"""

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')