def main():
"""
NAME
thellier_magic.py
DESCRIPTION
plots Thellier-Thellier, allowing interactive setting of bounds
and customizing of selection criteria. Saves and reads interpretations
from a pmag_specimen formatted table, default: thellier_specimens.txt
SYNTAX
thellier_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f MEAS, set magic_measurements input file
-fsp PRIOR, set pmag_specimen prior interpretations file
-fan ANIS, set rmag_anisotropy file for doing the anisotropy corrections
-fcr CRIT, set criteria file for grading.
-fmt [svg,png,jpg], format for images - default is svg
-sav, saves plots with out review (default format)
-spc SPEC, plots single specimen SPEC, saves plot with specified format
with optional -b bounds adn quits
-b BEG END: sets bounds for calculation
BEG: starting step for slope calculation
END: ending step for slope calculation
-z use only z component difference for pTRM calculation
DEFAULTS
MEAS: magic_measurements.txt
REDO: thellier_redo
CRIT: NONE
PRIOR: NONE
OUTPUT
figures:
ALL: numbers refer to temperature steps in command line window
1) Arai plot: closed circles are zero-field first/infield
open circles are infield first/zero-field
triangles are pTRM checks
squares are pTRM tail checks
VDS is vector difference sum
diamonds are bounds for interpretation
2) Zijderveld plot: closed (open) symbols are X-Y (X-Z) planes
X rotated to NRM direction
3) (De/Re)Magnetization diagram:
circles are NRM remaining
squares are pTRM gained
4) Optional: TRM acquisition
5) Optional: TDS normalization
command line window:
list is: temperature step numbers, temperatures (C), Dec, Inc, Int (units of magic_measuements)
list of possible commands: type letter followed by return to select option
saving of plots creates .svg format files with specimen_name, plot type as name
"""
#
# initializations
#
meas_file,critout,inspec="magic_measurements.txt","","thellier_specimens.txt"
first=1
inlt=0
version_num=pmag.get_version()
TDinit,Tinit,field,first_save=0,0,-1,1
user,comment,AniSpec="",'',""
ans,specimen,recnum,start,end=0,0,0,0,0
plots,pmag_out,samp_file,style=0,"","","svg"
fmt='.'+style
#
# default acceptance criteria
#
accept_keys=['specimen_int_ptrm_n','specimen_md','specimen_fvds','specimen_b_beta','specimen_dang','specimen_drats','specimen_Z']
accept={}
accept['specimen_int_ptrm_n']=2
accept['specimen_md']=10
accept['specimen_fvds']=0.35
accept['specimen_b_beta']=.1
accept['specimen_int_mad']=7
accept['specimen_dang']=10
accept['specimen_drats']=10
accept['specimen_Z']=10
#
# parse command line options
#
Zdiff,anis=0,0
spc,BEG,END="","",""
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index('-f')
meas_file=sys.argv[ind+1]
if '-fsp' in sys.argv:
ind=sys.argv.index('-fsp')
inspec=sys.argv[ind+1]
if '-fan' in sys.argv:
ind=sys.argv.index('-fan')
anisfile=sys.argv[ind+1]
anis=1
anis_data,file_type=pmag.magic_read(anisfile)
if pmagplotlib.verbose: print "Anisotropy data read in from ", anisfile
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt='.'+sys.argv[ind+1]
if '-sav' in sys.argv: plots=1
if '-z' in sys.argv: Zdiff=1
if '-spc' in sys.argv:
ind=sys.argv.index('-spc')
spc=sys.argv[ind+1]
if '-b' in sys.argv:
ind=sys.argv.index('-b')
BEG=int(sys.argv[ind+1])
END=int(sys.argv[ind+2])
if '-fcr' in sys.argv:
ind=sys.argv.index('-fcr')
critout=sys.argv[ind+1]
crit_data,file_type=pmag.magic_read(critout)
if pmagplotlib.verbose:
print "Acceptance criteria read in from ", critout
accept={}
accept['specimen_int_ptrm_n']=2.0
for critrec in crit_data:
if critrec["pmag_criteria_code"]=="IE-SPEC":
for key in accept_keys:
if key not in critrec.keys():
accept[key]=-1
else:
accept[key]=float(critrec[key])
try:
open(inspec,'rU')
PriorRecs,file_type=pmag.magic_read(inspec)
if file_type != 'pmag_specimens':
print file_type
print file_type,inspec," is not a valid pmag_specimens file "
sys.exit()
for rec in PriorRecs:
if 'magic_software_packages' not in rec.keys():rec['magic_software_packages']=""
except IOError:
PriorRecs=[]
if pmagplotlib.verbose:print "starting new specimen interpretation file: ",inspec
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()
backup=0
# define figure numbers for arai, zijderveld and
# de-,re-magization diagrams
AZD={}
AZD['deremag'], AZD['zijd'],AZD['arai'],AZD['eqarea']=1,2,3,4
pmagplotlib.plot_init(AZD['arai'],5,5)
pmagplotlib.plot_init(AZD['zijd'],5,5)
pmagplotlib.plot_init(AZD['deremag'],5,5)
pmagplotlib.plot_init(AZD['eqarea'],5,5)
#
#
#
# get list of unique specimen names
#
CurrRec=[]
sids=pmag.get_specs(meas_data)
# get plots for specimen s - default is just to step through arai diagrams
#
if spc!="": specimen =sids.index(spc)
while specimen < len(sids):
methcodes=[]
if pmagplotlib.verbose:
print sids[specimen],specimen+1, 'of ', len(sids)
MeasRecs=[]
s=sids[specimen]
datablock,trmblock,tdsrecs=[],[],[]
PmagSpecRec={}
if first==0:
for key in keys:PmagSpecRec[key]="" # make sure all new records have same set of keys
PmagSpecRec["er_analyst_mail_names"]=user
PmagSpecRec["specimen_correction"]='u'
#
# find the data from the meas_data file for this specimen
#
for rec in meas_data:
if rec["er_specimen_name"]==s:
MeasRecs.append(rec)
methods=rec["magic_method_codes"].split(":")
meths=[]
for meth in methods:
meths.append(meth.strip()) # take off annoying spaces
methods=""
for meth in meths:
if meth.strip() not in methcodes and "LP-" in meth:methcodes.append(meth.strip())
methods=methods+meth+":"
methods=methods[:-1]
rec["magic_method_codes"]=methods
if "LP-PI-TRM" in meths: datablock.append(rec)
if "LP-TRM" in meths: trmblock.append(rec)
if "LP-TRM-TD" in meths: tdsrecs.append(rec)
if len(trmblock)>2 and inspec!="":
if Tinit==0:
Tinit=1
AZD['TRM']=5
pmagplotlib.plot_init(AZD['TRM'],5,5)
elif Tinit==1: # clear the TRM figure if not needed
pmagplotlib.clearFIG(AZD['TRM'])
if len(tdsrecs)>2:
if TDinit==0:
TDinit=1
AZD['TDS']=6
pmagplotlib.plot_init(AZD['TDS'],5,5)
elif TDinit==1: # clear the TDS figure if not needed
pmagplotlib.clearFIG(AZD['TDS'])
if len(datablock) <4:
if backup==0:
specimen+=1
if pmagplotlib.verbose:
print 'skipping specimen - moving forward ', s
else:
specimen-=1
if pmagplotlib.verbose:
print 'skipping specimen - moving backward ', s
#
# collect info for the PmagSpecRec dictionary
#
else:
rec=datablock[0]
PmagSpecRec["er_citation_names"]="This study"
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 "magic_instrument_codes" not in rec.keys():rec["magic_instrument_codes"]=""
PmagSpecRec["magic_instrument_codes"]=rec["magic_instrument_codes"]
PmagSpecRec["measurement_step_unit"]="K"
if "magic_experiment_name" not in rec.keys():
rec["magic_experiment_name"]=""
else:
PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"]
meths=rec["magic_method_codes"].split()
# sort data into types
araiblock,field=pmag.sortarai(datablock,s,Zdiff)
first_Z=araiblock[0]
GammaChecks=araiblock[5]
if len(first_Z)<3:
if backup==0:
specimen+=1
if pmagplotlib.verbose:
print 'skipping specimen - moving forward ', s
else:
specimen-=1
if pmagplotlib.verbose:
print 'skipping specimen - moving backward ', s
else:
backup=0
zijdblock,units=pmag.find_dmag_rec(s,meas_data)
recnum=0
if pmagplotlib.verbose:
print "index step Dec Inc Int Gamma"
for plotrec in zijdblock:
if GammaChecks!="":
gamma=""
for g in GammaChecks:
if g[0]==plotrec[0]-273:
gamma=g[1]
break
if gamma!="":
print '%i %i %7.1f %7.1f %8.3e %7.1f' % (recnum,plotrec[0]-273,plotrec[1],plotrec[2],plotrec[3],gamma)
else:
print '%i %i %7.1f %7.1f %8.3e ' % (recnum,plotrec[0]-273,plotrec[1],plotrec[2],plotrec[3])
recnum += 1
pmagplotlib.plotAZ(AZD,araiblock,zijdblock,s,units[0])
if len(tdsrecs)>2: # a TDS experiment
tdsblock=[] # make a list for the TDS data
Mkeys=['measurement_magnitude','measurement_magn_moment','measurement_magn_volume','measuruement_magn_mass']
mkey,k="",0
while mkey=="" and k<len(Mkeys)-1: # find which type of intensity
key= Mkeys[k]
if key in tdsrecs[0].keys() and tdsrecs[0][key]!="": mkey=key
k+=1
if mkey=="":break # get outta here
Tnorm=""
for tdrec in tdsrecs:
meths=tdrec['magic_method_codes'].split(":")
for meth in meths: meth.replace(" ","") # strip off potential nasty spaces
if 'LT-T-I' in meths and Tnorm=="": # found first total TRM
Tnorm=float(tdrec[mkey]) # normalize by total TRM
tdsblock.append([273,zijdblock[0][3]/Tnorm,1.]) # put in the zero step
if 'LT-T-Z' in meths and Tnorm!="": # found a LP-TRM-TD demag step, now need complementary LT-T-Z from zijdblock
step=float(tdrec['treatment_temp'])
Tint=""
if mkey!="":
Tint=float(tdrec[mkey])
if Tint!="":
for zrec in zijdblock:
if zrec[0]==step: # found matching
tdsblock.append([step,zrec[3]/Tnorm,Tint/Tnorm])
break
if len(tdsblock)>2:
pmagplotlib.plotTDS(AZD['TDS'],tdsblock,s+':LP-PI-TDS:')
else:
print "Something wrong here"
if anis==1: # look up anisotropy data for this specimen
AniSpec=""
for aspec in anis_data:
if aspec["er_specimen_name"]==PmagSpecRec["er_specimen_name"]:
AniSpec=aspec
if pmagplotlib.verbose: print 'Found anisotropy record...'
break
if inspec !="":
if pmagplotlib.verbose: print 'Looking up saved interpretation....'
found = 0
for k in range(len(PriorRecs)):
try:
if PriorRecs[k]["er_specimen_name"]==s:
found =1
CurrRec.append(PriorRecs[k])
for j in range(len(zijdblock)):
if float(zijdblock[j][0])==float(PriorRecs[k]["measurement_step_min"]):start=j
if float(zijdblock[j][0])==float(PriorRecs[k]["measurement_step_max"]):end=j
pars,errcode=pmag.PintPars(araiblock,zijdblock,start,end)
pars['measurement_step_unit']="K"
pars['experiment_type']='LP-PI-TRM'
del PriorRecs[k] # put in CurrRec, take out of PriorRecs
if errcode!=1:
pars["specimen_lab_field_dc"]=field
pars["specimen_int"]=-1*field*pars["specimen_b"]
pars["er_specimen_name"]=s
if pmagplotlib.verbose:
print 'Saved interpretation: '
pars=pmag.scoreit(pars,PmagSpecRec,accept,'',0)
pmagplotlib.plotB(AZD,araiblock,zijdblock,pars)
if len(trmblock)>2:
blab=field
best=pars["specimen_int"]
Bs,TRMs=[],[]
for trec in trmblock:
Bs.append(float(trec['treatment_dc_field']))
TRMs.append(float(trec['measurement_magn_moment']))
NLpars=nlt.NLtrm(Bs,TRMs,best,blab,0) # calculate best fit parameters through TRM acquisition data, and get new banc
Mp,Bp=[],[]
for k in range(int(max(Bs)*1e6)):
Bp.append(float(k)*1e-6)
npred=nlt.TRM(Bp[-1],NLpars['xopt'][0],NLpars['xopt'][1]) # predicted NRM for this field
Mp.append(npred)
pmagplotlib.plotTRM(AZD['TRM'],Bs,TRMs,Bp,Mp,NLpars,trec['magic_experiment_name'])
PmagSpecRec['specimen_int']=NLpars['banc']
if pmagplotlib.verbose:
print 'Banc= ',float(NLpars['banc'])*1e6
pmagplotlib.drawFIGS(AZD)
if AniSpec!="":
AniSpecRec=pmag.thellier_anis_corr(PmagSpecRec,AniSpec)
print 'Anisotropy corrected intensity= ',float(AniSpecRec['specimen_int'])*1e6
else:
print 'error on specimen ',s
except:
pass
if pmagplotlib.verbose and found==0: print ' None found :( '
if spc!="":
if BEG!="":
pars,errcode=pmag.PintPars(araiblock,zijdblock,BEG,END)
pars['measurement_step_unit']="K"
pars["specimen_lab_field_dc"]=field
pars["specimen_int"]=-1*field*pars["specimen_b"]
pars["er_specimen_name"]=s
pars['specimen_grade']='' # ungraded
pmagplotlib.plotB(AZD,araiblock,zijdblock,pars)
if len(trmblock)>2:
if inlt==0:
inlt=1
blab=field
best=pars["specimen_int"]
Bs,TRMs=[],[]
for trec in trmblock:
Bs.append(float(trec['treatment_dc_field']))
TRMs.append(float(trec['measurement_magn_moment']))
NLpars=nlt.NLtrm(Bs,TRMs,best,blab,0) # calculate best fit parameters through TRM acquisition data, and get new banc
#
Mp,Bp=[],[]
for k in range(int(max(Bs)*1e6)):
Bp.append(float(k)*1e-6)
npred=nlt.TRM(Bp[-1],NLpars['xopt'][0],NLpars['xopt'][1]) # predicted NRM for this field
files={}
for key in AZD.keys():
files[key]=s+'_'+key+fmt
pmagplotlib.saveP(AZD,files)
sys.exit()
if plots==0:
ans='b'
while ans != "":
print """
s[a]ve plot, set [b]ounds for calculation, [d]elete current interpretation, [p]revious, [s]ample, [q]uit:
"""
ans=raw_input('Return for next specimen \n')
if ans=="":
specimen +=1
if ans=="d":
save_redo(PriorRecs,inspec)
CurrRec=[]
pmagplotlib.plotAZ(AZD,araiblock,zijdblock,s,units[0])
pmagplotlib.drawFIGS(AZD)
if ans=='a':
files={}
for key in AZD.keys():
files[key]=s+'_'+key+fmt
pmagplotlib.saveP(AZD,files)
ans=""
if ans=='q':
print "Good bye"
sys.exit()
if ans=='p':
specimen =specimen -1
backup = 1
ans=""
if ans=='s':
keepon=1
spec=raw_input('Enter desired specimen name (or first part there of): ')
while keepon==1:
try:
specimen =sids.index(spec)
keepon=0
except:
tmplist=[]
for qq in range(len(sids)):
if spec in sids[qq]:tmplist.append(sids[qq])
print specimen," not found, but this was: "
print tmplist
spec=raw_input('Select one or try again\n ')
ans=""
if ans=='b':
if end==0 or end >=len(zijdblock):end=len(zijdblock)-1
GoOn=0
while GoOn==0:
print 'Enter index of first point for calculation: ','[',start,']'
answer=raw_input('return to keep default ')
if answer != "":start=int(answer)
print 'Enter index of last point for calculation: ','[',end,']'
answer=raw_input('return to keep default ')
if answer != "":
end=int(answer)
if start >=0 and start <len(zijdblock)-2 and end >0 and end <len(zijdblock) or start>=end:
GoOn=1
else:
print "Bad endpoints - try again! "
start,end=0,len(zijdblock)
s=sids[specimen]
pars,errcode=pmag.PintPars(araiblock,zijdblock,start,end)
pars['measurement_step_unit']="K"
pars["specimen_lab_field_dc"]=field
pars["specimen_int"]=-1*field*pars["specimen_b"]
pars["er_specimen_name"]=s
pars=pmag.scoreit(pars,PmagSpecRec,accept,'',0)
PmagSpecRec["measurement_step_min"]='%8.3e' % (pars["measurement_step_min"])
PmagSpecRec["measurement_step_max"]='%8.3e' % (pars["measurement_step_max"])
PmagSpecRec["measurement_step_unit"]="K"
PmagSpecRec["specimen_int_n"]='%i'%(pars["specimen_int_n"])
PmagSpecRec["specimen_lab_field_dc"]='%8.3e'%(pars["specimen_lab_field_dc"])
PmagSpecRec["specimen_int"]='%9.4e '%(pars["specimen_int"])
PmagSpecRec["specimen_b"]='%5.3f '%(pars["specimen_b"])
PmagSpecRec["specimen_q"]='%5.1f '%(pars["specimen_q"])
PmagSpecRec["specimen_f"]='%5.3f '%(pars["specimen_f"])
PmagSpecRec["specimen_fvds"]='%5.3f'%(pars["specimen_fvds"])
PmagSpecRec["specimen_b_beta"]='%5.3f'%(pars["specimen_b_beta"])
PmagSpecRec["specimen_int_mad"]='%7.1f'%(pars["specimen_int_mad"])
PmagSpecRec["specimen_Z"]='%7.1f'%(pars["specimen_Z"])
PmagSpecRec["specimen_gamma"]='%7.1f'%(pars["specimen_gamma"])
PmagSpecRec["specimen_grade"]=pars["specimen_grade"]
if pars["method_codes"]!="":
tmpcodes=pars["method_codes"].split(":")
for t in tmpcodes:
if t.strip() not in methcodes:methcodes.append(t.strip())
PmagSpecRec["specimen_dec"]='%7.1f'%(pars["specimen_dec"])
PmagSpecRec["specimen_inc"]='%7.1f'%(pars["specimen_inc"])
PmagSpecRec["specimen_tilt_correction"]='-1'
PmagSpecRec["specimen_direction_type"]='l'
PmagSpecRec["direction_type"]='l' # this is redudant, but helpful - won't be imported
PmagSpecRec["specimen_dang"]='%7.1f '%(pars["specimen_dang"])
PmagSpecRec["specimen_drats"]='%7.1f '%(pars["specimen_drats"])
PmagSpecRec["specimen_int_ptrm_n"]='%i '%(pars["specimen_int_ptrm_n"])
PmagSpecRec["specimen_rsc"]='%6.4f '%(pars["specimen_rsc"])
PmagSpecRec["specimen_md"]='%i '%(int(pars["specimen_md"]))
if PmagSpecRec["specimen_md"]=='-1':PmagSpecRec["specimen_md"]=""
PmagSpecRec["specimen_b_sigma"]='%5.3f '%(pars["specimen_b_sigma"])
if "IE-TT" not in methcodes:methcodes.append("IE-TT")
methods=""
for meth in methcodes:
methods=methods+meth+":"
PmagSpecRec["magic_method_codes"]=methods[:-1]
PmagSpecRec["specimen_description"]=comment
PmagSpecRec["magic_software_packages"]=version_num
pmagplotlib.plotAZ(AZD,araiblock,zijdblock,s,units[0])
pmagplotlib.plotB(AZD,araiblock,zijdblock,pars)
if len(trmblock)>2:
blab=field
best=pars["specimen_int"]
Bs,TRMs=[],[]
for trec in trmblock:
Bs.append(float(trec['treatment_dc_field']))
TRMs.append(float(trec['measurement_magn_moment']))
NLpars=nlt.NLtrm(Bs,TRMs,best,blab,0) # calculate best fit parameters through TRM acquisition data, and get new banc
Mp,Bp=[],[]
for k in range(int(max(Bs)*1e6)):
Bp.append(float(k)*1e-6)
npred=nlt.TRM(Bp[-1],NLpars['xopt'][0],NLpars['xopt'][1]) # predicted NRM for this field
Mp.append(npred)
pmagplotlib.plotTRM(AZD['TRM'],Bs,TRMs,Bp,Mp,NLpars,trec['magic_experiment_name'])
print 'Non-linear TRM corrected intensity= ',float(NLpars['banc'])*1e6
pmagplotlib.drawFIGS(AZD)
pars["specimen_lab_field_dc"]=field
pars["specimen_int"]=-1*field*pars["specimen_b"]
saveit=raw_input("Save this interpretation? [y]/n \n")
if saveit!='n':
PriorRecs.append(PmagSpecRec) # put back an interpretation
specimen+=1
if first==1:
first=0
PriorRecs,keys=pmag.fillkeys(PriorRecs)
save_redo(PriorRecs,inspec)
ans=""
else:
specimen+=1
if fmt != ".pmag":
basename=s+'_thellier'+fmt
files={}
for key in AZD.keys():
files[key]=s+'_'+key+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['deremag']='DeReMag Plot'
titles['zijd']='Zijderveld Plot'
titles['arai']='Arai Plot'
AZD = pmagplotlib.addBorders(AZD,titles,black,purple)
pmagplotlib.saveP(AZD,files)
# pmagplotlib.combineFigs(s,files,3)
else: # save in pmag format
script="grep "+s+" output.mag | thellier -mfsi"
script=script+' %8.4e'%(field)
min='%i'%((pars["measurement_step_min"]-273))
Max='%i'%((pars["measurement_step_max"]-273))
script=script+" "+min+" "+Max
script=script+" |plotxy;cat mypost >>thellier.ps\n"
pltf.write(script)
pmag.domagicmag(outf,MeasRecs)
if len(CurrRec)>0:
for rec in CurrRec:
PriorRecs.append(rec)
CurrRec=[]
if plots!=1:
ans=raw_input(" Save last plot? 1/[0] ")
if ans=="1":
if fmt != ".pmag":
files={}
for key in AZD.keys():
files[key]=s+'_'+key+fmt
pmagplotlib.saveP(AZD,files)
else:
print "\n Good bye\n"
sys.exit()
if len(CurrRec)>0:PriorRecs.append(CurrRec) # put back an interpretation
if len(PriorRecs)>0:
save_redo(PriorRecs,inspec)
print 'Updated interpretations saved in ',inspec
if pmagplotlib.verbose:
print "Good bye"
def main():
"""
NAME
2G_bin_magic.py
DESCRIPTION
takes the binary 2G format magnetometer files and converts them to magic_measurements, er_samples.txt and er_sites.txt file
SYNTAX
2G_magic.py [command line options]
OPTIONS
-f FILE: specify input 2G (binary) file
-F FILE: specify magic_measurements output file, default is: magic_measurements.txt
-Fsa FILE: specify output file, default is: er_samples.txt
-Fsi FILE: specify output file, default is: er_sies.txt
-ncn NCON: specify naming convention: default is #2 below
-ocn OCON: specify orientation convention, default is #5 below
-mcd: specify sampling method codes as a colon delimited string: [default is: FS-FD:SO-POM]
FS-FD field sampling done with a drill
FS-H field sampling done with hand samples
FS-LOC-GPS field location done with GPS
FS-LOC-MAP field location done with map
SO-POM a Pomeroy orientation device was used
SO-ASC an ASC orientation device was used
SO-MAG orientation with magnetic compass
SO-SUN orientation with sun compass
-loc: location name, default="unknown"
-spc NUM : specify number of characters to designate a specimen, default = 0
-ins INST : specify instsrument name
-a: average replicate measurements
INPUT FORMAT
Input files are horrible mag binary format (who knows why?)
Orientation convention:
[1] Lab arrow azimuth= mag_azimuth; Lab arrow dip=-field_dip
i.e., field_dip is degrees from vertical down - the hade [default]
[2] Lab arrow azimuth = mag_azimuth-90; Lab arrow dip = -field_dip
i.e., mag_azimuth is strike and field_dip is hade
[3] Lab arrow azimuth = mag_azimuth; Lab arrow dip = 90-field_dip
i.e., lab arrow same as field arrow, but field_dip was a hade.
[4] lab azimuth and dip are same as mag_azimuth, field_dip
[5] lab azimuth is same as mag_azimuth,lab arrow dip=field_dip-90
[6] Lab arrow azimuth = mag_azimuth-90; Lab arrow dip = 90-field_dip
[7] all others you will have to either customize your
self or e-mail [email protected] for help.
Magnetic declination convention:
Az will use supplied declination to correct azimuth
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
OUTPUT
output saved in magic_measurements.txt & er_samples.txt formatted files
will overwrite any existing files
"""
#
# initialize variables
#
specnum = 0
ub_file, samp_file, or_con, corr, meas_file = "", "er_samples.txt", "3", "1", "magic_measurements.txt"
pos_file, site_file = "", "er_sites.txt"
noave = 1
args = sys.argv
bed_dip, bed_dip_dir = "", ""
samp_con, Z, average_bedding = "2", 1, "0"
meths = "FS-FD"
sclass, lithology, type = "", "", ""
user, inst = "", ""
DecCorr = 0.0
location_name = "unknown"
months = ["Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec"]
gmeths = ""
#
#
dir_path = "."
if "-WD" in args:
ind = args.index("-WD")
dir_path = sys.argv[ind + 1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-f" in args:
ind = args.index("-f")
mag_file = sys.argv[ind + 1]
if "-fpos" in args:
ind = args.index("-fpos")
pos_file = sys.argv[ind + 1]
if "-F" in args:
ind = args.index("-F")
meas_file = sys.argv[ind + 1]
if "-Fsa" in args:
ind = args.index("-Fsa")
samp_file = sys.argv[ind + 1]
if "-Fsi" in args:
ind = args.index("-Fsi")
site_file = sys.argv[ind + 1]
if "-ocn" in args:
ind = args.index("-ocn")
or_con = sys.argv[ind + 1]
if "-ncn" in args:
ind = args.index("-ncn")
samp_con = sys.argv[ind + 1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "7"
if "6" in samp_con:
try:
Samps, file_type = pmag.magic_read(dir_path + "/er_samples.txt")
except:
print "there is no er_samples.txt file available - you can't use naming convention #6"
sys.exit()
if "-mcd" in args:
ind = args.index("-mcd")
gmeths = sys.argv[ind + 1]
if "-loc" in args:
ind = args.index("-loc")
location_name = sys.argv[ind + 1]
if "-spc" in args:
ind = args.index("-spc")
specnum = int(args[ind + 1])
if specnum != 0:
specnum = -specnum
if "-ins" in args:
ind = args.index("-ins")
inst = args[ind + 1]
if "-a" in args:
noave = 0
#
#
mag_file = dir_path + "/" + mag_file
samp_file = dir_path + "/" + samp_file
site_file = dir_path + "/" + site_file
meas_file = dir_path + "/" + meas_file
samplist = []
try:
Samps, file_type = pmag.magic_read(samp_file)
for samp in Samps:
if samp["er_sample_name"] not in samplist:
samplist.append(samp["er_sample_name"])
except:
Samps = []
MagRecs = []
f = open(mag_file, "rU")
input = f.read()
f.close()
firstline, date = 1, ""
d = input.split("\xcd")
for line in d:
rec = line.split("\x00")
if firstline == 1:
firstline = 0
spec, vol = "", 1
for c in line[15:23]:
if c != "\x00":
spec = spec + c
# check for bad sample name
test = spec.split(".")
date = ""
if len(test) > 1:
spec = test[0]
kk = 24
while line[kk] != "\x01" and line[kk] != "\x00":
kk += 1
vcc = line[24:kk]
el = 10
while rec[el].strip() != "":
el += 1
date, comments = rec[el + 7], []
else:
el = 9
while rec[el] != "\x01":
el += 1
vcc, date, comments = rec[el - 3], rec[el + 7], []
specname = spec.lower()
print "importing ", specname
el += 8
while rec[el].isdigit() == False:
comments.append(rec[el])
el += 1
while rec[el] == "":
el += 1
az = float(rec[el])
el += 1
while rec[el] == "":
el += 1
pl = float(rec[el])
el += 1
while rec[el] == "":
el += 1
bed_dip_dir = float(rec[el])
el += 1
while rec[el] == "":
el += 1
bed_dip = float(rec[el])
el += 1
while rec[el] == "":
el += 1
if rec[el] == "\x01":
bed_dip = 180.0 - bed_dip
el += 1
while rec[el] == "":
el += 1
fold_az = float(rec[el])
el += 1
while rec[el] == "":
el += 1
fold_pl = rec[el]
el += 1
while rec[el] == "":
el += 1
if rec[el] != "" and rec[el] != "\x02" and rec[el] != "\x01":
deccorr = float(rec[el])
az += deccorr
bed_dip_dir += deccorr
fold_az += deccorr
if bed_dip_dir >= 360:
bed_dip_dir = bed_dip_dir - 360.0
if az >= 360.0:
az = az - 360.0
if fold_az >= 360.0:
fold_az = fold_az - 360.0
else:
deccorr = 0
if specnum != 0:
sample = specname[:specnum]
else:
sample = specname
SampRec = {}
SampRec["er_sample_name"] = sample
SampRec["er_location_name"] = location_name
SampRec["er_citation_names"] = "This study"
labaz, labdip = pmag.orient(az, pl, or_con) # convert to labaz, labpl
#
# parse information common to all orientation methods
#
SampRec["sample_bed_dip"] = "%7.1f" % (bed_dip)
SampRec["sample_bed_dip_direction"] = "%7.1f" % (bed_dip_dir)
SampRec["sample_dip"] = "%7.1f" % (labdip)
SampRec["sample_azimuth"] = "%7.1f" % (labaz)
if vcc.strip() != "":
vol = float(vcc) * 1e-6 # convert to m^3 from cc
SampRec["sample_volume"] = "%10.3e" % (vol) #
SampRec["sample_class"] = sclass
SampRec["sample_lithology"] = lithology
SampRec["sample_type"] = type
SampRec["sample_declination_correction"] = "%7.1f" % (deccorr)
methods = gmeths.split(":")
if deccorr != "0":
if "SO-MAG" in methods:
del methods[methods.index("SO-MAG")]
methods.append("SO-CMD-NORTH")
meths = ""
for meth in methods:
meths = meths + meth + ":"
meths = meths[:-1]
SampRec["magic_method_codes"] = meths
if int(samp_con) < 6:
site = pmag.parse_site(SampRec["er_sample_name"], samp_con, Z) # parse out the site name
SampRec["er_site_name"] = site
elif len(Samps) > 1:
site, location = "", ""
for samp in Samps:
if samp["er_sample_name"] == SampRec["er_sample_name"]:
site = samp["er_site_name"]
location = samp["er_location_name"]
break
SampRec["er_location_name"] = samp["er_location_name"]
SampRec["er_site_name"] = samp["er_site_name"]
if sample not in samplist:
samplist.append(sample)
Samps.append(SampRec)
else:
MagRec = {}
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"
meas_type = "LT-NO"
MagRec["measurement_flag"] = "g"
MagRec["measurement_standard"] = "u"
MagRec["measurement_number"] = "1"
MagRec["er_specimen_name"] = specname
MagRec["er_sample_name"] = SampRec["er_sample_name"]
MagRec["er_site_name"] = SampRec["er_site_name"]
MagRec["er_location_name"] = location_name
el, demag = 1, ""
treat = rec[el]
if treat[-1] == "C":
demag = "T"
elif treat != "NRM":
demag = "AF"
el += 1
while rec[el] == "":
el += 1
MagRec["measurement_dec"] = rec[el]
cdec = float(rec[el])
el += 1
while rec[el] == "":
el += 1
MagRec["measurement_inc"] = rec[el]
cinc = float(rec[el])
el += 1
while rec[el] == "":
el += 1
gdec = rec[el]
el += 1
while rec[el] == "":
el += 1
ginc = rec[el]
el = skip(2, el, rec) # skip bdec,binc
# el=skip(4,el,rec) # skip gdec,ginc,bdec,binc
# print 'moment emu: ',rec[el]
MagRec["measurement_magn_moment"] = "%10.3e" % (float(rec[el]) * 1e-3) # moment in Am^2 (from emu)
MagRec["measurement_magn_volume"] = "%10.3e" % (float(rec[el]) * 1e-3 / vol) # magnetization in A/m
el = skip(2, el, rec) # skip to xsig
MagRec["measurement_sd_x"] = "%10.3e" % (float(rec[el]) * 1e-3) # convert from emu
el = skip(3, el, rec) # skip to ysig
MagRec["measurement_sd_y"] = "%10.3e" % (float(rec[el]) * 1e-3) # convert from emu
el = skip(3, el, rec) # skip to zsig
MagRec["measurement_sd_z"] = "%10.3e" % (float(rec[el]) * 1e-3) # convert from emu
el += 1 # skip to positions
MagRec["measurement_positions"] = rec[el]
# el=skip(5,el,rec) # skip to date
# mm=str(months.index(date[0]))
# if len(mm)==1:
# mm='0'+str(mm)
# else:
# mm=str(mm)
# dstring=date[2]+':'+mm+':'+date[1]+":"+date[3]
# MagRec['measurement_date']=dstring
MagRec["magic_instrument_codes"] = inst
MagRec["er_analyst_mail_names"] = ""
MagRec["er_citation_names"] = "This study"
MagRec["magic_method_codes"] = meas_type
if demag == "AF":
MagRec["treatment_ac_field"] = "%8.3e" % (float(treat[:-2]) * 1e-3) # peak field in tesla
meas_type = "LT-AF-Z"
MagRec["treatment_dc_field"] = "0"
elif demag == "T":
MagRec["treatment_temp"] = "%8.3e" % (float(treat[:-1]) + 273.0) # temp in kelvin
meas_type = "LT-T-Z"
MagRec["magic_method_codes"] = meas_type
MagRecs.append(MagRec)
MagOuts = pmag.measurements_methods(MagRecs, noave)
pmag.magic_write(meas_file, MagOuts, "magic_measurements")
print "Measurements put in ", meas_file
SampsOut, sampkeys = pmag.fillkeys(Samps)
pmag.magic_write(samp_file, SampsOut, "er_samples")
Sites = []
for samp in Samps:
SiteRec = {}
SiteRec["er_site_name"] = samp["er_site_name"]
SiteRec["er_location_name"] = samp["er_location_name"]
SiteRec["site_definition"] = "s"
SiteRec["er_citation_names"] = "This study"
if "sample_class" in samp.keys():
SiteRec["site_class"] = samp["sample_class"]
if "sample_lithology" in samp.keys():
SiteRec["site_lithology"] = samp["sample_lithology"]
if "sample_type" in samp.keys():
SiteRec["site_lithology"] = samp["sample_lithology"]
if "sample_lat" in samp.keys():
SiteRec["site_lat"] = samp["sample_lat"]
else:
SiteRec["site_lat"] = "-999"
if "sample_lon" in samp.keys():
SiteRec["site_lon"] = samp["sample_lon"]
else:
SiteRec["site_lon"] = "-999"
if "sample_height" in samp.keys():
SiteRec["site_height"] = samp["sample_height"]
Sites.append(SiteRec)
pmag.magic_write(site_file, Sites, "er_sites")
def main(command_line=True, **kwargs):
"""
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('"')) + 273.0 # 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?"
return False, "no data found. bad magfile?"
def main():
"""
NAME
IODP_csv_magic.py
DESCRIPTION
converts ODP LIMS sample format files to magic_measurements format files
SYNTAX
IODP_csv_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
-Fsp FILE: specify output er_specimens.txt file, default is er_specimens.txt
-Fsa FILE: specify output er_samples.txt file, default is er_samples.txt
-Fsi FILE: specify output er_sites.txt file, default is er_sites.txt
-A : don't average replicate measurements
INPUTS
IODP .csv file format exported from LIMS database
"""
#
#
version_num=pmag.get_version()
meas_file='magic_measurements.txt'
spec_file='er_specimens.txt'
samp_file='er_samples.txt'
site_file='er_sites.txt'
csv_file=''
ErSpecs,ErSamps,ErSites,ErLocs,ErCits=[],[],[],[],[]
MagRecs=[]
citation="This study"
dir_path,demag='.','NRM'
args=sys.argv
noave=0
depth_method='a'
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
print "dir_path", dir_path
if "-h" in args:
print main.__doc__
sys.exit()
if "-A" in args: noave=1
if '-f' in args:
ind=args.index("-f")
# csv_file=args[ind+1] # original
csv_file=dir_path + '/' + args[ind+1] # LJ
if '-F' in args:
ind=args.index("-F")
meas_file=args[ind+1]
if '-Fsp' in args:
ind=args.index("-Fsp")
spec_file=dir_path+'/'+args[ind+1]
Specs,file_type=pmag.magic_read(spec_file)
else:
spec_file=dir_path+'/'+spec_file
if '-Fsi' in args:
ind=args.index("-Fsi")
site_file=args[ind+1]
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file=dir_path+'/'+args[ind+1]
ErSamps,file_type=pmag.magic_read(samp_file)
else:
samp_file=dir_path+'/'+samp_file
site_file=dir_path+'/'+site_file
meas_file=dir_path+'/'+meas_file
if csv_file=="":
filelist=os.listdir(dir_path) # read in list of files to import
else:
filelist=[csv_file]
specimens,samples,sites=[],[],[]
MagRecs,SpecRecs,SampRecs,SiteRecs=[],[],[],[]
for samp in ErSamps:
if samp['er_sample_name'] not in samples:
samples.append(samp['er_sample_name'])
SampRecs.append(samp)
print "filelist", filelist # LJ
for file in filelist: # parse each file
if file[-3:].lower()=='csv':
print 'processing: ',file
input=open(file,'rU').readlines()
keys=input[0].replace('\n','').split(',') # splits on underscores
if "Interval Top (cm) on SHLF" in keys:interval_key="Interval Top (cm) on SHLF"
if " Interval Bot (cm) on SECT" in keys:interval_key=" Interval Bot (cm) on SECT"
if "Top Depth (m)" in keys:depth_key="Top Depth (m)"
if "CSF-A Top (m)" in keys:depth_key="CSF-A Top (m)"
if "CSF-B Top (m)" in keys:
comp_depth_key="CSF-B Top (m)" # use this model if available
else:
comp_depth_key=""
if "Demag level (mT)" in keys:demag_key="Demag level (mT)"
if "Demag Level (mT)" in keys: demag_key="Demag Level (mT)"
if "Inclination (Tray- and Bkgrd-Corrected) (deg)" in keys:inc_key="Inclination (Tray- and Bkgrd-Corrected) (deg)"
if "Inclination background + tray corrected (deg)" in keys:inc_key="Inclination background + tray corrected (deg)"
if "Inclination background + tray corrected (\xc2\xb0)" in keys:inc_key="Inclination background + tray corrected (\xc2\xb0)"
if "Declination (Tray- and Bkgrd-Corrected) (deg)" in keys:dec_key="Declination (Tray- and Bkgrd-Corrected) (deg)"
if "Declination background + tray corrected (deg)" in keys:dec_key="Declination background + tray corrected (deg)"
if "Declination background + tray corrected (\xc2\xb0)" in keys:dec_key="Declination background + tray corrected (\xc2\xb0)"
if "Intensity (Tray- and Bkgrd-Corrected) (A/m)" in keys:int_key="Intensity (Tray- and Bkgrd-Corrected) (A/m)"
if "Intensity background + tray corrected (A/m)" in keys:int_key="Intensity background + tray corrected (A/m)"
if "Core Type" in keys:
type="Core Type"
else: type="Type"
for line in input[1:]:
InRec={}
for k in range(len(keys)):InRec[keys[k]]=line.split(',')[k]
try:
run_number=""
inst="ODP-SRM"
volume='15.59' # set default volume to this
MagRec,SpecRec,SampRec,SiteRec={},{},{},{}
expedition=InRec['Exp']
location=InRec['Site']+InRec['Hole']
# Maintain backward compatibility for the ever-changing LIMS format (Argh!)
while len(InRec['Core'])<3:
InRec['Core']='0'+InRec['Core']
if "Last Tray Measurment" in InRec.keys() and "Discrete" in InRec['Last Tray Measurement'] or 'dscr' in csv_file : # assume discrete sample
specimen=expedition+'-'+location+'-'+InRec['Core']+InRec[type]+"-"+InRec['Section']+'-'+InRec['Section Half']+'-'+InRec[interval_key]
else: # mark as continuous measurements
specimen=expedition+'-'+location+'-'+InRec['Core']+InRec[type]+"_"+InRec['Section']+InRec['Section Half']+'-'+InRec[interval_key]
SpecRec['er_expedition_name']=expedition
SpecRec['er_location_name']=location
SpecRec['er_site_name']=specimen
SpecRec['er_citation_names']=citation
for key in SpecRec.keys():SampRec[key]=SpecRec[key]
for key in SpecRec.keys():SiteRec[key]=SpecRec[key]
SampRec['sample_azimuth']='0'
SampRec['sample_dip']='0'
SampRec['sample_core_depth']=InRec[depth_key]
if comp_depth_key!='':
SampRec['sample_composite_depth']=InRec[comp_depth_key]
if "Discrete" in InRec['Last Tray Measurement']:
SampRec['magic_method_codes']='FS-C-DRILL-IODP:SP-SS-C:SO-V'
else:
SampRec['magic_method_codes']='FS-C-DRILL-IODP:SO-V'
SpecRec['er_specimen_name']=specimen
SpecRec['er_sample_name']=specimen
SampRec['er_sample_name']=specimen
SampRec['er_specimen_names']=specimen
SiteRec['er_specimen_names']=specimen
for key in SpecRec.keys():MagRec[key]=SpecRec[key]
# set up measurement record - default is NRM
MagRec['er_analyst_mail_names']=InRec['Test Entered By']
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"
SpecRec['er_specimen_alternatives']=InRec['Text Id']
if 'Sample Area (cm?)' in InRec.keys() and InRec['Sample Area (cm?)']!= "": volume=InRec['Sample Area (cm?)']
if InRec['Run Number']!= "": run_number=InRec['Run Number']
datestamp=InRec['Test Changed On'].split() # date time is second line of file
mmddyy=datestamp[0].split('/') # break into month day year
if len(mmddyy[0])==1: mmddyy[0]='0'+mmddyy[0] # make 2 characters
if len(mmddyy[1])==1: mmddyy[1]='0'+mmddyy[1] # make 2 characters
if len(datestamp[1])==1: datestamp[1]='0'+datestamp[1] # make 2 characters
date='20'+mmddyy[2]+':'+mmddyy[0]+":"+mmddyy[1] +':' +datestamp[1]+":00.00"
MagRec["measurement_date"]=date
MagRec["magic_method_codes"]='LT-NO'
if InRec[demag_key]!="0":
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst=inst+':ODP-SRM-AF' # measured on shipboard in-line 2G AF
treatment_value=float(InRec[demag_key].strip('"'))*1e-3 # convert mT => T
MagRec["treatment_ac_field"]=treatment_value # AF demag in treat mT => T
if InRec['Treatment Type']!="":
if 'Alternating Frequency' in InRec['Treatment Type']:
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst=inst+':ODP-DTECH' # measured on shipboard Dtech D2000
treatment_value=float(InRec['Treatment Value'])*1e-3 # convert mT => T
MagRec["treatment_ac_field"]=treatment_value # AF demag in treat mT => T
elif 'Thermal' in InRec['Treatment Type']:
MagRec['magic_method_codes'] = 'LT-T-Z'
inst=inst+':ODP-TDS' # measured on shipboard Schonstedt thermal demagnetizer
treatment_value=float(InRec['Treatment Value'])+273 # convert C => K
MagRec["treatment_temp"]='%8.3e'%(treatment_value) #
MagRec["measurement_standard"]='u' # assume all data are "good"
vol=float(volume)*1e-6 # convert from cc to m^3
if run_number!="":
MagRec['external_database_ids']=run_number
MagRec['external_database_names']='LIMS'
else:
MagRec['external_database_ids']=""
MagRec['external_database_names']=''
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_csd']=''
MagRec['measurement_positions']=''
MagRecs.append(MagRec)
if specimen not in specimens:
specimens.append(specimen)
SpecRecs.append(SpecRec)
if MagRec['er_sample_name'] not in samples:
samples.append(MagRec['er_sample_name'])
SampRecs.append(SampRec)
if MagRec['er_site_name'] not in sites:
sites.append(MagRec['er_site_name'])
SiteRecs.append(SiteRec)
except:
pass
if len(SpecRecs)>0:
pmag.magic_write(spec_file,SpecRecs,'er_specimens')
print 'specimens stored in ',spec_file
if len(SampRecs)>0:
SampOut,keys=pmag.fillkeys(SampRecs)
pmag.magic_write(samp_file,SampOut,'er_samples')
print 'samples stored in ',samp_file
if len(SiteRecs)>0:
pmag.magic_write(site_file,SiteRecs,'er_sites')
print 'sites stored in ',site_file
MagSort=pmag.sortbykeys(MagRecs,["er_specimen_name","treatment_ac_field"])
MagOuts=[]
for MagRec in MagSort:
MagRec["treatment_ac_field"]='%8.3e'%(MagRec['treatment_ac_field']) # convert to string
MagOuts.append(MagRec)
Fixed=pmag.measurements_methods(MagOuts,noave)
pmag.magic_write(meas_file,Fixed,'magic_measurements')
print 'data stored in ',meas_file
def main():
"""
NAME
ODP_dcs_magic.py
DESCRIPTION
converts ODP discrete sample format files to magic_measurements format files
SYNTAX
ODP_dsc_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsp FILE: specify output er_specimens.txt file, default is er_specimens.txt
-Fsa FILE: specify output er_samples.txt file for appending, default is er_samples.txt
-Fsi FILE: specify output er_sites.txt file, default is er_sites.txt
-dc B PHI THETA: dc lab field (in micro tesla) and phi,theta, default is none
NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment
-ac B : peak AF field (in mT) for ARM acquisition, default is none
-A : don't average replicate measurements
INPUT
Put data from separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.) in separate directory
"""
#
#
version_num=pmag.get_version()
meas_file='magic_measurements.txt'
spec_file='er_specimens.txt'
samp_file='er_samples.txt'
site_file='er_sites.txt'
ErSpecs,ErSamps,ErSites,ErLocs,ErCits=[],[],[],[],[]
MagRecs=[]
citation="This study"
dir_path,demag='.','NRM'
args=sys.argv
noave=0
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if "-h" in args:
print main.__doc__
sys.exit()
if "-A" in args: noave=1
if '-F' in args:
ind=args.index("-F")
meas_file=args[ind+1]
if '-Fsp' in args:
ind=args.index("-Fsp")
spec_file=args[ind+1]
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file=dir_path+'/'+args[ind+1]
ErSamps,file_type=pmag.magic_read(samp_file)
else:
samp_file=dir_path+'/'+samp_file
if '-LP' in args:
ind=args.index("-LP")
codelist=args[ind+1]
codes=codelist.split(':')
if "AF" in codes:
demag='AF'
if'-dc' not in args: methcode="LT-AF-Z"
if'-dc' in args: methcode="LT-AF-I"
if "T" in codes:
demag="T"
if '-dc' not in args: methcode="LT-T-Z"
if '-dc' in args: methcode="LT-T-I"
if "I" in codes:
methcode="LP-IRM"
if "S" in codes:
demag="S"
methcode="LP-PI-TRM:LP-PI-ALT-AFARM"
trm_labfield=labfield
ans=raw_input("DC lab field for ARM step: [50uT] ")
if ans=="":
arm_labfield=50e-6
else:
arm_labfield=float(ans)*1e-6
ans=raw_input("temperature for total trm step: [600 C] ")
if ans=="":
trm_peakT=600+273 # convert to kelvin
else:
trm_peakT=float(ans)+273 # convert to kelvin
if "G" in codes: methcode="LT-AF-G"
if "D" in codes: methcode="LT-AF-D"
if "TRM" in codes:
demag="T"
trm=1
if demag=="T" and "ANI" in codes:
methcode="LP-AN-TRM"
if demag=="AF" and "ANI" in codes:
methcode="LP-AN-ARM"
if labfield==0: labfield=50e-6
if peakfield==0: peakfield=.180
spec_file=dir_path+'/'+spec_file
site_file=dir_path+'/'+site_file
meas_file=dir_path+'/'+meas_file
filelist=os.listdir(dir_path) # read in list of files to import
specimens,samples,sites=[],[],[]
MagRecs,SpecRecs,SampRecs=[],[],[]
for samp in ErSamps:
if samp['er_sample_name'] not in samples:
samples.append(samp['er_sample_name'])
SampRecs.append(samp)
for file in filelist: # parse each file
if file[-3:].lower()=='dsc':
print 'processing: ',file
MagRec,SpecRec,SampRec={},{},{}
treatment_type,treatment_value,user="","",""
inst="ODP-SRM"
input=open(dir_path+'/'+file,'rU').readlines()
IDs=file.split('_') # splits on underscores
pieces=IDs[0].split('-')
expedition=pieces[0]
location=pieces[1]
if file[0]!='_':
while len(pieces[2])<4:pieces[2]='0'+pieces[2] # pad core to be 3 characters
specimen=""
else:
specimen="test"
for piece in pieces:
specimen=specimen+piece+'-'
specimen=specimen[:-1]
alt_spec=IDs[1] # alternate specimen is second field in field name
# set up specimen record for Er_specimens table
SpecRec['er_expedition_name']=expedition
SpecRec['er_location_name']=location
SpecRec['er_site_name']=specimen
SpecRec['er_sample_name']=specimen
SpecRec['er_citation_names']=citation
for key in SpecRec.keys():SampRec[key]=SpecRec[key]
SampRec['sample_azimuth']='0'
SampRec['sample_dip']='0'
SampRec['magic_method_codes']='FS-C-DRILL-IODP:FS-SS-C:SO-V'
SpecRec['er_specimen_name']=specimen
for key in SpecRec.keys():MagRec[key]=SpecRec[key]
# set up measurement record - default is NRM
MagRec['er_analyst_mail_names']=user
MagRec['magic_method_codes']='LT-NO'
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"]='' # set csd to blank
SpecRec['er_specimen_alternatives']=alt_spec
vol=7e-6 # assume 7 cc samples
datestamp=input[1].split() # date time is second line of file
mmddyy=datestamp[0].split('/') # break into month day year
date=mmddyy[2]+':'+mmddyy[0]+":"+mmddyy[1] +':' +datestamp[1]
MagRec["measurement_date"]=date
for k in range(len(input)):
fields= input[k].split("=")
if 'treatment_type' in fields[0]:
if "Alternating Frequency Demagnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-AF-Z'
inst=inst+':ODP-DTECH' # measured on shipboard AF DTECH D2000
treatment_type="AF"
if "Anhysteretic Remanent Magnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-AF-I'
inst=inst+':ODP-DTECH' # measured on shipboard AF DTECH D2000
treatment_type="ARM"
if "Isothermal Remanent Magnetization" in fields[1]:
MagRec['magic_method_codes'] = 'LT-IRM'
inst=inst+':ODP-IMP' # measured on shipboard ASC IMPULSE magnetizer
treatment_type="IRM"
if "treatment_value" in fields[0]:
values=fields[1].split(',')
value=values[0]
if value!=" \n":
if treatment_type=="AF":
treatment_value=float(value)*1e-3
MagRec["treatment_ac_field"]=treatment_value # AF demag in treat mT => T
elif treatment_type=="IRM":
treatment_value=float(value)*1e-3
MagRec["treatment_dc_field"]='%8.3e'%(treatment_value) # IRM treat mT => T
if treatment_type=="ARM":
treatment_value=float(value)*1e-3
dc_value=float(values[1])*1e-3
MagRec["treatment_ac_field"]=treatment_value # AF demag in treat mT => T
MagRec["treatment_dc_field"]='%8.3e'%(dc_value) # DC mT => T
if 'user' in fields[0]:
user=fields[-1]
MagRec["er_analyst_mail_names"]=user
if 'sample_orientation' in fields[0]:
MagRec["measurement_description"]=fields[-1]
MagRec["measurement_standard"]='u' # assume all data are "good"
if 'sample_area' in fields[0]: vol=float(fields[1])*1e-6 # takes volume (cc) and converts to m^3
if 'run_number' in fields[0]:
MagRec['external_database_ids']=fields[1] # run number is the LIMS measurement number
MagRec['external_database_names']='LIMS'
if input[k][0:7]=='<MULTI>':
rec=input[k+1].split(',') # list of data
for item in rec:
items=item.split('=')
if items[0].strip()=='demag_level' and treatment_value=="" :
treat= float(items[1])
if treat!=0:
MagRec['magic_method_codes']='LT-AF-Z'
inst=inst+':ODP-SRM-AF'
MagRec["treatment_ac_field"]=treat*1e-3 # AF demag in treat mT => T
if items[0].strip()=='inclination_w_tray_w_bkgrd': MagRec['measurement_inc']=items[1]
if items[0].strip()=='declination_w_tray_w_bkgrd': MagRec['measurement_dec']=items[1]
if items[0].strip()=='intensity_w_tray_w_bkgrd': MagRec['measurement_magn_moment']='%8.3e'%(float(items[1])*vol) # convert intensity from A/m to Am^2 using vol
if items[0].strip()=='x_stdev':MagRec['measurement_x_sd']=items[1]
if items[0].strip()=='y_stdev':MagRec['measurement_y_sd']=items[1]
if items[0].strip()=='z_stdev':MagRec['measurement_z_sd']=items[1]
MagRec['magic_instrument_codes']=inst
MagRec['measurement_number']='1'
MagRecs.append(MagRec)
if specimen not in specimens:
specimens.append(specimen)
SpecRecs.append(SpecRec)
if MagRec['er_sample_name'] not in samples:
samples.append(MagRec['er_sample_name'])
SampRecs.append(SampRec)
MagOuts=pmag.sort_diclist(MagRecs,'treatment_ac_field')
for MagRec in MagOuts:
MagRec["treatment_ac_field"]='%8.3e'%(MagRec["treatment_ac_field"]) # convert to string
pmag.magic_write(spec_file,SpecRecs,'er_specimens')
if len(SampRecs)>0:
SampOut,keys=pmag.fillkeys(SampRecs)
pmag.magic_write(samp_file,SampOut,'er_samples')
print 'samples stored in ',samp_file
pmag.magic_write(samp_file,SampRecs,'er_samples')
print 'specimens stored in ',spec_file
Fixed=pmag.measurements_methods(MagOuts,noave)
pmag.magic_write(meas_file,Fixed,'magic_measurements')
print 'data stored in ',meas_file
def main():
"""
ODP_samples_magic.py
OPTIONS:
-f FILE, input csv file
-Fsa FILE, output er_samples.txt file for updating, default is to overwrite er_samples.txt`
"""
samp_out="er_samples.txt"
dir_path='.'
if "-WD" in sys.argv:
ind=sys.argv.index("-WD")
dir_path=sys.argv[ind+1]
if "-h" in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index("-f")
samp_file=sys.argv[ind+1]
else:
print "must specify -f samp_file"
sys.exit()
samp_file=dir_path+'/'+samp_file
Samps=[]
if '-Fsa' in sys.argv:
ind=sys.argv.index("-Fsa")
samp_out=dir_path+'/'+sys.argv[ind+1]
Samps,file_type=pmag.magic_read(samp_out)
print len(Samps), ' read in from: ',samp_out
input=open(samp_file,"rU").readlines()
keys=input[0].replace('\n','').split(',')
ErSamples,samples=[],[]
for line in input[1:]:
ODPRec,SampRec={},{}
rec=line.replace('\n','').split(',')
for k in range(len(keys)):ODPRec[keys[k]]=rec[k]
SampRec['er_sample_alternatives']=ODPRec['Text Id']
label=ODPRec['Label Id'].split()
if len(label)>1 and 'PMAG' not in label[0]:
interval=label[1].split('/')[0]
pieces=label[0].split('-')
core=pieces[2]
while len(core)<4:core='0'+core
SampRec['magic_method_codes']='FS-C-DRILL-IODP:FS-SS-C:SO-V'
SampRec['er_sample_name']=pieces[0]+'-'+pieces[1]+'-'+core+'-'+pieces[3]+'-'+pieces[4]+'-'+interval
SampRec['er_site_name']=SampRec['er_sample_name']
pieces=SampRec['er_sample_name'].split('-')
SampRec['er_expedition_name']=pieces[0]
SampRec['er_location_name']=pieces[1]
SampRec['er_citation_names']="This study"
SampRec['sample_dip']="0"
SampRec['sample_azimuth']="0"
SampRec['sample_core_depth']=ODPRec['Top Depth (m)']
dates=ODPRec['Sample Date Logged'].split()
mmddyy=dates[0].split('/')
yyyy='20'+mmddyy[2]
mm=mmddyy[0]
if len(mm)==1:mm='0'+mm
dd=mmddyy[1]
if len(dd)==1:dd='0'+dd
date=yyyy+':'+mm+':'+dd+':'+dates[1]+":00.00"
SampRec['sample_date']=date
ErSamples.append(SampRec)
samples.append(SampRec['er_sample_name'])
if len(Samps)>0:
for samp in Samps:
if samp['er_sample_name'] not in samples:
ErSamples.append(samp)
Recs,keys=pmag.fillkeys(ErSamples)
pmag.magic_write(samp_out,Recs,'er_samples')
print('sample information written to er_samples.txt')
def main():
"""
ODP_samples_magic.py
OPTIONS:
-f FILE, input csv file
-Fsa FILE, output er_samples.txt file for updating, default is to overwrite er_samples.txt
"""
dir_path = "."
comp_depth_key = ""
if "-WD" in sys.argv:
ind = sys.argv.index("-WD")
dir_path = sys.argv[ind + 1]
if "-h" in sys.argv:
print main.__doc__
sys.exit()
if "-f" in sys.argv:
ind = sys.argv.index("-f")
samp_file = sys.argv[ind + 1]
else:
print "must specify -f samp_file"
sys.exit()
samp_file = dir_path + "/" + samp_file
Samps = []
if "-Fsa" in sys.argv:
ind = sys.argv.index("-Fsa")
samp_out = dir_path + "/" + sys.argv[ind + 1]
Samps, file_type = pmag.magic_read(samp_out)
print len(Samps), " read in from: ", samp_out
else:
samp_out = dir_path + "/er_samples.txt"
input = open(samp_file, "rU").readlines()
keys = input[0].replace("\n", "").split(",")
if "CSF-B Top (m)" in keys:
comp_depth_key = "CSF-B Top (m)"
if "Top Depth (m)" in keys: # incorporate changes to LIMS data model, while maintaining backward compatibility
depth_key = "Top Depth (m)"
elif "CSF-A Top (m)" in keys:
depth_key = "CSF-A Top (m)"
elif "Top depth CSF-A (m)" in keys:
depth_key = "Top depth CSF-A (m)"
if "Text Id" in keys:
text_key = "Text Id"
elif "Text identifier" in keys:
text_key = "Text identifier"
if "Sample Date Logged" in keys:
date_key = "Sample Date Logged"
elif "Sample date logged" in keys:
date_key = "Sample date logged"
ErSamples, samples, format = [], [], "old"
for line in input[1:]:
ODPRec, SampRec = {}, {}
interval, core = "", ""
rec = line.replace("\n", "").split(",")
for k in range(len(keys)):
ODPRec[keys[k]] = rec[k].strip('"')
SampRec["er_sample_alternatives"] = ODPRec[text_key]
if "Label Id" in keys: # old format
label = ODPRec["Label Id"].split()
if len(label) > 1:
interval = label[1].split("/")[0]
pieces = label[0].split("-")
core = pieces[2]
while len(core) < 4:
core = "0" + core # my way
else: # new format
format = "new"
pieces = [
ODPRec["Exp"],
ODPRec["Site"] + ODPRec["Hole"],
ODPRec["Core"] + ODPRec["Type"],
ODPRec["Sect"],
ODPRec["A/W"],
]
interval = ODPRec["Top offset (cm)"].split(".")[0].strip() # only integers allowed!
core = ODPRec["Core"] + ODPRec["Type"]
if core != "" and interval != "":
SampRec["magic_method_codes"] = "FS-C-DRILL-IODP:SP-SS-C:SO-V"
if format == "old":
SampRec["er_sample_name"] = (
pieces[0] + "-" + pieces[1] + "-" + core + "-" + pieces[3] + "-" + pieces[4] + "-" + interval
)
else:
SampRec["er_sample_name"] = (
pieces[0] + "-" + pieces[1] + "-" + core + "-" + pieces[3] + "_" + pieces[4] + "_" + interval
) # change in sample name convention
SampRec["er_site_name"] = SampRec["er_sample_name"]
# pieces=SampRec['er_sample_name'].split('-')
SampRec["er_expedition_name"] = pieces[0]
SampRec["er_location_name"] = pieces[1]
SampRec["er_citation_names"] = "This study"
SampRec["sample_dip"] = "0"
SampRec["sample_azimuth"] = "0"
SampRec["sample_core_depth"] = ODPRec[depth_key]
if comp_depth_key != "":
SampRec["sample_composite_depth"] = ODPRec[comp_depth_key]
dates = ODPRec[date_key].split()
if "/" in dates[0]: # have a date
mmddyy = dates[0].split("/")
yyyy = "20" + mmddyy[2]
mm = mmddyy[0]
if len(mm) == 1:
mm = "0" + mm
dd = mmddyy[1]
if len(dd) == 1:
dd = "0" + dd
date = yyyy + ":" + mm + ":" + dd + ":" + dates[1] + ":00.00"
else:
date = ""
SampRec["sample_date"] = date
ErSamples.append(SampRec)
samples.append(SampRec["er_sample_name"])
if len(Samps) > 0:
for samp in Samps:
if samp["er_sample_name"] not in samples:
ErSamples.append(samp)
Recs, keys = pmag.fillkeys(ErSamples)
pmag.magic_write(samp_out, Recs, "er_samples")
print "sample information written to: ", samp_out
def main():
"""
NAME
sufar4-asc_magic.py
DESCRIPTION
converts ascii files generated by SUFAR ver.4.0 to MagIC formated
files for use with PmagPy plotting software
SYNTAX
sufar4-asc_magic.py -h [command line options]
OPTIONS
-h: prints the help message and quits
-f FILE: specify .asc input file name
-F MFILE: specify magic_measurements output file
-Fa AFILE: specify rmag_anisotropy output file
-Fr RFILE: specify rmag_results output file
-Fs SFILE: specify er_specimens output file with location, sample, site, etc. information
-usr USER: specify who made the measurements
-loc LOC: specify location name for study
-ins INST: specify instrument used
-spc SPEC: specify number of characters to specify specimen from sample
-ncn NCON: specify naming convention: default is #2 below
-k15 : specify static 15 position mode - default is spinning
-new : replace all existing magic files
DEFAULTS
AFILE: rmag_anisotropy.txt
RFILE: rmag_results.txt
SFILE: default is to create new er_specimen.txt file
USER: ""
LOC: "unknown"
INST: ""
SPEC: 0 sample name is same as site (if SPEC is 1, sample is all but last character)
appends to 'er_specimens.txt, er_samples.txt, er_sites.txt' files
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
[8] This is a synthetic
[9] ODP naming convention
"""
citation = "This study"
cont = 0
samp_con, Z = "1", 1
AniRecSs, AniRecs, SpecRecs, SampRecs, SiteRecs, MeasRecs = [], [], [], [], [], []
user, locname, specfile = "", "unknown", "er_specimens.txt"
isspec, inst, specnum = "0", "", 0
spin, new = 1, 0
dir_path = "."
if "-WD" in sys.argv:
ind = sys.argv.index("-WD")
dir_path = sys.argv[ind + 1]
aoutput, routput, moutput = (
dir_path + "/rmag_anisotropy.txt",
dir_path + "/rmag_results.txt",
dir_path + "/magic_measurements.txt",
)
if "-h" in sys.argv:
print main.__doc__
sys.exit()
if "-usr" in sys.argv:
ind = sys.argv.index("-usr")
user = sys.argv[ind + 1]
if "-ncn" in sys.argv:
ind = sys.argv.index("-ncn")
samp_con = sys.argv[ind + 1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "7"
if "-k15" in sys.argv:
spin = 0
if "-ins" in sys.argv:
ind = sys.argv.index("-ins")
inst = sys.argv[ind + 1]
if "-f" in sys.argv:
ind = sys.argv.index("-f")
ascfile = dir_path + "/" + sys.argv[ind + 1]
if "-F" in sys.argv:
ind = sys.argv.index("-F")
moutput = dir_path + "/" + sys.argv[ind + 1]
if "-Fa" in sys.argv:
ind = sys.argv.index("-Fa")
aoutput = dir_path + "/" + sys.argv[ind + 1]
if "-Fr" in sys.argv:
ind = sys.argv.index("-Fr")
routput = dir_path + "/" + sys.argv[ind + 1]
if "-Fs" in sys.argv:
ind = sys.argv.index("-Fs")
specfile = dir_path + "/" + sys.argv[ind + 1]
isspec = "1"
elif "-loc" in sys.argv:
ind = sys.argv.index("-loc")
locname = sys.argv[ind + 1]
if "-spc" in sys.argv:
ind = sys.argv.index("-spc")
specnum = -(int(sys.argv[ind + 1]))
if specnum != 0:
specnum = -specnum
if isspec == "1":
specs, file_type = pmag.magic_read(specfile)
specnames, sampnames, sitenames = [], [], []
if "-new" not in sys.argv: # see if there are already specimen,sample, site files lying around
try:
SpecRecs, file_type = pmag.magic_read(dir_path + "/er_specimens.txt")
for spec in SpecRecs:
if spec["er_specimen_name"] not in specnames:
specnames.append(samp["er_specimen_name"])
except:
SpecRecs, specs = [], []
try:
SampRecs, file_type = pmag.magic_read(dir_path + "/er_samples.txt")
for samp in SampRecs:
if samp["er_sample_name"] not in sampnames:
sampnames.append(samp["er_sample_name"])
except:
sampnames, SampRecs = [], []
try:
SiteRecs, file_type = pmag.magic_read(dir_path + "/er_sites.txt")
for site in SiteRecs:
if site["er_site_names"] not in sitenames:
sitenames.append(site["er_site_name"])
except:
sitenames, SiteRecs = [], []
try:
input = open(ascfile, "rU")
except:
print "Error opening file: ", ascfile
Data = input.readlines()
k = 0
while k < len(Data):
line = Data[k]
words = line.split()
if "ANISOTROPY" in words: # first line of data for the spec
MeasRec, AniRec, SpecRec, SampRec, SiteRec = {}, {}, {}, {}, {}
specname = words[0]
AniRec["er_specimen_name"] = specname
if isspec == "1":
for spec in specs:
if spec["er_specimen_name"] == specname:
AniRec["er_sample_name"] = spec["er_sample_name"]
AniRec["er_site_name"] = spec["er_site_name"]
AniRec["er_location_name"] = spec["er_location_name"]
break
elif isspec == "0":
if specnum != 0:
sampname = specname[:specnum]
else:
sampname = specname
AniRec["er_sample_name"] = sampname
SpecRec["er_specimen_name"] = specname
SpecRec["er_sample_name"] = sampname
SampRec["er_sample_name"] = sampname
SiteRec["er_sample_name"] = sampname
SiteRec["site_description"] = "s"
if samp_con != "9":
AniRec["er_site_name"] = pmag.parse_site(AniRec["er_sample_name"], samp_con, Z)
SpecRec["er_site_name"] = pmag.parse_site(AniRec["er_sample_name"], samp_con, Z)
SampRec["er_site_name"] = pmag.parse_site(AniRec["er_sample_name"], samp_con, Z)
SiteRec["er_site_name"] = pmag.parse_site(AniRec["er_sample_name"], samp_con, Z)
else:
AniRec["er_site_name"] = specname
SpecRec["er_site_name"] = specname
SampRec["er_site_name"] = specname
SiteRec["er_site_name"] = specname
pieces = specname.split("-")
AniRec["er_expedition_name"] = pieces[0]
SpecRec["er_expedition_name"] = pieces[0]
SampRec["er_expedition_name"] = pieces[0]
SiteRec["er_expedition_name"] = pieces[0]
location = pieces[1]
AniRec["er_location_name"] = locname
SpecRec["er_location_name"] = locname
SampRec["er_location_name"] = locname
SiteRec["er_location_name"] = locname
AniRec["er_citation_names"] = "This study"
SpecRec["er_citation_names"] = "This study"
SampRec["er_citation_names"] = "This study"
SiteRec["er_citation_names"] = "This study"
AniRec["er_citation_names"] = "This study"
AniRec["magic_instrument_codes"] = inst
AniRec["magic_method_codes"] = "LP-X:AE-H:LP-AN-MS"
AniRec["magic_experiment_names"] = specname + ":" + "LP-AN-MS"
AniRec["er_analyst_mail_names"] = user
for key in AniRec.keys():
MeasRec[key] = AniRec[key]
MeasRec["measurement_flag"] = "g"
AniRec["anisotropy_flag"] = "g"
MeasRec["measurement_standard"] = "u"
MeasRec["measurement_description"] = "Bulk sucsecptibility measurement"
AniRec["anisotropy_type"] = "AMS"
AniRec["anisotropy_unit"] = "Normalized by trace - bulk in measurements table"
if spin == 1:
AniRec["anisotropy_n"] = "192"
else:
AniRec["anisotropy_n"] = "15"
if "Azi" in words and isspec == "0":
SampRec["sample_azimuth"] = words[1]
labaz = float(words[1])
if "Dip" in words:
SampRec["sample_dip"] = "%7.1f" % (-float(words[1]))
SpecRec["specimen_vol"] = "%8.3e" % (float(words[10]) * 1e-6) # convert actual volume to m^3 from cm^3
labdip = float(words[1])
if "T1" in words and "F1" in words:
k += 2 # read in fourth line down
line = Data[k]
rec = line.split()
dd = rec[1].split("/")
dip_direction = int(dd[0]) + 90
SampRec["sample_bed_dip_direction"] = "%i" % (dip_direction)
SampRec["sample_bed_dip"] = dd[1]
bed_dip = float(dd[1])
if "Mean" in words:
k += 4 # read in fourth line down
line = Data[k]
rec = line.split()
MeasRec["measurement_chi_volume"] = rec[1]
sigma = 0.01 * float(rec[2]) / 3.0
AniRec["anisotropy_sigma"] = "%7.4f" % (sigma)
AniRec["anisotropy_unit"] = "SI"
if "factors" in words:
k += 4 # read in second line down
line = Data[k]
rec = line.split()
if "Specimen" in words: # first part of specimen data
AniRec["anisotropy_s1"] = "%7.4f" % (float(words[5]) / 3.0) # eigenvalues sum to unity - not 3
AniRec["anisotropy_s2"] = "%7.4f" % (float(words[6]) / 3.0)
AniRec["anisotropy_s3"] = "%7.4f" % (float(words[7]) / 3.0)
k += 1
line = Data[k]
rec = line.split()
AniRec["anisotropy_s4"] = "%7.4f" % (float(rec[5]) / 3.0) # eigenvalues sum to unity - not 3
AniRec["anisotropy_s5"] = "%7.4f" % (float(rec[6]) / 3.0)
AniRec["anisotropy_s6"] = "%7.4f" % (float(rec[7]) / 3.0)
AniRec["anisotropy_tilt_correction"] = "-1"
AniRecs.append(AniRec)
AniRecG, AniRecT = {}, {}
for key in AniRec.keys():
AniRecG[key] = AniRec[key]
for key in AniRec.keys():
AniRecT[key] = AniRec[key]
sbar = []
sbar.append(float(AniRec["anisotropy_s1"]))
sbar.append(float(AniRec["anisotropy_s2"]))
sbar.append(float(AniRec["anisotropy_s3"]))
sbar.append(float(AniRec["anisotropy_s4"]))
sbar.append(float(AniRec["anisotropy_s5"]))
sbar.append(float(AniRec["anisotropy_s6"]))
sbarg = pmag.dosgeo(sbar, labaz, labdip)
AniRecG["anisotropy_s1"] = "%12.10f" % (sbarg[0])
AniRecG["anisotropy_s2"] = "%12.10f" % (sbarg[1])
AniRecG["anisotropy_s3"] = "%12.10f" % (sbarg[2])
AniRecG["anisotropy_s4"] = "%12.10f" % (sbarg[3])
AniRecG["anisotropy_s5"] = "%12.10f" % (sbarg[4])
AniRecG["anisotropy_s6"] = "%12.10f" % (sbarg[5])
AniRecG["anisotropy_tilt_correction"] = "0"
AniRecs.append(AniRecG)
if bed_dip != "" and bed_dip != 0: # have tilt correction
sbart = pmag.dostilt(sbarg, dip_direction, bed_dip)
AniRecT["anisotropy_s1"] = "%12.10f" % (sbart[0])
AniRecT["anisotropy_s2"] = "%12.10f" % (sbart[1])
AniRecT["anisotropy_s3"] = "%12.10f" % (sbart[2])
AniRecT["anisotropy_s4"] = "%12.10f" % (sbart[3])
AniRecT["anisotropy_s5"] = "%12.10f" % (sbart[4])
AniRecT["anisotropy_s6"] = "%12.10f" % (sbart[5])
AniRecT["anisotropy_tilt_correction"] = "100"
AniRecs.append(AniRecT)
MeasRecs.append(MeasRec)
if SpecRec["er_specimen_name"] not in specnames:
SpecRecs.append(SpecRec)
specnames.append(SpecRec["er_specimen_name"])
if SampRec["er_sample_name"] not in sampnames:
SampRecs.append(SampRec)
sampnames.append(SampRec["er_sample_name"])
if SiteRec["er_site_name"] not in sitenames:
SiteRecs.append(SiteRec)
sitenames.append(SiteRec["er_site_name"])
k += 1 # skip to next specimen
pmag.magic_write(aoutput, AniRecs, "rmag_anisotropy")
print "anisotropy tensors put in ", aoutput
pmag.magic_write(moutput, MeasRecs, "magic_measurements")
print "bulk measurements put in ", moutput
if isspec == "0":
SpecOut, keys = pmag.fillkeys(SpecRecs)
output = dir_path + "/er_specimens.txt"
pmag.magic_write(output, SpecOut, "er_specimens")
print "specimen info put in ", output
output = dir_path + "/er_samples.txt"
SampOut, keys = pmag.fillkeys(SampRecs)
pmag.magic_write(output, SampOut, "er_samples")
print "sample info put in ", output
output = dir_path + "/er_sites.txt"
SiteOut, keys = pmag.fillkeys(SiteRecs)
pmag.magic_write(output, SiteOut, "er_sites")
print "site info put in ", output
print """"
def main():
"""
NAME
agm_magic.py
DESCRIPTION
converts Micromag agm files to magic format
SYNTAX
agm_magic.py [-h] [command line options]
OPTIONS
-usr USER: identify user, default is "" - put in quotation marks!
-bak: this is a IRM backfield curve
-f FILE, specify input file, required
-fsa SAMPFILE, specify er_samples.txt file relating samples, site and locations names,default is none
-F MFILE, specify magic measurements formatted output file, default is agm_measurements.txt
-spn SPEC, specimen name, default is base of input file name, e.g. SPECNAME.agm
-spc NUM, specify number of characters to designate a specimen, default = 0
-Fsp SPECFILE : name of er_specimens.txt file for appending data to
[default: er_specimens.txt]
-ncn NCON,: specify naming convention: default is #1 below
-syn SYN, synthetic specimen name
-loc LOCNAME : specify location/study name,
should have either LOCNAME or SAMPFILE (unless synthetic)
-ins INST : specify which instrument was used (e.g, SIO-Maud), default is ""
-u units: [cgs,SI], default is cgs
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
[8] specimen is a synthetic - it has no sample, site, location information
NB: all others you will have to customize your self
or e-mail [email protected] for help.
OUTPUT
MagIC format files: magic_measurements, er_specimens, er_sample, er_site
"""
citation='This study'
MeasRecs=[]
units='cgs'
meth="LP-HYS"
version_num=pmag.get_version()
args=sys.argv
fmt='old'
er_sample_name,er_site_name,er_location_name="","",""
inst=""
er_location_name="unknown"
er_synthetic_name=""
user=""
er_site_name=""
dir_path='.'
if "-WD" in args:
ind=args.index("-WD")
dir_path=args[ind+1]
specfile=dir_path+'/er_specimens.txt'
output=dir_path+"/agm_measurements.txt"
if "-h" in args:
print main.__doc__
sys.exit()
if "-bak" in args:
meth="LP-IRM-DCD"
output=dir_path+"/irm_measurements.txt"
if "-new" in args: fmt='new'
if "-usr" in args:
ind=args.index("-usr")
user=args[ind+1]
if '-F' in args:
ind=args.index("-F")
output=dir_path+'/'+args[ind+1]
if '-f' in args:
ind=args.index("-f")
agm_file=dir_path+'/'+args[ind+1]
er_specimen_name=args[ind+1].split('.')[0]
else:
print "agm_file field is required option"
print main.__doc__
sys.exit()
if '-Fsp' in args:
ind=args.index("-Fsp")
specfile=dir_path+'/'+args[ind+1]
specnum,samp_con,Z=0,'1',1
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if specnum!=0:specnum=-specnum
if "-spn" in args:
ind=args.index("-spn")
er_specimen_name=args[ind+1]
elif "-syn" not in args:
print "you must specify a specimen name"
sys.exit()
if "-syn" in args:
ind=args.index("-syn")
er_synthetic_name=args[ind+1]
er_specimen_name=""
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-fsa" in args:
ind=args.index("-fsa")
sampfile=dir_path+'/'+args[ind+1]
Samps,file_type=pmag.magic_read(sampfile)
print 'sample_file successfully read in'
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="7"
if "-ins" in args:
ind=args.index("-ins")
inst=args[ind+1]
if "-u" in args:
ind=args.index("-u")
units=args[ind+1]
ErSpecRecs,filetype=pmag.magic_read(specfile)
ErSpecRec,MeasRec={},{}
ErSpecRec['er_citation_names']="This study"
ErSpecRec['er_specimen_name']=er_specimen_name
ErSpecRec['er_synthetic_name']=er_synthetic_name
if specnum!=0:
ErSpecRec["er_sample_name"]=er_specimen_name[:specnum]
else:
ErSpecRec["er_sample_name"]=er_specimen_name
if "-fsa" in args and er_synthetic_name=="":
for samp in Samps:
if samp["er_sample_name"] == ErSpecRec["er_sample_name"]:
ErSpecRec["er_location_name"]=samp["er_location_name"]
ErSpecRec["er_site_name"]=samp["er_site_name"]
break
elif int(samp_con)!=6 and int(samp_con)!=8:
site=pmag.parse_site(ErSpecRec['er_sample_name'],samp_con,Z)
ErSpecRec["er_site_name"]=site
ErSpecRec["er_location_name"]=er_location_name
ErSpecRec['er_scientist_mail_names']=user.strip()
insert=1
for rec in ErSpecRecs:
if rec['er_specimen_name']==er_specimen_name:
insert=0
break
if insert==1:
ErSpecRecs.append(ErSpecRec)
ErSpecRecs,keylist=pmag.fillkeys(ErSpecRecs)
pmag.magic_write(specfile,ErSpecRecs,'er_specimens')
print "specimen name put in ",specfile
f=open(agm_file,'rU')
Data=f.readlines()
if "ASCII" not in Data[0]:fmt='new'
measnum,start=1,""
if fmt=='new': # new Micromag formatted file
end=2
for skip in range(len(Data)):
line=Data[skip]
rec=line.split()
if 'Units' in line:units=rec[-1]
if "Raw" in rec:
start=skip+2
if "Field" in rec and "Moment" in rec and start=="":
start=skip+2
break
else:
start = 2
end=1
for i in range(start,len(Data)-end): # skip header stuff
MeasRec={}
for key in ErSpecRec.keys():
MeasRec[key]=ErSpecRec[key]
MeasRec['magic_instrument_codes']=inst
MeasRec['magic_method_codes']=meth
if 'er_synthetic_name' in MeasRec.keys() and MeasRec['er_synthetic_name']!="":
MeasRec['magic_experiment_name']=er_synthetic_name+':'+meth
else:
MeasRec['magic_experiment_name']=er_specimen_name+':'+meth
line=Data[i]
rec=line.split(',') # data comma delimited
if rec[0]!='\n':
if units=='cgs':
field =float(rec[0])*1e-4 # convert from oe to tesla
else:
field =float(rec[0]) # field in tesla
if meth=="LP-HYS":
MeasRec['measurement_lab_field_dc']='%10.3e'%(field)
MeasRec['treatment_dc_field']=''
else:
MeasRec['measurement_lab_field_dc']=''
MeasRec['treatment_dc_field']='%10.3e'%(field)
if units=='cgs':
MeasRec['measurement_magn_moment']='%10.3e'%(float(rec[1])*1e-3) # convert from emu to Am^2
else:
MeasRec['measurement_magn_moment']='%10.3e'%(float(rec[1])) # Am^2
MeasRec['treatment_temp']='273' # temp in kelvin
MeasRec['measurement_temp']='273' # temp in kelvin
MeasRec['measurement_flag']='g'
MeasRec['measurement_standard']='u'
MeasRec['measurement_number']='%i'%(measnum)
measnum+=1
MeasRec['magic_software_packages']=version_num
MeasRecs.append(MeasRec)
# now we have to relabel LP-HYS method codes. initial loop is LP-IMT, minor loops are LP-M - do this in measurements_methods function
if meth=='LP-HYS':
recnum=0
while float(MeasRecs[recnum]['measurement_lab_field_dc'])<float(MeasRecs[recnum+1]['measurement_lab_field_dc']) and recnum+1<len(MeasRecs): # this is LP-IMAG
MeasRecs[recnum]['magic_method_codes']='LP-IMAG'
MeasRecs[recnum]['magic_experiment_name']=MeasRecs[recnum]['er_specimen_name']+":"+'LP-IMAG'
recnum+=1
#
pmag.magic_write(output,MeasRecs,'magic_measurements')
print "results put in ",output
def main():
"""
NAME
azdip_magic.py
DESCRIPTION
takes space delimited AzDip file and converts to MagIC formatted tables
SYNTAX
azdip_magic.py [command line options]
OPTIONS
-f FILE: specify input file
-Fsa FILE: specify output file, default is: er_samples.txt
-ncn NCON: specify naming convention: default is #1 below
-mcd: specify sampling method codes as a colon delimited string: [default is: FS-FD]
FS-FD field sampling done with a drill
FS-H field sampling done with hand samples
FS-LOC-GPS field location done with GPS
FS-LOC-MAP field location done with map
SO-POM a Pomeroy orientation device was used
SO-ASC an ASC orientation device was used
SO-MAG orientation with magnetic compass
-loc: location name, default="unknown"
-app appends to existing er_samples.txt file, default is to overwrite
INPUT FORMAT
Input files must be space delimited:
Samp Az Dip Strike Dip
Orientation convention:
Lab arrow azimuth = mag_azimuth; Lab arrow dip = 90-field_dip
e.g. field_dip is degrees from horizontal of drill direction
Magnetic declination convention:
Az is already corrected in file
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
OUTPUT
output saved in er_samples.txt will overwrite any existing files
"""
#
# initialize variables
#
DEBUG = 0
version_num = pmag.get_version()
orient_file, samp_file, or_con, corr = "orient.txt", "er_samples.txt", "3", "1"
args = sys.argv
date, lat, lon = "", "", "" # date of sampling, latitude (pos North), longitude (pos East)
bed_dip, bed_dip_dir = "", ""
participantlist = ""
sites = [] # list of site names
Lats, Lons = [], [] # list of latitudes and longitudes
SampRecs, SiteRecs, ImageRecs, imagelist = [], [], [], [] # lists of Sample records and Site records
samp_con, Z, average_bedding = "1", 1, "0"
newbaseline, newbeddir, newbeddip = "", "", ""
meths = "FS-FD"
delta_u = "0"
sclass, lithology, type = "", "", ""
newclass, newlith, newtype = "", "", ""
user = ""
corr == "3"
DecCorr = 0.0
location_name = "unknown"
#
#
if "-h" in args:
print main.__doc__
sys.exit()
if "-f" in args:
ind = args.index("-f")
orient_file = sys.argv[ind + 1]
if "-Fsa" in args:
ind = args.index("-Fsa")
samp_file = sys.argv[ind + 1]
if "-ncn" in args:
ind = args.index("-ncn")
samp_con = sys.argv[ind + 1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z = samp_con.split("-")[1]
samp_con = "7"
if "-mcd" in args:
ind = args.index("-mcd")
meths = sys.argv[ind + 1]
if "-loc" in args:
ind = args.index("-loc")
location_name = sys.argv[ind + 1]
if "-app" in args:
try:
SampRecs, file_type = pmag.magic_read(samp_file)
print "sample data to be appended to: ", samp_file
except:
print "problem with existing samp file: ", samp_file, " will create new"
#
# read in file to convert
#
azfile = open(orient_file, "rU")
AzDipDat = azfile.readlines()
azfile.close()
SampOut, samplist = [], []
for line in AzDipDat:
orec = line.split()
if len(orec) > 2:
labaz, labdip = pmag.orient(float(orec[1]), float(orec[2]), or_con)
bed_dip = float(orec[4])
if bed_dip != 0:
bed_dip_dir = float(orec[3]) - 90.0 # assume dip to right of strike
else:
bed_dip_dir = float(orec[3]) # assume dip to right of strike
MagRec = {}
MagRec["er_location_name"] = location_name
MagRec["er_citation_names"] = "This study"
#
# parse information common to all orientation methods
#
MagRec["er_sample_name"] = orec[0]
MagRec["sample_bed_dip"] = "%7.1f" % (bed_dip)
MagRec["sample_bed_dip_direction"] = "%7.1f" % (bed_dip_dir)
MagRec["sample_dip"] = "%7.1f" % (labdip)
MagRec["sample_azimuth"] = "%7.1f" % (labaz)
methods = meths.replace(" ", "").split(":")
OR = 0
for method in methods:
type = method.split("-")
if "SO" in type:
OR = 1
if OR == 0:
meths = meths + ":SO-NO"
MagRec["magic_method_codes"] = meths
site = pmag.parse_site(orec[0], samp_con, Z) # parse out the site name
MagRec["er_site_name"] = site
MagRec["magic_software_packages"] = version_num
SampOut.append(MagRec)
if MagRec["er_sample_name"] not in samplist:
samplist.append(MagRec["er_sample_name"])
for samp in SampRecs:
if samp not in samplist:
SampOut.append(samp)
Samps, keys = pmag.fillkeys(SampOut)
pmag.magic_write(samp_file, Samps, "er_samples")
print "Data saved in ", samp_file
def main():
"""
NAME
curie_magic.py
DESCTIPTION
plots and interprets curie temperature data.
the 1st derivative is calculated from smoothed M-T curve
(convolution with trianfular window with width= <-w> degrees)
the 2nd derivative is calculated from smoothed 1st derivative curve
( using the same sliding window width)
the estinated curie temp. is the maximum of the 2nd derivative
- the temperature steps should be in multiples of 1.0 degrees
INPUT
magic_measurements formatted file
SYNTAX
curie_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE, sets M,T magic_measurements formatted file, default is MsT_measurements.txt
-F RMAG, sets Rmag_results format file for appending results, default is not
-w size of sliding window in degrees (default - 3 degrees)
-t <min> <max> temperature range (optional)
"""
fmt,dir_path='svg','.'
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
meas_file=dir_path+'/MsT_measurements.txt'
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index('-f')
meas_file=dir_path+'/'+sys.argv[ind+1]
Results,rmag_file=[],""
if '-F' in sys.argv:
ind=sys.argv.index('-F')
rmag_file=dir_path+'/'+sys.argv[ind+1]
try:
Results,file_type=pmag.magic_read(rmag_file)
if file_type!='rmag_results':
print 'bad results file, starting new one'
except:
pass
if '-w' in sys.argv:
ind=sys.argv.index('-w')
window_len=int(sys.argv[ind+1])
else:
window_len=3
if '-t' in sys.argv:
ind=sys.argv.index('-t')
t_begin=int(sys.argv[ind+1])
t_end=int(sys.argv[ind+2])
else:
t_begin=''
t_end=''
# read data from file
Data,file_type=pmag.magic_read(meas_file)
if file_type!='magic_measurements':
print 'bad measurements file'
sys.exit()
specs=[]
for rec in Data:
specname=""
if 'er_specimen_name' in rec.keys() and rec['er_specimen_name']!="":
specname=rec['er_specimen_name']
else:
rec['er_specimen_name']=""
if 'er_synthetic_name' in rec.keys() and rec['er_synthetic_name']!="":
specname=rec['er_synthetic_name']
else:
rec['er_synthetic_name']=""
if specname not in specs:specs.append(specname)
for spec in specs:
print 'processing: ',spec
M,T,curieT=[],[],0
for rec in Data:
if rec['er_specimen_name'] or rec['er_synthetic_name']==spec:
location,sample,site="","",""
if 'er_location_name' in rec.keys():location=rec['er_location_name']
if 'er_sample_name' in rec.keys():sample=rec['er_sample_name']
if 'er_site_name' in rec.keys():site=rec['er_site_name']
syn=""
if 'er_synthetic_name' in rec.keys():syn=rec['er_synthetic_name']
meths=rec['magic_method_codes'].strip().split(':')
expnames=rec['magic_experiment_name'].strip().split(':')
if 'LP-MW-I' in meths and 'Curie' in expnames:
method=rec['magic_method_codes']
expname=rec['magic_experiment_name']
T.append(float(rec['measurment_temp'])-273)
M.append(float(rec['measurement_magnitude']))
# cut the data if -t is one of the flags
if len(M)<10:
print 'not enough data for processing'
sys.exit()
if t_begin:
while T[0]<t_begin:
M.pop(0);T.pop(0)
while T[-1]>t_end:
M.pop(-1);T.pop(-1)
# prepare the signal:
# from M(T) array with unequal deltaT
# to M(T) array with deltaT=(1 degree).
# if delataT is larger, then points are added using linear fit between
# consecutive data points.
# exit if deltaT is not integer
i=0
while i<(len(T)-1):
if (T[i+1]-T[i])%1>0.001:
print "delta T should be integer, this program will not work!"
print "temperature range:",T[i],T[i+1]
sys.exit()
if (T[i+1]-T[i])==0.:
M[i]=average([M[i],M[i+1]])
M.pop(i+1);T.pop(i+1)
elif (T[i+1]-T[i])<0.:
M.pop(i+1);T.pop(i+1)
print "check data in T=%.0f ,M[T] is ignored"%(T[i])
elif (T[i+1]-T[i])>1.:
slope,b=polyfit([T[i],T[i+1]],[M[i],M[i+1]],1)
for j in range(int(T[i+1])-int(T[i])-1):
M.insert(i+1,slope*(T[i]+1.)+b)
T.insert(i+1,(T[i]+1.))
i=i+1
i=i+1
# calculate the smoothed signal
M=array(M,'f')
T=array(T,'f')
M_smooth=[]
M_smooth=smooth(M,window_len)
#plot the original data and the smooth data
PLT={'M_T':1,'der1':2,'der2':3,'Curie':4}
pmagplotlib.plot_init(PLT['M_T'],5,5)
string='M-T (sliding window=%i)'%int(window_len)
pmagplotlib.plotXY(PLT['M_T'],T,M,'--','Temperature C','Magnetization',string)
plot(T,M_smooth,'-')
#calculate first derivative
d1,T_d1=[],[]
for i in range(len(M_smooth)-1):
Dy=M_smooth[i-1]-M_smooth[i+1]
Dx=T[i-1]-T[i+1]
d1.append(Dy/Dx)
T_d1=T[1:len(T-1)]
d1=array(d1,'f')
d1_smooth=smooth(d1,window_len)
#plot the first derivative
pmagplotlib.plot_init(PLT['der1'],5,5)
string='1st dervative (sliding window=%i)'%int(window_len)
pmagplotlib.plotXY(PLT['der1'],T_d1,d1_smooth,'-','temperatue C','',string)
plot(T_d1,d1,'--b')
#calculate second derivative
d2,T_d2=[],[]
for i in range(len(d1_smooth)-1):
Dy=d1_smooth[i-1]-d1_smooth[i+1]
Dx=T[i-1]-T[i+1]
#print Dy/Dx
d2.append(Dy/Dx)
T_d2=T[2:len(T-2)]
d2=array(d2,'f')
d2_smooth=smooth(d2,window_len)
#plot the second derivative
pmagplotlib.plot_init(PLT['der2'],5,5)
string='2nd dervative (sliding window=%i)'%int(window_len)
pmagplotlib.plotXY(PLT['der2'],T_d2,d2,'-','temperatue C','',string)
d2=list(d2)
print 'second deriative maximum is at T=%i'%int(T_d2[d2.index(max(d2))])
# calculate Curie temperature for different width of sliding windows
curie,curie_1=[],[]
wn=range(5,50,1)
for win in wn:
# calculate the smoothed signal
M_smooth=[]
M_smooth=smooth(M,win)
#calculate first derivative
d1,T_d1=[],[]
for i in range(len(M_smooth)-1):
Dy=M_smooth[i-1]-M_smooth[i+1]
Dx=T[i-1]-T[i+1]
d1.append(Dy/Dx)
T_d1=T[1:len(T-1)]
d1=array(d1,'f')
d1_smooth=smooth(d1,win)
#calculate second derivative
d2,T_d2=[],[]
for i in range(len(d1_smooth)-1):
Dy=d1_smooth[i-1]-d1_smooth[i+1]
Dx=T[i-1]-T[i+1]
d2.append(Dy/Dx)
T_d2=T[2:len(T-2)]
d2=array(d2,'f')
d2_smooth=smooth(d2,win)
d2=list(d2)
d2_smooth=list(d2_smooth)
curie.append(T_d2[d2.index(max(d2))])
if curie[-1]>curieT:curieT=curie[-1] # find maximum curie T
curie_1.append(T_d2[d2_smooth.index(max(d2_smooth))])
#plot Curie temp for different sliding window length
pmagplotlib.plot_init(PLT['Curie'],5,5)
pmagplotlib.plotXY(PLT['Curie'],wn,curie,'.','sliding window width (degrees)','curie temp','Inferred Curie Temperatures')
print 'Curie T is: ',curieT
pmagplotlib.drawFIGS(PLT)
files={}
for key in PLT.keys():
files[key]=spec+'_'+key+'.'+fmt
ans=raw_input(" S[a]ve to save plot, [q]uit, or return to continue: ")
if ans=='q':sys.exit()
if ans=='a':
pmagplotlib.saveP(PLT,files)
if rmag_file!="":
ResRec={}
ResRec['rmag_result_name']='Curie T: '+spec
ResRec['er_location_names']=location
ResRec['er_sample_names']=sample
ResRec['er_site_names']=site
ResRec['er_synthetic_names']=syn
if syn!="":
ResRec['er_specimen_names']=spec
else:
ResRec['er_specimen_names']=""
ResRec['magic_experiment_names']=expname
ResRec['magic_method_codes']=method+':SM-2DMAX'
ResRec['critical_temp']='%10.1f'%(curieT)
ResRec['critical_temp_type']="Curie"
ResRec['er_citation_names']="This study"
Results.append(ResRec)
if len(Results)>0 and rmag_file!="":
ResOuts,keys=pmag.fillkeys(Results)
pmag.magic_write(rmag_file,ResOuts,'rmag_results')
print 'Results stored in ',rmag_file
def main():
"""
NAME
replace_AC_specimens.py
DESCRIPTION
finds anisotropy corrected data and
replaces that specimen with it.
puts in pmag_specimen format file
SYNTAX
replace_AC_specimens.py [command line options]
OPTIONS
-h prints help message and quits
-i allows interactive setting of file names
-fu TFILE uncorrected pmag_specimen format file with thellier interpretations
created by thellier_magic_redo.py
-fc AFILE anisotropy corrected pmag_specimen format file
created by thellier_magic_redo.py
-F FILE pmag_specimens format output file
DEFAULTS
TFILE: thellier_specimens.txt
AFILE: AC_specimens.txt
FILE: TorAC_specimens.txt
"""
dir_path='.'
tspec="thellier_specimens.txt"
aspec="AC_specimens.txt"
ofile="TorAC_specimens.txt"
critfile="pmag_criteria.txt"
ACSamplist,Samplist,sigmin=[],[],10000
GoodSamps,SpecOuts=[],[]
# get arguments from command line
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-fu' in sys.argv:
ind=sys.argv.index('-fu')
tspec=sys.argv[ind+1]
if '-fc' in sys.argv:
ind=sys.argv.index('-fc')
aspec=sys.argv[ind+1]
if '-F' in sys.argv:
ind=sys.argv.index('-F')
ofile=sys.argv[ind+1]
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
# read in pmag_specimens file
tspec=dir_path+'/'+tspec
aspec=dir_path+'/'+aspec
ofile=dir_path+'/'+ofile
Specs,file_type=pmag.magic_read(tspec)
Specs,file_type=pmag.magic_read(tspec)
Speclist=pmag.get_specs(Specs)
ACSpecs,file_type=pmag.magic_read(aspec)
ACspeclist=pmag.get_specs(ACSpecs)
for spec in Specs:
if spec["er_sample_name"] not in Samplist:Samplist.append(spec["er_sample_name"])
for spec in ACSpecs:
if spec["er_sample_name"] not in ACSamplist:ACSamplist.append(spec["er_sample_name"])
#
for samp in Samplist:
useAC,Ints,ACInts,GoodSpecs,AC,UC=0,[],[],[],[],[]
for spec in Specs:
if spec["er_sample_name"].lower()==samp.lower():
UC.append(spec)
if samp in ACSamplist:
for spec in ACSpecs:
if spec["er_sample_name"].lower()==samp.lower():
AC.append(spec)
if len(AC)>0:
AClist=[]
for spec in AC:
SpecOuts.append(spec)
AClist.append(spec['er_specimen_name'])
print 'using AC: ',spec['er_specimen_name'],'%7.1f'%(1e6*float(spec['specimen_int']))
for spec in UC:
if spec['er_specimen_name'] not in AClist:
SpecOuts.append(spec)
# print 'using UC: ',spec['er_specimen_name'],'%7.1f'%(1e6*float(spec['specimen_int']))
else:
for spec in UC:
SpecOuts.append(spec)
# print 'using UC: ',spec['er_specimen_name'],'%7.1f'%(1e6*float(spec['specimen_int']))
SpecOuts,keys=pmag.fillkeys(SpecOuts)
pmag.magic_write(ofile,SpecOuts,'pmag_specimens')
print 'thellier data assessed for AC correction put in ', ofile
def main():
"""
NAME
UR_jr6_magic.py
DESCRIPTION
converts University of Rome JR6 format files to magic_measurements format files
SYNTAX
UR_jr6_magic.py [command line options]
OPTIONS
-h: prints the help message and quits.
-F FILE: specify output measurements file, default is magic_measurements.txt
-Fsa FILE: specify output er_samples.txt file for appending, default is er_samples.txt
-dc B PHI THETA: dc lab field (in micro tesla) and phi,theta, default is none
NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment
-ac B : peak AF field (in mT) for ARM acquisition, default is none
-A : don't average replicate measurements
-spc NUM : specify number of characters to designate a specimen, default = 0
-loc LOCNAME : specify location/study name, must have either LOCNAME or SAMPFILE or be a synthetic
-mcd: specify sampling method codes as a colon delimited string: [default is: FS-FD:SO-POM:SO-SUN]
FS-FD field sampling done with a drill
FS-H field sampling done with hand samples
FS-LOC-GPS field location done with GPS
FS-LOC-MAP field location done with map
SO-POM a Pomeroy orientation device was used
SO-SUN orientations are from a sun compass
SO-MAG orientations are from a magnetic compass
SO-MAG-CMD orientations declination corrected magnetic compass
-ncn NCON: specify naming convention: default is #1 below
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
[8] synthetic - has no site name
[9] ODP naming convention
INPUT
Put data from separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.) in separate directory
"""
#
#
version_num=pmag.get_version()
er_location_name=""
ErSpecs,ErSamps,ErSites,ErLocs,ErCits=[],[],[],[],[]
MagRecs=[]
citation="This study"
dir_path,demag='.','NRM'
args=sys.argv
noave=0
specnum=0
sampmeths='FS-FD:SO-POM:SO-SUN'
samp_con,Z="4","2"
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
meas_file=dir_path+'/'+'magic_measurements.txt'
samp_file=dir_path+'/'+'er_samples.txt'
if "-h" in args:
print main.__doc__
sys.exit()
if "-A" in args: noave=1
if '-F' in args:
ind=args.index("-F")
meas_file=dir_path+'/'+args[ind+1]
if '-Fsa' in args:
ind=args.index("-Fsa")
samp_file=dir_path+'/'+args[ind+1]
ErSamps,file_type=pmag.magic_read(samp_file)
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "-mcd" in args:
ind=args.index("-mcd")
sampmeths=(sys.argv[ind+1])
if "-loc" in args:
ind=args.index("-loc")
er_location_name=args[ind+1]
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if specnum!=0:specnum=-specnum
if '-LP' in args:
ind=args.index("-LP")
codelist=args[ind+1]
codes=codelist.split(':')
if "AF" in codes:
demag='AF'
if'-dc' not in args: methcode="LT-AF-Z"
if'-dc' in args: methcode="LT-AF-I"
if "T" in codes:
demag="T"
if '-dc' not in args: methcode="LT-T-Z"
if '-dc' in args: methcode="LT-T-I"
if "I" in codes:
methcode="LP-IRM"
if "S" in codes:
demag="S"
methcode="LP-PI-TRM:LP-PI-ALT-AFARM"
trm_labfield=labfield
ans=raw_input("DC lab field for ARM step: [50uT] ")
if ans=="":
arm_labfield=50e-6
else:
arm_labfield=float(ans)*1e-6
ans=raw_input("temperature for total trm step: [600 C] ")
if ans=="":
trm_peakT=600+273 # convert to kelvin
else:
trm_peakT=float(ans)+273 # convert to kelvin
if "G" in codes: methcode="LT-AF-G"
if "D" in codes: methcode="LT-AF-D"
if "TRM" in codes:
demag="T"
trm=1
if demag=="T" and "ANI" in codes:
methcode="LP-AN-TRM"
if demag=="AF" and "ANI" in codes:
methcode="LP-AN-ARM"
if labfield==0: labfield=50e-6
if peakfield==0: peakfield=.180
filelist=os.listdir(dir_path) # read in list of files to import
samples=[]
MagRecs,SampRecs=[],[]
for samp in ErSamps:
if samp['er_sample_name'] not in samples:
samples.append(samp['er_sample_name'])
SampRecs.append(samp)
for file in filelist: # parse each file
parts=file.split('.')
if parts[1].upper()=='JR6':
print 'processing: ',file
treatment_type,treatment_value,user="","",""
inst="UR-JR6"
input=open(dir_path+'/'+file,'rU').readlines()
for line in input:
newline=line.replace('-',' -')
rec=newline.split()
MagRec,SampRec={},{}
specimen=rec[0]
if specnum!=0:
SampRec['er_sample_name']=specimen[:specnum]
else:
SampRec['er_sample_name']=specimen
er_site_name=pmag.parse_site(SampRec['er_sample_name'],samp_con,Z)
SampRec['er_site_name']=er_site_name
SampRec['er_location_name']=er_location_name
for key in SampRec.keys():MagRec[key]=SampRec[key]
SampRec['sample_azimuth']=rec[7]
SampRec['sample_dip']='-'+rec[8]
SampRec['sample_bed_dip_direction']=rec[9]
SampRec['sample_bed_dip']=rec[10]
SampRec['magic_method_codes']=sampmeths
MagRec['er_specimen_name']=specimen
MagRec['er_analyst_mail_names']=user
MagRec['magic_software_packages']=version_num
MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec["treatment_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"]='' # set csd to blank
MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin
MagRec['magic_method_codes']='LT-NO'
if rec[2]=='C':
temp=float(rec[1])+273.
if temp>298:
MagRec["treatment_temp"]='%8.3e' % (temp) # room temp in kelvin
MagRec['magic_method_codes']='LT-T-Z'
else: # measurement is in oe
AC=float(rec[1])*1e-4 # convert to tesla
if AC!=0.:
MagRec["treatment_ac_field"]='%8.3e' %(AC)
MagRec['magic_method_codes']='LT-AF-Z'
vol=10.8*1e-6 # standard Roma lab volume
MagRec['magic_instrument_codes']=inst
MagRec['measurement_number']='1'
mexp=10**(float(rec[6]))
x,y,z=mexp*float(rec[3]),mexp*float(rec[4]),mexp*float(rec[5])
Cart=[x,y,z]
Dir=pmag.cart2dir(Cart)
MagRec['measurement_dec']='%7.1f'%(Dir[0])
MagRec['measurement_inc']='%7.1f'%(Dir[1])
MagRec['measurement_magn_volume']='%8.3e'%(Dir[2])
MagRec['measurement_magn_moment']='%8.3e'%(Dir[2]*vol)
MagRec['measurement_description']='converted A/m to Am^2 using volume of '+str(vol)+' m^3'
MagRecs.append(MagRec)
if MagRec['er_sample_name'] not in samples:
samples.append(MagRec['er_sample_name'])
SampRecs.append(SampRec)
if len(SampRecs)>0:
SampOut,keys=pmag.fillkeys(SampRecs)
pmag.magic_write(samp_file,SampOut,'er_samples')
print 'samples stored in ',samp_file
Fixed=pmag.measurements_methods(MagRecs,noave)
pmag.magic_write(meas_file,Fixed,'magic_measurements')
print 'data stored in ',meas_file
def main(command_line=True, **kwargs):
"""
NAME
2G_bin_magic.py
DESCRIPTION
takes the binary 2G format magnetometer files and converts them to magic_measurements, er_samples.txt and er_sites.txt file
SYNTAX
2G_bin_magic.py [command line options]
OPTIONS
-f FILE: specify input 2G (binary) file
-F FILE: specify magic_measurements output file, default is: magic_measurements.txt
-Fsa FILE: specify output file, default is: er_samples.txt
-Fsi FILE: specify output file, default is: er_sites.txt
-ncn NCON: specify naming convention: default is #2 below
-ocn OCON: specify orientation convention, default is #5 below
-mcd: specify sampling method codes as a colon delimited string: [default is: FS-FD:SO-POM]
FS-FD field sampling done with a drill
FS-H field sampling done with hand samples
FS-LOC-GPS field location done with GPS
FS-LOC-MAP field location done with map
SO-POM a Pomeroy orientation device was used
SO-ASC an ASC orientation device was used
SO-MAG orientation with magnetic compass
SO-SUN orientation with sun compass
-loc: location name, default="unknown"
-spc NUM : specify number of characters to designate a specimen, default = 0
-ins INST : specify instsrument name
-a: average replicate measurements
INPUT FORMAT
Input files are horrible mag binary format (who knows why?)
Orientation convention:
[1] Lab arrow azimuth= mag_azimuth; Lab arrow dip=-field_dip
i.e., field_dip is degrees from vertical down - the hade [default]
[2] Lab arrow azimuth = mag_azimuth-90; Lab arrow dip = -field_dip
i.e., mag_azimuth is strike and field_dip is hade
[3] Lab arrow azimuth = mag_azimuth; Lab arrow dip = 90-field_dip
i.e., lab arrow same as field arrow, but field_dip was a hade.
[4] lab azimuth and dip are same as mag_azimuth, field_dip
[5] lab azimuth is same as mag_azimuth,lab arrow dip=field_dip-90
[6] Lab arrow azimuth = mag_azimuth-90; Lab arrow dip = 90-field_dip
[7] all others you will have to either customize your
self or e-mail [email protected] for help.
Magnetic declination convention:
Az will use supplied declination to correct azimuth
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name same as sample
[6] site is entered under a separate column
[7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY
NB: all others you will have to customize your self
or e-mail [email protected] for help.
OUTPUT
output saved in magic_measurements.txt & er_samples.txt formatted files
will overwrite any existing files
"""
#
# initialize variables
#
mag_file = ''
specnum=0
ub_file,samp_file,or_con,corr,meas_file = "","er_samples.txt","3","1","magic_measurements.txt"
pos_file,site_file="","er_sites.txt"
noave=1
args=sys.argv
bed_dip,bed_dip_dir="",""
samp_con,Z,average_bedding="2",1,"0"
meths='FS-FD'
sclass,lithology,_type="","",""
user,inst="",""
DecCorr=0.
location_name="unknown"
months=['Jan','Feb','Mar','Apr','May','Jun','Jul','Aug','Sep','Oct','Nov','Dec']
gmeths=""
#
#
dir_path='.'
if command_line:
if '-WD' in args:
ind=args.index("-WD")
dir_path=sys.argv[ind+1]
if "-h" in args:
print main.__doc__
return False
if "-f" in args:
ind=args.index("-f")
mag_file=sys.argv[ind+1]
if "-fpos" in args:
ind=args.index("-fpos")
pos_file=sys.argv[ind+1]
if "-F" in args:
ind=args.index("-F")
meas_file=sys.argv[ind+1]
if "-Fsa" in args:
ind=args.index("-Fsa")
samp_file=sys.argv[ind+1]
if "-Fsi" in args:
ind=args.index("-Fsi")
site_file=sys.argv[ind+1]
if "-ocn" in args:
ind=args.index("-ocn")
or_con=sys.argv[ind+1]
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "-mcd" in args:
ind=args.index("-mcd")
gmeths=(sys.argv[ind+1])
if "-loc" in args:
ind=args.index("-loc")
location_name=(sys.argv[ind+1])
if "-spc" in args:
ind=args.index("-spc")
specnum=int(args[ind+1])
if "-ins" in args:
ind=args.index("-ins")
inst=args[ind+1]
if "-a" in args:
noave=0
#
ID = False
if '-ID' in args:
ind = args.index('-ID')
ID = args[ind+1]
#
if not command_line:
dir_path = kwargs.get('dir_path', '.')
mag_file = kwargs.get('mag_file', '')
pos_file = kwargs.get('pos_file', '')
meas_file = kwargs.get('meas_file', 'magic_measurements.txt')
samp_file = kwargs.get('samp_file', 'er_samples.txt')
site_file = kwargs.get('site_file', 'er_sites.txt')
or_con = kwargs.get('or_con', '3')
samp_con = kwargs.get('samp_con', '2')
corr = kwargs.get('corr', '1')
gmeths = kwargs.get('gmeths', '')
location_name = kwargs.get('location_name', '')
specnum = int(kwargs.get('specnum', 0))
inst = kwargs.get('inst', '')
noave = kwargs.get('noave', 1) # default is DO average
ID = kwargs.get('ID', '')
# format and fix variables acquired from command line args or input with **kwargs
if specnum!=0:specnum=-specnum
if ID:
input_dir_path = ID
else:
input_dir_path = dir_path
if samp_con:
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
return False, "option [4] must be in form 4-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
return False, "option [7] must be in form 7-Z where Z is an integer"
else:
Z=samp_con.split("-")[1]
samp_con="7"
if "6" in samp_con:
try:
Samps,file_type=pmag.magic_read(os.path.join(input_dir_path, 'er_samples.txt'))
except:
print "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
return False, "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
if file_type == 'bad_file':
print "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
return False, "there is no er_samples.txt file in your input directory - you can't use naming convention #6"
if not mag_file:
print "mag file is required input"
return False, "mag file is required input"
output_dir_path = dir_path
mag_file = os.path.join(input_dir_path, mag_file)
samp_file = output_dir_path+'/'+samp_file
site_file = output_dir_path+'/'+site_file
meas_file= output_dir_path+'/'+meas_file
samplist=[]
try:
Samps,file_type=pmag.magic_read(samp_file)
for samp in Samps:
if samp['er_sample_name'] not in samplist: samplist.append(samp['er_sample_name'])
except:
Samps=[]
MagRecs=[]
try:
f=open(mag_file,'rU')
input=f.read()
f.close()
except Exception as ex:
print 'ex', ex
print "bad mag file"
return False, "bad mag file"
firstline,date=1,""
d=input.split('\xcd')
for line in d:
rec=line.split('\x00')
if firstline==1:
firstline=0
spec,vol="",1
for c in line[15:23]:
if c!='\x00':spec=spec+c
# check for bad sample name
test=spec.split('.')
date=""
if len(test)>1:
spec=test[0]
kk=24
while line[kk]!='\x01' and line[kk]!='\x00':
kk+=1
vcc=line[24:kk]
el=10
while rec[el].strip()!='':el+=1
date,comments=rec[el+7],[]
else:
el=9
while rec[el]!='\x01':el+=1
vcc,date,comments=rec[el-3],rec[el+7],[]
specname=spec.lower()
print 'importing ',specname
el+=8
while rec[el].isdigit()==False:
comments.append(rec[el])
el+=1
while rec[el]=="":el+=1
az=float(rec[el])
el+=1
while rec[el]=="":el+=1
pl=float(rec[el])
el+=1
while rec[el]=="":el+=1
bed_dip_dir=float(rec[el])
el+=1
while rec[el]=="":el+=1
bed_dip=float(rec[el])
el+=1
while rec[el]=="":el+=1
if rec[el]=='\x01':
bed_dip=180.-bed_dip
el+=1
while rec[el]=="":el+=1
fold_az=float(rec[el])
el+=1
while rec[el]=="":el+=1
fold_pl=rec[el]
el+=1
while rec[el]=="":el+=1
if rec[el]!="" and rec[el]!='\x02' and rec[el]!='\x01':
deccorr=float(rec[el])
az+=deccorr
bed_dip_dir+=deccorr
fold_az+=deccorr
if bed_dip_dir>=360:bed_dip_dir=bed_dip_dir-360.
if az>=360.:az=az-360.
if fold_az>=360.:fold_az=fold_az-360.
else:
deccorr=0
if specnum!=0:
sample=specname[:specnum]
else:
sample=specname
SampRec={}
SampRec["er_sample_name"]=sample
SampRec["er_location_name"]=location_name
SampRec["er_citation_names"]="This study"
labaz,labdip=pmag.orient(az,pl,or_con) # convert to labaz, labpl
#
# parse information common to all orientation methods
#
SampRec["sample_bed_dip"]='%7.1f'%(bed_dip)
SampRec["sample_bed_dip_direction"]='%7.1f'%(bed_dip_dir)
SampRec["sample_dip"]='%7.1f'%(labdip)
SampRec["sample_azimuth"]='%7.1f'%(labaz)
if vcc.strip()!="":vol=float(vcc)*1e-6 # convert to m^3 from cc
SampRec["sample_volume"]='%10.3e'%(vol) #
SampRec["sample_class"]=sclass
SampRec["sample_lithology"]=lithology
SampRec["sample_type"]=_type
SampRec["sample_declination_correction"]='%7.1f'%(deccorr)
methods=gmeths.split(':')
if deccorr!="0":
if 'SO-MAG' in methods:del methods[methods.index('SO-MAG')]
methods.append('SO-CMD-NORTH')
meths=""
for meth in methods:meths=meths+meth+":"
meths=meths[:-1]
SampRec["magic_method_codes"]=meths
if int(samp_con)<6 or int(samp_con) == 7:
site=pmag.parse_site(SampRec["er_sample_name"],samp_con,Z) # parse out the site name
SampRec["er_site_name"]=site
elif len(Samps)>1:
site,location="",""
for samp in Samps:
if samp["er_sample_name"] == SampRec["er_sample_name"]:
site=samp["er_site_name"]
location=samp["er_location_name"]
break
SampRec["er_location_name"]=samp["er_location_name"]
SampRec["er_site_name"]=samp["er_site_name"]
if sample not in samplist:
samplist.append(sample)
Samps.append(SampRec)
else:
MagRec={}
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'
meas_type="LT-NO"
MagRec["measurement_flag"]='g'
MagRec["measurement_standard"]='u'
MagRec["measurement_number"]='1'
MagRec["er_specimen_name"]=specname
MagRec["er_sample_name"]=SampRec['er_sample_name']
MagRec["er_site_name"]=SampRec['er_site_name']
MagRec["er_location_name"]=location_name
el,demag=1,''
treat=rec[el]
if treat[-1]=='C':
demag='T'
elif treat!='NRM':
demag='AF'
el+=1
while rec[el]=="":el+=1
MagRec["measurement_dec"]=rec[el]
cdec=float(rec[el])
el+=1
while rec[el]=="":el+=1
MagRec["measurement_inc"]=rec[el]
cinc=float(rec[el])
el+=1
while rec[el]=="":el+=1
gdec=rec[el]
el+=1
while rec[el]=="":el+=1
ginc=rec[el]
el=skip(2,el,rec) # skip bdec,binc
# el=skip(4,el,rec) # skip gdec,ginc,bdec,binc
# print 'moment emu: ',rec[el]
MagRec["measurement_magn_moment"]='%10.3e'% (float(rec[el])*1e-3) # moment in Am^2 (from emu)
MagRec["measurement_magn_volume"]='%10.3e'% (float(rec[el])*1e-3/vol) # magnetization in A/m
el=skip(2,el,rec) # skip to xsig
MagRec["measurement_sd_x"]='%10.3e'% (float(rec[el])*1e-3) # convert from emu
el=skip(3,el,rec) # skip to ysig
MagRec["measurement_sd_y"]='%10.3e'% (float(rec[el])*1e-3) # convert from emu
el=skip(3,el,rec) # skip to zsig
MagRec["measurement_sd_z"]='%10.3e'% (float(rec[el])*1e-3) # convert from emu
el+=1 # skip to positions
MagRec["measurement_positions"]=rec[el]
# el=skip(5,el,rec) # skip to date
# mm=str(months.index(date[0]))
# if len(mm)==1:
# mm='0'+str(mm)
# else:
# mm=str(mm)
# dstring=date[2]+':'+mm+':'+date[1]+":"+date[3]
# MagRec['measurement_date']=dstring
MagRec["magic_instrument_codes"]=inst
MagRec["er_analyst_mail_names"]=""
MagRec["er_citation_names"]="This study"
MagRec["magic_method_codes"]=meas_type
if demag=="AF":
MagRec["treatment_ac_field"]='%8.3e' %(float(treat[:-2])*1e-3) # peak field in tesla
meas_type="LT-AF-Z"
MagRec["treatment_dc_field"]='0'
elif demag=="T":
MagRec["treatment_temp"]='%8.3e' % (float(treat[:-1])+273.) # temp in kelvin
meas_type="LT-T-Z"
MagRec['magic_method_codes']=meas_type
MagRecs.append(MagRec)
MagOuts=pmag.measurements_methods(MagRecs,noave)
MagOuts, keylist = pmag.fillkeys(MagOuts)
pmag.magic_write(meas_file,MagOuts,'magic_measurements')
print "Measurements put in ",meas_file
SampsOut,sampkeys=pmag.fillkeys(Samps)
pmag.magic_write(samp_file,SampsOut,"er_samples")
Sites=[]
for samp in Samps:
SiteRec={}
SiteRec['er_site_name']=samp['er_site_name']
SiteRec['er_location_name']=samp['er_location_name']
SiteRec['site_definition']='s'
SiteRec['er_citation_names']='This study'
if 'sample_class' in samp.keys():SiteRec['site_class']=samp['sample_class']
if 'sample_lithology' in samp.keys():SiteRec['site_lithology']=samp['sample_lithology']
if 'sample_type' in samp.keys():SiteRec['site_lithology']=samp['sample_lithology']
if 'sample_lat' in samp.keys():
SiteRec['site_lat']=samp['sample_lat']
else:
SiteRec['site_lat']="-999"
if 'sample_lon' in samp.keys():
SiteRec['site_lon']=samp['sample_lon']
else:
SiteRec['site_lon']="-999"
if 'sample_height' in samp.keys():SiteRec['site_height']=samp['sample_height']
Sites.append(SiteRec)
pmag.magic_write(site_file,Sites,'er_sites')
return True, meas_file
def main():
"""
NAME
aniso_magic.py
DESCRIPTION
plots anisotropy data with either bootstrap or hext ellipses
SYNTAX
aniso_magic.py [-h] [command line options]
OPTIONS
-h plots help message and quits
-usr USER: set the user name
-f AFILE, specify rmag_anisotropy formatted file for input
-F RFILE, specify rmag_results formatted file for output
-x Hext [1963] and bootstrap
-B DON'T do bootstrap, do Hext
-par Tauxe [1998] parametric bootstrap
-v plot bootstrap eigenvectors instead of ellipses
-sit plot by site instead of entire file
-crd [s,g,t] coordinate system, default is specimen (g=geographic, t=tilt corrected)
-P don't make any plots - just make rmag_results table
-sav don't make the rmag_results table - just save all the plots
-fmt [svg, jpg, eps] format for output images, pdf default
-gtc DEC INC dec,inc of pole to great circle [down(up) in green (cyan)
-d Vi DEC INC; Vi (1,2,3) to compare to direction DEC INC
-nb N; specifies the number of bootstraps - default is 1000
DEFAULTS
AFILE: rmag_anisotropy.txt
RFILE: rmag_results.txt
plot bootstrap ellipses of Constable & Tauxe [1987]
NOTES
minor axis: circles
major axis: triangles
principal axis: squares
directions are plotted on the lower hemisphere
for bootstrapped eigenvector components: Xs: blue, Ys: red, Zs: black
"""
#
dir_path = "."
version_num = pmag.get_version()
verbose = pmagplotlib.verbose
args = sys.argv
ipar, ihext, ivec, iboot, imeas, isite, iplot, vec = 0, 0, 0, 1, 1, 0, 1, 0
hpars, bpars, PDir = [], [], []
CS, crd = "-1", "s"
nb = 1000
fmt = "pdf"
ResRecs = []
orlist = []
outfile, comp, Dir, gtcirc, PDir = "rmag_results.txt", 0, [], 0, []
infile = "rmag_anisotropy.txt"
if "-h" in args:
print main.__doc__
sys.exit()
if "-WD" in args:
ind = args.index("-WD")
dir_path = args[ind + 1]
if "-nb" in args:
ind = args.index("-nb")
nb = int(args[ind + 1])
if "-usr" in args:
ind = args.index("-usr")
user = args[ind + 1]
else:
user = ""
if "-B" in args:
iboot, ihext = 0, 1
if "-par" in args:
ipar = 1
if "-x" in args:
ihext = 1
if "-v" in args:
ivec = 1
if "-sit" in args:
isite = 1
if "-P" in args:
iplot = 0
if "-f" in args:
ind = args.index("-f")
infile = args[ind + 1]
if "-F" in args:
ind = args.index("-F")
outfile = args[ind + 1]
if "-crd" in sys.argv:
ind = sys.argv.index("-crd")
crd = sys.argv[ind + 1]
if crd == "g":
CS = "0"
if crd == "t":
CS = "100"
if "-fmt" in args:
ind = args.index("-fmt")
fmt = args[ind + 1]
if "-sav" in args:
plots = 1
verbose = 0
else:
plots = 0
if "-gtc" in args:
ind = args.index("-gtc")
d, i = float(args[ind + 1]), float(args[ind + 2])
PDir.append(d)
PDir.append(i)
if "-d" in args:
comp = 1
ind = args.index("-d")
vec = int(args[ind + 1]) - 1
Dir = [float(args[ind + 2]), float(args[ind + 3])]
#
# set up plots
#
if infile[0] != "/":
infile = dir_path + "/" + infile
if outfile[0] != "/":
outfile = dir_path + "/" + outfile
ANIS = {}
initcdf, inittcdf = 0, 0
ANIS["data"], ANIS["conf"] = 1, 2
if iboot == 1:
ANIS["tcdf"] = 3
if iplot == 1:
inittcdf = 1
pmagplotlib.plot_init(ANIS["tcdf"], 5, 5)
if comp == 1 and iplot == 1:
initcdf = 1
ANIS["vxcdf"], ANIS["vycdf"], ANIS["vzcdf"] = 4, 5, 6
pmagplotlib.plot_init(ANIS["vxcdf"], 5, 5)
pmagplotlib.plot_init(ANIS["vycdf"], 5, 5)
pmagplotlib.plot_init(ANIS["vzcdf"], 5, 5)
if iplot == 1:
pmagplotlib.plot_init(ANIS["conf"], 5, 5)
pmagplotlib.plot_init(ANIS["data"], 5, 5)
# read in the data
data, ifiletype = pmag.magic_read(infile)
for rec in data: # find all the orientation systems
if "anisotropy_tilt_correction" not in rec.keys():
rec["anisotropy_tilt_correction"] = "-1"
if rec["anisotropy_tilt_correction"] not in orlist:
orlist.append(rec["anisotropy_tilt_correction"])
if CS not in orlist:
if len(orlist) > 0:
CS = orlist[0]
else:
CS = "-1"
if CS == "-1":
crd = "s"
if CS == "0":
crd = "g"
if CS == "100":
crd = "t"
if verbose:
print "desired coordinate system not available, using available: ", crd
if isite == 1:
sitelist = []
for rec in data:
if rec["er_site_name"] not in sitelist:
sitelist.append(rec["er_site_name"])
sitelist.sort()
plt = len(sitelist)
else:
plt = 1
k = 0
while k < plt:
site = ""
sdata, Ss = [], [] # list of S format data
Locs, Sites, Samples, Specimens, Cits = [], [], [], [], []
if isite == 0:
sdata = data
else:
site = sitelist[k]
for rec in data:
if rec["er_site_name"] == site:
sdata.append(rec)
anitypes = []
csrecs = pmag.get_dictitem(sdata, "anisotropy_tilt_correction", CS, "T")
for rec in csrecs:
if rec["anisotropy_type"] not in anitypes:
anitypes.append(rec["anisotropy_type"])
if rec["er_location_name"] not in Locs:
Locs.append(rec["er_location_name"])
if rec["er_site_name"] not in Sites:
Sites.append(rec["er_site_name"])
if rec["er_sample_name"] not in Samples:
Samples.append(rec["er_sample_name"])
if rec["er_specimen_name"] not in Specimens:
Specimens.append(rec["er_specimen_name"])
if rec["er_citation_names"] not in Cits:
Cits.append(rec["er_citation_names"])
s = []
s.append(float(rec["anisotropy_s1"]))
s.append(float(rec["anisotropy_s2"]))
s.append(float(rec["anisotropy_s3"]))
s.append(float(rec["anisotropy_s4"]))
s.append(float(rec["anisotropy_s5"]))
s.append(float(rec["anisotropy_s6"]))
if s[0] <= 1.0:
Ss.append(s) # protect against crap
# tau,Vdirs=pmag.doseigs(s)
fpars = pmag.dohext(int(rec["anisotropy_n"]) - 6, float(rec["anisotropy_sigma"]), s)
ResRec = {}
ResRec["er_location_names"] = rec["er_location_name"]
ResRec["er_citation_names"] = rec["er_citation_names"]
ResRec["er_site_names"] = rec["er_site_name"]
ResRec["er_sample_names"] = rec["er_sample_name"]
ResRec["er_specimen_names"] = rec["er_specimen_name"]
ResRec["rmag_result_name"] = rec["er_specimen_name"] + ":" + rec["anisotropy_type"]
ResRec["er_analyst_mail_names"] = user
ResRec["tilt_correction"] = CS
ResRec["anisotropy_type"] = rec["anisotropy_type"]
ResRec["anisotropy_v1_dec"] = "%7.1f" % (fpars["v1_dec"])
ResRec["anisotropy_v2_dec"] = "%7.1f" % (fpars["v2_dec"])
ResRec["anisotropy_v3_dec"] = "%7.1f" % (fpars["v3_dec"])
ResRec["anisotropy_v1_inc"] = "%7.1f" % (fpars["v1_inc"])
ResRec["anisotropy_v2_inc"] = "%7.1f" % (fpars["v2_inc"])
ResRec["anisotropy_v3_inc"] = "%7.1f" % (fpars["v3_inc"])
ResRec["anisotropy_t1"] = "%10.8f" % (fpars["t1"])
ResRec["anisotropy_t2"] = "%10.8f" % (fpars["t2"])
ResRec["anisotropy_t3"] = "%10.8f" % (fpars["t3"])
ResRec["anisotropy_ftest"] = "%10.3f" % (fpars["F"])
ResRec["anisotropy_ftest12"] = "%10.3f" % (fpars["F12"])
ResRec["anisotropy_ftest23"] = "%10.3f" % (fpars["F23"])
ResRec["result_description"] = "F_crit: " + fpars["F_crit"] + "; F12,F23_crit: " + fpars["F12_crit"]
ResRec["anisotropy_type"] = pmag.makelist(anitypes)
ResRecs.append(ResRec)
if len(Ss) > 1:
title = "LO:_" + ResRec["er_location_names"] + "_SI:_" + site + "_SA:__SP:__CO:_" + crd
ResRec["er_location_names"] = pmag.makelist(Locs)
bpars, hpars = pmagplotlib.plotANIS(ANIS, Ss, iboot, ihext, ivec, ipar, title, iplot, comp, vec, Dir, nb)
if len(PDir) > 0:
pmagplotlib.plotC(ANIS["data"], PDir, 90.0, "g")
pmagplotlib.plotC(ANIS["conf"], PDir, 90.0, "g")
if verbose and plots == 0:
pmagplotlib.drawFIGS(ANIS)
ResRec["er_location_names"] = pmag.makelist(Locs)
if plots == 1:
save(ANIS, fmt, title)
ResRec = {}
ResRec["er_citation_names"] = pmag.makelist(Cits)
ResRec["er_location_names"] = pmag.makelist(Locs)
ResRec["er_site_names"] = pmag.makelist(Sites)
ResRec["er_sample_names"] = pmag.makelist(Samples)
ResRec["er_specimen_names"] = pmag.makelist(Specimens)
ResRec["rmag_result_name"] = pmag.makelist(Sites) + ":" + pmag.makelist(anitypes)
ResRec["anisotropy_type"] = pmag.makelist(anitypes)
ResRec["er_analyst_mail_names"] = user
ResRec["tilt_correction"] = CS
if isite == "0":
ResRec["result_description"] = "Study average using coordinate system: " + CS
if isite == "1":
ResRec["result_description"] = "Site average using coordinate system: " + CS
if hpars != [] and ihext == 1:
HextRec = {}
for key in ResRec.keys():
HextRec[key] = ResRec[key] # copy over stuff
HextRec["anisotropy_v1_dec"] = "%7.1f" % (hpars["v1_dec"])
HextRec["anisotropy_v2_dec"] = "%7.1f" % (hpars["v2_dec"])
HextRec["anisotropy_v3_dec"] = "%7.1f" % (hpars["v3_dec"])
HextRec["anisotropy_v1_inc"] = "%7.1f" % (hpars["v1_inc"])
HextRec["anisotropy_v2_inc"] = "%7.1f" % (hpars["v2_inc"])
HextRec["anisotropy_v3_inc"] = "%7.1f" % (hpars["v3_inc"])
HextRec["anisotropy_t1"] = "%10.8f" % (hpars["t1"])
HextRec["anisotropy_t2"] = "%10.8f" % (hpars["t2"])
HextRec["anisotropy_t3"] = "%10.8f" % (hpars["t3"])
HextRec["anisotropy_hext_F"] = "%7.1f " % (hpars["F"])
HextRec["anisotropy_hext_F12"] = "%7.1f " % (hpars["F12"])
HextRec["anisotropy_hext_F23"] = "%7.1f " % (hpars["F23"])
HextRec["anisotropy_v1_eta_semi_angle"] = "%7.1f " % (hpars["e12"])
HextRec["anisotropy_v1_eta_dec"] = "%7.1f " % (hpars["v2_dec"])
HextRec["anisotropy_v1_eta_inc"] = "%7.1f " % (hpars["v2_inc"])
HextRec["anisotropy_v1_zeta_semi_angle"] = "%7.1f " % (hpars["e13"])
HextRec["anisotropy_v1_zeta_dec"] = "%7.1f " % (hpars["v3_dec"])
HextRec["anisotropy_v1_zeta_inc"] = "%7.1f " % (hpars["v3_inc"])
HextRec["anisotropy_v2_eta_semi_angle"] = "%7.1f " % (hpars["e12"])
HextRec["anisotropy_v2_eta_dec"] = "%7.1f " % (hpars["v1_dec"])
HextRec["anisotropy_v2_eta_inc"] = "%7.1f " % (hpars["v1_inc"])
HextRec["anisotropy_v2_zeta_semi_angle"] = "%7.1f " % (hpars["e23"])
HextRec["anisotropy_v2_zeta_dec"] = "%7.1f " % (hpars["v3_dec"])
HextRec["anisotropy_v2_zeta_inc"] = "%7.1f " % (hpars["v3_inc"])
HextRec["anisotropy_v3_eta_semi_angle"] = "%7.1f " % (hpars["e12"])
HextRec["anisotropy_v3_eta_dec"] = "%7.1f " % (hpars["v1_dec"])
HextRec["anisotropy_v3_eta_inc"] = "%7.1f " % (hpars["v1_inc"])
HextRec["anisotropy_v3_zeta_semi_angle"] = "%7.1f " % (hpars["e23"])
HextRec["anisotropy_v3_zeta_dec"] = "%7.1f " % (hpars["v2_dec"])
HextRec["anisotropy_v3_zeta_inc"] = "%7.1f " % (hpars["v2_inc"])
HextRec["magic_method_codes"] = "LP-AN:AE-H"
if verbose:
print "Hext Statistics: "
print " tau_i, V_i_D, V_i_I, V_i_zeta, V_i_zeta_D, V_i_zeta_I, V_i_eta, V_i_eta_D, V_i_eta_I"
print HextRec["anisotropy_t1"], HextRec["anisotropy_v1_dec"], HextRec["anisotropy_v1_inc"], HextRec[
"anisotropy_v1_eta_semi_angle"
], HextRec["anisotropy_v1_eta_dec"], HextRec["anisotropy_v1_eta_inc"], HextRec[
"anisotropy_v1_zeta_semi_angle"
], HextRec[
"anisotropy_v1_zeta_dec"
], HextRec[
"anisotropy_v1_zeta_inc"
]
print HextRec["anisotropy_t2"], HextRec["anisotropy_v2_dec"], HextRec["anisotropy_v2_inc"], HextRec[
"anisotropy_v2_eta_semi_angle"
], HextRec["anisotropy_v2_eta_dec"], HextRec["anisotropy_v2_eta_inc"], HextRec[
"anisotropy_v2_zeta_semi_angle"
], HextRec[
"anisotropy_v2_zeta_dec"
], HextRec[
"anisotropy_v2_zeta_inc"
]
print HextRec["anisotropy_t3"], HextRec["anisotropy_v3_dec"], HextRec["anisotropy_v3_inc"], HextRec[
"anisotropy_v3_eta_semi_angle"
], HextRec["anisotropy_v3_eta_dec"], HextRec["anisotropy_v3_eta_inc"], HextRec[
"anisotropy_v3_zeta_semi_angle"
], HextRec[
"anisotropy_v3_zeta_dec"
], HextRec[
"anisotropy_v3_zeta_inc"
]
HextRec["magic_software_packages"] = version_num
ResRecs.append(HextRec)
if bpars != []:
BootRec = {}
for key in ResRec.keys():
BootRec[key] = ResRec[key] # copy over stuff
BootRec["anisotropy_v1_dec"] = "%7.1f" % (bpars["v1_dec"])
BootRec["anisotropy_v2_dec"] = "%7.1f" % (bpars["v2_dec"])
BootRec["anisotropy_v3_dec"] = "%7.1f" % (bpars["v3_dec"])
BootRec["anisotropy_v1_inc"] = "%7.1f" % (bpars["v1_inc"])
BootRec["anisotropy_v2_inc"] = "%7.1f" % (bpars["v2_inc"])
BootRec["anisotropy_v3_inc"] = "%7.1f" % (bpars["v3_inc"])
BootRec["anisotropy_t1"] = "%10.8f" % (bpars["t1"])
BootRec["anisotropy_t2"] = "%10.8f" % (bpars["t2"])
BootRec["anisotropy_t3"] = "%10.8f" % (bpars["t3"])
BootRec["anisotropy_v1_eta_inc"] = "%7.1f " % (bpars["v1_eta_inc"])
BootRec["anisotropy_v1_eta_dec"] = "%7.1f " % (bpars["v1_eta_dec"])
BootRec["anisotropy_v1_eta_semi_angle"] = "%7.1f " % (bpars["v1_eta"])
BootRec["anisotropy_v1_zeta_inc"] = "%7.1f " % (bpars["v1_zeta_inc"])
BootRec["anisotropy_v1_zeta_dec"] = "%7.1f " % (bpars["v1_zeta_dec"])
BootRec["anisotropy_v1_zeta_semi_angle"] = "%7.1f " % (bpars["v1_zeta"])
BootRec["anisotropy_v2_eta_inc"] = "%7.1f " % (bpars["v2_eta_inc"])
BootRec["anisotropy_v2_eta_dec"] = "%7.1f " % (bpars["v2_eta_dec"])
BootRec["anisotropy_v2_eta_semi_angle"] = "%7.1f " % (bpars["v2_eta"])
BootRec["anisotropy_v2_zeta_inc"] = "%7.1f " % (bpars["v2_zeta_inc"])
BootRec["anisotropy_v2_zeta_dec"] = "%7.1f " % (bpars["v2_zeta_dec"])
BootRec["anisotropy_v2_zeta_semi_angle"] = "%7.1f " % (bpars["v2_zeta"])
BootRec["anisotropy_v3_eta_inc"] = "%7.1f " % (bpars["v3_eta_inc"])
BootRec["anisotropy_v3_eta_dec"] = "%7.1f " % (bpars["v3_eta_dec"])
BootRec["anisotropy_v3_eta_semi_angle"] = "%7.1f " % (bpars["v3_eta"])
BootRec["anisotropy_v3_zeta_inc"] = "%7.1f " % (bpars["v3_zeta_inc"])
BootRec["anisotropy_v3_zeta_dec"] = "%7.1f " % (bpars["v3_zeta_dec"])
BootRec["anisotropy_v3_zeta_semi_angle"] = "%7.1f " % (bpars["v3_zeta"])
BootRec["anisotropy_hext_F"] = ""
BootRec["anisotropy_hext_F12"] = ""
BootRec["anisotropy_hext_F23"] = ""
BootRec["magic_method_codes"] = "LP-AN:AE-H:AE-BS" # regular bootstrap
if ipar == 1:
BootRec["magic_method_codes"] = "LP-AN:AE-H:AE-BS-P" # parametric bootstrap
if verbose:
print "Boostrap Statistics: "
print " tau_i, V_i_D, V_i_I, V_i_zeta, V_i_zeta_D, V_i_zeta_I, V_i_eta, V_i_eta_D, V_i_eta_I"
print BootRec["anisotropy_t1"], BootRec["anisotropy_v1_dec"], BootRec["anisotropy_v1_inc"], BootRec[
"anisotropy_v1_eta_semi_angle"
], BootRec["anisotropy_v1_eta_dec"], BootRec["anisotropy_v1_eta_inc"], BootRec[
"anisotropy_v1_zeta_semi_angle"
], BootRec[
"anisotropy_v1_zeta_dec"
], BootRec[
"anisotropy_v1_zeta_inc"
]
print BootRec["anisotropy_t2"], BootRec["anisotropy_v2_dec"], BootRec["anisotropy_v2_inc"], BootRec[
"anisotropy_v2_eta_semi_angle"
], BootRec["anisotropy_v2_eta_dec"], BootRec["anisotropy_v2_eta_inc"], BootRec[
"anisotropy_v2_zeta_semi_angle"
], BootRec[
"anisotropy_v2_zeta_dec"
], BootRec[
"anisotropy_v2_zeta_inc"
]
print BootRec["anisotropy_t3"], BootRec["anisotropy_v3_dec"], BootRec["anisotropy_v3_inc"], BootRec[
"anisotropy_v3_eta_semi_angle"
], BootRec["anisotropy_v3_eta_dec"], BootRec["anisotropy_v3_eta_inc"], BootRec[
"anisotropy_v3_zeta_semi_angle"
], BootRec[
"anisotropy_v3_zeta_dec"
], BootRec[
"anisotropy_v3_zeta_inc"
]
BootRec["magic_software_packages"] = version_num
ResRecs.append(BootRec)
k += 1
goon = 1
while goon == 1 and iplot == 1 and verbose:
if iboot == 1:
print "compare with [d]irection "
print " plot [g]reat circle, change [c]oord. system, change [e]llipse calculation, s[a]ve plots, [q]uit "
if isite == 1:
print " [p]revious, [s]ite, [q]uit, <return> for next "
ans = raw_input("")
if ans == "q":
sys.exit()
if ans == "e":
iboot, ipar, ihext, ivec = 1, 0, 0, 0
e = raw_input("Do Hext Statistics 1/[0]: ")
if e == "1":
ihext = 1
e = raw_input("Suppress bootstrap 1/[0]: ")
if e == "1":
iboot = 0
if iboot == 1:
e = raw_input("Parametric bootstrap 1/[0]: ")
if e == "1":
ipar = 1
e = raw_input("Plot bootstrap eigenvectors: 1/[0]: ")
if e == "1":
ivec = 1
if iplot == 1:
if inittcdf == 0:
ANIS["tcdf"] = 3
pmagplotlib.plot_init(ANIS["tcdf"], 5, 5)
inittcdf = 1
bpars, hpars = pmagplotlib.plotANIS(
ANIS, Ss, iboot, ihext, ivec, ipar, title, iplot, comp, vec, Dir, nb
)
if verbose and plots == 0:
pmagplotlib.drawFIGS(ANIS)
if ans == "c":
print "Current Coordinate system is: "
if CS == "-1":
print " Specimen"
if CS == "0":
print " Geographic"
if CS == "100":
print " Tilt corrected"
key = raw_input(" Enter desired coordinate system: [s]pecimen, [g]eographic, [t]ilt corrected ")
if key == "s":
CS = "-1"
if key == "g":
CS = "0"
if key == "t":
CS = "100"
if CS not in orlist:
if len(orlist) > 0:
CS = orlist[0]
else:
CS = "-1"
if CS == "-1":
crd = "s"
if CS == "0":
crd = "g"
if CS == "100":
crd = "t"
print "desired coordinate system not available, using available: ", crd
k -= 1
goon = 0
if ans == "":
if isite == 1:
goon = 0
else:
print "Good bye "
sys.exit()
if ans == "d":
if initcdf == 0:
initcdf = 1
ANIS["vxcdf"], ANIS["vycdf"], ANIS["vzcdf"] = 4, 5, 6
pmagplotlib.plot_init(ANIS["vxcdf"], 5, 5)
pmagplotlib.plot_init(ANIS["vycdf"], 5, 5)
pmagplotlib.plot_init(ANIS["vzcdf"], 5, 5)
Dir, comp = [], 1
print """
Input: Vi D I to compare eigenvector Vi with direction D/I
where Vi=1: principal
Vi=2: major
Vi=3: minor
D= declination of comparison direction
I= inclination of comparison direction"""
con = 1
while con == 1:
try:
vdi = raw_input("Vi D I: ").split()
vec = int(vdi[0]) - 1
Dir = [float(vdi[1]), float(vdi[2])]
con = 0
except IndexError:
print " Incorrect entry, try again "
bpars, hpars = pmagplotlib.plotANIS(
ANIS, Ss, iboot, ihext, ivec, ipar, title, iplot, comp, vec, Dir, nb
)
Dir, comp = [], 0
if ans == "g":
con, cnt = 1, 0
while con == 1:
try:
print " Input: input pole to great circle ( D I) to plot a great circle: "
di = raw_input(" D I: ").split()
PDir.append(float(di[0]))
PDir.append(float(di[1]))
con = 0
except:
cnt += 1
if cnt < 10:
print " enter the dec and inc of the pole on one line "
else:
print "ummm - you are doing something wrong - i give up"
sys.exit()
pmagplotlib.plotC(ANIS["data"], PDir, 90.0, "g")
pmagplotlib.plotC(ANIS["conf"], PDir, 90.0, "g")
if verbose and plots == 0:
pmagplotlib.drawFIGS(ANIS)
if ans == "p":
k -= 2
goon = 0
if ans == "q":
k = plt
goon = 0
if ans == "s":
keepon = 1
site = raw_input(" print site or part of site desired: ")
while keepon == 1:
try:
k = sitelist.index(site)
keepon = 0
except:
tmplist = []
for qq in range(len(sitelist)):
if site in sitelist[qq]:
tmplist.append(sitelist[qq])
print site, " not found, but this was: "
print tmplist
site = raw_input("Select one or try again\n ")
k = sitelist.index(site)
goon, ans = 0, ""
if ans == "a":
locs = pmag.makelist(Locs)
title = "LO:_" + locs + "_SI:__" + "_SA:__SP:__CO:_" + crd
save(ANIS, fmt, title)
goon = 0
else:
if verbose:
print "skipping plot - not enough data points"
k += 1
# put rmag_results stuff here
if len(ResRecs) > 0:
ResOut, keylist = pmag.fillkeys(ResRecs)
pmag.magic_write(outfile, ResOut, "rmag_results")
if verbose:
print " Good bye "
def main():
"""
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
else: print "No Results level table"
def save_redo(SpecRecs,inspec):
SpecRecs,keys=pmag.fillkeys(SpecRecs)
pmag.magic_write(inspec,SpecRecs,'pmag_specimens')
def main():
"""
NAME
orientation_magic.py
DESCRIPTION
takes tab delimited field notebook information and converts to MagIC formatted tables
SYNTAX
orientation_magic.py [command line options]
OPTIONS
-f FILE: specify input file, default is: orient.txt
-Fsa FILE: specify output file, default is: er_samples.txt
-Fsi FILE: specify output site location file, default is: er_sites.txt
-app append/update these data in existing er_samples.txt, er_sites.txt files
-ocn OCON: specify orientation convention, default is #1 below
-dcn DCON [DEC]: specify declination convention, default is #1 below
if DCON = 2, you must supply the declination correction
-BCN don't correct bedding_dip_dir for magnetic declination -already corrected
-ncn NCON: specify naming convention: default is #1 below
-a: averages all bedding poles and uses average for all samples: default is NO
-gmt HRS: specify hours to subtract from local time to get GMT: default is 0
-mcd: specify sampling method codes as a colon delimited string: [default is: FS-FD:SO-POM]
FS-FD field sampling done with a drill
FS-H field sampling done with hand samples
FS-LOC-GPS field location done with GPS
FS-LOC-MAP field location done with map
SO-POM a Pomeroy orientation device was used
SO-ASC an ASC orientation device was used
INPUT FORMAT
Input files must be tab delimited and have in the first line:
tab location_name
Note: The "location_name" will facilitate searching in the MagIC database. Data from different
"locations" should be put in separate files. The definition of a "location" is rather loose.
Also this is the word 'tab' not a tab, which will be indicated by '\t'.
The second line has the names of the columns (tab delimited), e.g.:
site_name sample_name mag_azimuth field_dip date lat long sample_lithology sample_type sample_class shadow_angle hhmm stratigraphic_height bedding_dip_direction bedding_dip GPS_baseline image_name image_look image_photographer participants method_codes site_description sample_description GPS_Az, sample_igsn, sample_texture, sample_cooling_rate, cooling_rate_corr, cooling_rate_mcd
Notes:
1) column order doesn't matter but the NAMES do.
2) sample_name, sample_lithology, sample_type, sample_class, lat and long are required. all others are optional.
3) If subsequent data are the same (e.g., date, bedding orientation, participants, stratigraphic_height),
you can leave the field blank and the program will fill in the last recorded information. BUT if you really want a blank stratigraphic_height, enter a '-1'. These will not be inherited and must be specified for each entry: image_name, look, photographer or method_codes
4) hhmm must be in the format: hh:mm and the hh must be in 24 hour time.
date must be mm/dd/yy (years < 50 will be converted to 20yy and >50 will be assumed 19yy)
5) image_name, image_look and image_photographer are colon delimited lists of file name (e.g., IMG_001.jpg) image look direction and the name of the photographer respectively. If all images had same look and photographer, just enter info once. The images will be assigned to the site for which they were taken - not at the sample level.
6) participants: Names of who helped take the samples. These must be a colon delimited list.
7) method_codes: Special method codes on a sample level, e.g., SO-GT5 which means the orientation is has an uncertainty of >5 degrees
for example if it broke off before orienting....
8) GPS_Az is the place to put directly determined GPS Azimuths, using, e.g., points along the drill direction.
9) sample_cooling_rate is the cooling rate in K per Ma
10) int_corr_cooling_rate
11) cooling_rate_mcd: data adjustment method code for cooling rate correction; DA-CR-EG is educated guess; DA-CR-PS is percent estimated from pilot samples; DA-CR-TRM is comparison between 2 TRMs acquired with slow and rapid cooling rates.
is the percent cooling rate factor to apply to specimens from this sample, DA-CR-XX is the method code
Orientation convention:
Samples are oriented in the field with a "field arrow" and measured in the laboratory with a "lab arrow". The lab arrow is the positive X direction of the right handed coordinate system of the specimen measurements. The lab and field arrows may not be the same. In the MagIC database, we require the orientation (azimuth and plunge) of the X direction of the measurements (lab arrow). Here are some popular conventions that convert the field arrow azimuth (mag_azimuth in the orient.txt file) and dip (field_dip in orient.txt) to the azimuth and plunge of the laboratory arrow (sample_azimuth and sample_dip in er_samples.txt). The two angles, mag_azimuth and field_dip are explained below.
[1] Standard Pomeroy convention of azimuth and hade (degrees from vertical down)
of the drill direction (field arrow). lab arrow azimuth= sample_azimuth = mag_azimuth;
lab arrow dip = sample_dip =-field_dip. i.e. the lab arrow dip is minus the hade.
[2] Field arrow is the strike of the plane orthogonal to the drill direction,
Field dip is the hade of the drill direction. Lab arrow azimuth = mag_azimuth-90
Lab arrow dip = -field_dip
[3] Lab arrow is the same as the drill direction;
hade was measured in the field.
Lab arrow azimuth = mag_azimuth; Lab arrow dip = 90-field_dip
[4] lab azimuth and dip are same as mag_azimuth, field_dip : use this for unoriented samples too
[5] Same as AZDIP convention explained below -
azimuth and inclination of the drill direction are mag_azimuth and field_dip;
lab arrow is as in [1] above.
lab azimuth is same as mag_azimuth,lab arrow dip=field_dip-90
[6] Lab arrow azimuth = mag_azimuth-90; Lab arrow dip = 90-field_dip
[7] all others you will have to either customize your
self or e-mail [email protected] for help.
Magnetic declination convention:
[1] Use the IGRF value at the lat/long and date supplied [default]
[2] Will supply declination correction
[3] mag_az is already corrected in file
[4] Correct mag_az but not bedding_dip_dir
Sample naming convention:
[1] XXXXY: where XXXX is an arbitrary length site designation and Y
is the single character sample designation. e.g., TG001a is the
first sample from site TG001. [default]
[2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length)
[3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length)
[4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX
[5] site name = sample name
[6] site name entered in site_name column in the orient.txt format input file
[7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY
NB: all others you will have to either customize your
self or e-mail [email protected] for help.
OUTPUT
output saved in er_samples.txt and er_sites.txt - will overwrite any existing files
"""
#
# initialize variables
#
stratpos=""
args=sys.argv
date,lat,lon="","","" # date of sampling, latitude (pos North), longitude (pos East)
bed_dip,bed_dip_dir="",""
participantlist=""
Lats,Lons=[],[] # list of latitudes and longitudes
SampOuts,SiteOuts,ImageOuts=[],[],[] # lists of Sample records and Site records
samplelist,sitelist,imagelist=[],[],[]
samp_con,Z,average_bedding,DecCorr="1",1,"0",0.
newbaseline,newbeddir,newbeddip="","",""
meths=''
delta_u="0"
sclass,lithology,type="","",""
newclass,newlith,newtype='','',''
user=""
BPs=[]# bedding pole declinations, bedding pole inclinations
#
#
dir_path,AddTo='.',0
if "-WD" in args:
ind=args.index("-WD")
dir_path=sys.argv[ind+1]
orient_file,samp_file,or_con,corr = dir_path+"/orient.txt",dir_path+"/er_samples.txt","1","1"
site_file=dir_path+"/er_sites.txt"
image_file=dir_path+"/er_images.txt"
SampRecs,SiteRecs,ImageRecs=[],[],[]
if "-h" in args:
print main.__doc__
sys.exit()
if "-f" in args:
ind=args.index("-f")
orient_file=dir_path+'/'+sys.argv[ind+1]
if "-Fsa" in args:
ind=args.index("-Fsa")
samp_file=dir_path+'/'+sys.argv[ind+1]
if "-Fsi" in args:
ind=args.index("-Fsi")
site_file=dir_path+'/'+sys.argv[ind+1]
if '-app' in args:
AddTo=1
try:
SampRecs,file_type=pmag.magic_read(samp_file)
print 'sample data to be appended to: ', samp_file
except:
print 'problem with existing file: ',samp_file, ' will create new.'
try:
SiteRecs,file_type=pmag.magic_read(site_file)
print 'site data to be appended to: ',site_file
except:
print 'problem with existing file: ',site_file,' will create new.'
try:
ImageRecs,file_type=pmag.magic_read(image_file)
print 'image data to be appended to: ',image_file
except:
print 'problem with existing file: ',image_file,' will create new.'
if "-ocn" in args:
ind=args.index("-ocn")
or_con=sys.argv[ind+1]
if "-dcn" in args:
ind=args.index("-dcn")
corr=sys.argv[ind+1]
if corr=="2":
DecCorr=float(sys.argv[ind+2])
elif corr=="3":
DecCorr=0.
if '-BCN' in args:
BedCorr=0
else:
BedCorr=1
if "-ncn" in args:
ind=args.index("-ncn")
samp_con=sys.argv[ind+1]
if "4" in samp_con:
if "-" not in samp_con:
print "option [4] must be in form 4-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="4"
if "7" in samp_con:
if "-" not in samp_con:
print "option [7] must be in form 7-Z where Z is an integer"
sys.exit()
else:
Z=samp_con.split("-")[1]
samp_con="7"
if "-gmt" in args:
ind=args.index("-gmt")
delta_u=(sys.argv[ind+1])
if "-mcd" in args:
ind=args.index("-mcd")
meths=(sys.argv[ind+1])
if "-a" in args: average_bedding="1"
#
# read in file to convert
#
OrData,location_name=pmag.magic_read(orient_file)
#
# step through the data sample by sample
#
for OrRec in OrData:
if 'mag_azimuth' not in OrRec.keys():OrRec['mag_azimuth']=""
if 'field_dip' not in OrRec.keys():OrRec['field_dip']=""
if OrRec['mag_azimuth']==" ":OrRec["mag_azimuth"]=""
if OrRec['field_dip']==" ":OrRec["field_dip"]=""
if 'sample_description' in OrRec.keys():
sample_description=OrRec['sample_description']
else:
sample_description=""
if 'sample_igsn' in OrRec.keys():
sample_igsn=OrRec['sample_igsn']
else:
sample_igsn=""
if 'sample_texture' in OrRec.keys():
sample_texture=OrRec['sample_texture']
else:
sample_texture=""
if 'sample_cooling_rate' in OrRec.keys():
sample_cooling_rate=OrRec['sample_cooling_rate']
else:
sample_cooling_rate=""
if 'cooling_rate_corr' in OrRec.keys():
cooling_rate_corr=OrRec['cooling_rate_corr']
if 'cooling_rate_mcd' in OrRec.keys():
cooling_rate_mcd=OrRec['cooling_rate_mcd']
else:
cooling_rate_mcd='DA-CR'
else:
cooling_rate_corr=""
cooling_rate_mcd=""
sample_orientation_flag='g'
if 'sample_orientation_flag' in OrRec.keys():
if OrRec['sample_orientation_flag']=='b' or OrRec["mag_azimuth"]=="":
sample_orientation_flag='b'
methcodes=meths # initialize method codes
if meths!='':
if 'method_codes' in OrRec.keys() and OrRec['method_codes'].strip()!="":methcodes=methcodes+":"+OrRec['method_codes'] # add notes
else:
if 'method_codes' in OrRec.keys() and OrRec['method_codes'].strip()!="":methcodes=OrRec['method_codes'] # add notes
codes=methcodes.replace(" ","").split(":")
MagRec={}
MagRec["er_location_name"]=location_name
MagRec["er_citation_names"]="This study"
MagRec['sample_orientation_flag']=sample_orientation_flag
MagRec['sample_igsn']=sample_igsn
MagRec['sample_texture']=sample_texture
MagRec['sample_cooling_rate']=sample_cooling_rate
MagRec['cooling_rate_corr']=cooling_rate_corr
MagRec['cooling_rate_mcd']=cooling_rate_mcd
#
# parse information common to all orientation methods
#
MagRec["er_sample_name"]=OrRec["sample_name"]
if "IGSN" in OrRec.keys():
MagRec["sample_igsn"]=OrRec["IGSN"]
else:
MagRec["sample_igsn"]=""
MagRec["sample_height"],MagRec["sample_bed_dip_direction"],MagRec["sample_bed_dip"]="","",""
if "er_sample_alternatives" in OrRec.keys():MagRec["er_sample_alternatives"]=OrRec["sample_alternatives"]
sample=OrRec["sample_name"]
if OrRec['mag_azimuth']=="" and OrRec['field_dip']!="":
OrRec['mag_azimuth']='999'
if OrRec["mag_azimuth"]!="":
labaz,labdip=pmag.orient(float(OrRec["mag_azimuth"]),float(OrRec["field_dip"]),or_con)
if labaz<0:labaz+=360.
else:
labaz,labdip="",""
if OrRec['mag_azimuth']=='999':labaz=""
if "GPS_baseline" in OrRec.keys() and OrRec['GPS_baseline']!="":newbaseline=OrRec["GPS_baseline"]
if newbaseline!="":baseline=float(newbaseline)
if 'participants' in OrRec.keys() and OrRec['participants']!="" and OrRec['participants']!=participantlist:
participantlist=OrRec['participants']
MagRec['er_scientist_mail_names']=participantlist
newlat=OrRec["lat"]
if newlat!="":lat=float(newlat)
if lat=="":
print "No latitude specified for ! ",sample
sys.exit()
MagRec["sample_lat"]='%11.5f'%(lat)
newlon=OrRec["long"]
if newlon!="":lon=float(newlon)
if lon=="":
print "No longitude specified for ! ",sample
sys.exit()
MagRec["sample_lon"]='%11.5f'%(lon)
if 'bedding_dip_direction' in OrRec.keys(): newbeddir=OrRec["bedding_dip_direction"]
if newbeddir!="":bed_dip_dir=OrRec['bedding_dip_direction']
if 'bedding_dip' in OrRec.keys(): newbeddip=OrRec["bedding_dip"]
if newbeddip!="":bed_dip=OrRec['bedding_dip']
MagRec["sample_bed_dip"]=bed_dip
MagRec["sample_bed_dip_direction"]=bed_dip_dir
if "sample_class" in OrRec.keys():newclass=OrRec["sample_class"]
if newclass!="":sclass=newclass
if sclass=="": sclass="Not Specified"
MagRec["sample_class"]=sclass
if "sample_lithology" in OrRec.keys():newlith=OrRec["sample_lithology"]
if newlith!="":lithology=newlith
if lithology=="": lithology="Not Specified"
MagRec["sample_lithology"]=lithology
if "sample_type" in OrRec.keys():newtype=OrRec["sample_type"]
if newtype!="":type=newtype
if type=="": type="Not Specified"
MagRec["sample_type"]=type
if labdip!="":
MagRec["sample_dip"]='%7.1f'%labdip
else:
MagRec["sample_dip"]=""
if "date" in OrRec.keys():
newdate=OrRec["date"]
if newdate!="":date=newdate
mmddyy=date.split('/')
yy=int(mmddyy[2])
if yy>50:
yy=1900+yy
else:
yy=2000+yy
decimal_year=yy+float(mmddyy[0])/12
sample_date='%i:%s:%s'%(yy,mmddyy[0],mmddyy[1])
MagRec["sample_date"]=sample_date
if labaz!="":
MagRec["sample_azimuth"]='%7.1f'%(labaz)
else:
MagRec["sample_azimuth"]=""
if "stratigraphic_height" in OrRec.keys():
if OrRec["stratigraphic_height"]!="":
MagRec["sample_height"]=OrRec["stratigraphic_height"]
stratpos=OrRec["stratigraphic_height"]
elif OrRec["stratigraphic_height"]=='-1':
MagRec["sample_height"]="" # make empty
else:
MagRec["sample_height"]=stratpos # keep last record if blank
#
if corr=="1" and MagRec['sample_azimuth']!="": # get magnetic declination (corrected with igrf value)
x,y,z,f=pmag.doigrf(lon,lat,0,decimal_year)
Dir=pmag.cart2dir( (x,y,z))
DecCorr=Dir[0]
if "bedding_dip" in OrRec.keys():
if OrRec["bedding_dip"]!="":
MagRec["sample_bed_dip"]=OrRec["bedding_dip"]
bed_dip=OrRec["bedding_dip"]
else:
MagRec["sample_bed_dip"]=bed_dip
else: MagRec["sample_bed_dip"]='0'
if "bedding_dip_direction" in OrRec.keys():
if OrRec["bedding_dip_direction"]!="" and BedCorr==1:
dd=float(OrRec["bedding_dip_direction"])+DecCorr
if dd>360.:dd=dd-360.
MagRec["sample_bed_dip_direction"]='%7.1f'%(dd)
dip_dir=MagRec["sample_bed_dip_direction"]
else:
MagRec["sample_bed_dip_direction"]=OrRec['bedding_dip_direction']
else: MagRec["sample_bed_dip_direction"]='0'
if average_bedding!="0": BPs.append([float(MagRec["sample_bed_dip_direction"]),float(MagRec["sample_bed_dip"])-90.,1.])
if MagRec['sample_azimuth']=="" and MagRec['sample_dip']=="":
MagRec["sample_declination_correction"]=''
methcodes=methcodes+':SO-NO'
MagRec["magic_method_codes"]=methcodes
MagRec['sample_description']=sample_description
#
# work on the site stuff too
if 'site_name' in OrRec.keys():
site=OrRec['site_name']
else:
site=pmag.parse_site(OrRec["sample_name"],samp_con,Z) # parse out the site name
MagRec["er_site_name"]=site
site_description="" # overwrite any prior description
if 'site_description' in OrRec.keys() and OrRec['site_description']!="":
site_description=OrRec['site_description'].replace(",",";")
if "image_name" in OrRec.keys():
images=OrRec["image_name"].split(":")
if "image_look" in OrRec.keys():
looks=OrRec['image_look'].split(":")
else:
looks=[]
if "image_photographer" in OrRec.keys():
photographers=OrRec['image_photographer'].split(":")
else:
photographers=[]
for image in images:
if image !="" and image not in imagelist:
imagelist.append(image)
ImageRec={}
ImageRec['er_image_name']=image
ImageRec['image_type']="outcrop"
ImageRec['image_date']=sample_date
ImageRec['er_citation_names']="This study"
ImageRec['er_location_name']=location_name
ImageRec['er_site_name']=MagRec['er_site_name']
k=images.index(image)
if len(looks)>k:
ImageRec['er_image_description']="Look direction: "+looks[k]
elif len(looks)>=1:
ImageRec['er_image_description']="Look direction: "+looks[-1]
else:
ImageRec['er_image_description']="Look direction: unknown"
if len(photographers)>k:
ImageRec['er_photographer_mail_names']=photographers[k]
elif len(photographers)>=1:
ImageRec['er_photographer_mail_names']=photographers[-1]
else:
ImageRec['er_photographer_mail_names']="unknown"
ImageOuts.append(ImageRec)
if site not in sitelist:
sitelist.append(site) # collect unique site names
SiteRec={}
SiteRec["er_site_name"]=site
SiteRec["site_definition"]="s"
SiteRec["er_location_name"]=location_name
SiteRec["er_citation_names"]="This study"
SiteRec["site_lat"]=MagRec["sample_lat"]
SiteRec["site_lon"]=MagRec["sample_lon"]
SiteRec["site_height"]=MagRec["sample_height"]
SiteRec["site_class"]=MagRec["sample_class"]
SiteRec["site_lithology"]=MagRec["sample_lithology"]
SiteRec["site_type"]=MagRec["sample_type"]
SiteRec["site_description"]=site_description
SiteOuts.append(SiteRec)
if sample not in samplelist:
samplelist.append(sample)
if MagRec['sample_azimuth']!="": # assume magnetic compass only
MagRec['magic_method_codes']=MagRec['magic_method_codes']+':SO-MAG'
MagRec['magic_method_codes']=MagRec['magic_method_codes'].strip(":")
SampOuts.append(MagRec)
if MagRec['sample_azimuth']!="" and corr!='3':
az=labaz+DecCorr
if az>360.:az=az-360.
CMDRec={}
for key in MagRec.keys():
CMDRec[key]=MagRec[key] # make a copy of MagRec
CMDRec["sample_azimuth"]='%7.1f'%(az)
CMDRec["magic_method_codes"]=methcodes+':SO-CMD-NORTH'
CMDRec["magic_method_codes"]=CMDRec['magic_method_codes'].strip(':')
CMDRec["sample_declination_correction"]='%7.1f'%(DecCorr)
if corr=='1':
CMDRec['sample_description']=sample_description+':Declination correction calculated from IGRF'
else:
CMDRec['sample_description']=sample_description+':Declination correction supplied by user'
CMDRec["sample_description"]=CMDRec['sample_description'].strip(':')
SampOuts.append(CMDRec)
if "mag_az_bs" in OrRec.keys() and OrRec["mag_az_bs"] !="" and OrRec["mag_az_bs"]!=" ":
SRec={}
for key in MagRec.keys():
SRec[key]=MagRec[key] # make a copy of MagRec
labaz=float(OrRec["mag_az_bs"])
az=labaz+DecCorr
if az>360.:az=az-360.
SRec["sample_azimuth"]='%7.1f'%(az)
SRec["sample_declination_correction"]='%7.1f'%(DecCorr)
SRec["magic_method_codes"]=methcodes+':SO-SIGHT-BACK:SO-CMD-NORTH'
SampOuts.append(SRec)
#
# check for suncompass data
#
if "shadow_angle" in OrRec.keys() and OrRec["shadow_angle"]!="": # there are sun compass data
if delta_u=="":
delta_u=raw_input("Enter hours to SUBTRACT from time for GMT: [0] ")
if delta_u=="":delta_u="0"
SunRec,sundata={},{}
shad_az=float(OrRec["shadow_angle"])
sundata["date"]='%i:%s:%s:%s'%(yy,mmddyy[0],mmddyy[1],OrRec["hhmm"])
# if eval(delta_u)<0:
# MagRec["sample_time_zone"]='GMT'+delta_u+' hours'
# else:
# MagRec["sample_time_zone"]='GMT+'+delta_u+' hours'
sundata["delta_u"]=delta_u
sundata["lon"]='%7.1f'%(lon)
sundata["lat"]='%7.1f'%(lat)
sundata["shadow_angle"]=OrRec["shadow_angle"]
sundec=pmag.dosundec(sundata)
for key in MagRec.keys():
SunRec[key]=MagRec[key] # make a copy of MagRec
SunRec["sample_azimuth"]='%7.1f'%(sundec)
SunRec["sample_declination_correction"]=''
SunRec["magic_method_codes"]=methcodes+':SO-SUN'
SunRec["magic_method_codes"]=SunRec['magic_method_codes'].strip(':')
SampOuts.append(SunRec)
#
# check for differential GPS data
#
if "prism_angle" in OrRec.keys() and OrRec["prism_angle"]!="": # there are diff GPS data
GPSRec={}
for key in MagRec.keys():
GPSRec[key]=MagRec[key] # make a copy of MagRec
prism_angle=float(OrRec["prism_angle"])
laser_angle=float(OrRec["laser_angle"])
if OrRec["GPS_baseline"]!="": baseline=float(OrRec["GPS_baseline"]) # new baseline
gps_dec=baseline+laser_angle+prism_angle-90.
while gps_dec>360.:
gps_dec=gps_dec-360.
while gps_dec<0:
gps_dec=gps_dec+360.
for key in MagRec.keys():
GPSRec[key]=MagRec[key] # make a copy of MagRec
GPSRec["sample_azimuth"]='%7.1f'%(gps_dec)
GPSRec["sample_declination_correction"]=''
GPSRec["magic_method_codes"]=methcodes+':SO-GPS-DIFF'
SampOuts.append(GPSRec)
if "GPS_Az" in OrRec.keys() and OrRec["GPS_Az"]!="": # there are differential GPS Azimuth data
GPSRec={}
for key in MagRec.keys():
GPSRec[key]=MagRec[key] # make a copy of MagRec
GPSRec["sample_azimuth"]='%7.1f'%(float(OrRec["GPS_Az"]))
GPSRec["sample_declination_correction"]=''
GPSRec["magic_method_codes"]=methcodes+':SO-GPS-DIFF'
SampOuts.append(GPSRec)
if average_bedding!="0":
fpars=pmag.fisher_mean(BPs)
print 'over-writing all bedding with average '
Samps=[]
for rec in SampOuts:
if average_bedding!="0":
rec['sample_bed_dip_direction']='%7.1f'%(fpars['dec'])
rec['sample_bed_dip']='%7.1f'%(fpars['inc']+90.)
Samps.append(rec)
else:
Samps.append(rec)
for rec in SampRecs:
if rec['er_sample_name'] not in samplelist: # overwrite prior for this sample
Samps.append(rec)
for rec in SiteRecs:
if rec['er_site_name'] not in sitelist: # overwrite prior for this sample
SiteOuts.append(rec)
for rec in ImageRecs:
if rec['er_image_name'] not in imagelist: # overwrite prior for this sample
ImageOuts.append(rec)
print 'saving data...'
SampsOut,keys=pmag.fillkeys(Samps)
Sites,keys=pmag.fillkeys(SiteOuts)
pmag.magic_write(samp_file,SampsOut,"er_samples")
pmag.magic_write(site_file,Sites,"er_sites")
print "Data saved in ", samp_file,' and ',site_file
if len(ImageOuts)>0:
Images,keys=pmag.fillkeys(ImageOuts)
pmag.magic_write(image_file,Images,"er_images")
print "Image info saved in ",image_file
def main():
"""
NAME
combine_magic.py
DESCRIPTION
Combines magic format files of the same type together.
SYNTAX
combine_magic.py [-h] [-i] -out filename -in file1 file2 ....
OPTIONS
-h prints help message
-i allows interactive entry of input and output filenames
-F specify output file name [must come BEFORE input file names]
-f specify input file names [ must come last]
"""
#
# set up magic meta data type requirements
#
filenames=[]
datasets=[]
dir_path='.'
#
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if "-h" in sys.argv:
print main.__doc__
sys.exit()
if "-F" in sys.argv:
ind=sys.argv.index("-F")
output=dir_path+'/'+sys.argv[ind+1]
if "-f" in sys.argv:
ind=sys.argv.index("-f")
for k in range(ind+1,len(sys.argv)):
filenames.append(dir_path+'/'+sys.argv[k])
for infile in filenames:
dataset,file_type=pmag.magic_read(infile)
print "File ",infile," read in with ",len(dataset), " records"
for rec in dataset:
datasets.append(rec)
if '-i' in sys.argv:
quit,dataset,datasets=0,[],[]
while quit==0:
infile=raw_input('\n\n Enter magic files for combining, <return> when done: ')
if infile=='':
quit = 1
break
dataset,file_type=pmag.magic_read(infile)
print "File ",infile," read in with ",len(dataset), " records"
for rec in dataset:
datasets.append(rec)
#
# collect all the keys from all the files
#
Recs,keys=pmag.fillkeys(datasets)
#
# write out the datasets into a combined file
#
pmag.magic_write(output,Recs,file_type)
print "All records stored in ",output
def main():
"""
NAME
customize_criteria.py
DESCRIPTION
Allows user to specify acceptance criteria, saves them in pmag_criteria.txt
SYNTAX
customize_criteria.py [-h][command line options]
OPTIONS
-h prints help message and quits
-f IFILE, reads in existing criteria
-F OFILE, writes to pmag_criteria format file
DEFAULTS
IFILE: pmag_criteria.txt
OFILE: pmag_criteria.txt
OUTPUT
creates a pmag_criteria.txt formatted output file
"""
infile,critout="","pmag_criteria.txt"
SpecCrit={}
#
# set some sort of quasi-reasonable default criteria
#
SpecCrit['pmag_criteria_code']='DE-SPEC'
SpecCrit['specimen_mad']='5.49'
SpecCrit['specimen_alpha95']='5.49'
SpecCrit['specimen_n']='4'
SpecIntCrit={}
SpecIntCrit['pmag_criteria_code']='IE-SPEC'
SpecIntCrit['specimen_int_ptrm_n']='2'
SpecIntCrit['specimen_drats']='20.5'
SpecIntCrit['specimen_b_beta']='0.1'
SpecIntCrit['specimen_md']='15'
SpecIntCrit['specimen_fvds']='0.7'
SpecIntCrit['specimen_q']='1.0'
SpecIntCrit['specimen_dang']='10.5'
SpecIntCrit['specimen_int_mad']='10.5'
SpecIntCrit['specimen_Z']='4'
#SpecIntCrit['measurement_step_min']='373'
#SpecIntCrit['measurement_step_max']='623'
SampCrit={}
SampCrit['pmag_criteria_code']='DE-SAMP'
SampCrit['sample_alpha95']='10.49'
SampIntCrit={}
SampIntCrit['pmag_criteria_code']='IE-SAMP'
SampIntCrit['sample_int_n']='2'
SampIntCrit['sample_int_sigma']='5.5e-6'
SampIntCrit['sample_int_sigma_perc']='15.5'
SiteIntCrit={}
SiteIntCrit['pmag_criteria_code']='IE-SITE'
SiteIntCrit['site_int_n']='2'
SiteIntCrit['site_int_sigma']='5.5e-6'
SiteIntCrit['site_int_sigma_perc']='15.5'
SiteCrit={}
SiteCrit['pmag_criteria_code']='DE-SITE'
SiteCrit['site_n']='5'
SiteCrit['site_n_lines']='4'
SiteCrit['site_k']='100'
SiteCrit['site_alpha95']='180'
NpoleCrit={}
NpoleCrit['pmag_criteria_code']='NPOLE'
NpoleCrit['site_polarity']="n"
RpoleCrit={}
RpoleCrit['pmag_criteria_code']='RPOLE'
RpoleCrit['site_polarity']="r"
# parse command line options
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index('-f')
infile=sys.argv[ind+1]
crit_data,file_type=pmag.magic_read(infile)
if file_type!='pmag_criteria':
print 'bad input file'
print main.__doc__
sys.exit()
for critrec in crit_data:
if critrec["pmag_criteria_code"]=="DE-SPEC": SpecCrit=critrec
if critrec["pmag_criteria_code"]=="IE-SPEC": SpecIntCrit=critrec
if critrec["pmag_criteria_code"]=="DE-SAMP": SampCrit=critrec
if critrec["pmag_criteria_code"]=="IE-SAMP": SampIntCrit=critrec
if critrec["pmag_criteria_code"]=="IE-SITE": SiteIntCrit=critrec
if critrec["pmag_criteria_code"]=="DE-SITE": SiteCrit=critrec
if critrec["pmag_criteria_code"]=="NPOLE": NpoleCrit=critrec
if critrec["pmag_criteria_code"]=="RPOLE": RpoleCrit=critrec
print "Acceptance criteria read in from ", infile
if '-F' in sys.argv:
ind=sys.argv.index('-F')
critout=sys.argv[ind+1]
Dcrit,Icrit,nocrit=0,0,0
custom='1'
crit=raw_input(" [0] Use no acceptance criteria?\n [1] full vector\n [2] direction only\n [3] intensity only \n ")
if crit=="0": nocrit=1
if crit=="1": Dcrit,Icrit=1,1
if crit=="2": Dcrit,Icrit=1,0
if crit=="3": Dcrit,Icrit=0,1
if nocrit==1:
print 'Using no selection criteria '
SpecCrit={}
SpecCrit['pmag_criteria_code']='DE-SPEC'
SpecCrit['specimen_mad']='180.'
SpecCrit['specimen_alpha95']='180.'
SpecCrit['specimen_n']='0'
SpecIntCrit={}
SpecIntCrit['pmag_criteria_code']='IE-SPEC'
SpecIntCrit['specimen_int_ptrm_n']='0'
SpecIntCrit['specimen_drats']='100'
SpecIntCrit['specimen_b_beta']='5'
SpecIntCrit['specimen_md']='100'
SpecIntCrit['specimen_fvds']='0'
SpecIntCrit['specimen_q']='0'
SpecIntCrit['specimen_dang']='180.'
SpecIntCrit['specimen_Z']='100.'
SpecIntCrit['specimen_int_mad']='180.'
#SpecIntCrit['measurement_step_min']='373'
SpecIntCrit['measurement_step_max']='0'
SampCrit={}
SampCrit['pmag_criteria_code']='DE-SAMP'
SampCrit['sample_alpha95']='180.'
SampIntCrit={}
SampIntCrit['pmag_criteria_code']='IE-SAMP'
SampIntCrit['sample_int_n']='0'
SampIntCrit['sample_int_sigma']='1000'
SampIntCrit['sample_int_sigma_perc']='500'
SiteIntCrit={}
SiteIntCrit['pmag_criteria_code']='IE-SITE'
SiteIntCrit['site_int_n']='0'
SiteIntCrit['site_int_sigma']='1000'
SiteIntCrit['site_int_sigma_perc']='500'
SiteCrit={}
SiteCrit['pmag_criteria_code']='DE-SITE'
SiteCrit['site_n']='0'
SiteCrit['site_n_lines']='0'
SiteCrit['site_k']='0'
SiteCrit['site_alpha95']='180'
NpoleCrit={}
NpoleCrit['pmag_criteria_code']='NPOLE'
NpoleCrit['site_polarity']="n"
RpoleCrit={}
RpoleCrit['pmag_criteria_code']='RPOLE'
RpoleCrit['site_polarity']="r"
while custom=='1':
if Dcrit==1:
for key in SpecCrit.keys():
if key!='pmag_criteria_code' and key!='er_citation_names' and key!='criteria_definition' and SpecCrit[key]!="":
print key, SpecCrit[key]
new=raw_input("Enter new criterion (return to keep default) ")
if new != "": SpecCrit[key]=(new)
for key in SampCrit.keys():
if key!='pmag_criteria_code' and key!='er_citation_names' and key!='criteria_definition' and SampCrit[key]!="":
print key, SampCrit[key]
new=raw_input("Enter new criterion (return to keep default) ")
if new != "": SampCrit[key]=(new)
for key in SiteCrit.keys():
if key!='pmag_criteria_code' and key!='er_citation_names' and key!='criteria_definition' and SiteCrit[key]!="":
print key, SiteCrit[key]
new=raw_input("Enter new criterion (return to keep default) ")
if new != "": SiteCrit[key]=(new)
if Icrit==1:
for key in SpecIntCrit.keys():
if key!='pmag_criteria_code' and key!='er_citation_names' and key!='criteria_definition' and SpecIntCrit[key]!="":
print key, SpecIntCrit[key]
new=raw_input("Enter new criterion (return to keep default) ")
if new != "": SpecIntCrit[key]=(new)
for key in SiteIntCrit.keys():
if key!='pmag_criteria_code' and key!='er_citation_names' and key!='criteria_definition' and SiteIntCrit[key]!="":
print key, SiteIntCrit[key]
new=raw_input("Enter new criterion (return to keep default) ")
if new != "": SiteIntCrit[key]=(new)
custom=raw_input("Customize criteria again ? 1/[0]")
SpecCrit['er_citation_names']="This study"
SpecIntCrit['er_citation_names']="This study"
SampCrit['er_citation_names']="This study"
SampIntCrit['er_citation_names']="This study"
SiteIntCrit['er_citation_names']="This study"
SiteCrit['er_citation_names']="This study"
NpoleCrit['er_citation_names']="This study"
RpoleCrit['er_citation_names']="This study"
SpecCrit['criteria_definition']="Criteria for selection of specimen direction"
SpecIntCrit['criteria_definition']="Criteria for selection of specimen intensity"
SampCrit['criteria_definition']="Criteria for selection of sample direction"
SiteIntCrit['criteria_definition']="Criteria for selection of site intensity"
SiteCrit['criteria_definition']="Criteria for selection of site direction"
NpoleCrit['criteria_definition']="Criteria for inclusion in normal mean"
RpoleCrit['criteria_definition']="Criteria for inclusion in reverse mean"
TmpCrits,PmagCrits=[],[]
TmpCrits.append(SpecCrit)
TmpCrits.append(SpecIntCrit)
TmpCrits.append(SampCrit)
TmpCrits.append(SampIntCrit)
TmpCrits.append(SiteIntCrit)
TmpCrits.append(SiteCrit)
TmpCrits.append(NpoleCrit)
TmpCrits.append(RpoleCrit)
#
# assemble criteria keys
#
PmagCrits,critkeys=pmag.fillkeys(TmpCrits)
pmag.magic_write(critout,PmagCrits,'pmag_criteria')
print "Criteria saved in pmag_criteria.txt"
pmag.magic_write(critout,TmpCrits,'pmag_criteria')
print "\n Pmag Criteria stored in ",critout,'\n'
