"""

NAME

zeq_magic_redo.py

DESCRIPTION

Calculate principal components through demagnetization data using bounds and calculation type stored in "redo" file

SYNTAX

zeq_magic_redo.py [command line options]

OPTIONS

-h prints help message

-usr USER: identify user, default is ""

-f: specify input file, default is magic_measurements.txt

-F: specify output file, default is zeq_specimens.txt

-fre REDO: specify redo file, default is "zeq_redo"

-fsa SAMPFILE: specify er_samples format file, default is "er_samples.txt"

-A : don't average replicate measurements, default is yes

-crd [s,g,t] :

specify coordinate system [s,g,t] [default is specimen coordinates]

are specimen, geographic, and tilt corrected respectively

NB: you must have a SAMPFILE in this directory to rotate from specimen coordinates

-leg: attaches "Recalculated from original measurements; supercedes published results. " to comment field

INPUTS

zeq_redo format file is:

specimen_name calculation_type[DE-BFL,DE-BFL-A,DE-BFL-O,DE-BFP,DE-FM] step_min step_max component_name[A,B,C]

"""

dir_path='.'

INCL=["LT-NO","LT-AF-Z","LT-T-Z","LT-M-Z"] # looking for demag data

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

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

geo,tilt=0,0

version_num=pmag.get_version()

args=sys.argv

if '-WD' in args:

ind=args.index('-WD')

dir_path=args[ind+1]

meas_file,pmag_file,mk_file= dir_path+"/"+"magic_measurements.txt",dir_path+"/"+"zeq_specimens.txt",dir_path+"/"+"zeq_redo"

samp_file,coord=dir_path+"/"+"er_samples.txt",""

if "-h" in args:

print main.__doc__

sys.exit()

if "-usr" in args:

ind=args.index("-usr")

user=sys.argv[ind+1]

if "-A" in args:doave=0

if "-leg" in args: comment="Recalculated from original measurements; supercedes published results. "

if "-f" in args:

ind=args.index("-f")

meas_file=dir_path+'/'+sys.argv[ind+1]

if "-F" in args:

ind=args.index("-F")

pmag_file=dir_path+'/'+sys.argv[ind+1]

if "-fre" in args:

ind=args.index("-fre")

mk_file=dir_path+"/"+args[ind+1]

try:

mk_f=open(mk_file,'rU')

except:

print "Bad redo file"

sys.exit()

mkspec,skipped=[],[]

speclist=[]

for line in mk_f.readlines():

tmp=line.split()

mkspec.append(tmp)

speclist.append(tmp[0])

if "-fsa" in args:

ind=args.index("-fsa")

samp_file=dir_path+'/'+sys.argv[ind+1]

if "-crd" in args:

ind=args.index("-crd")

coord=sys.argv[ind+1]

if coord=="g":geo,tilt=1,0

if coord=="t":geo,tilt=1,1

#

# now get down to bidness

if geo==1:

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()

#

#

#

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()

#

# sort the specimen names

#

k = 0

print 'Processing ',len(speclist), ' specimens - please wait'

PmagSpecs=[]

while k < len(speclist):

s=speclist[k]

recnum=0

PmagSpecRec={}

method_codes,inst_codes=[],[]

# find the data from the meas_data file for this sample

#

# collect info for the PmagSpecRec dictionary

#

meas_meth=[]

spec=pmag.get_dictitem(meas_data,'er_specimen_name',s,'T')

if len(spec)==0:

print 'no data found for specimen: ',s

print 'delete from zeq_redo input file...., then try again'

else:

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

skip=1

methods=rec["magic_method_codes"].split(":")

if len(set(methods) & set(INCL))>0:

PmagSpecRec["er_analyst_mail_names"]=user

PmagSpecRec["magic_software_packages"]=version_num

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"]

if "er_expedition_name" in rec.keys():PmagSpecRec["er_expedition_name"]=rec["er_expedition_name"]

PmagSpecRec["er_citation_names"]="This study"

if "magic_experiment_name" not in rec.keys(): rec["magic_experiment_name"]=""

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

if "magic_instrument_codes" not in rec.keys(): rec["magic_instrument_codes"]=""

inst=rec['magic_instrument_codes'].split(":")

for I in inst:

if I not in inst_codes: # copy over instruments

inst_codes.append(I)

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

for meth in meths:

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

if "LP-DIR-AF" in meas_meth or "LT-AF-Z" in meas_meth:

PmagSpecRec["measurement_step_unit"]="T"

if "LP-DIR-AF" not in method_codes:method_codes.append("LP-DIR-AF")

if "LP-DIR-T" in meas_meth or "LT-T-Z" in meas_meth:

PmagSpecRec["measurement_step_unit"]="K"

if "LP-DIR-T" not in method_codes:method_codes.append("LP-DIR-T")

if "LP-DIR-M" in meas_meth or "LT-M-Z" in meas_meth:

PmagSpecRec["measurement_step_unit"]="J"

if "LP-DIR-M" not in method_codes:method_codes.append("LP-DIR-M")

#

#

datablock,units=pmag.find_dmag_rec(s,spec) # fish out the demag data for this specimen

#

if len(datablock) <2 or s not in speclist :

k+=1

# print 'skipping ', s,len(datablock)

else:

#

# find replicate measurements at given treatment step and average them

#

# step_meth,avedata=pmag.vspec(data)

#

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

# if doave==1:

# method_codes.append("DE-VM")

# datablock=avedata

#

# do geo or stratigraphic correction now

#

if geo==1 or tilt==1:

# find top priority orientation method

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

if az_type not in method_codes:method_codes.append(az_type)

#

# if tilt selected, get stratigraphic correction

#

tiltblock,geoblock=[],[]

for rec in datablock:

if "sample_azimuth" in orient.keys() and orient["sample_azimuth"]!="":

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

geoblock.append([rec[0],d_geo,i_geo,rec[3],rec[4],rec[5]])

if tilt==1 and "sample_bed_dip_direction" in orient.keys():

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

tiltblock.append([rec[0],d_tilt,i_tilt,rec[3],rec[4],rec[5]])

elif tilt==1:

if PmagSpecRec["er_sample_name"] not in skipped:

print 'no tilt correction for ', PmagSpecRec["er_sample_name"],' skipping....'

skipped.append(PmagSpecRec["er_sample_name"])

else:

if PmagSpecRec["er_sample_name"] not in skipped:

print 'no geographic correction for ', PmagSpecRec["er_sample_name"],' skipping....'

skipped.append(PmagSpecRec["er_sample_name"])

#

# get beg_pca, end_pca, pca

if PmagSpecRec['er_sample_name'] not in skipped:

compnum=-1

for spec in mkspec:

if spec[0]==s:

CompRec={}

for key in PmagSpecRec.keys():CompRec[key]=PmagSpecRec[key]

compnum+=1

calculation_type=spec[1]

beg=float(spec[2])

end=float(spec[3])

if len(spec)>4:

comp_name=spec[4]

else:

comp_name=string.uppercase[compnum]

CompRec['specimen_comp_name']=comp_name

if beg < float(datablock[0][0]):beg=float(datablock[0][0])

if end > float(datablock[-1][0]):end=float(datablock[-1][0])

for l in range(len(datablock)):

if datablock[l][0]==beg:beg_pca=l

if datablock[l][0]==end:end_pca=l

if geo==1 and tilt==0:

mpars=pmag.domean(geoblock,beg_pca,end_pca,calculation_type)

if mpars["specimen_direction_type"]!="Error":

CompRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])

CompRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])

CompRec["specimen_tilt_correction"]='0'

if geo==1 and tilt==1:

mpars=pmag.domean(tiltblock,beg_pca,end_pca,calculation_type)

if mpars["specimen_direction_type"]!="Error":

CompRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])

CompRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])

CompRec["specimen_tilt_correction"]='100'

if geo==0 and tilt==0:

mpars=pmag.domean(datablock,beg_pca,end_pca,calculation_type)

if mpars["specimen_direction_type"]!="Error":

CompRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])

CompRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])

CompRec["specimen_tilt_correction"]='-1'

if mpars["specimen_direction_type"]=="Error":

pass

else:

CompRec["measurement_step_min"]='%8.3e '%(datablock[beg_pca][0])

try:

CompRec["measurement_step_max"]='%8.3e '%(datablock[end_pca][0] )

except:

print 'error in end_pca ',PmagSpecRec['er_specimen_name']

CompRec["specimen_correction"]='u'

if calculation_type!='DE-FM':

CompRec["specimen_mad"]='%7.1f '%(mpars["specimen_mad"])

CompRec["specimen_alpha95"]=""

else:

CompRec["specimen_mad"]=""

CompRec["specimen_alpha95"]='%7.1f '%(mpars["specimen_alpha95"])

CompRec["specimen_n"]='%i '%(mpars["specimen_n"])

CompRec["specimen_dang"]='%7.1f '%(mpars["specimen_dang"])

CompMeths=[]

for meth in method_codes:

if meth not in CompMeths:CompMeths.append(meth)

if calculation_type not in CompMeths:CompMeths.append(calculation_type)

if geo==1: CompMeths.append("DA-DIR-GEO")

if tilt==1: CompMeths.append("DA-DIR-TILT")

if "DE-BFP" not in calculation_type:

CompRec["specimen_direction_type"]='l'

else:

CompRec["specimen_direction_type"]='p'

CompRec["magic_method_codes"]=""

if len(CompMeths) != 0:

methstring=""

for meth in CompMeths:

methstring=methstring+ ":" +meth

CompRec["magic_method_codes"]=methstring.strip(':')

CompRec["specimen_description"]=comment

if len(inst_codes) != 0:

inststring=""

for inst in inst_codes:

inststring=inststring+ ":" +inst

CompRec["magic_instrument_codes"]=inststring.strip(':')

PmagSpecs.append(CompRec)

k+=1

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