec['er_sample_name'] == er_sample_name:
sampleFlag=1
break
if sampleFlag == 0:
ErSampRec['er_sample_name']=er_sample_name
ErSampRec['sample_azimuth']=specimenAngleDec
sample_dip=str(float(specimenAngleInc)-90.0) #convert to magic orientation
ErSampRec['sample_dip']=sample_dip
ErSampRec['magic_method_codes']=meth_code
ErSampRec['er_location_name']=er_location_name
ErSampRec['er_site_name']=er_site_name
ErSampRec['er_citation_names']='This study'
SampOuts.append(ErSampRec.copy())
MagRec={}
MagRec['measurement_description']='Date: '+date
MagRec["er_citation_names"]="This study"
MagRec['er_location_name']=er_location_name
MagRec['er_site_name']=er_site_name
MagRec['er_sample_name']=er_sample_name
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["er_specimen_name"]=er_specimen_name
MagRec["treatment_ac_field"]='0'
if demagLevel == 'NRM':
meas_type="LT-NO"
elif demagLevel[0] == 'A':
meas_type="LT-AF-Z"
treat=float(demagLevel[1:])
MagRec["treatment_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
elif demagLevel[0] == 'T':
meas_type="LT-T-Z"
treat=float(demagLevel[1:])
MagRec["treatment_temp"]='%8.3e' % (treat+273.) # temp in kelvin
else:
print "measurement type unknown", demag_level
return False, "measurement type unknown"
MagRec["measurement_magn_moment"]=str(intensityVol*volume) # Am^2
MagRec["measurement_magn_volume"]=intensityVolStr # A/m
MagRec["measurement_dec"]=specimenDec
MagRec["measurement_inc"]=specimenInc
MagRec['magic_method_codes']=meas_type
MagRecs.append(MagRec.copy())
#read lines till end of record
line=data.readline()
line=data.readline()
line=data.readline()
line=data.readline()
line=data.readline()
# read all the rest of the special characters. Some data files not consistantly formatted.
while (len(line) <=3 and line!=''):
line=data.readline()
#end of data while loop
MagOuts=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(samp_file,SampOuts,'er_samples')
print "sample orientations put in ",samp_file
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print "results put in ",meas_file
return True, meas_file
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(command_line=True, **kwargs):
"""
NAME
PMD_magic.py
DESCRIPTION
converts PMD (Enkin) format files to magic_measurements format files
SYNTAX
PMD_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt
-spc NUM : specify number of characters to designate a specimen, default = 1
-loc LOCNAME : specify location/study name
-A: don't average replicate measurements
-ncn NCON: specify naming convention
-mcd [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
INPUT
PMD format files
"""
# initialize some stuff
noave=0
inst=""
samp_con,Z='1',""
missing=1
demag="N"
er_location_name="unknown"
citation='This study'
args=sys.argv
meth_code="LP-NO"
specnum=-1
MagRecs=[]
version_num=pmag.get_version()
Samps=[] # keeps track of sample orientations
DIspec=[]
MagFiles=[]
user=""
mag_file=""
dir_path='.'
ErSamps=[]
SampOuts=[]
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print main.__doc__
return False
if '-F' in args:
ind=args.index("-F")
meas_file = args[ind+1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = args[ind+1]
#try:
# open(samp_file,'rU')
# ErSamps,file_type=pmag.magic_read(samp_file)
# print 'sample information will be appended to ', samp_file
#except:
# print samp_file,' not found: sample information will be stored in new er_samples.txt file'
# samp_file = output_dir_path+'/er_samples.txt'
if '-f' in args:
ind = args.index("-f")
mag_file= args[ind+1]
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind+1])
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-A" in args: noave=1
if "-mcd" in args:
ind=args.index("-mcd")
meth_code=args[ind+1]
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
specnum = kwargs.get('specnum', 0)
samp_con = kwargs.get('samp_con', '1')
er_location_name = kwargs.get('er_location_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
print samp_con
# format variables
mag_file = input_dir_path+"/" + mag_file
meas_file = output_dir_path+"/" + meas_file
samp_file = output_dir_path+"/" + samp_file
if specnum!=0:specnum=-specnum
if "4" in samp_con:
if "-" not in samp_con:
print "naming convention option [4] must be in form 4-Z where Z is an integer"
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
return False, "naming convention option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
# parse data
data=open(mag_file,'rU').readlines() # read in data from file
comment=data[0]
line=data[1].strip()
line=line.replace("=","= ") # make finding orientations easier
rec=line.split() # read in sample orientation, etc.
er_specimen_name=rec[0]
ErSampRec,ErSiteRec={},{} # make a sample record
if specnum!=0:
er_sample_name=rec[0][:specnum]
else:
er_sample_name=rec[0]
if len(ErSamps)>0: # need to copy existing
for samp in ErSamps:
if samp['er_sample_name']==er_sample_name:
ErSampRec=samp # we'll ammend this one
else:
SampOuts.append(samp) # keep all the others
if int(samp_con)<6:
er_site_name=pmag.parse_site(er_sample_name,samp_con,Z)
else:
if 'er_site_name' in ErSampRec.keys():er_site_name=ErSampREc['er_site_name']
if 'er_location_name' in ErSampRec.keys():er_location_name=ErSampREc['er_location_name']
az_ind=rec.index('a=')+1
ErSampRec['er_sample_name']=er_sample_name
ErSampRec['er_sample_description']=comment
ErSampRec['sample_azimuth']=rec[az_ind]
dip_ind=rec.index('b=')+1
dip=-float(rec[dip_ind])
ErSampRec['sample_dip']='%7.1f'%(dip)
strike_ind=rec.index('s=')+1
ErSampRec['sample_bed_dip_direction']='%7.1f'%(float(rec[strike_ind])+90.)
bd_ind=rec.index('d=')+1
ErSampRec['sample_bed_dip']=rec[bd_ind]
v_ind=rec.index('v=')+1
vol=rec[v_ind][:-3]
date=rec[-2]
time=rec[-1]
ErSampRec['magic_method_codes']=meth_code
if 'er_location_name' not in ErSampRec.keys():ErSampRec['er_location_name']=er_location_name
if 'er_site_name' not in ErSampRec.keys():ErSampRec['er_site_name']=er_site_name
if 'er_citation_names' not in ErSampRec.keys():ErSampRec['er_citation_names']='This study'
if 'magic_method_codes' not in ErSampRec.keys():ErSampRec['magic_method_codes']='SO-NO'
SampOuts.append(ErSampRec)
for k in range(3,len(data)): # read in data
line=data[k]
rec=line.split()
if len(rec)>1: # skip blank lines at bottom
MagRec={}
MagRec['measurement_description']='Date: '+date+' '+time
MagRec["er_citation_names"]="This study"
MagRec['er_location_name']=er_location_name
MagRec['er_site_name']=er_site_name
MagRec['er_sample_name']=er_sample_name
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["er_specimen_name"]=er_specimen_name
if rec[0]=='NRM':
meas_type="LT-NO"
elif rec[0][0]=='M' or rec[0][0]=='H':
meas_type="LT-AF-Z"
elif rec[0][0]=='T':
meas_type="LT-T-Z"
else:
print "measurement type unknown"
return False, "measurement type unknown"
X=[float(rec[1]),float(rec[2]),float(rec[3])]
Vec=pmag.cart2dir(X)
MagRec["measurement_magn_moment"]='%10.3e'% (Vec[2]) # Am^2
MagRec["measurement_magn_volume"]=rec[4] # A/m
MagRec["measurement_dec"]='%7.1f'%(Vec[0])
MagRec["measurement_inc"]='%7.1f'%(Vec[1])
MagRec["treatment_ac_field"]='0'
if meas_type!='LT-NO':
treat=float(rec[0][1:])
else:
treat=0
if meas_type=="LT-AF-Z":
MagRec["treatment_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
elif meas_type=="LT-T-Z":
MagRec["treatment_temp"]='%8.3e' % (treat+273.) # temp in kelvin
MagRec['magic_method_codes']=meas_type
MagRecs.append(MagRec)
MagOuts=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print "results put in ",meas_file
pmag.magic_write(samp_file,SampOuts,'er_samples')
print "sample orientations put in ",samp_file
return True, meas_file
def main():
"""
NAME
UMICH_magic.py
DESCRIPTION
converts UMICH .mag format files to magic_measurements format files
SYNTAX
UMICH_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify .mag format input file, required
-fsa SAMPFILE : specify er_samples.txt file relating samples, site and locations names,default is none
-F FILE: specify output file, default is magic_measurements.txt
-spc NUM : specify number of characters to designate a specimen, default = 0
-loc LOCNAME : specify location/study name, must have either LOCNAME or SAMPFILE or be a synthetic
-ncn NCON: specify naming convention: default is #1 below
-A: don't average replicate measurements
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
Format of UMICH .mag files:
Spec Treat CSD Intensity Declination Inclination metadata string
Spec: specimen name
Treat: treatment step
XXX T in Centigrade
XXX AF in mT
Intensity assumed to be total moment in 10^3 Am^2 (emu)
Declination: Declination in specimen coordinate system
Inclination: Declination in specimen coordinate system
metatdata string: mm/dd/yy;hh:mm;[dC,mT];xx.xx;UNITS;USER;INST;NMEAS
hh in 24 hours.
dC or mT units of treatment XXX (see Treat above) for thermal or AF respectively
xx.xxx DC field
UNITS of DC field (microT, mT)
INST: instrument code, number of axes, number of positions (e.g., G34 is 2G, three axes,
measured in four positions)
NMEAS: number of measurements in a single position (1,3,200...)
"""
# initialize some stuff
dir_path='.'
infile_type="mag"
noave=0
methcode,inst="",""
phi,theta,peakfield,labfield=0,0,0,0
pTRM,MD,samp_con,Z=0,0,'1',1
missing=1
demag="N"
er_location_name=""
citation='This study'
args=sys.argv
methcode="LP-NO"
samp_file,ErSamps='',[]
specnum=0
#
# get command line arguments
#
meas_file="magic_measurements.txt"
user=""
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
if '-F' in args:
ind=args.index("-F")
meas_file=dir_path+'/'+args[ind+1]
if '-f' in args:
ind=args.index("-f")
magfile=dir_path+'/'+args[ind+1]
try:
input=open(magfile,'rU')
except:
print "bad mag file name"
sys.exit()
else:
print "mag_file field is required option"
print main.__doc__
sys.exit()
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if specnum!=0:specnum=-specnum
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-fsa" in args:
ind=args.index("-fsa")
samp_file=dir_path+'/'+args[ind+1]
Samps,file_type=pmag.magic_read(samp_file)
if "-A" in args: noave=1
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
samp_con=sys.argv[ind+1]
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="7"
MagRecs,specs=[],[]
version_num=pmag.get_version()
if infile_type=="mag":
for line in input.readlines():
instcode=""
if len(line)>2:
MagRec={}
MagRec['er_location_name']=er_location_name
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["treatment_ac_field"]='0'
MagRec["treatment_dc_field"]='0'
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
meas_type="LT-NO"
rec=line.split()
labfield=0
code1=rec[6].split(';')
date=code1[0].split('/') # break date into mon/day/year
yy=int(date[2])
if yy <90:
yyyy=str(2000+yy)
else: yyyy=str(1900+yy)
mm=int(date[0])
if mm<10:
mm="0"+str(mm)
else: mm=str(mm)
dd=int(date[1])
if dd<10:
dd="0"+str(dd)
else: dd=str(dd)
time=code1[1].split(':')
hh=int(time[0])
if hh<10:
hh="0"+str(hh)
else: hh=str(hh)
min=int(time[1])
if min<10:
min= "0"+str(min)
else: min=str(min)
MagRec["measurement_date"]=yyyy+":"+mm+":"+dd+":"+hh+":"+min+":00.00"
MagRec["measurement_time_zone"]=''
instcode=''
if len(code1)>1:
MagRec["measurement_positions"]=code1[6][2]
else:
MagRec["measurement_positions"]=code1[7] # takes care of awkward format with bubba and flo being different
if user=="":user=code1[5]
if code1[2][-1]=='C': demag="T"
if code1[2]=='mT': demag="AF"
treat=rec[1].split('.')
if len(treat)==1:treat.append('0')
if demag=='T' and treat!=0:
meas_type="LT-T-Z"
MagRec["treatment_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
if demag=="AF":
meas_type="LT-AF-Z"
MagRec["treatment_ac_field"]='%8.3e' % (float(treat[0])*1e-3) # Af field in T
MagRec["treatment_dc_field"]='0'
MagRec["er_specimen_name"]=rec[0]
if rec[0] not in specs:specs.append(rec[0]) # get a list of specimen names
experiment=rec[0]+":"
MagRec["er_site_name"]=""
if specnum!=0:
MagRec["er_sample_name"]=rec[0][:specnum]
else:
MagRec["er_sample_name"]=rec[0]
if "-fsa" in args:
for samp in Samps:
if samp["er_sample_name"] == MagRec["er_sample_name"]:
MagRec["er_location_name"]=samp["er_location_name"]
MagRec["er_site_name"]=samp["er_site_name"]
break
elif int(samp_con)!=6:
site=pmag.parse_site(MagRec['er_sample_name'],samp_con,Z)
MagRec["er_site_name"]=site
if MagRec['er_site_name']=="":
print 'No site name found for: ',MagRec['er_specimen_name'],MagRec['er_sample_name']
if MagRec["er_location_name"]=="":
print 'no location name for: ',MagRec["er_specimen_name"]
if rec[1]==".00":rec[1]="0.00"
MagRec["measurement_csd"]=rec[2]
MagRec["measurement_magn_moment"]='%10.3e'% (float(rec[3])*1e-3) # moment in Am^2 (from emu)
MagRec["measurement_dec"]=rec[4]
MagRec["measurement_inc"]=rec[5]
MagRec["magic_instrument_codes"]=instcode
MagRec["er_analyst_mail_names"]=user
MagRec["er_citation_names"]=citation
MagRec["magic_method_codes"]=meas_type
MagRec["measurement_flag"]='g'
MagRec["er_specimen_name"]=rec[0]
MagRec["measurement_number"]='1'
MagRecs.append(MagRec)
MagOuts=[]
for spec in specs: # gather all demag types for this specimen
SpecRecs,meths,measnum=[],[],1
for rec in MagRecs:
if rec['er_specimen_name']==spec:
rec['measurement_number']=str(measnum)
measnum+=1
if rec['magic_method_codes'] not in meths:meths.append(rec['magic_method_codes'])
SpecRecs.append(rec)
expname=spec
if "LT-AF-Z" in meths:expname=expname+ ':LP-DIR-AF'
if "LT-T-Z" in meths:expname=expname+ ':LP-DIR-T'
for rec in SpecRecs:
rec['magic_experiment_name']=expname
MagOuts.append(rec)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print "results put in ",meas_file
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(command_line=True, **kwargs):
"""
NAME
CIT_magic.py
DESCRIPTION
converts CIT and .sam format files to magic_measurements format files
SYNTAX
CIT_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify .sam format input file, required
-fsi SITEFILE : specify file with site names and locations [tab delimited magic file]
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsp FILE: specify output er_specimens.txt file, default is er_specimens.txt
-Fsi FILE: specify output er_sites.txt file, default is er_sites.txt
-Fsa FILE: specify output er_samples.txt file, default is er_samples.txt # LORI
-n [gm,kg,cc,m3]: specify normalization
-A: don't average replicate measurements
-spc NUM : specify number of characters to designate a specimen, default = 0
-ncn NCON: specify naming convention
-loc LOCNAME : specify location/study name, must have either LOCNAME or SITEFILE or be a synthetic
-mcd [FS-FD:SO-MAG,.....] colon delimited list for method codes applied to all specimens in .sam file
-dc B PHI THETA: dc lab field (in micro tesla) and phi,theta, default is none
NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment
-ac B : peak AF field (in mT) for ARM acquisition, default is none
INPUT
Best to put separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.)
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) [default]
[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.
"""
#
#initialize variables
norm='cc'
samp_con,Z='3',1
meas_file='magic_measurements.txt'
spec_file='er_specimens.txt'
samp_file='er_samples.txt'
site_file='er_sites.txt'
ErSpecs,ErSamps,ErSites,ErLocs,ErCits=[],[],[],[],[]
MeasRecs=[]
specnum,units,locname=0,"1","unknown"
citation="This study"
dir_path='.'
args=sys.argv
if command_line:
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if "-h" in args:
print main.__doc__
return False
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
if '-F' in args:
ind=args.index("-F")
meas_file=args[ind+1]
if '-Fsp' in args:
ind=args.index("-Fsp")
spec_file=args[ind+1]
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file=args[ind+1]
if '-Fsi' in args: # LORI addition
ind=args.index("-Fsi")
site_file=args[ind+1]
if '-loc' in args:
ind=args.index("-loc")
locname=args[ind+1]
if '-mcd' in args:
ind=args.index("-mcd")
methods=args[ind+1]
else:
methods='SO-MAG'
if '-spc' in args:
ind=args.index("-spc")
specnum=-int(args[ind+1])
if '-n' in args:
ind=args.index("-n")
norm=args[ind+1]
if "-A" in args:
avg=1
else:
avg=0
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"
return False, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
if '-f' in args:
ind=args.index("-f")
magfile=args[ind+1]
if '-ID' in args:
ind = args.index('-ID')
input_dir_path = args[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
# LJ
# if you are running as a module:
elif not command_line:
dir_path = kwargs.get('dir_path', '.')
user = kwargs.get('user', '')
meas_file = kwargs.get('meas_file', 'magic_measurements.txt') # outfile
spec_file = kwargs.get('spec_file', 'er_specimens.txt') # specimen outfile
samp_file = kwargs.get('samp_file', 'er_samples.txt') # sample outfile
site_file = kwargs.get('site_file', 'er_sites.txt') # site outfile
locname = kwargs.get('locname', '')
methods = kwargs.get('methods', ['SO-MAG'])
specnum = -int(kwargs.get('specnum', 0))
norm = kwargs.get('norm', 'cc')
avg = kwargs.get('avg', 0) # 0 means do average, 1 means don't
samp_con = kwargs.get('samp_con', '3')
magfile = kwargs.get('magfile', '')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
# done with module-specific stuff
# formatting and checking variables
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, "naming convention option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
magfile = os.path.join(input_dir_path, magfile)
spec_file = os.path.join(output_dir_path, spec_file)
samp_file = os.path.join(output_dir_path, samp_file)
site_file = os.path.join(output_dir_path, site_file)
meas_file= os.path.join(output_dir_path, meas_file)
try:
file_input=open(magfile,'r')
except Exception as ex:
print "bad sam file name: ", magfile
return False, "bad sam file name"
File = file_input.readlines()
sids,ln,format=[],0,'CIT'
formats=['CIT','2G','APP','JRA']
ErLocRec={}
ErLocRec["er_location_name"]=locname
ErLocRec["er_citation_names"]=citation
comment=File[ln]
if comment=='CIT':
format=comment
ln+=1
comment=File[ln]
print comment
ln+=1
specimens,samples,sites=[],[],[]
if format=='CIT':
line=File[ln].split()
site_lat=line[0]
site_lon=line[1]
ErLocRec["location_begin_lat"]=site_lat
ErLocRec["location_begin_lon"]=site_lon
ErLocRec["location_end_lat"]=site_lat
ErLocRec["location_end_lon"]=site_lon
ErLocs.append(ErLocRec)
Cdec=float(line[2])
for k in range(ln+1,len(File)):
line=File[k]
rec=line.split()
specimen=rec[0]
specimens.append(specimen)
for specimen in specimens:
ErSpecRec,ErSampRec,ErSiteRec={},{},{}
if specnum!=0:
sample=specimen[:specnum]
else: sample=specimen
site=pmag.parse_site(sample,samp_con,Z)
ErSpecRec['er_specimen_name']=specimen
ErSpecRec['er_sample_name']=sample
ErSpecRec['er_site_name']=site
ErSpecRec['er_location_name']=locname
ErSpecRec['er_citation_names']=citation
ErSampRec['er_sample_name']=sample
ErSampRec['er_site_name']=site
ErSampRec['er_location_name']=locname
ErSampRec['er_citation_names']=citation
ErSampRec['magic_method_codes']=methods
ErSampRec['sample_declination_correction']='%7.1f'%(Cdec)
ErSiteRec['er_site_name']=site
ErSiteRec['er_location_name']=locname
ErSiteRec['er_citation_names']=citation
ErSiteRec['site_lat']=site_lat
ErSiteRec['site_lon']=site_lon
f=open(input_dir_path+'/'+specimen,'rU')
Lines=f.readlines()
comment=""
line=Lines[0].split()
if len(line)>2:
comment=line[2]
info=Lines[1].split()
vol=float(info[-1])
if vol!=1.0:
if norm=='cc':units="1"
if norm=='m3':units="2"
ErSpecRec['specimen_weight']=""
if units=="1" or "":
ErSpecRec['specimen_volume']='%10.3e'%(vol*1e-6)
else:
ErSpecRec['specimen_volume']='%10.3e'%(vol)
else:
if norm=='cc':units="1"
if norm=='m3':units="2"
ErSpecRec['specimen_volume']=""
if units=="1" or "":
ErSpecRec['specimen_weight']='%10.3e'%(vol*1e-3)
else:
ErSpecRec['specimen_weight']='%10.3e'%(vol)
dip=float(info[-2])
dip_direction=float(info[-3])+Cdec+90.
sample_dip=-float(info[-4])
sample_azimuth=float(info[-5])+Cdec-90.
if len(info)>5:
ErSampRec['sample_height']=info[-6]
else:
ErSampRec['sample_height']='0'
ErSampRec['sample_azimuth']='%7.1f'%(sample_azimuth)
ErSampRec['sample_dip']='%7.1f'%(sample_dip)
ErSampRec['sample_bed_dip']='%7.1f'%(dip)
ErSampRec['sample_bed_dip_direction']='%7.1f'%(dip_direction)
ErSampRec['sample_class']=''
ErSampRec['sample_type']=''
ErSampRec['sample_lithology']=''
if Cdec!=0 or Cdec!="":
ErSampRec['magic_method_codes']='SO-CMD-NORTH'
else:
ErSampRec['magic_method_codes']='SO-MAG'
for line in Lines[2:len(Lines)]:
#print 'line:', line
MeasRec=ErSpecRec.copy()
# Remove specimen_volume and specimen_weight as they do not exits in the magic_measurement table
del MeasRec["specimen_volume"]
del MeasRec["specimen_weight"]
treat_type=line[0:3]
treat=line[3:6]
#print 'treat:', treat
if treat_type.strip()=='NRM':
MeasRec['magic_method_codes']='LT-NO'
MeasRec['measurement_temp']='273'
MeasRec['treatment_temp']='273'
MeasRec['treatment_dc_field']='0'
MeasRec['treatment_ac_field']='0'
elif treat_type.strip()=='AF':
MeasRec['magic_method_codes']='LT-AF-Z'
MeasRec['measurement_temp']='273'
MeasRec['treatment_temp']='273'
MeasRec['treatment_dc_field']='0'
if treat == ' ':
MeasRec['treatment_ac_field']='0'
else:
MeasRec['treatment_ac_field']='%10.3e'%(float(treat)*1e-3)
elif treat_type.strip()=='TT':
MeasRec['magic_method_codes']='LT-T-Z'
MeasRec['measurement_temp']='273'
if treat == ' ':
MeasRec['treatment_temp']='273'
else:
MeasRec['treatment_temp']='%7.1f'%(float(treat)+273)
MeasRec['treatment_dc_field']='0'
MeasRec['treatment_ac_field']='0'
elif treat_type.strip()=='LT' or treat_type.strip()=='LN2':
MeasRec['magic_method_codes']='LT-LT-Z'
MeasRec['measurement_temp']='273'
MeasRec['treatment_temp']='77'
MeasRec['treatment_dc_field']='0'
MeasRec['treatment_ac_field']='0'
else:
print "trouble with your treatment steps"
MeasRec['measurement_dec']=line[46:51]
MeasRec['measurement_inc']=line[52:58]
M='%8.2e'%(float(line[31:39])*vol*1e-3) # convert to Am2
MeasRec['measurement_magn_moment']=M
MeasRec['measurement_sd_x']='%8.2e'%(float(line[58:67])*1e-8) #(convert e-5emu to Am2)
MeasRec['measurement_sd_y']='%8.2e'%(float(line[67:76])*1e-8)
MeasRec['measurement_sd_z']='%8.2e'%(float(line[76:85])*1e-8)
MeasRec['measurement_csd']='%7.1f'%(eval(line[41:46]))
MeasRec['magic_instrument_codes']=line[85:]
MeasRec["measurement_positions"]='1'
MeasRec['measurement_standard']='u'
MeasRecs.append(MeasRec)
ErSpecs.append(ErSpecRec)
if sample not in samples:
samples.append(sample)
ErSamps.append(ErSampRec)
site=pmag.parse_site(sample,samp_con,Z)
if site not in sites:
sites.append(site)
ErSites.append(ErSiteRec)
pmag.magic_write(spec_file,ErSpecs,'er_specimens')
print 'specimens stored in ',spec_file
pmag.magic_write(samp_file,ErSamps,'er_samples')
print 'samples stored in ',samp_file
pmag.magic_write(site_file,ErSites,'er_sites')
print 'sites stored in ', site_file
Fixed=pmag.measurements_methods(MeasRecs,avg)
pmag.magic_write(meas_file,Fixed,'magic_measurements')
print 'data stored in ',meas_file
return True, meas_file
def main():
"""
NAME
LDGO_magic.py
DESCRIPTION
converts LDGO format files to magic_measurements format files
SYNTAX
LDGO_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify .ldgo format input file, required
-fsa SAMPFILE : specify er_samples.txt file relating samples, site and locations names,default is none
-F FILE: specify output file, default is magic_measurements.txt
-Fsy: specify er_synthetics file, default is er_sythetics.txt
-Fsa: specify output er_samples file, default is NONE (only for LDGO formatted files)
-LP [colon delimited list of protocols, include all that apply]
AF: af demag
T: thermal including thellier but not trm acquisition
S: Shaw method
I: IRM (acquisition)
N: NRM only
TRM: trm acquisition
ANI: anisotropy experiment
D: double AF demag
G: triple AF demag (GRM protocol)
-V [1,2,3] units of IRM field in volts using ASC coil #1,2 or 3
-spc NUM : specify number of characters to designate a specimen, default = 0
-loc LOCNAME : specify location/study name, must have either LOCNAME or SAMPFILE or be a synthetic
-syn INST TYPE: sets these specimens as synthetics created at institution INST and of type TYPE
-ins INST : specify which demag instrument was used (e.g, SIO-Suzy or SIO-Odette),default is ""
-dc B PHI THETA: dc lab field (in micro tesla) and phi,theta, default is none
NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment
-ac B : peak AF field (in mT) for ARM acquisition, default is none
-ncn NCON: specify naming convention: default is #1 below
-A: don't average replicate measurements
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
[8] synthetic - has no site name
INPUT
Best to put separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.) in
seperate .mag files (eg. af.mag, thermal.mag, etc.)
Format of LDEO files:
isaf2.fix
LAT: .00 LON: .00
ID TREAT I CD J CDECL CINCL GDECL GINCL BDECL BINCL SUSC M/V
________________________________________________________________________________
is031c2 .0 SD 0 461.600 163.9 17.5 337.1 74.5 319.1 74.4 .0 .0
ID: specimen name
TREAT: treatment step
I: Instrument
CD: Circular standard devation
J: intensity. assumed to be total moment in 10^-4 (emu)
CDECL: Declination in specimen coordinate system
CINCL: Declination in specimen coordinate system
GDECL: Declination in geographic coordinate system
GINCL: Declination in geographic coordinate system
BDECL: Declination in bedding adjusted coordinate system
BINCL: Declination in bedding adjusted coordinate system
SUSC: magnetic susceptibility (in micro SI)a
M/V: mass or volume for nomalizing (0 won't normalize)
"""
# initialize some stuff
noave = 0
methcode, inst = "LP-NO", ""
phi, theta, peakfield, labfield = 0, 0, 0, 0
pTRM, MD, samp_con, Z = 0, 0, '1', 1
dec = [315, 225, 180, 135, 45, 90, 270, 270, 270, 90, 180, 180, 0, 0, 0]
inc = [0, 0, 0, 0, 0, -45, -45, 0, 45, 45, 45, -45, -90, -45, 45]
tdec = [0, 90, 0, 180, 270, 0, 0, 90, 0]
tinc = [0, 0, 90, 0, 0, -90, 0, 0, 90]
missing = 1
demag = "N"
er_location_name = ""
citation = 'This study'
args = sys.argv
fmt = 'old'
syn = 0
synfile = 'er_synthetics.txt'
samp_file, ErSamps = '', []
trm = 0
irm = 0
specnum = 0
coil = ""
#
# get command line arguments
#
meas_file = "magic_measurements.txt"
user = ""
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind = args.index("-usr")
user = args[ind + 1]
if '-F' in args:
ind = args.index("-F")
meas_file = args[ind + 1]
if '-Fsy' in args:
ind = args.index("-Fsy")
synfile = args[ind + 1]
if '-Fsa' in args:
ind = args.index("-Fsa")
samp_file = args[ind + 1]
try:
open(samp_file, 'rU')
ErSamps, file_type = pmag.magic_read(samp_file)
print 'sample information will be appended to new er_samples.txt file'
except:
print 'sample information will be stored in new er_samples.txt file'
if '-f' in args:
ind = args.index("-f")
magfile = args[ind + 1]
try:
input = open(magfile, 'rU')
except:
print "bad mag file name"
sys.exit()
else:
print "mag_file field is required option"
print main.__doc__
sys.exit()
if "-dc" in args:
ind = args.index("-dc")
labfield = float(args[ind + 1]) * 1e-6
phi = float(args[ind + 2])
theta = float(args[ind + 3])
if "-ac" in args:
ind = args.index("-ac")
peakfield = float(args[ind + 1]) * 1e-3
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind + 1])
if specnum != 0: specnum = -specnum
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if "-fsa" in args:
ind = args.index("-fsa")
Samps, file_type = pmag.magic_read(args[ind + 1])
if '-syn' in args:
syn = 1
ind = args.index("-syn")
institution = args[ind + 1]
syntype = args[ind + 2]
if '-fsy' in args:
ind = args.index("-fsy")
synfile = args[ind + 1]
if "-ins" in args:
ind = args.index("-ins")
inst = args[ind + 1]
if "-A" in args: noave = 1
if "-ncn" in args:
ind = args.index("-ncn")
samp_con = sys.argv[ind + 1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "4"
if '-LP' in args:
ind = args.index("-LP")
codelist = args[ind + 1]
codes = codelist.split(':')
if "AF" in codes:
demag = 'AF'
if '-dc' not in args: methcode = "LT-AF-Z"
if '-dc' in args: methcode = "LT-AF-I"
if "T" in codes:
demag = "T"
if '-dc' not in args: methcode = "LT-T-Z"
if '-dc' in args: methcode = "LT-T-I"
if "I" in codes:
methcode = "LP-IRM"
irmunits = "mT"
if "S" in codes:
demag = "S"
methcode = "LP-PI-TRM:LP-PI-ALT-AFARM"
trm_labfield = labfield
ans = raw_input("DC lab field for ARM step: [50uT] ")
if ans == "":
arm_labfield = 50e-6
else:
arm_labfield = float(ans) * 1e-6
ans = raw_input("temperature for total trm step: [600 C] ")
if ans == "":
trm_peakT = 600 + 273 # convert to kelvin
else:
trm_peakT = float(ans) + 273 # convert to kelvin
if "G" in codes: methcode = "LT-AF-G"
if "D" in codes: methcode = "LT-AF-D"
if "TRM" in codes:
demag = "T"
trm = 1
if "-V" in args:
methcode = "LP-IRM"
ind = args.index("-V")
irmunits = "V"
coil = args[ind + 1]
if coil not in ["1", "2", "3"]:
print main.__doc__
print 'not a valid coil specification'
sys.exit()
if demag == "T" and "ANI" in codes:
methcode = "LP-AN-TRM"
if demag == "AF" and "ANI" in codes:
methcode = "LP-AN-ARM"
if labfield == 0: labfield = 50e-6
if peakfield == 0: peakfield = .180
SynRecs, MagRecs = [], []
version_num = pmag.get_version()
if 1: # ldgo file format
#
# find start of data:
#
Samps = [] # keeps track of sample orientations
DIspec = []
Data, k = input.readlines(), 0
for k in range(len(Data)):
rec = Data[k].split()
if rec[0][0] == "_" or rec[0][0:2] == "!_":
break
start = k + 1
for k in range(start, len(Data)):
rec = Data[k].split()
if len(rec) > 0:
MagRec = {}
MagRec["treatment_temp"] = '%8.3e' % (273
) # room temp in kelvin
MagRec["measurement_temp"] = '%8.3e' % (
273) # room temp in kelvin
MagRec["treatment_ac_field"] = '0'
MagRec["treatment_dc_field"] = '0'
MagRec["treatment_dc_field_phi"] = '0'
MagRec["treatment_dc_field_theta"] = '0'
meas_type = "LT-NO"
MagRec["measurement_flag"] = 'g'
MagRec["measurement_standard"] = 'u'
MagRec["measurement_number"] = '1'
MagRec["er_specimen_name"] = rec[0]
if specnum != 0:
MagRec["er_sample_name"] = rec[0][:specnum]
else:
MagRec["er_sample_name"] = rec[0]
site = pmag.parse_site(MagRec['er_sample_name'], samp_con, Z)
MagRec["er_site_name"] = site
MagRec["er_location_name"] = er_location_name
MagRec["measurement_csd"] = rec[3]
MagRec["measurement_magn_moment"] = '%10.3e' % (
float(rec[4]) * 1e-7) # moment in Am^2 (from 10^-4 emu)
#
#if samp_file!="" and MagRec["er_sample_name"] not in Samps: # create er_samples.txt file with these data
# cdec,cinc=float(rec[5]),float(rec[6])
# gdec,ginc=float(rec[7]),float(rec[8])
# az,pl=pmag.get_azpl(cdec,cinc,gdec,ginc)
# bdec,binc=float(rec[9]),float(rec[10])
# if rec[7]!=rec[9] and rec[6]!=rec[8]:
# dipdir,dip=pmag.get_tilt(gdec,ginc,bdec,binc)
# else:
# dipdir,dip=0,0
# ErSampRec={}
# ErSampRec['er_location_name']=MagRec['er_location_name']
# ErSampRec['er_sample_name']=MagRec['er_sample_name']
# ErSampRec['er_site_name']=MagRec['er_site_name']
# ErSampRec['sample_azimuth']='%7.1f'%(az)
# ErSampRec['sample_dip']='%7.1f'%(pl)
# ErSampRec['sample_bed_dip_direction']='%7.1f'%(dipdir)
# ErSampRec['sample_bed_dip']='%7.1f'%(dip)
# ErSampRec['sample_description']='az,pl,dip_dir and dip recalculated from [c,g,b][dec,inc] in ldeo file'
# ErSampRec['magic_method_codes']='SO-REC'
# ErSamps.append(ErSampRec)
# Samps.append(ErSampRec['er_sample_name'])
MagRec["measurement_dec"] = rec[5]
MagRec["measurement_inc"] = rec[6]
MagRec["measurement_chi"] = '%10.3e' % (
float(rec[11]) * 1e-5
) #convert to SI (assume Bartington, 10-5 SI)
#MagRec["magic_instrument_codes"]=rec[2]
#MagRec["er_analyst_mail_names"]=""
MagRec["er_citation_names"] = "This study"
MagRec["magic_method_codes"] = meas_type
if demag == "AF":
if methcode != "LP-AN-ARM":
MagRec["treatment_ac_field"] = '%8.3e' % (
float(rec[1]) * 1e-3) # peak field in tesla
meas_type = "LT-AF-Z"
MagRec["treatment_dc_field"] = '0'
else: # AARM experiment
if treat[1][0] == '0':
meas_type = "LT-AF-Z"
MagRec["treatment_ac_field"] = '%8.3e' % (
peakfield) # peak field in tesla
else:
meas_type = "LT-AF-I"
ipos = int(treat[0]) - 1
MagRec["treatment_dc_field_phi"] = '%7.1f' % (
dec[ipos])
MagRec["treatment_dc_field_theta"] = '%7.1f' % (
inc[ipos])
MagRec["treatment_dc_field"] = '%8.3e' % (labfield)
MagRec["treatment_ac_field"] = '%8.3e' % (
peakfield) # peak field in tesla
elif demag == "T":
if rec[1][0] == ".": rec[1] = "0" + rec[1]
treat = rec[1].split('.')
if len(treat) == 1: treat.append('0')
MagRec["treatment_temp"] = '%8.3e' % (float(rec[1]) + 273.
) # temp in kelvin
meas_type = "LT-T-Z"
MagRec["treatment_temp"] = '%8.3e' % (
float(treat[0]) + 273.) # temp in kelvin
if trm == 0: # demag=T and not trmaq
if treat[1][0] == '0':
meas_type = "LT-T-Z"
else:
MagRec["treatment_dc_field"] = '%8.3e' % (
labfield
) # labfield in tesla (convert from microT)
MagRec["treatment_dc_field_phi"] = '%7.1f' % (
phi) # labfield phi
MagRec["treatment_dc_field_theta"] = '%7.1f' % (
theta) # labfield theta
if treat[1][0] == '1':
meas_type = "LT-T-I" # in-field thermal step
if treat[1][0] == '2':
meas_type = "LT-PTRM-I" # pTRM check
pTRM = 1
if treat[1][0] == '3':
MagRec[
"treatment_dc_field"] = '0' # this is a zero field step
meas_type = "LT-PTRM-MD" # pTRM tail check
else:
meas_type = "LT-T-I" # trm acquisition experiment
MagRec['magic_method_codes'] = meas_type
MagRecs.append(MagRec)
MagOuts = pmag.measurements_methods(MagRecs, noave)
pmag.magic_write(meas_file, MagOuts, 'magic_measurements')
print "results put in ", meas_file
if samp_file != "":
pmag.magic_write(samp_file, ErSamps, 'er_samples')
print "sample orientations put in ", samp_file
if len(SynRecs) > 0:
pmag.magic_write(synfile, SynRecs, 'er_synthetics')
print "synthetics put in ", synfile
def main():
"""
NAME
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
susar4-asc_magic.py
DESCRIPTION
converts ascii files generated by SUSAR ver.4.0 to MagIC formated
files for use with PmagPy plotting software
SYNTAX
susar4-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: ""
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.
"""
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',"PGL-KLY3",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 '-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 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()
print words
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":
AniRec['er_sample_name']=specname[:specnum]
SpecRec['er_specimen_name']=specname
SpecRec['er_sample_name']=specname[:specnum]
SampRec['er_sample_name']=specname[:specnum]
SiteRec['er_sample_name']=specname[:specnum]
SiteRec['site_description']='s'
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)
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"
AniRec['anisotropy_unit']='SI'
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])-90.
if 'T1' in words and 'F1' in words:
k+=2 # read in fourth line down
line=Data[k]
rec=line.split()
dd,dip_direction=0,0
if len(rec)>0:
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()
if len(rec)>0:
MeasRec['measurement_chi_volume']=rec[1]
sigma=.01*float(rec[2])/3.
AniRec['anisotropy_sigma']='%7.4f'%(sigma)
if "susceptibilities" in words: # first part of specimen data
line=Data[k+2]
rec=line.split()
AniRec['anisotropy_s1']='%7.4f'%(float(rec[1])/3.) # eigenvalues sum to unity - not 3
AniRec['anisotropy_s2']='%7.4f'%(float(rec[2])/3.)
AniRec['anisotropy_s3']='%7.4f'%(float(rec[3])/3.)
k+=2
line=Data[k]
rec=line.split()
AniRec['anisotropy_s4']='%7.4f'%(float(rec[0])/3.) # eigenvalues sum to unity - not 3
AniRec['anisotropy_s5']='%7.4f'%(float(rec[1])/3.)
AniRec['anisotropy_s6']='%7.4f'%(float(rec[2])/3.)
AniRec['anisotropy_tilt_correction']='-1'
AniRecs.append(AniRec)
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":
output=dir_path+"/er_specimens.txt"
pmag.magic_write(output,SpecRecs,'er_specimens')
print "specimen info put in ",output
output=dir_path+"/er_samples.txt"
pmag.magic_write(output,SampRecs,'er_samples')
print "sample info put in ",output
output=dir_path+"/er_sites.txt"
pmag.magic_write(output,SiteRecs,'er_sites')
print "site info put in ",output
print """"
def main():
"""
NAME
CIT_magic.py
DESCRIPTION
converts CalTech (CIT) .sam format files to magic_measurements format files
SYNTAX
CIT_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify .sam format input file, required
-fsi SITEFILE : specify file with site names and locations [tab delimited magic file]
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsp FILE: specify output er_specimens.txt file, default is er_specimens.txt
-Fsi FILE: specify output er_sites.txt file, default is er_sites.txt
-n [gm,kg,cc,m3]: specify normalization
-spc NUM : specify number of characters to designate a specimen, default = 0
-ncn NCON: specify naming convention
-loc LOCNAME : specify location/study name, must have either LOCNAME or SITEFILE or be a synthetic
-dc B PHI THETA: dc lab field (in micro tesla) and phi,theta, default is none
NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment
-ac B : peak AF field (in mT) for ARM acquisition, default is none
INPUT
Best to put separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.)
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] 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.
"""
#
#
norm='cc'
samp_con,Z='3',1
meas_file='magic_measurements.txt'
spec_file='er_specimens.txt'
samp_file='er_samples.txt'
site_file='er_sites.txt'
ErSpecs,ErSamps,ErSites,ErLocs,ErCits=[],[],[],[],[]
MeasRecs=[]
specnum,units,locname=0,"1","unknown"
citation="This study"
dir_path='.'
args=sys.argv
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
if '-F' in args:
ind=args.index("-F")
meas_file=args[ind+1]
if '-Fsp' in args:
ind=args.index("-Fsp")
spec_file=args[ind+1]
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file=args[ind+1]
if '-loc' in args:
ind=args.index("-loc")
locname=args[ind+1]
if '-spc' in args:
ind=args.index("-spc")
specnum=-int(args[ind+1])
if '-n' in args:
ind=args.index("-n")
norm=args[ind+1]
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="7"
if '-f' in args:
ind=args.index("-f")
magfile=args[ind+1]
magfile=dir_path+'/'+magfile
spec_file=dir_path+'/'+spec_file
samp_file=dir_path+'/'+samp_file
site_file=dir_path+'/'+site_file
meas_file=dir_path+'/'+meas_file
try:
input=open(magfile,'r')
except:
print "bad sam file name"
sys.exit()
File=input.readlines()
sids,ln,format=[],0,'CIT'
formats=['CIT','2G','APP','JRA']
ErLocRec={}
ErLocRec["er_location_name"]=locname
ErLocRec["er_citation_name"]=citation
comment=File[ln]
if comment=='CIT':
format=comment
ln+=1
comment=File[ln]
print comment
ln+=1
specimens,samples,sites=[],[],[]
if format=='CIT':
line=File[ln].split()
site_lat=line[0]
site_lon=line[1]
ErLocRec["location_begin_lat"]=site_lat
ErLocRec["location_begin_lon"]=site_lon
ErLocRec["location_end_lat"]=site_lat
ErLocRec["location_end_lon"]=site_lon
ErLocs.append(ErLocRec)
Cdec=float(line[2])
if len(line)>4:
fa_az=line[3]
fa_pl=line[4]
if len(line)>6:
bed_dip_dir='%7.1f'%(float(line[5]+90.))
bed_dip=line[6]
for k in range(ln+1,len(File)):
line=File[k]
rec=line.split()
specimen=rec[0]
specimens.append(specimen)
else:
print 'file type not yet supported'
sys.exit()
for specimen in specimens:
ErSpecRec,ErSampRec,ErSiteRec={},{},{}
if specnum!=0:
sample=specimen[:specnum]
else: sample=specimen
site=pmag.parse_site(sample,samp_con,Z)
ErSpecRec['er_specimen_name']=specimen
ErSpecRec['er_sample_name']=sample
ErSpecRec['er_site_name']=site
ErSpecRec['er_location_name']=locname
ErSpecRec['er_citation_name']=citation
ErSampRec['er_sample_name']=sample
ErSampRec['er_site_name']=site
ErSampRec['er_location_name']=locname
ErSampRec['er_citation_name']=citation
for k in range(ln+1,len(File)):
line=File[k]
rec=line.split()
specimen=rec[0]
specimens.append(specimen)
for specimen in specimens:
ErSpecRec,ErSampRec,ErSiteRec={},{},{}
if specnum!=0:
sample=specimen[:specnum]
else: sample=specimen
site=pmag.parse_site(sample,samp_con,Z)
ErSpecRec['er_specimen_name']=specimen
ErSpecRec['er_sample_name']=sample
ErSpecRec['er_site_name']=site
ErSpecRec['er_location_name']=locname
ErSpecRec['er_citation_name']=citation
ErSampRec['er_sample_name']=sample
ErSampRec['er_site_name']=site
ErSampRec['er_location_name']=locname
ErSampRec['er_citation_name']=citation
ErSiteRec['er_site_name']=site
ErSiteRec['er_location_name']=locname
ErSiteRec['er_citation_name']=citation
ErSiteRec['site_lat']=site_lat
ErSiteRec['site_lon']=site_lon
f=open(dir_path+'/'+specimen,'rU')
Lines=f.readlines()
comment=Lines[0][10:]
if len(line)>2:comment=line[2]
info=Lines[1].split()
vol=float(info[-1])
if vol!=1.0:
if norm=='cc':units="1"
if norm=='m3':units="2"
ErSampRec['specimen_weight']=""
if units=="1" or "":
ErSampRec['specimen_volume']='%10.3e'%(vol*1e-6)
else:
ErSampRec['specimen_volume']='%10.3e'%(vol)
else:
if norm=='cc':units="1"
if norm=='m3':units="2"
ErSampRec['specimen_volume']=""
if units=="1" or "":
ErSampRec['specimen_weight']='%10.3e'%(vol*1e-3)
else:
ErSampRec['specimen_weight']='%10.3e'%(vol)
dip=float(info[-2])
dip_direction=float(info[-3])+Cdec+90.
sample_dip=-float(info[-4])
sample_azimuth=float(info[-5])+Cdec-90.
if len(info)>5:
ErSampRec['sample_height']=info[-6]
else:
ErSampRec['sample_height']='0'
ErSampRec['sample_azimuth']='%7.1f'%(sample_azimuth)
ErSampRec['sample_dip']='%7.1f'%(sample_dip)
ErSampRec['sample_bed_dip']='%7.1f'%(dip)
ErSampRec['sample_bed_dip_direction']='%7.1f'%(dip_direction)
ErSampRec['sample_class']=''
ErSampRec['sample_type']=''
ErSampRec['sample_lithology']=''
if Cdec!=0 or Cdec!="":
ErSampRec['magic_method_codes']='SO-CMD-NORTH'
else:
ErSampRec['magic_method_codes']='SO-MAG'
for line in Lines[2:len(Lines)-1]:
MeasRec=ErSpecRec.copy()
treat_type=line[0:3]
treat=line[3:6]
if treat_type.strip()=='NRM' or treat==" ":
MeasRec['magic_method_codes']='LT-NO'
MeasRec['measurement_temp']='273'
MeasRec['treatment_temp']='273'
MeasRec['treatment_dc_field']='0'
MeasRec['treatment_ac_field']='0'
elif treat_type.strip()=='AF':
MeasRec['magic_method_codes']='LT-AF-Z'
MeasRec['measurement_temp']='273'
MeasRec['treatment_temp']='273'
MeasRec['treatment_dc_field']='0'
MeasRec['treatment_ac_field']='%10.3e'%(float(treat)*1e-3)
elif treat_type.strip()=='TT':
MeasRec['magic_method_codes']='LT-T-Z'
MeasRec['measurement_temp']='273'
MeasRec['treatment_temp']='%7.1f'%(float(treat)+273)
MeasRec['treatment_dc_field']='0'
MeasRec['treatment_ac_field']='0'
else:
print "trouble with your treatment steps"
MeasRec['measurement_dec']=line[46:51]
MeasRec['measurement_inc']=line[52:58]
int='%8.2e'%(float(line[31:39])*vol*1e-3) # convert to Am2
MeasRec['measurement_magn_moment']=int
MeasRec['measurement_x_sd']='%8.2e'%(float(line[58:67])*1e-8) #(convert e-5emu to Am2)
MeasRec['measurement_y_sd']='%8.2e'%(float(line[67:76])*1e-8)
MeasRec['measurement_z_sd']='%8.2e'%(float(line[76:85])*1e-8)
MeasRec['measurement_csd']='%7.1f'%(eval(line[41:46]))
MeasRec['magic_instrument_codes']=line[85:]
MeasRecs.append(MeasRec)
ErSpecs.append(ErSpecRec)
if sample not in samples:
samples.append(sample)
ErSamps.append(ErSampRec)
site=pmag.parse_site(sample,samp_con,Z)
if site not in sites:
sites.append(site)
ErSites.append(ErSiteRec)
pmag.magic_write(spec_file,ErSpecs,'er_specimens')
print 'specimens stored in ',spec_file
pmag.magic_write(samp_file,ErSamps,'er_samples')
print 'samples stored in ',samp_file
pmag.magic_write(site_file,ErSites,'er_sites')
Fixed=pmag.measurements_methods(MeasRecs,0)
pmag.magic_write(meas_file,Fixed,'magic_measurements')
print 'data stored in ',meas_file
def main():
"""
NAME
mag_magic.py
DESCRIPTION
converts SIO .mag format files to magic_measurements format files
SYNTAX
mag_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify .mag format input file, required
-fsa SAMPFILE : specify er_samples.txt file relating samples, site and locations names,default is none
-F FILE: specify output file, default is magic_measurements.txt
-Fsy: specify er_synthetics file, default is er_sythetics.txt
-Fsa: specify output er_samples file, default is NONE (only for LDGO formatted files)
-LP [colon delimited list of protocols, include all that apply]
AF: af demag
S: Shaw method
T: thermal including thellier but not trm acquisition
N: NRM only
TRM: trm acquisition
ANI: anisotropy experiment
D: double AF demag
G: triple AF demag (GRM protocol)
-spc NUM : specify number of characters to designate a specimen, default = 0
-loc LOCNAME : specify location/study name, must have either LOCNAME or SAMPFILE or be a synthetic
-syn INST TYPE: sets these specimens as synthetics created at institution INST and of type TYPE
-ins INST : specify which demag instrument was used (e.g, SIO-Suzy or SIO-Odette),default is ""
-dc B PHI THETA: dc lab field (in micro tesla) and phi,theta, default is none
NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment
-ac B : peak AF field (in mT) for ARM acquisition, default is none
-FT [SIO,LDGO] : file type. default is SIO (.mag file format)
-ncn NCON: specify naming convention: default is #1 below
-A: don't average replicate measurements
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
[8] synthetic - has no site name
[9] ODP naming convention
INPUT
Best to put separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.) in
seperate .mag files (eg. af.mag, thermal.mag, etc.)
Format of SIO .mag files:
Spec Treat CSD Intensity Declination Inclination [optional metadata string]
Spec: specimen name
Treat: treatment step
XXX T in Centigrade
XXX AF in mT
for special experiments:
Thellier:
XXX.0 first zero field step
XXX.1 first in field step [XXX.0 and XXX.1 can be done in any order]
XXX.2 second in-field step at lower temperature (pTRM check)
XXX.3 second zero-field step after infield (pTRM check step)
XXX.3 MUST be done in this order [XXX.0, XXX.1 [optional XXX.2] XXX.3]
AARM:
X.00 baseline step (AF in zero bias field - high peak field)
X.1 ARM step (in field step) where
X is the step number in the 15 position scheme
(see Appendix to Lecture 13 - Lectures in Paleomagnetism, 2007)
TRM:
XXX.YYY XXX is temperature step of total TRM
YYY is dc field in microtesla
Shaw:
XXX.YY XXX is AF field
YY=00 is AF of NRM
YY=01 is AF of ARM1
YY=02 is AF of TRM
YY=03 is AF of ARM2
specify temperature and field of Total TRM step on command line
Intensity assumed to be total moment in 10^3 Am^2 (emu)
Declination: Declination in specimen coordinate system
Inclination: Declination in specimen coordinate system
Optional metatdata string: mm/dd/yy;hh:mm;[dC,mT];xx.xx;UNITS;USER;INST;NMEAS
hh in 24 hours.
dC or mT units of treatment XXX (see Treat above) for thermal or AF respectively
xx.xxx DC field
UNITS of DC field (microT, mT)
INST: instrument code, number of axes, number of positions (e.g., G34 is 2G, three axes,
measured in four positions)
NMEAS: number of measurements in a single position (1,3,200...)
Format of LDGO files:
SPEC TREAT INST CSD Intensity CDECL CINCL [GDECL GINCL BDECL BINCL SUSC ]
"""
# initialize some stuff
infile_type="mag"
noave=0
methcode,inst="",""
phi,theta,peakfield,labfield=0,0,0,0
pTRM,MD,samp_con,Z=0,0,'1',1
dec=[315,225,180,135,45,90,270,270,270,90,180,180,0,0,0]
inc=[0,0,0,0,0,-45,-45,0,45,45,45,-45,-90,-45,45]
missing=1
demag="N"
er_location_name=""
citation='This study'
args=sys.argv
methcode="LP-NO"
fmt='old'
syn=0
synfile='er_synthetics.txt'
samp_file,ErSamps='',[]
trm=0
irm=0
specnum=0
#
# get command line arguments
#
meas_file="magic_measurements.txt"
user=""
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
if '-F' in args:
ind=args.index("-F")
meas_file=args[ind+1]
if '-Fsy' in args:
ind=args.index("-Fsy")
synfile=args[ind+1]
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file=args[ind+1]
try:
open(samp_file,'rU')
ErSamps,file_type=pmag.magic_read(samp_file)
print 'sample information will be appended to new er_samples.txt file'
except:
print 'sample information will be stored in new er_samples.txt file'
if '-f' in args:
ind=args.index("-f")
magfile=args[ind+1]
try:
input=open(magfile,'rU')
except:
print "bad mag file name"
sys.exit()
else:
print "mag_file field is required option"
print main.__doc__
sys.exit()
if "-dc" in args:
ind=args.index("-dc")
labfield=float(args[ind+1])*1e-6
phi=float(args[ind+2])
theta=float(args[ind+3])
if "-ac" in args:
ind=args.index("-ac")
peakfield=float(args[ind+1])*1e-3
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if specnum!=0:specnum=-specnum
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-fsa" in args:
ind=args.index("-fsa")
Samps,file_type=pmag.magic_read(args[ind+1])
if '-syn' in args:
syn=1
ind=args.index("-syn")
institution=args[ind+1]
syntype=args[ind+2]
if '-fsy' in args:
ind=args.index("-fsy")
synfile=args[ind+1]
if "-ins" in args:
ind=args.index("-ins")
inst=args[ind+1]
if '-FT' in args:
ind=args.index("-FT")
FT=args[ind+1]
if FT=="LDGO":infile_type="ldgo" # default is "mag"
if "-A" in args: noave=1
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
if '-LP' in args:
ind=args.index("-LP")
codelist=args[ind+1]
codes=codelist.split(':')
if "AF" in codes:
demag='AF'
if'-dc' not in args: methcode="LT-AF-Z"
if'-dc' in args: methcode="LT-AF-I"
if "T" in codes:
demag="T"
if '-dc' not in args: methcode="LT-T-Z"
if '-dc' in args: methcode="LT-T-I"
if "I" in codes:
methcode="LP-IRM"
if "S" in codes:
demag="S"
methcode="LP-PI-TRM:LP-PI-ALT-AFARM"
trm_labfield=labfield
ans=raw_input("DC lab field for ARM step: [50uT] ")
if ans=="":
arm_labfield=50e-6
else:
arm_labfield=float(ans)*1e-6
ans=raw_input("temperature for total trm step: [600 C] ")
if ans=="":
trm_peakT=600+273 # convert to kelvin
else:
trm_peakT=float(ans)+273 # convert to kelvin
if "G" in codes: methcode="LT-AF-G"
if "D" in codes: methcode="LT-AF-D"
if "TRM" in codes:
demag="T"
trm=1
if demag=="T" and "ANI" in codes:
methcode="LP-AN-TRM"
if demag=="AF" and "ANI" in codes:
methcode="LP-AN-ARM"
if labfield==0: labfield=50e-6
if peakfield==0: peakfield=.180
SynRecs,MagRecs=[],[]
version_num=pmag.get_version()
if infile_type=="mag":
for line in input.readlines():
instcode=""
if len(line)>2:
SynRec={}
MagRec={}
MagRec['er_location_name']=er_location_name
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["treatment_ac_field"]='0'
MagRec["treatment_dc_field"]='0'
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
meas_type="LT-NO"
rec=line.split()
if len(rec)>6:
code1=rec[6].split(';') # break e.g., 10/15/02;7:45 indo date and time
if len(code1)==2: # old format with AM/PM
missing=0
code2=code1[0].split('/') # break date into mon/day/year
code3=rec[7].split(';') # break e.g., AM;C34;200 into time;instr/axes/measuring pos;number of measurements
yy=int(code2[2])
if yy <90:
yyyy=str(2000+yy)
else: yyyy=str(1900+yy)
mm=int(code2[0])
if mm<10:
mm="0"+str(mm)
else: mm=str(mm)
dd=int(code2[1])
if dd<10:
dd="0"+str(dd)
else: dd=str(dd)
time=code1[1].split(':')
hh=int(time[0])
if code3[0]=="PM":hh=hh+12
if hh<10:
hh="0"+str(hh)
else: hh=str(hh)
min=int(time[1])
if min<10:
min= "0"+str(min)
else: min=str(min)
MagRec["measurement_date"]=yyyy+":"+mm+":"+dd+":"+hh+":"+min+":00.00"
MagRec["measurement_time_zone"]='SAN'
if inst=="":
if code3[1][0]=='C':instcode='SIO-bubba'
if code3[1][0]=='G':instcode='SIO-flo'
else:
instcode=''
MagRec["measurement_positions"]=code3[1][2]
elif len(code1)>2: # newest format (cryo7 or later)
labfield=0
fmt='new'
date=code1[0].split('/') # break date into mon/day/year
yy=int(date[2])
if yy <90:
yyyy=str(2000+yy)
else: yyyy=str(1900+yy)
mm=int(date[0])
if mm<10:
mm="0"+str(mm)
else: mm=str(mm)
dd=int(date[1])
if dd<10:
dd="0"+str(dd)
else: dd=str(dd)
time=code1[1].split(':')
hh=int(time[0])
if hh<10:
hh="0"+str(hh)
else: hh=str(hh)
min=int(time[1])
if min<10:
min= "0"+str(min)
else: min=str(min)
MagRec["measurement_date"]=yyyy+":"+mm+":"+dd+":"+hh+":"+min+":00.00"
MagRec["measurement_time_zone"]='SAN'
if inst=="":
if code1[6][0]=='C':instcode='SIO-bubba'
if code1[6][0]=='G':instcode='SIO-flo'
else:
instcode=''
if len(code1)>1:
MagRec["measurement_positions"]=code1[6][2]
else:
MagRec["measurement_positions"]=code1[7] # takes care of awkward format with bubba and flo being different
if user=="":user=code1[5]
if code1[2][-1]=='C': demag="T"
if code1[2]=='mT':
if methcode=="LP-IRM":
labfield=float(code1[3])*1e-3
if rec[1][0]!="-":
phi,theta=0.,90.
else:
phi,theta=0.,-90.
meas_type="LT-IRM"
MagRec["treatment_dc_field"]='%8.3e'%(labfield)
MagRec["treatment_dc_field_phi"]='%7.1f'%(phi)
MagRec["treatment_dc_field_theta"]='%7.1f'%(theta)
else:
demag="AF"
labfield=float(code1[3])*1e-6
if code1[4]=='microT' and labfield!=0.:
phi,theta=0.,90.
if demag=="T": meas_type="LT-T-I"
if demag=="AF": meas_type="LT-AF-I"
MagRec["treatment_dc_field"]='%8.3e'%(labfield)
MagRec["treatment_dc_field_phi"]='%7.1f'%(phi)
MagRec["treatment_dc_field_theta"]='%7.1f'%(theta)
if code1[4]=='' or labfield==0.:
if demag=='T':meas_type="LT-T-Z"
if demag=="AF":meas_type="LT-AF-Z"
MagRec["treatment_dc_field"]='0'
if syn==0:
MagRec["er_specimen_name"]=rec[0]
MagRec["er_synthetic_name"]=""
MagRec["er_site_name"]=""
if specnum!=0:
MagRec["er_sample_name"]=rec[0][:specnum]
else:
MagRec["er_sample_name"]=rec[0]
if "-fsa" in args:
for samp in Samps:
if samp["er_sample_name"] == MagRec["er_sample_name"]:
MagRec["er_location_name"]=samp["er_location_name"]
MagRec["er_site_name"]=samp["er_site_name"]
break
elif int(samp_con)!=6:
site=pmag.parse_site(MagRec['er_sample_name'],samp_con,Z)
MagRec["er_site_name"]=site
if MagRec['er_site_name']=="":
print 'No site name found for: ',MagRec['er_specimen_name'],MagRec['er_sample_name']
if MagRec["er_location_name"]=="":
print 'no location name for: ',MagRec["er_specimen_name"]
else:
if specnum!=0:
MagRec["er_sample_name"]=rec[0][:specnum]
else:
MagRec["er_sample_name"]=rec[0]
MagRec["er_site_name"]=""
MagRec["er_synthetic_name"]=MagRec["er_specimen_name"]
SynRec["er_synthetic_name"]=MagRec["er_specimen_name"]
site=pmag.parse_site(MagRec['er_sample_name'],samp_con,Z)
SynRec["synthetic_parent_sample"]=site
SynRec["er_citation_names"]="This study"
SynRec["synthetic_institution"]=institution
SynRec["synthetic_type"]=syntype
SynRecs.append(SynRec)
if rec[1]==".00":rec[1]="0.00"
treat=rec[1].split('.')
if float(rec[1])==0:
pass
elif demag=="AF":
if methcode != "LP-AN-ARM":
MagRec["treatment_ac_field"]='%8.3e' %(float(rec[1])*1e-3) # peak field in tesla
meas_type="LT-AF-Z"
MagRec["treatment_dc_field"]='0'
else: # AARM experiment
if treat[1][0]=='0':
meas_type="LT-AF-Z"
MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
MagRec["treatment_dc_field"]='%8.3e'%(0)
if labfield!=0: print "Warning - inconsistency in mag file with lab field - overriding file with 0"
else:
meas_type="LT-AF-I"
ipos=int(treat[0])-1
MagRec["treatment_dc_field_phi"]='%7.1f' %(dec[ipos])
MagRec["treatment_dc_field_theta"]='%7.1f'% (inc[ipos])
MagRec["treatment_dc_field"]='%8.3e'%(labfield)
MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
elif demag=="S": # Shaw experiment
if treat[1][1]=='0':
if int(treat[0])!=0:
MagRec["treatment_ac_field"]='%8.3e' % (float(treat[0])*1e-3) # AF field in tesla
MagRec["treatment_dc_field"]='0'
meas_type="LT-AF-Z" # first AF
else:
meas_type="LT-NO"
MagRec["treatment_ac_field"]='0'
MagRec["treatment_dc_field"]='0'
elif treat[1][1]=='1':
if int(treat[0])==0:
MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
MagRec["treatment_dc_field"]='%8.3e'%(arm_labfield)
MagRec["treatment_dc_field_phi"]='%7.1f'%(phi)
MagRec["treatment_dc_field_theta"]='%7.1f'%(theta)
meas_type="LT-AF-I"
else:
MagRec["treatment_ac_field"]='%8.3e' % ( float(treat[0])*1e-3) # AF field in tesla
MagRec["treatment_dc_field"]='0'
meas_type="LT-AF-Z"
elif treat[1][1]=='2':
if int(treat[0])==0:
MagRec["treatment_ac_field"]='0'
MagRec["treatment_dc_field"]='%8.3e'%(trm_labfield)
MagRec["treatment_dc_field_phi"]='%7.1f'%(phi)
MagRec["treatment_dc_field_theta"]='%7.1f'%(theta)
MagRec["treatment_temp"]='%8.3e' % (trm_peakT)
meas_type="LT-T-I"
else:
MagRec["treatment_ac_field"]='%8.3e' % ( float(treat[0])*1e-3) # AF field in tesla
MagRec["treatment_dc_field"]='0'
meas_type="LT-AF-Z"
elif treat[1][1]=='3':
if int(treat[0])==0:
MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
MagRec["treatment_dc_field"]='%8.3e'%(arm_labfield)
MagRec["treatment_dc_field_phi"]='%7.1f'%(phi)
MagRec["treatment_dc_field_theta"]='%7.1f'%(theta)
meas_type="LT-AF-I"
else:
MagRec["treatment_ac_field"]='%8.3e' % ( float(treat[0])*1e-3) # AF field in tesla
MagRec["treatment_dc_field"]='0'
meas_type="LT-AF-Z"
else:
if len(treat)==1:treat.append('0')
MagRec["treatment_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
if trm==0: # demag=T and not trmaq
if treat[1][0]=='0':
meas_type="LT-T-Z"
else:
MagRec["treatment_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MagRec["treatment_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MagRec["treatment_dc_field_theta"]='%7.1f' % (theta) # labfield theta
if treat[1][0]=='1':meas_type="LT-T-I" # in-field thermal step
if treat[1][0]=='2':
meas_type="LT-PTRM-I" # pTRM check
pTRM=1
if treat[1][0]=='3':
MagRec["treatment_dc_field"]='0' # this is a zero field step
meas_type="LT-PTRM-MD" # pTRM tail check
else:
labfield=float(treat[1])*1e-6
MagRec["treatment_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MagRec["treatment_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MagRec["treatment_dc_field_theta"]='%7.1f' % (theta) # labfield theta
meas_type="LT-T-I:LP-TRM" # trm acquisition experiment
MagRec["measurement_csd"]=rec[2]
MagRec["measurement_magn_moment"]='%10.3e'% (float(rec[3])*1e-3) # moment in Am^2 (from emu)
MagRec["measurement_dec"]=rec[4]
MagRec["measurement_inc"]=rec[5]
MagRec["magic_instrument_codes"]=instcode
MagRec["er_analyst_mail_names"]=user
MagRec["er_citation_names"]=citation
MagRec["magic_method_codes"]=meas_type
MagRec["measurement_flag"]='g'
MagRec["er_specimen_name"]=rec[0]
if 'std' in rec[0]:
MagRec["measurement_standard"]='s'
else:
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["er_specimen_name"],meas_type
MagRecs.append(MagRec)
elif infile_type=="ldgo":
#
# find start of data:
#
Samps=[] # keeps track of sample orientations
DIspec=[]
Data,k=input.readlines(),0
for k in range(len(Data)):
rec=Data[k].split()
if rec[0][0]=="_" or rec[0][0:2]=="!_":
break
start=k+1
for k in range(start,len(Data)):
rec=Data[k].split()
if len(rec)>0:
MagRec={}
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["treatment_ac_field"]='0'
MagRec["treatment_dc_field"]='0'
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
meas_type="LT-NO"
MagRec["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["er_specimen_name"]=rec[0]
if specnum!=0:
MagRec["er_sample_name"]=rec[0][:specnum]
else:
MagRec["er_sample_name"]=rec[0]
site=pmag.parse_site(MagRec['er_sample_name'],samp_con,Z)
MagRec["er_site_name"]=site
MagRec["er_site_name"]=MagRec['er_sample_name'][0:-2]
MagRec["er_location_name"]=er_location_name
MagRec["measurement_csd"]=rec[3]
MagRec["measurement_magn_moment"]='%10.3e'% (float(rec[4])*1e-7) # moment in Am^2 (from 10^-4 emu)
#
if samp_file!="" and MagRec["er_sample_name"] not in Samps: # create er_samples.txt file with these data
cdec,cinc=float(rec[5]),float(rec[6])
gdec,ginc=float(rec[7]),float(rec[8])
az,pl=pmag.get_azpl(cdec,cinc,gdec,ginc)
bdec,binc=float(rec[9]),float(rec[10])
if rec[7]!=rec[9] and rec[6]!=rec[8]:
dipdir,dip=pmag.get_tilt(gdec,ginc,bdec,binc)
else:
dipdir,dip=0,0
ErSampRec={}
ErSampRec['er_location_name']=MagRec['er_location_name']
ErSampRec['er_sample_name']=MagRec['er_sample_name']
ErSampRec['er_site_name']=MagRec['er_site_name']
ErSampRec['sample_azimuth']='%7.1f'%(az)
ErSampRec['sample_dip']='%7.1f'%(pl)
ErSampRec['sample_bed_dip_direction']='%7.1f'%(dipdir)
ErSampRec['sample_bed_dip']='%7.1f'%(dip)
ErSampRec['sample_description']='az,pl,dip_dir and dip recalculated from [c,g,b][dec,inc] in ldeo file'
ErSampRec['magic_method_codes']='SO-REC'
ErSamps.append(ErSampRec)
Samps.append(ErSampRec['er_sample_name'])
MagRec["measurement_dec"]=rec[5]
MagRec["measurement_inc"]=rec[6]
MagRec["magic_instrument_codes"]=rec[2]
MagRec["er_analyst_mail_names"]=""
MagRec["er_citation_names"]="This study"
MagRec["magic_method_codes"]=meas_type
if demag=="AF":
if methcode != "LP-AN-ARM":
MagRec["treatment_ac_field"]='%8.3e' %(float(rec[1])*1e-3) # peak field in tesla
meas_type="LT-AF-Z"
MagRec["treatment_dc_field"]='0'
else: # AARM experiment
if treat[1][0]=='0':
meas_type="LT-AF-Z"
MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
else:
meas_type="LT-AF-I"
ipos=int(treat[0])-1
MagRec["treatment_dc_field_phi"]='%7.1f' %(dec[ipos])
MagRec["treatment_dc_field_theta"]='%7.1f'% (inc[ipos])
MagRec["treatment_dc_field"]='%8.3e'%(labfield)
MagRec["treatment_ac_field"]='%8.3e' %(peakfield) # peak field in tesla
elif demag=="T":
if rec[1][0]==".":rec[1]="0"+rec[1]
treat=rec[1].split('.')
if len(treat)==1:treat.append('0')
MagRec["treatment_temp"]='%8.3e' % (float(rec[1])+273.) # temp in kelvin
meas_type="LT-T-Z"
MagRec["treatment_temp"]='%8.3e' % (float(treat[0])+273.) # temp in kelvin
if trm==0: # demag=T and not trmaq
if treat[1][0]=='0':
meas_type="LT-T-Z"
else:
MagRec["treatment_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MagRec["treatment_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MagRec["treatment_dc_field_theta"]='%7.1f' % (theta) # labfield theta
if treat[1][0]=='1':meas_type="LT-T-I" # in-field thermal step
if treat[1][0]=='2':
meas_type="LT-PTRM-I" # pTRM check
pTRM=1
if treat[1][0]=='3':
MagRec["treatment_dc_field"]='0' # this is a zero field step
meas_type="LT-PTRM-MD" # pTRM tail check
else:
meas_type="LT-T-I" # trm acquisition experiment
MagRec['magic_method_codes']=meas_type
MagRecs.append(MagRec)
MagOuts=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print "results put in ",meas_file
if samp_file!="":
pmag.magic_write(samp_file,ErSamps,'er_samples')
print "sample orientations put in ",samp_file
if len(SynRecs)>0:
pmag.magic_write(synfile,SynRecs,'er_synthetics')
print "synthetics put in ",synfile
