"""

NAME

nrm_specimens_magic.py

DESCRIPTION

converts NRM data in a magic_measurements type file to

geographic and tilt corrected data in a pmag_specimens type file

SYNTAX

nrm_specimens_magic.py [-h][command line options]

OPTIONS:

-h prints the help message and quits

-f MFILE: specify input file

-fsa SFILE: specify er_samples format file [with orientations]

-F PFILE: specify output file

-A do not average replicate measurements

-crd [g, t]: specify coordinate system ([g]eographic or [t]ilt adjusted)

NB: you must have the SFILE in this directory

DEFAULTS

MFILE: magic_measurements.txt

PFILE: nrm_specimens.txt

SFILE: er_samples.txt

coord: specimen

average replicate measurements?: YES

"""

#

# define some variables

#

beg,end,pole,geo,tilt,askave,save=0,0,[],0,0,0,0

samp_file=1

args=sys.argv

geo,tilt,orient=0,0,0

doave=1

user,comment,doave,coord="","",1,""

meas_file="magic_measurements.txt"

pmag_file="nrm_specimens.txt"

samp_file="er_samples.txt"

if "-h" in args:

print main.__doc__

sys.exit()

if "-A" in args: doave=0

if "-f" in args:

ind=args.index("-f")

meas_file=sys.argv[ind+1]

if "-F" in args:

ind=args.index("-F")

pmag_file=sys.argv[ind+1]

speclist=[]

if "-fsa" in args:

ind=args.index("-fsa")

samp_file=sys.argv[ind+1]

if "-crd" in args:

ind=args.index("-crd")

coord=sys.argv[ind+1]

if coord=="g":

geo,orient=1,1

if coord=="t":

tilt,orient,geo=1,1,1

#

# read in data

if samp_file!="":

samp_data,file_type=pmag.magic_read(samp_file)

if file_type != 'er_samples':

print file_type

print "This is not a valid er_samples file "

sys.exit()

else: print samp_file,' read in with ',len(samp_data),' records'

else:

print 'no orientations - will create file in specimen coordinates'

geo,tilt,orient=0,0,0

#

#

meas_data,file_type=pmag.magic_read(meas_file)

if file_type != 'magic_measurements':

print file_type

print file_type,"This is not a valid magic_measurements file "

sys.exit()

#

if orient==1:

# set orientation priorities

SO_methods=[]

orientation_priorities={'0':'SO-SUN','1':'SO-GPS-DIFF','2':'SO-SIGHT-BACK','3':'SO-CMD-NORTH','4':'SO-MAG'}

for rec in samp_data:

if "magic_method_codes" in rec:

methlist=rec["magic_method_codes"]

for meth in methlist.split(":"):

if "SO" in meth and "SO-POM" not in meth.strip():

if meth.strip() not in SO_methods: SO_methods.append(meth.strip())

#

# sort the sample names

#

sids=pmag.get_specs(meas_data)

#

#

PmagSpecRecs=[]

for s in sids:

skip=0

recnum=0

PmagSpecRec={}

PmagSpecRec["er_analyst_mail_names"]=user

method_codes,inst_code=[],""

# find the data from the meas_data file for this sample

#

# collect info for the PmagSpecRec dictionary

#

meas_meth=[]

for rec in meas_data: # copy of vital stats to PmagSpecRec from first spec record

if rec["er_specimen_name"]==s:

PmagSpecRec["er_specimen_name"]=s

PmagSpecRec["er_sample_name"]=rec["er_sample_name"]

PmagSpecRec["er_site_name"]=rec["er_site_name"]

PmagSpecRec["er_location_name"]=rec["er_location_name"]

PmagSpecRec["er_citation_names"]="This study"

PmagSpecRec["magic_instrument_codes"]=""

if "magic_experiment_name" not in rec.keys():

rec["magic_experiment_name"]=""

if "magic_instrument_codes" not in rec.keys():

rec["magic_instrument_codes"]=""

else:

PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"]

if len(rec["magic_instrument_codes"]) > len(inst_code):

inst_code=rec["magic_instrument_codes"]

PmagSpecRec["magic_instrument_codes"]=inst_code # copy over instruments

break

#

# now check for correct method labels for all measurements

#

nrm_data=[]

for meas_rec in meas_data:

if meas_rec['er_specimen_name']==PmagSpecRec['er_specimen_name']:

meths=meas_rec["magic_method_codes"].split(":")

for meth in meths:

if meth.strip() not in meas_meth:meas_meth.append(meth)

if "LT-NO" in meas_meth:nrm_data.append(meas_rec)

#

data,units=pmag.find_dmag_rec(s,nrm_data)

#

datablock=data

#

# find replicate measurements at NRM step and average them

#

Specs=[]

if doave==1:

step_meth,avedata=pmag.vspec(data)

if len(avedata) != len(datablock):

method_codes.append("DE-VM")

SpecRec=avedata[0]

print 'averaging data '

else: SpecRec=data[0]

Specs.append(SpecRec)

else:

for spec in data:Specs.append(spec)

for SpecRec in Specs:

#

# do geo or stratigraphic correction now

#

if geo==1:

#

# find top priority orientation method

redo,p=1,0

if len(SO_methods)<=1:

az_type=SO_methods[0]

orient=pmag.find_samp_rec(PmagSpecRec["er_sample_name"],samp_data,az_type)

if orient["sample_azimuth"] !="": method_codes.append(az_type)

redo=0

while redo==1:

if p>=len(orientation_priorities):

print "no orientation data for ",s

skip,redo=1,0

break

az_type=orientation_priorities[str(p)]

orient=pmag.find_samp_rec(PmagSpecRec["er_sample_name"],samp_data,az_type)

if orient["sample_azimuth"] !="":

method_codes.append(az_type.strip())

redo=0

elif orient["sample_azimuth"] =="":

p+=1

#

# if stratigraphic selected, get stratigraphic correction

#

if skip==0 and orient["sample_azimuth"]!="" and orient["sample_dip"]!="":

d_geo,i_geo=pmag.dogeo(SpecRec[1],SpecRec[2],orient["sample_azimuth"],orient["sample_dip"])

SpecRec[1]=d_geo

SpecRec[2]=i_geo

if tilt==1 and "sample_bed_dip" in orient.keys() and orient['sample_bed_dip']!="":

d_tilt,i_tilt=pmag.dotilt(d_geo,i_geo,orient["sample_bed_dip_direction"],orient["sample_bed_dip"])

SpecRec[1]=d_tilt

SpecRec[2]=i_tilt

if skip==0:

PmagSpecRec["specimen_dec"]='%7.1f ' %(SpecRec[1])

PmagSpecRec["specimen_inc"]='%7.1f ' %(SpecRec[2])

if geo==1 and tilt==0:PmagSpecRec["specimen_tilt_correction"]='0'

if geo==1 and tilt==1: PmagSpecRec["specimen_tilt_correction"]='100'

if geo==0 and tilt==0: PmagSpecRec["specimen_tilt_correction"]='-1'

PmagSpecRec["specimen_direction_type"]='l'

PmagSpecRec["magic_method_codes"]="LT-NO"

if len(method_codes) != 0:

methstring=""

for meth in method_codes:

methstring=methstring+ ":" +meth

PmagSpecRec["magic_method_codes"]=methstring[1:]

PmagSpecRec["specimen_description"]="NRM data"

PmagSpecRecs.append(PmagSpecRec)

pmag.magic_write(pmag_file,PmagSpecRecs,'pmag_specimens')