"""

NAME

specimens_results_magic.py

DESCRIPTION

combines pmag_specimens.txt file with age, location, acceptance criteria and

outputs pmag_results table along with other MagIC tables necessary for uploading to the database

SYNTAX

specimens_results_magic.py [command line options]

OPTIONS

-h prints help message and quits

-usr USER: identify user, default is ""

-f: specimen input magic_measurements format file, default is "magic_measurements.txt"

-fsp: specimen input pmag_specimens format file, default is "pmag_specimens.txt"

-fsm: sample input er_samples format file, default is "er_samples.txt"

-fsi: specimen input er_sites format file, default is "er_sites.txt"

-fla: specify a file with paleolatitudes for calculating VADMs, default is not to calculate VADMS

format is: site_name paleolatitude (space delimited file)

-fa AGES: specify er_ages format file with age information

-crd [s,g,t,b]: specify coordinate system

(s, specimen, g geographic, t, tilt corrected, b, geographic and tilt corrected)

Default is to assume geographic

NB: only the tilt corrected data will appear on the results table, if both g and t are selected.

-cor [AC:CR:NL]: colon delimited list of required data adjustments for all specimens

included in intensity calculations (anisotropy, cooling rate, non-linear TRM)

unless specified, corrections will not be applied

-pri [TRM:ARM] colon delimited list of priorities for anisotropy correction (-cor must also be set to include AC). default is TRM, then ARM

-age MIN MAX UNITS: specify age boundaries and units

-exc: use exiting selection criteria (in pmag_criteria.txt file), default is default criteria

-C: no acceptance criteria

-aD: average directions per sample, default is NOT

-aI: average multiple specimen intensities per sample, default is by site

-aC: average all components together, default is NOT

-pol: calculate polarity averages

-sam: save sample level vgps and v[a]dms, default is by site

-xSi: skip the site level intensity calculation

-p: plot directions and look at intensities by site, default is NOT

-fmt: specify output for saved images, default is svg (only if -p set)

-lat: use present latitude for calculating VADMs, default is not to calculate VADMs

-xD: skip directions

-xI: skip intensities

OUPUT

writes pmag_samples, pmag_sites, pmag_results tables

"""

# set defaults

Comps=[] # list of components

version_num=pmag.get_version()

args=sys.argv

DefaultAge=["none"]

skipdirs,coord,excrit,custom,vgps,average,Iaverage,plotsites,opt=1,0,0,0,0,0,0,0,0

get_model_lat=0 # this skips VADM calculation altogether, when get_model_lat=1, uses present day

fmt='svg'

dir_path="."

model_lat_file=""

Caverage=0

infile='pmag_specimens.txt'

measfile="magic_measurements.txt"

sampfile="er_samples.txt"

sitefile="er_sites.txt"

agefile="er_ages.txt"

specout="er_specimens.txt"

sampout="pmag_samples.txt"

siteout="pmag_sites.txt"

resout="pmag_results.txt"

critout="pmag_criteria.txt"

instout="magic_instruments.txt"

sigcutoff,OBJ="",""

noDir,noInt=0,0

polarity=0

coords=['0']

Dcrit,Icrit,nocrit=0,0,0

corrections=[]

nocorrection=['DA-NL','DA-AC','DA-CR']

priorities=['DA-AC-ARM','DA-AC-TRM'] # priorities for anisotropy correction

# get command line stuff

if "-h" in args:

print main.__doc__

sys.exit()

if '-WD' in args:

ind=args.index("-WD")

dir_path=args[ind+1]

if '-cor' in args:

ind=args.index('-cor')

cors=args[ind+1].split(':') # list of required data adjustments

for cor in cors:

nocorrection.remove('DA-'+cor)

corrections.append('DA-'+cor)

if '-pri' in args:

ind=args.index('-pri')

priorities=args[ind+1].split(':') # list of required data adjustments

for p in priorities:

p='DA-AC-'+p

if '-f' in args:

ind=args.index("-f")

measfile=args[ind+1]

if '-fsp' in args:

ind=args.index("-fsp")

infile=args[ind+1]

if '-fsi' in args:

ind=args.index("-fsi")

sitefile=args[ind+1]

if "-crd" in args:

ind=args.index("-crd")

coord=args[ind+1]

if coord=='s':coords=['-1']

if coord=='g':coords=['0']

if coord=='t':coords=['100']

if coord=='b':coords=['0','100']

if "-usr" in args:

ind=args.index("-usr")

user=sys.argv[ind+1]

else: user=""

if "-C" in args: Dcrit,Icrit,nocrit=1,1,1 # no selection criteria

if "-sam" in args: vgps=1 # save sample level VGPS/VADMs

if "-xSi" in args:

nositeints=1 # skip site level intensity

else:

nositeints=0

if "-age" in args:

ind=args.index("-age")

DefaultAge[0]=args[ind+1]

DefaultAge.append(args[ind+2])

DefaultAge.append(args[ind+3])

Daverage,Iaverage,Caverage=0,0,0

if "-aD" in args: Daverage=1 # average by sample directions

if "-aI" in args: Iaverage=1 # average by sample intensities

if "-aC" in args: Caverage=1 # average all components together ??? why???

if "-pol" in args: polarity=1 # calculate averages by polarity

if '-xD' in args:noDir=1

if '-xI' in args:

noInt=1

elif "-fla" in args:

if '-lat' in args:

print "you should set a paleolatitude file OR use present day lat - not both"

sys.exit()

ind=args.index("-fla")

model_lat_file=dir_path+'/'+args[ind+1]

get_model_lat=2

mlat=open(model_lat_file,'rU')

ModelLats=[]

for line in mlat.readlines():

ModelLat={}

tmp=line.split()

ModelLat["er_site_name"]=tmp[0]

ModelLat["site_model_lat"]=tmp[1]

ModelLat["er_sample_name"]=tmp[0]

ModelLat["sample_lat"]=tmp[1]

ModelLats.append(ModelLat)

get_model_lat=2

elif '-lat' in args:

get_model_lat=1

if "-p" in args:

plotsites=1

if "-fmt" in args:

ind=args.index("-fmt")

fmt=args[ind+1]

if noDir==0: # plot by site - set up plot window

import pmagplotlib

EQ={}

EQ['eqarea']=1

pmagplotlib.plot_init(EQ['eqarea'],5,5) # define figure 1 as equal area projection

pmagplotlib.plotNET(EQ['eqarea']) # I don't know why this has to be here, but otherwise the first plot never plots...

pmagplotlib.drawFIGS(EQ)

if '-WD' in args:

infile=dir_path+'/'+infile

measfile=dir_path+'/'+measfile

instout=dir_path+'/'+instout

sampfile=dir_path+'/'+sampfile

sitefile=dir_path+'/'+sitefile

agefile=dir_path+'/'+agefile

specout=dir_path+'/'+specout

sampout=dir_path+'/'+sampout

siteout=dir_path+'/'+siteout

resout=dir_path+'/'+resout

critout=dir_path+'/'+critout

if "-exc" in args: # use existing pmag_criteria file

if "-C" in args:

print 'you can not use both existing and no criteria - choose either -exc OR -C OR neither (for default)'

sys.exit()

crit_data,file_type=pmag.magic_read(critout)

print "Acceptance criteria read in from ", critout

else : # use default criteria (if nocrit set, then get really loose criteria as default)

crit_data=pmag.default_criteria(nocrit)

if nocrit==0:

print "Acceptance criteria are defaults"

else:

print "No acceptance criteria used "

accept={}

for critrec in crit_data:

for key in critrec.keys():

if 'sample_int_sigma_uT' in critrec.keys():

critrec['sample_int_sigma']='%10.3e'%(eval(critrec['sample_int_sigma_uT'])*1e-6)

if key not in accept.keys() and critrec[key]!='':

accept[key]=critrec[key]

#

#

if "-exc" not in args and "-C" not in args:

print "args",args

pmag.magic_write(critout,[accept],'pmag_criteria')

print "\n Pmag Criteria stored in ",critout,'\n'

#

# now we're done slow dancing

#

SiteNFO,file_type=pmag.magic_read(sitefile) # read in site data - has the lats and lons

SampNFO,file_type=pmag.magic_read(sampfile) # read in site data - has the lats and lons

height_nfo=pmag.get_dictitem(SiteNFO,'site_height','','F') # find all the sites with height info.

if agefile !="":AgeNFO,file_type=pmag.magic_read(agefile) # read in the age information

Data,file_type=pmag.magic_read(infile) # read in specimen interpretations

IntData=pmag.get_dictitem(Data,'specimen_int','','F') # retrieve specimens with intensity data

comment,orient="",[]

samples,sites=[],[]

for rec in Data: # run through the data filling in missing keys and finding all components, coordinates available

# fill in missing fields, collect unique sample and site names

if 'er_sample_name' not in rec.keys():

rec['er_sample_name']=""

elif rec['er_sample_name'] not in samples:

samples.append(rec['er_sample_name'])

if 'er_site_name' not in rec.keys():

rec['er_site_name']=""

elif rec['er_site_name'] not in sites:

sites.append(rec['er_site_name'])

if 'specimen_int' not in rec.keys():rec['specimen_int']=''

if 'specimen_comp_name' not in rec.keys() or rec['specimen_comp_name']=="":rec['specimen_comp_name']='A'

if rec['specimen_comp_name'] not in Comps:Comps.append(rec['specimen_comp_name'])

rec['specimen_tilt_correction']=rec['specimen_tilt_correction'].strip('\n')

if "specimen_tilt_correction" not in rec.keys(): rec["specimen_tilt_correction"]="-1" # assume sample coordinates

if rec["specimen_tilt_correction"] not in orient: orient.append(rec["specimen_tilt_correction"]) # collect available coordinate systems

if "specimen_direction_type" not in rec.keys(): rec["specimen_direction_type"]='l' # assume direction is line - not plane

if "specimen_dec" not in rec.keys(): rec["specimen_direction_type"]='' # if no declination, set direction type to blank

if "specimen_n" not in rec.keys(): rec["specimen_n"]='' # put in n

if "specimen_alpha95" not in rec.keys(): rec["specimen_alpha95"]='' # put in alpha95

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

#

# start parsing data into SpecDirs, SpecPlanes, SpecInts

SpecInts,SpecDirs,SpecPlanes=[],[],[]

samples.sort() # get sorted list of samples and sites

sites.sort()

if noInt==0: # don't skip intensities

IntData=pmag.get_dictitem(Data,'specimen_int','','F') # retrieve specimens with intensity data

if nocrit==0: # use selection criteria

for rec in IntData: # do selection criteria

kill=pmag.grade(rec,accept,'specimen_int')

if len(kill)==0: SpecInts.append(rec) # intensity record to be included in sample, site calculations

else:

SpecInts=IntData[:] # take everything - no selection criteria

# check for required data adjustments

if len(corrections)>0 and len(SpecInts)>0:

for cor in corrections:

SpecInts=pmag.get_dictitem(SpecInts,'magic_method_codes',cor,'has') # only take specimens with the required corrections

if len(nocorrection)>0 and len(SpecInts)>0:

for cor in nocorrection:

SpecInts=pmag.get_dictitem(SpecInts,'magic_method_codes',cor,'not') # exclude the corrections not specified for inclusion

# take top priority specimen of its name in remaining specimens (only one per customer)

PrioritySpecInts=[]

specimens=pmag.get_specs(SpecInts) # get list of uniq specimen names

for spec in specimens:

ThisSpecRecs=pmag.get_dictitem(SpecInts,'er_specimen_name',spec,'T') # all the records for this specimen

if len(ThisSpecRecs)==1:

PrioritySpecInts.append(ThisSpecRecs[0])

elif len(ThisSpecRecs)>1: # more than one

prec=[]

for p in priorities:

ThisSpecRecs=pmag.get_dictitem(SpecInts,'magic_method_codes',p,'has') # all the records for this specimen

if len(ThisSpecRecs)>0:prec.append(ThisSpecRecs[0])

PrioritySpecInts.append(prec[0]) # take the best one

SpecInts=PrioritySpecInts # this has the first specimen record

if noDir==0: # don't skip directions

AllDirs=pmag.get_dictitem(Data,'specimen_direction_type','','F') # retrieve specimens with directed lines and planes

Ns=pmag.get_dictitem(AllDirs,'specimen_n','','F') # get all specimens with specimen_n information

if nocrit!=1: # use selection criteria

for rec in Ns: # look through everything with specimen_n for "good" data

kill=pmag.grade(rec,accept,'specimen_dir')

if len(kill)==0: # nothing killed it

SpecDirs.append(rec)

else: # no criteria

SpecDirs=AllDirs[:] # take them all

# SpecDirs is now the list of all specimen directions (lines and planes) that pass muster

#

PmagSamps,SampDirs=[],[] # list of all sample data and list of those that pass the DE-SAMP criteria

PmagSites,PmagResults=[],[] # list of all site data and selected results

SampInts=[]

for samp in samples: # run through the sample names

if Daverage==1: # average by sample if desired

SampDir=pmag.get_dictitem(SpecDirs,'er_sample_name',samp,'T') # get all the directional data for this sample

if len(SampDir)>0: # there are some directions

for coord in coords: # step through desired coordinate systems

CoordDir=pmag.get_dictitem(SampDir,'specimen_tilt_correction',coord,'T') # get all the directions for this sample

if len(CoordDir)>0: # there are some with this coordinate system

if Caverage==0: # look component by component

for comp in Comps:

CompDir=pmag.get_dictitem(CoordDir,'specimen_comp_name',comp,'T') # get all directions from this component

if len(CompDir)>0: # there are some

PmagSampRec=pmag.lnpbykey(CompDir,'sample','specimen') # get a sample average from all specimens

PmagSampRec["er_location_name"]=CompDir[0]['er_location_name'] # decorate the sample record

PmagSampRec["er_site_name"]=CompDir[0]['er_site_name']

PmagSampRec["er_sample_name"]=samp

PmagSampRec["er_citation_names"]="This study"

PmagSampRec["er_analyst_mail_names"]=user

PmagSampRec['magic_software_packages']=version_num

if nocrit!=1:PmagSampRec['pmag_criteria_codes']="ACCEPT"

if agefile != "": PmagSampRec= pmag.get_age(PmagSampRec,"er_site_name","sample_inferred_",AgeNFO,DefaultAge)

site_height=pmag.get_dictitem(height_nfo,'er_site_name',PmagSampRec['er_site_name'],'T')

if len(site_height)>0:PmagSampRec["sample_height"]=site_height[0]['site_height'] # add in height if available

PmagSampRec['sample_comp_name']=comp

PmagSampRec['sample_tilt_correction']=coord

PmagSampRec['er_specimen_names']= pmag.get_list(CompDir,'er_specimen_name') # get a list of the specimen names used

PmagSampRec['magic_method_codes']= pmag.get_list(CompDir,'magic_method_codes') # get a list of the methods used

if nocrit!=1: # apply selection criteria

kill=pmag.grade(PmagSampRec,accept,'sample_dir')

else:

kill=[]

if len(kill)==0:

SampDirs.append(PmagSampRec)

if vgps==1: # if sample level VGP info desired, do that now

PmagResRec=pmag.getsampVGP(PmagSampRec,SiteNFO)

if PmagResRec!="":PmagResults.append(PmagResRec)

PmagSamps.append(PmagSampRec)

if Caverage==1: # average all components together basically same as above

PmagSampRec=pmag.lnpbykey(CoordDir,'sample','specimen')

PmagSampRec["er_location_name"]=CoordDir[0]['er_location_name']

PmagSampRec["er_site_name"]=CoordDir[0]['er_site_name']

PmagSampRec["er_sample_name"]=samp

PmagSampRec["er_citation_names"]="This study"

PmagSampRec["er_analyst_mail_names"]=user

PmagSampRec['magic_software_packages']=version_num

if nocrit!=1:PmagSampRec['pmag_criteria_codes']=""

if agefile != "": PmagSampRec= pmag.get_age(PmagSampRec,"er_site_name","sample_inferred_",AgeNFO,DefaultAge)

site_height=pmag.get_dictitem(height_nfo,'er_site_name',site,'T')

if len(site_height)>0:PmagSampRec["sample_height"]=site_height[0]['site_height'] # add in height if available

PmagSampRec['sample_tilt_correction']=coord

PmagSampRec['sample_comp_name']= pmag.get_list(CoordDir,'specimen_comp_name') # get components used

PmagSampRec['er_specimen_names']= pmag.get_list(CoordDir,'er_specimen_name') # get specimne names averaged

PmagSampRec['magic_method_codes']= pmag.get_list(CoordDir,'magic_method_codes') # assemble method codes

if nocrit!=1: # apply selection criteria

kill=pmag.grade(PmagSampRec,accept,'sample_dir')

if len(kill)==0: # passes the mustard

SampDirs.append(PmagSampRec)

if vgps==1:

PmagResRec=pmag.getsampVGP(PmagSampRec,SiteNFO)

if PmagResRec!="":PmagResults.append(PmagResRec)

else: # take everything

SampDirs.append(PmagSampRec)

if vgps==1:

PmagResRec=pmag.getsampVGP(PmagSampRec,SiteNFO)

if PmagResRec!="":PmagResults.append(PmagResRec)

PmagSamps.append(PmagSampRec)

if Iaverage==1: # average by sample if desired

SampI=pmag.get_dictitem(SpecInts,'er_sample_name',samp,'T') # get all the intensity data for this sample

if len(SampI)>0: # there are some

PmagSampRec=pmag.average_int(SampI,'specimen','sample') # get average intensity stuff

PmagSampRec["sample_description"]="sample intensity" # decorate sample record

PmagSampRec["sample_direction_type"]=""

PmagSampRec['er_site_name']=SampI[0]["er_site_name"]

PmagSampRec['er_sample_name']=samp

PmagSampRec['er_location_name']=SampI[0]["er_location_name"]

PmagSampRec["er_citation_names"]="This study"

PmagSampRec["er_analyst_mail_names"]=user

if agefile != "": PmagSampRec=pmag.get_age(PmagSampRec,"er_site_name","sample_inferred_", AgeNFO,DefaultAge)

site_height=pmag.get_dictitem(height_nfo,'er_site_name',PmagSampRec['er_site_name'],'T')

if len(site_height)>0:PmagSampRec["sample_height"]=site_height[0]['site_height'] # add in height if available

PmagSampRec['er_specimen_names']= pmag.get_list(SampI,'er_specimen_name')

PmagSampRec['magic_method_codes']= pmag.get_list(SampI,'magic_method_codes')

if nocrit!=1: # apply criteria!

kill=pmag.grade(PmagSampRec,accept,'sample_int')

if len(kill)==0:

PmagSampRec['pmag_criteria_codes']="ACCEPT"

SampInts.append(PmagSampRec)

PmagSamps.append(PmagSampRec)

else:PmagSampRec={} # sample rejected

else: # no criteria

SampInts.append(PmagSampRec)

PmagSamps.append(PmagSampRec)

PmagSampRec['pmag_criteria_codes']=""

if vgps==1 and get_model_lat!=0 and PmagSampRec!={}: #

if get_model_lat==1: # use sample latitude

PmagResRec=pmag.getsampVDM(PmagSampRec,SampNFO)

del(PmagResRec['model_lat']) # get rid of the model lat key

elif get_model_lat==2: # use model latitude

PmagResRec=pmag.getsampVDM(PmagSampRec,ModelLats)

if PmagResRec!={}:PmagResRec['magic_method_codes']=PmagResRec['magic_method_codes']+":IE-MLAT"

if PmagResRec!={}:

PmagResRec['er_specimen_names']=PmagSampRec['er_specimen_names']

PmagResRec['er_sample_names']=PmagSampRec['er_sample_name']

PmagResRec['pmag_criteria_codes']='ACCEPT'

PmagResRec['average_int_sigma_perc']=PmagSampRec['sample_int_sigma_perc']

PmagResRec['average_int_sigma']=PmagSampRec['sample_int_sigma']

PmagResRec['average_int_n']=PmagSampRec['sample_int_n']

PmagResRec['vadm_n']=PmagSampRec['sample_int_n']

PmagResRec['data_type']='i'

PmagResults.append(PmagResRec)

if len(PmagSamps)>0:

TmpSamps,keylist=pmag.fillkeys(PmagSamps) # fill in missing keys from different types of records

pmag.magic_write(sampout,TmpSamps,'pmag_samples') # save in sample output file

print ' sample averages written to ',sampout

#

#create site averages from specimens or samples as specified

#

for site in sites:

if Daverage==0: key,dirlist='specimen',SpecDirs # if specimen averages at site level desired

if Daverage==1: key,dirlist='sample',SampDirs # if sample averages at site level desired

tmp=pmag.get_dictitem(dirlist,'er_site_name',site,'T') # get all the sites with directions

tmp1=pmag.get_dictitem(tmp,key+'_tilt_correction',coords[-1],'T') # use only the last coordinate if Caverage==0

sd=pmag.get_dictitem(SiteNFO,'er_site_name',site,'T') # fish out site information (lat/lon, etc.)

if len(sd)>0:

sitedat=sd[0]

if Caverage==0: # do component wise averaging

for comp in Comps:

siteD=pmag.get_dictitem(tmp1,key+'_comp_name',comp,'T') # get all components comp

if len(siteD)>0: # there are some for this site and component name

PmagSiteRec=pmag.lnpbykey(siteD,'site',key) # get an average for this site

PmagSiteRec['site_comp_name']=comp # decorate the site record

PmagSiteRec["er_location_name"]=siteD[0]['er_location_name']

PmagSiteRec["er_site_name"]=siteD[0]['er_site_name']

PmagSiteRec['site_tilt_correction']=coords[-1]

PmagSiteRec['site_comp_name']= pmag.get_list(siteD,key+'_comp_name')

if Daverage==1:

PmagSiteRec['er_sample_names']= pmag.get_list(siteD,'er_sample_name')

else:

PmagSiteRec['er_specimen_names']= pmag.get_list(siteD,'er_specimen_name')

# determine the demagnetization code (DC3,4 or 5) for this site

AFnum=len(pmag.get_dictitem(siteD,'magic_method_codes','LP-DIR-AF','has'))

Tnum=len(pmag.get_dictitem(siteD,'magic_method_codes','LP-DIR-T','has'))

DC=3

if AFnum>0:DC+=1

if Tnum>0:DC+=1

PmagSiteRec['magic_method_codes']= pmag.get_list(siteD,'magic_method_codes')+':'+ 'LP-DC'+str(DC)

PmagSiteRec['magic_method_codes'].strip(":")

if plotsites==1:

print PmagSiteRec['er_site_name']

pmagplotlib.plotSITE(EQ['eqarea'],PmagSiteRec,siteD,key) # plot and list the data

pmagplotlib.drawFIGS(EQ)

PmagSites.append(PmagSiteRec)

else: # last component only

siteD=tmp1[:] # get the last orientation system specified

if len(siteD)>0: # there are some

PmagSiteRec=pmag.lnpbykey(siteD,'site',key) # get the average for this site

PmagSiteRec["er_location_name"]=siteD[0]['er_location_name'] # decorate the record

PmagSiteRec["er_site_name"]=siteD[0]['er_site_name']

PmagSiteRec['site_comp_name']=comp

PmagSiteRec['site_tilt_correction']=coords[-1]

PmagSiteRec['site_comp_name']= pmag.get_list(siteD,key+'_comp_name')

PmagSiteRec['er_specimen_names']= pmag.get_list(siteD,'er_specimen_name')

PmagSiteRec['er_sample_names']= pmag.get_list(siteD,'er_sample_name')

AFnum=len(pmag.get_dictitem(siteD,'magic_method_codes','LP-DIR-AF','has'))

Tnum=len(pmag.get_dictitem(siteD,'magic_method_codes','LP-DIR-T','has'))

DC=3

if AFnum>0:DC+=1

if Tnum>0:DC+=1

PmagSiteRec['magic_method_codes']= pmag.get_list(siteD,'magic_method_codes')+':'+ 'LP-DC'+str(DC)

PmagSiteRec['magic_method_codes'].strip(":")

if Daverage==0:PmagSiteRec['site_comp_name']= pmag.get_list(siteD,key+'_comp_name')

if plotsites==1:

pmagplotlib.plotSITE(EQ['eqarea'],PmagSiteRec,siteD,key)

pmagplotlib.drawFIGS(EQ)

PmagSites.append(PmagSiteRec)

else:

print 'site information not found in er_sites for site, ',site,' site will be skipped'

for PmagSiteRec in PmagSites: # now decorate each dictionary some more, and calculate VGPs etc. for results table

PmagSiteRec["er_citation_names"]="This study"

PmagSiteRec["er_analyst_mail_names"]=user

PmagSiteRec['magic_software_packages']=version_num

if agefile != "": PmagSiteRec= pmag.get_age(PmagSiteRec,"er_site_name","site_inferred_",AgeNFO,DefaultAge)

PmagSiteRec['pmag_criteria_codes']='ACCEPT'

if 'site_n_lines' in PmagSiteRec.keys() and 'site_n_planes' in PmagSiteRec.keys() and PmagSiteRec['site_n_lines']!="" and PmagSiteRec['site_n_planes']!="":

if int(PmagSiteRec["site_n_planes"])>0:

PmagSiteRec["magic_method_codes"]=PmagSiteRec['magic_method_codes']+":DE-FM-LP"

elif int(PmagSiteRec["site_n_lines"])>2:

PmagSiteRec["magic_method_codes"]=PmagSiteRec['magic_method_codes']+":DE-FM"

kill=pmag.grade(PmagSiteRec,accept,'site_dir')

if len(kill)==0:

PmagResRec={} # set up dictionary for the pmag_results table entry

PmagResRec['data_type']='i' # decorate it a bit

PmagResRec['magic_software_packages']=version_num

PmagSiteRec['site_description']='Site direction included in results table'

PmagResRec['pmag_criteria_codes']='ACCEPT'

dec=float(PmagSiteRec["site_dec"])

inc=float(PmagSiteRec["site_inc"])

if 'site_alpha95' in PmagSiteRec.keys() and PmagSiteRec['site_alpha95']!="":

a95=float(PmagSiteRec["site_alpha95"])

else:a95=180.

sitedat=pmag.get_dictitem(SiteNFO,'er_site_name',PmagSiteRec['er_site_name'],'T')[0] # fish out site information (lat/lon, etc.)

lat=float(sitedat['site_lat'])

lon=float(sitedat['site_lon'])

plong,plat,dp,dm=pmag.dia_vgp(dec,inc,a95,lat,lon) # get the VGP for this site

if PmagSiteRec['site_tilt_correction']=='-1':C=' (spec coord) '

if PmagSiteRec['site_tilt_correction']=='0':C=' (geog. coord) '

if PmagSiteRec['site_tilt_correction']=='100':C=' (strat. coord) '

PmagResRec["pmag_result_name"]="VGP Site: "+PmagSiteRec["er_site_name"] # decorate some more

PmagResRec["result_description"]="Site VGP, coord system = "+str(coord)+' component: '+comp

PmagResRec['er_site_names']=PmagSiteRec['er_site_name']

PmagResRec['pmag_criteria_codes']='ACCEPT'

PmagResRec['er_citation_names']='This study'

PmagResRec['er_analyst_mail_names']=user

PmagResRec["er_location_names"]=PmagSiteRec["er_location_name"]

if Daverage==1:

PmagResRec["er_sample_names"]=PmagSiteRec["er_sample_names"]

else:

PmagResRec["er_specimen_names"]=PmagSiteRec["er_specimen_names"]

PmagResRec["tilt_correction"]=PmagSiteRec['site_tilt_correction']

PmagResRec["pole_comp_name"]=PmagSiteRec['site_comp_name']

PmagResRec["average_dec"]=PmagSiteRec["site_dec"]

PmagResRec["average_inc"]=PmagSiteRec["site_inc"]

PmagResRec["average_alpha95"]=PmagSiteRec["site_alpha95"]

PmagResRec["average_n"]=PmagSiteRec["site_n"]

PmagResRec["average_n_lines"]=PmagSiteRec["site_n_lines"]

PmagResRec["average_n_planes"]=PmagSiteRec["site_n_planes"]

PmagResRec["vgp_n"]=PmagSiteRec["site_n"]

PmagResRec["average_k"]=PmagSiteRec["site_k"]

PmagResRec["average_r"]=PmagSiteRec["site_r"]

PmagResRec["average_lat"]='%10.4f ' %(lat)

PmagResRec["average_lon"]='%10.4f ' %(lon)

if agefile != "": PmagResRec= pmag.get_age(PmagResRec,"er_site_names","average_",AgeNFO,DefaultAge)

site_height=pmag.get_dictitem(height_nfo,'er_site_name',site,'T')

if len(site_height)>0:PmagResRec["average_height"]=site_height[0]['site_height']

PmagResRec["vgp_lat"]='%7.1f ' % (plat)

PmagResRec["vgp_lon"]='%7.1f ' % (plong)

PmagResRec["vgp_dp"]='%7.1f ' % (dp)

PmagResRec["vgp_dm"]='%7.1f ' % (dm)

PmagResRec["magic_method_codes"]= PmagSiteRec["magic_method_codes"]

if PmagSiteRec['site_tilt_correction']=='0':PmagSiteRec['magic_method_codes']=PmagSiteRec['magic_method_codes']+":DA-DIR-GEO"

if PmagSiteRec['site_tilt_correction']=='100':PmagSiteRec['magic_method_codes']=PmagSiteRec['magic_method_codes']+":DA-DIR-TILT"

PmagSiteRec['site_polarity']=""

if polarity==1: # assign polarity based on angle of pole lat to spin axis - may want to re-think this sometime

angle=pmag.angle([0,0],[0,(90-plat)])

if angle <= 55.: PmagSiteRec["site_polarity"]='n'

if angle > 55. and angle < 125.: PmagSiteRec["site_polarity"]='t'

if angle >= 125.: PmagSiteRec["site_polarity"]='r'

PmagResults.append(PmagResRec)

if noInt!=1 and nositeints!=1:

for site in sites: # now do intensities for each site

if plotsites==1:print site

if Iaverage==0: key,intlist='specimen',SpecInts # if using specimen level data

if Iaverage==1: key,intlist='sample',PmagSamps # if using sample level data

Ints=pmag.get_dictitem(intlist,'er_site_name',site,'T') # get all the intensities for this site

if len(Ints)>0: # there are some

PmagSiteRec=pmag.average_int(Ints,key,'site') # get average intensity stuff for site table

PmagResRec=pmag.average_int(Ints,key,'average') # get average intensity stuff for results table

if plotsites==1: # if site by site examination requested - print this site out to the screen

for rec in Ints:print rec['er_'+key+'_name'],' %7.1f'%(1e6*float(rec[key+'_int']))

if len(Ints)>1:

print 'Average: ','%7.1f'%(1e6*float(PmagResRec['average_int'])),'N: ',len(Ints)

print 'Sigma: ','%7.1f'%(1e6*float(PmagResRec['average_int_sigma'])),'Sigma %: ',PmagResRec['average_int_sigma_perc']

raw_input('Press any key to continue\n')

er_location_name=Ints[0]["er_location_name"]

PmagSiteRec["er_location_name"]=er_location_name # decorate the records

PmagSiteRec["er_citation_names"]="This study"

PmagResRec["er_location_names"]=er_location_name

PmagResRec["er_citation_names"]="This study"

PmagSiteRec["er_analyst_mail_names"]=user

PmagResRec["er_analyst_mail_names"]=user

PmagResRec["data_type"]='i'

if Iaverage==0:

PmagSiteRec['er_specimen_names']= pmag.get_list(Ints,'er_specimen_name') # list of all specimens used

PmagResRec['er_specimen_names']= pmag.get_list(Ints,'er_specimen_name')

PmagSiteRec['er_sample_names']= pmag.get_list(Ints,'er_sample_name') # list of all samples used

PmagResRec['er_sample_names']= pmag.get_list(Ints,'er_sample_name')

PmagSiteRec['er_site_name']= site

PmagResRec['er_site_names']= site

PmagSiteRec['magic_method_codes']= pmag.get_list(Ints,'magic_method_codes')

PmagResRec['magic_method_codes']= pmag.get_list(Ints,'magic_method_codes')

kill=pmag.grade(PmagSiteRec,accept,'site_int')

if nocrit==1 or len(kill)==0:

b,sig=float(PmagResRec['average_int']),""

if(PmagResRec['average_int_sigma'])!="":sig=float(PmagResRec['average_int_sigma'])

sdir=pmag.get_dictitem(PmagResults,'er_site_names',site,'T') # fish out site direction

if len(sdir)>0 and sdir[-1]['average_inc']!="": # get the VDM for this record using last average inclination (hope it is the right one!)

inc=float(sdir[0]['average_inc']) #

mlat=pmag.magnetic_lat(inc) # get magnetic latitude using dipole formula

PmagResRec["vdm"]='%8.3e '% (pmag.b_vdm(b,mlat)) # get VDM with magnetic latitude

PmagResRec["vdm_n"]=PmagResRec['average_int_n']

if 'average_int_sigma' in PmagResRec.keys() and PmagResRec['average_int_sigma']!="":

vdm_sig=pmag.b_vdm(float(PmagResRec['average_int_sigma']),mlat)

PmagResRec["vdm_sigma"]='%8.3e '% (vdm_sig)

else:

PmagResRec["vdm_sigma"]=""

mlat="" # define a model latitude

if get_model_lat==1: # use present site latitude

mlats=pmag.get_dictitem(SiteNFO,'er_site_name',site,'T')

if len(mlats)>0: mlat=mlats[0]['site_lat']

elif get_model_lat==2: # use a model latitude from some plate reconstruction model (or something)

mlats=pmag.get_dictitem(ModelLats,'er_site_name',site,'T')

if len(mlats)>0: PmagResRec['model_lat']=mlats[0]['site_model_lat']

mlat=PmagResRec['model_lat']

if mlat!="":

PmagResRec["vadm"]='%8.3e '% (pmag.b_vdm(b,float(mlat))) # get the VADM using the desired latitude

if sig!="":

vdm_sig=pmag.b_vdm(float(PmagResRec['average_int_sigma']),float(mlat))

PmagResRec["vadm_sigma"]='%8.3e '% (vdm_sig)

PmagResRec["vadm_n"]=PmagResRec['average_int_n']

else:

PmagResRec["vadm_sigma"]=""

sitedat=pmag.get_dictitem(SiteNFO,'er_site_name',PmagSiteRec['er_site_name'],'T') # fish out site information (lat/lon, etc.)

if len(sitedat)>0:

sitedat=sitedat[0]

PmagResRec['average_lat']=sitedat['site_lat']

PmagResRec['average_lon']=sitedat['site_lon']

else:

PmagResRec['average_lon']='UNKNOWN'

PmagResRec['average_lon']='UNKNOWN'

PmagResRec['magic_software_packages']=version_num

PmagResRec["pmag_result_name"]="V[A]DM: Site "+site

PmagResRec["result_description"]="V[A]DM of site"

PmagResRec["pmag_criteria_codes"]="ACCEPT"

if agefile != "": PmagResRec= pmag.get_age(PmagResRec,"er_site_names","average_",AgeNFO,DefaultAge)

site_height=pmag.get_dictitem(height_nfo,'er_site_name',site,'T')

if len(site_height)>0:PmagResRec["average_height"]=site_height[0]['site_height']

PmagSites.append(PmagSiteRec)

PmagResults.append(PmagResRec)

if len(PmagSites)>0:

Tmp,keylist=pmag.fillkeys(PmagSites)

pmag.magic_write(siteout,Tmp,'pmag_sites')

print ' sites written to ',siteout

else: print "No Site level table"

if len(PmagResults)>0:

TmpRes,keylist=pmag.fillkeys(PmagResults)

pmag.magic_write(resout,TmpRes,'pmag_results')

print ' results written to ',resout