"""

NAME

pmag_results_extract.py

DESCRIPTION

make a tab delimited output file from pmag_results table

SYNTAX

pmag_results_extract.py [command line options]

OPTIONS

-h prints help message and quits

-f RFILE, specify pmag_results table; default is pmag_results.txt

-fa AFILE, specify er_ages table; default is NONE

-fsp SFILE, specify pmag_specimens table, default is NONE

-fcr CFILE, specify pmag_criteria table, default is NONE

-g include specimen_grade in table - only works for PmagPy generated pmag_specimen formatted files.

-tex, output in LaTeX format

"""

dir_path='.'

res_file='pmag_results.txt'

crit_file=''

spec_file=''

age_file=""

latex=0

grade=0

if '-h' in sys.argv:

print main.__doc__

sys.exit()

if '-WD' in sys.argv:

ind = sys.argv.index('-WD')

dir_path=sys.argv[ind+1]

if '-f' in sys.argv:

ind = sys.argv.index('-f')

res_file=sys.argv[ind+1]

if '-fsp' in sys.argv:

ind = sys.argv.index('-fsp')

spec_file=sys.argv[ind+1]

if '-fcr' in sys.argv:

ind = sys.argv.index('-fcr')

crit_file=sys.argv[ind+1]

if '-fa' in sys.argv:

ind = sys.argv.index('-fa')

age_file=sys.argv[ind+1]

if '-g' in sys.argv:grade=1

if '-tex' in sys.argv:

latex=1

outfile='Directions.tex'

Ioutfile='Intensities.tex'

Soutfile='SiteNfo.tex'

Specout='Specimens.tex'

Critout='Criteria.tex'

else:

latex=0

outfile='Directions.txt'

Ioutfile='Intensities.txt'

Soutfile='SiteNfo.txt'

Specout='Specimens.txt'

Critout='Criteria.txt'

res_file=dir_path+'/'+res_file

if crit_file!="":crit_file=dir_path+'/'+crit_file

if spec_file!="":spec_file=dir_path+'/'+spec_file

# open output files

outfile=dir_path+'/'+outfile

Ioutfile=dir_path+'/'+Ioutfile

Soutfile=dir_path+'/'+Soutfile

Specout=dir_path+'/'+Specout

Critout=dir_path+'/'+Critout

f=open(outfile,'w')

sf=open(Soutfile,'w')

fI=open(Ioutfile,'w')

cr=open(Critout,'w')

# set up column headers

Sites,file_type=pmag.magic_read(res_file)

if crit_file!="":

Crits,file_type=pmag.magic_read(crit_file)

else:

Crits=[]

SiteCols=["Site","Samples","Location","Lat. (N)","Long. (E)","Age ","Age sigma","Units"]

SiteKeys=["er_site_names","er_sample_names","average_lat","average_lon","average_age","average_age_sigma","average_age_unit"]

DirCols=["Site","Samples",'Comp.',"%TC","Dec.","Inc.","Nl","Np","k ","R","a95","PLat","PLong"]

DirKeys=["er_site_names","er_sample_names","pole_comp_name","tilt_correction","average_dec","average_inc","average_n_lines","average_n_planes","average_k","average_r","average_alpha95","vgp_lat","vgp_lon"]

IntCols=["Site","Specimens","Samples","N","B (uT)","sigma","sigma perc","VADM","VADM sigma"]

IntKeys=["er_site_names","er_specimen_names","er_sample_names","average_int_n","average_int","average_int_sigma",'average_int_sigma_perc',"vadm","vadm_sigma"]

AllowedKeys=['specimen_frac','specimen_scat','specimen_gap_max','measurement_step_min', 'measurement_step_max', 'measurement_step_unit', 'specimen_polarity', 'specimen_nrm', 'specimen_direction_type', 'specimen_comp_nmb', 'specimen_mad', 'specimen_alpha95', 'specimen_n', 'specimen_int_sigma', 'specimen_int_sigma_perc', 'specimen_int_rel_sigma', 'specimen_int_rel_sigma_perc', 'specimen_int_mad', 'specimen_int_n', 'specimen_w', 'specimen_q', 'specimen_f', 'specimen_fvds', 'specimen_b_sigma', 'specimen_b_beta', 'specimen_g', 'specimen_dang', 'specimen_md', 'specimen_ptrm', 'specimen_drat', 'specimen_drats', 'specimen_rsc', 'specimen_viscosity_index', 'specimen_magn_moment', 'specimen_magn_volume', 'specimen_magn_mass', 'specimen_int_ptrm_n', 'specimen_delta', 'specimen_theta', 'specimen_gamma', 'sample_polarity', 'sample_nrm', 'sample_direction_type', 'sample_comp_nmb', 'sample_sigma', 'sample_alpha95', 'sample_n', 'sample_n_lines', 'sample_n_planes', 'sample_k', 'sample_r', 'sample_tilt_correction', 'sample_int_sigma', 'sample_int_sigma_perc', 'sample_int_rel_sigma', 'sample_int_rel_sigma_perc', 'sample_int_n', 'sample_magn_moment', 'sample_magn_volume', 'sample_magn_mass', 'site_polarity', 'site_nrm', 'site_direction_type', 'site_comp_nmb', 'site_sigma', 'site_alpha95', 'site_n', 'site_n_lines', 'site_n_planes', 'site_k', 'site_r', 'site_tilt_correction', 'site_int_sigma', 'site_int_sigma_perc', 'site_int_rel_sigma', 'site_int_rel_sigma_perc', 'site_int_n', 'site_magn_moment', 'site_magn_volume', 'site_magn_mass', 'average_age_min', 'average_age_max', 'average_age_sigma', 'average_age_unit', 'average_sigma', 'average_alpha95', 'average_n', 'average_nn', 'average_k', 'average_r', 'average_int_sigma', 'average_int_rel_sigma', 'average_int_rel_sigma_perc', 'average_int_n', 'average_int_nn', 'vgp_dp', 'vgp_dm', 'vgp_sigma', 'vgp_alpha95', 'vgp_n', 'vdm_sigma', 'vdm_n', 'vadm_sigma', 'vadm_n']

if crit_file!="":

crit=Crits[0] # get a list of useful keys

for key in crit.keys():

if key not in AllowedKeys:del(crit[key])

for key in crit.keys():

if crit[key]=='' or eval(crit[key])>1000 or eval(crit[key])==0:del(crit[key]) # get rid of all blank or too big ones or too little ones

CritKeys=crit.keys()

if spec_file!="":

Specs,file_type=pmag.magic_read(spec_file)

fsp=open(Specout,'w') # including specimen intensities if desired

SpecCols=["Site","Specimen","B (uT)","MAD","Beta","N","Q","DANG","f-vds","DRATS","T (C)"]

SpecKeys=['er_site_name','er_specimen_name','specimen_int','specimen_int_mad','specimen_b_beta','specimen_int_n','specimen_q','specimen_dang','specimen_fvds','specimen_drats','trange']

Xtra=['specimen_frac','specimen_scat','specimen_gmax']

if grade:

SpecCols.append('Grade')

SpecKeys.append('specimen_grade')

for x in Xtra: # put in the new intensity keys if present

if x in Specs[0].keys():

SpecKeys.append(x)

newkey=""

for k in x.split('_')[1:]:newkey=newkey+k+'_'

SpecCols.append(newkey.strip('_'))

SpecCols.append('Corrections')

SpecKeys.append('corrections')

Micro=['specimen_int','average_int','average_int_sigma'] # these should be multiplied by 1e6

Zeta=['vadm','vadm_sigma'] # these should be multiplied by 1e21

# write out the header information for each output file

if latex: #write out the latex header stuff

sep=' & '

end='\\\\'

f.write('\\begin{table}\n')

sf.write('\\begin{table}\n')

fI.write('\\begin{table}\n')

if crit_file!="":cr.write('\\begin{table}\n')

if spec_file!="": fsp.write('\\begin{table}\n')

tabstring='\\begin{tabular}{'

fstring=tabstring

for k in range(len(SiteCols)):fstring=fstring+'r'

f.write(fstring+'}\n')

f.write('\hline\n')

fstring=tabstring

for k in range(len(DirCols)):fstring=fstring+'r'

sf.write(fstring+'}\n')

sf.write('\hline\n')

fstring=tabstring

for k in range(len(IntCols)):fstring=fstring+'r'

fI.write(fstring+'}\n')

fI.write('\hline\n')

fstring=tabstring

if crit_file!="":

for k in range(len(CritKeys)):fstring=fstring+'r'

cr.write(fstring+'}\n')

cr.write('\hline\n')

if spec_file!="":

fstring=tabstring

for k in range(len(SpecCols)):fstring=fstring+'r'

fsp.write(fstring+'}\n')

fsp.write('\hline\n')

else: # just set the tab and line endings for tab delimited

sep=' \t '

end=''

# now write out the actual column headers

Soutstring,Doutstring,Ioutstring,Spoutstring,Croutstring="","","","",""

for k in range(len(SiteCols)): Soutstring=Soutstring+SiteCols[k]+sep

Soutstring=Soutstring+end

Soutstring=Soutstring.strip(sep) +"\n"

sf.write(Soutstring)

for k in range(len(DirCols)): Doutstring=Doutstring+DirCols[k]+sep

Doutstring=Doutstring+end

Doutstring=Doutstring.strip(sep) +"\n"

f.write(Doutstring)

for k in range(len(IntCols)): Ioutstring=Ioutstring+IntCols[k]+sep

Ioutstring=Ioutstring+end

Ioutstring=Ioutstring.strip(sep) +"\n"

fI.write(Ioutstring)

if crit_file!="":

for k in range(len(CritKeys)): Croutstring=Croutstring+CritKeys[k]+sep

Croutstring=Croutstring+end

Croutstring=Croutstring.strip(sep) +"\n"

cr.write(Croutstring)

if spec_file!="":

for k in range(len(SpecCols)): Spoutstring=Spoutstring+SpecCols[k]+sep

Spoutstring=Spoutstring+end

Spoutstring=Spoutstring.strip(sep) +"\n"

fsp.write(Spoutstring)

if latex: # put in a horizontal line in latex file

f.write('\hline\n')

sf.write('\hline\n')

fI.write('\hline\n')

if crit_file!="":cr.write('\hline\n')

if spec_file!="": fsp.write('\hline\n')

# do criteria

if crit_file!="":

for crit in Crits: #

Croutstring=""

for key in CritKeys:

Croutstring=Croutstring+crit[key]+sep

Croutstring=Croutstring.strip(sep) +end

cr.write(Croutstring+'\n')

# do directions

VGPs=pmag.get_dictitem(Sites,'vgp_lat','','F') # get all results with VGPs

for site in VGPs:

if len(site['er_site_names'].split(":"))==1:

if 'er_sample_names' not in site.keys():site['er_sample_names']=''

if 'pole_comp_name' not in site.keys(): site['pole_comp_name']="A"

if 'average_n_lines' not in site.keys():site['average_n_lines']=site['average_nn']

if 'average_n_planes' not in site.keys():site['average_n_planes']=""

Soutstring,Doutstring="",""

for key in SiteKeys:

if key in site.keys():Soutstring=Soutstring+site[key]+sep

Soutstring=Soutstring.strip(sep) +end

sf.write(Soutstring+'\n')

for key in DirKeys:

if key in site.keys():Doutstring=Doutstring+site[key]+sep

Doutstring=Doutstring.strip(sep) +end

f.write(Doutstring+'\n')

# now do intensities

VADMs=pmag.get_dictitem(Sites,'vadm','','F')

for site in VADMs: # do results level stuff

if site not in VGPs:

Soutstring=""

for key in SiteKeys:

if key in site.keys():

Soutstring=Soutstring+site[key]+sep

else: Soutstring=Soutstring + " " + sep

Soutstring=Soutstring.strip(sep) +end

sf.write(Soutstring+'\n')

if len(site['er_site_names'].split(":"))==1:

if 'average_int_sigma_perc' not in site.keys():site['average_int_sigma_perc']="0"

if site["average_int_sigma"]=="":site["average_int_sigma"]="0"

if site["average_int_sigma_perc"]=="":site["average_int_sigma_perc"]="0"

if site["vadm"]=="":site["vadm"]="0"

if site["vadm_sigma"]=="":site["vadm_sigma"]="0"

for key in site.keys(): # reformat vadms, intensities

if key in Micro: site[key]='%7.1f'%(float(site[key])*1e6)

if key in Zeta: site[key]='%7.1f'%(float(site[key])*1e-21)

outstring=""

for key in IntKeys:

if key not in site.keys():site[key]=""

outstring=outstring+site[key]+sep

outstring=outstring.strip(sep)+end +'\n'

fI.write(outstring)

# VDMs=pmag.get_dictitem(Sites,'vdm','','F') # get non-blank VDMs

# for site in VDMs: # do results level stuff

# if len(site['er_site_names'].split(":"))==1:

# if 'average_int_sigma_perc' not in site.keys():site['average_int_sigma_perc']="0"

# if site["average_int_sigma"]=="":site["average_int_sigma"]="0"

# if site["average_int_sigma_perc"]=="":site["average_int_sigma_perc"]="0"

# if site["vadm"]=="":site["vadm"]="0"

# if site["vadm_sigma"]=="":site["vadm_sigma"]="0"

# for key in site.keys(): # reformat vadms, intensities

# if key in Micro: site[key]='%7.1f'%(float(site[key])*1e6)

# if key in Zeta: site[key]='%7.1f'%(float(site[key])*1e-21)

# outstring=""

# for key in IntKeys:

# outstring=outstring+site[key]+sep

# fI.write(outstring.strip(sep)+'\n')

if spec_file!="":

SpecsInts=pmag.get_dictitem(Specs,'specimen_int','','F')

for spec in SpecsInts:

spec['trange']= '%i'%(int(float(spec['measurement_step_min'])-273))+'-'+'%i'%(int(float(spec['measurement_step_max'])-273))

meths=spec['magic_method_codes'].split(':')

corrections=''

for meth in meths:

if 'DA' in meth:corrections=corrections+meth[3:]+':'

corrections=corrections.strip(':')

if corrections.strip()=="":corrections="None"

spec['corrections']=corrections

outstring=""

for key in SpecKeys:

if key in Micro: spec[key]='%7.1f'%(float(spec[key])*1e6)

if key in Zeta: spec[key]='%7.1f'%(float(spec[key])*1e-21)

outstring=outstring+spec[key]+sep

fsp.write(outstring.strip(sep)+end+'\n')

#

if latex: # write out the tail stuff

f.write('\hline\n')

sf.write('\hline\n')

fI.write('\hline\n')

f.write('\end{tabular}\n')

sf.write('\end{tabular}\n')

fI.write('\end{tabular}\n')

f.write('\end{table}\n')

fI.write('\end{table}\n')

if spec_file!="":

fsp.write('\hline\n')

fsp.write('\end{tabular}\n')

fsp.write('\end{table}\n')

f.close()

sf.close()

fI.close()

print 'data saved in: ',outfile,Ioutfile,Soutfile

if spec_file!="":

fsp.close()

print 'specimen data saved in: ',Specout

if crit_file!="":

cr.close()