def main():
"""
NAME
watsons_v.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
watsons_v.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:
print "Watson's V, Vcrit: "
print ' %10.1f %10.1f' % (V, Vp[k])
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'] = 'watsons_v_' + file1 + '_' + file2 + '.' + fmt
else:
files['cdf'] = 'watsons_v_' + 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
revtest_magic.py
DESCRIPTION
calculates bootstrap statistics to test for antipodality
INPUT FORMAT
takes dec/inc data from 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 criteria file to set acceptance criteria (only available for data model 3)
-fmt [svg,png,jpg], sets format for image output
-sav saves plot and quits
-DM [2, 3] MagIC data model num, default is 3
"""
if '-h' in sys.argv: # check if help is needed
print(main.__doc__)
sys.exit() # graceful quit
dir_path = pmag.get_named_arg("-WD", ".")
coord = pmag.get_named_arg("-crd",
"0") # default to geographic coordinates
if coord == 's':
coord = '-1'
elif coord == 'g':
coord = '0'
elif coord == 't':
coord = '100'
fmt = pmag.get_named_arg("-fmt", "svg")
if '-sav' in sys.argv:
plot = 1
data_model = int(float(pmag.get_named_arg("-DM")))
if data_model == 2:
infile = pmag.get_named_arg("-f", "pmag_sites.txt")
critfile = "pmag_criteria.txt"
tilt_corr_col = 'site_tilt_correction'
dec_col = "site_dec"
inc_col = "site_inc"
crit_code_col = "pmag_criteria_code"
else:
infile = pmag.get_named_arg("-f", "sites.txt")
critfile = "criteria.txt"
tilt_corr_col = "dir_tilt_correction"
dec_col = "dir_dec"
inc_col = "dir_inc"
crit_code_col = "criterion"
D = []
#
infile = pmag.resolve_file_name(infile, dir_path)
dir_path = os.path.split(infile)[0]
critfile = pmag.resolve_file_name(critfile, dir_path)
#
if data_model == 2:
Accept = ['site_k', 'site_alpha95', 'site_n', 'site_n_lines']
else:
Accept = [
'dir_k', 'dir_alpha95', 'dir_n_samples', 'dir_n_specimens_line'
]
data, file_type = pmag.magic_read(infile)
if 'sites' not in file_type:
print("Error opening file", file_type)
sys.exit()
# ordata,file_type=pmag.magic_read(orfile)
SiteCrits = []
if '-exc' in sys.argv and data_model != 2:
crits, file_type = pmag.magic_read(critfile)
for crit in crits:
if crit[crit_code_col] == "DE-SITE":
SiteCrit = crit
SiteCrits.append(SiteCrit)
elif '-exc' in sys.argv and data_model == 2:
print(
'-W- You have selected the -exc option, which is not available with MagIC data model 2.'
)
for rec in data:
if rec[tilt_corr_col] == coord:
Dec = float(rec[dec_col])
Inc = float(rec[inc_col])
if '-exc' in sys.argv and data_model != 2:
fail = False
for SiteCrit in SiteCrits:
for key in Accept:
if key not in SiteCrit['table_column']:
continue
if key not in rec:
continue
if SiteCrit['criterion_value'] != "":
op = OPS[SiteCrit['criterion_operation']]
if not op(float(rec[key]),
float(SiteCrit['criterion_value'])):
fail = True
if not fail:
D.append([Dec, Inc, 1.])
else:
D.append([Dec, Inc, 1.])
# set up plots
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.plot_com(CDF, BDI1, BDI2, [""])
files = {}
for key in list(CDF.keys()):
files[key] = 'REV' + '_' + key + '.' + fmt
if plot == 0:
pmagplotlib.draw_figs(CDF)
ans = input("s[a]ve plots, [q]uit: ")
if ans == 'a':
pmagplotlib.save_plots(CDF, files)
else:
pmagplotlib.save_plots(CDF, files)
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 list(CDF.keys()):
files[key]='REV'+'_'+key+'.'+fmt
if plot==0:
pmagplotlib.drawFIGS(CDF)
ans= 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
watsons_v.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
watsons_v.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:
print "Watson's V, Vcrit: "
print ' %10.1f %10.1f'%(V,Vp[k])
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']='watsons_v_'+file1+'_'+file2+'.'+fmt
else:
files['cdf']='watsons_v_'+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
watsons_f.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
watsons_f.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 '%7.2f %7.2f' % (F, Fcrit)
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
-sav saves plot and quits
"""
D, fmt, plot = [], 'svg', 0
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 '-sav' in sys.argv: plot = 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, [""])
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)
else:
pmagplotlib.saveP(CDF, files)
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
watsons_f.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
watsons_f.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 '%7.2f %7.2f'%(F,Fcrit)
def main():
"""
NAME
revtest_magic.py
DESCRIPTION
calculates bootstrap statistics to test for antipodality
INPUT FORMAT
takes dec/inc data from 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 criteria file to set acceptance criteria (only available for data model 3)
-fmt [svg,png,jpg], sets format for image output
-sav saves plot and quits
-DM [2, 3] MagIC data model num, default is 3
"""
if '-h' in sys.argv: # check if help is needed
print(main.__doc__)
sys.exit() # graceful quit
dir_path = pmag.get_named_arg("-WD", ".")
coord = pmag.get_named_arg("-crd", "0") # default to geographic coordinates
if coord == 's':
coord = '-1'
elif coord == 'g':
coord = '0'
elif coord == 't':
coord = '100'
fmt = pmag.get_named_arg("-fmt", "svg")
if '-sav' in sys.argv:
plot = 1
data_model = int(float(pmag.get_named_arg("-DM")))
if data_model == 2:
infile = pmag.get_named_arg("-f", "pmag_sites.txt")
critfile = "pmag_criteria.txt"
tilt_corr_col = 'site_tilt_correction'
dec_col = "site_dec"
inc_col = "site_inc"
crit_code_col = "pmag_criteria_code"
else:
infile = pmag.get_named_arg("-f", "sites.txt")
critfile = "criteria.txt"
tilt_corr_col = "dir_tilt_correction"
dec_col = "dir_dec"
inc_col = "dir_inc"
crit_code_col = "criterion"
D = []
#
infile = pmag.resolve_file_name(infile, dir_path)
dir_path = os.path.split(infile)[0]
critfile = pmag.resolve_file_name(critfile, dir_path)
#
if data_model == 2:
Accept = ['site_k', 'site_alpha95', 'site_n', 'site_n_lines']
else:
Accept = ['dir_k', 'dir_alpha95', 'dir_n_samples', 'dir_n_specimens_line']
data, file_type = pmag.magic_read(infile)
if 'sites' not in file_type:
print("Error opening file", file_type)
sys.exit()
# ordata,file_type=pmag.magic_read(orfile)
SiteCrits = []
if '-exc' in sys.argv and data_model != 2:
crits, file_type = pmag.magic_read(critfile)
for crit in crits:
if crit[crit_code_col] == "DE-SITE":
SiteCrit = crit
SiteCrits.append(SiteCrit)
elif '-exc' in sys.argv and data_model == 2:
print('-W- You have selected the -exc option, which is not available with MagIC data model 2.')
for rec in data:
if rec[tilt_corr_col] == coord:
Dec = float(rec[dec_col])
Inc = float(rec[inc_col])
if '-exc' in sys.argv and data_model != 2:
fail = False
for SiteCrit in SiteCrits:
for key in Accept:
if key not in SiteCrit['table_column']:
continue
if key not in rec:
continue
if SiteCrit['criterion_value'] != "":
op = OPS[SiteCrit['criterion_operation']]
if not op(float(rec[key]), float(SiteCrit['criterion_value'])):
fail = True
if not fail:
D.append([Dec, Inc, 1.])
else:
D.append([Dec, Inc, 1.])
# set up plots
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.plot_com(CDF, BDI1, BDI2, [""])
files = {}
for key in list(CDF.keys()):
files[key] = 'REV'+'_'+key+'.'+fmt
if plot == 0:
pmagplotlib.draw_figs(CDF)
ans = input("s[a]ve plots, [q]uit: ")
if ans == 'a':
pmagplotlib.save_plots(CDF, files)
else:
pmagplotlib.save_plots(CDF, files)
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
-sav saves plot and quits
"""
D,fmt,plot=[],'svg',0
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 '-sav' in sys.argv:plot=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,[""])
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)
else:
pmagplotlib.saveP(CDF,files)
sys.exit()
