"""

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: