def main():
"""
NAME
revtest.py
DESCRIPTION
calculates bootstrap statistics to test for antipodality
INPUT FORMAT
takes dec/inc as first two columns in space delimited file
SYNTAX
revtest.py [-h] [-i] [command line options]
OPTION
-h prints help message and quits
-i for interactive entry of file names from command line
-f FILE, sets input filename on command line
-fmt [svg,png,jpg], sets format for image output
"""
D,fmt=[],'svg'
if '-h' in sys.argv: # check if help is needed
print main.__doc__
sys.exit() # graceful quit
if '-i' in sys.argv: # ask for filename
file=raw_input("Enter file name with dec, inc data: ")
f=open(file,'rU')
data=f.readlines()
elif '-f' in sys.argv:
ind=sys.argv.index('-f')
file=sys.argv[ind+1]
f=open(file,'rU')
data=f.readlines()
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
for line in data:
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])
D.append([Dec,Inc,1.])
# set up plots
d=""
CDF={'X':1,'Y':2,'Z':3}
pmagplotlib.plot_init(CDF['X'],5,5)
pmagplotlib.plot_init(CDF['Y'],5,5)
pmagplotlib.plot_init(CDF['Z'],5,5)
#
# flip reverse mode
#
D1,D2=pmag.flip(D)
counter,NumSims=0,500
#
# get bootstrapped means for each data set
#
print 'doing first mode, be patient'
BDI1=pmag.di_boot(D1)
print 'doing second mode, be patient'
BDI2=pmag.di_boot(D2)
pmagplotlib.plotCOM(CDF,BDI1,BDI2,[""])
pmagplotlib.drawFIGS(CDF)
ans= raw_input("s[a]ve plots, [q]uit: ")
if ans=='a':
files={}
for key in CDF.keys():
files[key]='REV'+'_'+key+'.'+fmt
pmagplotlib.saveP(CDF,files)
else:
print 'good bye'
sys.exit()
def main():
"""
NAME
revtest_magic.py
DESCRIPTION
calculates bootstrap statistics to test for antipodality
INPUT FORMAT
takes dec/inc data from pmag_sites table
SYNTAX
revtest_magic.py [command line options]
OPTION
-h prints help message and quits
-f FILE, sets pmag_sites filename on command line
-crd [s,g,t], set coordinate system, default is geographic
-exc use pmag_criteria.txt to set acceptance criteria
-fmt [svg,png,jpg], sets format for image output
"""
D,fmt=[],'svg'
coord='0'
infile='pmag_sites.txt'
critfile='pmag_criteria.txt'
dir_path='.'
if '-h' in sys.argv: # check if help is needed
print main.__doc__
sys.exit() # graceful quit
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-f' in sys.argv:
ind=sys.argv.index('-f')
infile=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 '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
#
infile=dir_path+'/'+infile
critfile=dir_path+'/'+critfile
Accept=['site_k','site_alpha95','site_n','site_n_lines']
data,file_type=pmag.magic_read(infile)
if file_type!='pmag_sites':
print "Error opening file"
sys.exit()
# 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
for rec in data:
if rec['site_tilt_correction']==coord:
Dec=float(rec['site_dec'])
Inc=float(rec['site_inc'])
if '-exc' in sys.argv:
for key in Accept:
if SiteCrit[key]!="":
if float(rec[key])<=float(SiteCrit[key]):
D.append([Dec,Inc,1.])
else:
D.append([Dec,Inc,1.])
# set up plots
d=""
CDF={'X':1,'Y':2,'Z':3}
pmagplotlib.plot_init(CDF['X'],5,5)
pmagplotlib.plot_init(CDF['Y'],5,5)
pmagplotlib.plot_init(CDF['Z'],5,5)
#
# flip reverse mode
#
D1,D2=pmag.flip(D)
counter,NumSims=0,500
#
# get bootstrapped means for each data set
#
if len(D1) < 5 or len(D2) < 5:
print 'not enough data in two different modes for reversals test'
sys.exit()
print 'doing first mode, be patient'
BDI1=pmag.di_boot(D1)
print 'doing second mode, be patient'
BDI2=pmag.di_boot(D2)
pmagplotlib.plotCOM(CDF,BDI1,BDI2,[""])
pmagplotlib.drawFIGS(CDF)
ans= raw_input("s[a]ve plots, [q]uit: ")
if ans=='a':
files={}
for key in CDF.keys():
files[key]='REV'+'_'+key+'.'+fmt
pmagplotlib.saveP(CDF,files)
else:
print 'good bye'
sys.exit()
def main():
"""
NAME
revtest.py
DESCRIPTION
calculates bootstrap statistics to test for antipodality
INPUT FORMAT
takes dec/inc as first two columns in space delimited file
SYNTAX
revtest.py [-h] [command line options]
OPTION
-h prints help message and quits
-f FILE, sets input filename on command line
-fmt [svg,png,jpg], sets format for image output
-sav saves the figures silently and quits
"""
fmt,plot='svg',0
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]
data=numpy.loadtxt(file).transpose()
D=numpy.array([data[0],data[1]]).transpose()
else:
print '-f is a required switch'
print main.__doc__
print sys.exit()
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
if '-sav' in sys.argv:plot=1
# set up plots
d=""
CDF={'X':1,'Y':2,'Z':3}
pmagplotlib.plot_init(CDF['X'],5,5)
pmagplotlib.plot_init(CDF['Y'],5,5)
pmagplotlib.plot_init(CDF['Z'],5,5)
#
# flip reverse mode
#
D1,D2=pmag.flip(D)
counter,NumSims=0,500
#
# get bootstrapped means for each data set
#
print 'doing first mode, be patient'
BDI1=pmag.di_boot(D1)
print 'doing second mode, be patient'
BDI2=pmag.di_boot(D2)
pmagplotlib.plotCOM(CDF,BDI1,BDI2,[""])
files={}
for key in CDF.keys():
files[key]='REV'+'_'+key+'.'+fmt
if plot==0:
pmagplotlib.drawFIGS(CDF)
ans= raw_input("s[a]ve plots, [q]uit: ")
if ans=='a':
pmagplotlib.saveP(CDF,files)
print 'good bye'
sys.exit()
else:
pmagplotlib.saveP(CDF,files)
def main():
"""
NAME
watsonsF.py
DESCRIPTION
calculates Watson's F statistic from input files
INPUT FORMAT
takes dec/inc as first two columns in two space delimited files
SYNTAX
watsonsF.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
OUTPUT
Watson's F, critical value from F-tables for 2, 2(N-2) degrees of freedom
"""
D,D1,D2=[],[],[]
Flip=0
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 '-f' in sys.argv:
ind=sys.argv.index('-f')
file1=sys.argv[ind+1]
if '-f2' in sys.argv:
ind=sys.argv.index('-f2')
file2=sys.argv[ind+1]
f=open(file1,'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])
D1.append([Dec,Inc,1.])
D.append([Dec,Inc,1.])
f.close()
if Flip==0:
f=open(file2,'rU')
for line in f.readlines():
rec=line.split()
Dec,Inc=float(rec[0]),float(rec[1])
D2.append([Dec,Inc,1.])
D.append([Dec,Inc,1.])
f.close()
else:
D1,D2=pmag.flip(D1)
for d in D2: D.append(d)
#
# first calculate the fisher means and cartesian coordinates of each set of Directions
#
pars_0=pmag.fisher_mean(D)
pars_1=pmag.fisher_mean(D1)
pars_2=pmag.fisher_mean(D2)
#
# get F statistic for these
#
N= len(D)
R=pars_0['r']
R1=pars_1['r']
R2=pars_2['r']
F=(N-2)*((R1+R2-R)/(N-R1-R2))
Fcrit=pmag.fcalc(2,2*(N-2))
print F,Fcrit
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 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)
