"""

NAME

IODP_dscr_magic.py

DESCRIPTION

converts ODP LIMS discrete sample format files to magic_measurements format files

SYNTAX

IODP_descr_magic.py [command line options]

OPTIONS

-h: prints the help message and quits.

-f FILE: specify input .csv file, default is all in directory

-F FILE: specify output measurements file, default is magic_measurements.txt

-A : don't average replicate measurements

INPUTS

IODP discrete sample .csv file format exported from LIMS database

"""

#

# initialize defaults

version_num=pmag.get_version()

meas_file='magic_measurements.txt'

csv_file=''

MagRecs,Specs=[],[]

citation="This study"

dir_path,demag='.','NRM'

args=sys.argv

noave=0

# get command line args

if command_line:

if '-WD' in args:

ind=args.index("-WD")

dir_path=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

if "-h" in args:

print main.__doc__

return False

if "-A" in args: noave=1

if '-f' in args:

ind=args.index("-f")

csv_file=args[ind+1]

if '-F' in args:

ind=args.index("-F")

meas_file=args[ind+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 # rename dir_path after input_dir_path is set

noave = kwargs.get('noave', 0) # default (0) is DO average

csv_file = kwargs.get('csv_file', '')

meas_file = kwargs.get('meas_file', 'magic_measurements.txt')

# format variables

meas_file= os.path.join(output_dir_path, meas_file)

if csv_file=="":

filelist=os.listdir(input_dir_path) # read in list of files to import

else:

csv_file = os.path.join(input_dir_path, csv_file)

filelist=[csv_file]

# parsing the data

file_found = False

for file in filelist: # parse each file

if file[-3:].lower()=='csv':

file_found = True

print 'processing: ',file

input=open(file,'rU').readlines()

keys=input[0].replace('\n','').split(',') # splits on underscores

interval_key="Offset (cm)"

demag_key="Demag level (mT)"

offline_demag_key="Treatment Value (mT or °C)"

offline_treatment_type="Treatment type"

run_key="Test No."

if "Inclination background + tray corrected (deg)" in keys: inc_key="Inclination background + tray corrected (deg)"

if "Inclination background & tray corrected (deg)" in keys: inc_key="Inclination background & tray corrected (deg)"

if "Declination background + tray corrected (deg)" in keys: dec_key="Declination background + tray corrected (deg)"

if "Declination background & tray corrected (deg)" in keys: dec_key="Declination background & tray corrected (deg)"

if "Intensity background + tray corrected (A/m)" in keys: int_key="Intensity background + tray corrected (A/m)"

if "Intensity background & tray corrected (A/m)" in keys: int_key="Intensity background & tray corrected (A/m)"

type="Type"

sect_key="Sect"

half_key="A/W"

# need to add volume_key to LORE format!

if "Sample volume (cm^3)" in keys:volume_key="Sample volume (cm^3)"

if "Sample volume (cc)" in keys:volume_key="Sample volume (cc)"

if "Sample volume (cm³)" in keys:volume_key="Sample volume (cm³)"

for line in input[1:]:

InRec={}

for k in range(len(keys)):InRec[keys[k]]=line.split(',')[k]

inst="IODP-SRM"

MagRec={}

expedition=InRec['Exp']

location=InRec['Site']+InRec['Hole']

offsets=InRec[interval_key].split('.') # maintain consistency with er_samples convention of using top interval

if len(offsets)==1:

offset=int(offsets[0])

else:

offset=int(offsets[0])-1

#interval=str(offset+1)# maintain consistency with er_samples convention of using top interval

interval=str(offset)# maintain consistency with er_samples convention of using top interval

specimen=expedition+'-'+location+'-'+InRec['Core']+InRec[type]+"-"+InRec[sect_key]+'_'+InRec[half_key]+'_'+interval

if specimen not in Specs:Specs.append(specimen)

MagRec['er_expedition_name']=expedition

MagRec['er_location_name']=location

MagRec['er_site_name']=specimen

MagRec['er_citation_names']=citation

MagRec['er_specimen_name']=specimen

MagRec['er_sample_name']=specimen

MagRec['er_site_name']=specimen

# set up measurement record - default is NRM

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"]='0' # assume all data are "good"

volume=InRec[volume_key]

MagRec["magic_method_codes"]='LT-NO'

sort_by='treatment_ac_field' # set default to AF demag

if InRec[demag_key]!="0":

MagRec['magic_method_codes'] = 'LT-AF-Z'

inst=inst+':IODP-SRM-AF' # measured on shipboard in-line 2G AF

treatment_value=float(InRec[demag_key].strip('"'))*1e-3 # convert mT => T

if sort_by =="treatment_ac_field":

MagRec["treatment_ac_field"]=treatment_value # AF demag in treat mT => T

else:

MagRec["treatment_ac_field"]=str(treatment_value)# AF demag in treat mT => T

elif offline_treatment_type in InRec.keys() and InRec[offline_treatment_type]!="":

if "Lowrie" in InRec['Comments']:

MagRec['magic_method_codes'] = 'LP-IRM-3D'

treatment_value=float(InRec[offline_demag_key].strip('"'))+273. # convert C => K

MagRec["treatment_temp"]=treatment_value

MagRec["treatment_ac_field"]="0"

sort_by='treatment_temp'

elif 'Isothermal' in InRec[offline_treatment_type]:

MagRec['magic_method_codes'] = 'LT-IRM'

treatment_value=float(InRec[offline_demag_key].strip('"'))*1e-3 # convert mT => T

MagRec["treatment_dc_field"]=treatment_value

MagRec["treatment_ac_field"]="0"

sort_by='treatment_dc_field'

MagRec["measurement_standard"]='u' # assume all data are "good"

vol=float(volume)*1e-6 # convert from cc to m^3

if run_key in InRec.keys():

run_number=InRec[run_key]

MagRec['external_database_ids']=run_number

MagRec['external_database_names']='LIMS'

else:

MagRec['external_database_ids']=""

MagRec['external_database_names']=''

MagRec['measurement_description']='sample orientation: '+InRec['Sample orientation']

MagRec['measurement_inc']=InRec[inc_key].strip('"')

MagRec['measurement_dec']=InRec[dec_key].strip('"')

intens= InRec[int_key].strip('"')

MagRec['measurement_magn_moment']='%8.3e'%(float(intens)*vol) # convert intensity from A/m to Am^2 using vol

MagRec['magic_instrument_codes']=inst

MagRec['measurement_number']='1'

MagRec['measurement_positions']=''

MagRecs.append(MagRec)

if not file_found:

print "No .csv files were found"

return False, "No .csv files were found"

MagOuts=[]

for spec in Specs:

Speclist=pmag.get_dictitem(MagRecs,'er_specimen_name',spec,'T')

sorted=pmag.sort_diclist(Speclist,sort_by)

for rec in sorted:

for key in rec.keys(): rec[key]=str(rec[key])

MagOuts.append(rec)

Fixed=pmag.measurements_methods(MagOuts,noave)

Out,keys=pmag.fillkeys(Fixed)

if pmag.magic_write(meas_file,Out,'magic_measurements'):

print 'data stored in ',meas_file

return True, meas_file

else:

print 'no data found. bad magfile?'