"""

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 ltauxe@ucsd.edu 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')