def main():
"""
NAME
fishrot.py
DESCRIPTION
generates set of Fisher distribed data from specified distribution
SYNTAX
fishrot.py [-h][-i][command line options]
OPTIONS
-h prints help message and quits
-i for interactive entry
-k kappa specify kappa, default is 20
-n N specify N, default is 100
-D D specify mean Dec, default is 0
-I I specify mean Inc, default is 90
where:
kappa: fisher distribution concentration parameter
N: number of directions desired
OUTPUT
dec, inc
"""
N,kappa,D,I=100,20.,0.,90.
if len(sys.argv)!=0 and '-h' in sys.argv:
print main.__doc__
sys.exit()
elif '-i' in sys.argv:
ans=raw_input(' Kappa: ')
kappa=float(ans)
ans=raw_input(' N: ')
N=int(ans)
ans=raw_input(' Mean Dec: ')
D=float(ans)
ans=raw_input(' Mean Inc: ')
I=float(ans)
else:
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 '-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])
for k in range(N):
dec,inc= pmag.fshdev(kappa) # send kappa to fshdev
drot,irot=pmag.dodirot(dec,inc,D,I)
print '%7.1f %7.1f ' % (drot,irot)
def get_fish(dir):
"""
generate fisher distributed points according to the supplied parameters
(includes dec,inc,n,k) in a pandas object.
"""
tempD,tempI=[],[]
for k in range(int(dir.n)):
dec,inc=pmag.fshdev(dir.k)
drot,irot=pmag.dodirot(dec,inc,dir.dec,dir.inc)
tempD.append(drot)
tempI.append(irot)
return np.column_stack((tempD,tempI))
def fishrot(kappa,N,D,I): #from Pmagpy
"""
Description: generates set of Fisher distributed data from specified distribution
Input: kappa (fisher distribution concentration parameter), number of desired subsamples, Dec and Inc
Output: list with N pairs of Dec, Inc.
"""
out_d=[]
out=[]
for k in range(N):
dec,inc= pmag.fshdev(kappa) # send kappa to fshdev
drot,irot=pmag.dodirot(dec,inc,D,I)
out_d=[drot,irot]
out.append(out_d)
return out
def ifishrot(k=20,n=100,Dec=0,Inc=90):
"""
Generates Fisher distributed unit vectors from a specified distribution
using the pmag.py fshdev and dodirot functions
Parameters
----------
k kappa precision parameter (default is 20)
n number of vectors to determine (default is 100)
Dec mean declination of data set (default is 0)
Inc mean inclination of data set (default is 90)
"""
directions=[]
for data in range(n):
dec,inc=pmag.fshdev(k)
drot,irot=pmag.dodirot(dec,inc,Dec,Inc)
directions.append([drot,irot,1.])
return directions
def main():
"""
NAME
EI.py [command line options]
DESCRIPTION
Finds bootstrap confidence bounds on Elongation and Inclination data
SYNTAX
EI.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE specifies input file
-p do parametric bootstrap
INPUT
dec/inc pairs
OUTPUT
makes a plot of the E/I pair and bootstrapped confidence bounds
along with the E/I trend predicted by the TK03 field model
prints out:
Io (mean inclination), I_lower and I_upper are 95% confidence bounds on inclination
Eo (elongation), E_lower and E_upper are 95% confidence bounds on elongation
Edec,Einc are the elongation direction
"""
par=0
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-f' in sys.argv:
ind=sys.argv.index('-f')
file=open(sys.argv[ind+1],'rU')
if '-p' in sys.argv: par=1
rseed,nb,data=10,5000,[]
upper,lower=int(round(.975*nb)),int(round(.025*nb))
Es,Is=[],[]
PLTS={'eq':1,'ei':2}
pmagplotlib.plot_init(PLTS['eq'],5,5)
pmagplotlib.plot_init(PLTS['ei'],5,5)
# poly_tab= [ 3.07448925e-06, -3.49555831e-04, -1.46990847e-02, 2.90905483e+00]
poly_new= [ 3.15976125e-06, -3.52459817e-04, -1.46641090e-02, 2.89538539e+00]
# poly_cp88= [ 5.34558576e-06, -7.70922659e-04, 5.18529685e-03, 2.90941351e+00]
# poly_qc96= [ 7.08210133e-06, -8.79536536e-04, 1.09625547e-03, 2.92513660e+00]
# poly_cj98=[ 6.56675431e-06, -7.91823539e-04, -1.08211350e-03, 2.80557710e+00]
# poly_tk03_g20= [ 4.96757685e-06, -6.02256097e-04, -5.96103272e-03, 2.84227449e+00]
# poly_tk03_g30= [ 7.82525963e-06, -1.39781724e-03, 4.47187092e-02, 2.54637535e+00]
# poly_gr99_g=[ 1.24362063e-07, -1.69383384e-04, -4.24479223e-03, 2.59257437e+00]
# poly_gr99_e=[ 1.26348154e-07, 2.01691452e-04, -4.99142308e-02, 3.69461060e+00]
E_EI,E_tab,E_new,E_cp88,E_cj98,E_qc96,E_tk03_g20=[],[],[],[],[],[],[]
E_tk03_g30,E_gr99_g,E_gr99_e=[],[],[]
I2=range(0,90,5)
for inc in I2:
E_new.append(EI(inc,poly_new)) # use the polynomial from Tauxe et al. (2008)
pmagplotlib.plotEI(PLTS['ei'],E_new,I2,1)
if '-f' in sys.argv:
random.seed(rseed)
for line in file.readlines():
rec=line.split()
dec=float(rec[0])
inc=float(rec[1])
if par==1:
if len(rec)==4:
N=(int(rec[2])) # append n
K=float(rec[3]) # append k
rec=[dec,inc,N,K]
data.append(rec)
else:
rec=[dec,inc]
data.append(rec)
pmagplotlib.plotEQ(PLTS['eq'],data,'Data')
ppars=pmag.doprinc(data)
n=ppars["N"]
Io=ppars['inc']
Edec=ppars['Edir'][0]
Einc=ppars['Edir'][1]
Eo=(ppars['tau2']/ppars['tau3'])
b=0
print 'doing bootstrap - be patient'
while b<nb:
bdata=[]
for j in range(n):
boot=random.randint(0,n-1)
random.jumpahead(rseed)
if par==1:
DIs=[]
D,I,N,K=data[boot][0],data[boot][1],data[boot][2],data[boot][3]
for k in range(N):
dec,inc=pmag.fshdev(K)
drot,irot=pmag.dodirot(dec,inc,D,I)
DIs.append([drot,irot])
fpars=pmag.fisher_mean(DIs)
bdata.append([fpars['dec'],fpars['inc'],1.]) # replace data[boot] with parametric dec,inc
else:
bdata.append(data[boot])
ppars=pmag.doprinc(bdata)
Is.append(ppars['inc'])
Es.append(ppars['tau2']/ppars['tau3'])
b+=1
if b%100==0:print b
Is.sort()
Es.sort()
x,std=pmag.gausspars(Es)
stderr=std/math.sqrt(len(data))
pmagplotlib.plotX(PLTS['ei'],Io,Eo,Is[lower],Is[upper],Es[lower],Es[upper],'b-')
# pmagplotlib.plotX(PLTS['ei'],Io,Eo,Is[lower],Is[upper],Eo-stderr,Eo+stderr,'b-')
print 'Io, Eo, I_lower, I_upper, E_lower, E_upper, Edec, Einc'
print '%7.1f %4.2f %7.1f %7.1f %4.2f %4.2f %7.1f %7.1f' %(Io,Eo,Is[lower],Is[upper],Es[lower],Es[upper], Edec,Einc)
# print '%7.1f %4.2f %7.1f %7.1f %4.2f %4.2f' %(Io,Eo,Is[lower],Is[upper],Eo-stderr,Eo+stderr)
pmagplotlib.drawFIGS(PLTS)
files,fmt={},'svg'
for key in PLTS.keys():
files[key]=key+'.'+fmt
ans=raw_input(" S[a]ve to save plot, [q]uit without saving: ")
if ans=="a": pmagplotlib.saveP(PLTS,files)
def main():
"""
NAME
foldtest.py
DESCRIPTION
does a fold test (Tauxe, 2010) on data
INPUT FORMAT
dec inc dip_direction dip
SYNTAX
foldtest.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE file with input data
-F FILE for confidence bounds on fold test
-u ANGLE (circular standard deviation) for uncertainty on bedding poles
-b MIN MAX bounds for quick search of percent untilting [default is -10 to 150%]
-n NB number of bootstrap samples [default is 1000]
-fmt FMT, specify format - default is svg
OUTPUT PLOTS
Geographic: is an equal area projection of the input data in
original coordinates
Stratigraphic: is an equal area projection of the input data in
tilt adjusted coordinates
% Untilting: The dashed (red) curves are representative plots of
maximum eigenvalue (tau_1) as a function of untilting
The solid line is the cumulative distribution of the
% Untilting required to maximize tau for all the
bootstrapped data sets. The dashed vertical lines
are 95% confidence bounds on the % untilting that yields
the most clustered result (maximum tau_1).
Command line: prints out the bootstrapped iterations and
finally the confidence bounds on optimum untilting.
If the 95% conf bounds include 0, then a pre-tilt magnetization is indicated
If the 95% conf bounds include 100, then a post-tilt magnetization is indicated
If the 95% conf bounds exclude both 0 and 100, syn-tilt magnetization is
possible as is vertical axis rotation or other pathologies
Geographic: is an equal area projection of the input data in
OPTIONAL OUTPUT FILE:
The output file has the % untilting within the 95% confidence bounds
nd the number of bootstrap samples
"""
kappa=0
fmt='svg'
nb=1000 # number of bootstraps
min,max=-10,150
if '-h' in sys.argv: # check if help is needed
print main.__doc__
sys.exit() # graceful quit
if '-F' in sys.argv:
ind=sys.argv.index('-F')
outfile=open(sys.argv[ind+1],'w')
else:
outfile=""
if '-f' in sys.argv:
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
DIDDs=numpy.loadtxt(file)
else:
print main.__doc__
sys.exit()
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
if '-b' in sys.argv:
ind=sys.argv.index('-b')
min=float(sys.argv[ind+1])
max=float(sys.argv[ind+2])
if '-n' in sys.argv:
ind=sys.argv.index('-n')
nb=int(sys.argv[ind+1])
if '-u' in sys.argv:
ind=sys.argv.index('-u')
csd=float(sys.argv[ind+1])
kappa=(81./csd)**2
#
# get to work
#
PLTS={'geo':1,'strat':2,'taus':3} # make plot dictionary
pmagplotlib.plot_init(PLTS['geo'],5,5)
pmagplotlib.plot_init(PLTS['strat'],5,5)
pmagplotlib.plot_init(PLTS['taus'],5,5)
pmagplotlib.plotEQ(PLTS['geo'],DIDDs,'Geographic')
D,I=pmag.dotilt_V(DIDDs)
TCs=numpy.array([D,I]).transpose()
pmagplotlib.plotEQ(PLTS['strat'],TCs,'Stratigraphic')
pmagplotlib.drawFIGS(PLTS)
Percs=range(min,max)
Cdf,Untilt=[],[]
pylab.figure(num=PLTS['taus'])
print 'doing ',nb,' iterations...please be patient.....'
for n in range(nb): # do bootstrap data sets - plot first 25 as dashed red line
if n%50==0:print n
Taus=[] # set up lists for taus
PDs=pmag.pseudo(DIDDs)
if kappa!=0:
for k in range(len(PDs)):
d,i=pmag.fshdev(kappa)
dipdir,dip=pmag.dodirot(d,i,PDs[k][2],PDs[k][3])
PDs[k][2]=dipdir
PDs[k][3]=dip
for perc in Percs:
tilt=numpy.array([1.,1.,1.,0.01*perc])
D,I=pmag.dotilt_V(PDs*tilt)
TCs=numpy.array([D,I]).transpose()
ppars=pmag.doprinc(TCs) # get principal directions
Taus.append(ppars['tau1'])
if n<25:pylab.plot(Percs,Taus,'r--')
Untilt.append(Percs[Taus.index(numpy.max(Taus))]) # tilt that gives maximum tau
Cdf.append(float(n)/float(nb))
pylab.plot(Percs,Taus,'k')
pylab.xlabel('% Untilting')
pylab.ylabel('tau_1 (red), CDF (green)')
Untilt.sort() # now for CDF of tilt of maximum tau
pylab.plot(Untilt,Cdf,'g')
lower=int(.025*nb)
upper=int(.975*nb)
pylab.axvline(x=Untilt[lower],ymin=0,ymax=1,linewidth=1,linestyle='--')
pylab.axvline(x=Untilt[upper],ymin=0,ymax=1,linewidth=1,linestyle='--')
tit= '%i - %i %s'%(Untilt[lower],Untilt[upper],'Percent Unfolding')
print tit
print 'range of all bootstrap samples: ', Untilt[0], ' - ', Untilt[-1]
pylab.title(tit)
outstring= '%i - %i; %i\n'%(Untilt[lower],Untilt[upper],nb)
if outfile!="":outfile.write(outstring)
pmagplotlib.drawFIGS(PLTS)
ans= raw_input('S[a]ve all figures, <Return> to quit ')
if ans!='a':
print "Good bye"
sys.exit()
else:
files={}
for key in PLTS.keys():
files[key]=('foldtest_'+'%s'%(key.strip()[:2])+'.'+fmt)
pmagplotlib.saveP(PLTS,files)
def main():
"""
NAME
watsonsV.py
DESCRIPTION
calculates Watson's V statistic from input files
INPUT FORMAT
takes dec/inc as first two columns in two space delimited files
SYNTAX
watsonsV.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE (with optional second)
-f2 FILE (second file)
-ant, flip antipodal directions to opposite direction
in first file if only one file or flip all in second, if two files
-P (don't save or show plot)
-sav save figure and quit silently
-fmt [png,svg,eps,pdf,jpg] format for saved figure
OUTPUT
Watson's V and the Monte Carlo Critical Value Vc.
in plot, V is solid and Vc is dashed.
"""
Flip=0
show,plot=1,0
fmt='svg'
file2=""
if '-h' in sys.argv: # check if help is needed
print main.__doc__
sys.exit() # graceful quit
if '-ant' in sys.argv: Flip=1
if '-sav' in sys.argv: show,plot=0,1 # don't display, but do save plot
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
if '-P' in sys.argv: show=0 # don't display or save plot
if '-f' in sys.argv:
ind=sys.argv.index('-f')
file1=sys.argv[ind+1]
data=numpy.loadtxt(file1).transpose()
D1=numpy.array([data[0],data[1]]).transpose()
else:
print "-f is required"
print main.__doc__
sys.exit()
if '-f2' in sys.argv:
ind=sys.argv.index('-f2')
file2=sys.argv[ind+1]
data2=numpy.loadtxt(file2).transpose()
D2=numpy.array([data2[0],data2[1]]).transpose()
if Flip==1:
D2,D=pmag.flip(D2) # D2 are now flipped
if len(D2)!=0:
if len(D)!=0:
D2=numpy.concatenate(D,D2) # put all in D2
elif len(D)!=0:
D2=D
else:
print 'length of second file is zero'
sys.exit()
elif Flip==1:D2,D1=pmag.flip(D1) # peel out antipodal directions, put in D2
#
counter,NumSims=0,5000
#
# first calculate the fisher means and cartesian coordinates of each set of Directions
#
pars_1=pmag.fisher_mean(D1)
pars_2=pmag.fisher_mean(D2)
#
# get V statistic for these
#
V=pmag.vfunc(pars_1,pars_2)
#
# do monte carlo simulation of datasets with same kappas, but common mean
#
Vp=[] # set of Vs from simulations
if show==1:print "Doing ",NumSims," simulations"
for k in range(NumSims):
counter+=1
if counter==50:
if show==1:print k+1
counter=0
Dirp=[]
# get a set of N1 fisher distributed vectors with k1, calculate fisher stats
for i in range(pars_1["n"]):
Dirp.append(pmag.fshdev(pars_1["k"]))
pars_p1=pmag.fisher_mean(Dirp)
# get a set of N2 fisher distributed vectors with k2, calculate fisher stats
Dirp=[]
for i in range(pars_2["n"]):
Dirp.append(pmag.fshdev(pars_2["k"]))
pars_p2=pmag.fisher_mean(Dirp)
# get the V for these
Vk=pmag.vfunc(pars_p1,pars_p2)
Vp.append(Vk)
#
# sort the Vs, get Vcrit (95th one)
#
Vp.sort()
k=int(.95*NumSims)
if show==1:
print "Watson's V, Vcrit: "
print ' %10.1f %10.1f'%(V,Vp[k])
if show==1 or plot==1:
CDF={'cdf':1}
pmagplotlib.plot_init(CDF['cdf'],5,5)
pmagplotlib.plotCDF(CDF['cdf'],Vp,"Watson's V",'r',"")
pmagplotlib.plotVs(CDF['cdf'],[V],'g','-')
pmagplotlib.plotVs(CDF['cdf'],[Vp[k]],'b','--')
if plot==0:pmagplotlib.drawFIGS(CDF)
files={}
if file2!="":
files['cdf']='WatsonsV_'+file1+'_'+file2+'.'+fmt
else:
files['cdf']='WatsonsV_'+file1+'.'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['cdf']='Cumulative Distribution'
CDF = pmagplotlib.addBorders(CDF,titles,black,purple)
pmagplotlib.saveP(CDF,files)
elif plot==0:
ans=raw_input(" S[a]ve to save plot, [q]uit without saving: ")
if ans=="a": pmagplotlib.saveP(CDF,files)
if plot==1: # save and quit silently
pmagplotlib.saveP(CDF,files)
def watson_common_mean(Data1,Data2,NumSims=5000,plot='no'):
"""
Conduct a Watson V test for a common mean on two declination, inclination data sets
This function calculates Watson's V statistic from input files through Monte Carlo
simulation in order to test whether two populations of directional data could have
been drawn from a common mean. The critical angle between the two sample mean
directions and the corresponding McFadden and McElhinny (1990) classification is printed.
Required Arguments
----------
Data1 : a list of directional data [dec,inc]
Data2 : a list of directional data [dec,inc]
Optional Arguments
----------
NumSims : number of Monte Carlo simulations (default is 5000)
plot : the default is no plot ('no'). Putting 'yes' will the plot the CDF from
the Monte Carlo simulations.
"""
pars_1=pmag.fisher_mean(Data1)
pars_2=pmag.fisher_mean(Data2)
cart_1=pmag.dir2cart([pars_1["dec"],pars_1["inc"],pars_1["r"]])
cart_2=pmag.dir2cart([pars_2['dec'],pars_2['inc'],pars_2["r"]])
Sw=pars_1['k']*pars_1['r']+pars_2['k']*pars_2['r'] # k1*r1+k2*r2
xhat_1=pars_1['k']*cart_1[0]+pars_2['k']*cart_2[0] # k1*x1+k2*x2
xhat_2=pars_1['k']*cart_1[1]+pars_2['k']*cart_2[1] # k1*y1+k2*y2
xhat_3=pars_1['k']*cart_1[2]+pars_2['k']*cart_2[2] # k1*z1+k2*z2
Rw=np.sqrt(xhat_1**2+xhat_2**2+xhat_3**2)
V=2*(Sw-Rw)
# keep weighted sum for later when determining the "critical angle"
# let's save it as Sr (notation of McFadden and McElhinny, 1990)
Sr=Sw
# do monte carlo simulation of datasets with same kappas as data,
# but a common mean
counter=0
Vp=[] # set of Vs from simulations
for k in range(NumSims):
# get a set of N1 fisher distributed vectors with k1,
# calculate fisher stats
Dirp=[]
for i in range(pars_1["n"]):
Dirp.append(pmag.fshdev(pars_1["k"]))
pars_p1=pmag.fisher_mean(Dirp)
# get a set of N2 fisher distributed vectors with k2,
# calculate fisher stats
Dirp=[]
for i in range(pars_2["n"]):
Dirp.append(pmag.fshdev(pars_2["k"]))
pars_p2=pmag.fisher_mean(Dirp)
# get the V for these
Vk=pmag.vfunc(pars_p1,pars_p2)
Vp.append(Vk)
# sort the Vs, get Vcrit (95th percentile one)
Vp.sort()
k=int(.95*NumSims)
Vcrit=Vp[k]
# equation 18 of McFadden and McElhinny, 1990 calculates the critical
# value of R (Rwc)
Rwc=Sr-(Vcrit/2)
# following equation 19 of McFadden and McElhinny (1990) the critical
# angle is calculated. If the observed angle (also calculated below)
# between the data set means exceeds the critical angle the hypothesis
# of a common mean direction may be rejected at the 95% confidence
# level. The critical angle is simply a different way to present
# Watson's V parameter so it makes sense to use the Watson V parameter
# in comparison with the critical value of V for considering the test
# results. What calculating the critical angle allows for is the
# classification of McFadden and McElhinny (1990) to be made
# for data sets that are consistent with sharing a common mean.
k1=pars_1['k']
k2=pars_2['k']
R1=pars_1['r']
R2=pars_2['r']
critical_angle=np.degrees(np.arccos(((Rwc**2)-((k1*R1)**2)
-((k2*R2)**2))/
(2*k1*R1*k2*R2)))
D1=(pars_1['dec'],pars_1['inc'])
D2=(pars_2['dec'],pars_2['inc'])
angle=pmag.angle(D1,D2)
print "Results of Watson V test: "
print ""
print "Watson's V: " '%.1f' %(V)
print "Critical value of V: " '%.1f' %(Vcrit)
if V<Vcrit:
print '"Pass": Since V is less than Vcrit, the null hypothesis'
print 'that the two populations are drawn from distributions'
print 'that share a common mean direction can not be rejected.'
elif V>Vcrit:
print '"Fail": Since V is greater than Vcrit, the two means can'
print 'be distinguished at the 95% confidence level.'
print ""
print "M&M1990 classification:"
print ""
print "Angle between data set means: " '%.1f'%(angle)
print "Critical angle for M&M1990: " '%.1f'%(critical_angle)
if V>Vcrit:
print ""
elif V<Vcrit:
if critical_angle<5:
print "The McFadden and McElhinny (1990) classification for"
print "this test is: 'A'"
elif critical_angle<10:
print "The McFadden and McElhinny (1990) classification for"
print "this test is: 'B'"
elif critical_angle<20:
print "The McFadden and McElhinny (1990) classification for"
print "this test is: 'C'"
else:
print "The McFadden and McElhinny (1990) classification for"
print "this test is: 'INDETERMINATE;"
if plot=='yes':
CDF={'cdf':1}
#pmagplotlib.plot_init(CDF['cdf'],5,5)
p1 = pmagplotlib.plotCDF(CDF['cdf'],Vp,"Watson's V",'r',"")
p2 = pmagplotlib.plotVs(CDF['cdf'],[V],'g','-')
p3 = pmagplotlib.plotVs(CDF['cdf'],[Vp[k]],'b','--')
pmagplotlib.drawFIGS(CDF)
def main():
"""
NAME
revtest_MM1990.py
DESCRIPTION
calculates Watson's V statistic from input files through Monte Carlo simulation in order to test whether normal and reversed populations could have been drawn from a common mean (equivalent to watsonV.py). Also provides the critical angle between the two sample mean directions and the corresponding McFadden and McElhinny (1990) classification.
INPUT FORMAT
takes dec/inc as first two columns in two space delimited files (one file for normal directions, one file for reversed directions).
SYNTAX
revtest_MM1990.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE
-f2 FILE
-P (don't plot the Watson V cdf)
OUTPUT
Watson's V between the two populations and the Monte Carlo Critical Value Vc.
M&M1990 angle, critical angle and classification
Plot of Watson's V CDF from Monte Carlo simulation (red line), V is solid and Vc is dashed.
"""
D1, D2 = [], []
plot = 1
Flip = 1
if "-h" in sys.argv: # check if help is needed
print main.__doc__
sys.exit() # graceful quit
if "-P" in sys.argv:
plot = 0
if "-f" in sys.argv:
ind = sys.argv.index("-f")
file1 = sys.argv[ind + 1]
f1 = open(file1, "rU")
for line in f1.readlines():
rec = line.split()
Dec, Inc = float(rec[0]), float(rec[1])
D1.append([Dec, Inc, 1.0])
f1.close()
if "-f2" in sys.argv:
ind = sys.argv.index("-f2")
file2 = sys.argv[ind + 1]
f2 = open(file2, "rU")
print "be patient, your computer is doing 5000 simulations..."
for line in f2.readlines():
rec = line.split()
Dec, Inc = float(rec[0]), float(rec[1])
D2.append([Dec, Inc, 1.0])
f2.close()
# take the antipode for the directions in file 2
D2_flip = []
for rec in D2:
d, i = (rec[0] - 180.0) % 360.0, -rec[1]
D2_flip.append([d, i, 1.0])
pars_1 = pmag.fisher_mean(D1)
pars_2 = pmag.fisher_mean(D2_flip)
cart_1 = pmag.dir2cart([pars_1["dec"], pars_1["inc"], pars_1["r"]])
cart_2 = pmag.dir2cart([pars_2["dec"], pars_2["inc"], pars_2["r"]])
Sw = pars_1["k"] * pars_1["r"] + pars_2["k"] * pars_2["r"] # k1*r1+k2*r2
xhat_1 = pars_1["k"] * cart_1[0] + pars_2["k"] * cart_2[0] # k1*x1+k2*x2
xhat_2 = pars_1["k"] * cart_1[1] + pars_2["k"] * cart_2[1] # k1*y1+k2*y2
xhat_3 = pars_1["k"] * cart_1[2] + pars_2["k"] * cart_2[2] # k1*z1+k2*z2
Rw = numpy.sqrt(xhat_1 ** 2 + xhat_2 ** 2 + xhat_3 ** 2)
V = 2 * (Sw - Rw)
#
# keep weighted sum for later when determining the "critical angle" let's save it as Sr (notation of McFadden and McElhinny, 1990)
#
Sr = Sw
#
# do monte carlo simulation of datasets with same kappas, but common mean
#
counter, NumSims = 0, 5000
Vp = [] # set of Vs from simulations
for k in range(NumSims):
#
# get a set of N1 fisher distributed vectors with k1, calculate fisher stats
#
Dirp = []
for i in range(pars_1["n"]):
Dirp.append(pmag.fshdev(pars_1["k"]))
pars_p1 = pmag.fisher_mean(Dirp)
#
# get a set of N2 fisher distributed vectors with k2, calculate fisher stats
#
Dirp = []
for i in range(pars_2["n"]):
Dirp.append(pmag.fshdev(pars_2["k"]))
pars_p2 = pmag.fisher_mean(Dirp)
#
# get the V for these
#
Vk = pmag.vfunc(pars_p1, pars_p2)
Vp.append(Vk)
#
# sort the Vs, get Vcrit (95th percentile one)
#
Vp.sort()
k = int(0.95 * NumSims)
Vcrit = Vp[k]
#
# equation 18 of McFadden and McElhinny, 1990 calculates the critical value of R (Rwc)
#
Rwc = Sr - (Vcrit / 2)
#
# following equation 19 of McFadden and McElhinny (1990) the critical angle is calculated.
#
k1 = pars_1["k"]
k2 = pars_2["k"]
R1 = pars_1["r"]
R2 = pars_2["r"]
critical_angle = numpy.degrees(
numpy.arccos(((Rwc ** 2) - ((k1 * R1) ** 2) - ((k2 * R2) ** 2)) / (2 * k1 * R1 * k2 * R2))
)
D1_mean = (pars_1["dec"], pars_1["inc"])
D2_mean = (pars_2["dec"], pars_2["inc"])
angle = pmag.angle(D1_mean, D2_mean)
#
# print the results of the test
#
print ""
print "Results of Watson V test: "
print ""
print "Watson's V: " "%.1f" % (V)
print "Critical value of V: " "%.1f" % (Vcrit)
if V < Vcrit:
print '"Pass": Since V is less than Vcrit, the null hypothesis that the two populations are drawn from distributions that share a common mean direction (antipodal to one another) cannot be rejected.'
elif V > Vcrit:
print '"Fail": Since V is greater than Vcrit, the two means can be distinguished at the 95% confidence level.'
print ""
print "M&M1990 classification:"
print ""
print "Angle between data set means: " "%.1f" % (angle)
print "Critical angle of M&M1990: " "%.1f" % (critical_angle)
if V > Vcrit:
print ""
elif V < Vcrit:
if critical_angle < 5:
print "The McFadden and McElhinny (1990) classification for this test is: 'A'"
elif critical_angle < 10:
print "The McFadden and McElhinny (1990) classification for this test is: 'B'"
elif critical_angle < 20:
print "The McFadden and McElhinny (1990) classification for this test is: 'C'"
else:
print "The McFadden and McElhinny (1990) classification for this test is: 'INDETERMINATE;"
if plot == 1:
CDF = {"cdf": 1}
pmagplotlib.plot_init(CDF["cdf"], 5, 5)
p1 = pmagplotlib.plotCDF(CDF["cdf"], Vp, "Watson's V", "r", "")
p2 = pmagplotlib.plotVs(CDF["cdf"], [V], "g", "-")
p3 = pmagplotlib.plotVs(CDF["cdf"], [Vp[k]], "b", "--")
pmagplotlib.drawFIGS(CDF)
files, fmt = {}, "svg"
if file2 != "":
files["cdf"] = "WatsonsV_" + file1 + "_" + file2 + "." + fmt
else:
files["cdf"] = "WatsonsV_" + file1 + "." + fmt
if pmagplotlib.isServer:
black = "#000000"
purple = "#800080"
titles = {}
titles["cdf"] = "Cumulative Distribution"
CDF = pmagplotlib.addBorders(CDF, titles, black, purple)
pmagplotlib.saveP(CDF, files)
else:
ans = raw_input(" S[a]ve to save plot, [q]uit without saving: ")
if ans == "a":
pmagplotlib.saveP(CDF, files)
def watson_common_mean(Data1, Data2, NumSims=5000, plot='no'):
"""
Conduct a Watson V test for a common mean on two declination, inclination data sets
This function calculates Watson's V statistic from input files through Monte Carlo
simulation in order to test whether two populations of directional data could have
been drawn from a common mean. The critical angle between the two sample mean
directions and the corresponding McFadden and McElhinny (1990) classification is printed.
Required Arguments
----------
Data1 : a list of directional data [dec,inc]
Data2 : a list of directional data [dec,inc]
Optional Arguments
----------
NumSims : number of Monte Carlo simulations (default is 5000)
plot : the default is no plot ('no'). Putting 'yes' will the plot the CDF from
the Monte Carlo simulations.
"""
pars_1 = pmag.fisher_mean(Data1)
pars_2 = pmag.fisher_mean(Data2)
cart_1 = pmag.dir2cart([pars_1["dec"], pars_1["inc"], pars_1["r"]])
cart_2 = pmag.dir2cart([pars_2['dec'], pars_2['inc'], pars_2["r"]])
Sw = pars_1['k'] * pars_1['r'] + pars_2['k'] * pars_2['r'] # k1*r1+k2*r2
xhat_1 = pars_1['k'] * cart_1[0] + pars_2['k'] * cart_2[0] # k1*x1+k2*x2
xhat_2 = pars_1['k'] * cart_1[1] + pars_2['k'] * cart_2[1] # k1*y1+k2*y2
xhat_3 = pars_1['k'] * cart_1[2] + pars_2['k'] * cart_2[2] # k1*z1+k2*z2
Rw = np.sqrt(xhat_1**2 + xhat_2**2 + xhat_3**2)
V = 2 * (Sw - Rw)
# keep weighted sum for later when determining the "critical angle"
# let's save it as Sr (notation of McFadden and McElhinny, 1990)
Sr = Sw
# do monte carlo simulation of datasets with same kappas as data,
# but a common mean
counter = 0
Vp = [] # set of Vs from simulations
for k in range(NumSims):
# get a set of N1 fisher distributed vectors with k1,
# calculate fisher stats
Dirp = []
for i in range(pars_1["n"]):
Dirp.append(pmag.fshdev(pars_1["k"]))
pars_p1 = pmag.fisher_mean(Dirp)
# get a set of N2 fisher distributed vectors with k2,
# calculate fisher stats
Dirp = []
for i in range(pars_2["n"]):
Dirp.append(pmag.fshdev(pars_2["k"]))
pars_p2 = pmag.fisher_mean(Dirp)
# get the V for these
Vk = pmag.vfunc(pars_p1, pars_p2)
Vp.append(Vk)
# sort the Vs, get Vcrit (95th percentile one)
Vp.sort()
k = int(.95 * NumSims)
Vcrit = Vp[k]
# equation 18 of McFadden and McElhinny, 1990 calculates the critical
# value of R (Rwc)
Rwc = Sr - (Vcrit / 2)
# following equation 19 of McFadden and McElhinny (1990) the critical
# angle is calculated. If the observed angle (also calculated below)
# between the data set means exceeds the critical angle the hypothesis
# of a common mean direction may be rejected at the 95% confidence
# level. The critical angle is simply a different way to present
# Watson's V parameter so it makes sense to use the Watson V parameter
# in comparison with the critical value of V for considering the test
# results. What calculating the critical angle allows for is the
# classification of McFadden and McElhinny (1990) to be made
# for data sets that are consistent with sharing a common mean.
k1 = pars_1['k']
k2 = pars_2['k']
R1 = pars_1['r']
R2 = pars_2['r']
critical_angle = np.degrees(
np.arccos(((Rwc**2) - ((k1 * R1)**2) - ((k2 * R2)**2)) /
(2 * k1 * R1 * k2 * R2)))
D1 = (pars_1['dec'], pars_1['inc'])
D2 = (pars_2['dec'], pars_2['inc'])
angle = pmag.angle(D1, D2)
print "Results of Watson V test: "
print ""
print "Watson's V: " '%.1f' % (V)
print "Critical value of V: " '%.1f' % (Vcrit)
if V < Vcrit:
print '"Pass": Since V is less than Vcrit, the null hypothesis'
print 'that the two populations are drawn from distributions'
print 'that share a common mean direction can not be rejected.'
elif V > Vcrit:
print '"Fail": Since V is greater than Vcrit, the two means can'
print 'be distinguished at the 95% confidence level.'
print ""
print "M&M1990 classification:"
print ""
print "Angle between data set means: " '%.1f' % (angle)
print "Critical angle for M&M1990: " '%.1f' % (critical_angle)
if V > Vcrit:
print ""
elif V < Vcrit:
if critical_angle < 5:
print "The McFadden and McElhinny (1990) classification for"
print "this test is: 'A'"
elif critical_angle < 10:
print "The McFadden and McElhinny (1990) classification for"
print "this test is: 'B'"
elif critical_angle < 20:
print "The McFadden and McElhinny (1990) classification for"
print "this test is: 'C'"
else:
print "The McFadden and McElhinny (1990) classification for"
print "this test is: 'INDETERMINATE;"
if plot == 'yes':
CDF = {'cdf': 1}
#pmagplotlib.plot_init(CDF['cdf'],5,5)
p1 = pmagplotlib.plotCDF(CDF['cdf'], Vp, "Watson's V", 'r', "")
p2 = pmagplotlib.plotVs(CDF['cdf'], [V], 'g', '-')
p3 = pmagplotlib.plotVs(CDF['cdf'], [Vp[k]], 'b', '--')
pmagplotlib.drawFIGS(CDF)
def spitout(kappa):
dec,inc= pmag.fshdev(kappa) # send kappa to fshdev
print '%7.1f %7.1f ' % (dec,inc)
return
def main():
"""
NAME
watsonsV.py
DESCRIPTION
calculates Watson's V statistic from input files
INPUT FORMAT
takes dec/inc as first two columns in two space delimited files
SYNTAX
watsonsV.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE (with optional second)
-f2 FILE (second file)
-ant, flip antipodal directions in FILE to opposite direction
-P (don't plot)
OUTPUT
Watson's V and the Monte Carlo Critical Value Vc.
in plot, V is solid and Vc is dashed.
"""
D1,D2=[],[]
Flip=0
plot=1
if '-h' in sys.argv: # check if help is needed
print main.__doc__
sys.exit() # graceful quit
if '-ant' in sys.argv: Flip=1
if '-P' in sys.argv: plot=0
if '-f' in sys.argv:
ind=sys.argv.index('-f')
file1=sys.argv[ind+1]
f=open(file1,'rU')
for line in f.readlines():
rec=line.split()
Dec,Inc=float(rec[0]),float(rec[1])
D1.append([Dec,Inc,1.])
f.close()
if '-f2' in sys.argv:
ind=sys.argv.index('-f2')
file2=sys.argv[ind+1]
f=open(file2,'rU')
for line in f.readlines():
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
Dec,Inc=float(rec[0]),float(rec[1])
if Flip==0:
D2.append([Dec,Inc,1.])
else:
D1.append([Dec,Inc,1.])
f.close()
if Flip==1:
D1,D2=pmag.flip(D1)
#
counter,NumSims=0,5000
#
# first calculate the fisher means and cartesian coordinates of each set of Directions
#
pars_1=pmag.fisher_mean(D1)
pars_2=pmag.fisher_mean(D2)
#
# get V statistic for these
#
V=pmag.vfunc(pars_1,pars_2)
#
# do monte carlo simulation of datasets with same kappas, but common mean
#
Vp=[] # set of Vs from simulations
if plot==1:print "Doing ",NumSims," simulations"
for k in range(NumSims):
counter+=1
if counter==50:
if plot==1:print k+1
counter=0
Dirp=[]
# get a set of N1 fisher distributed vectors with k1, calculate fisher stats
for i in range(pars_1["n"]):
Dirp.append(pmag.fshdev(pars_1["k"]))
pars_p1=pmag.fisher_mean(Dirp)
# get a set of N2 fisher distributed vectors with k2, calculate fisher stats
Dirp=[]
for i in range(pars_2["n"]):
Dirp.append(pmag.fshdev(pars_2["k"]))
pars_p2=pmag.fisher_mean(Dirp)
# get the V for these
Vk=pmag.vfunc(pars_p1,pars_p2)
Vp.append(Vk)
#
# sort the Vs, get Vcrit (95th one)
#
Vp.sort()
k=int(.95*NumSims)
print "Watson's V, Vcrit: "
print ' %10.1f %10.1f'%(V,Vp[k])
if plot==1:
CDF={'cdf':1}
pmagplotlib.plot_init(CDF['cdf'],5,5)
pmagplotlib.plotCDF(CDF['cdf'],Vp,"Watson's V",'r',"")
pmagplotlib.plotVs(CDF['cdf'],[V],'g','-')
pmagplotlib.plotVs(CDF['cdf'],[Vp[k]],'b','--')
pmagplotlib.drawFIGS(CDF)
files,fmt={},'svg'
if file2!="":
files['cdf']='WatsonsV_'+file1+'_'+file2+'.'+fmt
else:
files['cdf']='WatsonsV_'+file1+'.'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['cdf']='Cumulative Distribution'
CDF = pmagplotlib.addBorders(CDF,titles,black,purple)
pmagplotlib.saveP(CDF,files)
else:
ans=raw_input(" S[a]ve to save plot, [q]uit without saving: ")
if ans=="a": pmagplotlib.saveP(CDF,files)
def main():
"""
NAME
foldtest.py
DESCRIPTION
does a fold test (Tauxe, 2008) on data
INPUT FORMAT
dec inc dip_direction dip
SYNTAX
foldtest.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE
-u ANGLE (circular standard deviation) for uncertainty on bedding poles
-b MIN MAX bounds for quick search of percent untilting [default is -10 to 150%]
-n NB number of bootstrap samples [default is 1000]
OUTPUT
Geographic: is an equal area projection of the input data in
original coordinates
Stratigraphic: is an equal area projection of the input data in
tilt adjusted coordinates
% Untilting: The dashed (red) curves are representative plots of
maximum eigenvalue (tau_1) as a function of untilting
The solid line is the cumulative distribution of the
% Untilting required to maximize tau for all the
bootstrapped data sets. The dashed vertical lines
are 95% confidence bounds on the % untilting that yields
the most clustered result (maximum tau_1).
Command line: prints out the bootstrapped iterations and
finally the confidence bounds on optimum untilting.
If the 95% conf bounds include 0, then a pre-tilt magnetization is indicated
If the 95% conf bounds include 100, then a post-tilt magnetization is indicated
If the 95% conf bounds exclude both 0 and 100, syn-tilt magnetization is
possible as is vertical axis rotation or other pathologies
"""
kappa=0
nb=1000 # number of bootstraps
min,max=-10,150
if '-h' in sys.argv: # check if help is needed
print main.__doc__
sys.exit() # graceful quit
if '-f' in sys.argv:
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
f=open(file,'rU')
data=f.readlines()
else:
print main.__doc__
sys.exit()
if '-b' in sys.argv:
ind=sys.argv.index('-b')
min=float(sys.argv[ind+1])
max=float(sys.argv[ind+2])
if '-n' in sys.argv:
ind=sys.argv.index('-n')
nb=int(sys.argv[ind+1])
if '-u' in sys.argv:
ind=sys.argv.index('-u')
csd=float(sys.argv[ind+1])
kappa=(81./csd)**2
#
# get to work
#
PLTS={'geo':1,'strat':2,'taus':3} # make plot dictionary
pmagplotlib.plot_init(PLTS['geo'],5,5)
pmagplotlib.plot_init(PLTS['strat'],5,5)
pmagplotlib.plot_init(PLTS['taus'],5,5)
DIDDs= [] # set up list for dec inc dip_direction, dip
for line in data: # read in the data from standard input
rec=line.split() # split each line on space to get records
DIDDs.append([float(rec[0]),float(rec[1]),float(rec[2]),float(rec[3])])
pmagplotlib.plotEQ(PLTS['geo'],DIDDs,'Geographic')
TCs=[]
for k in range(len(DIDDs)):
drot,irot=pmag.dotilt(DIDDs[k][0],DIDDs[k][1],DIDDs[k][2],DIDDs[k][3])
TCs.append([drot,irot,1.])
pmagplotlib.plotEQ(PLTS['strat'],TCs,'Stratigraphic')
Percs=range(min,max)
Cdf,Untilt=[],[]
pylab.figure(num=PLTS['taus'])
print 'doing ',nb,' iterations...please be patient.....'
for n in range(nb): # do bootstrap data sets - plot first 25 as dashed red line
if n%50==0:print n
Taus=[] # set up lists for taus
PDs=pmag.pseudo(DIDDs)
if kappa!=0:
for k in range(len(PDs)):
d,i=pmag.fshdev(kappa)
dipdir,dip=pmag.dodirot(d,i,PDs[k][2],PDs[k][3])
PDs[k][2]=dipdir
PDs[k][3]=dip
for perc in Percs:
tilt=0.01*perc
TCs=[]
for k in range(len(PDs)):
drot,irot=pmag.dotilt(PDs[k][0],PDs[k][1],PDs[k][2],tilt*PDs[k][3])
TCs.append([drot,irot,1.])
ppars=pmag.doprinc(TCs) # get principal directions
Taus.append(ppars['tau1'])
if n<25:pylab.plot(Percs,Taus,'r--')
Untilt.append(Percs[Taus.index(numpy.max(Taus))]) # tilt that gives maximum tau
Cdf.append(float(n)/float(nb))
pylab.plot(Percs,Taus,'k')
pylab.xlabel('% Untilting')
pylab.ylabel('tau_1 (red), CDF (green)')
Untilt.sort() # now for CDF of tilt of maximum tau
pylab.plot(Untilt,Cdf,'g')
lower=int(.025*nb)
upper=int(.975*nb)
pylab.axvline(x=Untilt[lower],ymin=0,ymax=1,linewidth=1,linestyle='--')
pylab.axvline(x=Untilt[upper],ymin=0,ymax=1,linewidth=1,linestyle='--')
tit= '%i - %i %s'%(Untilt[lower],Untilt[upper],'Percent Unfolding')
print tit
print 'range of all bootstrap samples: ', Untilt[0], ' - ', Untilt[-1]
pylab.title(tit)
try:
raw_input('Return to save all figures, cntl-d to quit\n')
except:
print "Good bye"
sys.exit()
files={}
for key in PLTS.keys():
files[key]=('fold_'+'%s'%(key.strip()[:2])+'.svg')
pmagplotlib.saveP(PLTS,files)
def main():
"""
NAME
foldtest_magic.py
DESCRIPTION
does a fold test (Tauxe, 2010) on data
INPUT FORMAT
pmag_specimens format file, er_samples.txt format file (for bedding)
SYNTAX
foldtest_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f pmag_sites formatted file [default is pmag_sites.txt]
-fsa er_samples formatted file [default is er_samples.txt]
-exc use pmag_criteria.txt to set acceptance criteria
-n NB, set number of bootstraps, default is 1000
-b MIN, MAX, set bounds for untilting, default is -10, 150
-fmt FMT, specify format - default is svg
OUTPUT
Geographic: is an equal area projection of the input data in
original coordinates
Stratigraphic: is an equal area projection of the input data in
tilt adjusted coordinates
% Untilting: The dashed (red) curves are representative plots of
maximum eigenvalue (tau_1) as a function of untilting
The solid line is the cumulative distribution of the
% Untilting required to maximize tau for all the
bootstrapped data sets. The dashed vertical lines
are 95% confidence bounds on the % untilting that yields
the most clustered result (maximum tau_1).
Command line: prints out the bootstrapped iterations and
finally the confidence bounds on optimum untilting.
If the 95% conf bounds include 0, then a pre-tilt magnetization is indicated
If the 95% conf bounds include 100, then a post-tilt magnetization is indicated
If the 95% conf bounds exclude both 0 and 100, syn-tilt magnetization is
possible as is vertical axis rotation or other pathologies
"""
kappa=0
nb=1000 # number of bootstraps
min,max=-10,150
dir_path='.'
infile,orfile='pmag_sites.txt','er_samples.txt'
critfile='pmag_criteria.txt'
fmt='svg'
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-h' in sys.argv: # check if help is needed
print main.__doc__
sys.exit() # graceful quit
if '-n' in sys.argv:
ind=sys.argv.index('-n')
nb=int(sys.argv[ind+1])
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
if '-b' in sys.argv:
ind=sys.argv.index('-b')
min=int(sys.argv[ind+1])
max=int(sys.argv[ind+2])
if '-f' in sys.argv:
ind=sys.argv.index('-f')
infile=sys.argv[ind+1]
if '-fsa' in sys.argv:
ind=sys.argv.index('-fsa')
orfile=sys.argv[ind+1]
orfile=dir_path+'/'+orfile
infile=dir_path+'/'+infile
critfile=dir_path+'/'+critfile
data,file_type=pmag.magic_read(infile)
ordata,file_type=pmag.magic_read(orfile)
if '-exc' in sys.argv:
crits,file_type=pmag.magic_read(critfile)
for crit in crits:
if crit['pmag_criteria_code']=="DE-SITE":
SiteCrit=crit
break
# get to work
#
PLTS={'geo':1,'strat':2,'taus':3} # make plot dictionary
pmagplotlib.plot_init(PLTS['geo'],5,5)
pmagplotlib.plot_init(PLTS['strat'],5,5)
pmagplotlib.plot_init(PLTS['taus'],5,5)
GEOrecs=pmag.get_dictitem(data,'site_tilt_correction','0','T')
if len(GEOrecs)>0: # have some geographic data
DIDDs= [] # set up list for dec inc dip_direction, dip
for rec in GEOrecs: # parse data
dip,dip_dir=0,-1
Dec=float(rec['site_dec'])
Inc=float(rec['site_inc'])
orecs=pmag.get_dictitem(ordata,'er_site_name',rec['er_site_name'],'T')
if len(orecs)>0:
if orecs[0]['sample_bed_dip_direction']!="":dip_dir=float(orecs[0]['sample_bed_dip_direction'])
if orecs[0]['sample_bed_dip']!="":dip=float(orecs[0]['sample_bed_dip'])
if dip!=0 and dip_dir!=-1:
if '-exc' in sys.argv:
keep=1
for key in SiteCrit.keys():
if 'site' in key and SiteCrit[key]!="" and rec[key]!="" and key!='site_alpha95':
if float(rec[key])<float(SiteCrit[key]):
keep=0
print rec['er_site_name'],key,rec[key]
if key=='site_alpha95' and SiteCrit[key]!="" and rec[key]!="":
if float(rec[key])>float(SiteCrit[key]):
keep=0
if keep==1: DIDDs.append([Dec,Inc,dip_dir,dip])
else:
DIDDs.append([Dec,Inc,dip_dir,dip])
else:
print 'no geographic directional data found'
sys.exit()
pmagplotlib.plotEQ(PLTS['geo'],DIDDs,'Geographic')
data=numpy.array(DIDDs)
D,I=pmag.dotilt_V(data)
TCs=numpy.array([D,I]).transpose()
pmagplotlib.plotEQ(PLTS['strat'],TCs,'Stratigraphic')
pmagplotlib.drawFIGS(PLTS)
Percs=range(min,max)
Cdf,Untilt=[],[]
pylab.figure(num=PLTS['taus'])
print 'doing ',nb,' iterations...please be patient.....'
for n in range(nb): # do bootstrap data sets - plot first 25 as dashed red line
if n%50==0:print n
Taus=[] # set up lists for taus
PDs=pmag.pseudo(DIDDs)
if kappa!=0:
for k in range(len(PDs)):
d,i=pmag.fshdev(kappa)
dipdir,dip=pmag.dodirot(d,i,PDs[k][2],PDs[k][3])
PDs[k][2]=dipdir
PDs[k][3]=dip
for perc in Percs:
tilt=numpy.array([1.,1.,1.,0.01*perc])
D,I=pmag.dotilt_V(PDs*tilt)
TCs=numpy.array([D,I]).transpose()
ppars=pmag.doprinc(TCs) # get principal directions
Taus.append(ppars['tau1'])
if n<25:pylab.plot(Percs,Taus,'r--')
Untilt.append(Percs[Taus.index(numpy.max(Taus))]) # tilt that gives maximum tau
Cdf.append(float(n)/float(nb))
pylab.plot(Percs,Taus,'k')
pylab.xlabel('% Untilting')
pylab.ylabel('tau_1 (red), CDF (green)')
Untilt.sort() # now for CDF of tilt of maximum tau
pylab.plot(Untilt,Cdf,'g')
lower=int(.025*nb)
upper=int(.975*nb)
pylab.axvline(x=Untilt[lower],ymin=0,ymax=1,linewidth=1,linestyle='--')
pylab.axvline(x=Untilt[upper],ymin=0,ymax=1,linewidth=1,linestyle='--')
tit= '%i - %i %s'%(Untilt[lower],Untilt[upper],'Percent Unfolding')
print tit
pylab.title(tit)
pmagplotlib.drawFIGS(PLTS)
ans= raw_input('S[a]ve all figures, <Return> to quit \n ')
if ans!='a':
print "Good bye"
sys.exit()
files={}
for key in PLTS.keys():
files[key]=('foldtest_'+'%s'%(key.strip()[:2])+'.'+fmt)
pmagplotlib.saveP(PLTS,files)
#!/usr/bin/env python
import pmag, matplotlib, math
matplotlib.use("TkAgg")
import pylab
k = 29.2
Dels, A95s, CSDs, Ns = [], [], [], range(4, 31)
DIs = []
for i in range(31):
dec, inc = pmag.fshdev(k)
DIs.append([dec, inc])
pars = pmag.fisher_mean(DIs)
pDIs = []
for i in range(3):
pDIs.append(DIs[i])
for n in Ns:
pDIs.append(DIs[n])
fpars = pmag.fisher_mean(pDIs)
A95s.append(fpars['alpha95'])
CSDs.append(fpars['csd'])
Dels.append((180. / math.pi) * math.acos(fpars['r'] / float(n)))
pylab.plot(Ns, A95s, 'ro')
pylab.plot(Ns, A95s, 'r-')
pylab.plot(Ns, CSDs, 'bs')
pylab.plot(Ns, CSDs, 'b-')
pylab.plot(Ns, Dels, 'g^')
pylab.plot(Ns, Dels, 'g-')
pylab.axhline(pars['csd'], color='k')
pylab.show()
raw_input()
def common_dir_MM90(dir1,dir2,NumSims=5000,plot='no'):
dir1['r']=get_R(dir1)
dir2['r']=get_R(dir2)
#largely based on iWatsonV routine of Swanson-Hyell in IPMag
cart_1=pmag.dir2cart([dir1["dec"],dir1["inc"],dir1["r"]])
cart_2=pmag.dir2cart([dir2['dec'],dir2['inc'],dir2["r"]])
Sw=dir1['k']*dir1['r']+dir2['k']*dir2['r'] # k1*r1+k2*r2
xhat_1=dir1['k']*cart_1[0]+dir2['k']*cart_2[0] # k1*x1+k2*x2
xhat_2=dir1['k']*cart_1[1]+dir2['k']*cart_2[1] # k1*y1+k2*y2
xhat_3=dir1['k']*cart_1[2]+dir2['k']*cart_2[2] # k1*z1+k2*z2
Rw=np.sqrt(xhat_1**2+xhat_2**2+xhat_3**2)
V=2*(Sw-Rw)
# keep weighted sum for later when determining the "critical angle"
# let's save it as Sr (notation of McFadden and McElhinny, 1990)
Sr=Sw
# do monte carlo simulation of datasets with same kappas as data,
# but a common mean
counter=0
Vp=[] # set of Vs from simulations
for k in range(NumSims):
# get a set of N1 fisher distributed vectors with k1,
# calculate fisher stats
Dirp=[]
for i in range(int(dir1["n"])):
Dirp.append(pmag.fshdev(dir1["k"]))
pars_p1=pmag.fisher_mean(Dirp)
# get a set of N2 fisher distributed vectors with k2,
# calculate fisher stats
Dirp=[]
for i in range(int(dir2["n"])):
Dirp.append(pmag.fshdev(dir2["k"]))
pars_p2=pmag.fisher_mean(Dirp)
# get the V for these
Vk=pmag.vfunc(pars_p1,pars_p2)
Vp.append(Vk)
# sort the Vs, get Vcrit (95th percentile one)
Vp.sort()
k=int(.95*NumSims)
Vcrit=Vp[k]
# equation 18 of McFadden and McElhinny, 1990 calculates the critical
# value of R (Rwc)
Rwc=Sr-(Vcrit/2)
# following equation 19 of McFadden and McElhinny (1990) the critical
# angle is calculated. If the observed angle (also calculated below)
# between the data set means exceeds the critical angle the hypothesis
# of a common mean direction may be rejected at the 95% confidence
# level. The critical angle is simply a different way to present
# Watson's V parameter so it makes sense to use the Watson V parameter
# in comparison with the critical value of V for considering the test
# results. What calculating the critical angle allows for is the
# classification of McFadden and McElhinny (1990) to be made
# for data sets that are consistent with sharing a common mean.
k1=dir1['k']
k2=dir2['k']
R1=dir1['r']
R2=dir2['r']
critical_angle=np.degrees(np.arccos(((Rwc**2)-((k1*R1)**2)
-((k2*R2)**2))/
(2*k1*R1*k2*R2)))
D1=(dir1['dec'],dir1['inc'])
D2=(dir2['dec'],dir2['inc'])
angle=pmag.angle(D1,D2)
if V<Vcrit:
outcome='Pass'
if critical_angle<5: MM90class='A'
elif critical_angle<10: MM90class='B'
elif critical_angle<20: MM90class='C'
else: MM90class='INDETERMINATE'
else:
outcome='Fail'
MM90class='FAIL'
result=pd.Series([outcome,V,Vcrit,angle[0],critical_angle,MM90class], index=['Outcome','VWatson','Vcrit','angle','critangle','MM90class'])
if plot=='yes':
CDF={'cdf':1}
#pmagplotlib.plot_init(CDF['cdf'],5,5)
p1 = pmagplotlib.plotCDF(CDF['cdf'],Vp,"Watson's V",'r',"")
p2 = pmagplotlib.plotVs(CDF['cdf'],[V],'g','-')
p3 = pmagplotlib.plotVs(CDF['cdf'],[Vp[k]],'b','--')
pmagplotlib.drawFIGS(CDF)
return result