def main():
"""
NAME
change_case_magic.py
DESCRIPTION
picks out key and converts to upper or lower case
SYNTAX
change_case_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE: specify input magic format file
-F FILE: specify output magic format file , default is to overwrite input file
-keys KEY1:KEY2 specify colon delimited list of keys to convert
-[U,l] : specify [U]PPER or [l]ower case, default is lower
"""
dir_path = "./"
change = "l"
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 "-f" in sys.argv:
ind = sys.argv.index("-f")
magic_file = dir_path + "/" + sys.argv[ind + 1]
else:
print main.__doc__
sys.exit()
if "-F" in sys.argv:
ind = sys.argv.index("-F")
out_file = dir_path + "/" + sys.argv[ind + 1]
else:
out_file = magic_file
if "-keys" in sys.argv:
ind = sys.argv.index("-keys")
grab_keys = sys.argv[ind + 1].split(":")
else:
print main.__doc__
sys.exit()
if "-U" in sys.argv:
change = "U"
#
#
# get data read in
Data, file_type = pmag.magic_read(magic_file)
if len(Data) > 0:
for grab_key in grab_keys:
for rec in Data:
if change == "l":
rec[grab_key] = rec[grab_key].lower()
else:
rec[grab_key] = rec[grab_key].upper()
else:
print "bad file name"
pmag.magic_write(out_file, Data, file_type)
def main():
"""
NAME
extract_methods.py
DESCRIPTION
reads in a magic table and creates a file with method codes
SYNTAX
extract_methods.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify magic format input file, default is magic_measurements.txt
-F FILE: specify method code output file, default is magic_methods.txt
"""
citation='This study'
args=sys.argv
outfile='magic_methods.txt'
infile='magic_measurements.txt'
#
# get command line arguments
#
dir_path='.'
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if "-h" in args:
print main.__doc__
sys.exit()
if '-F' in args:
ind=args.index("-F")
outfile=args[ind+1]
if '-f' in args:
ind=args.index("-f")
infile=args[ind+1]
infile=dir_path+'/'+infile
outfile=dir_path+'/'+outfile
data,file_type=pmag.magic_read(infile)
MethRecs=[]
methods=[]
for rec in data:
meths=rec['magic_method_codes'].split(":")
for meth in meths:
if meth not in methods:
MethRec={}
methods.append(meth)
MethRec['magic_method_code']=meth
MethRecs.append(MethRec)
pmag.magic_write(outfile,MethRecs,'magic_methods')
def main():
"""
ODP_fix_sample_names.py
DESCRIPTION:
pads core to three digits and makes upper case
OPTIONS:
-f FILE, input ODP magic file for sample name conversion
"""
dir_path='.'
if '-WD' in sys.argv:
ind=sys.argv.index("-WD")
dir_path=sys.argv[ind+1]
if '-f' in sys.argv:
ind=sys.argv.index("-f")
infile=dir_path+'/'+sys.argv[ind+1]
else:
print "must specify -f input_file"
sys.exit()
Data,file_type=pmag.magic_read(infile)
Fixed=[]
for rec in Data:
pieces=rec['er_specimen_name'].split('-')
if len(pieces)==6:
while len(pieces[2])<4:pieces[2]='0'+pieces[2] # pad core to be 3 characters
specimen=""
for piece in pieces:
specimen=specimen+piece+'-'
specimen=specimen[:-1].upper()
rec['er_specimen_name']=specimen
rec['er_sample_name']=specimen
rec['er_site_name']=specimen
rec['er_location_name']=pieces[1]
rec['er_expedition_name']=pieces[0]
Fixed.append(rec)
else:
print 'problem with this data record: ',rec['er_specimen_name']
print 'deleting from file ', infile
pmag.magic_write(infile,Fixed,file_type)
print 'new specimen names written to: ',infile
def main():
"""
NAME
HUJI_magic.py
DESCRIPTION
converts HUJI format files to magic_measurements format files
SYNTAX
HUJI_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify input file, required
-F FILE: specify output file, default is magic_measurements.txt
-LP [colon delimited list of protocols, include all that apply]
AF: af demag
T: thermal including thellier but not trm acquisition
N: NRM only
TRM: trm acquisition
ANI: anisotropy experiment
CR: cooling rate experiment.
The treatment coding of the measurement file should be: XXX.00,XXX.10, XXX.20 ...XX.70 etc. (XXX.00 is optional)
where XXX in the temperature and .10,.20... are running numbers of the cooling rates steps.
XXX.00 is optional zerofield baseline. XXX.70 is alteration check.
syntax in sio_magic is: -LP CR xxx,yyy,zzz,.....xx
where xx, yyy,zzz...xxx are cooling time in [K/minutes], seperated by comma, ordered at the same order as XXX.10,XXX.20 ...XX.70
if you use a zerofield step then no need to specify the cooling rate for the zerofield
-spc NUM : specify number of characters to designate a specimen, default = 0
-loc LOCNAME : specify location/study name, must have either LOCNAME or SAMPFILE or be a synthetic
-dc B PHI THETA: dc lab field (in micro tesla) and phi,theta, default is none
NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment
# to do! -ac B : peak AF field (in mT) for ARM acquisition, default is none
-ncn NCON: specify naming convention: default is #1 below
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
[8] synthetic - has no site name
[9] ODP naming convention
INPUT
separate experiments ( AF, thermal, thellier, trm aquisition) should be seperate files
(eg. af.txt, thermal.txt, etc.)
HUJI masurement file format (space delimited text):
Spec lab-running-numbe-code Date Hour Treatment-type(T/N/A) Treatment(XXX.XX) dec(geo) inc(geo) dec(tilt) inc(tilt)
---------
conventions:
Spec: specimen name
Treat: treatment step
XXX T in Centigrade
XXX AF in mT
for special experiments:
Thellier:
XXX.0 first zero field step
XXX.1 first in field step [XXX.0 and XXX.1 can be done in any order]
XXX.2 second in-field step at lower temperature (pTRM check)
ATRM:
X.00 optional baseline
X.1 ATRM step (+X)
X.2 ATRM step (+Y)
X.3 ATRM step (+Z)
X.4 ATRM step (-X)
X.5 ATRM step (-Y)
X.6 ATRM step (-Z)
X.7 optional alteration check (+X)
TRM:
XXX.YYY XXX is temperature step of total TRM
YYY is dc field in microtesla
Intensity assumed to be total moment in 10^3 Am^2 (emu)
Declination: Declination in specimen coordinate system
Inclination: Inclination in specimen coordinate system
Optional metatdata string: mm/dd/yy;hh:mm;[dC,mT];xx.xx;UNITS;USER;INST;NMEAS
hh in 24 hours.
dC or mT units of treatment XXX (see Treat above) for thermal or AF respectively
xx.xxx DC field
UNITS of DC field (microT, mT)
INST: instrument code, number of axes, number of positions (e.g., G34 is 2G, three axes,
measured in four positions)
NMEAS: number of measurements in a single position (1,3,200...)
"""
args=sys.argv
meas_file="magic_measurements.txt"
user=""
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
else:
user=""
if '-F' in args:
ind=args.index("-F")
meas_file=args[ind+1]
if '-f' in args:
ind=args.index("-f")
magfile=args[ind+1]
try:
input=open(magfile,'rU')
except:
print "bad mag file name"
sys.exit()
else:
print "mag_file field is required option"
print main.__doc__
sys.exit()
if "-dc" in args:
ind=args.index("-dc")
labfield=float(args[ind+1])*1e-6
phi=float(args[ind+2])
theta=float(args[ind+3])
if "-ac" in args:
ind=args.index("-ac")
peakfield=float(args[ind+1])*1e-3
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if specnum!=0:specnum=-specnum
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4-" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z=int(samp_con.split("-")[1])
samp_con="4"
if "7-" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z=int(samp_con.split("-")[1])
samp_con="7"
# lab process:
if '-LP' in args:
ind=args.index("-LP")
codelist=args[ind+1]
codes=codelist.split(':')
if "AF" in codes:
demag='AF'
LPcode="LP-DIR-AF"
if "T" in codes:
demag="T"
if '-dc' not in args: LPcode="LP-DIR-T"
if '-dc' in args: LPcode="LP-PI-TRM"
if "ANI" in codes:
if '-dc' not in args:
print "missing option -dc exiting"
exit()
LPcode="LP-AN-TRM"
if "TRM" in codes:
demag="T"
LPcode="LP-TRM"
#trm=1
if "CR" in codes:
demag="T"
# dc should be in the code
if '-dc' not in args:
print "missing option -dc exiting"
exit()
LPcode="LP-TRM-CR" # TRM in different cooling rates
ind=args.index("-LP")
CR_cooling_times=args[ind+2].split(",")
#print CR_cooling_time ,"CR_cooling_time"
version_num=pmag.get_version()
MagRecs=[]
#--------------------------------------
# Read the file
# Assumption:
# 1. different lab protocolsa are in different files
# 2. measurements are in the correct order
#--------------------------------------
Data={}
line_no=0
for line in input.readlines():
line_no+=1
this_line_data={}
line_no+=1
instcode=""
if len(line)<2:
continue
if line[0]=="#": #HUJI way of marking bad data points
continue
rec=line.strip('\n').split()
specimen=rec[0]
date=rec[2].split("/")
hour=rec[3].split(":")
treatment_type=rec[4]
treatment=rec[5].split(".")
dec=rec[6]
inc=rec[7]
dec_tilted=rec[8]
inc_tilted=rec[9]
moment_emu=float(rec[10])
if specimen not in Data.keys():
Data[specimen]=[]
# check duplicate treatments:
# if yes, delete the first and use the second
if len(Data[specimen])>0:
if treatment==Data[specimen][-1]['treatment']:
del(Data[specimen][-1])
print "-W- Identical treatimens in file %s magfile line %i: specimen %s, treatment %s deleting the first. " %(magfile, line_no, specimen,".".join(treatment))
this_line_data={}
this_line_data['specimen']=specimen
this_line_data['date']=date
this_line_data['hour']=hour
this_line_data['treatment_type']=treatment_type
this_line_data['treatment']=treatment
this_line_data['dec']=dec
this_line_data['inc']=inc
this_line_data['dec_tilted']=dec_tilted
this_line_data['inc_tilted']=inc_tilted
this_line_data['moment_emu']=moment_emu
Data[specimen].append(this_line_data)
print "-I- done reading file %s"%magfile
#--------------------------------------
# Convert to MagIC
#--------------------------------------
specimens_list=Data.keys()
specimens_list.sort()
MagRecs=[]
for specimen in specimens_list:
for i in range(len(Data[specimen])):
#print LPcode
this_line_data=Data[specimen][i]
methcode=""
MagRec={}
MagRec["er_specimen_name"]=this_line_data['specimen']
if specnum!=0:
MagRec["er_sample_name"]=this_line_data['specimen'][:specnum]
else:
MagRec["er_sample_name"]=this_line_data['specimen']
if samp_con=="1":
MagRec["er_site_name"]=MagRec["er_sample_name"][:-1]
elif samp_con=="2":
parts=MagRec["er_sample_name"].split('-')
MagRec["er_site_name"]= parts[0]
elif samp_con=="3":
parts=MagRec["er_sample_name"].split('.')
MagRec["er_site_name"]= parts[0]
elif samp_con=='4':
MagRec["er_site_name"]=MagRec["er_sample_name"][0:-Z]
elif samp_con=='5':
MagRec["er_site_name"]=MagRec["er_sample_name"]
elif samp_con=='7':
MagRec["er_site_name"]=MagRec["er_sample_name"][0:Z]
else:
MagRec["er_site_name"]=MagRec["er_sample_name"] # site=sample by default
if "-loc" in args:
MagRec['er_location_name']=er_location_name
else:
MagRec['er_location_name']=MagRec["er_site_name"]
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_magn_moment"]='%10.3e'% (float(this_line_data['moment_emu'])*1e-3) # moment in Am^2 (from emu)
MagRec["measurement_dec"]=this_line_data['dec']
MagRec["measurement_inc"]=this_line_data['inc']
date=this_line_data['date']
hour=this_line_data['hour']
if float(date[2])>80:
yyyy="19"+date[2]
else:
yyyy="20"+date[2]
if len (date[0])==1:
date[0]="0"+date[0]
if len (date[1])==1:
date[1]="0"+date[1]
MagRec["measurement_date"]=":".join([yyyy,date[0],date[1],hour[0],hour[1],"00.00"])
#print MagRec["measurement_date"]," Ron check please"
MagRec["measurement_time_zone"]='JER'
MagRec['er_analyst_mail_names'] =user
MagRec["er_citation_names"]="This study"
MagRec["magic_instrument_codes"]="HUJI-2G"
MagRec["measurement_flag"]="g"
MagRec["measurement_positions"]="1"
MagRec["measurement_positions"]="1"
MagRec["measurement_standard"]="u"
MagRec["measurement_description"]=""
MagRec["treatment_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
#----------------------------------------
# AF demag
# do not support AARM yet
#----------------------------------------
if demag=="AF":
# demag in zero field
if LPcode != "LP-AN-ARM":
MagRec["treatment_ac_field"]='%8.3e' %(float(this_line_data['treatment'][0])*1e-3) # peak field in tesla
MagRec["treatment_dc_field"]='0'
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
if treatment_type=="N":
methcode="LP-DIR-AF:LT-NO"
elif treatment_type=="A":
methcode="LP-DIR-AF:LT-AF-Z"
else:
print "ERROR in treatment field line %i... exiting until you fix the problem" %line_no
exit()
# AARM experiment
else:
print "Dont supprot AARM in HUJI format yet. sorry... do be DONE"
MagRec["magic_method_codes"]=methcode
MagRec["magic_experiment_name"]=specimen+ ":" + LPcode
MagRec["measurement_number"]="%i"%i
MagRec["measurement_description"]=""
MagRecs.append(MagRec)
#continue
#----------------------------------------
# Thermal:
# Thellier experiment: "IZ", "ZI", "IZZI", pTRM checks
# Thermal demag
# Thermal cooling rate experiment
# Thermal NLT
#----------------------------------------
if demag=="T":
treatment=this_line_data['treatment']
treatment_type=this_line_data['treatment_type']
#----------------------------------------
# Thellier experimet
#----------------------------------------
if LPcode == "LP-PI-TRM" : # Thelllier experiment
MagRec["magic_experiment_name"]=specimen+ ":" + LPcode
methcode=LPcode
if treatment_type=="N" or ( (treatment[1]=='0' or treatment[1]=='00') and float(treatment[0])==0):
LT_code="LT-NO"
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
MagRec["treatment_dc_field"]='0'
MagRec["treatment_temp"]='273.'
elif treatment[1]=='0' or treatment[1]=='00':
LT_code="LT-T-Z"
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
MagRec["treatment_dc_field"]='%8.3e'%(0)
MagRec["treatment_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
# check if this is ZI or IZ:
# check if the same temperature already measured:
methcode="LP-PI-TRM:LP-PI-TRM-ZI"
for j in range (0,i):
if Data[specimen][j]['treatment'][0] == treatment[0]:
if Data[specimen][j]['treatment'][1] == '1' or Data[specimen][j]['treatment'][1] == '10':
methcode="LP-PI-TRM:LP-PI-TRM-IZ"
else:
methcode="LP-PI-TRM:LP-PI-TRM-ZI"
elif treatment[1]=='1' or treatment[1]=='10':
LT_code="LT-T-I"
MagRec["treatment_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MagRec["treatment_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MagRec["treatment_dc_field_theta"]='%7.1f' % (theta) # labfield theta
MagRec["treatment_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
# check if this is ZI or IZ:
# check if the same temperature already measured:
methcode="LP-PI-TRM:LP-PI-TRM-IZ"
for j in range (0,i):
if Data[specimen][j]['treatment'][0] == treatment[0]:
if Data[specimen][j]['treatment'][1] == '0' or Data[specimen][j]['treatment'][1] == '00':
methcode="LP-PI-TRM:LP-PI-TRM-ZI"
else:
methcode="LP-PI-TRM:LP-PI-TRM-IZ"
elif treatment[1]=='2' or treatment[1]=='20':
LT_code="LT-PTRM-I"
MagRec["treatment_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MagRec["treatment_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MagRec["treatment_dc_field_theta"]='%7.1f' % (theta) # labfield theta
MagRec["treatment_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
methcode="LP-PI-TRM:LP-PI-TRM-IZ"
else:
print "ERROR in treatment field line %i... exiting until you fix the problem" %line_no
exit()
MagRec["magic_method_codes"]=LT_code+":"+methcode
MagRec["measurement_number"]="%i"%i
MagRec["measurement_description"]=""
MagRecs.append(MagRec)
#continue
#----------------------------------------
# demag experimet
#----------------------------------------
if LPcode == "LP-DIR-T" :
MagRec["magic_experiment_name"]=specimen+ ":" + LPcode
methcode=LPcode
if treatment_type=="N":
LT_code="LT-NO"
else:
LT_code="LT-T-Z"
methcode=LPcode+":"+"LT-T-Z"
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
MagRec["treatment_dc_field"]='%8.3e'%(0)
MagRec["treatment_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
MagRec["magic_method_codes"]=LT_code+":"+methcode
MagRec["measurement_number"]="%i"%i
MagRec["measurement_description"]=""
MagRecs.append(MagRec)
#continue
#----------------------------------------
# ATRM measurements
# The direction of the magnetization is used to determine the
# direction of the lab field.
#----------------------------------------
if LPcode =="LP-AN-TRM" :
MagRec["magic_experiment_name"]=specimen+ ":" + LPcode
methcode=LPcode
if float(treatment[1])==0:
MagRec["magic_method_codes"]="LP-AN-TRM:LT-T-Z"
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
MagRec["treatment_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
MagRec["treatment_dc_field"]='0'
else:
if float(treatment[1])==7:
# alteration check
methcode="LP-AN-TRM:LT-PTRM-I"
MagRec["measurement_number"]='7'# -z
else:
MagRec["magic_method_codes"]="LP-AN-TRM:LT-T-I"
inc=float(MagRec["measurement_inc"]);dec=float(MagRec["measurement_dec"])
if abs(inc)<45 and (dec<45 or dec>315): # +x
tdec,tinc=0,0
MagRec["measurement_number"]='1'
if abs(inc)<45 and (dec<135 and dec>45):
tdec,tinc=90,0
MagRec["measurement_number"]='2' # +y
if inc>45 :
tdec,tinc=0,90
MagRec["measurement_number"]='3' # +z
if abs(inc)<45 and (dec<225 and dec>135):
tdec,tinc=180,0
MagRec["measurement_number"]='4' # -x
if abs(inc)<45 and (dec<315 and dec>225):
tdec,tinc=270,0
MagRec["measurement_number"]='5'# -y
if inc<-45 :
tdec,tinc=0,-90
MagRec["measurement_number"]='6'# -z
MagRec["treatment_dc_field_phi"]='%7.1f' %(tdec)
MagRec["treatment_dc_field_theta"]='%7.1f'% (tinc)
MagRec["treatment_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
MagRec["treatment_dc_field"]='%8.3e'%(labfield)
MagRec["measurement_description"]=""
MagRecs.append(MagRec)
#continue
#----------------------------------------
# NLT measurements
# or TRM acquisistion experiment
#----------------------------------------
if LPcode == "LP-TRM" :
MagRec["magic_experiment_name"]=specimen+ ":" + LPcode
MagRec["magic_method_codes"]="LP-TRM:LT-T-I"
if float(treatment[1])==0:
labfield=0
else:
labfield=float(float(treatment[1]))*1e-6
MagRec["treatment_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
MagRec["treatment_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MagRec["treatment_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MagRec["treatment_dc_field_theta"]='%7.1f' % (theta) # labfield theta
MagRec["measurement_number"]="%i"%i
MagRec["measurement_description"]=""
MagRecs.append(MagRec)
#continue
#----------------------------------------
# Cooling rate experiments
#----------------------------------------
if LPcode =="LP-TRM-CR":
index=int(treatment[1][0])
#print index,"index"
#print CR_cooling_times,"CR_cooling_times"
#print CR_cooling_times[index-1]
#print CR_cooling_times[0:index-1]
CR_cooling_time=CR_cooling_times[index-1]
if CR_cooling_time in CR_cooling_times[0:index-1]:
MagRec["magic_method_codes"]="LP-TRM-CR"+":" +"LT-PTRM-I"
else:
MagRec["magic_method_codes"]="LP-TRM-CR"
MagRec["magic_experiment_name"]=specimen+ ":" + LPcode
MagRec["treatment_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
MagRec["treatment_dc_field"]='%8.3e' % (labfield) # labfield in tesla (convert from microT)
MagRec["treatment_dc_field_phi"]='%7.1f' % (phi) # labfield phi
MagRec["treatment_dc_field_theta"]='%7.1f' % (theta) # labfield theta
MagRec["measurement_number"]="%i"%index
MagRec["measurement_description"]="%i minutes cooling time"%int(CR_cooling_time)
MagRecs.append(MagRec)
#continue
pmag.magic_write(meas_file,MagRecs,'magic_measurements')
print "-I- results put in ",meas_file
def main():
"""
NAME
download_magic.py
DESCRIPTION
unpacks a magic formatted smartbook .txt file from the MagIC database into the
tab delimited MagIC format txt files for use with the MagIC-Py programs.
SYNTAX
download_magic.py command line options]
INPUT
takes either the upload.txt file created by upload_magic.py or the file
exported by the MagIC v2.2 console software (downloaded from the MagIC database
or output by the Console on your PC).
OPTIONS
-h prints help message and quits
-i allows interactive entry of filename
-f FILE specifies input file name
"""
dir_path='.'
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-i' in sys.argv:
file=raw_input("Magic txt file for unpacking? ")
elif '-f' in sys.argv:
ind=sys.argv.index("-f")
file=sys.argv[ind+1]
else:
print main.__doc__
sys.exit()
f=open(dir_path+'/'+file,'rU')
File=f.readlines()
LN=0
type_list=[]
filenum=0
while LN<len(File)-1:
line=File[LN]
file_type=line.split('\t')[1]
file_type=file_type.lower()
if file_type=='delimited':file_type=Input[skip].split('\t')[2]
if file_type[-1]=="\n":file_type=file_type[:-1]
print 'working on: ',file_type
if file_type not in type_list:
type_list.append(file_type)
else:
filenum+=1
LN+=1
line=File[LN]
keys=line.split('\t')
LN+=1
Recs=[]
while LN<len(File):
line=File[LN]
if line[:4]==">>>>" and len(Recs)>0:
if filenum==0:
outfile=dir_path+"/"+file_type.strip()+'.txt'
else:
outfile=dir_path+"/"+file_type.strip()+'_'+str(filenum)+'.txt'
NewRecs=[]
for rec in Recs:
if 'magic_method_codes' in rec.keys():
meths=rec['magic_method_codes'].split(":")
if len(meths)>0:
methods=""
for meth in meths: methods=methods+meth.strip()+":" # get rid of nasty spaces!!!!!!
rec['magic_method_codes']=methods[:-1]
NewRecs.append(rec)
pmag.magic_write(outfile,Recs,file_type)
print file_type," data put in ",outfile
Recs=[]
LN+=1
break
else:
rec=line.split('\t')
Rec={}
for k in range(len(keys)):
Rec[keys[k]]=rec[k]
Recs.append(Rec)
LN+=1
def main(command_line=True, **kwargs):
"""
NAME
BGC_magic.py
DESCRIPTION
converts Berkeley Geochronology Center (BGC) format files to magic_measurements format files
SYNTAX
BGC_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt (Not working yet)
-loc LOCNAME : specify location/study name
-site SITENAME : specify site name
-A: don't average replicate measurements
-mcd [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented
-v NUM : specify the volume in cc of the sample, default 2.5^3cc. Will use vol in data file if volume!=0 in file.
INPUT
BGC paleomag format file
"""
# initialize some stuff
noave = 0
volume = 0.025 ** 3 # default volume is a 2.5cm cube
# inst=""
# samp_con,Z='1',""
# missing=1
# demag="N"
er_location_name = "unknown"
er_site_name = "unknown"
# citation='This study'
args = sys.argv
meth_code = "LP-NO"
# specnum=1
version_num = pmag.get_version()
mag_file = ""
dir_path = "."
MagRecs = []
SampOuts = []
samp_file = "er_samples.txt"
meas_file = "magic_measurements.txt"
meth_code = ""
#
# get command line arguments
#
if command_line:
if "-WD" in sys.argv:
ind = sys.argv.index("-WD")
dir_path = sys.argv[ind + 1]
if "-ID" in sys.argv:
ind = sys.argv.index("-ID")
input_dir_path = sys.argv[ind + 1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print main.__doc__
return False
if "-F" in args:
ind = args.index("-F")
meas_file = args[ind + 1]
if "-Fsa" in args:
ind = args.index("-Fsa")
samp_file = args[ind + 1]
# try:
# open(samp_file,'rU')
# ErSamps,file_type=pmag.magic_read(samp_file)
# print 'sample information will be appended to ', samp_file
# except:
# print samp_file,' not found: sample information will be stored in new er_samples.txt file'
# samp_file = output_dir_path+'/er_samples.txt'
if "-f" in args:
ind = args.index("-f")
mag_file = args[ind + 1]
if "-loc" in args:
ind = args.index("-loc")
er_location_name = args[ind + 1]
if "-site" in args:
ind = args.index("-site")
er_site_name = args[ind + 1]
if "-A" in args:
noave = 1
if "-mcd" in args:
ind = args.index("-mcd")
meth_code = args[ind + 1]
# samp_con='5'
if "-v" in args:
ind = args.index("-v")
volume = float(args[ind + 1]) * 1e-6 # enter volume in cc, convert to m^3
if not command_line:
dir_path = kwargs.get("dir_path", ".")
input_dir_path = kwargs.get("input_dir_path", dir_path)
output_dir_path = dir_path
meas_file = kwargs.get("meas_file", "magic_measurements.txt")
mag_file = kwargs.get("mag_file")
samp_file = kwargs.get("samp_file", "er_samples.txt")
er_location_name = kwargs.get("er_location_name", "")
er_site_name = kwargs.get("er_site_name", "")
noave = kwargs.get("noave", 0) # default (0) means DO average
meth_code = kwargs.get("meth_code", "LP-NO")
volume = float(kwargs.get("volume", 0))
if not volume:
volume = 0.025 ** 3 # default volume is a 2.5 cm cube, translated to meters cubed
else:
# convert cm^3 to m^3
volume *= 1e-6
# format variables
if not mag_file:
return False, "You must provide a BCG format file"
mag_file = os.path.join(input_dir_path, mag_file)
meas_file = os.path.join(output_dir_path, meas_file)
samp_file = os.path.join(output_dir_path, samp_file)
ErSampRec = {}
# parse data
# Open up the BGC file and read the header information
print "mag_file in BGC_magic", mag_file
pre_data = open(mag_file, "rU")
line = pre_data.readline()
line_items = line.split(" ")
sample_name = line_items[2]
sample_name = sample_name.replace("\n", "")
line = pre_data.readline()
line = pre_data.readline()
line_items = line.split("\t")
sample_azimuth = float(line_items[1])
sample_dip = 90.0 - float(line_items[2])
sample_bed_dip = line_items[3]
sample_bed_azimuth = line_items[4]
sample_lon = line_items[5]
sample_lat = line_items[6]
tmp_volume = line_items[7]
if tmp_volume != 0.0:
volume = float(tmp_volume) * 1e-6
pre_data.close()
data = pd.read_csv(mag_file, sep="\t", header=3, index_col=False)
# print "\ndata\n", data
cart = np.array([data["X"], data["Y"], data["Z"]]).transpose()
direction = pmag.cart2dir(cart).transpose()
data["measurement_dec"] = direction[0]
data["measurement_inc"] = direction[1]
data["measurement_magn_moment"] = direction[2] * 1000 * volume # the data are in EMU - this converts to Am^2
data["measurement_magn_volume"] = direction[2] * 1000 # EMU - data converted to A/m
# DGEOs, IGEOs = [], []
# print "len(data)=",len(data)
# for ind in range(len(data)):
# dgeo,igeo=pmag.dogeo(data.ix[ind]['measurement_dec'],data.ix[ind]['measurement_inc'],90-sample_azimuth,sample_dip)
# DGEOs.append(dgeo)
# IGEOs.append(igeo)
# data['specimen_dec']=DGEOs
# data['specimen_inc']=IGEOs
# data['specimen_tilt']='1'
# print "data specimn_dec=",DGEOs
# print "data specimn_inc=",IGEOs
# Configure the er_sample table
ErSampRec["er_sample_name"] = sample_name
ErSampRec["sample_azimuth"] = sample_azimuth
ErSampRec["sample_dip"] = sample_dip
ErSampRec["sample_bed_dip_direction"] = sample_bed_azimuth
ErSampRec["sample_bed_dip"] = sample_bed_dip
ErSampRec["sample_lat"] = sample_lat
ErSampRec["sample_lon"] = sample_lon
ErSampRec["magic_method_codes"] = meth_code
ErSampRec["er_location_name"] = er_location_name
ErSampRec["er_site_name"] = er_site_name
ErSampRec["er_citation_names"] = "This study"
SampOuts.append(ErSampRec.copy())
# Configure the magic_measurements table
for rowNum, row in data.iterrows():
MagRec = {}
MagRec["measurement_description"] = "Date: " + str(row["Date"]) + " Time: " + str(row["Time"])
MagRec["er_citation_names"] = "This study"
MagRec["er_location_name"] = er_location_name
MagRec["er_site_name"] = er_site_name
MagRec["er_sample_name"] = sample_name
MagRec["magic_software_packages"] = version_num
MagRec["treatment_temp"] = "%8.3e" % (273) # room temp in kelvin
MagRec["measurement_temp"] = "%8.3e" % (273) # room temp in kelvin
MagRec["measurement_flag"] = "g"
MagRec["measurement_standard"] = "u"
MagRec["measurement_number"] = "1"
MagRec["er_specimen_name"] = sample_name
MagRec["treatment_ac_field"] = "0"
if row["DM Val"] == "0":
meas_type = "LT-NO"
elif int(row["DM Type"]) > 0.0:
meas_type = "LT-AF-Z"
treat = float(row["DM Val"])
MagRec["treatment_ac_field"] = "%8.3e" % (treat * 1e-3) # convert from mT to tesla
elif int(row["DM Type"]) == -1:
meas_type = "LT-T-Z"
treat = float(row["DM Val"])
MagRec["treatment_temp"] = "%8.3e" % (treat + 273.0) # temp in kelvin
else:
print "measurement type unknown:", row["DM Type"], " in row ", rowNum
MagRec["measurement_magn_moment"] = str(row["measurement_magn_moment"])
MagRec["measurement_magn_volume"] = str(row["measurement_magn_volume"])
MagRec["measurement_dec"] = str(row["measurement_dec"])
MagRec["measurement_inc"] = str(row["measurement_inc"])
MagRec["magic_method_codes"] = meas_type
MagRec["measurement_csd"] = "0.0" # added due to magic.write error
MagRec["measurement_positions"] = "1" # added due to magic.write error
MagRecs.append(MagRec.copy())
pmag.magic_write(samp_file, SampOuts, "er_samples")
print "sample orientations put in ", samp_file
MagOuts = pmag.measurements_methods(MagRecs, noave)
pmag.magic_write(meas_file, MagOuts, "magic_measurements")
print "results put in ", meas_file
print "exit!"
return True, meas_file
def main():
"""
NAME
thellier_magic_redo.py
DESCRIPTION
Calculates paleointensity parameters for thellier-thellier type data using bounds
stored in the "redo" file
SYNTAX
thellier_magic_redo [command line options]
OPTIONS
-h prints help message
-usr USER: identify user, default is ""
-fcr CRIT, set criteria for grading
-f IN: specify input file, default is magic_measurements.txt
-fre REDO: specify redo file, default is "thellier_redo"
-F OUT: specify output file, default is thellier_specimens.txt
-leg: attaches "Recalculated from original measurements; supercedes published results. " to comment field
-CR PERC TYPE: apply a blanket cooling rate correction if none supplied in the er_samples.txt file
PERC should be a percentage of original (say reduce to 90%)
TYPE should be one of the following:
EG (for educated guess); PS (based on pilots); TRM (based on comparison of two TRMs)
-ANI: perform anisotropy correction
-fsa SAMPFILE: er_samples.txt file with cooling rate correction information, default is NO CORRECTION
-Fcr CRout: specify pmag_specimen format file for cooling rate corrected data
-fan ANIFILE: specify rmag_anisotropy format file, default is rmag_anisotropy.txt
-Fac ACout: specify pmag_specimen format file for anisotropy corrected data
default is AC_specimens.txt
-fnl NLTFILE: specify magic_measurments format file, default is magic_measurements.txt
-Fnl NLTout: specify pmag_specimen format file for non-linear trm corrected data
default is NLT_specimens.txt
-z use z component differenences for pTRM calculation
INPUT
a thellier_redo file is Specimen_name Tmin Tmax (where Tmin and Tmax are in Centigrade)
"""
dir_path = "."
critout = ""
version_num = pmag.get_version()
field, first_save = -1, 1
spec, recnum, start, end = 0, 0, 0, 0
crfrac = 0
NltRecs, PmagSpecs, AniSpecRecs, NltSpecRecs, CRSpecs = [], [], [], [], []
meas_file, pmag_file, mk_file = "magic_measurements.txt", "thellier_specimens.txt", "thellier_redo"
anis_file = "rmag_anisotropy.txt"
anisout, nltout = "AC_specimens.txt", "NLT_specimens.txt"
crout = "CR_specimens.txt"
nlt_file = ""
samp_file = ""
comment, user = "", "unknown"
anis, nltrm = 0, 0
jackknife = 0 # maybe in future can do jackknife
args = sys.argv
Zdiff = 0
if "-WD" in args:
ind = args.index("-WD")
dir_path = args[ind + 1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind = args.index("-usr")
user = sys.argv[ind + 1]
if "-leg" in args:
comment = "Recalculated from original measurements; supercedes published results. "
cool = 0
if "-CR" in args:
cool = 1
ind = args.index("-CR")
crfrac = 0.01 * float(sys.argv[ind + 1])
crtype = "DA-CR-" + sys.argv[ind + 2]
if "-Fcr" in args:
ind = args.index("-Fcr")
crout = sys.argv[ind + 1]
if "-f" in args:
ind = args.index("-f")
meas_file = sys.argv[ind + 1]
if "-F" in args:
ind = args.index("-F")
pmag_file = sys.argv[ind + 1]
if "-fre" in args:
ind = args.index("-fre")
mk_file = args[ind + 1]
if "-fsa" in args:
ind = args.index("-fsa")
samp_file = dir_path + "/" + args[ind + 1]
Samps, file_type = pmag.magic_read(samp_file)
SampCRs = pmag.get_dictitem(Samps, "cooling_rate_corr", "", "F") # get samples cooling rate corrections
cool = 1
if file_type != "er_samples":
print "not a valid er_samples.txt file"
sys.exit()
#
#
if "-ANI" in args:
anis = 1
ind = args.index("-ANI")
if "-Fac" in args:
ind = args.index("-Fac")
anisout = args[ind + 1]
if "-fan" in args:
ind = args.index("-fan")
anis_file = args[ind + 1]
#
if "-NLT" in args:
if "-Fnl" in args:
ind = args.index("-Fnl")
nltout = args[ind + 1]
if "-fnl" in args:
ind = args.index("-fnl")
nlt_file = args[ind + 1]
if "-z" in args:
Zdiff = 1
if "-fcr" in sys.argv:
ind = args.index("-fcr")
critout = sys.argv[ind + 1]
#
# start reading in data:
#
meas_file = dir_path + "/" + meas_file
mk_file = dir_path + "/" + mk_file
accept = pmag.default_criteria(1)[0] # set criteria to none
if critout != "":
critout = dir_path + "/" + critout
crit_data, file_type = pmag.magic_read(critout)
if file_type != "pmag_criteria":
print "bad pmag_criteria file, using no acceptance criteria"
print "Acceptance criteria read in from ", critout
for critrec in crit_data:
if "sample_int_sigma_uT" in critrec.keys(): # accommodate Shaar's new criterion
critrec["sample_int_sigma"] = "%10.3e" % (eval(critrec["sample_int_sigma_uT"]) * 1e-6)
for key in critrec.keys():
if key not in accept.keys() and critrec[key] != "":
accept[key] = critrec[key]
meas_data, file_type = pmag.magic_read(meas_file)
if file_type != "magic_measurements":
print file_type
print file_type, "This is not a valid magic_measurements file "
sys.exit()
try:
mk_f = open(mk_file, "rU")
except:
print "Bad redo file"
sys.exit()
mkspec = []
speclist = []
for line in mk_f.readlines():
tmp = line.split()
mkspec.append(tmp)
speclist.append(tmp[0])
if anis == 1:
anis_file = dir_path + "/" + anis_file
anis_data, file_type = pmag.magic_read(anis_file)
if file_type != "rmag_anisotropy":
print file_type
print file_type, "This is not a valid rmag_anisotropy file "
sys.exit()
if nlt_file == "":
nlt_data = pmag.get_dictitem(
meas_data, "magic_method_codes", "LP-TRM", "has"
) # look for trm acquisition data in the meas_data file
else:
nlt_file = dir_path + "/" + nlt_file
nlt_data, file_type = pmag.magic_read(nlt_file)
if len(nlt_data) > 0:
nltrm = 1
#
# sort the specimen names and step through one by one
#
sids = pmag.get_specs(meas_data)
#
print "Processing ", len(speclist), " specimens - please wait "
while spec < len(speclist):
s = speclist[spec]
recnum = 0
datablock = []
PmagSpecRec = {}
PmagSpecRec["er_analyst_mail_names"] = user
PmagSpecRec["er_citation_names"] = "This study"
PmagSpecRec["magic_software_packages"] = version_num
methcodes, inst_code = [], ""
#
# find the data from the meas_data file for this specimen
#
datablock = pmag.get_dictitem(meas_data, "er_specimen_name", s, "T")
datablock = pmag.get_dictitem(
datablock, "magic_method_codes", "LP-PI-TRM", "has"
) # pick out the thellier experiment data
if len(datablock) > 0:
for rec in datablock:
if "magic_instrument_codes" not in rec.keys():
rec["magic_instrument_codes"] = "unknown"
#
# collect info for the PmagSpecRec dictionary
#
rec = datablock[0]
PmagSpecRec["er_specimen_name"] = s
PmagSpecRec["er_sample_name"] = rec["er_sample_name"]
PmagSpecRec["er_site_name"] = rec["er_site_name"]
PmagSpecRec["er_location_name"] = rec["er_location_name"]
PmagSpecRec["measurement_step_unit"] = "K"
PmagSpecRec["specimen_correction"] = "u"
if "er_expedition_name" in rec.keys():
PmagSpecRec["er_expedition_name"] = rec["er_expedition_name"]
if "magic_instrument_codes" not in rec.keys():
PmagSpecRec["magic_instrument_codes"] = "unknown"
else:
PmagSpecRec["magic_instrument_codes"] = rec["magic_instrument_codes"]
if "magic_experiment_name" not in rec.keys():
rec["magic_experiment_name"] = ""
else:
PmagSpecRec["magic_experiment_names"] = rec["magic_experiment_name"]
meths = rec["magic_experiment_name"].split(":")
for meth in meths:
if meth.strip() not in methcodes and "LP-" in meth:
methcodes.append(meth.strip())
#
# sort out the data into first_Z, first_I, ptrm_check, ptrm_tail
#
araiblock, field = pmag.sortarai(datablock, s, Zdiff)
first_Z = araiblock[0]
first_I = araiblock[1]
ptrm_check = araiblock[2]
ptrm_tail = araiblock[3]
if len(first_I) < 3 or len(first_Z) < 4:
spec += 1
print "skipping specimen ", s
else:
#
# get start, end
#
for redospec in mkspec:
if redospec[0] == s:
b, e = float(redospec[1]), float(redospec[2])
break
if e > float(first_Z[-1][0]):
e = float(first_Z[-1][0])
for recnum in range(len(first_Z)):
if first_Z[recnum][0] == b:
start = recnum
if first_Z[recnum][0] == e:
end = recnum
nsteps = end - start
if nsteps > 2:
zijdblock, units = pmag.find_dmag_rec(s, meas_data)
pars, errcode = pmag.PintPars(datablock, araiblock, zijdblock, start, end, accept)
if "specimen_scat" in pars.keys():
PmagSpecRec["specimen_scat"] = pars["specimen_scat"]
if "specimen_frac" in pars.keys():
PmagSpecRec["specimen_frac"] = "%5.3f" % (pars["specimen_frac"])
if "specimen_gmax" in pars.keys():
PmagSpecRec["specimen_gmax"] = "%5.3f" % (pars["specimen_gmax"])
pars["measurement_step_unit"] = units
pars["specimen_lab_field_dc"] = field
pars["specimen_int"] = -1 * field * pars["specimen_b"]
PmagSpecRec["measurement_step_min"] = "%8.3e" % (pars["measurement_step_min"])
PmagSpecRec["measurement_step_max"] = "%8.3e" % (pars["measurement_step_max"])
PmagSpecRec["specimen_int_n"] = "%i" % (pars["specimen_int_n"])
PmagSpecRec["specimen_lab_field_dc"] = "%8.3e" % (pars["specimen_lab_field_dc"])
PmagSpecRec["specimen_int"] = "%9.4e " % (pars["specimen_int"])
PmagSpecRec["specimen_b"] = "%5.3f " % (pars["specimen_b"])
PmagSpecRec["specimen_q"] = "%5.1f " % (pars["specimen_q"])
PmagSpecRec["specimen_f"] = "%5.3f " % (pars["specimen_f"])
PmagSpecRec["specimen_fvds"] = "%5.3f" % (pars["specimen_fvds"])
PmagSpecRec["specimen_b_beta"] = "%5.3f" % (pars["specimen_b_beta"])
PmagSpecRec["specimen_int_mad"] = "%7.1f" % (pars["specimen_int_mad"])
PmagSpecRec["specimen_Z"] = "%7.1f" % (pars["specimen_Z"])
PmagSpecRec["specimen_gamma"] = "%7.1f" % (pars["specimen_gamma"])
if pars["method_codes"] != "" and pars["method_codes"] not in methcodes:
methcodes.append(pars["method_codes"])
PmagSpecRec["specimen_dec"] = "%7.1f" % (pars["specimen_dec"])
PmagSpecRec["specimen_inc"] = "%7.1f" % (pars["specimen_inc"])
PmagSpecRec["specimen_tilt_correction"] = "-1"
PmagSpecRec["specimen_direction_type"] = "l"
PmagSpecRec["direction_type"] = "l" # this is redudant, but helpful - won't be imported
PmagSpecRec["specimen_dang"] = "%7.1f " % (pars["specimen_dang"])
PmagSpecRec["specimen_drats"] = "%7.1f " % (pars["specimen_drats"])
PmagSpecRec["specimen_drat"] = "%7.1f " % (pars["specimen_drat"])
PmagSpecRec["specimen_int_ptrm_n"] = "%i " % (pars["specimen_int_ptrm_n"])
PmagSpecRec["specimen_rsc"] = "%6.4f " % (pars["specimen_rsc"])
PmagSpecRec["specimen_md"] = "%i " % (int(pars["specimen_md"]))
if PmagSpecRec["specimen_md"] == "-1":
PmagSpecRec["specimen_md"] = ""
PmagSpecRec["specimen_b_sigma"] = "%5.3f " % (pars["specimen_b_sigma"])
if "IE-TT" not in methcodes:
methcodes.append("IE-TT")
methods = ""
for meth in methcodes:
methods = methods + meth + ":"
PmagSpecRec["magic_method_codes"] = methods.strip(":")
PmagSpecRec["magic_software_packages"] = version_num
PmagSpecRec["specimen_description"] = comment
if critout != "":
kill = pmag.grade(PmagSpecRec, accept, "specimen_int")
if len(kill) > 0:
Grade = "F" # fails
else:
Grade = "A" # passes
PmagSpecRec["specimen_grade"] = Grade
else:
PmagSpecRec["specimen_grade"] = "" # not graded
if nltrm == 0 and anis == 0 and cool != 0: # apply cooling rate correction
SCR = pmag.get_dictitem(
SampCRs, "er_sample_name", PmagSpecRec["er_sample_name"], "T"
) # get this samples, cooling rate correction
CrSpecRec = pmag.cooling_rate(PmagSpecRec, SCR, crfrac, crtype)
if CrSpecRec["er_specimen_name"] != "none":
CrSpecs.append(CrSpecRec)
PmagSpecs.append(PmagSpecRec)
NltSpecRec = ""
#
# check on non-linear TRM correction
#
if nltrm == 1:
#
# find the data from the nlt_data list for this specimen
#
TRMs, Bs = [], []
NltSpecRec = ""
NltRecs = pmag.get_dictitem(
nlt_data, "er_specimen_name", PmagSpecRec["er_specimen_name"], "has"
) # fish out all the NLT data for this specimen
if len(NltRecs) > 2:
for NltRec in NltRecs:
Bs.append(float(NltRec["treatment_dc_field"]))
TRMs.append(float(NltRec["measurement_magn_moment"]))
NLTpars = nlt.NLtrm(
Bs,
TRMs,
float(PmagSpecRec["specimen_int"]),
float(PmagSpecRec["specimen_lab_field_dc"]),
0,
)
if NLTpars["banc"] > 0:
NltSpecRec = {}
for key in PmagSpecRec.keys():
NltSpecRec[key] = PmagSpecRec[key]
NltSpecRec["specimen_int"] = "%9.4e" % (NLTpars["banc"])
NltSpecRec["magic_method_codes"] = PmagSpecRec["magic_method_codes"] + ":DA-NL"
NltSpecRec["specimen_correction"] = "c"
NltSpecRec["specimen_grade"] = PmagSpecRec["specimen_grade"]
NltSpecRec["magic_software_packages"] = version_num
print NltSpecRec["er_specimen_name"], " Banc= ", float(NLTpars["banc"]) * 1e6
if anis == 0 and cool != 0:
SCR = pmag.get_dictitem(
SampCRs, "er_sample_name", NltSpecRec["er_sample_name"], "T"
) # get this samples, cooling rate correction
CrSpecRec = pmag.cooling_rate(NltSpecRec, SCR, crfrac, crtype)
if CrSpecRec["er_specimen_name"] != "none":
CrSpecs.append(CrSpecRec)
NltSpecRecs.append(NltSpecRec)
#
# check on anisotropy correction
if anis == 1:
if NltSpecRec != "":
Spc = NltSpecRec
else: # find uncorrected data
Spc = PmagSpecRec
AniSpecs = pmag.get_dictitem(
anis_data, "er_specimen_name", PmagSpecRec["er_specimen_name"], "T"
)
if len(AniSpecs) > 0:
AniSpec = AniSpecs[0]
AniSpecRec = pmag.doaniscorr(Spc, AniSpec)
AniSpecRec["specimen_grade"] = PmagSpecRec["specimen_grade"]
AniSpecRec["magic_instrument_codes"] = PmagSpecRec["magic_instrument_codes"]
AniSpecRec["specimen_correction"] = "c"
AniSpecRec["magic_software_packages"] = version_num
if cool != 0:
SCR = pmag.get_dictitem(
SampCRs, "er_sample_name", AniSpecRec["er_sample_name"], "T"
) # get this samples, cooling rate correction
CrSpecRec = pmag.cooling_rate(AniSpecRec, SCR, crfrac, crtype)
if CrSpecRec["er_specimen_name"] != "none":
CrSpecs.append(CrSpecRec)
AniSpecRecs.append(AniSpecRec)
elif anis == 1:
AniSpecs = pmag.get_dictitem(
anis_data, "er_specimen_name", PmagSpecRec["er_specimen_name"], "T"
)
if len(AniSpecs) > 0:
AniSpec = AniSpecs[0]
AniSpecRec = pmag.doaniscorr(PmagSpecRec, AniSpec)
AniSpecRec["specimen_grade"] = PmagSpecRec["specimen_grade"]
AniSpecRec["magic_instrument_codes"] = PmagSpecRec["magic_instrument_codes"]
AniSpecRec["specimen_correction"] = "c"
AniSpecRec["magic_software_packages"] = version_num
if crfrac != 0:
CrSpecRec = {}
for key in AniSpecRec.keys():
CrSpecRec[key] = AniSpecRec[key]
inten = frac * float(CrSpecRec["specimen_int"])
CrSpecRec["specimen_int"] = "%9.4e " % (
inten
) # adjust specimen intensity by cooling rate correction
CrSpecRec["magic_method_codes"] = CrSpecRec["magic_method_codes"] + ":DA-CR-" + crtype
CRSpecs.append(CrSpecRec)
AniSpecRecs.append(AniSpecRec)
spec += 1
else:
print "skipping ", s
spec += 1
pmag_file = dir_path + "/" + pmag_file
pmag.magic_write(pmag_file, PmagSpecs, "pmag_specimens")
print "uncorrected thellier data saved in: ", pmag_file
if anis == 1 and len(AniSpecRecs) > 0:
anisout = dir_path + "/" + anisout
pmag.magic_write(anisout, AniSpecRecs, "pmag_specimens")
print "anisotropy corrected data saved in: ", anisout
if nltrm == 1 and len(NltSpecRecs) > 0:
nltout = dir_path + "/" + nltout
pmag.magic_write(nltout, NltSpecRecs, "pmag_specimens")
print "non-linear TRM corrected data saved in: ", nltout
if crfrac != 0:
crout = dir_path + "/" + crout
pmag.magic_write(crout, CRSpecs, "pmag_specimens")
print "cooling rate corrected data saved in: ", crout
def main():
"""
NAME
zeq_magic_redo.py
DESCRIPTION
Calculate principal components through demagnetization data using bounds and calculation type stored in "redo" file
SYNTAX
zeq_magic_redo.py [command line options]
OPTIONS
-h prints help message
-usr USER: identify user, default is ""
-f: specify input file, default is magic_measurements.txt
-F: specify output file, default is zeq_specimens.txt
-fre REDO: specify redo file, default is "zeq_redo"
-fsa SAMPFILE: specify er_samples format file, default is "er_samples.txt"
-A : don't average replicate measurements, default is yes
-crd [s,g,t] :
specify coordinate system [s,g,t] [default is specimen coordinates]
are specimen, geographic, and tilt corrected respectively
NB: you must have a SAMPFILE in this directory to rotate from specimen coordinates
-leg: attaches "Recalculated from original measurements; supercedes published results. " to comment field
INPUTS
zeq_redo format file is:
specimen_name calculation_type[DE-BFL,DE-BFL-A,DE-BFL-O,DE-BFP,DE-FM] step_min step_max component_name[A,B,C]
"""
dir_path='.'
INCL=["LT-NO","LT-AF-Z","LT-T-Z","LT-M-Z"] # looking for demag data
beg,end,pole,geo,tilt,askave,save=0,0,[],0,0,0,0
user,doave,comment= "",1,""
geo,tilt=0,0
version_num=pmag.get_version()
args=sys.argv
if '-WD' in args:
ind=args.index('-WD')
dir_path=args[ind+1]
meas_file,pmag_file,mk_file= dir_path+"/"+"magic_measurements.txt",dir_path+"/"+"zeq_specimens.txt",dir_path+"/"+"zeq_redo"
samp_file,coord=dir_path+"/"+"er_samples.txt",""
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=sys.argv[ind+1]
if "-A" in args:doave=0
if "-leg" in args: comment="Recalculated from original measurements; supercedes published results. "
if "-f" in args:
ind=args.index("-f")
meas_file=dir_path+'/'+sys.argv[ind+1]
if "-F" in args:
ind=args.index("-F")
pmag_file=dir_path+'/'+sys.argv[ind+1]
if "-fre" in args:
ind=args.index("-fre")
mk_file=dir_path+"/"+args[ind+1]
try:
mk_f=open(mk_file,'rU')
except:
print "Bad redo file"
sys.exit()
mkspec,skipped=[],[]
speclist=[]
for line in mk_f.readlines():
tmp=line.split()
mkspec.append(tmp)
speclist.append(tmp[0])
if "-fsa" in args:
ind=args.index("-fsa")
samp_file=dir_path+'/'+sys.argv[ind+1]
if "-crd" in args:
ind=args.index("-crd")
coord=sys.argv[ind+1]
if coord=="g":geo,tilt=1,0
if coord=="t":geo,tilt=1,1
#
# now get down to bidness
if geo==1:
samp_data,file_type=pmag.magic_read(samp_file)
if file_type != 'er_samples':
print file_type
print "This is not a valid er_samples file "
sys.exit()
# set orientation priorities
SO_methods=[]
for rec in samp_data:
if "magic_method_codes" in rec:
methlist=rec["magic_method_codes"]
for meth in methlist.split(":"):
if "SO" in meth and "SO-POM" not in meth.strip():
if meth.strip() not in SO_methods: SO_methods.append(meth.strip())
SO_priorities=pmag.set_priorities(SO_methods,0)
#
#
#
meas_data,file_type=pmag.magic_read(meas_file)
if file_type != 'magic_measurements':
print file_type
print file_type,"This is not a valid magic_measurements file "
sys.exit()
#
# sort the specimen names
#
k = 0
print 'Processing ',len(speclist), ' specimens - please wait'
PmagSpecs=[]
while k < len(speclist):
s=speclist[k]
recnum=0
PmagSpecRec={}
method_codes,inst_codes=[],[]
# find the data from the meas_data file for this sample
#
# collect info for the PmagSpecRec dictionary
#
meas_meth=[]
for rec in meas_data: # copy of vital stats to PmagSpecRec from first spec record in demag block
skip=1
if rec["er_specimen_name"]==s:
methods=rec["magic_method_codes"].split(":")
if len(set(methods) & set(INCL))>0:
PmagSpecRec["er_analyst_mail_names"]=user
PmagSpecRec["magic_software_packages"]=version_num
PmagSpecRec["er_specimen_name"]=s
PmagSpecRec["er_sample_name"]=rec["er_sample_name"]
PmagSpecRec["er_site_name"]=rec["er_site_name"]
PmagSpecRec["er_location_name"]=rec["er_location_name"]
PmagSpecRec["er_citation_names"]="This study"
if "magic_experiment_name" not in rec.keys(): rec["magic_experiment_name"]=""
PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"]
if "magic_instrument_codes" not in rec.keys(): rec["magic_instrument_codes"]=""
inst=rec['magic_instrument_codes'].split(":")
for I in inst:
if I not in inst_codes: # copy over instruments
inst_codes.append(I)
meths=rec["magic_method_codes"].split(":")
for meth in meths:
if meth.strip() not in meas_meth:meas_meth.append(meth)
if "LP-DIR-AF" in meas_meth or "LT-AF-Z" in meas_meth:
PmagSpecRec["measurement_step_unit"]="T"
if "LP-DIR-AF" not in method_codes:method_codes.append("LP-DIR-AF")
if "LP-DIR-T" in meas_meth or "LT-T-Z" in meas_meth:
PmagSpecRec["measurement_step_unit"]="K"
if "LP-DIR-T" not in method_codes:method_codes.append("LP-DIR-T")
if "LP-DIR-M" in meas_meth or "LT-M-Z" in meas_meth:
PmagSpecRec["measurement_step_unit"]="J"
if "LP-DIR-M" not in method_codes:method_codes.append("LP-DIR-M")
if PmagSpecRec=={}:
print 'no data found for specimen: ',s
print 'delete from zeq_redo input file...., then try again'
sys.exit()
#
#
data,units=pmag.find_dmag_rec(s,meas_data)
#
datablock=data
noskip=1
if len(datablock) <2 or s not in speclist :
noskip=0
k+=1
# print 'skipping ', s,len(datablock)
if noskip:
#
# find replicate measurements at given treatment step and average them
#
# step_meth,avedata=pmag.vspec(data)
#
# if len(avedata) != len(datablock):
# if doave==1:
# method_codes.append("DE-VM")
# datablock=avedata
#
# do geo or stratigraphic correction now
#
if geo==1:
# find top priority orientation method
redo,p=1,0
if len(SO_methods)<=1:
az_type=SO_methods[0]
orient=pmag.find_samp_rec(PmagSpecRec["er_sample_name"],samp_data,az_type)
if orient["sample_azimuth"] !="": method_codes.append(az_type)
redo=0
while redo==1:
if p>=len(SO_priorities):
print "no orientation data for ",s
orient["sample_azimuth"]=""
orient["sample_dip"]=""
method_codes.append("SO-NO")
redo=0
else:
az_type=SO_methods[SO_methods.index(SO_priorities[p])]
orient=pmag.find_samp_rec(PmagSpecRec["er_sample_name"],samp_data,az_type)
if orient["sample_azimuth"] !="":
method_codes.append(az_type)
redo=0
p+=1
#
# if tilt selected, get stratigraphic correction
#
tiltblock,geoblock=[],[]
for rec in datablock:
if "sample_azimuth" in orient.keys() and orient["sample_azimuth"]!="":
d_geo,i_geo=pmag.dogeo(rec[1],rec[2],orient["sample_azimuth"],orient["sample_dip"])
geoblock.append([rec[0],d_geo,i_geo,rec[3],rec[4],rec[5]])
if tilt==1 and "sample_bed_dip_direction" in orient.keys():
d_tilt,i_tilt=pmag.dotilt(d_geo,i_geo,orient["sample_bed_dip_direction"],orient["sample_bed_dip"])
tiltblock.append([rec[0],d_tilt,i_tilt,rec[3],rec[4],rec[5]])
elif tilt==1:
if PmagSpecRec["er_sample_name"] not in skipped:
print 'no tilt correction for ', PmagSpecRec["er_sample_name"],' skipping....'
skipped.append(PmagSpecRec["er_sample_name"])
else:
if PmagSpecRec["er_sample_name"] not in skipped:
print 'no geographic correction for ', PmagSpecRec["er_sample_name"],' skipping....'
skipped.append(PmagSpecRec["er_sample_name"])
#
# get beg_pca, end_pca, pca
if PmagSpecRec['er_sample_name'] not in skipped:
compnum=-1
for spec in mkspec:
if spec[0]==s:
CompRec={}
for key in PmagSpecRec.keys():CompRec[key]=PmagSpecRec[key]
compnum+=1
calculation_type=spec[1]
beg=float(spec[2])
end=float(spec[3])
if len(spec)>4:
comp_name=spec[4]
else:
comp_name=string.uppercase[compnum]
CompRec['specimen_comp_name']=comp_name
if beg < float(datablock[0][0]):beg=float(datablock[0][0])
if end > float(datablock[-1][0]):end=float(datablock[-1][0])
for l in range(len(datablock)):
if datablock[l][0]==beg:beg_pca=l
if datablock[l][0]==end:end_pca=l
if geo==1 and tilt==0:
mpars=pmag.domean(geoblock,beg_pca,end_pca,calculation_type)
if mpars["specimen_direction_type"]!="Error":
CompRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
CompRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
CompRec["specimen_tilt_correction"]='0'
if geo==1 and tilt==1:
mpars=pmag.domean(tiltblock,beg_pca,end_pca,calculation_type)
if mpars["specimen_direction_type"]!="Error":
CompRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
CompRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
CompRec["specimen_tilt_correction"]='100'
if geo==0 and tilt==0:
mpars=pmag.domean(datablock,beg_pca,end_pca,calculation_type)
if mpars["specimen_direction_type"]!="Error":
CompRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
CompRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
CompRec["specimen_tilt_correction"]='-1'
if mpars["specimen_direction_type"]=="Error":
pass
else:
CompRec["measurement_step_min"]='%8.3e '%(datablock[beg_pca][0])
try:
CompRec["measurement_step_max"]='%8.3e '%(datablock[end_pca][0] )
except:
print 'error in end_pca ',PmagSpecRec['er_specimen_name']
CompRec["specimen_correction"]='u'
if calculation_type!='DE-FM':
CompRec["specimen_mad"]='%7.1f '%(mpars["specimen_mad"])
CompRec["specimen_alpha95"]=""
else:
CompRec["specimen_mad"]=""
CompRec["specimen_alpha95"]='%7.1f '%(mpars["specimen_alpha95"])
CompRec["specimen_n"]='%i '%(mpars["specimen_n"])
CompMeths=[]
for meth in method_codes:
if meth not in CompMeths:CompMeths.append(meth)
if calculation_type not in CompMeths:CompMeths.append(calculation_type)
if geo==1: CompMeths.append("DA-DIR-GEO")
if tilt==1: CompMeths.append("DA-DIR-TILT")
if "DE-BFP" not in calculation_type:
CompRec["specimen_direction_type"]='l'
else:
CompRec["specimen_direction_type"]='p'
CompRec["magic_method_codes"]=""
if len(CompMeths) != 0:
methstring=""
for meth in CompMeths:
methstring=methstring+ ":" +meth
CompRec["magic_method_codes"]=methstring.strip(':')
CompRec["specimen_description"]=comment
if len(inst_codes) != 0:
inststring=""
for inst in inst_codes:
inststring=inststring+ ":" +inst
CompRec["magic_instrument_codes"]=inststring.strip(':')
PmagSpecs.append(CompRec)
k+=1
pmag.magic_write(pmag_file,PmagSpecs,'pmag_specimens')
print "Recalculated specimen data stored in ",pmag_file
def main():
"""
NAME
sort_specimens.py
DESCRIPTION
Reads in a pmag_specimen formatted file and separates it into different components (A,B...etc.)
SYNTAX
sort_specimens.py [-h] [command line options]
INPUT
takes pmag_specimens.txt formatted input file
OPTIONS
-h: prints help message and quits
-f FILE: specify input file, default is 'pmag_specimens.txt'
OUTPUT
makes pmag_specimen formatted files with input filename plus _X_Y
where X is the component name and Y is s,g,t for coordinate system
"""
dir_path='.'
inspec="pmag_specimens.txt"
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 '-f' in sys.argv:
ind=sys.argv.index('-f')
inspec=sys.argv[ind+1]
basename=inspec.split('.')[:-1]
inspec=dir_path+"/"+inspec
ofile_base=dir_path+"/"+basename[0]
#
# read in data
#
prior_spec_data,file_type=pmag.magic_read(inspec)
if file_type != 'pmag_specimens':
print file_type, " this is not a valid pmag_specimens file"
sys.exit()
# get list of specimens in file, components, coordinate systems available
specs,comps,coords=[],[],[]
for spec in prior_spec_data:
if spec['er_specimen_name'] not in specs:specs.append(spec['er_specimen_name'])
if 'specimen_comp_name' not in spec.keys():spec['specimen_comp_name']='A'
if 'specimen_tilt_correction' not in spec.keys():spec['tilt_correction']='-1' # assume specimen coordinates
if spec['specimen_comp_name'] not in comps:comps.append(spec['specimen_comp_name'])
if spec['specimen_tilt_correction'] not in coords:coords.append(spec['specimen_tilt_correction'])
# work on separating out components, coordinate systems by specimen
for coord in coords:
print coord
for comp in comps:
print comp
speclist=[]
for spec in prior_spec_data:
if spec['specimen_tilt_correction']==coord and spec['specimen_comp_name']==comp:speclist.append(spec)
ofile=ofile_base+'_'+coord+'_'+comp+'.txt'
pmag.magic_write(ofile,speclist,'pmag_specimens')
print 'coordinate system: ',coord,' component name: ',comp,' saved in ',ofile
def main():
"""
NAME
magic_select.py
DESCRIPTION
picks out records and dictitem options saves to magic_special file
SYNTAX
magic_select.py [command line optins]
OPTIONS
-h prints help message and quits
-f FILE: specify input magic format file
-F FILE: specify output magic format file
-key KEY string [T,F,has, not, eval,min,max]
returns records where the value of the key either:
matches exactly the string (T)
does not match the string (F)
contains the string (has)
does not contain the string (not)
the value equals the numerical value of the string (eval)
the value is greater than the numerical value of the string (min)
the value is less than the numerical value of the string (max)
NOTES
for age range:
use KEY: age (converts to Ma, takes mid point of low, high if no value for age.
for paleolat:
use KEY: model_lat (uses lat, if age<5 Ma, else, model_lat, or attempts calculation from average_inc if no model_lat.) returns estimate in model_lat key
"""
dir_path="."
flag=''
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 '-f' in sys.argv:
ind=sys.argv.index('-f')
magic_file=dir_path+'/'+sys.argv[ind+1]
else:
print main.__doc__
sys.exit()
if '-F' in sys.argv:
ind=sys.argv.index('-F')
outfile=dir_path+'/'+sys.argv[ind+1]
else:
print main.__doc__
sys.exit()
if '-key' in sys.argv:
ind=sys.argv.index('-key')
grab_key=sys.argv[ind+1]
v=sys.argv[ind+2]
flag=sys.argv[ind+3]
else:
print main.__doc__
print '-key is required'
sys.exit()
#
# get data read in
Data,file_type=pmag.magic_read(magic_file)
if grab_key =='age':
grab_key='average_age'
Data=pmag.convert_ages(Data)
if grab_key =='model_lat':
Data=pmag.convert_lat(Data)
Data=pmag.convert_ages(Data)
Selection=pmag.get_dictitem(Data,grab_key,v,flag)
if len(Selection)>0:
pmag.magic_write(outfile,Selection,file_type)
print len(Selection),' records written to ',outfile
else:
print 'no data matched your criteria'
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
UCSC_magic.py
DESCRIPTION
converts UCSC format files to MagIC formatted files
SYNTAX
UCSC_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify UCSC format input file, required
-F FILE: specify output file, default is magic_measurements.txt
-A: don't average replicate measurements
"""
global k,Data
k,Data,measNum=0,[],0
ErLocs,ErSites,ErSamps,ErSpecs,MagRecs=[],[],[],[],[] # MagIC formatted info
# initialize some stuff
noave=0
args=sys.argv
ErLocs,ErSites,ErSamps,ErSpecs,MagicMeas=[],[],[],[],[] # MagIC formatted info
dir_path='.'
#
# get command line arguments
#
if '-WD' in args: # set working directory (only for within MagIC.py GUI)
ind=args.index("-WD")
dir_path=args[ind+1]
loc_file,site_file,samp_file,spec_file,meas_file=dir_path+"/er_locations.txt",dir_path+"/er_sites.txt",dir_path+"/er_samples.txt",dir_path+"/er_specimens.txt",dir_path+"/magic_measurements.txt"
if "-h" in args:
print main.__doc__
sys.exit()
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 "-A" in args: noave=1
InData=input.readlines()
Data=[]
for line in InData:
if line!="\n" and line!="":
Data.append(line) # strip out annoying blank lines
LocRec=parseloc() # peel off the location info
ErLoc={}
ErLoc['er_location_name']=LocRec['name']
ErLoc['er_citation_name']="This study"
ErLoc['location_type']="outcrop"
ErLoc['location_begin_lat']=LocRec['northLatitude']
ErLoc['location_begin_lon']=LocRec['eastLongitude']
ErLoc['location_begin_elevation']=convert2meters(LocRec['altitude'],LocRec['altitudeUnits'])
ErLoc['location_description']=LocRec['comments']
ErLocs.append(ErLoc)
while "</locality>" not in Data[k]:
ErSite={}
SiteRec=parsesite()
if SiteRec=='done': break
print SiteRec['name']
ErSite['er_citation_name']="This study"
ErSite['er_location_name']=ErLoc['er_location_name']
ErSite['site_definition']='s' # this means a single site as opposed to composite site
ErSite['er_site_name']=SiteRec['name']
ErSite['site_type']=""
ErSite['site_class']=""
ErSite['site_lithology']=""
ErSite['site_lat']=SiteRec['northLatitude']
ErSite['site_lon']=SiteRec['eastLongitude']
ErSite['site_elevation']=convert2meters(SiteRec['altitude'],SiteRec['altitudeUnits'])
ErSite['site_description']=SiteRec['comments']
ErSites.append(ErSite)
samples=[] # this is a list for unique sample names
while '</site>' not in Data[k] and k<len(Data):
ErSpec={}
SpecRec=parsespec()
print SpecRec['name']
ErSpec['er_specimen_name']=SpecRec['name']
ErSpec['er_citation_name']="This study"
ErSpec['er_location_name']=ErLoc['er_location_name']
ErSpec['er_citation_names']="This study"
ErSpec['er_site_name']=ErSite['er_site_name']
er_sample_name=ErSpec['er_specimen_name'][:-1]
ErSpec['er_sample_name']=er_sample_name
ErSpec['specimen_volume']=SpecRec['volume'] # volume in m^3
ErSpecs.append(ErSpec)
MeasRecs=parsesteps()
print len(MeasRecs),' measurements'
if er_sample_name not in samples: # new sample name
samples.append(er_sample_name)
ErSamp={}
ErSamp['er_sample_name']=er_sample_name
ErSamp['er_citation_name']="This study"
ErSamp['er_location_name']=ErLoc['er_location_name']
ErSamp['er_site_name']=ErSite['er_site_name']
ErSamp['sample_lat']=ErSite['site_lat']
ErSamp['sample_lon']=ErSite['site_lon']
ErSamp['sample_elevation']=ErSite['site_elevation']
ErSamp['sample_date']=parsedate(SpecRec['dateCollected'])
# ErSamp['sample_time_zone']=LocRec['gmtOffset']+"+GMT"
ErSamp['sample_bed_dip_direction']=str(float(SpecRec['strike'])+90.)
ErSamp['sample_bed_dip']=SpecRec['dip']
ErSamp['sample_height']=SpecRec['stratigraphicLevel']
ErSamp['sample_description']=SpecRec['comments']
ErSamp['sample_declination_correction']=LocRec['regionalDeclination']
if 'calculatedSunAz' in SpecRec.keys():
ErSamp['sample_azimuth']=SpecRec['calculatedSunAz']
ErSamp['magic_method_codes']='SO-SUN'
az,pl=pmag.get_azpl(float(MeasRecs[0]['coreDec']),float(MeasRecs[0]['coreInc']),float(MeasRecs[0]['geoDec']),float(MeasRecs[0]['geoInc']))
ErSamp['sample_azimuth']=str(az)
ErSamp['sample_dip']=str(pl)
ErSamps.append(ErSamp)
for MeasRec in MeasRecs:
MagRec={}
measNum+=1
MagRec['er_citation_names']="This study"
MagRec['measurement_number']='%i'%(measNum)
MagRec['er_location_name']=ErSpec['er_location_name']
MagRec['er_site_name']=ErSpec['er_site_name']
MagRec['er_sample_name']=ErSpec['er_sample_name']
MagRec['er_specimen_name']=ErSpec['er_specimen_name']
MagRec['measurement_date']=parsedate(MeasRec['date'])
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'
step=MeasRec['stepType']
if step=='AF':
MagRec["magic_method_codes"]="LT-AF-Z" # lab treatment, af in zero field
MagRec['magic_experiment_name']=MagRec['er_specimen_name']+":LT-AF-Z"
elif step=="TH": # I'm guessing here
MagRec["magic_method_codes"]="LT-T-Z" # this is "lab treatment, thermal in zero field
MagRec['magic_experiment_name']=MagRec['er_specimen_name']+":LT-T-Z"
else:
MagRec["magic_method_codes"]="LT-NO" # no lab treatment - NRM
MagRec['magic_experiment_name']=MagRec['er_specimen_name']+":LT-NO"
MagRec['measurement_dec']=MeasRec['coreDec']
MagRec['measurement_inc']=MeasRec['coreInc']
MagRec['measurement_magn_volume']=MeasRec['J'] # intensity in A/m
MagRec['measurement_magn_moment']=str(float(MeasRec['J'])*float(ErSpec['specimen_volume'])) # intensity in Am^2
MagRec['measurement_chi_volume']=MeasRec['susceptibility'] # assuming dimensionless SI CHECK THIS
MagRec['magic_software_packages']=MeasRec['measuringRoutine'] #
if step=="AF": MagRec["treatment_ac_field"]=str(1e-3*float(MeasRec['stepLevel'])) # stepLevel in tesla
if step=="TH":
stepLevel=float(MeasRec['stepLevel']) +273
MagRec["treatment_temp"]='%8.3e' % (stepLevel) # treatment step in kelvin
MagRec["measurement_csd"]=MeasRec['Q_95'] # I think this is the csd
MagRec["magic_instrument_codes"]='UCSC-'+MeasRec['instrument']
MagRec["er_analyst_mail_names"]=MeasRec['operator']
MagRec["measurement_flag"]='g' # good measurement flag
MagRec["measurement_standard"]='u' # # unknown - as opposed to standard
MagRecs.append(MagRec)
pmag.magic_write(loc_file,ErLocs,'er_locations')
print "results put in ",loc_file
pmag.magic_write(site_file,ErSites,'er_sites')
print "results put in ",site_file
pmag.magic_write(samp_file,ErSamps,'er_samples')
print "results put in ",samp_file
pmag.magic_write(spec_file,ErSpecs,'er_specimens')
print "results put in ",spec_file
pmag.magic_write(meas_file,MagRecs,'magic_measurements')
print "results put in ",meas_file
def main(command_line=True, **kwargs):
"""
NAME
IODP_jr6_magic.py
DESCRIPTION
converts shipboard .jr6 format files to magic_measurements format files
SYNTAX
IODP_jr6_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-f FILE: specify input file, or
-F FILE: specify output file, default is magic_measurements.txt
-fsa FILE: specify er_samples.txt file for sample name lookup ,
default is 'er_samples.txt'
-loc HOLE : specify hole name (U1456A)
-A: don't average replicate measurements
INPUT
JR6 .jr6 format file
"""
def fix_separation(filename, new_filename):
old_file = open(filename, 'rU')
data = old_file.readlines()
new_data = []
for line in data:
new_line = line.replace('-', ' -')
new_line = new_line.replace(' ', ' ')
new_data.append(new_line)
new_file = open(new_filename, 'w')
for s in new_data:
new_file.write(s)
old_file.close()
new_file.close()
return new_filename
def old_fix_separation(filename, new_filename):
old_file = open(filename, 'rU')
data = old_file.readlines()
new_data = []
for line in data:
new_line = []
for i in line.split():
if '-' in i[1:]:
lead_char = '-' if i[0] == '-' else ''
if lead_char:
v = i[1:].split('-')
else:
v = i.split('-')
new_line.append(lead_char + v[0])
new_line.append('-' + v[1])
else:
new_line.append(i)
new_line = (' '.join(new_line)) + '\n'
new_data.append(new_line)
new_file = open(new_filename, 'w')
for s in new_data:
new_file.write(s)
new_file.close()
old_file.close()
return new_filename
# initialize some stuff
noave=0
volume=2.5**3 #default volume is a 2.5cm cube
inst=""
samp_con,Z='5',""
missing=1
demag="N"
er_location_name="unknown"
citation='This study'
args=sys.argv
meth_code="LP-NO"
version_num=pmag.get_version()
dir_path='.'
MagRecs=[]
samp_file = 'er_samples.txt'
meas_file = 'magic_measurements.txt'
mag_file = ''
#
# get command line arguments
#
if command_line:
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-ID' in sys.argv:
ind = sys.argv.index('-ID')
input_dir_path = sys.argv[ind+1]
else:
input_dir_path = dir_path
output_dir_path = dir_path
if "-h" in args:
print main.__doc__
return False
if '-F' in args:
ind=args.index("-F")
meas_file = args[ind+1]
if '-fsa' in args:
ind = args.index("-fsa")
samp_file = args[ind+1]
if samp_file[0]!='/':
samp_file = os.path.join(input_dir_path, samp_file)
try:
open(samp_file,'rU')
ErSamps,file_type=pmag.magic_read(samp_file)
except:
print samp_file,' not found: '
print ' download csv file and import to MagIC with IODP_samples_magic.py'
if '-f' in args:
ind = args.index("-f")
mag_file= args[ind+1]
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-A" in args:
noave=1
if not command_line:
dir_path = kwargs.get('dir_path', '.')
input_dir_path = kwargs.get('input_dir_path', dir_path)
output_dir_path = dir_path
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
mag_file = kwargs.get('mag_file', '')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
specnum = kwargs.get('specnum', 1)
samp_con = kwargs.get('samp_con', '1')
if len(str(samp_con)) > 1:
samp_con, Z = samp_con.split('-')
else:
Z = ''
er_location_name = kwargs.get('er_location_name', '')
noave = kwargs.get('noave', 0) # default (0) means DO average
meth_code = kwargs.get('meth_code', "LP-NO")
# format variables
meth_code=meth_code+":FS-C-DRILL-IODP:SP-SS-C:SO-V"
meth_code=meth_code.strip(":")
if mag_file:
mag_file = os.path.join(input_dir_path, mag_file)
samp_file = os.path.join(input_dir_path, samp_file)
meas_file = os.path.join(output_dir_path, meas_file)
# validate variables
if not mag_file:
print "You must provide an IODP_jr6 format file"
return False, "You must provide an IODP_jr6 format file"
if not os.path.exists(mag_file):
print 'The input file you provided: {} does not exist.\nMake sure you have specified the correct filename AND correct input directory name.'.format(os.path.join(input_dir_path, mag_file))
return False, 'The input file you provided: {} does not exist.\nMake sure you have specified the correct filename AND correct input directory name.'.format(magfile)
if not os.path.exists(samp_file):
print 'samp_file', samp_file
print "Your input directory:\n{}\nmust contain an er_samples.txt file, or you must explicitly provide one".format(input_dir_path)
return False, "Your input directory:\n{}\nmust contain an er_samples.txt file, or you must explicitly provide one".format(input_dir_path)
# parse data
temp = os.path.join(output_dir_path, 'temp.txt')
fix_separation(mag_file, temp)
#os.rename('temp.txt', mag_file)
#data = open(mag_file, 'rU').readlines()
data=pd.read_csv(temp, delim_whitespace=True,header=None)
os.remove(temp)
samples,filetype = pmag.magic_read(samp_file)
data.columns=['specname','step','negz','y','x','expon','sample_azimuth','sample_dip','sample_bed_dip_direction','sample_bed_dip','bed_dip_dir2','bed_dip2','param1','param2','param3','param4','measurement_csd']
cart=np.array([data['x'],data['y'],-data['negz']]).transpose()
dir= pmag.cart2dir(cart).transpose()
data['measurement_dec']=dir[0]
data['measurement_inc']=dir[1]
data['measurement_magn_volume']=dir[2]*(10.0**data['expon']) # A/m - data in A/m
data['measurement_flag']='g'
data['measurement_standard']='u'
data['measurement_number']='1'
data['measurement_temp']='273'
data['er_location_name']=er_location_name
for rowNum, row in data.iterrows():
MagRec={}
spec_text_id=row['specname'].split('_')[1]
SampRecs=pmag.get_dictitem(samples,'er_sample_alternatives',spec_text_id,'has') # retrieve sample record for this specimen
if len(SampRecs)>0: # found one
MagRec['er_specimen_name']=SampRecs[0]['er_sample_name']
MagRec['er_sample_name']=MagRec['er_specimen_name']
MagRec['er_site_name']=MagRec['er_specimen_name']
MagRec["er_citation_names"]="This study"
MagRec['er_location_name']=er_location_name
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["treatment_ac_field"]='0'
volume=float(SampRecs[0]['sample_volume'])
moment=row['measurement_magn_volume'] * volume
MagRec["measurement_magn_moment"]=str(moment)
MagRec["measurement_magn_volume"]=str(row['measurement_magn_volume'])
MagRec["measurement_dec"]='%7.1f'%(row['measurement_dec'])
MagRec["measurement_inc"]='%7.1f'%(row['measurement_inc'])
if row['step'] == 'NRM':
meas_type="LT-NO"
elif row['step'][0:2] == 'AD':
meas_type="LT-AF-Z"
treat=float(row['step'][2:])
MagRec["treatment_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
elif row['step'][0] == 'TD':
meas_type="LT-T-Z"
treat=float(row['step'][2:])
MagRec["treatment_temp"]='%8.3e' % (treat+273.) # temp in kelvin
elif row['step'][0:3]=='ARM': #
meas_type="LT-AF-I"
treat=float(row['step'][3:])
MagRec["treatment_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
MagRec["treatment_dc_field"]='%8.3e' %(50e-6) # assume 50uT DC field
MagRec["measurement_description"]='Assumed DC field - actual unknown'
elif row['step'][0:3]=='IRM': #
meas_type="LT-IRM"
treat=float(row['step'][3:])
MagRec["treatment_dc_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla
else:
print 'unknown treatment type for ',row
return False, 'unknown treatment type for ',row
MagRec['magic_method_codes']=meas_type
MagRecs.append(MagRec.copy())
else:
print 'sample name not found: ',row['specname']
MagOuts=pmag.measurements_methods(MagRecs,noave)
file_created, error_message = pmag.magic_write(meas_file,MagOuts,'magic_measurements')
if file_created:
return True, meas_file
else:
return False, 'Results not written to file'
def main():
"""
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
site_edit_magic.py
DESCRIPTION
makes equal area projections site by site
from pmag_specimens.txt file with
Fisher confidence ellipse using McFadden and McElhinny (1988)
technique for combining lines and planes
allows testing and reject specimens for bad orientations
SYNTAX
site_edit_magic.py [command line options]
OPTIONS
-h: prints help and quits
-f: specify pmag_specimen format file, default is pmag_specimens.txt
-fsa: specify er_samples.txt file
-exc: use existing pmag_criteria.txt file
-N: reset all sample flags to good
OUPUT
edited er_samples.txt file
"""
dir_path='.'
FIG={} # plot dictionary
FIG['eqarea']=1 # eqarea is figure 1
in_file='pmag_specimens.txt'
sampfile='er_samples.txt'
out_file=""
fmt,plot='svg',1
Crits=""
M,N=180.,1
repeat=''
renew=0
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-f' in sys.argv:
ind=sys.argv.index("-f")
in_file=sys.argv[ind+1]
if '-fsa' in sys.argv:
ind=sys.argv.index("-fsa")
sampfile=sys.argv[ind+1]
if '-exc' in sys.argv:
Crits,file_type=pmag.magic_read(dir_path+'/pmag_criteria.txt')
for crit in Crits:
if crit['pmag_criteria_code']=='DE-SPEC':
M=float(crit['specimen_mad'])
N=float(crit['specimen_n'])
if '-fmt' in sys.argv:
ind=sys.argv.index("-fmt")
fmt=sys.argv[ind+1]
if '-N' in sys.argv: renew=1
#
if in_file[0]!="/":in_file=dir_path+'/'+in_file
if sampfile[0]!="/":sampfile=dir_path+'/'+sampfile
crd='s'
Specs,file_type=pmag.magic_read(in_file)
if file_type!='pmag_specimens':
print ' bad pmag_specimen input file'
sys.exit()
Samps,file_type=pmag.magic_read(sampfile)
if file_type!='er_samples':
print ' bad er_samples input file'
sys.exit()
SO_methods=[]
for rec in Samps:
if 'sample_orientation_flag' not in rec.keys(): rec['sample_orientation_flag']='g'
if 'sample_description' not in rec.keys(): rec['sample_description']=''
if renew==1:
rec['sample_orientation_flag']='g'
description=rec['sample_description']
if '#' in description:
newdesc=""
c=0
while description[c]!='#' and c<len(description)-1: # look for first pound sign
newdesc=newdesc+description[c]
c+=1
while description[c]=='#':
c+=1# skip first set of pound signs
while description[c]!='#':c+=1 # find second set of pound signs
while description[c]=='#' and c<len(description)-1:c+=1 # skip second set of pound signs
while c<len(description)-1: # look for first pound sign
newdesc=newdesc+description[c]
c+=1
rec['sample_description']=newdesc # edit out old comment about orientations
if "magic_method_codes" in rec:
methlist=rec["magic_method_codes"]
for meth in methlist.split(":"):
if "SO" in meth.strip() and "SO-POM" not in meth.strip():
if meth.strip() not in SO_methods: SO_methods.append(meth.strip())
pmag.magic_write(sampfile,Samps,'er_samples')
SO_priorities=pmag.set_priorities(SO_methods,0)
sitelist=[]
for rec in Specs:
if rec['er_site_name'] not in sitelist: sitelist.append(rec['er_site_name'])
sitelist.sort()
EQ={}
EQ['eqarea']=1
pmagplotlib.plot_init(EQ['eqarea'],5,5)
k=0
while k<len(sitelist):
site=sitelist[k]
print site
data=[]
ThisSiteSpecs=pmag.get_dictitem(Specs,'er_site_name',site,'T')
ThisSiteSpecs=pmag.get_dictitem(ThisSiteSpecs,'specimen_tilt_correction','-1','T') # get all the unoriented data
for spec in ThisSiteSpecs:
if spec['specimen_mad']!="" and spec['specimen_n']!="" and float(spec['specimen_mad'])<=M and float(spec['specimen_n'])>=N:
# good spec, now get orientation....
redo,p=1,0
if len(SO_methods)<=1:
az_type=SO_methods[0]
orient=pmag.find_samp_rec(spec["er_sample_name"],Samps,az_type)
redo=0
while redo==1:
if p>=len(SO_priorities):
print "no orientation data for ",spec['er_sample_name']
orient["sample_azimuth"]=""
orient["sample_dip"]=""
redo=0
else:
az_type=SO_methods[SO_methods.index(SO_priorities[p])]
orient=pmag.find_samp_rec(spec["er_sample_name"],Samps,az_type)
if orient["sample_azimuth"] !="":
redo=0
p+=1
if orient['sample_azimuth']!="":
rec={}
for key in spec.keys():rec[key]=spec[key]
rec['dec'],rec['inc']=pmag.dogeo(float(spec['specimen_dec']),float(spec['specimen_inc']),float(orient['sample_azimuth']),float(orient['sample_dip']))
rec["tilt_correction"]='1'
crd='g'
rec['sample_azimuth']=orient['sample_azimuth']
rec['sample_dip']=orient['sample_dip']
data.append(rec)
if len(data)>2:
print 'specimen, dec, inc, n_meas/MAD,| method codes '
for i in range(len(data)):
print '%s: %7.1f %7.1f %s / %s | %s' % (data[i]['er_specimen_name'], data[i]['dec'], data[i]['inc'], data[i]['specimen_n'], data[i]['specimen_mad'], data[i]['magic_method_codes'])
fpars=pmag.dolnp(data,'specimen_direction_type')
print "\n Site lines planes kappa a95 dec inc"
print site, fpars["n_lines"], fpars["n_planes"], fpars["K"], fpars["alpha95"], fpars["dec"], fpars["inc"], fpars["R"]
if out_file!="":
if float(fpars["alpha95"])<=acutoff and float(fpars["K"])>=kcutoff:
out.write('%s %s %s\n'%(fpars["dec"],fpars['inc'],fpars['alpha95']))
pmagplotlib.plotLNP(EQ['eqarea'],site,data,fpars,'specimen_direction_type')
pmagplotlib.drawFIGS(EQ)
if k!=0 and repeat!='y':
ans=raw_input("s[a]ve plot, [q]uit, [e]dit specimens, [p]revious site, <return> to continue:\n ")
elif k==0 and repeat!='y':
ans=raw_input("s[a]ve plot, [q]uit, [e]dit specimens, <return> to continue:\n ")
if ans=="p": k-=2
if ans=="a":
files={}
files['eqarea']=site+'_'+crd+'_eqarea'+'.'+fmt
pmagplotlib.saveP(EQ,files)
if ans=="q": sys.exit()
if ans=="e" and Samps==[]:
print "can't edit samples without orientation file, sorry"
elif ans=="e":
# k-=1
testspec=raw_input("Enter name of specimen to check: ")
for spec in data:
if spec['er_specimen_name']==testspec:
# first test wrong direction of drill arrows (flip drill direction in opposite direction and re-calculate d,i
d,i=pmag.dogeo(float(spec['specimen_dec']),float(spec['specimen_inc']),float(spec['sample_azimuth'])-180.,-float(spec['sample_dip']))
XY=pmag.dimap(d,i)
pmagplotlib.plotXY(EQ['eqarea'],[XY[0]],[XY[1]],sym='g^')
# first test wrong end of compass (take az-180.)
d,i=pmag.dogeo(float(spec['specimen_dec']),float(spec['specimen_inc']),float(spec['sample_azimuth'])-180.,float(spec['sample_dip']))
XY=pmag.dimap(d,i)
pmagplotlib.plotXY(EQ['eqarea'],[XY[0]],[XY[1]],sym='kv')
# did the sample spin in the hole?
# now spin around specimen's z
X_up,Y_up,X_d,Y_d=[],[],[],[]
for incr in range(0,360,5):
d,i=pmag.dogeo(float(spec['specimen_dec'])+incr,float(spec['specimen_inc']),float(spec['sample_azimuth']),float(spec['sample_dip']))
XY=pmag.dimap(d,i)
if i>=0:
X_d.append(XY[0])
Y_d.append(XY[1])
else:
X_up.append(XY[0])
Y_up.append(XY[1])
pmagplotlib.plotXY(EQ['eqarea'],X_d,Y_d,sym='b.')
pmagplotlib.plotXY(EQ['eqarea'],X_up,Y_up,sym='c.')
pmagplotlib.drawFIGS(EQ)
break
print "Triangle: wrong arrow for drill direction."
print "Delta: wrong end of compass."
print "Small circle: wrong mark on sample. [cyan upper hemisphere]"
deleteme=raw_input("Mark this sample as bad? y/[n] ")
if deleteme=='y':
reason=raw_input("Reason: [1] broke, [2] wrong drill direction, [3] wrong compass direction, [4] bad mark, [5] displaced block [6] other ")
if reason=='1':
description=' sample broke while drilling'
if reason=='2':
description=' wrong drill direction '
if reason=='3':
description=' wrong compass direction '
if reason=='4':
description=' bad mark in field'
if reason=='5':
description=' displaced block'
if reason=='6':
description=raw_input('Enter brief reason for deletion: ')
for samp in Samps:
if samp['er_sample_name']==spec['er_sample_name']:
samp['sample_orientation_flag']='b'
samp['sample_description']=samp['sample_description']+' ## direction deleted because: '+description+'##' # mark description
pmag.magic_write(sampfile,Samps,'er_samples')
repeat=raw_input("Mark another sample, this site? y/[n] ")
if repeat=='y': k-=1
else:
print 'skipping site - not enough data with specified coordinate system'
k+=1
print "sample flags stored in ",sampfile
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
aniso_magic.py
DESCRIPTION
plots anisotropy data with either bootstrap or hext ellipses
SYNTAX
aniso_magic.py [-h] [command line options]
OPTIONS
-h plots help message and quits
-usr USER: set the user name
-f AFILE, specify rmag_anisotropy formatted file for input
-F RFILE, specify rmag_results formatted file for output
-x Hext [1963] and bootstrap
-B DON'T do bootstrap, do Hext
-par Tauxe [1998] parametric bootstrap
-v plot bootstrap eigenvectors instead of ellipses
-sit plot by site instead of entire file
-crd [s,g,t] coordinate system, default is specimen (g=geographic, t=tilt corrected)
-P don't make any plots - just make rmag_results table
-sav don't make the rmag_results table - just save all the plots
-fmt [svg, jpg, eps] format for output images, pdf default
-gtc DEC INC dec,inc of pole to great circle [down(up) in green (cyan)
-d Vi DEC INC; Vi (1,2,3) to compare to direction DEC INC
-nb N; specifies the number of bootstraps - default is 1000
DEFAULTS
AFILE: rmag_anisotropy.txt
RFILE: rmag_results.txt
plot bootstrap ellipses of Constable & Tauxe [1987]
NOTES
minor axis: circles
major axis: triangles
principal axis: squares
directions are plotted on the lower hemisphere
for bootstrapped eigenvector components: Xs: blue, Ys: red, Zs: black
"""
#
dir_path = "."
version_num = pmag.get_version()
verbose = pmagplotlib.verbose
args = sys.argv
ipar, ihext, ivec, iboot, imeas, isite, iplot, vec = 0, 0, 0, 1, 1, 0, 1, 0
hpars, bpars, PDir = [], [], []
CS, crd = "-1", "s"
nb = 1000
fmt = "pdf"
ResRecs = []
orlist = []
outfile, comp, Dir, gtcirc, PDir = "rmag_results.txt", 0, [], 0, []
infile = "rmag_anisotropy.txt"
if "-h" in args:
print main.__doc__
sys.exit()
if "-WD" in args:
ind = args.index("-WD")
dir_path = args[ind + 1]
if "-nb" in args:
ind = args.index("-nb")
nb = int(args[ind + 1])
if "-usr" in args:
ind = args.index("-usr")
user = args[ind + 1]
else:
user = ""
if "-B" in args:
iboot, ihext = 0, 1
if "-par" in args:
ipar = 1
if "-x" in args:
ihext = 1
if "-v" in args:
ivec = 1
if "-sit" in args:
isite = 1
if "-P" in args:
iplot = 0
if "-f" in args:
ind = args.index("-f")
infile = args[ind + 1]
if "-F" in args:
ind = args.index("-F")
outfile = args[ind + 1]
if "-crd" in sys.argv:
ind = sys.argv.index("-crd")
crd = sys.argv[ind + 1]
if crd == "g":
CS = "0"
if crd == "t":
CS = "100"
if "-fmt" in args:
ind = args.index("-fmt")
fmt = args[ind + 1]
if "-sav" in args:
plots = 1
verbose = 0
else:
plots = 0
if "-gtc" in args:
ind = args.index("-gtc")
d, i = float(args[ind + 1]), float(args[ind + 2])
PDir.append(d)
PDir.append(i)
if "-d" in args:
comp = 1
ind = args.index("-d")
vec = int(args[ind + 1]) - 1
Dir = [float(args[ind + 2]), float(args[ind + 3])]
#
# set up plots
#
if infile[0] != "/":
infile = dir_path + "/" + infile
if outfile[0] != "/":
outfile = dir_path + "/" + outfile
ANIS = {}
initcdf, inittcdf = 0, 0
ANIS["data"], ANIS["conf"] = 1, 2
if iboot == 1:
ANIS["tcdf"] = 3
if iplot == 1:
inittcdf = 1
pmagplotlib.plot_init(ANIS["tcdf"], 5, 5)
if comp == 1 and iplot == 1:
initcdf = 1
ANIS["vxcdf"], ANIS["vycdf"], ANIS["vzcdf"] = 4, 5, 6
pmagplotlib.plot_init(ANIS["vxcdf"], 5, 5)
pmagplotlib.plot_init(ANIS["vycdf"], 5, 5)
pmagplotlib.plot_init(ANIS["vzcdf"], 5, 5)
if iplot == 1:
pmagplotlib.plot_init(ANIS["conf"], 5, 5)
pmagplotlib.plot_init(ANIS["data"], 5, 5)
# read in the data
data, ifiletype = pmag.magic_read(infile)
for rec in data: # find all the orientation systems
if "anisotropy_tilt_correction" not in rec.keys():
rec["anisotropy_tilt_correction"] = "-1"
if rec["anisotropy_tilt_correction"] not in orlist:
orlist.append(rec["anisotropy_tilt_correction"])
if CS not in orlist:
if len(orlist) > 0:
CS = orlist[0]
else:
CS = "-1"
if CS == "-1":
crd = "s"
if CS == "0":
crd = "g"
if CS == "100":
crd = "t"
if verbose:
print "desired coordinate system not available, using available: ", crd
if isite == 1:
sitelist = []
for rec in data:
if rec["er_site_name"] not in sitelist:
sitelist.append(rec["er_site_name"])
sitelist.sort()
plt = len(sitelist)
else:
plt = 1
k = 0
while k < plt:
site = ""
sdata, Ss = [], [] # list of S format data
Locs, Sites, Samples, Specimens, Cits = [], [], [], [], []
if isite == 0:
sdata = data
else:
site = sitelist[k]
for rec in data:
if rec["er_site_name"] == site:
sdata.append(rec)
anitypes = []
csrecs = pmag.get_dictitem(sdata, "anisotropy_tilt_correction", CS, "T")
for rec in csrecs:
if rec["anisotropy_type"] not in anitypes:
anitypes.append(rec["anisotropy_type"])
if rec["er_location_name"] not in Locs:
Locs.append(rec["er_location_name"])
if rec["er_site_name"] not in Sites:
Sites.append(rec["er_site_name"])
if rec["er_sample_name"] not in Samples:
Samples.append(rec["er_sample_name"])
if rec["er_specimen_name"] not in Specimens:
Specimens.append(rec["er_specimen_name"])
if rec["er_citation_names"] not in Cits:
Cits.append(rec["er_citation_names"])
s = []
s.append(float(rec["anisotropy_s1"]))
s.append(float(rec["anisotropy_s2"]))
s.append(float(rec["anisotropy_s3"]))
s.append(float(rec["anisotropy_s4"]))
s.append(float(rec["anisotropy_s5"]))
s.append(float(rec["anisotropy_s6"]))
if s[0] <= 1.0:
Ss.append(s) # protect against crap
# tau,Vdirs=pmag.doseigs(s)
fpars = pmag.dohext(int(rec["anisotropy_n"]) - 6, float(rec["anisotropy_sigma"]), s)
ResRec = {}
ResRec["er_location_names"] = rec["er_location_name"]
ResRec["er_citation_names"] = rec["er_citation_names"]
ResRec["er_site_names"] = rec["er_site_name"]
ResRec["er_sample_names"] = rec["er_sample_name"]
ResRec["er_specimen_names"] = rec["er_specimen_name"]
ResRec["rmag_result_name"] = rec["er_specimen_name"] + ":" + rec["anisotropy_type"]
ResRec["er_analyst_mail_names"] = user
ResRec["tilt_correction"] = CS
ResRec["anisotropy_type"] = rec["anisotropy_type"]
ResRec["anisotropy_v1_dec"] = "%7.1f" % (fpars["v1_dec"])
ResRec["anisotropy_v2_dec"] = "%7.1f" % (fpars["v2_dec"])
ResRec["anisotropy_v3_dec"] = "%7.1f" % (fpars["v3_dec"])
ResRec["anisotropy_v1_inc"] = "%7.1f" % (fpars["v1_inc"])
ResRec["anisotropy_v2_inc"] = "%7.1f" % (fpars["v2_inc"])
ResRec["anisotropy_v3_inc"] = "%7.1f" % (fpars["v3_inc"])
ResRec["anisotropy_t1"] = "%10.8f" % (fpars["t1"])
ResRec["anisotropy_t2"] = "%10.8f" % (fpars["t2"])
ResRec["anisotropy_t3"] = "%10.8f" % (fpars["t3"])
ResRec["anisotropy_ftest"] = "%10.3f" % (fpars["F"])
ResRec["anisotropy_ftest12"] = "%10.3f" % (fpars["F12"])
ResRec["anisotropy_ftest23"] = "%10.3f" % (fpars["F23"])
ResRec["result_description"] = "F_crit: " + fpars["F_crit"] + "; F12,F23_crit: " + fpars["F12_crit"]
ResRec["anisotropy_type"] = pmag.makelist(anitypes)
ResRecs.append(ResRec)
if len(Ss) > 1:
title = "LO:_" + ResRec["er_location_names"] + "_SI:_" + site + "_SA:__SP:__CO:_" + crd
ResRec["er_location_names"] = pmag.makelist(Locs)
bpars, hpars = pmagplotlib.plotANIS(ANIS, Ss, iboot, ihext, ivec, ipar, title, iplot, comp, vec, Dir, nb)
if len(PDir) > 0:
pmagplotlib.plotC(ANIS["data"], PDir, 90.0, "g")
pmagplotlib.plotC(ANIS["conf"], PDir, 90.0, "g")
if verbose and plots == 0:
pmagplotlib.drawFIGS(ANIS)
ResRec["er_location_names"] = pmag.makelist(Locs)
if plots == 1:
save(ANIS, fmt, title)
ResRec = {}
ResRec["er_citation_names"] = pmag.makelist(Cits)
ResRec["er_location_names"] = pmag.makelist(Locs)
ResRec["er_site_names"] = pmag.makelist(Sites)
ResRec["er_sample_names"] = pmag.makelist(Samples)
ResRec["er_specimen_names"] = pmag.makelist(Specimens)
ResRec["rmag_result_name"] = pmag.makelist(Sites) + ":" + pmag.makelist(anitypes)
ResRec["anisotropy_type"] = pmag.makelist(anitypes)
ResRec["er_analyst_mail_names"] = user
ResRec["tilt_correction"] = CS
if isite == "0":
ResRec["result_description"] = "Study average using coordinate system: " + CS
if isite == "1":
ResRec["result_description"] = "Site average using coordinate system: " + CS
if hpars != [] and ihext == 1:
HextRec = {}
for key in ResRec.keys():
HextRec[key] = ResRec[key] # copy over stuff
HextRec["anisotropy_v1_dec"] = "%7.1f" % (hpars["v1_dec"])
HextRec["anisotropy_v2_dec"] = "%7.1f" % (hpars["v2_dec"])
HextRec["anisotropy_v3_dec"] = "%7.1f" % (hpars["v3_dec"])
HextRec["anisotropy_v1_inc"] = "%7.1f" % (hpars["v1_inc"])
HextRec["anisotropy_v2_inc"] = "%7.1f" % (hpars["v2_inc"])
HextRec["anisotropy_v3_inc"] = "%7.1f" % (hpars["v3_inc"])
HextRec["anisotropy_t1"] = "%10.8f" % (hpars["t1"])
HextRec["anisotropy_t2"] = "%10.8f" % (hpars["t2"])
HextRec["anisotropy_t3"] = "%10.8f" % (hpars["t3"])
HextRec["anisotropy_hext_F"] = "%7.1f " % (hpars["F"])
HextRec["anisotropy_hext_F12"] = "%7.1f " % (hpars["F12"])
HextRec["anisotropy_hext_F23"] = "%7.1f " % (hpars["F23"])
HextRec["anisotropy_v1_eta_semi_angle"] = "%7.1f " % (hpars["e12"])
HextRec["anisotropy_v1_eta_dec"] = "%7.1f " % (hpars["v2_dec"])
HextRec["anisotropy_v1_eta_inc"] = "%7.1f " % (hpars["v2_inc"])
HextRec["anisotropy_v1_zeta_semi_angle"] = "%7.1f " % (hpars["e13"])
HextRec["anisotropy_v1_zeta_dec"] = "%7.1f " % (hpars["v3_dec"])
HextRec["anisotropy_v1_zeta_inc"] = "%7.1f " % (hpars["v3_inc"])
HextRec["anisotropy_v2_eta_semi_angle"] = "%7.1f " % (hpars["e12"])
HextRec["anisotropy_v2_eta_dec"] = "%7.1f " % (hpars["v1_dec"])
HextRec["anisotropy_v2_eta_inc"] = "%7.1f " % (hpars["v1_inc"])
HextRec["anisotropy_v2_zeta_semi_angle"] = "%7.1f " % (hpars["e23"])
HextRec["anisotropy_v2_zeta_dec"] = "%7.1f " % (hpars["v3_dec"])
HextRec["anisotropy_v2_zeta_inc"] = "%7.1f " % (hpars["v3_inc"])
HextRec["anisotropy_v3_eta_semi_angle"] = "%7.1f " % (hpars["e12"])
HextRec["anisotropy_v3_eta_dec"] = "%7.1f " % (hpars["v1_dec"])
HextRec["anisotropy_v3_eta_inc"] = "%7.1f " % (hpars["v1_inc"])
HextRec["anisotropy_v3_zeta_semi_angle"] = "%7.1f " % (hpars["e23"])
HextRec["anisotropy_v3_zeta_dec"] = "%7.1f " % (hpars["v2_dec"])
HextRec["anisotropy_v3_zeta_inc"] = "%7.1f " % (hpars["v2_inc"])
HextRec["magic_method_codes"] = "LP-AN:AE-H"
if verbose:
print "Hext Statistics: "
print " tau_i, V_i_D, V_i_I, V_i_zeta, V_i_zeta_D, V_i_zeta_I, V_i_eta, V_i_eta_D, V_i_eta_I"
print HextRec["anisotropy_t1"], HextRec["anisotropy_v1_dec"], HextRec["anisotropy_v1_inc"], HextRec[
"anisotropy_v1_eta_semi_angle"
], HextRec["anisotropy_v1_eta_dec"], HextRec["anisotropy_v1_eta_inc"], HextRec[
"anisotropy_v1_zeta_semi_angle"
], HextRec[
"anisotropy_v1_zeta_dec"
], HextRec[
"anisotropy_v1_zeta_inc"
]
print HextRec["anisotropy_t2"], HextRec["anisotropy_v2_dec"], HextRec["anisotropy_v2_inc"], HextRec[
"anisotropy_v2_eta_semi_angle"
], HextRec["anisotropy_v2_eta_dec"], HextRec["anisotropy_v2_eta_inc"], HextRec[
"anisotropy_v2_zeta_semi_angle"
], HextRec[
"anisotropy_v2_zeta_dec"
], HextRec[
"anisotropy_v2_zeta_inc"
]
print HextRec["anisotropy_t3"], HextRec["anisotropy_v3_dec"], HextRec["anisotropy_v3_inc"], HextRec[
"anisotropy_v3_eta_semi_angle"
], HextRec["anisotropy_v3_eta_dec"], HextRec["anisotropy_v3_eta_inc"], HextRec[
"anisotropy_v3_zeta_semi_angle"
], HextRec[
"anisotropy_v3_zeta_dec"
], HextRec[
"anisotropy_v3_zeta_inc"
]
HextRec["magic_software_packages"] = version_num
ResRecs.append(HextRec)
if bpars != []:
BootRec = {}
for key in ResRec.keys():
BootRec[key] = ResRec[key] # copy over stuff
BootRec["anisotropy_v1_dec"] = "%7.1f" % (bpars["v1_dec"])
BootRec["anisotropy_v2_dec"] = "%7.1f" % (bpars["v2_dec"])
BootRec["anisotropy_v3_dec"] = "%7.1f" % (bpars["v3_dec"])
BootRec["anisotropy_v1_inc"] = "%7.1f" % (bpars["v1_inc"])
BootRec["anisotropy_v2_inc"] = "%7.1f" % (bpars["v2_inc"])
BootRec["anisotropy_v3_inc"] = "%7.1f" % (bpars["v3_inc"])
BootRec["anisotropy_t1"] = "%10.8f" % (bpars["t1"])
BootRec["anisotropy_t2"] = "%10.8f" % (bpars["t2"])
BootRec["anisotropy_t3"] = "%10.8f" % (bpars["t3"])
BootRec["anisotropy_v1_eta_inc"] = "%7.1f " % (bpars["v1_eta_inc"])
BootRec["anisotropy_v1_eta_dec"] = "%7.1f " % (bpars["v1_eta_dec"])
BootRec["anisotropy_v1_eta_semi_angle"] = "%7.1f " % (bpars["v1_eta"])
BootRec["anisotropy_v1_zeta_inc"] = "%7.1f " % (bpars["v1_zeta_inc"])
BootRec["anisotropy_v1_zeta_dec"] = "%7.1f " % (bpars["v1_zeta_dec"])
BootRec["anisotropy_v1_zeta_semi_angle"] = "%7.1f " % (bpars["v1_zeta"])
BootRec["anisotropy_v2_eta_inc"] = "%7.1f " % (bpars["v2_eta_inc"])
BootRec["anisotropy_v2_eta_dec"] = "%7.1f " % (bpars["v2_eta_dec"])
BootRec["anisotropy_v2_eta_semi_angle"] = "%7.1f " % (bpars["v2_eta"])
BootRec["anisotropy_v2_zeta_inc"] = "%7.1f " % (bpars["v2_zeta_inc"])
BootRec["anisotropy_v2_zeta_dec"] = "%7.1f " % (bpars["v2_zeta_dec"])
BootRec["anisotropy_v2_zeta_semi_angle"] = "%7.1f " % (bpars["v2_zeta"])
BootRec["anisotropy_v3_eta_inc"] = "%7.1f " % (bpars["v3_eta_inc"])
BootRec["anisotropy_v3_eta_dec"] = "%7.1f " % (bpars["v3_eta_dec"])
BootRec["anisotropy_v3_eta_semi_angle"] = "%7.1f " % (bpars["v3_eta"])
BootRec["anisotropy_v3_zeta_inc"] = "%7.1f " % (bpars["v3_zeta_inc"])
BootRec["anisotropy_v3_zeta_dec"] = "%7.1f " % (bpars["v3_zeta_dec"])
BootRec["anisotropy_v3_zeta_semi_angle"] = "%7.1f " % (bpars["v3_zeta"])
BootRec["anisotropy_hext_F"] = ""
BootRec["anisotropy_hext_F12"] = ""
BootRec["anisotropy_hext_F23"] = ""
BootRec["magic_method_codes"] = "LP-AN:AE-H:AE-BS" # regular bootstrap
if ipar == 1:
BootRec["magic_method_codes"] = "LP-AN:AE-H:AE-BS-P" # parametric bootstrap
if verbose:
print "Boostrap Statistics: "
print " tau_i, V_i_D, V_i_I, V_i_zeta, V_i_zeta_D, V_i_zeta_I, V_i_eta, V_i_eta_D, V_i_eta_I"
print BootRec["anisotropy_t1"], BootRec["anisotropy_v1_dec"], BootRec["anisotropy_v1_inc"], BootRec[
"anisotropy_v1_eta_semi_angle"
], BootRec["anisotropy_v1_eta_dec"], BootRec["anisotropy_v1_eta_inc"], BootRec[
"anisotropy_v1_zeta_semi_angle"
], BootRec[
"anisotropy_v1_zeta_dec"
], BootRec[
"anisotropy_v1_zeta_inc"
]
print BootRec["anisotropy_t2"], BootRec["anisotropy_v2_dec"], BootRec["anisotropy_v2_inc"], BootRec[
"anisotropy_v2_eta_semi_angle"
], BootRec["anisotropy_v2_eta_dec"], BootRec["anisotropy_v2_eta_inc"], BootRec[
"anisotropy_v2_zeta_semi_angle"
], BootRec[
"anisotropy_v2_zeta_dec"
], BootRec[
"anisotropy_v2_zeta_inc"
]
print BootRec["anisotropy_t3"], BootRec["anisotropy_v3_dec"], BootRec["anisotropy_v3_inc"], BootRec[
"anisotropy_v3_eta_semi_angle"
], BootRec["anisotropy_v3_eta_dec"], BootRec["anisotropy_v3_eta_inc"], BootRec[
"anisotropy_v3_zeta_semi_angle"
], BootRec[
"anisotropy_v3_zeta_dec"
], BootRec[
"anisotropy_v3_zeta_inc"
]
BootRec["magic_software_packages"] = version_num
ResRecs.append(BootRec)
k += 1
goon = 1
while goon == 1 and iplot == 1 and verbose:
if iboot == 1:
print "compare with [d]irection "
print " plot [g]reat circle, change [c]oord. system, change [e]llipse calculation, s[a]ve plots, [q]uit "
if isite == 1:
print " [p]revious, [s]ite, [q]uit, <return> for next "
ans = raw_input("")
if ans == "q":
sys.exit()
if ans == "e":
iboot, ipar, ihext, ivec = 1, 0, 0, 0
e = raw_input("Do Hext Statistics 1/[0]: ")
if e == "1":
ihext = 1
e = raw_input("Suppress bootstrap 1/[0]: ")
if e == "1":
iboot = 0
if iboot == 1:
e = raw_input("Parametric bootstrap 1/[0]: ")
if e == "1":
ipar = 1
e = raw_input("Plot bootstrap eigenvectors: 1/[0]: ")
if e == "1":
ivec = 1
if iplot == 1:
if inittcdf == 0:
ANIS["tcdf"] = 3
pmagplotlib.plot_init(ANIS["tcdf"], 5, 5)
inittcdf = 1
bpars, hpars = pmagplotlib.plotANIS(
ANIS, Ss, iboot, ihext, ivec, ipar, title, iplot, comp, vec, Dir, nb
)
if verbose and plots == 0:
pmagplotlib.drawFIGS(ANIS)
if ans == "c":
print "Current Coordinate system is: "
if CS == "-1":
print " Specimen"
if CS == "0":
print " Geographic"
if CS == "100":
print " Tilt corrected"
key = raw_input(" Enter desired coordinate system: [s]pecimen, [g]eographic, [t]ilt corrected ")
if key == "s":
CS = "-1"
if key == "g":
CS = "0"
if key == "t":
CS = "100"
if CS not in orlist:
if len(orlist) > 0:
CS = orlist[0]
else:
CS = "-1"
if CS == "-1":
crd = "s"
if CS == "0":
crd = "g"
if CS == "100":
crd = "t"
print "desired coordinate system not available, using available: ", crd
k -= 1
goon = 0
if ans == "":
if isite == 1:
goon = 0
else:
print "Good bye "
sys.exit()
if ans == "d":
if initcdf == 0:
initcdf = 1
ANIS["vxcdf"], ANIS["vycdf"], ANIS["vzcdf"] = 4, 5, 6
pmagplotlib.plot_init(ANIS["vxcdf"], 5, 5)
pmagplotlib.plot_init(ANIS["vycdf"], 5, 5)
pmagplotlib.plot_init(ANIS["vzcdf"], 5, 5)
Dir, comp = [], 1
print """
Input: Vi D I to compare eigenvector Vi with direction D/I
where Vi=1: principal
Vi=2: major
Vi=3: minor
D= declination of comparison direction
I= inclination of comparison direction"""
con = 1
while con == 1:
try:
vdi = raw_input("Vi D I: ").split()
vec = int(vdi[0]) - 1
Dir = [float(vdi[1]), float(vdi[2])]
con = 0
except IndexError:
print " Incorrect entry, try again "
bpars, hpars = pmagplotlib.plotANIS(
ANIS, Ss, iboot, ihext, ivec, ipar, title, iplot, comp, vec, Dir, nb
)
Dir, comp = [], 0
if ans == "g":
con, cnt = 1, 0
while con == 1:
try:
print " Input: input pole to great circle ( D I) to plot a great circle: "
di = raw_input(" D I: ").split()
PDir.append(float(di[0]))
PDir.append(float(di[1]))
con = 0
except:
cnt += 1
if cnt < 10:
print " enter the dec and inc of the pole on one line "
else:
print "ummm - you are doing something wrong - i give up"
sys.exit()
pmagplotlib.plotC(ANIS["data"], PDir, 90.0, "g")
pmagplotlib.plotC(ANIS["conf"], PDir, 90.0, "g")
if verbose and plots == 0:
pmagplotlib.drawFIGS(ANIS)
if ans == "p":
k -= 2
goon = 0
if ans == "q":
k = plt
goon = 0
if ans == "s":
keepon = 1
site = raw_input(" print site or part of site desired: ")
while keepon == 1:
try:
k = sitelist.index(site)
keepon = 0
except:
tmplist = []
for qq in range(len(sitelist)):
if site in sitelist[qq]:
tmplist.append(sitelist[qq])
print site, " not found, but this was: "
print tmplist
site = raw_input("Select one or try again\n ")
k = sitelist.index(site)
goon, ans = 0, ""
if ans == "a":
locs = pmag.makelist(Locs)
title = "LO:_" + locs + "_SI:__" + "_SA:__SP:__CO:_" + crd
save(ANIS, fmt, title)
goon = 0
else:
if verbose:
print "skipping plot - not enough data points"
k += 1
# put rmag_results stuff here
if len(ResRecs) > 0:
ResOut, keylist = pmag.fillkeys(ResRecs)
pmag.magic_write(outfile, ResOut, "rmag_results")
if verbose:
print " Good bye "
def main():
"""
NAME
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
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
combine_magic.py
DESCRIPTION
Combines magic format files of the same type together.
SYNTAX
combine_magic.py [-h] [-i] -out filename -in file1 file2 ....
OPTIONS
-h prints help message
-i allows interactive entry of input and output filenames
-F specify output file name [must come BEFORE input file names]
-f specify input file names [ must come last]
"""
#
# set up magic meta data type requirements
#
filenames=[]
datasets=[]
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 "-F" in sys.argv:
ind=sys.argv.index("-F")
output=dir_path+'/'+sys.argv[ind+1]
if "-f" in sys.argv:
ind=sys.argv.index("-f")
for k in range(ind+1,len(sys.argv)):
filenames.append(dir_path+'/'+sys.argv[k])
for infile in filenames:
dataset,file_type=pmag.magic_read(infile)
print "File ",infile," read in with ",len(dataset), " records"
for rec in dataset:
datasets.append(rec)
if '-i' in sys.argv:
quit,dataset,datasets=0,[],[]
while quit==0:
infile=raw_input('\n\n Enter magic files for combining, <return> when done: ')
if infile=='':
quit = 1
break
dataset,file_type=pmag.magic_read(infile)
print "File ",infile," read in with ",len(dataset), " records"
for rec in dataset:
datasets.append(rec)
#
# collect all the keys from all the files
#
Recs,keys=pmag.fillkeys(datasets)
#
# write out the datasets into a combined file
#
pmag.magic_write(output,Recs,file_type)
print "All records stored in ",output
def save_redo(SpecRecs,inspec):
SpecRecs,keys=pmag.fillkeys(SpecRecs)
pmag.magic_write(inspec,SpecRecs,'pmag_specimens')
def main():
"""
NAME
FLA_magic.py
DESCRIPTION
import data files from the Univ. Florida, Gainesvile format to magic
SYNTAX
FLA_magic.py
"""
if '-h' in sys.argv:
print main.__doc__
sys.exit()
meas_type,methcode,instcode,experiment_name,izzi="LT-NO","","","",0
phi,theta,peakfield,labfield=0,0,0,0
pTRM,MD,ispec=0,0,0
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]
er_location_name=raw_input("Enter the location name for this study, or <return> for none ")
if er_location_name=="":
er_sites_file=raw_input("Enter site location file name, or <return> for none ")
if er_sites_file=="":
er_location_name="none"
else:
site_locations,file_type=pmag.magic_read(er_sites_file)
magfile=raw_input("Enter florida measurement filename for processing ")
print "Enter whether [A]F or [T]hermal de-(re)magnetization "
ans=raw_input(" <return> for NRMs only ")
inst=""
methcode="LT-NO"
if ans=="A":
inst="UFG-AF"
methcode="LT-AF-Z"
if ans=="T":
inst="UFG-thermal"
methcode="LT-T-Z"
if ans=="":methcode="LT-NO"
input=open(magfile,'r')
MagRecs=[]
for line in input.readlines():
print line
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"]='%8.3e' %(peakfield) # peak field in tesla
MagRec["treatment_dc_field"]='%8.3e' %(labfield) # lab field in tesla
MagRec["treatment_dc_field_phi"]='%7.1f' %(phi)
MagRec["treatment_dc_field_theta"]='%7.1f'% (theta)
rec=line.split()
MagRec["er_specimen_name"]=rec[0]
MagRec["er_sample_name"]=rec[0]
sitetmp=rec[0].split('.') # Florida naming convention splits on '.' between site and sample
MagRec["er_site_name"]=sitetmp[0]
MagRec["er_location_name"]="none"
if er_location_name!="":
MagRec["er_location_name"]=er_location_name
else:
for site in site_locations:
if site["er_site_name"] == MagRec["er_site_name"]:
MagRec["er_location_name"]=site["er_location_name"]
if inst=="UFG-AF":
MagRec["treatment_ac_field"]='%8.3e' % ( float(rec[1])*1e-4) # AF field in tesla from Oersted in Florida convention
meas_type="LT-AF-Z"
MagRec["treatment_dc_field"]='0'
else:
MagRec["treatment_temp"]='%8.3e' % (float(rec[1])+273.) # temp in kelvin
meas_type="LT-T-Z"
MagRec["measurement_magn_moment"]='%10.3e'% ((float(rec[4])/100)*1e-5) # moment in Am^2 (from 50xA/m and assuming 5cc sample in Florida convention)
MagRec["measurement_dec"]=rec[7]
MagRec["measurement_inc"]=rec[8]
MagRec["magic_method_codes"]=meas_type
MagRecs.append(MagRec)
output=raw_input("Filename for output [magic_measurements.txt] ")
if output=="":output="magic_measurements.txt"
MagOuts=pmag.measurements_methods(MagRecs,0)
pmag.magic_write(output,MagOuts,'magic_measurements')
print "results put in ",output
def main():
"""
NAME
UCSC_leg_magic.py
DESCRIPTION
converts UCSC legacy format files to magic_measurements format files
SYNTAX
UCSC_leg_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-usr USER: identify user, default is ""
-f FILE: specify input file, or
-fin INDEX: specify index file for reading whole directory: default is index.txt
-F FILE: specify output file, default is magic_measurements.txt
-Fsa: specify er_samples format file for appending, default is new er_samples.txt
-spc NUM : specify number of characters to designate a specimen, default = 1
-loc LOCNAME : specify location/study name
-A: don't average replicate measurements
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXXYYY: YYY is sample designation with Z characters from site XXX
[5] sample = site
[6] all others you will have to either customize your
self or e-mail [email protected] for help.
INPUT
Format of UCSC legacy files:
Spec Treat CDec CInc GDec GInc SDec SInc Int [optional A95]
Treat is HX where X is AF field in Oe, TX where X is T in C, or NRM
Intensity assumed to be total moment in (emu/cc) with a 10cc specimen volume
CDec: Declination in specimen coordinate system
CInc: Declination in specimen coordinate system
GDec: Declination in geographic coordinate system
GInc: Declination in geographic coordinate system
SDec: Declination in stratigraphic coordinate system
SInc: Declination in stratigraphic coordinate system
index file: must be formatted:
FILENAME SITE
"""
# initialize some stuff
noave=0
methcode,inst="",""
samp_con,Z='4',3
missing=1
demag="N"
er_location_name=""
citation='This study'
args=sys.argv
methcode="LP-NO"
specnum=-1
MagRecs=[]
version_num=pmag.get_version()
Samps=[] # keeps track of sample orientations
DIspec=[]
MagFiles=[]
#
# get command line arguments
#
user=""
mag_file=""
ind_file=""
dir_path='.'
ErSamps,ErSites=[],[]
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
samp_file=dir_path+'/er_samples.txt'
site_file=dir_path+'/er_sites.txt'
meas_file=dir_path+"/magic_measurements.txt"
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
if '-F' in args:
ind=args.index("-F")
meas_file=dir_path+'/'+args[ind+1]
if '-Fsi' in args:
ind=args.index("-Fsi")
site_file=dirpath+'.'+args[ind+1]
try:
open(site_file,'rU')
ErSites,file_type=pmag.magic_read(site_file)
print 'site information will be appended to ', site_file
except:
print site_file,' not found: site information will be stored in new er_sites.txt file'
site_file=dir_path+'/er_sites.txt'
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file=dirpath+'/'+args[ind+1]
try:
open(samp_file,'rU')
ErSamps,file_type=pmag.magic_read(samp_file)
print 'sample information will be appended to ', samp_file
except:
print samp_file,' not found: sample information will be stored in new er_samples.txt file'
samp_file=dir_path+'/er_samples.txt'
if '-f' in args:
ind=args.index("-f")
mag_file=args[ind+1]
site=mag_file.split('.')[0]
magfile=dir_path+'/'+mag_file
try:
input=open(magfile,'rU')
MagFiles.append([magfile,site])
except:
print "bad input file name"
sys.exit()
elif '-fin' in args:
ind=args.index("-fin")
ind_file=args[ind+1]
ind_file=dir_path+'/'+ind_file
try:
index_file=open(ind_file,'rU')
except:
print "bad index file name"
sys.exit()
elif '-fin' not in args:
ind_file=dir_path+'/index.txt'
try:
index_file=open(ind_file,'rU')
except:
print "bad index file name"
sys.exit()
if ind_file!="":
Files=index_file.readlines()
for file in Files:
rec=file.split()
MagFiles.append(rec)
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if specnum!=0:specnum=-specnum
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
else:
print "-loc is required option"
print main.__doc__
sys.exit()
if "-A" in args: noave=1
Sites=[]
for file in MagFiles:
site=file[1] # attach site name either from file name or from index file
if site not in Sites:
Sites.append(site)
ErSiteRec={'er_location_name': er_location_name,'er_site_name':site,'er_citation_names':citation,'site_definition':'s','site_lat':'','site_lon':"",'site_class':"",'site_lithology':"",'site_type':""}
ErSites.append(ErSiteRec)
print 'processing file: ',file[0],' for site: ',site
data=open(dir_path+'/'+file[0],'rU').readlines() # read in data from file
firstrec=data[0].split()
if firstrec[0]=='FILE': # this file has a header, must look for start of data
for k in range(len(data)):
if data[k][0]=='-': break
else:
k=-1
while k<len(data)-1:
k+=1
line=data[k]
if len(line)>2: # skip stupid terminal lines
line=line.replace(' T ',' T') # make columns consistent
line=line.replace(' H ',' H') # make columns consistent
line=line.replace(' T ',' T') # make columns consistent
line=line.replace(' H ',' H') # make columns consistent
rec=line.split()
if len(rec)<2: break # skip junk
MagRec={}
MagRec['er_location_name']=er_location_name
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["treatment_ac_field"]='0'
meas_type="LT-NO"
MagRec["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["er_specimen_name"]=rec[0]
if specnum!=0:
MagRec["er_sample_name"]=rec[0][:specnum]
else:
MagRec["er_sample_name"]=rec[0]
# site=pmag.parse_site(MagRec['er_sample_name'],samp_con,Z)
MagRec["er_site_name"]=site
MagRec["measurement_magn_moment"]='%10.3e'% (float(rec[8])*1e-4) # # int is in emu/cc; assuming 10cc, this converts to Am^2
#
if samp_file!="" and MagRec["er_sample_name"] not in Samps: # create er_samples.txt file with these data
cdec,cinc=float(rec[2]),float(rec[3])
gdec,ginc=float(rec[4]),float(rec[5])
az,pl=pmag.get_azpl(cdec,cinc,gdec,ginc)
bdec,binc=float(rec[6]),float(rec[7])
if rec[4]!=rec[6] and rec[5]!=rec[7]:
dipdir,dip=pmag.get_tilt(gdec,ginc,bdec,binc)
else:
dipdir,dip=0,0
ErSampRec={}
ErSampRec['er_citation_names']='This study'
ErSampRec['er_location_name']=MagRec['er_location_name']
ErSampRec['er_site_name']=MagRec['er_site_name']
ErSampRec['er_sample_name']=MagRec['er_sample_name']
ErSampRec['sample_azimuth']='%7.1f'%(az)
ErSampRec['sample_dip']='%7.1f'%(pl)
ErSampRec['sample_bed_dip_direction']='%7.1f'%(dipdir)
ErSampRec['sample_bed_dip']='%7.1f'%(dip)
ErSampRec['sample_description']='az,pl,dip_dir and dip recalculated from [c,g,b][dec,inc] in UCSC legacy file'
ErSampRec['magic_method_codes']='SO-NO'
ErSamps.append(ErSampRec)
Samps.append(ErSampRec['er_sample_name'])
MagRec["measurement_dec"]=rec[2]
MagRec["measurement_inc"]=rec[3]
MagRec["er_analyst_mail_names"]=""
MagRec["er_citation_names"]="This study"
demag=rec[1][0]
if demag!='N':
treat=float(rec[1][1:])
else:
treat=0
if demag=="H":
MagRec["treatment_ac_field"]='%8.3e' %(treat*1e-4) # convert from oe to tesla
meas_type="LT-AF-Z"
elif demag=="T":
MagRec["treatment_temp"]='%8.3e' % (treat+273.) # temp in kelvin
meas_type="LT-T-Z"
MagRec['magic_method_codes']=meas_type
MagRecs.append(MagRec)
MagOuts=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print "results put in ",meas_file
pmag.magic_write(samp_file,ErSamps,'er_samples')
print "sample orientations put in ",samp_file
pmag.magic_write(site_file,ErSites,'er_sites')
print "site names put in ",site_file
def main():
"""
NAME
generic_magic.py
DESCRIPTION
converts magnetometer files in generic format to magic_measurements format
SYNTAX
generic_magic.py [command line options]
OPTIONS
-h
prints the help message and quits.
-usr USER
identify user, default is ""
-f FILE:
specify path to input file, required
-fsa SAMPFILE:
specify er_samples.txt file for sample orientation data. default is er_samples.txt
-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
-exp EXPERIMENT-TYPE
Demag:
AF and/or Thermal
PI:
paleointenisty thermal experiment (ZI/IZ/IZZI)
ATRM n:
ATRM in n positions
AARM n:
AARM in n positions
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 rates in [K/minutes], seperated by comma, ordered at the same order as XXX.10,XXX.20 ...XX.70
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
NLT:
non-linear-TRM experiment
-samp X Y
specimen-sample naming convention.
X=0 Y=n: specimen is distiguished from sample by n initial characters.
(example: if n=4 then and specimen = mgf13a then sample = mgf13)
X=1 Y=n: specimen is distiguished from sample by n terminate characters.
(example: if n=1 then and specimen = mgf13a then sample = mgf13)
X=2 Y=c: specimen is distiguishing from sample by a delimiter.
(example: if c=- then annd specimen = mgf13-a then sample = mgf13)
-site X Y
sample-site naming convention.
X=0 Y=n: sample is distiguished from site by n initial characters.
(example: if n=3 then and sample = mgf13 then sample = mgf)
X=1 Y=n: sample is distiguished from site by n terminate characters.
(example: if n=2 and sample = mgf13 then site = mgf)
X=2 Y=c: specimen is distiguishing from sample by a delimiter.
(example: if c='-' and sample = 'mgf-13' then site = mgf)
-loc LOCNAM
specify location/study name.
-dc B PHI THETA:
B: dc lab field (in micro tesla)
PHI (declination). takes numbers from 0 to 360
THETA (inclination). takes numbers from -90 to 90
NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment.
-A: don't average replicate measurements. Take the last measurement from replicate measurements.
-WD working directory
INPUT
A generic file is a tab-delimited file. Each columns should have a header.
The file must include the follwing headers. The order of the columns is not important.
specimen:
string specifying specimen name
treatment:
a number with one or two decimal point (X.Y)
coding for thermal demagnetization:
0.0 or 0 is NRM.
X is temperature in celcsius
Y is always 0
coding for AF demagnetization:
0.0 or 0 is NRM.
X is AF peak field in mT
Y is always 0
coding for Thellier-type experiment:
0.0 or 0 is NRM
X is temperature in celcsius
Y=0: zerofield
Y=1: infield
Y=2: pTRM check
Y=3: pTRM tail check
Y=4: Additivity check
# Ron, Add also 5 for Thellier protocol
treatment_type:
N: NRM
A: AF
T: Thermal
moment:
magnetic moment in emu !!
In addition. at least one of the following headers are requiered:
dec_s:
declination in specimen coordinate system (0 to 360)
inc_s:
inclination in specimen coordinate system (-90 to 90)
Testing:
1) make a genetric file with AF
2) make a genetric file with Thermal
3) make a genetric file with Thermal + AF
4) make a genetric file with IZZI
5) check duplicates option
"""
#--------------------------------------
# functions
#--------------------------------------
def sort_magic_file(path,ignore_lines_n,sort_by_this_name):
'''
reads a file with headers. Each line is stored as a dictionary following the headers.
Lines are sorted in DATA by the sort_by_this_name header
DATA[sort_by_this_name]=[dictionary1,dictionary2,...]
'''
DATA={}
fin=open(path,'rU')
#ignore first lines
for i in range(ignore_lines_n):
fin.readline()
#header
line=fin.readline()
header=line.strip('\n').split('\t')
#print header
for line in fin.readlines():
if line[0]=="#":
continue
tmp_data={}
tmp_line=line.strip('\n').split('\t')
#print tmp_line
for i in range(len(tmp_line)):
if i>= len(header):
continue
tmp_data[header[i]]=tmp_line[i]
DATA[tmp_data[sort_by_this_name]]=tmp_data
fin.close()
return(DATA)
def read_generic_file(path,average_replicates):
'''
reads a generic file format. If average_replicates==True average replicate measurements.
Rrturns a Data dictionary with measurements line sorted by specimen
Data[specimen_name][dict1,dict2,...]
'''
Data={}
Fin=open(path,'rU')
header=Fin.readline().strip('\n').split('\t')
duplicates=[]
for line in Fin.readlines():
tmp_data={}
#found_duplicate=False
l=line.strip('\n').split('\t')
for i in range(min(len(header),len(l))):
tmp_data[header[i]]=l[i]
specimen=tmp_data['specimen']
if specimen not in Data.keys():
Data[specimen]=[]
Data[specimen].append(tmp_data)
# search fro duplicates
for specimen in Data.keys():
x=len(Data[specimen])-1
new_data=[]
duplicates=[]
for i in range(1,x):
while i< len(Data[specimen]) and Data[specimen][i]['treatment']==Data[specimen][i-1]['treatment'] and Data[specimen][i]['treatment_type']==Data[specimen][i-1]['treatment_type']:
duplicates.append(Data[specimen][i])
del(Data[specimen][i])
if len(duplicates)>0:
if average_replicates:
duplicates.append(Data[specimen][i-1])
Data[specimen][i-1]=average_duplicates(duplicates)
print "-W- WARNING: averaging %i duplicates for specimen %s treatmant %s"%(len(duplicates),specimen,duplicates[-1]['treatment'])
duplicates=[]
else:
Data[specimen][i-1]=duplicates[-1]
print "-W- WARNING: found %i duplicates for specimen %s treatmant %s. Taking the last measurement only"%(len(duplicates),specimen,duplicates[-1]['treatment'])
duplicates=[]
if i==len(Data[specimen])-1:
break
# if tmp_data['treatment']==Data[specimen][-1]['treatment'] and tmp_data['treatment_type']==Data[specimen][-1]['treatment_type']:
#
## check replicates
#if tmp_data['treatment']==Data[specimen][-1]['treatment'] and tmp_data['treatment_type']==Data[specimen][-1]['treatment_type']:
# #found_duplicate=True
# duplicates.append(Data[specimen][-1])
# duplicates.append(tmp_data)
# del(Data[specimen][-1])
# continue
#else:
# if len(duplicates)>0:
# if average_replicates:
# Data[specimen].append(average_duplicates(duplicates))
# print "-W- WARNING: averaging %i duplicates for specimen %s treatmant %s"%(len(duplicates),specimen,duplicates[-1]['treatment'])
# else:
# Data[specimen].append(duplicates[-1])
# print "-W- WARNING: found %i duplicates for specimen %s treatmant %s. Taking the last measurement only"%(len(duplicates),specimen,duplicates[-1]['treatment'])
# duplicates=[]
# Data[specimen].append(tmp_data)
return(Data)
def average_duplicates(duplicates):
'''
avarage replicate measurements.
'''
carts_s,carts_g,carts_t=[],[],[]
for rec in duplicates:
moment=float(rec['moment'])
if 'dec_s' in rec.keys() and 'inc_s' in rec.keys():
if rec['dec_s']!="" and rec['inc_s']!="":
dec_s=float(rec['dec_s'])
inc_s=float(rec['inc_s'])
cart_s=pmag.dir2cart([dec_s,inc_s,moment])
carts_s.append(cart_s)
if 'dec_g' in rec.keys() and 'inc_g' in rec.keys():
if rec['dec_g']!="" and rec['inc_g']!="":
dec_g=float(rec['dec_g'])
inc_g=float(rec['inc_g'])
cart_g=pmag.dir2cart([dec_g,inc_g,moment])
carts_g.append(cart_g)
if 'dec_t' in rec.keys() and 'inc_t' in rec.keys():
if rec['dec_t']!="" and rec['inc_t']!="":
dec_t=float(rec['dec_t'])
inc_t=float(rec['inc_t'])
cart_t=pmag.dir2cart([dec_t,inc_t,moment])
carts_t.append(cart_t)
if len(carts_s)>0:
carts=scipy.array(carts_s)
x_mean=scipy.mean(carts[:,0])
y_mean=scipy.mean(carts[:,1])
z_mean=scipy.mean(carts[:,2])
mean_dir=pmag.cart2dir([x_mean,y_mean,z_mean])
mean_dec_s="%.2f"%mean_dir[0]
mean_inc_s="%.2f"%mean_dir[1]
mean_moment="%10.3e"%mean_dir[2]
else:
mean_dec_s,mean_inc_s="",""
if len(carts_g)>0:
carts=scipy.array(carts_g)
x_mean=scipy.mean(carts[:,0])
y_mean=scipy.mean(carts[:,1])
z_mean=scipy.mean(carts[:,2])
mean_dir=pmag.cart2dir([x_mean,y_mean,z_mean])
mean_dec_g="%.2f"%mean_dir[0]
mean_inc_g="%.2f"%mean_dir[1]
mean_moment="%10.3e"%mean_dir[2]
else:
mean_dec_g,mean_inc_g="",""
if len(carts_t)>0:
carts=scipy.array(carts_t)
x_mean=scipy.mean(carts[:,0])
y_mean=scipy.mean(carts[:,1])
z_mean=scipy.mean(carts[:,2])
mean_dir=pmag.cart2dir([x_mean,y_mean,z_mean])
mean_dec_t="%.2f"%mean_dir[0]
mean_inc_t="%.2f"%mean_dir[1]
mean_moment="%10.3e"%mean_dir[2]
else:
mean_dec_t,mean_inc_t="",""
meanrec={}
for key in duplicates[0].keys():
if key in ['dec_s','inc_s','dec_g','inc_g','dec_t','inc_t','moment']:
continue
else:
meanrec[key]=duplicates[0][key]
meanrec['dec_s']=mean_dec_s
meanrec['dec_g']=mean_dec_g
meanrec['dec_t']=mean_dec_t
meanrec['inc_s']=mean_inc_s
meanrec['inc_g']=mean_inc_g
meanrec['inc_t']=mean_inc_t
meanrec['moment']=mean_moment
return meanrec
def get_upper_level_name(name,nc):
'''
get sample/site name from specimen/sample using naming convention
'''
if float(nc[0])==0:
if float(nc[1])!=0:
number_of_char=int(nc[1])
high_name=name[:number_of_char]
else:
high_name=name
elif float(nc[0])==1:
if float(nc[1])!=0:
number_of_char=int(nc[1])*-1
high_name=name[:number_of_char]
else:
high_name=name
elif float(nc[0])==2:
d=str(nc[1])
name_splitted=name.split(d)
if len(name_splitted)==1:
high_name=name_splitted[0]
else:
high_name=d.join(name_splitted[:-1])
else:
high_name=name
return high_name
def merge_pmag_recs(old_recs):
recs={}
recs=copy.deepcopy(old_recs)
headers=[]
for rec in recs:
for key in rec.keys():
if key not in headers:
headers.append(key)
for rec in recs:
for header in headers:
if header not in rec.keys():
rec[header]=""
return recs
#--------------------------------------
# get command line arguments
#--------------------------------------
args=sys.argv
user=""
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
else:
user=""
if '-F' in args:
ind=args.index("-F")
meas_file=args[ind+1]
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file=args[ind+1]
else:
samp_file="er_samples.txt"
if '-f' in args:
ind=args.index("-f")
magfile=args[ind+1]
try:
input=open(magfile,'rU')
except:
print "bad mag file:",magfile
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
labfield_phi=float(args[ind+2])
labfield_theta=float(args[ind+3])
if '-exp' in args:
ind=args.index("-exp")
experiment=args[ind+1]
else:
print "-LP is required option"
print main.__doc__
sys.exit()
if experiment=='ATRM':
ind=args.index("ATRM")
atrm_n_pos=int(args[ind+1])
if experiment=='AARM':
ind=args.index("AARM")
aarm_n_pos=int(args[ind+1])
if experiment=='CR':
ind=args.index("CR")
coolling_times=args[ind+1]
coolling_times_list=coolling_times.split(',')
if "-samp" in args:
ind=args.index("-samp")
sample_nc=[]
sample_nc.append(args[ind+1])
sample_nc.append(args[ind+2])
if "-site" in args:
ind=args.index("-site")
site_nc=[]
site_nc.append(args[ind+1])
site_nc.append(args[ind+2])
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
else:
er_location_name=""
if "-A" in args:
noave=1
else:
noave=0
if "-WD" in args:
ind=args.index("-WD")
WD=args[ind+1]
os.chdir(WD)
#--------------------------------------
# read data from er_samples.txt
#--------------------------------------
#if "-fsa" in args:
# ind=args.index("-fsa")
# er_sample_file=args[ind+1]
#else:
# er_sample_file="er_samples.txt"
er_sample_data={}
#er_sample_data=sort_magic_file(samp_file,1,'er_sample_name')
try:
er_sample_data=sort_magic_file(samp_file,1,'er_sample_name')
print "-I- Found er_samples.txt"
print '-I- sample information will be appended to existing er_samples.txt file'
except:
print "-I- Cant find file er_samples.txt"
print '-I- sample information will be stored in new er_samples.txt file'
#--------------------------------------
# read data from generic file
#--------------------------------------
if noave:
mag_data=read_generic_file(magfile,False)
else:
mag_data=read_generic_file(magfile,True)
#--------------------------------------
# for each specimen get the data, and translate it to MagIC format
#--------------------------------------
ErSamplesRecs=[]
MagRecs=[]
specimens_list=mag_data.keys()
specimens_list.sort()
for specimen in specimens_list:
measurement_running_number=0
this_specimen_treatments=[] # a list of all treatments
MagRecs_this_specimen=[]
LP_this_specimen=[] # a list of all lab protocols
IZ,ZI=0,0 # counter for IZ and ZI steps
for meas_line in mag_data[specimen]:
#------------------
# trivial MagRec data
#------------------
MagRec={}
MagRec['er_citation_names']="This study"
MagRec["er_specimen_name"]=meas_line['specimen']
MagRec["er_sample_name"]=get_upper_level_name(MagRec["er_specimen_name"],sample_nc)
MagRec["er_site_name"]=get_upper_level_name(MagRec["er_sample_name"],site_nc)
MagRec['er_location_name']=er_location_name
MagRec['er_analyst_mail_names']=user
MagRec["magic_instrument_codes"]=""
MagRec["measurement_flag"]='g'
MagRec["measurement_number"]="%i"%measurement_running_number
MagRec["measurement_magn_moment"]='%10.3e'%(float(meas_line["moment"])*1e-3) # in Am^2
MagRec["measurement_temp"]='273.' # room temp in kelvin
#------------------
# decode treatments from treatment column in the generic file
#------------------
treatment=[]
treatment_code=str(meas_line['treatment']).split(".")
treatment.append(float(treatment_code[0]))
if len(treatment_code)==1:
treatment.append(0)
else:
treatment.append(float(treatment_code[1]))
#------------------
# lab field direction
#------------------
if experiment in ['PI','NLT','CR']:
if float(treatment[1])==0:
MagRec["treatment_dc_field"]="0"
MagRec["treatment_dc_field_phi"]="0"
MagRec["treatment_dc_field_theta"]="0"
else:
MagRec["treatment_dc_field"]='%8.3e'%(float(labfield))
MagRec["treatment_dc_field_phi"]="%.2f"%(float(labfield_phi))
MagRec["treatment_dc_field_theta"]="%.2f"%(float(labfield_theta))
else:
MagRec["treatment_dc_field"]=""
MagRec["treatment_dc_field_phi"]=""
MagRec["treatment_dc_field_theta"]=""
#------------------
# treatment temperature/peak field
#------------------
if experiment == 'Demag':
if meas_line['treatment_type']=='A':
MagRec['treatment_temp']="273."
MagRec["treatment_ac_field"]="%.3e"%(treatment[0]*1e-3)
elif meas_line['treatment_type']=='N':
MagRec['treatment_temp']="273."
MagRec["treatment_ac_field"]=""
else:
MagRec['treatment_temp']="%.2f"%(treatment[0]+273.)
MagRec["treatment_ac_field"]=""
else:
MagRec['treatment_temp']="%.2f"%(treatment[0]+273.)
MagRec["treatment_ac_field"]=""
#---------------------
# Lab treatment
# Lab protocol
#---------------------
#---------------------
# Lab treatment and lab protocoal for NRM:
#---------------------
if float(meas_line['treatment'])==0:
LT="LT-NO"
LP="" # will be filled later after finishing reading all measurements line
#---------------------
# Lab treatment and lab protocoal for paleointensity experiment
#---------------------
elif experiment =='PI':
LP="LP-PI-TRM"
if treatment[1]==0:
LT="LT-T-Z"
elif treatment[1]==1 or treatment[1]==10: # infield
LT="LT-T-I"
elif treatment[1]==2 or treatment[1]==20: # pTRM check
LT="LT-PTRM-I"
LP=LP+":"+"LP-PI-ALT-PTRM"
elif treatment[1]==3 or treatment[1]==30: # Tail check
LT="LT-PTRM-MD"
LP=LP+":"+"LP-PI-BT-MD"
elif treatment[1]==4 or treatment[1]==40: # Additivity check
LT="LT-PTRM-AC"
LP=LP+":"+"LP-PI-BT-MD"
else:
print "-E- unknown measurement code specimen %s treatmemt %s"%(meas_line['specimen'],meas_line['treatment'])
MagRec={}
continue
# save all treatment in a list
# we will use this later to distinguidh between ZI / IZ / and IZZI
this_specimen_treatments.append(float(meas_line['treatment']))
if LT=="LT-T-Z":
if float(treatment[0]+0.1) in this_specimen_treatments:
LP=LP+":"+"LP-PI-IZ"
if LT=="LT-T-I":
if float(treatment[0]+0.0) in this_specimen_treatments:
LP=LP+":"+"LP-PI-ZI"
#---------------------
# Lab treatment and lab protocoal for demag experiment
#---------------------
elif "Demag" in experiment:
if meas_line['treatment_type']=='A':
LT="LT-AF-Z"
LP="LP-DIR-AF"
else:
LT="LT-T-Z"
LP="LP-DIR-T"
#---------------------
# Lab treatment and lab protocoal for ATRM experiment
#---------------------
elif experiment in ['ATRM','AARM']:
if experiment=='ATRM':
LP="LP-AN-TRM"
n_pos=atrm_n_pos
if n_pos!=6:
print "the program does not support ATRM in %i position."%n_pos
continue
if experiment=='AARM':
#MagRec['treatment_temp']="273."
#MagRec["treatment_ac_field"]=""
LP="LP-AN-ARM"
n_pos=aarm_n_pos
if n_pos!=6:
print "the program does not support AARM in %i position."%n_pos
continue
if treatment[1]==0:
if experiment=='ATRM':
LT="LT-T-Z"
MagRec['treatment_temp']="%.2f"%(treatment[0]+273.)
MagRec["treatment_ac_field"]=""
else:
LT="LT-AF-Z"
MagRec['treatment_temp']="273."
MagRec["treatment_ac_field"]="%.3e"%(treatment[0]*1e-3)
MagRec["treatment_dc_field"]='0'
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
else:
if experiment=='ATRM':
if float(treatment[1])==70 or float(treatment[1])==7: # alteration check as final measurement
LT="LT-PTRM-I"
else:
LT="LT-T-I"
else:
LT="LT-AF-I"
MagRec["treatment_dc_field"]='%8.3e'%(float(labfield))
# 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)
tdec=[0,90,0,180,270,0,0,90,0]
tinc=[0,0,90,0,0,-90,0,0,90]
if treatment[1] < 10:
ipos_code=int(treatment[1])-1
else:
ipos_code=int(treatment[1]/10)-1
# (2) using the magnetization
if meas_line["dec_s"]!="":
DEC=float(meas_line["dec_s"])
INC=float(meas_line["inc_s"])
elif meas_line["dec_g"]!="":
DEC=float(meas_line["dec_g"])
INC=float(meas_line["inc_g"])
elif meas_line["dec_t"]!="":
DEC=float(meas_line["dec_t"])
INC=float(meas_line["inc_t"])
if DEC<0 and DEC>-359:
DEC=360.+DEC
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
# check it
if treatment[1]!= 7 and treatment[1]!= 70:
if ipos_guess!=ipos_code:
print "-W- WARNING: check specimen %s step %s, anistropy measurements, coding does not match the direction of the lab field"%(specimen,meas_line['treatment'])
MagRec["treatment_dc_field_phi"]='%7.1f' %(tdec[ipos])
MagRec["treatment_dc_field_theta"]='%7.1f'% (tinc[ipos])
#---------------------
# Lab treatment and lab protocoal for cooling rate experiment
#---------------------
elif experiment == "CR":
coolling_times_list
LP="LP-CR-TRM"
MagRec["treatment_temp"]='%8.3e' % (float(treatment[0])+273.) # temp in kelvin
if treatment[1]==0:
LT="LT-T-Z"
MagRec["treatment_dc_field"]="0"
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
else:
if treatment[1]==7: # alteration check as final measurement
LT="LT-PTRM-I"
else:
LT="LT-T-I"
MagRec["treatment_dc_field"]='%8.3e'%(labfield)
MagRec["treatment_dc_field_phi"]='%7.1f' % (labfield_phi) # labfield phi
MagRec["treatment_dc_field_theta"]='%7.1f' % (labfield_theta) # labfield theta
indx=int(treatment[1])-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"
#---------------------
# Lab treatment and lab protocoal for NLT experiment
#---------------------
elif 'NLT' in experiment :
print "Dont support yet NLT rate experiment file. Contact [email protected]"
#---------------------
# magic_method_codes for this measurement only
# LP will be fixed after all measurement lines are read
#---------------------
MagRec["magic_method_codes"]=LT+":"+LP
#---------------------
# Demag experiments only:
# search if orientation data exists in er_samples.txt
# if not: create one and save
#---------------------
# see if core azimuth and tilt-corrected data are in er_samples.txt
sample=MagRec["er_sample_name"]
found_sample_azimuth,found_sample_dip,found_sample_bed_dip_direction,found_sample_bed_dip=False,False,False,False
if sample in er_sample_data.keys():
if "sample_azimuth" in er_sample_data[sample].keys() and er_sample_data[sample]['sample_azimuth'] !="":
sample_azimuth=float(er_sample_data[sample]['sample_azimuth'])
found_sample_azimuth=True
if "sample_dip" in er_sample_data[sample].keys() and er_sample_data[sample]['sample_dip']!="":
sample_dip=float(er_sample_data[sample]['sample_dip'])
found_sample_dip=True
if "sample_bed_dip_direction" in er_sample_data[sample].keys() and er_sample_data[sample]['sample_bed_dip_direction']!="":
sample_bed_dip_direction=float(er_sample_data[sample]['sample_bed_dip_direction'])
found_sample_bed_dip_direction=True
if "sample_bed_dip" in er_sample_data[sample].keys() and er_sample_data[sample]['sample_bed_dip']!="":
sample_bed_dip=float(er_sample_data[sample]['sample_bed_dip'])
found_sample_bed_dip=True
else:
er_sample_data[sample]={}
#--------------------
# deal with specimen orientation and different coordinate system
#--------------------
found_s,found_geo,found_tilt=False,False,False
if "dec_s" in meas_line.keys() and "inc_s" in meas_line.keys():
if meas_line["dec_s"]!="" and meas_line["inc_s"]!="":
found_s=True
MagRec["measurement_dec"]=meas_line["dec_s"]
MagRec["measurement_inc"]=meas_line["inc_s"]
if "dec_g" in meas_line.keys() and "inc_g" in meas_line.keys():
if meas_line["dec_g"]!="" and meas_line["inc_g"]!="":
found_geo=True
if "dec_t" in meas_line.keys() and "inc_t" in meas_line.keys():
if meas_line["dec_t"]!="" and meas_line["inc_t"]!="":
found_tilt=True
#-----------------------------
# specimen coordinates: no
# geographic coordinates: yes
#-----------------------------
if found_geo and not found_s:
MagRec["measurement_dec"]=meas_line["dec_g"]
MagRec["measurement_inc"]=meas_line["inc_g"]
# core azimuth/plunge is not in er_samples.txt
if not found_sample_dip or not found_sample_azimuth:
er_sample_data[sample]['sample_azimuth']="0"
er_sample_data[sample]['sample_dip']="0"
# core azimuth/plunge is in er_samples.txt
else:
sample_azimuth=float(er_sample_data[sample]['sample_azimuth'])
sample_dip=float(er_sample_data[sample]['sample_dip'])
if sample_azimuth!=0 and sample_dip!=0:
print "-W- WARNING: delete core azimuth/plunge in er_samples.txt\n\
becasue dec_s and inc_s are unavaialable"
#-----------------------------
# specimen coordinates: no
# geographic coordinates: no
#-----------------------------
if not found_geo and not found_s:
print "-E- ERROR: sample %s does not have dec_s/inc_s or dec_g/inc_g. Ignore specimen %s "%(sample,specimen)
break
#-----------------------------
# specimen coordinates: yes
# geographic coordinates: yes
#
# commant: Ron, this need to be tested !!
#-----------------------------
if found_geo and found_s:
cdec,cinc=float(meas_line["dec_s"]),float(meas_line["inc_s"])
gdec,ginc=float(meas_line["dec_g"]),float(meas_line["inc_g"])
az,pl=pmag.get_azpl(cdec,cinc,gdec,ginc)
# core azimuth/plunge is not in er_samples.txt:
# calculate core az/pl and add it to er_samples.txt
if not found_sample_dip or not found_sample_azimuth:
er_sample_data[sample]['sample_azimuth']="%.1f"%az
er_sample_data[sample]['sample_dip']="%.1f"%pl
# core azimuth/plunge is in er_samples.txt
else:
if float(er_sample_data[sample]['sample_azimuth'])!= az:
print "-E- ERROR in sample_azimuth sample %s. Check it! using the value in er_samples.txt"%sample
if float(er_sample_data[sample]['sample_dip'])!= pl:
print "-E- ERROR in sample_dip sample %s. Check it! using the value in er_samples.txt"%sample
#-----------------------------
# specimen coordinates: yes
# geographic coordinates: no
#-----------------------------
if not found_geo and found_s:
if found_sample_dip and found_sample_azimuth:
pass
# (nothing to do)
else:
if "Demag" in experiment:
print "-W- WARNING: missing sample_dip or sample_azimuth for sample %s"%sample
#-----------------------------
# tilt-corrected coordinates: yes
# geographic coordinates: no
#-----------------------------
if found_tilt and not found_geo:
print "-E- ERROR: missing geographic data for sample %s. Ignoring tilt-corrected data "%sample
if found_tilt and found_geo:
dec_geo,inc_geo=float(meas_line["dec_g"]),float(meas_line["inc_g"])
dec_tilt,inc_tilt=float(meas_line["dec_t"]),float(meas_line["inc_t"])
if dec_geo==dec_tilt and inc_geo==inc_tilt:
DipDir,Dip=0.,0.
else:
DipDir,Dip=pmag.get_tilt(dec_geo,inc_geo,dec_tilt,inc_tilt)
if not found_sample_bed_dip_direction or not found_sample_bed_dip:
print "-I- calculating dip and dip direction used for tilt correction sample %s. results are put in er_samples.txt"%sample
er_sample_data[sample]['sample_bed_dip_direction']="%.1f"%DipDir
er_sample_data[sample]['sample_bed_dip']="%.1f"%Dip
#-----------------------------
# er_samples method codes
# geographic coordinates: no
#-----------------------------
if found_tilt or found_geo:
er_sample_data[sample]['magic_method_codes']="SO-NO"
#-----------------
# er_samples_data
#-----------------
if sample in er_sample_data.keys():
er_sample_data[sample]['er_sample_name']=sample
er_sample_data[sample]['er_site_name']=MagRec["er_site_name"]
er_sample_data[sample]['er_location_name']=MagRec["er_location_name"]
#MagRec["magic_method_codes"]=LT
MagRecs_this_specimen.append(MagRec)
#if LP!="" and LP not in LP_this_specimen:
# LP_this_specimen.append(LP)
measurement_running_number+=1
#-------
#-------
# after reading all the measurements lines for this specimen
# 1) add magic_experiment_name
# 2) fix magic_method_codes with the correct lab protocol
#-------
LP_this_specimen=[]
for MagRec in MagRecs_this_specimen:
magic_method_codes=MagRec["magic_method_codes"].split(":")
for code in magic_method_codes:
if "LP" in code and code not in LP_this_specimen:
LP_this_specimen.append(code)
# check IZ/ZI/IZZI
if "LP-PI-ZI" in LP_this_specimen and "LP-PI-IZ" in LP_this_specimen:
LP_this_specimen.remove("LP-PI-ZI")
LP_this_specimen.remove("LP-PI-IZ")
LP_this_specimen.append("LP-PI-BT-IZZI")
# add the right LP codes and fix experiment name
for MagRec in MagRecs_this_specimen:
MagRec["magic_experiment_name"]=MagRec["er_specimen_name"]+":"+":".join(LP_this_specimen)
magic_method_codes=MagRec["magic_method_codes"].split(":")
LT=""
for code in magic_method_codes:
if code[:3]=="LT-":
LT=code;
break
MagRec["magic_method_codes"]=LT+":"+":".join(LP_this_specimen)
MagRecs.append(MagRec)
#--
# write magic_measurements.txt
#--
MagRecs_fixed=merge_pmag_recs(MagRecs)
pmag.magic_write(meas_file,MagRecs_fixed,'magic_measurements')
print "-I- MagIC file is saved in %s"%meas_file
#--
# write er_samples.txt
#--
ErSamplesRecs=[]
samples=er_sample_data.keys()
samples.sort()
for sample in samples:
ErSamplesRecs.append(er_sample_data[sample])
ErSamplesRecs_fixed=merge_pmag_recs(ErSamplesRecs)
pmag.magic_write("er_samples.txt",ErSamplesRecs_fixed,'er_samples')
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
thellier_magic_redo.py
DESCRIPTION
Calculates paleointensity parameters for thellier-thellier type data using bounds
stored in the "redo" file
SYNTAX
thellier_magic_redo [command line options]
OPTIONS
-h prints help message
-usr USER: identify user, default is ""
-fcr CRIT, set criteria for grading
-f IN: specify input file, default is magic_measurements.txt
-fre REDO: specify redo file, default is "thellier_redo"
-F OUT: specify output file, default is thellier_specimens.txt
-leg: attaches "Recalculated from original measurements; supercedes published results. " to comment field
-CR PERC TYPE: apply a cooling rate correction.
PERC should be a percentage of original (say reduce to 90%)
TYPE should be one of the following:
EG (for educated guess); PS (based on pilots); TRM (based on comparison of two TRMs)
-Fcr CRout: specify pmag_specimen format file for cooling rate corrected data
-ANI: there are anisotropy data to correct thellier results
-fan ANIFILE: specify rmag_anisotropy format file, default is rmag_anisotropy.txt
-Fac ACout: specify pmag_specimen format file for anisotropy corrected data
default is AC_specimens.txt
-NLT: there are non-linear trm data in the measurements file to correct thellier results
-fnl NLTFILE: specify magic_measurments format file, default is magic_measurements.txt
-Fnl NLTout: specify pmag_specimen format file for non-linear trm corrected data
default is NLT_specimens.txt
-z use z component differenences for pTRM calculation
"""
dir_path='.'
critout=""
version_num=pmag.get_version()
field,first_save=-1,1
spec,recnum,start,end=0,0,0,0
frac=0
NltRecs,PmagSpecs,AniSpecRecs,NltSpecRecs,CRSpecs=[],[],[],[],[]
meas_file,pmag_file,mk_file="magic_measurements.txt","thellier_specimens.txt","thellier_redo"
anis_file="rmag_anisotropy.txt"
anisout,nltout="AC_specimens.txt","NLT_specimens.txt"
crout="CR_specimens.txt"
nlt_file=""
comment,user="","unknown"
anis,nltrm=0,0
jackknife=0 # maybe in future can do jackknife
args=sys.argv
Zdiff=0
if '-WD' in args:
ind=args.index('-WD')
dir_path=args[ind+1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=sys.argv[ind+1]
if "-leg" in args: comment="Recalculated from original measurements; supercedes published results. "
if "-CR" in args:
ind=args.index("-CR")
frac=.01*float(sys.argv[ind+1])
crtype=sys.argv[ind+2]
if "-Fcr" in args:
ind=args.index("-Fcr")
crout=sys.argv[ind+1]
if "-f" in args:
ind=args.index("-f")
meas_file=sys.argv[ind+1]
if "-F" in args:
ind=args.index("-F")
pmag_file=sys.argv[ind+1]
if "-fre" in args:
ind=args.index("-fre")
mk_file=args[ind+1]
#
#
if "-ANI" in args:
anis=1
ind=args.index("-ANI")
if "-Fac" in args:
ind=args.index("-Fac")
anisout=args[ind+1]
if "-fan" in args:
ind=args.index("-fan")
anis_file=args[ind+1]
#
if "-NLT" in args:
nltrm=1
if "-Fnl" in args:
ind=args.index("-Fnl")
nltout=args[ind+1]
if "-fnl" in args:
ind=args.index("-fnl")
nlt_file=args[ind+1]
if "-z" in args: Zdiff=1
if '-fcr' in sys.argv:
ind=args.index("-fcr")
critout=sys.argv[ind+1]
#
# start reading in data:
#
meas_file=dir_path+"/"+meas_file
mk_file=dir_path+"/"+mk_file
critout=dir_path+"/"+critout
try:
open(critout,'rU')
accept_keys=['specimen_int_ptrm_n','specimen_md','specimen_fvds','specimen_b_beta','specimen_dang','specimen_drats','specimen_Z']
crit_data,file_type=pmag.magic_read(critout)
print "Acceptance criteria read in from ", critout
accept={}
accept['specimen_int_ptrm_n']=2.0
for critrec in crit_data:
if critrec["pmag_criteria_code"]=="IE-SPEC":
for key in accept_keys:
if key not in critrec.keys():
accept[key]=-1
else:
accept[key]=float(critrec[key])
except:
critout="" # no acceptance criteria specified
meas_data,file_type=pmag.magic_read(meas_file)
if file_type != 'magic_measurements':
print file_type
print file_type,"This is not a valid magic_measurements file "
sys.exit()
try:
mk_f=open(mk_file,'rU')
except:
print "Bad redo file"
sys.exit()
mkspec=[]
speclist=[]
for line in mk_f.readlines():
tmp=line.split()
mkspec.append(tmp)
speclist.append(tmp[0])
if anis==1:
anis_file=dir_path+"/"+anis_file
anis_data,file_type=pmag.magic_read(anis_file)
if file_type != 'rmag_anisotropy':
print file_type
print file_type,"This is not a valid rmag_anisotropy file "
sys.exit()
if nlt_file=="":
nlt_data=meas_data # look for trm acquisition data in the meas_data file
else:
nlt_file=dir_path+"/"+nlt_file
nlt_data,file_type=pmag.magic_read(nlt_file)
#
# sort the specimen names and step through one by one
#
sids=pmag.get_specs(meas_data)
#
print 'Processing ',len(speclist),' specimens - please wait '
while spec < len(speclist):
s=speclist[spec]
recnum=0
datablock=[]
PmagSpecRec={}
PmagSpecRec["er_analyst_mail_names"]=user
PmagSpecRec["er_citation_names"]="This study"
PmagSpecRec["magic_software_packages"]=version_num
methcodes,inst_code=[],""
#
# find the data from the meas_data file for this specimen
#
for rec in meas_data:
if rec["er_specimen_name"].lower()==s.lower():
if "magic_instrument_codes" not in rec.keys():
rec["magic_instrument_codes"]="unknown"
meths=rec["magic_method_codes"]
for meth in meths:meth.strip() # get rid of annoying spaces in method codes
if "LP-PI-TRM" in meths: datablock.append(rec)
#
# collect info for the PmagSpecRec dictionary
#
if len(datablock)>0:
rec=datablock[0]
PmagSpecRec["er_specimen_name"]=s
PmagSpecRec["er_sample_name"]=rec["er_sample_name"]
PmagSpecRec["er_site_name"]=rec["er_site_name"]
PmagSpecRec["er_location_name"]=rec["er_location_name"]
PmagSpecRec["measurement_step_unit"]="K"
PmagSpecRec["specimen_correction"]='u'
if "magic_instrument_codes" not in rec.keys():
PmagSpecRec["magic_instrument_codes"]="unknown"
else:
PmagSpecRec["magic_instrument_codes"]=rec["magic_instrument_codes"]
if "magic_experiment_name" not in rec.keys():
rec["magic_experiment_name"]=""
else:
PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"]
meths=rec["magic_experiment_name"].split(":")
for meth in meths:
if meth.strip() not in methcodes and "LP-" in meth:methcodes.append(meth.strip())
#
# sort out the data into first_Z, first_I, ptrm_check, ptrm_tail
#
araiblock,field=pmag.sortarai(datablock,s,Zdiff)
first_Z=araiblock[0]
first_I=araiblock[1]
ptrm_check=araiblock[2]
ptrm_tail=araiblock[3]
if len(first_I)<3 or len(first_Z)<4:
spec+=1
print 'skipping specimen ', s
else:
#
# get start, end
#
for redospec in mkspec:
if redospec[0]==s:
b,e=float(redospec[1]),float(redospec[2])
break
if e > float(first_Z[-1][0]):e=float(first_Z[-1][0])
for recnum in range(len(first_Z)):
if first_Z[recnum][0]==b:start=recnum
if first_Z[recnum][0]==e:end=recnum
nsteps=end-start
if nsteps>2:
zijdblock,units=pmag.find_dmag_rec(s,meas_data)
pars,errcode=pmag.PintPars(araiblock,zijdblock,start,end)
pars['measurement_step_unit']=units
pars["specimen_lab_field_dc"]=field
pars["specimen_int"]=-1*field*pars["specimen_b"]
PmagSpecRec["measurement_step_min"]='%8.3e' % (pars["measurement_step_min"])
PmagSpecRec["measurement_step_max"]='%8.3e' % (pars["measurement_step_max"])
PmagSpecRec["specimen_int_n"]='%i'%(pars["specimen_int_n"])
PmagSpecRec["specimen_lab_field_dc"]='%8.3e'%(pars["specimen_lab_field_dc"])
PmagSpecRec["specimen_int"]='%9.4e '%(pars["specimen_int"])
PmagSpecRec["specimen_b"]='%5.3f '%(pars["specimen_b"])
PmagSpecRec["specimen_q"]='%5.1f '%(pars["specimen_q"])
PmagSpecRec["specimen_f"]='%5.3f '%(pars["specimen_f"])
PmagSpecRec["specimen_fvds"]='%5.3f'%(pars["specimen_fvds"])
PmagSpecRec["specimen_b_beta"]='%5.3f'%(pars["specimen_b_beta"])
PmagSpecRec["specimen_int_mad"]='%7.1f'%(pars["specimen_int_mad"])
PmagSpecRec["specimen_Z"]='%7.1f'%(pars["specimen_Z"])
PmagSpecRec["specimen_gamma"]='%7.1f'%(pars["specimen_gamma"])
if pars["method_codes"]!="" and pars["method_codes"] not in methcodes: methcodes.append(pars["method_codes"])
PmagSpecRec["specimen_dec"]='%7.1f'%(pars["specimen_dec"])
PmagSpecRec["specimen_inc"]='%7.1f'%(pars["specimen_inc"])
PmagSpecRec["specimen_tilt_correction"]='-1'
PmagSpecRec["specimen_direction_type"]='l'
PmagSpecRec["direction_type"]='l' # this is redudant, but helpful - won't be imported
PmagSpecRec["specimen_dang"]='%7.1f '%(pars["specimen_dang"])
PmagSpecRec["specimen_drats"]='%7.1f '%(pars["specimen_drats"])
PmagSpecRec["specimen_int_ptrm_n"]='%i '%(pars["specimen_int_ptrm_n"])
PmagSpecRec["specimen_rsc"]='%6.4f '%(pars["specimen_rsc"])
PmagSpecRec["specimen_md"]='%i '%(int(pars["specimen_md"]))
if PmagSpecRec["specimen_md"]=='-1':PmagSpecRec["specimen_md"]=""
PmagSpecRec["specimen_b_sigma"]='%5.3f '%(pars["specimen_b_sigma"])
if "IE-TT" not in methcodes:methcodes.append("IE-TT")
methods=""
for meth in methcodes:
methods=methods+meth+":"
PmagSpecRec["magic_method_codes"]=methods[:-1]
PmagSpecRec["magic_software_packages"]=version_num
PmagSpecRec["specimen_description"]=comment
if critout!="":
score,kill=pmag.grade(PmagSpecRec,accept)
Grade=""
if score==len(accept.keys()):Grade='A'
if score==len(accept.keys())-1:Grade='B'
if score==len(accept.keys())-2:Grade='C'
if score==len(accept.keys())-3:Grade='D'
if score<=len(accept.keys())-4:Grade='F'
PmagSpecRec["specimen_grade"]=Grade
else:
PmagSpecRec["specimen_grade"]=""
if nltrm==0 and anis==0 and frac!=0: # apply cooling rate correction
CrSpecRec={}
for key in PmagSpecRec.keys():CrSpecRec[key]=PmagSpecRec[key]
inten=frac*float(CrSpecRec['specimen_int'])
CrSpecRec["specimen_int"]='%9.4e '%(inten) # adjust specimen intensity by cooling rate correction
CrSpecRec['magic_method_codes'] = CrSpecRec['magic_method_codes']+':DA-CR-'+crtype
CrSpecRec["specimen_correction"]='c'
CRSpecs.append(CrSpecRec)
PmagSpecs.append(PmagSpecRec)
NltSpecRec=""
#
# check on non-linear TRM correction
#
if nltrm==1:
#
# find the data from the nlt_data list for this specimen
#
TRMs,Bs=[],[]
NltSpecRec=""
NltRecs=[]
for NltRec in nlt_data:
if NltRec['er_specimen_name']==PmagSpecRec["er_specimen_name"]:
meths=NltRec["magic_method_codes"].split(":")
for meth in meths:meth.strip()
if "LP-TRM" in meths: NltRecs.append(NltRec)
if len(NltRecs) > 2:
for NltRec in NltRecs:
Bs.append(float(NltRec['treatment_dc_field']))
TRMs.append(float(NltRec['measurement_magn_moment']))
NLTpars=nlt.NLtrm(Bs,TRMs,float(PmagSpecRec['specimen_int']),float(PmagSpecRec['specimen_lab_field_dc']),0)
if NLTpars['banc']>0:
NltSpecRec={}
for key in PmagSpecRec.keys():
NltSpecRec[key]=PmagSpecRec[key]
NltSpecRec['specimen_int']='%9.4e'%(NLTpars['banc'])
NltSpecRec['magic_method_codes']=PmagSpecRec["magic_method_codes"]+":DA-NL"
NltSpecRec["specimen_correction"]='c'
NltSpecRec['specimen_grade']=PmagSpecRec['specimen_grade']
NltSpecRec["magic_software_packages"]=version_num
print NltSpecRec['er_specimen_name'], ' Banc= ',float(NLTpars['banc'])*1e6
if anis==0 and frac!=0:
CrSpecRec={}
for key in NltSpecRec.keys():CrSpecRec[key]=NltSpecRec[key]
inten=frac*float(CrSpecRec['specimen_int'])
CrSpecRec["specimen_int"]='%9.4e '%(inten) # adjust specimen intensity by cooling rate correction
CrSpecRec['magic_method_codes'] = CrSpecRec['magic_method_codes']+':DA-CR-'+crtype
CRSpecs.append(CrSpecRec)
NltSpecRecs.append(NltSpecRec)
#
# check on anisotropy correction
if anis==1:
if NltSpecRec!="":
Spc=NltSpecRec
else: # find uncorrected data
Spc=PmagSpecRec
for AniSpec in anis_data:
if AniSpec["er_specimen_name"]==PmagSpecRec["er_specimen_name"]:
AniSpecRec=pmag.thellier_anis_corr(Spc,AniSpec)
AniSpecRec['specimen_grade']=PmagSpecRec['specimen_grade']
inst_codes=Spc["magic_instrument_codes"]
if "magic_instrument_codes" in AniSpec.keys():
if inst_codes=="unknown":
inst_codes=AniSpec["magic_instrument_codes"]
else:
inst_codes=inst_codes+":"+AniSpec["magic_instrument_codes"]
AniSpecRec["magic_instrument_codes"]=inst_codes
AniSpecRec["specimen_correction"]='c'
AniSpecRec["magic_software_packages"]=version_num
if frac!=0:
CrSpecRec={}
for key in AniSpecRec.keys():CrSpecRec[key]=AniSpecRec[key]
inten=frac*float(CrSpecRec['specimen_int'])
CrSpecRec["specimen_int"]='%9.4e '%(inten) # adjust specimen intensity by cooling rate correction
CrSpecRec['magic_method_codes'] = CrSpecRec['magic_method_codes']+':DA-CR-'+crtype
CRSpecs.append(CrSpecRec)
AniSpecRecs.append(AniSpecRec)
break
elif anis==1:
for AniSpec in anis_data:
if AniSpec["er_specimen_name"]==PmagSpecRec["er_specimen_name"]:
AniSpecRec=pmag.thellier_anis_corr(PmagSpecRec,AniSpec)
AniSpecRec['specimen_grade']=PmagSpecRec['specimen_grade']
inst_codes=PmagSpecRec["magic_instrument_codes"]
if "magic_instrument_codes" in AniSpec.keys():
if inst_codes=="unknown":
inst_codes=AniSpec["magic_instrument_codes"]
else:
inst_codes=inst_codes+":"+AniSpec["magic_instrument_codes"]
AniSpecRec["magic_instrument_codes"]=inst_codes
AniSpecRec["specimen_correction"]='c'
AniSpecRec["magic_software_packages"]=version_num
if frac!=0:
CrSpecRec={}
for key in AniSpecRec.keys():CrSpecRec[key]=AniSpecRec[key]
inten=frac*float(CrSpecRec['specimen_int'])
CrSpecRec["specimen_int"]='%9.4e '%(inten) # adjust specimen intensity by cooling rate correction
CrSpecRec['magic_method_codes'] = CrSpecRec['magic_method_codes']+':DA-CR-'+crtype
CRSpecs.append(CrSpecRec)
AniSpecRecs.append(AniSpecRec)
break
spec +=1
else:
print "skipping ",s
spec+=1
pmag_file=dir_path+'/'+pmag_file
pmag.magic_write(pmag_file,PmagSpecs,'pmag_specimens')
if anis==1:
anisout=dir_path+'/'+anisout
pmag.magic_write(anisout,AniSpecRecs,'pmag_specimens')
if nltrm==1:
nltout=dir_path+'/'+nltout
pmag.magic_write(nltout,NltSpecRecs,'pmag_specimens')
if frac!=0:
crout=dir_path+'/'+crout
pmag.magic_write(crout,CRSpecs,'pmag_specimens')
def main():
"""
ODP_samples_magic.py
OPTIONS:
-f FILE, input csv file
-Fsa FILE, output er_samples.txt file for updating, default is to overwrite er_samples.txt`
"""
samp_out="er_samples.txt"
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 '-f' in sys.argv:
ind=sys.argv.index("-f")
samp_file=sys.argv[ind+1]
else:
print "must specify -f samp_file"
sys.exit()
samp_file=dir_path+'/'+samp_file
Samps=[]
if '-Fsa' in sys.argv:
ind=sys.argv.index("-Fsa")
samp_out=dir_path+'/'+sys.argv[ind+1]
Samps,file_type=pmag.magic_read(samp_out)
print len(Samps), ' read in from: ',samp_out
input=open(samp_file,"rU").readlines()
keys=input[0].replace('\n','').split(',')
ErSamples,samples=[],[]
for line in input[1:]:
ODPRec,SampRec={},{}
rec=line.replace('\n','').split(',')
for k in range(len(keys)):ODPRec[keys[k]]=rec[k]
SampRec['er_sample_alternatives']=ODPRec['Text Id']
label=ODPRec['Label Id'].split()
if len(label)>1 and 'PMAG' not in label[0]:
interval=label[1].split('/')[0]
pieces=label[0].split('-')
core=pieces[2]
while len(core)<4:core='0'+core
SampRec['magic_method_codes']='FS-C-DRILL-IODP:FS-SS-C:SO-V'
SampRec['er_sample_name']=pieces[0]+'-'+pieces[1]+'-'+core+'-'+pieces[3]+'-'+pieces[4]+'-'+interval
SampRec['er_site_name']=SampRec['er_sample_name']
pieces=SampRec['er_sample_name'].split('-')
SampRec['er_expedition_name']=pieces[0]
SampRec['er_location_name']=pieces[1]
SampRec['er_citation_names']="This study"
SampRec['sample_dip']="0"
SampRec['sample_azimuth']="0"
SampRec['sample_core_depth']=ODPRec['Top Depth (m)']
dates=ODPRec['Sample Date Logged'].split()
mmddyy=dates[0].split('/')
yyyy='20'+mmddyy[2]
mm=mmddyy[0]
if len(mm)==1:mm='0'+mm
dd=mmddyy[1]
if len(dd)==1:dd='0'+dd
date=yyyy+':'+mm+':'+dd+':'+dates[1]+":00.00"
SampRec['sample_date']=date
ErSamples.append(SampRec)
samples.append(SampRec['er_sample_name'])
if len(Samps)>0:
for samp in Samps:
if samp['er_sample_name'] not in samples:
ErSamples.append(samp)
Recs,keys=pmag.fillkeys(ErSamples)
pmag.magic_write(samp_out,Recs,'er_samples')
print('sample information written to er_samples.txt')
def main():
"""
NAME
pt_rot.py
DESCRIPTION
rotates pt according to specified age and plate
SYNTAX
pt_rot.py [command line options]
OPTIONS
-h prints help and quits
-f file with lon lat plate age Dplate as space delimited input
Dplate is the destination plate coordinates desires
- default is "fixed south africa"
Dplate should be one of: [nwaf, neaf,saf,aus, eur, ind, sam, ant, grn, nam]
-ff file Efile, file has lat lon data file and Efile has sequential rotation poles: Elat Elon Omega
-F OFILE, output pmag_results formatted file with rotated points stored in vgp_lon, vgp_lat
default is to print out rotated lon, lat to standard output
"""
dir_path='.'
PTS=[]
ResRecs=[]
ofile=""
Dplates=['nwaf', 'neaf','saf','aus', 'eur', 'ind', 'sam', 'ant', 'grn', 'nam']
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 '-F' in sys.argv:
ind = sys.argv.index('-F')
ofile=dir_path+'/'+sys.argv[ind+1]
if '-f' in sys.argv:
ind = sys.argv.index('-f')
file=dir_path+'/'+sys.argv[ind+1]
f=open(file,'rU')
data=f.readlines()
elif '-ff' in sys.argv:
ind = sys.argv.index('-ff')
file=dir_path+'/'+sys.argv[ind+1]
f=open(file,'rU')
data=f.readlines()
Efile=dir_path+'/'+sys.argv[ind+2]
f=open(Efile,'rU')
edata=f.readlines()
Poles=[]
for p in edata:
rec=p.split()
pole=[float(rec[0]),float(rec[1]),float(rec[2])]
Poles.append(pole)
else:
data=sys.stdin.readlines()
for line in data:
PtRec={}
rec=line.split()
PtRec['site_lat']=rec[0]
PtRec['site_lon']=rec[1]
if '-ff' in sys.argv:
pt_lat,pt_lon=float(rec[0]),float(rec[1])
for pole in Poles:
ptrot= pmag.PTrot(pole,[pt_lat],[pt_lon])
pt_lat=ptrot[0][0]
pt_lon=ptrot[1][0]
if ofile=="":
print ptrot[1][0], ptrot[0][0]
else:
ResRec={'vgp_lat': '%7.1f'%(ptrot[0][0]),'vgp_lon':'%7.1f'%( ptrot[1][0])}
ResRecs.append(ResRec)
else:
PtRec['cont']=rec[2]
if PtRec['cont']=='af':PtRec['cont']='saf' # use fixed south africa
PtRec['age']=rec[3]
if len(rec)>4:
PtRec['dcont']=rec[4]
PTS.append(PtRec)
if '-ff' not in sys.argv:
for pt in PTS:
pole='not specified'
pt_lat=float(pt['site_lat'])
pt_lon=float(pt['site_lon'])
age=float(pt['age'])
ptrot=[[pt_lat],[pt_lon]]
if pt['cont']=='ib':
pole=frp.get_pole(pt['cont'],age)
ptrot= pmag.PTrot(pole,[pt_lat],[pt_lon])
pt_lat=ptrot[0][0]
pt_lon=ptrot[1][0]
pt['cont']='eur'
if pt['cont']!='saf':
pole1=frp.get_pole(pt['cont'],age)
ptrot= pmag.PTrot(pole1,[pt_lat],[pt_lon])
if 'dcont' in pt.keys():
pt_lat=ptrot[0][0]
pt_lon=ptrot[1][0]
pole=frp.get_pole(pt['dcont'],age)
pole[2]=-pole[2]
ptrot= pmag.PTrot(pole,[pt_lat],[pt_lon])
if ofile=="":
print ptrot[1][0], ptrot[0][0]
else:
ResRec={'vgp_lat': '%7.1f'%(ptrot[0][0]),'vgp_lon':'%7.1f'%( ptrot[1][0])}
ResRecs.append(ResRec)
else:
if 'dcont' in pt.keys():
pole=frp.get_pole(pt['dcont'],age)
pole[2]=-pole[2]
ptrot= pmag.PTrot(pole,[pt_lat],[pt_lon])
if ofile=="":
print ptrot[1][0], ptrot[0][0]
else:
ResRec={'vgp_lat': '%7.1f'%(ptrot[0][0]),'vgp_lon':'%7.1f'%( ptrot[1][0])}
ResRecs.append(ResRec)
else:
if ofile=="":
print ptrot[1][0], ptrot[0][0]
else:
ResRec={'vgp_lat': '%7.1f'%(ptrot[0][0]),'vgp_lon':'%7.1f'%( ptrot[1][0])}
ResRecs.append(ResRec)
if len(ResRecs)>0:
pmag.magic_write(ofile,ResRecs,'pmag_results')
def main():
"""
NAME
download_magic.py
DESCRIPTION
unpacks a magic formatted smartbook .txt file from the MagIC database into the
tab delimited MagIC format txt files for use with the MagIC-Py programs.
SYNTAX
download_magic.py command line options]
INPUT
takes either the upload.txt file created by upload_magic.py or the file
exported by the MagIC v2.2 console software (downloaded from the MagIC database
or output by the Console on your PC).
OPTIONS
-h prints help message and quits
-i allows interactive entry of filename
-f FILE specifies input file name
"""
dir_path='.'
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-i' in sys.argv:
file=raw_input("Magic txt file for unpacking? ")
elif '-f' in sys.argv:
ind=sys.argv.index("-f")
file=sys.argv[ind+1]
else:
print main.__doc__
sys.exit()
f=open(dir_path+'/'+file,'rU')
File=f.readlines()
LN=0
type_list=[]
filenum=0
while LN<len(File)-1:
line=File[LN]
file_type=line.split('\t')[1]
file_type=file_type.lower()
if file_type=='delimited':file_type=Input[skip].split('\t')[2]
if file_type[-1]=="\n":file_type=file_type[:-1]
print 'working on: ',repr(file_type)
if file_type not in type_list:
type_list.append(file_type)
else:
filenum+=1
LN+=1
line=File[LN]
keys=line.replace('\n','').split('\t')
LN+=1
Recs=[]
while LN<len(File):
line=File[LN]
if line[:4]==">>>>" and len(Recs)>0:
if filenum==0:
outfile=dir_path+"/"+file_type.strip()+'.txt'
else:
outfile=dir_path+"/"+file_type.strip()+'_'+str(filenum)+'.txt'
NewRecs=[]
for rec in Recs:
if 'magic_method_codes' in rec.keys():
meths=rec['magic_method_codes'].split(":")
if len(meths)>0:
methods=""
for meth in meths: methods=methods+meth.strip()+":" # get rid of nasty spaces!!!!!!
rec['magic_method_codes']=methods[:-1]
NewRecs.append(rec)
pmag.magic_write(outfile,Recs,file_type)
print file_type," data put in ",outfile
if file_type =='pmag_specimens' and 'magic_measurements.txt' in File and 'measurement_step_min' in File and 'measurement_step_max' in File: # sort out zeq_specimens and thellier_specimens
os.system('mk_redo.py')
os.system('zeq_magic_redo.py')
os.system('thellier_magic_redo.py')
type_list.append('zeq_specimens')
type_list.append('thellier_specimens')
Recs=[]
LN+=1
break
else:
rec=line.split('\t')
Rec={}
if len(rec)==len(keys):
for k in range(len(rec)):
Rec[keys[k]]=rec[k]
Recs.append(Rec)
else:
print 'WARNING: problem in file with line: '
print line
print 'skipping....'
LN+=1
if len(Recs)>0:
if filenum==0:
outfile=dir_path+"/"+file_type.strip()+'.txt'
else:
outfile=dir_path+"/"+file_type.strip()+'_'+str(filenum)+'.txt'
NewRecs=[]
for rec in Recs:
if 'magic_method_codes' in rec.keys():
meths=rec['magic_method_codes'].split(":")
if len(meths)>0:
methods=""
for meth in meths: methods=methods+meth.strip()+":" # get rid of nasty spaces!!!!!!
rec['magic_method_codes']=methods[:-1]
NewRecs.append(rec)
pmag.magic_write(outfile,Recs,file_type)
print file_type," data put in ",outfile
# look through locations table and create separate directories for each location
locs,locnum=[],1
if 'er_locations' in type_list:
locs,file_type=pmag.magic_read(dir_path+'/er_locations.txt')
if len(locs)>0: # at least one location
for loc in locs:
print 'location_'+str(locnum)+": ",loc['er_location_name']
lpath=dir_path+'/Location_'+str(locnum)
locnum+=1
try:
os.mkdir(lpath)
except:
print 'directory ',lpath,' already exists - overwrite everything [y/n]?'
ans=raw_input()
if ans=='n':sys.exit()
for f in type_list:
print 'unpacking: ',dir_path+'/'+f+'.txt'
recs,file_type=pmag.magic_read(dir_path+'/'+f+'.txt')
print len(recs),' read in'
if 'results' not in f:
lrecs=pmag.get_dictitem(recs,'er_location_name',loc['er_location_name'],'T')
if len(lrecs)>0:
pmag.magic_write(lpath+'/'+f+'.txt',lrecs,file_type)
print len(lrecs),' stored in ',lpath+'/'+f+'.txt'
else:
lrecs=pmag.get_dictitem(recs,'er_location_names',loc['er_location_name'],'T')
if len(lrecs)>0:
pmag.magic_write(lpath+'/'+f+'.txt',lrecs,file_type)
print len(lrecs),' stored in ',lpath+'/'+f+'.txt'
def main():
"""
NAME
ODP_srm_magic.py
DESCRIPTION
converts ODP measurement format files to magic_measurements format files
SYNTAX
ODP_srm_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsa FILE: specify output er_sample.txt file, default is er_sample.txt
-A : don't average replicate measurements
INPUT
put data from a single core into a directory. depths will be below core top
"""
#
#
version_num=pmag.get_version()
meas_file='magic_measurements.txt'
samp_file='er_samples.txt'
ErSpecs,ErSamps,ErSites,ErLocs,ErCits=[],[],[],[],[]
MagRecs=[]
citation="This study"
dir_path,demag='.','NRM'
args=sys.argv
noave=0,
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-A" in args: noave=1
if '-F' in args:
ind=args.index("-F")
meas_file=args[ind+1]
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file=args[ind+1]
if '-LP' in args:
ind=args.index("-LP")
codelist=args[ind+1]
codes=codelist.split(':')
if "AF" in codes:
demag='AF'
if'-dc' not in args: methcode="LT-AF-Z"
if'-dc' in args: methcode="LT-AF-I"
if "T" in codes:
demag="T"
if '-dc' not in args: methcode="LT-T-Z"
if '-dc' in args: methcode="LT-T-I"
if "I" in codes:
methcode="LP-IRM"
if "S" in codes:
demag="S"
methcode="LP-PI-TRM:LP-PI-ALT-AFARM"
trm_labfield=labfield
ans=raw_input("DC lab field for ARM step: [50uT] ")
if ans=="":
arm_labfield=50e-6
else:
arm_labfield=float(ans)*1e-6
ans=raw_input("temperature for total trm step: [600 C] ")
if ans=="":
trm_peakT=600+273 # convert to kelvin
else:
trm_peakT=float(ans)+273 # convert to kelvin
if "G" in codes: methcode="LT-AF-G"
if "D" in codes: methcode="LT-AF-D"
if "TRM" in codes:
demag="T"
trm=1
if demag=="T" and "ANI" in codes:
methcode="LP-AN-TRM"
if demag=="AF" and "ANI" in codes:
methcode="LP-AN-ARM"
if labfield==0: labfield=50e-6
if peakfield==0: peakfield=.180
samp_file=dir_path+'/'+samp_file
meas_file=dir_path+'/'+meas_file
filelist=os.listdir(dir_path) # read in list of files to import
specimens,samples,sites=[],[],[]
MagRecs,SpecRecs,SampRecs=[],[],[]
for file in filelist: # parse each file
if file[-3:].lower()=='srm':
print 'processing: ',file
Nfo=file.split('_')[0].split('-')
try:
sect=int(Nfo[3][:-1])
except:
sect=1
input=open(file,'rU').readlines()
MagRec,SpecRec,SampRec={},{},{}
alt_spec,treatment_type,treatment_value,user="","","",""
inst="ODP-SRM"
SampRec['sample_azimuth']='0'
SampRec['sample_dip']='0'
SampRec['magic_method_code']='FS-C-DRILL-IODP:SP-SS-C'
MagRec['er_analyst_mail_names']=user
MagRec['magic_method_codes']='LT-NO'
MagRec['magic_software_packages']=version_num
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["treatment_ac_field"]='0'
MagRec["treatment_dc_field"]='0'
MagRec["treatment_dc_field_phi"]='0'
MagRec["treatment_dc_field_theta"]='0'
MagRec["measurement_flag"]='g' # assume all data are "good"
MagRec["measurement_standard"]='u' # assume all data are "good"
MagRec["measurement_csd"]='' # set csd to blank
SpecRec['er_specimen_alternatives']=alt_spec
vol=7e-6 # assume 7 cc samples
datestamp=input[1].split() # date time is second line of file
mmddyy=datestamp[0].split('/') # break into month day year
date=mmddyy[2]+':'+mmddyy[0]+":"+mmddyy[1] +':' +datestamp[1]
MagRec["measurement_date"]=date
treatment_value,inst="","ODP-SRM"
k=0
while 1:
fields= input[k].replace('\n','').split("=")
if 'treatment_type' in fields[0]:
if "Alternating Frequency Demagnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst=inst+':ODP-DTECH' # measured on shipboard AF DTECH D2000
if "treatment_value" in fields[0]:
value=fields[1]
if value!=" ":
treatment_value=float(value)*1e-3
MagRec["treatment_ac_field"]='%8.3e'%(treatment_value) # AF demag in treat mT => T
if 'user' in fields[0]:
user=fields[-1]
MagRec["er_analyst_mail_names"]=user
MagRec["measurement_standard"]='u' # assume all data are "good"
if 'sample_area' in fields[0]: vol=float(fields[1])*1e-6 # takes volume (cc) and converts to m^3
if 'run_number' in fields[0]:
MagRec['external_database_ids']=fields[1] # run number is the LIMS measurement number
MagRec['external_database_names']='LIMS'
k+=1
if input[k][0:7]=='<MULTI>':
break
while 1:
k+=1
line = input[k]
if line[0:5]=='<RAW>':
break
treatment_value=""
rec=line.replace('\n','').split(',') # list of data
if len(rec)>2:
MeasRec,SampRec={},{'core_depth':'0','er_sample_name':'0','er_site_name':'0','er_location_name':'location'}
for key in MagRec.keys():MeasRec[key]=MagRec[key]
for item in rec:
items=item.split('=')
if 'demag_level' in items[0]:
treat= float(items[1])
if treat!=0:
MeasRec['magic_method_codes']='LT-AF-Z'
inst=inst+':ODP-SRM-AF'
MeasRec["treatment_ac_field"]='%8.3e'%(treat*1e-3) # AF demag in treat mT => T
if 'inclination_w_tray_w_bkgrd' in items[0]: MeasRec['measurement_inc']=items[1]
if 'declination_w_tray_w_bkgrd' in items[0]: MeasRec['measurement_dec']=items[1]
if 'intensity_w_tray_w_bkgrd' in items[0]: MeasRec['measurement_magn_moment']='%8.3e'%(float(items[1])*vol) # convert intensity from A/m to Am^2 using vol
MeasRec['magic_instrument_codes']=inst
if 'offset' in items[0]:
depth='%7.3f'%(float(sect-1)*1.5+float(items[1]))
SampRec['core_depth']=depth
MeasRec['er_specimen_name']=depth
MeasRec['er_sample_name']=depth
MeasRec['er_site_name']=depth
MeasRec['er_location_name']='location'
SampRec['er_sample_name']=depth
SampRec['er_site_name']=depth
SampRec['er_location_name']='location'
MeasRec['measurement_number']='1'
SampRecs.append(SampRec)
MagRecs.append(MeasRec)
pmag.magic_write(samp_file,SampRecs,'er_samples')
print 'samples stored in ',samp_file
Fixed=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(meas_file,Fixed,'magic_measurements')
print 'data stored in ',meas_file
def main():
"""
NAME
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
