"""

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.) # 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!"