def simulations_GGP(lat,GGPmodel,Nsim,plot=True):
""" Gerenates four arrays that are directions (dec, inc), x and y equal area coordinates of rotated directions (x,y),
rotated directions (dec,inc), x and y equal area coordinates of rotated directions
input
- lat latitude you want generate the directions list
- GGPmodel: dictionary like GGP_QC96_GAD = {"g10" : -30, "g20" : 0.0, "g30" : 0.0, "sig10" : 3.0, "sig11": 3.0,
"sig20" : 1.3 , "sig21" : 4.3, "sig22" : 1.3, "alpha": 27.7, "beta": 1.0, "name":'QC96_GAD'}
- Nsim number of simulations you want
output:
lista_sim, lista_xy, lista_r, lista_xyr """
dec_r=180
pol=-GGPmodel['g10']/abs(GGPmodel['g10'])
if pol<0:
dec_r=0
lista_sim = dii_fromGGPmodels(Nsim,lat,GGPmodel)
m = psv.m_TAF(GGPmodel, lat)
Binc = np.rad2deg(np.arctan(m[2]/abs(m[0])))
lista_r = np.zeros(np.shape(lista_sim))
for j in range(len(lista_sim)):
lista_r[j,0],lista_r[j,1] = pmag.dotilt(lista_sim[j,0],lista_sim[j,1],dec_r,(90-Binc))
lista_xyr = np.zeros([len(lista_sim),2])
lista_xy = np.zeros([len(lista_sim),2])
for j in range(len(lista_sim)):
lista_xyr[j,0:2] = pmag.dimap(lista_r[j,0],lista_r[j,1])
lista_xy[j,0:2] = pmag.dimap(lista_sim[j,0],lista_sim[j,1])
if plot==True:
plot_syn_directions(lista_sim, lista_xy, lista_r, lista_xyr,GGPmodel['name'],lat)
return lista_sim, lista_xy, lista_r, lista_xyr
def main():
"""
NAME
di_tilt.py
DESCRIPTION
rotates geographic coordinate dec, inc data to stratigraphic
coordinates using the dip and dip direction (strike+90, dip if dip to right of strike)
INPUT FORMAT
declination inclination dip_direction dip
SYNTAX
di_tilt.py [-h][-i][-f FILE] [< filename ]
OPTIONS
-h prints help message and quits
-i for interactive data entry
-f FILE command line entry of file name
-F OFILE, specify output file, default is standard output
OUTPUT:
declination inclination
"""
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-F' in sys.argv:
ind = sys.argv.index('-F')
ofile = sys.argv[ind + 1]
out = open(ofile, 'w')
print ofile, ' opened for output'
else:
ofile = ""
if '-i' in sys.argv: # interactive flag
while 1:
try:
Dec = float(raw_input("Declination: <cntl-D> to quit "))
except:
print "\n Good-bye\n"
sys.exit()
Inc = float(raw_input("Inclination: "))
Dip_dir = float(raw_input("Dip direction: "))
Dip = float(raw_input("Dip: "))
print '%7.1f %7.1f' % (pmag.dotilt(Dec, Inc, Dip_dir, Dip))
elif '-f' in sys.argv:
ind = sys.argv.index('-f')
file = sys.argv[ind + 1]
data = numpy.loadtxt(file)
else:
data = numpy.loadtxt(
sys.stdin, dtype=numpy.float) # read in the data from the datafile
D, I = pmag.dotilt_V(data)
for k in range(len(D)):
if ofile == "":
print '%7.1f %7.1f' % (D[k], I[k])
else:
out.write('%7.1f %7.1f\n' % (D[k], I[k]))
def main():
"""
NAME
di_tilt.py
DESCRIPTION
rotates geographic coordinate dec, inc data to stratigraphic
coordinates using the dip and dip direction (strike+90, dip if dip to right of strike)
INPUT FORMAT
declination inclination dip_direction dip
SYNTAX
di_tilt.py [-h][-i][-f FILE] [< filename ]
OPTIONS
-h prints help message and quits
-i for interactive data entry
-f FILE command line entry of file name
-F OFILE, specify output file, default is standard output
OUTPUT:
declination inclination
"""
if "-h" in sys.argv:
print main.__doc__
sys.exit()
if "-F" in sys.argv:
ind = sys.argv.index("-F")
ofile = sys.argv[ind + 1]
out = open(ofile, "w")
print ofile, " opened for output"
else:
ofile = ""
if "-i" in sys.argv: # interactive flag
while 1:
try:
Dec = float(raw_input("Declination: <cntl-D> to quit "))
except:
print "\n Good-bye\n"
sys.exit()
Inc = float(raw_input("Inclination: "))
Dip_dir = float(raw_input("Dip direction: "))
Dip = float(raw_input("Dip: "))
print "%7.1f %7.1f" % (pmag.dotilt(Dec, Inc, Dip_dir, Dip))
elif "-f" in sys.argv:
ind = sys.argv.index("-f")
file = sys.argv[ind + 1]
data = numpy.loadtxt(file)
else:
data = numpy.loadtxt(sys.stdin, dtype=numpy.float) # read in the data from the datafile
D, I = pmag.dotilt_V(data)
for k in range(len(D)):
if ofile == "":
print "%7.1f %7.1f" % (D[k], I[k])
else:
out.write("%7.1f %7.1f\n" % (D[k], I[k]))
def main():
"""
NAME
fishqq.py
DESCRIPTION
makes qq plot from dec,inc input data
INPUT FORMAT
takes dec/inc pairs in space delimited file
SYNTAX
fishqq.py [command line options]
OPTIONS
-h help message
-f FILE, specify file on command line
-F FILE, specify output file for statistics
-sav save and quit [saves as input file name plus fmt extension]
-fmt specify format for output [png, eps, svg, pdf]
OUTPUT:
Dec Inc N Mu Mu_crit Me Me_crit Y/N
where direction is the principal component and Y/N is Fisherian or not
separate lines for each mode with N >=10 (N and R)
"""
fmt,plot='svg',0
outfile=""
if '-h' in sys.argv: # check if help is needed
print(main.__doc__)
sys.exit() # graceful quit
elif '-f' in sys.argv: # ask for filename
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
f=open(file,'r')
data=f.readlines()
if '-F' in sys.argv:
ind=sys.argv.index('-F')
outfile=open(sys.argv[ind+1],'w') # open output file
if '-sav' in sys.argv: plot=1
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
DIs,nDIs,rDIs= [],[],[] # set up list for data
for line in data: # read in the data from standard input
if '\t' in line:
rec=line.split('\t') # split each line on space to get records
else:
rec=line.split() # split each line on space to get records
DIs.append([float(rec[0]),float(rec[1])]) # append data to Inc
# split into two modes
ppars=pmag.doprinc(DIs) # get principal directions
for rec in DIs:
angle=pmag.angle([rec[0],rec[1]],[ppars['dec'],ppars['inc']])
if angle>90.:
rDIs.append(rec)
else:
nDIs.append(rec)
#
if len(rDIs) >=10 or len(nDIs) >=10:
D1,I1=[],[]
QQ={'unf1':1,'exp1':2}
pmagplotlib.plot_init(QQ['unf1'],5,5)
pmagplotlib.plot_init(QQ['exp1'],5,5)
if len(nDIs) < 10:
ppars=pmag.doprinc(rDIs) # get principal directions
Drbar,Irbar=ppars['dec']-180.,-ppars['inc']
Nr=len(rDIs)
for di in rDIs:
d,irot=pmag.dotilt(di[0],di[1],Drbar-180.,90.-Irbar) # rotate to mean
drot=d-180.
if drot<0:drot=drot+360.
D1.append(drot)
I1.append(irot)
Dtit='Mode 2 Declinations'
Itit='Mode 2 Inclinations'
else:
ppars=pmag.doprinc(nDIs) # get principal directions
Dnbar,Inbar=ppars['dec'],ppars['inc']
Nn=len(nDIs)
for di in nDIs:
d,irot=pmag.dotilt(di[0],di[1],Dnbar-180.,90.-Inbar) # rotate to mean
drot=d-180.
if drot<0:drot=drot+360.
D1.append(drot)
I1.append(irot)
Dtit='Mode 1 Declinations'
Itit='Mode 1 Inclinations'
Mu_n,Mu_ncr=pmagplotlib.plot_qq_unf(QQ['unf1'],D1,Dtit) # make plot
Me_n,Me_ncr=pmagplotlib.plot_qq_exp(QQ['exp1'],I1,Itit) # make plot
#print Mu_n,Mu_ncr,Me_n, Me_ncr
if outfile!="":
# Dec Inc N Mu Mu_crit Me Me_crit Y/N
if Mu_n<=Mu_ncr and Me_n<=Me_ncr:
F='Y'
else:
F='N'
outstring='%7.1f %7.1f %i %5.3f %5.3f %5.3f %5.3f %s \n'%(Dnbar,Inbar,Nn,Mu_n,Mu_ncr,Me_n,Me_ncr,F)
outfile.write(outstring)
else:
print('you need N> 10 for at least one mode')
sys.exit()
if len(rDIs)>10 and len(nDIs)>10:
D2,I2=[],[]
QQ['unf2']=3
QQ['exp2']=4
pmagplotlib.plot_init(QQ['unf2'],5,5)
pmagplotlib.plot_init(QQ['exp2'],5,5)
ppars=pmag.doprinc(rDIs) # get principal directions
Drbar,Irbar=ppars['dec']-180.,-ppars['inc']
Nr=len(rDIs)
for di in rDIs:
d,irot=pmag.dotilt(di[0],di[1],Drbar-180.,90.-Irbar) # rotate to mean
drot=d-180.
if drot<0:drot=drot+360.
D2.append(drot)
I2.append(irot)
Dtit='Mode 2 Declinations'
Itit='Mode 2 Inclinations'
Mu_r,Mu_rcr=pmagplotlib.plot_qq_unf(QQ['unf2'],D2,Dtit) # make plot
Me_r,Me_rcr=pmagplotlib.plot_qq_exp(QQ['exp2'],I2,Itit) # make plot
if outfile!="":
# Dec Inc N Mu Mu_crit Me Me_crit Y/N
if Mu_r<=Mu_rcr and Me_r<=Me_rcr:
F='Y'
else:
F='N'
outstring='%7.1f %7.1f %i %5.3f %5.3f %5.3f %5.3f %s \n'%(Drbar,Irbar,Nr,Mu_r,Mu_rcr,Me_r,Me_rcr,F)
outfile.write(outstring)
files={}
for key in list(QQ.keys()):
files[key]=file+'_'+key+'.'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['eq']='Equal Area Plot'
EQ = pmagplotlib.add_borders(EQ,titles,black,purple)
pmagplotlib.save_plots(QQ,files)
elif plot==1:
pmagplotlib.save_plots(QQ,files)
else:
pmagplotlib.draw_figs(QQ)
ans=input(" S[a]ve to save plot, [q]uit without saving: ")
if ans=="a": pmagplotlib.save_plots(QQ,files)
def main():
"""
NAME
scalc.py
DESCRIPTION
calculates Sb from VGP Long,VGP Lat,Directional kappa,Site latitude data
SYNTAX
scalc -h [command line options] [< standard input]
INPUT
takes space delimited files with PLong, PLat,[kappa, N_site, slat]
OPTIONS
-h prints help message and quits
-f FILE: specify input file
-c cutoff: specify VGP colatitude cutoff value
-k cutoff: specify kappa cutoff
-v : use the VanDammme criterion
-a: use antipodes of reverse data: default is to use only normal
-C: use all data without regard to polarity
-b: do a bootstrap for confidence
-p: do relative to principle axis
NOTES
if kappa, N_site, lat supplied, will consider within site scatter
OUTPUT
N Sb Sb_lower Sb_upper Co-lat. Cutoff
"""
coord, kappa, cutoff = "0", 0, 90.
nb, anti, boot = 1000, 0, 0
all = 0
n = 0
v = 0
spin = 1
coord_key = 'tilt_correction'
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind = sys.argv.index("-f")
in_file = sys.argv[ind + 1]
f = open(in_file, 'rU')
lines = f.readlines()
else:
lines = sys.stdin.readlines()
if '-c' in sys.argv:
ind = sys.argv.index('-c')
cutoff = float(sys.argv[ind + 1])
if '-k' in sys.argv:
ind = sys.argv.index('-k')
kappa = float(sys.argv[ind + 1])
if '-n' in sys.argv:
ind = sys.argv.index('-n')
n = int(sys.argv[ind + 1])
if '-a' in sys.argv: anti = 1
if '-C' in sys.argv: cutoff = 180. # no cutoff
if '-b' in sys.argv: boot = 1
if '-v' in sys.argv: v = 1
if '-p' in sys.argv: spin = 0
#
#
# find desired vgp lat,lon, kappa,N_site data:
#
A, Vgps, slats, Pvgps = 180., [], [], []
for line in lines:
if '\t' in line:
rec = line.replace('\n', '').split(
'\t') # split each line on space to get records
else:
rec = line.replace(
'\n', '').split() # split each line on space to get records
vgp = {}
vgp['vgp_lon'], vgp['vgp_lat'] = rec[0], rec[1]
Pvgps.append([float(rec[0]), float(rec[1])])
if anti == 1:
if float(vgp['vgp_lat']) < 0:
vgp['vgp_lat'] = '%7.1f' % (-1 * float(vgp['vgp_lat']))
vgp['vgp_lon'] = '%7.1f' % (float(vgp['vgp_lon']) - 180.)
if len(rec) == 5:
vgp['average_k'], vgp['average_nn'], vgp['average_lat'] = rec[
2], rec[3], rec[4]
slats.append(float(rec[4]))
else:
vgp['average_k'], vgp['average_nn'], vgp[
'average_lat'] = "0", "0", "0"
if 90. - (float(vgp['vgp_lat'])) <= cutoff and float(
vgp['average_k']) >= kappa and int(vgp['average_nn']) >= n:
Vgps.append(vgp)
if spin == 0: # do transformation to pole
ppars = pmag.doprinc(Pvgps)
for vgp in Vgps:
vlon, vlat = pmag.dotilt(float(vgp['vgp_lon']),
float(vgp['vgp_lat']),
ppars['dec'] - 180., 90. - ppars['inc'])
vgp['vgp_lon'] = vlon
vgp['vgp_lat'] = vlat
vgp['average_k'] = "0"
S_B = pmag.get_Sb(Vgps)
A = cutoff
if v == 1:
thetamax, A = 181., 180.
vVgps, cnt = [], 0
for vgp in Vgps:
vVgps.append(vgp) # make a copy of Vgps
while thetamax > A:
thetas = []
A = 1.8 * S_B + 5
cnt += 1
for vgp in vVgps:
thetas.append(90. - (float(vgp['vgp_lat'])))
thetas.sort()
thetamax = thetas[-1]
if thetamax < A: break
nVgps = []
for vgp in vVgps:
if 90. - (float(vgp['vgp_lat'])) < thetamax: nVgps.append(vgp)
vVgps = []
for vgp in nVgps:
vVgps.append(vgp)
S_B = pmag.get_Sb(vVgps)
Vgps = []
for vgp in vVgps:
Vgps.append(vgp) # make a new Vgp list
SBs, Ns = [], []
if boot == 1:
print 'please be patient... bootstrapping'
for i in range(nb): # now do bootstrap
BVgps = []
for k in range(len(Vgps)):
ind = random.randint(0, len(Vgps) - 1)
random.jumpahead(int(ind * 1000))
BVgps.append(Vgps[ind])
SBs.append(pmag.get_Sb(BVgps))
SBs.sort()
low = int(.025 * nb)
high = int(.975 * nb)
print len(Vgps), '%7.1f %7.1f %7.1f %7.1f ' % (S_B, SBs[low],
SBs[high], A)
else:
print len(Vgps), '%7.1f %7.1f ' % (S_B, A)
if len(slats) > 2:
stats = pmag.gausspars(slats)
print 'mean lat = ', '%7.1f' % (stats[0])
def main():
"""
NAME
di_rot.py
DESCRIPTION
rotates set of directions to new coordinate system
SYNTAX
di_rot.py [command line options]
OPTIONS
-h prints help message and quits
-f specify input file, default is standard input
-F specify output file, default is standard output
-D D specify Dec of new coordinate system, default is 0
-I I specify Inc of new coordinate system, default is 90
INTPUT/OUTPUT
dec inc [space delimited]
"""
D,I=0.,90.
outfile=""
infile=""
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]
data=numpy.loadtxt(infile)
else:
data=numpy.loadtxt(sys.stdin,dtype=numpy.float)
if '-F' in sys.argv:
ind=sys.argv.index('-F')
outfile=sys.argv[ind+1]
out=open(outfile,'w')
if '-D' in sys.argv:
ind=sys.argv.index('-D')
D=float(sys.argv[ind+1])
if '-I' in sys.argv:
ind=sys.argv.index('-I')
I=float(sys.argv[ind+1])
if len(data.shape)>1: # 2-D array
N=data.shape[0]
DipDir,Dip=numpy.ones(N,dtype=numpy.float).transpose()*(D-180.),numpy.ones(N,dtype=numpy.float).transpose()*(90.-I)
data=data.transpose()
data=numpy.array([data[0],data[1],DipDir ,Dip]).transpose()
drot,irot=pmag.dotilt_V(data)
drot=(drot-180.)%360. #
for k in range(N):
if outfile=="":
print '%7.1f %7.1f ' % (drot[k],irot[k])
else:
out.write('%7.1f %7.1f\n' % (drot[k],irot[k]))
else:
d,i=pmag.dotilt(data[0],data[1],(D-180.),90.-I)
if outfile=="":
print '%7.1f %7.1f ' % ((d-180.)%360.,i)
else:
out.write('%7.1f %7.1f\n' % ((d-180.)%360.,i))
def main():
"""
NAME
nrm_specimens_magic.py
DESCRIPTION
converts NRM data in a magic_measurements type file to
geographic and tilt corrected data in a pmag_specimens type file
SYNTAX
nrm_specimens_magic.py [-h][command line options]
OPTIONS:
-h prints the help message and quits
-f MFILE: specify input file
-fsa SFILE: specify er_samples format file [with orientations]
-F PFILE: specify output file
-A do not average replicate measurements
-crd [g, t]: specify coordinate system ([g]eographic or [t]ilt adjusted)
NB: you must have the SFILE in this directory
DEFAULTS
MFILE: magic_measurements.txt
PFILE: nrm_specimens.txt
SFILE: er_samples.txt
coord: specimen
average replicate measurements?: YES
"""
#
# define some variables
#
beg,end,pole,geo,tilt,askave,save=0,0,[],0,0,0,0
samp_file=1
args=sys.argv
geo,tilt,orient=0,0,0
doave=1
user,comment,doave,coord="","",1,""
dir_path='.'
if "-h" in args:
print main.__doc__
sys.exit()
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
meas_file=dir_path+"/magic_measurements.txt"
pmag_file=dir_path+"/nrm_specimens.txt"
samp_file=dir_path+"/er_samples.txt"
if "-A" in args: doave=0
if "-f" in args:
ind=args.index("-f")
meas_file=sys.argv[ind+1]
if "-F" in args:
ind=args.index("-F")
pmag_file=dir_path+'/'+sys.argv[ind+1]
speclist=[]
if "-fsa" in args:
ind=args.index("-fsa")
samp_file=dir_path+'/'+sys.argv[ind+1]
if "-crd" in args:
ind=args.index("-crd")
coord=sys.argv[ind+1]
if coord=="g":
geo,orient=1,1
if coord=="t":
tilt,orient,geo=1,1,1
#
# read in data
if samp_file!="":
samp_data,file_type=pmag.magic_read(samp_file)
if file_type != 'er_samples':
print file_type
print "This is not a valid er_samples file "
sys.exit()
else: print samp_file,' read in with ',len(samp_data),' records'
else:
print 'no orientations - will create file in specimen coordinates'
geo,tilt,orient=0,0,0
#
#
meas_data,file_type=pmag.magic_read(meas_file)
if file_type != 'magic_measurements':
print file_type
print file_type,"This is not a valid magic_measurements file "
sys.exit()
#
if orient==1:
# set orientation priorities
SO_methods=[]
orientation_priorities={'0':'SO-SUN','1':'SO-GPS-DIFF','2':'SO-SIGHT-BACK','3':'SO-CMD-NORTH','4':'SO-MAG'}
for rec in samp_data:
if "magic_method_codes" in rec:
methlist=rec["magic_method_codes"]
for meth in methlist.split(":"):
if "SO" in meth and "SO-POM" not in meth.strip():
if meth.strip() not in SO_methods: SO_methods.append(meth.strip())
#
# sort the sample names
#
sids=pmag.get_specs(meas_data)
#
#
PmagSpecRecs=[]
for s in sids:
skip=0
recnum=0
PmagSpecRec={}
PmagSpecRec["er_analyst_mail_names"]=user
method_codes,inst_code=[],""
# find the data from the meas_data file for this sample
#
# collect info for the PmagSpecRec dictionary
#
meas_meth=[]
for rec in meas_data: # copy of vital stats to PmagSpecRec from first spec record
if rec["er_specimen_name"]==s:
PmagSpecRec["er_specimen_name"]=s
PmagSpecRec["er_sample_name"]=rec["er_sample_name"]
PmagSpecRec["er_site_name"]=rec["er_site_name"]
PmagSpecRec["er_location_name"]=rec["er_location_name"]
PmagSpecRec["er_citation_names"]="This study"
PmagSpecRec["magic_instrument_codes"]=""
if "magic_experiment_name" not in rec.keys():
rec["magic_experiment_name"]=""
if "magic_instrument_codes" not in rec.keys():
rec["magic_instrument_codes"]=""
else:
PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"]
if len(rec["magic_instrument_codes"]) > len(inst_code):
inst_code=rec["magic_instrument_codes"]
PmagSpecRec["magic_instrument_codes"]=inst_code # copy over instruments
break
#
# now check for correct method labels for all measurements
#
nrm_data=[]
for meas_rec in meas_data:
if meas_rec['er_specimen_name']==PmagSpecRec['er_specimen_name']:
meths=meas_rec["magic_method_codes"].split(":")
for meth in meths:
if meth.strip() not in meas_meth:meas_meth.append(meth)
if "LT-NO" in meas_meth:nrm_data.append(meas_rec)
#
data,units=pmag.find_dmag_rec(s,nrm_data)
#
datablock=data
#
# find replicate measurements at NRM step and average them
#
Specs=[]
if doave==1:
step_meth,avedata=pmag.vspec(data)
if len(avedata) != len(datablock):
method_codes.append("DE-VM")
SpecRec=avedata[0]
print 'averaging data '
else: SpecRec=data[0]
Specs.append(SpecRec)
else:
for spec in data:Specs.append(spec)
for SpecRec in Specs:
#
# do geo or stratigraphic correction now
#
if geo==1:
#
# find top priority orientation method
redo,p=1,0
if len(SO_methods)<=1:
az_type=SO_methods[0]
orient=pmag.find_samp_rec(PmagSpecRec["er_sample_name"],samp_data,az_type)
if orient["sample_azimuth"] !="": method_codes.append(az_type)
redo=0
while redo==1:
if p>=len(orientation_priorities):
print "no orientation data for ",s
skip,redo=1,0
break
az_type=orientation_priorities[str(p)]
orient=pmag.find_samp_rec(PmagSpecRec["er_sample_name"],samp_data,az_type)
if orient["sample_azimuth"] !="":
method_codes.append(az_type.strip())
redo=0
elif orient["sample_azimuth"] =="":
p+=1
#
# if stratigraphic selected, get stratigraphic correction
#
if skip==0 and orient["sample_azimuth"]!="" and orient["sample_dip"]!="":
d_geo,i_geo=pmag.dogeo(SpecRec[1],SpecRec[2],orient["sample_azimuth"],orient["sample_dip"])
SpecRec[1]=d_geo
SpecRec[2]=i_geo
if tilt==1 and "sample_bed_dip" in orient.keys() and orient['sample_bed_dip']!="":
d_tilt,i_tilt=pmag.dotilt(d_geo,i_geo,orient["sample_bed_dip_direction"],orient["sample_bed_dip"])
SpecRec[1]=d_tilt
SpecRec[2]=i_tilt
if skip==0:
PmagSpecRec["specimen_dec"]='%7.1f ' %(SpecRec[1])
PmagSpecRec["specimen_inc"]='%7.1f ' %(SpecRec[2])
if geo==1 and tilt==0:PmagSpecRec["specimen_tilt_correction"]='0'
if geo==1 and tilt==1: PmagSpecRec["specimen_tilt_correction"]='100'
if geo==0 and tilt==0: PmagSpecRec["specimen_tilt_correction"]='-1'
PmagSpecRec["specimen_direction_type"]='l'
PmagSpecRec["magic_method_codes"]="LT-NO"
if len(method_codes) != 0:
methstring=""
for meth in method_codes:
methstring=methstring+ ":" +meth
PmagSpecRec["magic_method_codes"]=methstring[1:]
PmagSpecRec["specimen_description"]="NRM data"
PmagSpecRecs.append(PmagSpecRec)
pmag.magic_write(pmag_file,PmagSpecRecs,'pmag_specimens')
print "Data saved in ",pmag_file
def main():
"""
NAME
zeq_magic_redo.py
DESCRIPTION
Calculate principal components through demagnetization data using bounds and calculation type stored in "redo" file
SYNTAX
zeq_magic_redo.py [command line options]
OPTIONS
-h prints help message
-usr USER: identify user, default is ""
-f: specify input file, default is magic_measurements.txt
-F: specify output file, default is zeq_specimens.txt
-fre REDO: specify redo file, default is "zeq_redo"
-fsa SAMPFILE: specify er_samples format file, default is "er_samples.txt"
-A : don't average replicate measurements, default is yes
-crd [s,g,t] :
specify coordinate system [s,g,t] [default is specimen coordinates]
are specimen, geographic, and tilt corrected respectively
NB: you must have a SAMPFILE in this directory to rotate from specimen coordinates
-leg: attaches "Recalculated from original measurements; supercedes published results. " to comment field
INPUTS
zeq_redo format file is:
specimen_name calculation_type[DE-BFL,DE-BFL-A,DE-BFL-O,DE-BFP,DE-FM] step_min step_max component_name[A,B,C]
"""
dir_path='.'
INCL=["LT-NO","LT-AF-Z","LT-T-Z","LT-M-Z"] # looking for demag data
beg,end,pole,geo,tilt,askave,save=0,0,[],0,0,0,0
user,doave,comment= "",1,""
geo,tilt=0,0
version_num=pmag.get_version()
args=sys.argv
if '-WD' in args:
ind=args.index('-WD')
dir_path=args[ind+1]
meas_file,pmag_file,mk_file= dir_path+"/"+"magic_measurements.txt",dir_path+"/"+"zeq_specimens.txt",dir_path+"/"+"zeq_redo"
samp_file,coord=dir_path+"/"+"er_samples.txt",""
if "-h" in args:
print(main.__doc__)
sys.exit()
if "-usr" in args:
ind=args.index("-usr")
user=sys.argv[ind+1]
if "-A" in args:doave=0
if "-leg" in args: comment="Recalculated from original measurements; supercedes published results. "
if "-f" in args:
ind=args.index("-f")
meas_file=dir_path+'/'+sys.argv[ind+1]
if "-F" in args:
ind=args.index("-F")
pmag_file=dir_path+'/'+sys.argv[ind+1]
if "-fre" in args:
ind=args.index("-fre")
mk_file=dir_path+"/"+args[ind+1]
try:
mk_f=open(mk_file,'r')
except:
print("Bad redo file")
sys.exit()
mkspec,skipped=[],[]
speclist=[]
for line in mk_f.readlines():
tmp=line.split()
mkspec.append(tmp)
speclist.append(tmp[0])
if "-fsa" in args:
ind=args.index("-fsa")
samp_file=dir_path+'/'+sys.argv[ind+1]
if "-crd" in args:
ind=args.index("-crd")
coord=sys.argv[ind+1]
if coord=="g":geo,tilt=1,0
if coord=="t":geo,tilt=1,1
#
# now get down to bidness
if geo==1:
samp_data,file_type=pmag.magic_read(samp_file)
if file_type != 'er_samples':
print(file_type)
print("This is not a valid er_samples file ")
sys.exit()
#
#
#
meas_data,file_type=pmag.magic_read(meas_file)
if file_type != 'magic_measurements':
print(file_type)
print(file_type,"This is not a valid magic_measurements file ")
sys.exit()
#
# sort the specimen names
#
k = 0
print('Processing ',len(speclist), ' specimens - please wait')
PmagSpecs=[]
while k < len(speclist):
s=speclist[k]
recnum=0
PmagSpecRec={}
method_codes,inst_codes=[],[]
# find the data from the meas_data file for this sample
#
# collect info for the PmagSpecRec dictionary
#
meas_meth=[]
spec=pmag.get_dictitem(meas_data,'er_specimen_name',s,'T')
if len(spec)==0:
print('no data found for specimen: ',s)
print('delete from zeq_redo input file...., then try again')
else:
for rec in spec: # copy of vital stats to PmagSpecRec from first spec record in demag block
skip=1
methods=rec["magic_method_codes"].split(":")
if len(set(methods) & set(INCL))>0:
PmagSpecRec["er_analyst_mail_names"]=user
PmagSpecRec["magic_software_packages"]=version_num
PmagSpecRec["er_specimen_name"]=s
PmagSpecRec["er_sample_name"]=rec["er_sample_name"]
PmagSpecRec["er_site_name"]=rec["er_site_name"]
PmagSpecRec["er_location_name"]=rec["er_location_name"]
if "er_expedition_name" in list(rec.keys()):PmagSpecRec["er_expedition_name"]=rec["er_expedition_name"]
PmagSpecRec["er_citation_names"]="This study"
if "magic_experiment_name" not in list(rec.keys()): rec["magic_experiment_name"]=""
PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"]
if "magic_instrument_codes" not in list(rec.keys()): rec["magic_instrument_codes"]=""
inst=rec['magic_instrument_codes'].split(":")
for I in inst:
if I not in inst_codes: # copy over instruments
inst_codes.append(I)
meths=rec["magic_method_codes"].split(":")
for meth in meths:
if meth.strip() not in meas_meth:meas_meth.append(meth)
if "LP-DIR-AF" in meas_meth or "LT-AF-Z" in meas_meth:
PmagSpecRec["measurement_step_unit"]="T"
if "LP-DIR-AF" not in method_codes:method_codes.append("LP-DIR-AF")
if "LP-DIR-T" in meas_meth or "LT-T-Z" in meas_meth:
PmagSpecRec["measurement_step_unit"]="K"
if "LP-DIR-T" not in method_codes:method_codes.append("LP-DIR-T")
if "LP-DIR-M" in meas_meth or "LT-M-Z" in meas_meth:
PmagSpecRec["measurement_step_unit"]="J"
if "LP-DIR-M" not in method_codes:method_codes.append("LP-DIR-M")
#
#
datablock,units=pmag.find_dmag_rec(s,spec) # fish out the demag data for this specimen
#
if len(datablock) <2 or s not in speclist :
k+=1
# print 'skipping ', s,len(datablock)
else:
#
# find replicate measurements at given treatment step and average them
#
# step_meth,avedata=pmag.vspec(data)
#
# if len(avedata) != len(datablock):
# if doave==1:
# method_codes.append("DE-VM")
# datablock=avedata
#
# do geo or stratigraphic correction now
#
if geo==1 or tilt==1:
# find top priority orientation method
orient,az_type=pmag.get_orient(samp_data,PmagSpecRec["er_sample_name"])
if az_type not in method_codes:method_codes.append(az_type)
#
# if tilt selected, get stratigraphic correction
#
tiltblock,geoblock=[],[]
for rec in datablock:
if "sample_azimuth" in list(orient.keys()) and orient["sample_azimuth"]!="":
d_geo,i_geo=pmag.dogeo(rec[1],rec[2],float(orient["sample_azimuth"]),float(orient["sample_dip"]))
geoblock.append([rec[0],d_geo,i_geo,rec[3],rec[4],rec[5]])
if tilt==1 and "sample_bed_dip_direction" in list(orient.keys()):
d_tilt,i_tilt=pmag.dotilt(d_geo,i_geo,float(orient["sample_bed_dip_direction"]),float(orient["sample_bed_dip"]))
tiltblock.append([rec[0],d_tilt,i_tilt,rec[3],rec[4],rec[5]])
elif tilt==1:
if PmagSpecRec["er_sample_name"] not in skipped:
print('no tilt correction for ', PmagSpecRec["er_sample_name"],' skipping....')
skipped.append(PmagSpecRec["er_sample_name"])
else:
if PmagSpecRec["er_sample_name"] not in skipped:
print('no geographic correction for ', PmagSpecRec["er_sample_name"],' skipping....')
skipped.append(PmagSpecRec["er_sample_name"])
#
# get beg_pca, end_pca, pca
if PmagSpecRec['er_sample_name'] not in skipped:
compnum=-1
for spec in mkspec:
if spec[0]==s:
CompRec={}
for key in list(PmagSpecRec.keys()):CompRec[key]=PmagSpecRec[key]
compnum+=1
calculation_type=spec[1]
beg=float(spec[2])
end=float(spec[3])
if len(spec)>4:
comp_name=spec[4]
else:
comp_name=string.uppercase[compnum]
CompRec['specimen_comp_name']=comp_name
if beg < float(datablock[0][0]):beg=float(datablock[0][0])
if end > float(datablock[-1][0]):end=float(datablock[-1][0])
for l in range(len(datablock)):
if datablock[l][0]==beg:beg_pca=l
if datablock[l][0]==end:end_pca=l
if geo==1 and tilt==0:
mpars=pmag.domean(geoblock,beg_pca,end_pca,calculation_type)
if mpars["specimen_direction_type"]!="Error":
CompRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
CompRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
CompRec["specimen_tilt_correction"]='0'
if geo==1 and tilt==1:
mpars=pmag.domean(tiltblock,beg_pca,end_pca,calculation_type)
if mpars["specimen_direction_type"]!="Error":
CompRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
CompRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
CompRec["specimen_tilt_correction"]='100'
if geo==0 and tilt==0:
mpars=pmag.domean(datablock,beg_pca,end_pca,calculation_type)
if mpars["specimen_direction_type"]!="Error":
CompRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
CompRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
CompRec["specimen_tilt_correction"]='-1'
if mpars["specimen_direction_type"]=="Error":
pass
else:
CompRec["measurement_step_min"]='%8.3e '%(datablock[beg_pca][0])
try:
CompRec["measurement_step_max"]='%8.3e '%(datablock[end_pca][0] )
except:
print('error in end_pca ',PmagSpecRec['er_specimen_name'])
CompRec["specimen_correction"]='u'
if calculation_type!='DE-FM':
CompRec["specimen_mad"]='%7.1f '%(mpars["specimen_mad"])
CompRec["specimen_alpha95"]=""
else:
CompRec["specimen_mad"]=""
CompRec["specimen_alpha95"]='%7.1f '%(mpars["specimen_alpha95"])
CompRec["specimen_n"]='%i '%(mpars["specimen_n"])
CompRec["specimen_dang"]='%7.1f '%(mpars["specimen_dang"])
CompMeths=[]
for meth in method_codes:
if meth not in CompMeths:CompMeths.append(meth)
if calculation_type not in CompMeths:CompMeths.append(calculation_type)
if geo==1: CompMeths.append("DA-DIR-GEO")
if tilt==1: CompMeths.append("DA-DIR-TILT")
if "DE-BFP" not in calculation_type:
CompRec["specimen_direction_type"]='l'
else:
CompRec["specimen_direction_type"]='p'
CompRec["magic_method_codes"]=""
if len(CompMeths) != 0:
methstring=""
for meth in CompMeths:
methstring=methstring+ ":" +meth
CompRec["magic_method_codes"]=methstring.strip(':')
CompRec["specimen_description"]=comment
if len(inst_codes) != 0:
inststring=""
for inst in inst_codes:
inststring=inststring+ ":" +inst
CompRec["magic_instrument_codes"]=inststring.strip(':')
PmagSpecs.append(CompRec)
k+=1
pmag.magic_write(pmag_file,PmagSpecs,'pmag_specimens')
print("Recalculated specimen data stored in ",pmag_file)
def main():
"""
NAME
zeq_magic.py
DESCRIPTION
reads in magic_measurements formatted file, makes plots of remanence decay
during demagnetization experiments. Reads in prior interpretations saved in
a pmag_specimens formatted file and allows re-interpretations of best-fit lines
and planes and saves (revised or new) interpretations in a pmag_specimens file.
interpretations are saved in the coordinate system used. Also allows judicious editting of
measurements to eliminate "bad" measurements. These are marked as such in the magic_measurements
input file. they are NOT deleted, just ignored.
SYNTAX
zeq_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f MEASFILE: sets magic_measurements format input file, default: magic_measurements.txt
-fsp SPECFILE: sets pmag_specimens format file with prior interpreations, default: zeq_specimens.txt
-Fp PLTFILE: sets filename for saved plot, default is name_type.fmt (where type is zijd, eqarea or decay curve)
-crd [s,g,t]: sets coordinate system, g=geographic, t=tilt adjusted, default: specimen coordinate system
-fsa SAMPFILE: sets er_samples format file with orientation information, default: er_samples.txt
-spc SPEC plots single specimen SPEC, saves plot with specified format
with optional -dir settings and quits
-dir [L,P,F][beg][end]: sets calculation type for principal component analysis, default is none
beg: starting step for PCA calculation
end: ending step for PCA calculation
[L,P,F]: calculation type for line, plane or fisher mean
must be used with -spc option
-fmt FMT: set format of saved plot [png,svg,jpg]
-A: suppresses averaging of replicate measurements, default is to average
-sav: saves all plots without review
SCREEN OUTPUT:
Specimen, N, a95, StepMin, StepMax, Dec, Inc, calculation type
"""
# initialize some variables
doave,e,b=1,0,0 # average replicates, initial end and beginning step
plots,coord=0,'s'
noorient=0
version_num=pmag.get_version()
verbose=pmagplotlib.verbose
beg_pca,end_pca,direction_type="","",'l'
calculation_type,fmt="","svg"
user,spec_keys,locname="",[],''
plot_file=""
sfile=""
plot_file=""
PriorRecs=[] # empty list for prior interpretations
backup=0
specimen="" # can skip everything and just plot one specimen with bounds e,b
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
else:
dir_path='.'
inspec=dir_path+'/'+'zeq_specimens.txt'
meas_file,geo,tilt,ask,samp_file=dir_path+'/magic_measurements.txt',0,0,0,dir_path+'/er_samples.txt'
if '-f' in sys.argv:
ind=sys.argv.index('-f')
meas_file=dir_path+'/'+sys.argv[ind+1]
if '-fsp' in sys.argv:
ind=sys.argv.index('-fsp')
inspec=dir_path+'/'+sys.argv[ind+1]
if '-fsa' in sys.argv:
ind=sys.argv.index('-fsa')
samp_file=dir_path+'/'+sys.argv[ind+1]
sfile='ok'
if '-crd' in sys.argv:
ind=sys.argv.index('-crd')
coord=sys.argv[ind+1]
if coord=='g' or coord=='t':
samp_data,file_type=pmag.magic_read(samp_file)
if file_type=='er_samples':sfile='ok'
geo=1
if coord=='t':tilt=1
if '-spc' in sys.argv:
ind=sys.argv.index('-spc')
specimen=sys.argv[ind+1]
if '-dir' in sys.argv:
ind=sys.argv.index('-dir')
direction_type=sys.argv[ind+1]
beg_pca=int(sys.argv[ind+2])
end_pca=int(sys.argv[ind+3])
if direction_type=='L':calculation_type='DE-BFL'
if direction_type=='P':calculation_type='DE-BFP'
if direction_type=='F':calculation_type='DE-FM'
if '-Fp' in sys.argv:
ind=sys.argv.index('-Fp')
plot_file=dir_path+'/'+sys.argv[ind+1]
if '-A' in sys.argv: doave=0
if '-sav' in sys.argv:
plots=1
verbose=0
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
#
first_save=1
meas_data,file_type=pmag.magic_read(meas_file)
changeM,changeS=0,0 # check if data or interpretations have changed
if file_type != 'magic_measurements':
print file_type
print file_type,"This is not a valid magic_measurements file "
sys.exit()
for rec in meas_data:
if "magic_method_codes" not in rec.keys(): rec["magic_method_codes"]=""
methods=""
tmp=rec["magic_method_codes"].replace(" ","").split(":")
for meth in tmp:
methods=methods+meth+":"
rec["magic_method_codes"]=methods[:-1] # get rid of annoying spaces in Anthony's export files
if "magic_instrument_codes" not in rec.keys() :rec["magic_instrument_codes"]=""
PriorSpecs=[]
PriorRecs,file_type=pmag.magic_read(inspec)
if len(PriorRecs)==0:
if verbose:print "starting new file ",inspec
for Rec in PriorRecs:
if 'magic_software_packages' not in Rec.keys():Rec['magic_software_packages']=""
if Rec['er_specimen_name'] not in PriorSpecs:
if 'specimen_comp_name' not in Rec.keys():Rec['specimen_comp_name']="A"
PriorSpecs.append(Rec['er_specimen_name'])
else:
if 'specimen_comp_name' not in Rec.keys():Rec['specimen_comp_name']="A"
if "magic_method_codes" in Rec.keys():
methods=[]
tmp=Rec["magic_method_codes"].replace(" ","").split(":")
for meth in tmp:
methods.append(meth)
if 'DE-FM' in methods:
Rec['calculation_type']='DE-FM' # this won't be imported but helps
if 'DE-BFL' in methods:
Rec['calculation_type']='DE-BFL'
if 'DE-BFL-A' in methods:
Rec['calculation_type']='DE-BFL-A'
if 'DE-BFL-O' in methods:
Rec['calculation_type']='DE-BFL-O'
if 'DE-BFP' in methods:
Rec['calculation_type']='DE-BFP'
else:
Rec['calculation_type']='DE-BFL' # default is to assume a best-fit line
#
# get list of unique specimen names
#
sids=pmag.get_specs(meas_data)
#
# set up plots, angle sets X axis to horizontal, direction_type 'l' is best-fit line
# direction_type='p' is great circle
#
#
# draw plots for sample s - default is just to step through zijderveld diagrams
#
#
# define figure numbers for equal area, zijderveld,
# and intensity vs. demagnetiztion step respectively
ZED={}
ZED['eqarea'],ZED['zijd'], ZED['demag']=1,2,3
pmagplotlib.plot_init(ZED['eqarea'],5,5)
pmagplotlib.plot_init(ZED['zijd'],6,5)
pmagplotlib.plot_init(ZED['demag'],5,5)
save_pca=0
if specimen=="":
k = 0
else:
k=sids.index(specimen)
angle,direction_type="",""
setangle=0
CurrRecs=[]
while k < len(sids):
CurrRecs=[]
if setangle==0:angle=""
method_codes,inst_code=[],""
s=sids[k]
PmagSpecRec={}
PmagSpecRec["er_analyst_mail_names"]=user
PmagSpecRec['magic_software_packages']=version_num
PmagSpecRec['specimen_description']=""
PmagSpecRec['magic_method_codes']=""
if verbose and s!="":print s, k , 'out of ',len(sids)
#
# collect info for the PmagSpecRec dictionary
#
s_meas=pmag.get_dictitem(meas_data,'er_specimen_name',s,'T') # fish out this specimen
s_meas=pmag.get_dictitem(s_meas,'magic_method_codes','Z','has') # fish out zero field steps
if len(s_meas)>0:
for rec in s_meas: # fix up a few things for the output record
PmagSpecRec["magic_instrument_codes"]=rec["magic_instrument_codes"] # copy over instruments
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"]
locname=rec['er_location_name']
if 'er_expedition_name' in rec.keys(): PmagSpecRec["er_expedition_name"]=rec["er_expedition_name"]
PmagSpecRec["magic_method_codes"]=rec["magic_method_codes"]
if "magic_experiment_name" not in rec.keys():
PmagSpecRec["magic_experiment_names"]=""
else:
PmagSpecRec["magic_experiment_names"]=rec["magic_experiment_name"]
break
#
# find the data from the meas_data file for this specimen
#
data,units=pmag.find_dmag_rec(s,meas_data)
PmagSpecRec["measurement_step_unit"]= units
u=units.split(":")
if "T" in units:PmagSpecRec["magic_method_codes"]=PmagSpecRec["magic_method_codes"]+":LP-DIR-AF"
if "K" in units:PmagSpecRec["magic_method_codes"]=PmagSpecRec["magic_method_codes"]+":LP-DIR-T"
if "J" in units:PmagSpecRec["magic_method_codes"]=PmagSpecRec["magic_method_codes"]+":LP-DIR-M"
#
# find prior interpretation
#
if len(CurrRecs)==0: # check if already in
beg_pca,end_pca="",""
calculation_type=""
if inspec !="":
if verbose: print " looking up previous interpretations..."
precs=pmag.get_dictitem(PriorRecs,'er_specimen_name',s,'T') # get all the prior recs with this specimen name
precs=pmag.get_dictitem(precs,'magic_method_codes','LP-DIR','has') # get the directional data
PriorRecs=pmag.get_dictitem(PriorRecs,'er_specimen_name',s,'F') # take them all out of prior recs
# get the ones that meet the current coordinate system
for prec in precs:
if 'specimen_tilt_correction' not in prec.keys() or prec['specimen_tilt_correction']=='-1':
crd='s'
elif prec['specimen_tilt_correction']=='0':
crd='g'
elif prec['specimen_tilt_correction']=='100':
crd='t'
else:
crd='?'
CurrRec={}
for key in prec.keys():CurrRec[key]=prec[key]
CurrRecs.append(CurrRec) # put in CurrRecs
method_codes= CurrRec["magic_method_codes"].replace(" ","").split(':')
calculation_type='DE-BFL'
if 'DE-FM' in method_codes: calculation_type='DE-FM'
if 'DE-BFP' in method_codes: calculation_type='DE-BFP'
if 'DE-BFL-A' in method_codes: calculation_type='DE-BFL-A'
if 'specimen_dang' not in CurrRec.keys():
if verbose:print 'Run mk_redo.py and zeq_magic_redo.py to get the specimen_dang values'
CurrRec['specimen_dang']=-1
if calculation_type!='DE-FM' and crd==coord: # not a fisher mean
if verbose:print "Specimen N MAD DANG start end dec inc type component coordinates"
if units=='K':
if verbose:print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %s %s %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_mad"]),float(CurrRec["specimen_dang"]),float(CurrRec["measurement_step_min"])-273,float(CurrRec["measurement_step_max"])-273,float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,CurrRec['specimen_comp_name'],crd)
elif units=='T':
if verbose:print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %s %s %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_mad"]),float(CurrRec["specimen_dang"]),float(CurrRec["measurement_step_min"])*1e3,float(CurrRec["measurement_step_max"])*1e3,float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,CurrRec['specimen_comp_name'],crd)
elif 'T' in units and 'K' in units:
if float(CurrRec['measurement_step_min'])<1.0 :
min=float(CurrRec['measurement_step_min'])*1e3
else:
min=float(CurrRec['measurement_step_min'])-273
if float(CurrRec['measurement_step_max'])<1.0 :
max=float(CurrRec['measurement_step_max'])*1e3
else:
max=float(CurrRec['measurement_step_max'])-273
if verbose:print '%s %i %7.1f %i %i %7.1f %7.1f %7.1f, %s %s\n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_mad"]),float(CurrRec['specimen_dang']),min,max,float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,crd)
elif 'J' in units:
if verbose:print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f %s %s %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_mad"]),float(CurrRec['specimen_dang']),float(CurrRec["measurement_step_min"]),float(CurrRec["measurement_step_max"]),float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,CurrRec['specimen_comp_name'],crd)
elif calculation_type=='DE-FM' and crd==coord: # fisher mean
if verbose:print "Specimen a95 DANG start end dec inc type component coordinates"
if units=='K':
if verbose:print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %s %s %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_alpha95"]),float(CurrRec["measurement_step_min"])-273,float(CurrRec["measurement_step_max"])-273,float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,CurrRec['specimen_comp_name'],crd)
elif units=='T':
if verbose:print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %s %s %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_alpha95"]),float(CurrRec["measurement_step_min"])*1e3,float(CurrRec["measurement_step_max"])*1e3,float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,CurrRec['specimen_comp_name'],crd)
elif 'T' in units and 'K' in units:
if float(CurrRec['measurement_step_min'])<1.0 :
min=float(CurrRec['measurement_step_min'])*1e3
else:
min=float(CurrRec['measurement_step_min'])-273
if float(CurrRec['measurement_step_max'])<1.0 :
max=float(CurrRec['measurement_step_max'])*1e3
else:
max=float(CurrRec['measurement_step_max'])-273
if verbose:print '%s %i %7.1f %i %i %7.1f %7.1f %s %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_alpha95"]),min,max,float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,crd)
elif 'J' in units:
if verbose:print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %s %s %s \n' % (CurrRec["er_specimen_name"],int(CurrRec["specimen_n"]),float(CurrRec["specimen_mad"]),float(CurrRec["measurement_step_min"]),float(CurrRec["measurement_step_max"]),float(CurrRec["specimen_dec"]),float(CurrRec["specimen_inc"]),calculation_type,CurrRec['specimen_comp_name'],crd)
if len(CurrRecs)==0:beg_pca,end_pca="",""
datablock=data
noskip=1
if len(datablock) <3:
noskip=0
if backup==0:
k+=1
else:
k-=1
if len(CurrRecs)>0:
for rec in CurrRecs:
PriorRecs.append(rec)
CurrRecs=[]
else:
backup=0
if noskip:
#
# find replicate measurements at given treatment step and average them
#
# step_meth,avedata=pmag.vspec(data)
# if len(avedata) != len(datablock):
# if doave==1:
# method_codes.append("DE-VM")
# datablock=avedata
# #
# do geo or stratigraphic correction now
#
if geo==1:
#
# find top priority orientation method
orient,az_type=pmag.get_orient(samp_data,PmagSpecRec["er_sample_name"])
if az_type=='SO-NO':
if verbose: print "no orientation data for ",s
orient["sample_azimuth"]=0
orient["sample_dip"]=0
noorient=1
method_codes.append("SO-NO")
orient["sample_azimuth"]=0
orient["sample_dip"]=0
orient["sample_bed_dip_azimuth"]=0
orient["sample_bed_dip"]=0
noorient=1
method_codes.append("SO-NO")
else:
noorient=0
#
# if stratigraphic selected, get stratigraphic correction
#
tiltblock,geoblock=[],[]
for rec in datablock:
d_geo,i_geo=pmag.dogeo(rec[1],rec[2],float(orient["sample_azimuth"]),float(orient["sample_dip"]))
geoblock.append([rec[0],d_geo,i_geo,rec[3],rec[4],rec[5],rec[6]])
if tilt==1 and "sample_bed_dip" in orient.keys() and float(orient['sample_bed_dip'])!=0:
d_tilt,i_tilt=pmag.dotilt(d_geo,i_geo,float(orient["sample_bed_dip_direction"]),float(orient["sample_bed_dip"]))
tiltblock.append([rec[0],d_tilt,i_tilt,rec[3],rec[4],rec[5],rec[6]])
if tilt==1: plotblock=tiltblock
if geo==1 and tilt==0:plotblock=geoblock
if geo==0 and tilt==0: plotblock=datablock
#
# set the end pca point to last point if not set
if e==0 or e>len(plotblock)-1: e=len(plotblock)-1
if angle=="": angle=plotblock[0][1] # rotate to NRM declination
title=s+'_s'
if geo==1 and tilt==0 and noorient!=1:title=s+'_g'
if tilt==1 and noorient!=1:title=s+'_t'
pmagplotlib.plotZED(ZED,plotblock,angle,title,units)
if verbose:pmagplotlib.drawFIGS(ZED)
if len(CurrRecs)!=0:
for prec in CurrRecs:
if 'calculation_type' not in prec.keys():
calculation_type=''
else:
calculation_type=prec["calculation_type"]
direction_type=prec["specimen_direction_type"]
if calculation_type !="":
beg_pca,end_pca="",""
for j in range(len(datablock)):
if data[j][0]==float(prec["measurement_step_min"]):beg_pca=j
if data[j][0]==float(prec["measurement_step_max"]):end_pca=j
if beg_pca=="" or end_pca=="":
if verbose:
print "something wrong with prior interpretation "
break
if calculation_type!="":
if beg_pca=="":beg_pca=0
if end_pca=="":end_pca=len(plotblock)-1
if geo==1 and tilt==0:
mpars=pmag.domean(geoblock,beg_pca,end_pca,calculation_type)
if mpars["specimen_direction_type"]!="Error":
pmagplotlib.plotDir(ZED,mpars,geoblock,angle)
if verbose:pmagplotlib.drawFIGS(ZED)
if geo==1 and tilt==1:
mpars=pmag.domean(tiltblock,beg_pca,end_pca,calculation_type)
if mpars["specimen_direction_type"]!="Error":
pmagplotlib.plotDir(ZED,mpars,tiltblock,angle)
if verbose:pmagplotlib.drawFIGS(ZED)
if geo==0 and tilt==0:
mpars=pmag.domean(datablock,beg_pca,end_pca,calculation_type)
if mpars["specimen_direction_type"]!="Error":
pmagplotlib.plotDir(ZED,mpars,plotblock,angle)
if verbose:pmagplotlib.drawFIGS(ZED)
#
# print out data for this sample to screen
#
recnum=0
for plotrec in plotblock:
if units=='T' and verbose: print '%s: %i %7.1f %s %8.3e %7.1f %7.1f %s' % (plotrec[5], recnum,plotrec[0]*1e3," mT",plotrec[3],plotrec[1],plotrec[2],plotrec[6])
if units=="K" and verbose: print '%s: %i %7.1f %s %8.3e %7.1f %7.1f %s' % (plotrec[5], recnum,plotrec[0]-273,' C',plotrec[3],plotrec[1],plotrec[2],plotrec[6])
if units=="J" and verbose: print '%s: %i %7.1f %s %8.3e %7.1f %7.1f %s' % (plotrec[5], recnum,plotrec[0],' J',plotrec[3],plotrec[1],plotrec[2],plotrec[6])
if 'K' in units and 'T' in units:
if plotrec[0]>=1. and verbose: print '%s: %i %7.1f %s %8.3e %7.1f %7.1f %s' % (plotrec[5], recnum,plotrec[0]-273,' C',plotrec[3],plotrec[1],plotrec[2],plotrec[6])
if plotrec[0]<1. and verbose: print '%s: %i %7.1f %s %8.3e %7.1f %7.1f %s' % (plotrec[5], recnum,plotrec[0]*1e3," mT",plotrec[3],plotrec[1],plotrec[2],plotrec[6])
recnum += 1
if specimen!="":
if plot_file=="":
basename=locname+'_'+s
else:
basename=plot_file
files={}
for key in ZED.keys():
files[key]=basename+'_'+key+'.'+fmt
pmagplotlib.saveP(ZED,files)
sys.exit()
else: # interactive
if plots==0:
ans='b'
k+=1
changeS=0
while ans != "":
if len(CurrRecs)==0:
print """
g/b: indicates good/bad measurement. "bad" measurements excluded from calculation
set s[a]ve plot, [b]ounds for pca and calculate, [p]revious, [s]pecimen,
change [h]orizontal projection angle, change [c]oordinate systems,
[e]dit data, [q]uit:
"""
else:
print """
g/b: indicates good/bad measurement. "bad" measurements excluded from calculation
set s[a]ve plot, [b]ounds for pca and calculate, [p]revious, [s]pecimen,
change [h]orizontal projection angle, change [c]oordinate systems,
[d]elete current interpretation(s), [e]dit data, [q]uit:
"""
ans=raw_input('<Return> for next specimen \n')
setangle=0
if ans=='d': # delete this interpretation
CurrRecs=[]
k-=1 # replot same specimen
ans=""
changeS=1
if ans=='q':
if changeM==1:
ans=raw_input('Save changes to magic_measurements.txt? y/[n] ')
if ans=='y':
pmag.magic_write(meas_file,meas_data,'magic_measurements')
print "Good bye"
sys.exit()
if ans=='a':
if plot_file=="":
basename=locname+'_'+s+'_'
else:
basename=plot_file
files={}
for key in ZED.keys():
files[key]=basename+'_'+coord+'_'+key+'.'+fmt
pmagplotlib.saveP(ZED,files)
ans=""
if ans=='p':
k-=2
ans=""
backup=1
if ans=='c':
k-=1 # replot same block
if tilt==0 and geo ==1:print "You are currently viewing geographic coordinates "
if tilt==1 and geo ==1:print "You are currently viewing stratigraphic coordinates "
if tilt==0 and geo ==0: print "You are currently viewing sample coordinates "
print "\n Which coordinate system do you wish to view? "
coord=raw_input(" <Return> specimen, [g] geographic, [t] tilt corrected ")
if coord=="g":geo,tilt=1,0
if coord=="t":
geo=1
tilt=1
if coord=="":
coord='s'
geo=0
tilt=0
if geo==1 and sfile=="":
samp_file=raw_input(" Input er_samples file for sample orientations [er_samples.txt] " )
if samp_file=="":samp_file="er_samples.txt"
samp_data,file_type=pmag.magic_read(samp_file)
if file_type != 'er_samples':
print file_type
print "This is not a valid er_samples file - coordinate system not changed"
else:
sfile="ok"
ans=""
if ans=='s':
keepon=1
sample=raw_input('Enter desired specimen name (or first part there of): ')
while keepon==1:
try:
k =sids.index(sample)
keepon=0
except:
tmplist=[]
for qq in range(len(sids)):
if sample in sids[qq]:tmplist.append(sids[qq])
print sample," not found, but this was: "
print tmplist
sample=raw_input('Select one or try again\n ')
angle,direction_type="",""
setangle=0
ans=""
if ans=='h':
k-=1
angle=raw_input("Enter desired declination for X axis 0-360 ")
angle=float(angle)
if angle==0:angle=0.001
s=sids[k]
setangle=1
ans=""
if ans=='e':
k-=1
ans=""
recnum=0
for plotrec in plotblock:
if plotrec[0]<=200 and verbose: print '%s: %i %7.1f %s %8.3e %7.1f %7.1f ' % (plotrec[5], recnum,plotrec[0]*1e3," mT",plotrec[3],plotrec[1],plotrec[2])
if plotrec[0]>200 and verbose: print '%s: %i %7.1f %s %8.3e %7.1f %7.1f ' % (plotrec[5], recnum,plotrec[0]-273,' C',plotrec[3],plotrec[1],plotrec[2])
recnum += 1
answer=raw_input('Enter index of point to change from bad to good or vice versa: ')
try:
ind=int(answer)
meas_data=pmag.mark_dmag_rec(s,ind,meas_data)
changeM=1
except:
'bad entry, try again'
if ans=='b':
if end_pca=="":end_pca=len(plotblock)-1
if beg_pca=="":beg_pca=0
k-=1 # stay on same sample until through
GoOn=0
while GoOn==0:
print 'Enter index of first point for pca: ','[',beg_pca,']'
answer=raw_input('return to keep default ')
if answer != "":
beg_pca=int(answer)
print 'Enter index of last point for pca: ','[',end_pca,']'
answer=raw_input('return to keep default ')
try:
end_pca=int(answer)
if plotblock[beg_pca][5]=='b' or plotblock[end_pca][5]=='b':
print "Can't select 'bad' measurement for PCA bounds -try again"
end_pca=len(plotblock)-1
beg_pca=0
elif beg_pca >=0 and beg_pca<=len(plotblock)-2 and end_pca>0 and end_pca<len(plotblock):
GoOn=1
else:
print beg_pca,end_pca, " are bad entry of indices - try again"
end_pca=len(plotblock)-1
beg_pca=0
except:
print beg_pca,end_pca, " are bad entry of indices - try again"
end_pca=len(plotblock)-1
beg_pca=0
GoOn=0
while GoOn==0:
if calculation_type!="":
print "Prior calculation type = ",calculation_type
ct=raw_input('Enter new Calculation Type: best-fit line, plane or fisher mean [l]/p/f : ' )
if ct=="" or ct=="l":
direction_type="l"
calculation_type="DE-BFL"
GoOn=1
elif ct=='p':
direction_type="p"
calculation_type="DE-BFP"
GoOn=1
elif ct=='f':
direction_type="l"
calculation_type="DE-FM"
GoOn=1
else:
print "bad entry of calculation type: try again. "
pmagplotlib.plotZED(ZED,plotblock,angle,s,units)
if verbose:pmagplotlib.drawFIGS(ZED)
if geo==1 and tilt==0:
mpars=pmag.domean(geoblock,beg_pca,end_pca,calculation_type)
if mpars['specimen_direction_type']=='Error':break
PmagSpecRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
PmagSpecRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
if "SO-NO" not in method_codes:
PmagSpecRec["specimen_tilt_correction"]='0'
method_codes.append("DA-DIR-GEO")
else:
PmagSpecRec["specimen_tilt_correction"]='-1'
pmagplotlib.plotDir(ZED,mpars,geoblock,angle)
if verbose:pmagplotlib.drawFIGS(ZED)
if geo==1 and tilt==1:
mpars=pmag.domean(tiltblock,beg_pca,end_pca,calculation_type)
if mpars['specimen_direction_type']=='Error':break
PmagSpecRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
PmagSpecRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
if "SO-NO" not in method_codes:
PmagSpecRec["specimen_tilt_correction"]='100'
method_codes.append("DA-DIR-TILT")
else:
PmagSpecRec["specimen_tilt_correction"]='-1'
pmagplotlib.plotDir(ZED,mpars,tiltblock,angle)
if verbose:pmagplotlib.drawFIGS(ZED)
if geo==0 and tilt==0:
mpars=pmag.domean(datablock,beg_pca,end_pca,calculation_type)
if mpars['specimen_direction_type']=='Error':break
PmagSpecRec["specimen_dec"]='%7.1f ' %(mpars["specimen_dec"])
PmagSpecRec["specimen_inc"]='%7.1f ' %(mpars["specimen_inc"])
PmagSpecRec["specimen_tilt_correction"]='-1'
pmagplotlib.plotDir(ZED,mpars,plotblock,angle)
if verbose:pmagplotlib.drawFIGS(ZED)
PmagSpecRec["measurement_step_min"]='%8.3e ' %(mpars["measurement_step_min"])
PmagSpecRec["measurement_step_max"]='%8.3e ' %(mpars["measurement_step_max"])
PmagSpecRec["specimen_correction"]='u'
PmagSpecRec["specimen_dang"]='%7.1f ' %(mpars['specimen_dang'])
print 'DANG: ',PmagSpecRec["specimen_dang"]
if calculation_type!='DE-FM':
PmagSpecRec["specimen_mad"]='%7.1f ' %(mpars["specimen_mad"])
PmagSpecRec["specimen_alpha95"]=""
else:
PmagSpecRec["specimen_alpha95"]='%7.1f ' %(mpars["specimen_alpha95"])
PmagSpecRec["specimen_mad"]=""
PmagSpecRec["specimen_n"]='%i ' %(mpars["specimen_n"])
PmagSpecRec["specimen_direction_type"]=direction_type
PmagSpecRec["calculation_type"]=calculation_type # redundant and won't be imported - just for convenience
method_codes=PmagSpecRec["magic_method_codes"].split(':')
if len(method_codes) != 0:
methstring=""
for meth in method_codes:
ctype=meth.split('-')
if 'DE' not in ctype:methstring=methstring+ ":" +meth # don't include old direction estimation methods
methstring=methstring+':'+calculation_type
PmagSpecRec["magic_method_codes"]= methstring.strip(':')
print 'Method codes: ',PmagSpecRec['magic_method_codes']
if calculation_type!='DE-FM':
if units=='K':
print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_mad"]),float(PmagSpecRec["specimen_dang"]),float(PmagSpecRec["measurement_step_min"])-273,float(PmagSpecRec["measurement_step_max"])-273,float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
elif units== 'T':
print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_mad"]),float(PmagSpecRec["specimen_dang"]),float(PmagSpecRec["measurement_step_min"])*1e3,float(PmagSpecRec["measurement_step_max"])*1e3,float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
elif 'T' in units and 'K' in units:
if float(PmagSpecRec['measurement_step_min'])<1.0 :
min=float(PmagSpecRec['measurement_step_min'])*1e3
else:
min=float(PmagSpecRec['measurement_step_min'])-273
if float(PmagSpecRec['measurement_step_max'])<1.0 :
max=float(PmagSpecRec['measurement_step_max'])*1e3
else:
max=float(PmagSpecRec['measurement_step_max'])-273
print '%s %i %7.1f %i %i %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_mad"]),float(PmagSpecRec["specimen_dang"]),min,max,float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
else:
print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_mad"]),float(PmagSpecRec["specimen_dang"]),float(PmagSpecRec["measurement_step_min"]),float(PmagSpecRec["measurement_step_max"]),float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
else:
if 'K' in units:
print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_alpha95"]),float(PmagSpecRec["specimen_dang"]),float(PmagSpecRec["measurement_step_min"])-273,float(PmagSpecRec["measurement_step_max"])-273,float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
elif 'T' in units:
print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_alpha95"]),float(PmagSpecRec["specimen_dang"]),float(PmagSpecRec["measurement_step_min"])*1e3,float(PmagSpecRec["measurement_step_max"])*1e3,float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
elif 'T' in units and 'K' in units:
if float(PmagSpecRec['measurement_step_min'])<1.0 :
min=float(PmagSpecRec['measurement_step_min'])*1e3
else:
min=float(PmagSpecRec['measurement_step_min'])-273
if float(PmagSpecRec['measurement_step_max'])<1.0 :
max=float(PmagSpecRec['measurement_step_max'])*1e3
else:
max=float(PmagSpecRec['measurement_step_max'])-273
print '%s %i %7.1f %i %i %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_alpha95"]),min,max,float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
else:
print '%s %i %7.1f %7.1f %7.1f %7.1f %7.1f, %s \n' % (PmagSpecRec["er_specimen_name"],int(PmagSpecRec["specimen_n"]),float(PmagSpecRec["specimen_alpha95"]),float(PmagSpecRec["measurement_step_min"]),float(PmagSpecRec["measurement_step_max"]),float(PmagSpecRec["specimen_dec"]),float(PmagSpecRec["specimen_inc"]),calculation_type)
saveit=raw_input("Save this interpretation? [y]/n \n")
if saveit!="n":
changeS=1
#
# put in details
#
angle,direction_type,setangle="","",0
if len(CurrRecs)>0:
replace=raw_input(" [0] add new component, or [1] replace existing interpretation(s) [default is replace] ")
if replace=="1" or replace=="":
CurrRecs=[]
PmagSpecRec['specimen_comp_name']='A'
CurrRecs.append(PmagSpecRec)
else:
print 'These are the current component names for this specimen: '
for trec in CurrRecs:print trec['specimen_comp_name']
compnum=raw_input("Enter new component name: ")
PmagSpecRec['specimen_comp_name']=compnum
print "Adding new component: ",PmagSpecRec['specimen_comp_name']
CurrRecs.append(PmagSpecRec)
else:
PmagSpecRec['specimen_comp_name']='A'
CurrRecs.append(PmagSpecRec)
k+=1
ans=""
else:
ans=""
else: # plots=1
k+=1
files={}
locname.replace('/','-')
print PmagSpecRec
for key in ZED.keys():
files[key]="LO:_"+locname+'_SI:_'+PmagSpecRec['er_site_name']+'_SA:_'+PmagSpecRec['er_sample_name']+'_SP:_'+s+'_CO:_'+coord+'_TY:_'+key+'_.'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['demag']='DeMag Plot'
titles['zijd']='Zijderveld Plot'
titles['eqarea']='Equal Area Plot'
ZED = pmagplotlib.addBorders(ZED,titles,black,purple)
pmagplotlib.saveP(ZED,files)
if len(CurrRecs)>0:
for rec in CurrRecs: PriorRecs.append(rec)
if changeS==1:
if len(PriorRecs)>0:
save_redo(PriorRecs,inspec)
else:
os.system('rm '+inspec)
CurrRecs,beg_pca,end_pca=[],"","" # next up
changeS=0
else: k+=1 # skip record - not enough data
if changeM==1:
pmag.magic_write(meas_file,meas_data,'magic_measurements')
def main():
"""
NAME
scalc_magic.py
DESCRIPTION
calculates Sb from pmag_results files
SYNTAX
scalc_magic -h [command line options]
INPUT
takes magic formatted pmag_results table
pmag_result_name must start with "VGP: Site"
must have average_lat if spin axis is reference
OPTIONS
-h prints help message and quits
-f FILE: specify input results file, default is 'pmag_results.txt'
-c cutoff: specify VGP colatitude cutoff value
-k cutoff: specify kappa cutoff
-crd [s,g,t]: specify coordinate system, default is geographic
-v : use the VanDammme criterion
-a: use antipodes of reverse data: default is to use only normal
-C: use all data without regard to polarity
-r: use reverse data only
-p: do relative to principle axis
-b: do bootstrap confidence bounds
OUTPUT:
if option -b used: N, S_B, lower and upper bounds
otherwise: N, S_B, cutoff
"""
in_file = 'pmag_results.txt'
coord, kappa, cutoff = "0", 1., 90.
nb, anti, spin, v, boot = 1000, 0, 1, 0, 0
coord_key = 'tilt_correction'
rev = 0
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-f' in sys.argv:
ind = sys.argv.index("-f")
in_file = sys.argv[ind + 1]
if '-c' in sys.argv:
ind = sys.argv.index('-c')
cutoff = float(sys.argv[ind + 1])
if '-k' in sys.argv:
ind = sys.argv.index('-k')
kappa = float(sys.argv[ind + 1])
if '-crd' in sys.argv:
ind = sys.argv.index("-crd")
coord = sys.argv[ind + 1]
if coord == 's': coord = "-1"
if coord == 'g': coord = "0"
if coord == 't': coord = "100"
if '-a' in sys.argv: anti = 1
if '-C' in sys.argv: cutoff = 180. # no cutoff
if '-r' in sys.argv: rev = 1
if '-p' in sys.argv: spin = 0
if '-v' in sys.argv: v = 1
if '-b' in sys.argv: boot = 1
data, file_type = pmag.magic_read(in_file)
#
#
# find desired vgp lat,lon, kappa,N_site data:
#
#
#
A, Vgps, Pvgps = 180., [], []
VgpRecs = pmag.get_dictitem(data, 'vgp_lat', '',
'F') # get all non-blank vgp latitudes
VgpRecs = pmag.get_dictitem(VgpRecs, 'vgp_lon', '',
'F') # get all non-blank vgp longitudes
SiteRecs = pmag.get_dictitem(VgpRecs, 'data_type', 'i',
'T') # get VGPs (as opposed to averaged)
SiteRecs = pmag.get_dictitem(SiteRecs, coord_key, coord,
'T') # get right coordinate system
for rec in SiteRecs:
if anti == 1:
if 90. - abs(float(rec['vgp_lat'])) <= cutoff and float(
rec['average_k']) >= kappa:
if float(rec['vgp_lat']) < 0:
rec['vgp_lat'] = '%7.1f' % (-1 * float(rec['vgp_lat']))
rec['vgp_lon'] = '%7.1f' % (float(rec['vgp_lon']) - 180.)
Vgps.append(rec)
Pvgps.append([float(rec['vgp_lon']), float(rec['vgp_lat'])])
elif rev == 0: # exclude normals
if 90. - (float(rec['vgp_lat'])) <= cutoff and float(
rec['average_k']) >= kappa:
Vgps.append(rec)
Pvgps.append([float(rec['vgp_lon']), float(rec['vgp_lat'])])
else: # include normals
if 90. - abs(float(rec['vgp_lat'])) <= cutoff and float(
rec['average_k']) >= kappa:
if float(rec['vgp_lat']) < 0:
rec['vgp_lat'] = '%7.1f' % (-1 * float(rec['vgp_lat']))
rec['vgp_lon'] = '%7.1f' % (float(rec['vgp_lon']) - 180.)
Vgps.append(rec)
Pvgps.append(
[float(rec['vgp_lon']),
float(rec['vgp_lat'])])
if spin == 0: # do transformation to pole
ppars = pmag.doprinc(Pvgps)
for vgp in Vgps:
vlon, vlat = pmag.dotilt(float(vgp['vgp_lon']),
float(vgp['vgp_lat']),
ppars['dec'] - 180., 90. - ppars['inc'])
vgp['vgp_lon'] = vlon
vgp['vgp_lat'] = vlat
vgp['average_k'] = "0"
S_B = pmag.get_Sb(Vgps)
A = cutoff
if v == 1:
thetamax, A = 181., 180.
vVgps, cnt = [], 0
for vgp in Vgps:
vVgps.append(vgp) # make a copy of Vgps
while thetamax > A:
thetas = []
A = 1.8 * S_B + 5
cnt += 1
for vgp in vVgps:
thetas.append(90. - (float(vgp['vgp_lat'])))
thetas.sort()
thetamax = thetas[-1]
if thetamax < A: break
nVgps = []
for vgp in vVgps:
if 90. - (float(vgp['vgp_lat'])) < thetamax: nVgps.append(vgp)
vVgps = []
for vgp in nVgps:
vVgps.append(vgp)
S_B = pmag.get_Sb(vVgps)
Vgps = []
for vgp in vVgps:
Vgps.append(vgp) # make a new Vgp list
SBs = []
if boot == 1:
for i in range(nb): # now do bootstrap
BVgps = []
if i % 100 == 0: print(i, ' out of ', nb)
for k in range(len(Vgps)):
random.seed()
ind = random.randint(0, len(Vgps) - 1)
BVgps.append(Vgps[ind])
SBs.append(pmag.get_Sb(BVgps))
SBs.sort()
low = int(.025 * nb)
high = int(.975 * nb)
print(len(Vgps),
'%7.1f _ %7.1f ^ %7.1f %7.1f' % (S_B, SBs[low], SBs[high], A))
else:
print(len(Vgps), '%7.1f %7.1f ' % (S_B, A))
def main():
"""
NAME
zeq_magic_redo.py
DESCRIPTION
Calculate principal components through demagnetization data using bounds and calculation type stored in "redo" file
SYNTAX
zeq_magic_redo.py [command line options]
OPTIONS
-h prints help message
-usr USER: identify user, default is ""
-f: specify input file, default is magic_measurements.txt
-F: specify output file, default is zeq_specimens.txt
-fre REDO: specify redo file, default is "zeq_redo"
-fsa SAMPFILE: specify er_samples format file, default is "er_samples.txt"
-A : don't average replicate measurements, default is yes
-crd [s,g,t] :
specify coordinate system [s,g,t] [default is specimen coordinates]
are specimen, geographic, and tilt corrected respectively
NB: you must have a SAMPFILE in this directory to rotate from specimen coordinates
-leg: attaches "Recalculated from original measurements; supercedes published results. " to comment field
INPUTS
zeq_redo format file is:
specimen_name calculation_type[DE-BFL,DE-BFL-A,DE-BFL-O,DE-BFP,DE-FM] step_min step_max component_name[A,B,C]
"""
dir_path = '.'
INCL = ["LT-NO", "LT-AF-Z", "LT-T-Z", "LT-M-Z"] # looking for demag data
beg, end, pole, geo, tilt, askave, save = 0, 0, [], 0, 0, 0, 0
user, doave, comment = "", 1, ""
geo, tilt = 0, 0
version_num = pmag.get_version()
args = sys.argv
if '-WD' in args:
ind = args.index('-WD')
dir_path = args[ind + 1]
meas_file, pmag_file, mk_file = dir_path + "/" + "magic_measurements.txt", dir_path + "/" + "zeq_specimens.txt", dir_path + "/" + "zeq_redo"
samp_file, coord = dir_path + "/" + "er_samples.txt", ""
if "-h" in args:
print(main.__doc__)
sys.exit()
if "-usr" in args:
ind = args.index("-usr")
user = sys.argv[ind + 1]
if "-A" in args: doave = 0
if "-leg" in args:
comment = "Recalculated from original measurements; supercedes published results. "
if "-f" in args:
ind = args.index("-f")
meas_file = dir_path + '/' + sys.argv[ind + 1]
if "-F" in args:
ind = args.index("-F")
pmag_file = dir_path + '/' + sys.argv[ind + 1]
if "-fre" in args:
ind = args.index("-fre")
mk_file = dir_path + "/" + args[ind + 1]
try:
mk_f = open(mk_file, 'r')
except:
print("Bad redo file")
sys.exit()
mkspec, skipped = [], []
speclist = []
for line in mk_f.readlines():
tmp = line.split()
mkspec.append(tmp)
speclist.append(tmp[0])
if "-fsa" in args:
ind = args.index("-fsa")
samp_file = dir_path + '/' + sys.argv[ind + 1]
if "-crd" in args:
ind = args.index("-crd")
coord = sys.argv[ind + 1]
if coord == "g": geo, tilt = 1, 0
if coord == "t": geo, tilt = 1, 1
#
# now get down to bidness
if geo == 1:
samp_data, file_type = pmag.magic_read(samp_file)
if file_type != 'er_samples':
print(file_type)
print("This is not a valid er_samples file ")
sys.exit()
#
#
#
meas_data, file_type = pmag.magic_read(meas_file)
if file_type != 'magic_measurements':
print(file_type)
print(file_type, "This is not a valid magic_measurements file ")
sys.exit()
#
# sort the specimen names
#
k = 0
print('Processing ', len(speclist), ' specimens - please wait')
PmagSpecs = []
while k < len(speclist):
s = speclist[k]
recnum = 0
PmagSpecRec = {}
method_codes, inst_codes = [], []
# find the data from the meas_data file for this sample
#
# collect info for the PmagSpecRec dictionary
#
meas_meth = []
spec = pmag.get_dictitem(meas_data, 'er_specimen_name', s, 'T')
if len(spec) == 0:
print('no data found for specimen: ', s)
print('delete from zeq_redo input file...., then try again')
else:
for rec in spec: # copy of vital stats to PmagSpecRec from first spec record in demag block
skip = 1
methods = rec["magic_method_codes"].split(":")
if len(set(methods) & set(INCL)) > 0:
PmagSpecRec["er_analyst_mail_names"] = user
PmagSpecRec["magic_software_packages"] = version_num
PmagSpecRec["er_specimen_name"] = s
PmagSpecRec["er_sample_name"] = rec["er_sample_name"]
PmagSpecRec["er_site_name"] = rec["er_site_name"]
PmagSpecRec["er_location_name"] = rec["er_location_name"]
if "er_expedition_name" in list(rec.keys()):
PmagSpecRec["er_expedition_name"] = rec[
"er_expedition_name"]
PmagSpecRec["er_citation_names"] = "This study"
if "magic_experiment_name" not in list(rec.keys()):
rec["magic_experiment_name"] = ""
PmagSpecRec["magic_experiment_names"] = rec[
"magic_experiment_name"]
if "magic_instrument_codes" not in list(rec.keys()):
rec["magic_instrument_codes"] = ""
inst = rec['magic_instrument_codes'].split(":")
for I in inst:
if I not in inst_codes: # copy over instruments
inst_codes.append(I)
meths = rec["magic_method_codes"].split(":")
for meth in meths:
if meth.strip() not in meas_meth:
meas_meth.append(meth)
if "LP-DIR-AF" in meas_meth or "LT-AF-Z" in meas_meth:
PmagSpecRec["measurement_step_unit"] = "T"
if "LP-DIR-AF" not in method_codes:
method_codes.append("LP-DIR-AF")
if "LP-DIR-T" in meas_meth or "LT-T-Z" in meas_meth:
PmagSpecRec["measurement_step_unit"] = "K"
if "LP-DIR-T" not in method_codes:
method_codes.append("LP-DIR-T")
if "LP-DIR-M" in meas_meth or "LT-M-Z" in meas_meth:
PmagSpecRec["measurement_step_unit"] = "J"
if "LP-DIR-M" not in method_codes:
method_codes.append("LP-DIR-M")
#
#
datablock, units = pmag.find_dmag_rec(
s, spec) # fish out the demag data for this specimen
#
if len(datablock) < 2 or s not in speclist:
k += 1
# print 'skipping ', s,len(datablock)
else:
#
# find replicate measurements at given treatment step and average them
#
# step_meth,avedata=pmag.vspec(data)
#
# if len(avedata) != len(datablock):
# if doave==1:
# method_codes.append("DE-VM")
# datablock=avedata
#
# do geo or stratigraphic correction now
#
if geo == 1 or tilt == 1:
# find top priority orientation method
orient, az_type = pmag.get_orient(
samp_data, PmagSpecRec["er_sample_name"])
if az_type not in method_codes: method_codes.append(az_type)
#
# if tilt selected, get stratigraphic correction
#
tiltblock, geoblock = [], []
for rec in datablock:
if "sample_azimuth" in list(
orient.keys()) and orient["sample_azimuth"] != "":
d_geo, i_geo = pmag.dogeo(
rec[1], rec[2], float(orient["sample_azimuth"]),
float(orient["sample_dip"]))
geoblock.append(
[rec[0], d_geo, i_geo, rec[3], rec[4], rec[5]])
if tilt == 1 and "sample_bed_dip_direction" in list(
orient.keys()):
d_tilt, i_tilt = pmag.dotilt(
d_geo, i_geo,
float(orient["sample_bed_dip_direction"]),
float(orient["sample_bed_dip"]))
tiltblock.append([
rec[0], d_tilt, i_tilt, rec[3], rec[4], rec[5]
])
elif tilt == 1:
if PmagSpecRec["er_sample_name"] not in skipped:
print('no tilt correction for ',
PmagSpecRec["er_sample_name"],
' skipping....')
skipped.append(PmagSpecRec["er_sample_name"])
else:
if PmagSpecRec["er_sample_name"] not in skipped:
print('no geographic correction for ',
PmagSpecRec["er_sample_name"],
' skipping....')
skipped.append(PmagSpecRec["er_sample_name"])
#
# get beg_pca, end_pca, pca
if PmagSpecRec['er_sample_name'] not in skipped:
compnum = -1
for spec in mkspec:
if spec[0] == s:
CompRec = {}
for key in list(PmagSpecRec.keys()):
CompRec[key] = PmagSpecRec[key]
compnum += 1
calculation_type = spec[1]
beg = float(spec[2])
end = float(spec[3])
if len(spec) > 4:
comp_name = spec[4]
else:
comp_name = string.uppercase[compnum]
CompRec['specimen_comp_name'] = comp_name
if beg < float(datablock[0][0]):
beg = float(datablock[0][0])
if end > float(datablock[-1][0]):
end = float(datablock[-1][0])
for l in range(len(datablock)):
if datablock[l][0] == beg: beg_pca = l
if datablock[l][0] == end: end_pca = l
if geo == 1 and tilt == 0:
mpars = pmag.domean(geoblock, beg_pca, end_pca,
calculation_type)
if mpars["specimen_direction_type"] != "Error":
CompRec["specimen_dec"] = '%7.1f ' % (
mpars["specimen_dec"])
CompRec["specimen_inc"] = '%7.1f ' % (
mpars["specimen_inc"])
CompRec["specimen_tilt_correction"] = '0'
if geo == 1 and tilt == 1:
mpars = pmag.domean(tiltblock, beg_pca, end_pca,
calculation_type)
if mpars["specimen_direction_type"] != "Error":
CompRec["specimen_dec"] = '%7.1f ' % (
mpars["specimen_dec"])
CompRec["specimen_inc"] = '%7.1f ' % (
mpars["specimen_inc"])
CompRec["specimen_tilt_correction"] = '100'
if geo == 0 and tilt == 0:
mpars = pmag.domean(datablock, beg_pca, end_pca,
calculation_type)
if mpars["specimen_direction_type"] != "Error":
CompRec["specimen_dec"] = '%7.1f ' % (
mpars["specimen_dec"])
CompRec["specimen_inc"] = '%7.1f ' % (
mpars["specimen_inc"])
CompRec["specimen_tilt_correction"] = '-1'
if mpars["specimen_direction_type"] == "Error":
pass
else:
CompRec["measurement_step_min"] = '%8.3e ' % (
datablock[beg_pca][0])
try:
CompRec["measurement_step_max"] = '%8.3e ' % (
datablock[end_pca][0])
except:
print('error in end_pca ',
PmagSpecRec['er_specimen_name'])
CompRec["specimen_correction"] = 'u'
if calculation_type != 'DE-FM':
CompRec["specimen_mad"] = '%7.1f ' % (
mpars["specimen_mad"])
CompRec["specimen_alpha95"] = ""
else:
CompRec["specimen_mad"] = ""
CompRec["specimen_alpha95"] = '%7.1f ' % (
mpars["specimen_alpha95"])
CompRec["specimen_n"] = '%i ' % (
mpars["specimen_n"])
CompRec["specimen_dang"] = '%7.1f ' % (
mpars["specimen_dang"])
CompMeths = []
for meth in method_codes:
if meth not in CompMeths:
CompMeths.append(meth)
if calculation_type not in CompMeths:
CompMeths.append(calculation_type)
if geo == 1: CompMeths.append("DA-DIR-GEO")
if tilt == 1: CompMeths.append("DA-DIR-TILT")
if "DE-BFP" not in calculation_type:
CompRec["specimen_direction_type"] = 'l'
else:
CompRec["specimen_direction_type"] = 'p'
CompRec["magic_method_codes"] = ""
if len(CompMeths) != 0:
methstring = ""
for meth in CompMeths:
methstring = methstring + ":" + meth
CompRec[
"magic_method_codes"] = methstring.strip(
':')
CompRec["specimen_description"] = comment
if len(inst_codes) != 0:
inststring = ""
for inst in inst_codes:
inststring = inststring + ":" + inst
CompRec[
"magic_instrument_codes"] = inststring.strip(
':')
PmagSpecs.append(CompRec)
k += 1
pmag.magic_write(pmag_file, PmagSpecs, 'pmag_specimens')
print("Recalculated specimen data stored in ", pmag_file)
def main():
"""
NAME
fishqq.py
DESCRIPTION
makes qq plot from dec,inc input data
INPUT FORMAT
takes dec/inc pairs in space delimited file
SYNTAX
fishqq.py [command line options]
OPTIONS
-h help message
-f FILE, specify file on command line
-F FILE, specify output file for statistics
-sav save and quit [saves as input file name plus fmt extension]
-fmt specify format for output [png, eps, svg, pdf]
OUTPUT:
Dec Inc N Mu Mu_crit Me Me_crit Y/N
where direction is the principal component and Y/N is Fisherian or not
separate lines for each mode with N >=10 (N and R)
"""
fmt,plot='svg',0
outfile=""
if '-h' in sys.argv: # check if help is needed
print main.__doc__
sys.exit() # graceful quit
elif '-f' in sys.argv: # ask for filename
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
f=open(file,'rU')
data=f.readlines()
if '-F' in sys.argv:
ind=sys.argv.index('-F')
outfile=open(sys.argv[ind+1],'w') # open output file
if '-sav' in sys.argv: plot=1
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
DIs,nDIs,rDIs= [],[],[] # set up list for data
for line in data: # read in the data from standard input
if '\t' in line:
rec=line.split('\t') # split each line on space to get records
else:
rec=line.split() # split each line on space to get records
DIs.append([float(rec[0]),float(rec[1])]) # append data to Inc
# split into two modes
ppars=pmag.doprinc(DIs) # get principal directions
for rec in DIs:
angle=pmag.angle([rec[0],rec[1]],[ppars['dec'],ppars['inc']])
if angle>90.:
rDIs.append(rec)
else:
nDIs.append(rec)
#
if len(rDIs) >=10 or len(nDIs) >=10:
D1,I1=[],[]
QQ={'unf1':1,'exp1':2}
pmagplotlib.plot_init(QQ['unf1'],5,5)
pmagplotlib.plot_init(QQ['exp1'],5,5)
if len(nDIs) < 10:
ppars=pmag.doprinc(rDIs) # get principal directions
Drbar,Irbar=ppars['dec']-180.,-ppars['inc']
Nr=len(rDIs)
for di in rDIs:
d,irot=pmag.dotilt(di[0],di[1],Drbar-180.,90.-Irbar) # rotate to mean
drot=d-180.
if drot<0:drot=drot+360.
D1.append(drot)
I1.append(irot)
Dtit='Mode 2 Declinations'
Itit='Mode 2 Inclinations'
else:
ppars=pmag.doprinc(nDIs) # get principal directions
Dnbar,Inbar=ppars['dec'],ppars['inc']
Nn=len(nDIs)
for di in nDIs:
d,irot=pmag.dotilt(di[0],di[1],Dnbar-180.,90.-Inbar) # rotate to mean
drot=d-180.
if drot<0:drot=drot+360.
D1.append(drot)
I1.append(irot)
Dtit='Mode 1 Declinations'
Itit='Mode 1 Inclinations'
Mu_n,Mu_ncr=pmagplotlib.plotQQunf(QQ['unf1'],D1,Dtit) # make plot
Me_n,Me_ncr=pmagplotlib.plotQQexp(QQ['exp1'],I1,Itit) # make plot
#print Mu_n,Mu_ncr,Me_n, Me_ncr
if outfile!="":
# Dec Inc N Mu Mu_crit Me Me_crit Y/N
if Mu_n<=Mu_ncr and Me_n<=Me_ncr:
F='Y'
else:
F='N'
outstring='%7.1f %7.1f %i %5.3f %5.3f %5.3f %5.3f %s \n'%(Dnbar,Inbar,Nn,Mu_n,Mu_ncr,Me_n,Me_ncr,F)
outfile.write(outstring)
else:
print 'you need N> 10 for at least one mode'
sys.exit()
if len(rDIs)>10 and len(nDIs)>10:
D2,I2=[],[]
QQ['unf2']=3
QQ['exp2']=4
pmagplotlib.plot_init(QQ['unf2'],5,5)
pmagplotlib.plot_init(QQ['exp2'],5,5)
ppars=pmag.doprinc(rDIs) # get principal directions
Drbar,Irbar=ppars['dec']-180.,-ppars['inc']
Nr=len(rDIs)
for di in rDIs:
d,irot=pmag.dotilt(di[0],di[1],Drbar-180.,90.-Irbar) # rotate to mean
drot=d-180.
if drot<0:drot=drot+360.
D2.append(drot)
I2.append(irot)
Dtit='Mode 2 Declinations'
Itit='Mode 2 Inclinations'
Mu_r,Mu_rcr=pmagplotlib.plotQQunf(QQ['unf2'],D2,Dtit) # make plot
Me_r,Me_rcr=pmagplotlib.plotQQexp(QQ['exp2'],I2,Itit) # make plot
if outfile!="":
# Dec Inc N Mu Mu_crit Me Me_crit Y/N
if Mu_r<=Mu_rcr and Me_r<=Me_rcr:
F='Y'
else:
F='N'
outstring='%7.1f %7.1f %i %5.3f %5.3f %5.3f %5.3f %s \n'%(Drbar,Irbar,Nr,Mu_r,Mu_rcr,Me_r,Me_rcr,F)
outfile.write(outstring)
files={}
for key in QQ.keys():
files[key]=file+'_'+key+'.'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['eq']='Equal Area Plot'
EQ = pmagplotlib.addBorders(EQ,titles,black,purple)
pmagplotlib.saveP(QQ,files)
elif plot==1:
pmagplotlib.saveP(QQ,files)
else:
pmagplotlib.drawFIGS(QQ)
ans=raw_input(" S[a]ve to save plot, [q]uit without saving: ")
if ans=="a": pmagplotlib.saveP(QQ,files)
def main():
"""
NAME
scalc.py
DESCRIPTION
calculates Sb from VGP Long,VGP Lat,Directional kappa,Site latitude data
SYNTAX
scalc -h [command line options] [< standard input]
INPUT
takes space delimited files with PLong, PLat,[kappa, N_site, slat]
OPTIONS
-h prints help message and quits
-f FILE: specify input file
-c cutoff: specify VGP colatitude cutoff value
-k cutoff: specify kappa cutoff
-v : use the VanDammme criterion
-a: use antipodes of reverse data: default is to use only normal
-C: use all data without regard to polarity
-b: do a bootstrap for confidence
-p: do relative to principle axis
NOTES
if kappa, N_site, lat supplied, will consider within site scatter
OUTPUT
N Sb Sb_lower Sb_upper Co-lat. Cutoff
"""
coord,kappa,cutoff="0",0,90.
nb,anti,boot=1000,0,0
all=0
n=0
v=0
spin=1
coord_key='tilt_correction'
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index("-f")
in_file=sys.argv[ind+1]
f=open(in_file,'rU')
lines=f.readlines()
else:
lines=sys.stdin.readlines()
if '-c' in sys.argv:
ind=sys.argv.index('-c')
cutoff=float(sys.argv[ind+1])
if '-k' in sys.argv:
ind=sys.argv.index('-k')
kappa=float(sys.argv[ind+1])
if '-n' in sys.argv:
ind=sys.argv.index('-n')
n=int(sys.argv[ind+1])
if '-a' in sys.argv: anti=1
if '-C' in sys.argv: cutoff=180. # no cutoff
if '-b' in sys.argv: boot=1
if '-v' in sys.argv: v=1
if '-p' in sys.argv: spin=0
#
#
# find desired vgp lat,lon, kappa,N_site data:
#
A,Vgps,slats,Pvgps=180.,[],[],[]
for line in lines:
if '\t' in line:
rec=line.replace('\n','').split('\t') # split each line on space to get records
else:
rec=line.replace('\n','').split() # split each line on space to get records
vgp={}
vgp['vgp_lon'],vgp['vgp_lat']=rec[0],rec[1]
Pvgps.append([float(rec[0]),float(rec[1])])
if anti==1:
if float(vgp['vgp_lat'])<0:
vgp['vgp_lat']='%7.1f'%(-1*float(vgp['vgp_lat']))
vgp['vgp_lon']='%7.1f'%(float(vgp['vgp_lon'])-180.)
if len(rec)==5:
vgp['average_k'],vgp['average_nn'],vgp['average_lat']=rec[2],rec[3],rec[4]
slats.append(float(rec[4]))
else:
vgp['average_k'],vgp['average_nn'],vgp['average_lat']="0","0","0"
if 90.-(float(vgp['vgp_lat']))<=cutoff and float(vgp['average_k'])>=kappa and int(vgp['average_nn'])>=n: Vgps.append(vgp)
if spin==0: # do transformation to pole
ppars=pmag.doprinc(Pvgps)
for vgp in Vgps:
vlon,vlat=pmag.dotilt(float(vgp['vgp_lon']),float(vgp['vgp_lat']),ppars['dec']-180.,90.-ppars['inc'])
vgp['vgp_lon']=vlon
vgp['vgp_lat']=vlat
vgp['average_k']="0"
S_B= pmag.get_Sb(Vgps)
A=cutoff
if v==1:
thetamax,A=181.,180.
vVgps,cnt=[],0
for vgp in Vgps:vVgps.append(vgp) # make a copy of Vgps
while thetamax>A:
thetas=[]
A=1.8*S_B+5
cnt+=1
for vgp in vVgps:thetas.append(90.-(float(vgp['vgp_lat'])))
thetas.sort()
thetamax=thetas[-1]
if thetamax<A:break
nVgps=[]
for vgp in vVgps:
if 90.-(float(vgp['vgp_lat']))<thetamax:nVgps.append(vgp)
vVgps=[]
for vgp in nVgps:vVgps.append(vgp)
S_B= pmag.get_Sb(vVgps)
Vgps=[]
for vgp in vVgps:Vgps.append(vgp) # make a new Vgp list
SBs,Ns=[],[]
if boot==1:
print 'please be patient... bootstrapping'
for i in range(nb): # now do bootstrap
BVgps=[]
for k in range(len(Vgps)):
ind=random.randint(0,len(Vgps)-1)
random.jumpahead(int(ind*1000))
BVgps.append(Vgps[ind])
SBs.append(pmag.get_Sb(BVgps))
SBs.sort()
low=int(.025*nb)
high=int(.975*nb)
print len(Vgps),'%7.1f %7.1f %7.1f %7.1f '%(S_B,SBs[low],SBs[high],A)
else:
print len(Vgps),'%7.1f %7.1f '%(S_B,A)
if len(slats)>2:
stats= pmag.gausspars(slats)
print 'mean lat = ','%7.1f'%(stats[0])
def main():
"""
NAME
scalc_magic.py
DESCRIPTION
calculates Sb from pmag_results files
SYNTAX
scalc_magic -h [command line options]
INPUT
takes magic formatted pmag_results table
pmag_result_name must start with "VGP: Site"
must have average_lat if spin axis is reference
OPTIONS
-h prints help message and quits
-f FILE: specify input results file, default is 'pmag_results.txt'
-c cutoff: specify VGP colatitude cutoff value
-k cutoff: specify kappa cutoff
-crd [s,g,t]: specify coordinate system, default is geographic
-v : use the VanDammme criterion
-a: use antipodes of reverse data: default is to use only normal
-C: use all data without regard to polarity
-r: use reverse data only
-p: do relative to principle axis
-b: do bootstrap confidence bounds
OUTPUT:
if option -b used: N, S_B, lower and upper bounds
otherwise: N, S_B, cutoff
"""
in_file='pmag_results.txt'
coord,kappa,cutoff="0",1.,90.
nb,anti,spin,v,boot=1000,0,1,0,0
coord_key='tilt_correction'
rev=0
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index("-f")
in_file=sys.argv[ind+1]
if '-c' in sys.argv:
ind=sys.argv.index('-c')
cutoff=float(sys.argv[ind+1])
if '-k' in sys.argv:
ind=sys.argv.index('-k')
kappa=float(sys.argv[ind+1])
if '-crd' in sys.argv:
ind=sys.argv.index("-crd")
coord=sys.argv[ind+1]
if coord=='s':coord="-1"
if coord=='g':coord="0"
if coord=='t':coord="100"
if '-a' in sys.argv: anti=1
if '-C' in sys.argv: cutoff=180. # no cutoff
if '-r' in sys.argv: rev=1
if '-p' in sys.argv: spin=0
if '-v' in sys.argv: v=1
if '-b' in sys.argv: boot=1
data,file_type=pmag.magic_read(in_file)
#
#
# find desired vgp lat,lon, kappa,N_site data:
#
#
#
A,Vgps,Pvgps=180.,[],[]
VgpRecs=pmag.get_dictitem(data,'vgp_lat','','F') # get all non-blank vgp latitudes
VgpRecs=pmag.get_dictitem(VgpRecs,'vgp_lon','','F') # get all non-blank vgp longitudes
SiteRecs=pmag.get_dictitem(VgpRecs,'data_type','i','T') # get VGPs (as opposed to averaged)
SiteRecs=pmag.get_dictitem(SiteRecs,coord_key,coord,'T') # get right coordinate system
for rec in SiteRecs:
if anti==1:
if 90.-abs(float(rec['vgp_lat']))<=cutoff and float(rec['average_k'])>=kappa:
if float(rec['vgp_lat'])<0:
rec['vgp_lat']='%7.1f'%(-1*float(rec['vgp_lat']))
rec['vgp_lon']='%7.1f'%(float(rec['vgp_lon'])-180.)
Vgps.append(rec)
Pvgps.append([float(rec['vgp_lon']),float(rec['vgp_lat'])])
elif rev==0: # exclude normals
if 90.-(float(rec['vgp_lat']))<=cutoff and float(rec['average_k'])>=kappa:
Vgps.append(rec)
Pvgps.append([float(rec['vgp_lon']),float(rec['vgp_lat'])])
else: # include normals
if 90.-abs(float(rec['vgp_lat']))<=cutoff and float(rec['average_k'])>=kappa:
if float(rec['vgp_lat'])<0:
rec['vgp_lat']='%7.1f'%(-1*float(rec['vgp_lat']))
rec['vgp_lon']='%7.1f'%(float(rec['vgp_lon'])-180.)
Vgps.append(rec)
Pvgps.append([float(rec['vgp_lon']),float(rec['vgp_lat'])])
if spin==0: # do transformation to pole
ppars=pmag.doprinc(Pvgps)
for vgp in Vgps:
vlon,vlat=pmag.dotilt(float(vgp['vgp_lon']),float(vgp['vgp_lat']),ppars['dec']-180.,90.-ppars['inc'])
vgp['vgp_lon']=vlon
vgp['vgp_lat']=vlat
vgp['average_k']="0"
S_B= pmag.get_Sb(Vgps)
A=cutoff
if v==1:
thetamax,A=181.,180.
vVgps,cnt=[],0
for vgp in Vgps:vVgps.append(vgp) # make a copy of Vgps
while thetamax>A:
thetas=[]
A=1.8*S_B+5
cnt+=1
for vgp in vVgps:thetas.append(90.-(float(vgp['vgp_lat'])))
thetas.sort()
thetamax=thetas[-1]
if thetamax<A:break
nVgps=[]
for vgp in vVgps:
if 90.-(float(vgp['vgp_lat']))<thetamax:nVgps.append(vgp)
vVgps=[]
for vgp in nVgps:vVgps.append(vgp)
S_B= pmag.get_Sb(vVgps)
Vgps=[]
for vgp in vVgps:Vgps.append(vgp) # make a new Vgp list
SBs=[]
if boot==1:
for i in range(nb): # now do bootstrap
BVgps=[]
if i%100==0: print(i,' out of ',nb)
for k in range(len(Vgps)):
random.seed()
ind=random.randint(0,len(Vgps)-1)
BVgps.append(Vgps[ind])
SBs.append(pmag.get_Sb(BVgps))
SBs.sort()
low=int(.025*nb)
high=int(.975*nb)
print(len(Vgps),'%7.1f _ %7.1f ^ %7.1f %7.1f'%(S_B,SBs[low],SBs[high],A))
else:
print(len(Vgps),'%7.1f %7.1f '%(S_B,A))
def main():
"""
NAME
nrm_specimens_magic.py
DESCRIPTION
converts NRM data in a magic_measurements type file to
geographic and tilt corrected data in a pmag_specimens type file
SYNTAX
nrm_specimens_magic.py [-h][command line options]
OPTIONS:
-h prints the help message and quits
-f MFILE: specify input file
-fsa SFILE: specify er_samples format file [with orientations]
-F PFILE: specify output file
-A do not average replicate measurements
-crd [g, t]: specify coordinate system ([g]eographic or [t]ilt adjusted)
NB: you must have the SFILE in this directory
DEFAULTS
MFILE: magic_measurements.txt
PFILE: nrm_specimens.txt
SFILE: er_samples.txt
coord: specimen
average replicate measurements?: YES
"""
#
# define some variables
#
beg, end, pole, geo, tilt, askave, save = 0, 0, [], 0, 0, 0, 0
samp_file = 1
args = sys.argv
geo, tilt, orient = 0, 0, 0
doave = 1
user, comment, doave, coord = "", "", 1, ""
dir_path = "."
if "-h" in args:
print main.__doc__
sys.exit()
if "-WD" in sys.argv:
ind = sys.argv.index("-WD")
dir_path = sys.argv[ind + 1]
meas_file = dir_path + "/magic_measurements.txt"
pmag_file = dir_path + "/nrm_specimens.txt"
samp_file = dir_path + "/er_samples.txt"
if "-A" in args:
doave = 0
if "-f" in args:
ind = args.index("-f")
meas_file = sys.argv[ind + 1]
if "-F" in args:
ind = args.index("-F")
pmag_file = dir_path + "/" + sys.argv[ind + 1]
speclist = []
if "-fsa" in args:
ind = args.index("-fsa")
samp_file = dir_path + "/" + sys.argv[ind + 1]
if "-crd" in args:
ind = args.index("-crd")
coord = sys.argv[ind + 1]
if coord == "g":
geo, orient = 1, 1
if coord == "t":
tilt, orient, geo = 1, 1, 1
#
# read in data
if samp_file != "":
samp_data, file_type = pmag.magic_read(samp_file)
if file_type != "er_samples":
print file_type
print "This is not a valid er_samples file "
sys.exit()
else:
print samp_file, " read in with ", len(samp_data), " records"
else:
print "no orientations - will create file in specimen coordinates"
geo, tilt, orient = 0, 0, 0
#
#
meas_data, file_type = pmag.magic_read(meas_file)
if file_type != "magic_measurements":
print file_type
print file_type, "This is not a valid magic_measurements file "
sys.exit()
#
if orient == 1:
# set orientation priorities
SO_methods = []
orientation_priorities = {
"0": "SO-SUN",
"1": "SO-GPS-DIFF",
"2": "SO-SIGHT-BACK",
"3": "SO-CMD-NORTH",
"4": "SO-MAG",
}
for rec in samp_data:
if "magic_method_codes" in rec:
methlist = rec["magic_method_codes"]
for meth in methlist.split(":"):
if "SO" in meth and "SO-POM" not in meth.strip():
if meth.strip() not in SO_methods:
SO_methods.append(meth.strip())
#
# sort the sample names
#
sids = pmag.get_specs(meas_data)
#
#
PmagSpecRecs = []
for s in sids:
skip = 0
recnum = 0
PmagSpecRec = {}
PmagSpecRec["er_analyst_mail_names"] = user
method_codes, inst_code = [], ""
# find the data from the meas_data file for this sample
#
# collect info for the PmagSpecRec dictionary
#
meas_meth = []
for rec in meas_data: # copy of vital stats to PmagSpecRec from first spec record
if rec["er_specimen_name"] == s:
PmagSpecRec["er_specimen_name"] = s
PmagSpecRec["er_sample_name"] = rec["er_sample_name"]
PmagSpecRec["er_site_name"] = rec["er_site_name"]
PmagSpecRec["er_location_name"] = rec["er_location_name"]
PmagSpecRec["er_citation_names"] = "This study"
PmagSpecRec["magic_instrument_codes"] = ""
if "magic_experiment_name" not in rec.keys():
rec["magic_experiment_name"] = ""
if "magic_instrument_codes" not in rec.keys():
rec["magic_instrument_codes"] = ""
else:
PmagSpecRec["magic_experiment_names"] = rec["magic_experiment_name"]
if len(rec["magic_instrument_codes"]) > len(inst_code):
inst_code = rec["magic_instrument_codes"]
PmagSpecRec["magic_instrument_codes"] = inst_code # copy over instruments
break
#
# now check for correct method labels for all measurements
#
nrm_data = []
for meas_rec in meas_data:
if meas_rec["er_specimen_name"] == PmagSpecRec["er_specimen_name"]:
meths = meas_rec["magic_method_codes"].split(":")
for meth in meths:
if meth.strip() not in meas_meth:
meas_meth.append(meth)
if "LT-NO" in meas_meth:
nrm_data.append(meas_rec)
#
data, units = pmag.find_dmag_rec(s, nrm_data)
#
datablock = data
#
# find replicate measurements at NRM step and average them
#
Specs = []
if doave == 1:
step_meth, avedata = pmag.vspec(data)
if len(avedata) != len(datablock):
method_codes.append("DE-VM")
SpecRec = avedata[0]
print "averaging data "
else:
SpecRec = data[0]
Specs.append(SpecRec)
else:
for spec in data:
Specs.append(spec)
for SpecRec in Specs:
#
# do geo or stratigraphic correction now
#
if geo == 1:
#
# find top priority orientation method
redo, p = 1, 0
if len(SO_methods) <= 1:
az_type = SO_methods[0]
orient = pmag.find_samp_rec(PmagSpecRec["er_sample_name"], samp_data, az_type)
if orient["sample_azimuth"] != "":
method_codes.append(az_type)
redo = 0
while redo == 1:
if p >= len(orientation_priorities):
print "no orientation data for ", s
skip, redo = 1, 0
break
az_type = orientation_priorities[str(p)]
orient = pmag.find_samp_rec(PmagSpecRec["er_sample_name"], samp_data, az_type)
if orient["sample_azimuth"] != "":
method_codes.append(az_type.strip())
redo = 0
elif orient["sample_azimuth"] == "":
p += 1
#
# if stratigraphic selected, get stratigraphic correction
#
if skip == 0 and orient["sample_azimuth"] != "" and orient["sample_dip"] != "":
d_geo, i_geo = pmag.dogeo(SpecRec[1], SpecRec[2], orient["sample_azimuth"], orient["sample_dip"])
SpecRec[1] = d_geo
SpecRec[2] = i_geo
if tilt == 1 and "sample_bed_dip" in orient.keys() and orient["sample_bed_dip"] != "":
d_tilt, i_tilt = pmag.dotilt(
d_geo, i_geo, orient["sample_bed_dip_direction"], orient["sample_bed_dip"]
)
SpecRec[1] = d_tilt
SpecRec[2] = i_tilt
if skip == 0:
PmagSpecRec["specimen_dec"] = "%7.1f " % (SpecRec[1])
PmagSpecRec["specimen_inc"] = "%7.1f " % (SpecRec[2])
if geo == 1 and tilt == 0:
PmagSpecRec["specimen_tilt_correction"] = "0"
if geo == 1 and tilt == 1:
PmagSpecRec["specimen_tilt_correction"] = "100"
if geo == 0 and tilt == 0:
PmagSpecRec["specimen_tilt_correction"] = "-1"
PmagSpecRec["specimen_direction_type"] = "l"
PmagSpecRec["magic_method_codes"] = "LT-NO"
if len(method_codes) != 0:
methstring = ""
for meth in method_codes:
methstring = methstring + ":" + meth
PmagSpecRec["magic_method_codes"] = methstring[1:]
PmagSpecRec["specimen_description"] = "NRM data"
PmagSpecRecs.append(PmagSpecRec)
pmag.magic_write(pmag_file, PmagSpecRecs, "pmag_specimens")
print "Data saved in ", pmag_file
def main():
"""
NAME
di_rot.py
DESCRIPTION
rotates set of directions to new coordinate system
SYNTAX
di_rot.py [command line options]
OPTIONS
-h prints help message and quits
-f specify input file, default is standard input
-F specify output file, default is standard output
-D D specify Dec of new coordinate system, default is 0
-I I specify Inc of new coordinate system, default is 90
INTPUT/OUTPUT
dec inc [space delimited]
"""
D, I = 0., 90.
outfile = ""
infile = ""
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]
data = numpy.loadtxt(infile)
else:
data = numpy.loadtxt(sys.stdin, dtype=numpy.float)
if '-F' in sys.argv:
ind = sys.argv.index('-F')
outfile = sys.argv[ind + 1]
out = open(outfile, 'w')
if '-D' in sys.argv:
ind = sys.argv.index('-D')
D = float(sys.argv[ind + 1])
if '-I' in sys.argv:
ind = sys.argv.index('-I')
I = float(sys.argv[ind + 1])
if len(data.shape) > 1: # 2-D array
N = data.shape[0]
DipDir, Dip = numpy.ones(N, dtype=numpy.float).transpose() * (
D - 180.), numpy.ones(N, dtype=numpy.float).transpose() * (90. - I)
data = data.transpose()
data = numpy.array([data[0], data[1], DipDir, Dip]).transpose()
drot, irot = pmag.dotilt_V(data)
drot = (drot - 180.) % 360. #
for k in range(N):
if outfile == "":
print '%7.1f %7.1f ' % (drot[k], irot[k])
else:
out.write('%7.1f %7.1f\n' % (drot[k], irot[k]))
else:
d, i = pmag.dotilt(data[0], data[1], (D - 180.), 90. - I)
if outfile == "":
print '%7.1f %7.1f ' % ((d - 180.) % 360., i)
else:
out.write('%7.1f %7.1f\n' % ((d - 180.) % 360., i))