def main():
"""
NAME
pyscu_draw.py
DESCRIPTION
plot the data calculated in pyscu_calc.py
INPUT
ouput files from pyscu_calc.py
You must open the *_main.txt
interactive data entry using Easygui
(http://easygui.sourceforge.net/)
"""
print(
'\nThis program uses the PmagPy and pySCu softwares utilities\n\tTauxe et al. 2016, G3, http://dx.doi.org/10.1002/2016GC006307\n\tCalvín et al. 2017, C&G, http://dx.doi.org/10.1016/j.cageo.2017.07.002'
)
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
infile = eg.fileopenbox(msg="Open File",
title="Control: fileopenbox",
default='')
outfile = infile[:-9]
infile_m = infile[:-8] + 'mat.txt'
infile_ref = infile[:-8] + 'Ref.txt'
infile_inter = infile[:-8] + 'inter.txt'
infile_sci = infile[:-8] + 'SCIs.txt'
if path.exists(infile_ref): Ref = 'true'
else: Ref = 'false'
if path.exists(infile_m): matrix = 'true'
else: matrix = 'false'
if path.exists(infile_inter): inter = 'true'
else: inter = 'false'
if path.exists(infile_sci): SCIs = 'true'
else: SCIs = 'false'
if Ref == 'false':
campos = [
'Dec', 'Inc', 'Eta', 'Dec_Eta', 'Inc_Eta', 'Zeta', 'Dec_Zeta',
'Inc_Zeta'
]
ref = []
ref = eg.multenterbox(
msg=
"I can't found the file with the reference direction \n Please, input the Kent parameters of it",
title='Interactive entry of the remagnetization direction',
fields=campos,
values=(0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0))
if Ref == 'false' and ref != None:
print(ref)
ref[0] = float(ref[0])
ref[1] = float(ref[1])
ref[2] = float(ref[2])
ref[3] = float(ref[3])
ref[4] = float(ref[4])
ref[5] = float(ref[5])
ref[6] = float(ref[6])
ref[7] = float(ref[7])
iRef = 'true'
print(ref)
ans_mat = eg.boolbox(msg='Do you want to plot te A matrix?',
title='Control: boolbox',
choices=('Yes', 'No'))
preS = eg.buttonbox(
msg=
'Doy you want plot the SCI solutions (s), the intersections (i) or none (n)',
title='Control: buttonbox',
choices=('s', 'i', 'n'))
if matrix == 'false' and ans_mat == True:
print("\nTake care, I don't found the file", infile_m,
' whit the A/N matriz data')
if inter == 'false' and preS == 'i':
print("\nTake care, I don't found the file", infile_inter,
' whit the intersections directions')
if SCIs == 'false' and preS == 's':
print("\nTake care, I don't found the file", infile_sci,
' whit the SCIs directions')
out_name_bbc = outfile + '_bbc.svg'
out_name_bfd = outfile + '_bfd.svg'
out_name_atbc = outfile + '_atbc.svg'
out_name_mat = outfile + '_mat.svg'
print('\nPlease, wait a moment')
print('\nPlots will be saved as', out_name_bbc, ', ', out_name_bfd,
'...\n')
#Saving the data in different list
site, sc, geo, tilt, bfd = scu.getInFile_main(infile) #main file
n = len(site)
if Ref == 'true': #reference direction
reader = csv.reader(open(infile_ref), delimiter=' ')
dat_Ref = list(reader)
ref = [
float(dat_Ref[1][1]),
float(dat_Ref[1][2]),
float(dat_Ref[1][3]),
float(dat_Ref[1][5]),
float(dat_Ref[1][6]),
float(dat_Ref[1][4]),
float(dat_Ref[1][7]),
float(dat_Ref[1][8]),
float(dat_Ref[1][11])
]
if inter == 'true' and preS == 'i': #intersections directions
reader = csv.reader(open(infile_inter), delimiter=' ')
dat_inter_h = list(reader)
dat_inter = dat_inter_h[1:]
if SCIs == 'true' and preS == 's': #intersections directions
reader = csv.reader(open(infile_sci), delimiter=' ')
dat_SCIs_h = list(reader)
dat_SCIs = dat_SCIs_h[1:]
if matrix == 'true' and ans_mat == True: #A/n values
X, Y, Z, minA, maxA = scu.getInFile_mat(infile_m)
#Drawing...
plt.figure(num=1, figsize=(6, 6), facecolor='white')
#Plotting the BBC directions, the SCs and the reference
pmagpl.plotNET(1)
pylab.figtext(.02, .045, 'pySCu v3.1')
plt.text(0.85, 0.7, 'BBC', fontsize=13)
plt.scatter(0.8, 0.74, color='r', marker='s', s=30)
plt.text(0.70, 0.85, 'n=' + str(n), fontsize=13)
for dato in sc: #The SCs
scu.smallcirc(dato, 1)
for dato in geo: #The BBC directions
scu.plot_di_mean(dato[0],
dato[1],
dato[2],
color='r',
marker='s',
markersize=8,
label='Geo',
legend='no',
zorder=3)
#You can change the marker (+, ., o, *, p, s, x, D, h, ^), the color (b, g, r, c, m, y, k, w) or the size as you prefere
if Ref == 'true' or iRef == 'true': #The reference
scu.plotCONF(ref)
plt.text(0.51, -1.05, 'Reference', fontsize=13)
plt.scatter(0.45, -1, color='m', marker='*', s=100)
plt.title('Before Bedding Correction', fontsize=20)
plt.savefig(out_name_bbc)
#Plotting the ATBC directions, the SCs and the reference
plt.figure(num=2, figsize=(6, 6), facecolor='white')
pmagpl.plotNET(2)
pylab.figtext(.02, .045, 'pySCu v3.1')
plt.text(0.85, 0.7, 'ATBC', fontsize=13)
plt.scatter(0.8, 0.745, color='g', marker='^', s=40)
plt.text(0.70, 0.85, 'n=' + str(n), fontsize=13)
for dato in sc:
scu.smallcirc(dato, 1)
if Ref == 'true' or iRef == 'true':
scu.plotCONF(ref)
plt.text(0.51, -1.05, 'Reference', fontsize=13)
plt.scatter(0.45, -1, color='m', marker='*', s=100)
for dato in tilt:
scu.plot_di_mean(dato[0],
dato[1],
dato[2],
color='g',
marker='^',
markersize=9,
label='Tilt',
legend='no',
zorder=3)
plt.savefig(out_name_atbc)
#Plotting the BFD directions, the SCs and the reference
plt.figure(num=3, figsize=(6, 6), facecolor='white')
pmagpl.plotNET(3)
pylab.figtext(.02, .045, 'pySCu v3.1')
plt.text(0.85, 0.7, 'BFD', fontsize=13)
plt.scatter(0.8, 0.74, color='b', marker='o', s=30)
plt.text(0.70, 0.85, 'n=' + str(n), fontsize=13)
for dato in sc:
scu.smallcirc(dato, 1)
for dato in bfd:
scu.plot_di_mean(dato[0],
dato[1],
dato[2],
color='b',
marker='o',
markersize=5,
label='BFD',
legend='no',
zorder=3)
if Ref == 'true' or iRef == 'true': #Ploting the reference and the leyend
scu.plotCONF(ref)
plt.text(0.51, -1.05, 'Reference', fontsize=13)
plt.scatter(0.45, -1, color='m', marker='*', s=100)
plt.savefig(out_name_bfd)
#Plotting the A/n contour plot and/or the intersections
if (ans_mat == True and matrix == 'true') or (
preS == 'i' and inter == 'true') or (preS == 's'
and SCIs == 'true'):
plt.figure(num=4, figsize=(6, 6), facecolor='white')
pmagpl.plotNET(4)
pylab.figtext(.02, .045, 'pySCu v3.1')
fig4 = 'true'
else:
fig4 = 'false'
if ans_mat == True and matrix == 'true': #plotting the A/n contour plot
max_z = max(Z)
max_z_s = max_z + (5 - max_z % 5) + 0.1
min_z = min(Z)
min_z_s = min_z - (min_z % 5)
levels5 = np.arange(min_z_s, max_z_s, 5)
levels1 = np.arange(min_z_s, max_z_s, 1)
CS = plt.tricontourf(
X, Y, Z, vmin=min_z, vmax=max_z, cmap='Blues', levels=levels1
) #Other colormaps (as 'rainbow') are possibles. Change 'Blues' for the choosed colormap
cbar = plt.colorbar(CS, orientation='horizontal', pad=0.05)
CS2 = plt.tricontour(X,
Y,
Z,
colors='k',
linewidths=.5,
levels=levels5)
#plt.clabel(CS2,levels=levels5, inline=1, fmt='%1.0f', fontsize=10)
cbar.ax.set_xlabel('A/n value' + ' (' + str(round(minA, 1)) + '-' +
str(round(maxA, 1)) + ')')
#cbar.add_lines(CS2)
plt.axis((-1.35, 1.35, -1.35, 1.35))
else:
for dato in sc:
scu.smallcirc(dato, 1)
if preS == 'i' and inter == 'true': #plotting the intersections
text_i = 'SCs intersec. (n=' + str(len(dat_inter)) + ')'
plt.text(-0.3, -1.2, text_i, fontsize=12)
plt.scatter(-0.38, -1.12, color='k', marker='.', s=50)
for dato in dat_inter:
scu.plot_di_mean(float(dato[0]),
float(dato[1]),
0.,
color='k',
marker='.',
markersize=1,
label='Intersections',
legend='no')
if preS == 's' and SCIs == 'true': #plotting the SCIs
text_s = 'SCIs solutions (n=' + str(len(dat_SCIs)) + ')'
plt.text(-0.3, -1.2, text_s, fontsize=12)
plt.scatter(-0.38, -1.12, color='k', marker='.', s=50)
for dato in dat_SCIs:
scu.plot_di_mean(float(dato[0]),
float(dato[1]),
0.,
color='k',
marker='.',
markersize=1,
label='SCIs',
legend='no')
if fig4 == 'true' and (Ref == 'true' or iRef
== 'true'): #Plotting the reference and the leyend
scu.plotCONF(ref)
plt.text(0.6, 0.83, 'Reference', fontsize=13)
plt.scatter(0.93, 0.73, color='m', marker='*', s=100)
text_rat = 'mr/mp=' + str(ref[8]) + ';'
plt.text(-1.37, -1.2, text_rat, fontsize=12)
if fig4 == 'true':
plt.savefig(out_name_mat)
plt.show()
def main():
"""
NAME
eqarea_magic.py
DESCRIPTION
makes equal area projections from declination/inclination data
SYNTAX
eqarea_magic.py [command line options]
INPUT
takes magic formatted pmag_results, pmag_sites, pmag_samples or pmag_specimens
OPTIONS
-h prints help message and quits
-f FILE: specify input magic format file from magic,default='pmag_results.txt'
supported types=[magic_measurements,pmag_specimens, pmag_samples, pmag_sites, pmag_results, magic_web]
-obj OBJ: specify level of plot [all, sit, sam, spc], default is all
-crd [s,g,t]: specify coordinate system, [s]pecimen, [g]eographic, [t]ilt adjusted
default is geographic, unspecified assumed geographic
-fmt [svg,png,jpg] format for output plots
-ell [F,K,B,Be,Bv] plot Fisher, Kent, Bingham, Bootstrap ellipses or Boostrap eigenvectors
-c plot as colour contour
-sav save plot and quit quietly
NOTE
all: entire file; sit: site; sam: sample; spc: specimen
"""
FIG = {} # plot dictionary
FIG['eqarea'] = 1 # eqarea is figure 1
in_file, plot_key, coord, crd = 'pmag_results.txt', 'all', "0", 'g'
plotE, contour = 0, 0
dir_path = '.'
fmt = 'svg'
verbose = pmagplotlib.verbose
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]
pmagplotlib.plot_init(FIG['eqarea'], 5, 5)
if '-f' in sys.argv:
ind = sys.argv.index("-f")
in_file = dir_path + "/" + sys.argv[ind + 1]
if '-obj' in sys.argv:
ind = sys.argv.index('-obj')
plot_by = sys.argv[ind + 1]
if plot_by == 'all': plot_key = 'all'
if plot_by == 'sit': plot_key = 'er_site_name'
if plot_by == 'sam': plot_key = 'er_sample_name'
if plot_by == 'spc': plot_key = 'er_specimen_name'
if '-c' in sys.argv: contour = 1
plots = 0
if '-sav' in sys.argv:
plots = 1
verbose = 0
if '-ell' in sys.argv:
plotE = 1
ind = sys.argv.index('-ell')
ell_type = sys.argv[ind + 1]
if ell_type == 'F': dist = 'F'
if ell_type == 'K': dist = 'K'
if ell_type == 'B': dist = 'B'
if ell_type == 'Be': dist = 'BE'
if ell_type == 'Bv':
dist = 'BV'
FIG['bdirs'] = 2
pmagplotlib.plot_init(FIG['bdirs'], 5, 5)
if '-crd' in sys.argv:
ind = sys.argv.index("-crd")
crd = sys.argv[ind + 1]
if crd == 's': coord = "-1"
if crd == 'g': coord = "0"
if crd == 't': coord = "100"
if '-fmt' in sys.argv:
ind = sys.argv.index("-fmt")
fmt = sys.argv[ind + 1]
Dec_keys = ['site_dec', 'sample_dec', 'specimen_dec', 'measurement_dec', 'average_dec', 'none']
Inc_keys = ['site_inc', 'sample_inc', 'specimen_inc', 'measurement_inc', 'average_inc', 'none']
Tilt_keys = ['tilt_correction', 'site_tilt_correction', 'sample_tilt_correction', 'specimen_tilt_correction',
'none']
Dir_type_keys = ['', 'site_direction_type', 'sample_direction_type', 'specimen_direction_type']
Name_keys = ['er_specimen_name', 'er_sample_name', 'er_site_name', 'pmag_result_name']
data, file_type = pmag.magic_read(in_file)
if file_type == 'pmag_results' and plot_key != "all": plot_key = plot_key + 's' # need plural for results table
if verbose:
print len(data), ' records read from ', in_file
#
#
# find desired dec,inc data:
#
dir_type_key = ''
#
# get plotlist if not plotting all records
#
plotlist = []
if plot_key != "all":
plots = pmag.get_dictitem(data, plot_key, '', 'F')
for rec in plots:
if rec[plot_key] not in plotlist:
plotlist.append(rec[plot_key])
plotlist.sort()
else:
plotlist.append('All')
for plot in plotlist:
if verbose: print plot
DIblock = []
GCblock = []
SLblock, SPblock = [], []
title = plot
mode = 1
dec_key, inc_key, tilt_key, name_key, k = "", "", "", "", 0
if plot != "All":
odata = pmag.get_dictitem(data, plot_key, plot, 'T')
else:
odata = data # data for this obj
for dec_key in Dec_keys:
Decs = pmag.get_dictitem(odata, dec_key, '', 'F') # get all records with this dec_key not blank
if len(Decs) > 0: break
for inc_key in Inc_keys:
Incs = pmag.get_dictitem(Decs, inc_key, '', 'F') # get all records with this inc_key not blank
if len(Incs) > 0: break
for tilt_key in Tilt_keys:
if tilt_key in Incs[0].keys(): break # find the tilt_key for these records
if tilt_key == 'none': # no tilt key in data, need to fix this with fake data which will be unknown tilt
tilt_key = 'tilt_correction'
for rec in Incs: rec[tilt_key] = ''
cdata = pmag.get_dictitem(Incs, tilt_key, coord, 'T') # get all records matching specified coordinate system
if coord == '0': # geographic
udata = pmag.get_dictitem(Incs, tilt_key, '', 'T') # get all the blank records - assume geographic
if len(cdata) == 0: crd = ''
if len(udata) > 0:
for d in udata: cdata.append(d)
crd = crd + 'u'
for name_key in Name_keys:
Names = pmag.get_dictitem(cdata, name_key, '', 'F') # get all records with this name_key not blank
if len(Names) > 0: break
for dir_type_key in Dir_type_keys:
Dirs = pmag.get_dictitem(cdata, dir_type_key, '', 'F') # get all records with this direction type
if len(Dirs) > 0: break
if dir_type_key == "": dir_type_key = 'direction_type'
locations, site, sample, specimen = "", "", "", ""
for rec in cdata: # pick out the data
if 'er_location_name' in rec.keys() and rec['er_location_name'] != "" and rec[
'er_location_name'] not in locations: locations = locations + rec['er_location_name'].replace("/",
"") + "_"
if 'er_location_names' in rec.keys() and rec['er_location_names'] != "":
locs = rec['er_location_names'].split(':')
for loc in locs:
if loc not in locations: locations = locations + loc.replace("/", "") + '_'
if plot_key == 'er_site_name' or plot_key == 'er_sample_name' or plot_key == 'er_specimen_name':
site = rec['er_site_name']
if plot_key == 'er_sample_name' or plot_key == 'er_specimen_name':
sample = rec['er_sample_name']
if plot_key == 'er_specimen_name':
specimen = rec['er_specimen_name']
if plot_key == 'er_site_names' or plot_key == 'er_sample_names' or plot_key == 'er_specimen_names':
site = rec['er_site_names']
if plot_key == 'er_sample_names' or plot_key == 'er_specimen_names':
sample = rec['er_sample_names']
if plot_key == 'er_specimen_names':
specimen = rec['er_specimen_names']
if dir_type_key not in rec.keys() or rec[dir_type_key] == "": rec[dir_type_key] = 'l'
if 'magic_method_codes' not in rec.keys(): rec['magic_method_codes'] = ""
DIblock.append([float(rec[dec_key]), float(rec[inc_key])])
SLblock.append([rec[name_key], rec['magic_method_codes']])
if rec[tilt_key] == coord and rec[dir_type_key] != 'l' and rec[dec_key] != "" and rec[inc_key] != "":
GCblock.append([float(rec[dec_key]), float(rec[inc_key])])
SPblock.append([rec[name_key], rec['magic_method_codes']])
if len(DIblock) == 0 and len(GCblock) == 0:
if verbose: print "no records for plotting"
sys.exit()
if verbose:
for k in range(len(SLblock)):
print '%s %s %7.1f %7.1f' % (SLblock[k][0], SLblock[k][1], DIblock[k][0], DIblock[k][1])
for k in range(len(SPblock)):
print '%s %s %7.1f %7.1f' % (SPblock[k][0], SPblock[k][1], GCblock[k][0], GCblock[k][1])
if len(DIblock) > 0:
if contour == 0:
pmagplotlib.plotEQ(FIG['eqarea'], DIblock, title)
else:
pmagplotlib.plotEQcont(FIG['eqarea'], DIblock)
else:
pmagplotlib.plotNET(FIG['eqarea'])
if len(GCblock) > 0:
for rec in GCblock: pmagplotlib.plotC(FIG['eqarea'], rec, 90., 'g')
if plotE == 1:
ppars = pmag.doprinc(DIblock) # get principal directions
nDIs, rDIs, npars, rpars = [], [], [], []
for rec in DIblock:
angle = pmag.angle([rec[0], rec[1]], [ppars['dec'], ppars['inc']])
if angle > 90.:
rDIs.append(rec)
else:
nDIs.append(rec)
if dist == 'B': # do on whole dataset
etitle = "Bingham confidence ellipse"
bpars = pmag.dobingham(DIblock)
for key in bpars.keys():
if key != 'n' and verbose: print " ", key, '%7.1f' % (bpars[key])
if key == 'n' and verbose: print " ", key, ' %i' % (bpars[key])
npars.append(bpars['dec'])
npars.append(bpars['inc'])
npars.append(bpars['Zeta'])
npars.append(bpars['Zdec'])
npars.append(bpars['Zinc'])
npars.append(bpars['Eta'])
npars.append(bpars['Edec'])
npars.append(bpars['Einc'])
if dist == 'F':
etitle = "Fisher confidence cone"
if len(nDIs) > 2:
fpars = pmag.fisher_mean(nDIs)
for key in fpars.keys():
if key != 'n' and verbose: print " ", key, '%7.1f' % (fpars[key])
if key == 'n' and verbose: print " ", key, ' %i' % (fpars[key])
mode += 1
npars.append(fpars['dec'])
npars.append(fpars['inc'])
npars.append(fpars['alpha95']) # Beta
npars.append(fpars['dec'])
isign = abs(fpars['inc']) / fpars['inc']
npars.append(fpars['inc'] - isign * 90.) #Beta inc
npars.append(fpars['alpha95']) # gamma
npars.append(fpars['dec'] + 90.) # Beta dec
npars.append(0.) #Beta inc
if len(rDIs) > 2:
fpars = pmag.fisher_mean(rDIs)
if verbose: print "mode ", mode
for key in fpars.keys():
if key != 'n' and verbose: print " ", key, '%7.1f' % (fpars[key])
if key == 'n' and verbose: print " ", key, ' %i' % (fpars[key])
mode += 1
rpars.append(fpars['dec'])
rpars.append(fpars['inc'])
rpars.append(fpars['alpha95']) # Beta
rpars.append(fpars['dec'])
isign = abs(fpars['inc']) / fpars['inc']
rpars.append(fpars['inc'] - isign * 90.) #Beta inc
rpars.append(fpars['alpha95']) # gamma
rpars.append(fpars['dec'] + 90.) # Beta dec
rpars.append(0.) #Beta inc
if dist == 'K':
etitle = "Kent confidence ellipse"
if len(nDIs) > 3:
kpars = pmag.dokent(nDIs, len(nDIs))
if verbose: print "mode ", mode
for key in kpars.keys():
if key != 'n' and verbose: print " ", key, '%7.1f' % (kpars[key])
if key == 'n' and verbose: print " ", key, ' %i' % (kpars[key])
mode += 1
npars.append(kpars['dec'])
npars.append(kpars['inc'])
npars.append(kpars['Zeta'])
npars.append(kpars['Zdec'])
npars.append(kpars['Zinc'])
npars.append(kpars['Eta'])
npars.append(kpars['Edec'])
npars.append(kpars['Einc'])
if len(rDIs) > 3:
kpars = pmag.dokent(rDIs, len(rDIs))
if verbose: print "mode ", mode
for key in kpars.keys():
if key != 'n' and verbose: print " ", key, '%7.1f' % (kpars[key])
if key == 'n' and verbose: print " ", key, ' %i' % (kpars[key])
mode += 1
rpars.append(kpars['dec'])
rpars.append(kpars['inc'])
rpars.append(kpars['Zeta'])
rpars.append(kpars['Zdec'])
rpars.append(kpars['Zinc'])
rpars.append(kpars['Eta'])
rpars.append(kpars['Edec'])
rpars.append(kpars['Einc'])
else: # assume bootstrap
if dist == 'BE':
if len(nDIs) > 5:
BnDIs = pmag.di_boot(nDIs)
Bkpars = pmag.dokent(BnDIs, 1.)
if verbose: print "mode ", mode
for key in Bkpars.keys():
if key != 'n' and verbose: print " ", key, '%7.1f' % (Bkpars[key])
if key == 'n' and verbose: print " ", key, ' %i' % (Bkpars[key])
mode += 1
npars.append(Bkpars['dec'])
npars.append(Bkpars['inc'])
npars.append(Bkpars['Zeta'])
npars.append(Bkpars['Zdec'])
npars.append(Bkpars['Zinc'])
npars.append(Bkpars['Eta'])
npars.append(Bkpars['Edec'])
npars.append(Bkpars['Einc'])
if len(rDIs) > 5:
BrDIs = pmag.di_boot(rDIs)
Bkpars = pmag.dokent(BrDIs, 1.)
if verbose: print "mode ", mode
for key in Bkpars.keys():
if key != 'n' and verbose: print " ", key, '%7.1f' % (Bkpars[key])
if key == 'n' and verbose: print " ", key, ' %i' % (Bkpars[key])
mode += 1
rpars.append(Bkpars['dec'])
rpars.append(Bkpars['inc'])
rpars.append(Bkpars['Zeta'])
rpars.append(Bkpars['Zdec'])
rpars.append(Bkpars['Zinc'])
rpars.append(Bkpars['Eta'])
rpars.append(Bkpars['Edec'])
rpars.append(Bkpars['Einc'])
etitle = "Bootstrapped confidence ellipse"
elif dist == 'BV':
sym = {'lower': ['o', 'c'], 'upper': ['o', 'g'], 'size': 3, 'edgecolor': 'face'}
if len(nDIs) > 5:
BnDIs = pmag.di_boot(nDIs)
pmagplotlib.plotEQsym(FIG['bdirs'], BnDIs, 'Bootstrapped Eigenvectors', sym)
if len(rDIs) > 5:
BrDIs = pmag.di_boot(rDIs)
if len(nDIs) > 5: # plot on existing plots
pmagplotlib.plotDIsym(FIG['bdirs'], BrDIs, sym)
else:
pmagplotlib.plotEQ(FIG['bdirs'], BrDIs, 'Bootstrapped Eigenvectors')
if dist == 'B':
if len(nDIs) > 3 or len(rDIs) > 3: pmagplotlib.plotCONF(FIG['eqarea'], etitle, [], npars, 0)
elif len(nDIs) > 3 and dist != 'BV':
pmagplotlib.plotCONF(FIG['eqarea'], etitle, [], npars, 0)
if len(rDIs) > 3:
pmagplotlib.plotCONF(FIG['eqarea'], etitle, [], rpars, 0)
elif len(rDIs) > 3 and dist != 'BV':
pmagplotlib.plotCONF(FIG['eqarea'], etitle, [], rpars, 0)
if verbose: pmagplotlib.drawFIGS(FIG)
#
files = {}
locations = locations[:-1]
for key in FIG.keys():
filename = 'LO:_' + locations + '_SI:_' + site + '_SA:_' + sample + '_SP:_' + specimen + '_CO:_' + crd + '_TY:_' + key + '_.' + fmt
files[key] = filename
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles = {}
titles['eq'] = 'Equal Area Plot'
FIG = pmagplotlib.addBorders(FIG, titles, black, purple)
pmagplotlib.saveP(FIG, files)
elif verbose:
ans = raw_input(" S[a]ve to save plot, [q]uit, Return to continue: ")
if ans == "q": sys.exit()
if ans == "a":
pmagplotlib.saveP(FIG, files)
if plots:
pmagplotlib.saveP(FIG, files)
def main():
"""
NAME
specimens_results_magic.py
DESCRIPTION
combines pmag_specimens.txt file with age, location, acceptance criteria and
outputs pmag_results table along with other MagIC tables necessary for uploading to the database
SYNTAX
specimens_results_magic.py [command line options]
OPTIONS
-h prints help message and quits
-usr USER: identify user, default is ""
-f: specimen input magic_measurements format file, default is "magic_measurements.txt"
-fsp: specimen input pmag_specimens format file, default is "pmag_specimens.txt"
-fsm: sample input er_samples format file, default is "er_samples.txt"
-fsi: specimen input er_sites format file, default is "er_sites.txt"
-fla: specify a file with paleolatitudes for calculating VADMs, default is not to calculate VADMS
format is: site_name paleolatitude (space delimited file)
-fa AGES: specify er_ages format file with age information
-crd [s,g,t,b]: specify coordinate system
(s, specimen, g geographic, t, tilt corrected, b, geographic and tilt corrected)
Default is to assume geographic
NB: only the tilt corrected data will appear on the results table, if both g and t are selected.
-cor [AC:CR:NL]: colon delimited list of required data adjustments for all specimens
included in intensity calculations (anisotropy, cooling rate, non-linear TRM)
unless specified, corrections will not be applied
-pri [TRM:ARM] colon delimited list of priorities for anisotropy correction (-cor must also be set to include AC). default is TRM, then ARM
-age MIN MAX UNITS: specify age boundaries and units
-exc: use exiting selection criteria (in pmag_criteria.txt file), default is default criteria
-C: no acceptance criteria
-aD: average directions per sample, default is NOT
-aI: average multiple specimen intensities per sample, default is by site
-aC: average all components together, default is NOT
-pol: calculate polarity averages
-sam: save sample level vgps and v[a]dms, default is by site
-xSi: skip the site level intensity calculation
-p: plot directions and look at intensities by site, default is NOT
-fmt: specify output for saved images, default is svg (only if -p set)
-lat: use present latitude for calculating VADMs, default is not to calculate VADMs
-xD: skip directions
-xI: skip intensities
OUPUT
writes pmag_samples, pmag_sites, pmag_results tables
"""
# set defaults
Comps = [] # list of components
version_num = pmag.get_version()
args = sys.argv
DefaultAge = ["none"]
skipdirs, coord, excrit, custom, vgps, average, Iaverage, plotsites, opt = 1, 0, 0, 0, 0, 0, 0, 0, 0
get_model_lat = 0 # this skips VADM calculation altogether, when get_model_lat=1, uses present day
fmt = 'svg'
dir_path = "."
model_lat_file = ""
Caverage = 0
infile = 'pmag_specimens.txt'
measfile = "magic_measurements.txt"
sampfile = "er_samples.txt"
sitefile = "er_sites.txt"
agefile = "er_ages.txt"
specout = "er_specimens.txt"
sampout = "pmag_samples.txt"
siteout = "pmag_sites.txt"
resout = "pmag_results.txt"
critout = "pmag_criteria.txt"
instout = "magic_instruments.txt"
sigcutoff, OBJ = "", ""
noDir, noInt = 0, 0
polarity = 0
coords = ['0']
Dcrit, Icrit, nocrit = 0, 0, 0
corrections = []
nocorrection = ['DA-NL', 'DA-AC', 'DA-CR']
priorities = ['DA-AC-ARM',
'DA-AC-TRM'] # priorities for anisotropy correction
# get command line stuff
if "-h" in args:
print main.__doc__
sys.exit()
if '-WD' in args:
ind = args.index("-WD")
dir_path = args[ind + 1]
if '-cor' in args:
ind = args.index('-cor')
cors = args[ind + 1].split(':') # list of required data adjustments
for cor in cors:
nocorrection.remove('DA-' + cor)
corrections.append('DA-' + cor)
if '-pri' in args:
ind = args.index('-pri')
priorities = args[ind + 1].split(
':') # list of required data adjustments
for p in priorities:
p = 'DA-AC-' + p
if '-f' in args:
ind = args.index("-f")
measfile = args[ind + 1]
if '-fsp' in args:
ind = args.index("-fsp")
infile = args[ind + 1]
if '-fsi' in args:
ind = args.index("-fsi")
sitefile = args[ind + 1]
if "-crd" in args:
ind = args.index("-crd")
coord = args[ind + 1]
if coord == 's': coords = ['-1']
if coord == 'g': coords = ['0']
if coord == 't': coords = ['100']
if coord == 'b': coords = ['0', '100']
if "-usr" in args:
ind = args.index("-usr")
user = sys.argv[ind + 1]
else:
user = ""
if "-C" in args: Dcrit, Icrit, nocrit = 1, 1, 1 # no selection criteria
if "-sam" in args: vgps = 1 # save sample level VGPS/VADMs
if "-xSi" in args:
nositeints = 1 # skip site level intensity
else:
nositeints = 0
if "-age" in args:
ind = args.index("-age")
DefaultAge[0] = args[ind + 1]
DefaultAge.append(args[ind + 2])
DefaultAge.append(args[ind + 3])
Daverage, Iaverage, Caverage = 0, 0, 0
if "-aD" in args: Daverage = 1 # average by sample directions
if "-aI" in args: Iaverage = 1 # average by sample intensities
if "-aC" in args:
Caverage = 1 # average all components together ??? why???
if "-pol" in args: polarity = 1 # calculate averages by polarity
if '-xD' in args: noDir = 1
if '-xI' in args:
noInt = 1
elif "-fla" in args:
if '-lat' in args:
print "you should set a paleolatitude file OR use present day lat - not both"
sys.exit()
ind = args.index("-fla")
model_lat_file = dir_path + '/' + args[ind + 1]
get_model_lat = 2
mlat = open(model_lat_file, 'rU')
ModelLats = []
for line in mlat.readlines():
ModelLat = {}
tmp = line.split()
ModelLat["er_site_name"] = tmp[0]
ModelLat["site_model_lat"] = tmp[1]
ModelLat["er_sample_name"] = tmp[0]
ModelLat["sample_lat"] = tmp[1]
ModelLats.append(ModelLat)
get_model_lat = 2
elif '-lat' in args:
get_model_lat = 1
if "-p" in args:
plotsites = 1
if "-fmt" in args:
ind = args.index("-fmt")
fmt = args[ind + 1]
if noDir == 0: # plot by site - set up plot window
import pmagplotlib
EQ = {}
EQ['eqarea'] = 1
pmagplotlib.plot_init(
EQ['eqarea'], 5, 5) # define figure 1 as equal area projection
pmagplotlib.plotNET(
EQ['eqarea']
) # I don't know why this has to be here, but otherwise the first plot never plots...
pmagplotlib.drawFIGS(EQ)
if '-WD' in args:
infile = dir_path + '/' + infile
measfile = dir_path + '/' + measfile
instout = dir_path + '/' + instout
sampfile = dir_path + '/' + sampfile
sitefile = dir_path + '/' + sitefile
agefile = dir_path + '/' + agefile
specout = dir_path + '/' + specout
sampout = dir_path + '/' + sampout
siteout = dir_path + '/' + siteout
resout = dir_path + '/' + resout
critout = dir_path + '/' + critout
if "-exc" in args: # use existing pmag_criteria file
if "-C" in args:
print 'you can not use both existing and no criteria - choose either -exc OR -C OR neither (for default)'
sys.exit()
crit_data, file_type = pmag.magic_read(critout)
print "Acceptance criteria read in from ", critout
else: # use default criteria (if nocrit set, then get really loose criteria as default)
crit_data = pmag.default_criteria(nocrit)
if nocrit == 0:
print "Acceptance criteria are defaults"
else:
print "No acceptance criteria used "
accept = {}
for critrec in crit_data:
for key in critrec.keys():
# need to migrate specimen_dang to specimen_int_dang for intensity data using old format
if 'IE-SPEC' in critrec.keys() and 'specimen_dang' in critrec.keys(
) and 'specimen_int_dang' not in critrec.keys():
critrec['specimen_int_dang'] = critrec['specimen_dang']
del critrec['specimen_dang']
# need to get rid of ron shaars sample_int_sigma_uT
if 'sample_int_sigma_uT' in critrec.keys():
critrec['sample_int_sigma'] = '%10.3e' % (
eval(critrec['sample_int_sigma_uT']) * 1e-6)
if key not in accept.keys() and critrec[key] != '':
accept[key] = critrec[key]
#
#
if "-exc" not in args and "-C" not in args:
print "args", args
pmag.magic_write(critout, [accept], 'pmag_criteria')
print "\n Pmag Criteria stored in ", critout, '\n'
#
# now we're done slow dancing
#
SiteNFO, file_type = pmag.magic_read(
sitefile) # read in site data - has the lats and lons
SampNFO, file_type = pmag.magic_read(
sampfile) # read in site data - has the lats and lons
height_nfo = pmag.get_dictitem(SiteNFO, 'site_height', '',
'F') # find all the sites with height info.
if agefile != "":
AgeNFO, file_type = pmag.magic_read(
agefile) # read in the age information
Data, file_type = pmag.magic_read(
infile) # read in specimen interpretations
IntData = pmag.get_dictitem(Data, 'specimen_int', '',
'F') # retrieve specimens with intensity data
comment, orient = "", []
samples, sites = [], []
for rec in Data: # run through the data filling in missing keys and finding all components, coordinates available
# fill in missing fields, collect unique sample and site names
if 'er_sample_name' not in rec.keys():
rec['er_sample_name'] = ""
elif rec['er_sample_name'] not in samples:
samples.append(rec['er_sample_name'])
if 'er_site_name' not in rec.keys():
rec['er_site_name'] = ""
elif rec['er_site_name'] not in sites:
sites.append(rec['er_site_name'])
if 'specimen_int' not in rec.keys(): rec['specimen_int'] = ''
if 'specimen_comp_name' not in rec.keys(
) or rec['specimen_comp_name'] == "":
rec['specimen_comp_name'] = 'A'
if rec['specimen_comp_name'] not in Comps:
Comps.append(rec['specimen_comp_name'])
rec['specimen_tilt_correction'] = rec[
'specimen_tilt_correction'].strip('\n')
if "specimen_tilt_correction" not in rec.keys():
rec["specimen_tilt_correction"] = "-1" # assume sample coordinates
if rec["specimen_tilt_correction"] not in orient:
orient.append(rec["specimen_tilt_correction"]
) # collect available coordinate systems
if "specimen_direction_type" not in rec.keys():
rec["specimen_direction_type"] = 'l' # assume direction is line - not plane
if "specimen_dec" not in rec.keys():
rec["specimen_direction_type"] = '' # if no declination, set direction type to blank
if "specimen_n" not in rec.keys(): rec["specimen_n"] = '' # put in n
if "specimen_alpha95" not in rec.keys():
rec["specimen_alpha95"] = '' # put in alpha95
if "magic_method_codes" not in rec.keys():
rec["magic_method_codes"] = ''
#
# start parsing data into SpecDirs, SpecPlanes, SpecInts
SpecInts, SpecDirs, SpecPlanes = [], [], []
samples.sort() # get sorted list of samples and sites
sites.sort()
if noInt == 0: # don't skip intensities
IntData = pmag.get_dictitem(
Data, 'specimen_int', '',
'F') # retrieve specimens with intensity data
if nocrit == 0: # use selection criteria
for rec in IntData: # do selection criteria
kill = pmag.grade(rec, accept, 'specimen_int')
if len(kill) == 0:
SpecInts.append(
rec
) # intensity record to be included in sample, site calculations
else:
SpecInts = IntData[:] # take everything - no selection criteria
# check for required data adjustments
if len(corrections) > 0 and len(SpecInts) > 0:
for cor in corrections:
SpecInts = pmag.get_dictitem(
SpecInts, 'magic_method_codes', cor,
'has') # only take specimens with the required corrections
if len(nocorrection) > 0 and len(SpecInts) > 0:
for cor in nocorrection:
SpecInts = pmag.get_dictitem(
SpecInts, 'magic_method_codes', cor, 'not'
) # exclude the corrections not specified for inclusion
# take top priority specimen of its name in remaining specimens (only one per customer)
PrioritySpecInts = []
specimens = pmag.get_specs(SpecInts) # get list of uniq specimen names
for spec in specimens:
ThisSpecRecs = pmag.get_dictitem(
SpecInts, 'er_specimen_name', spec,
'T') # all the records for this specimen
if len(ThisSpecRecs) == 1:
PrioritySpecInts.append(ThisSpecRecs[0])
elif len(ThisSpecRecs) > 1: # more than one
prec = []
for p in priorities:
ThisSpecRecs = pmag.get_dictitem(
SpecInts, 'magic_method_codes', p,
'has') # all the records for this specimen
if len(ThisSpecRecs) > 0: prec.append(ThisSpecRecs[0])
PrioritySpecInts.append(prec[0]) # take the best one
SpecInts = PrioritySpecInts # this has the first specimen record
if noDir == 0: # don't skip directions
AllDirs = pmag.get_dictitem(
Data, 'specimen_direction_type', '',
'F') # retrieve specimens with directed lines and planes
Ns = pmag.get_dictitem(
AllDirs, 'specimen_n', '',
'F') # get all specimens with specimen_n information
if nocrit != 1: # use selection criteria
for rec in Ns: # look through everything with specimen_n for "good" data
kill = pmag.grade(rec, accept, 'specimen_dir')
if len(kill) == 0: # nothing killed it
SpecDirs.append(rec)
else: # no criteria
SpecDirs = AllDirs[:] # take them all
# SpecDirs is now the list of all specimen directions (lines and planes) that pass muster
#
PmagSamps, SampDirs = [], [
] # list of all sample data and list of those that pass the DE-SAMP criteria
PmagSites, PmagResults = [], [
] # list of all site data and selected results
SampInts = []
for samp in samples: # run through the sample names
if Daverage == 1: # average by sample if desired
SampDir = pmag.get_dictitem(
SpecDirs, 'er_sample_name', samp,
'T') # get all the directional data for this sample
if len(SampDir) > 0: # there are some directions
for coord in coords: # step through desired coordinate systems
CoordDir = pmag.get_dictitem(
SampDir, 'specimen_tilt_correction', coord,
'T') # get all the directions for this sample
if len(CoordDir
) > 0: # there are some with this coordinate system
if Caverage == 0: # look component by component
for comp in Comps:
CompDir = pmag.get_dictitem(
CoordDir, 'specimen_comp_name', comp, 'T'
) # get all directions from this component
if len(CompDir) > 0: # there are some
PmagSampRec = pmag.lnpbykey(
CompDir, 'sample', 'specimen'
) # get a sample average from all specimens
PmagSampRec["er_location_name"] = CompDir[0][
'er_location_name'] # decorate the sample record
PmagSampRec["er_site_name"] = CompDir[0][
'er_site_name']
PmagSampRec["er_sample_name"] = samp
PmagSampRec[
"er_citation_names"] = "This study"
PmagSampRec["er_analyst_mail_names"] = user
PmagSampRec[
'magic_software_packages'] = version_num
if nocrit != 1:
PmagSampRec[
'pmag_criteria_codes'] = "ACCEPT"
if agefile != "":
PmagSampRec = pmag.get_age(
PmagSampRec, "er_site_name",
"sample_inferred_", AgeNFO,
DefaultAge)
site_height = pmag.get_dictitem(
height_nfo, 'er_site_name',
PmagSampRec['er_site_name'], 'T')
if len(site_height) > 0:
PmagSampRec[
"sample_height"] = site_height[0][
'site_height'] # add in height if available
PmagSampRec['sample_comp_name'] = comp
PmagSampRec[
'sample_tilt_correction'] = coord
PmagSampRec[
'er_specimen_names'] = pmag.get_list(
CompDir, 'er_specimen_name'
) # get a list of the specimen names used
PmagSampRec[
'magic_method_codes'] = pmag.get_list(
CompDir, 'magic_method_codes'
) # get a list of the methods used
if nocrit != 1: # apply selection criteria
kill = pmag.grade(
PmagSampRec, accept, 'sample_dir')
else:
kill = []
if len(kill) == 0:
SampDirs.append(PmagSampRec)
if vgps == 1: # if sample level VGP info desired, do that now
PmagResRec = pmag.getsampVGP(
PmagSampRec, SiteNFO)
if PmagResRec != "":
PmagResults.append(PmagResRec)
PmagSamps.append(PmagSampRec)
if Caverage == 1: # average all components together basically same as above
PmagSampRec = pmag.lnpbykey(
CoordDir, 'sample', 'specimen')
PmagSampRec["er_location_name"] = CoordDir[0][
'er_location_name']
PmagSampRec["er_site_name"] = CoordDir[0][
'er_site_name']
PmagSampRec["er_sample_name"] = samp
PmagSampRec["er_citation_names"] = "This study"
PmagSampRec["er_analyst_mail_names"] = user
PmagSampRec[
'magic_software_packages'] = version_num
if nocrit != 1:
PmagSampRec['pmag_criteria_codes'] = ""
if agefile != "":
PmagSampRec = pmag.get_age(
PmagSampRec, "er_site_name",
"sample_inferred_", AgeNFO, DefaultAge)
site_height = pmag.get_dictitem(
height_nfo, 'er_site_name', site, 'T')
if len(site_height) > 0:
PmagSampRec["sample_height"] = site_height[0][
'site_height'] # add in height if available
PmagSampRec['sample_tilt_correction'] = coord
PmagSampRec['sample_comp_name'] = pmag.get_list(
CoordDir,
'specimen_comp_name') # get components used
PmagSampRec['er_specimen_names'] = pmag.get_list(
CoordDir, 'er_specimen_name'
) # get specimne names averaged
PmagSampRec['magic_method_codes'] = pmag.get_list(
CoordDir,
'magic_method_codes') # assemble method codes
if nocrit != 1: # apply selection criteria
kill = pmag.grade(PmagSampRec, accept,
'sample_dir')
if len(kill) == 0: # passes the mustard
SampDirs.append(PmagSampRec)
if vgps == 1:
PmagResRec = pmag.getsampVGP(
PmagSampRec, SiteNFO)
if PmagResRec != "":
PmagResults.append(PmagResRec)
else: # take everything
SampDirs.append(PmagSampRec)
if vgps == 1:
PmagResRec = pmag.getsampVGP(
PmagSampRec, SiteNFO)
if PmagResRec != "":
PmagResults.append(PmagResRec)
PmagSamps.append(PmagSampRec)
if Iaverage == 1: # average by sample if desired
SampI = pmag.get_dictitem(
SpecInts, 'er_sample_name', samp,
'T') # get all the intensity data for this sample
if len(SampI) > 0: # there are some
PmagSampRec = pmag.average_int(
SampI, 'specimen', 'sample') # get average intensity stuff
PmagSampRec[
"sample_description"] = "sample intensity" # decorate sample record
PmagSampRec["sample_direction_type"] = ""
PmagSampRec['er_site_name'] = SampI[0]["er_site_name"]
PmagSampRec['er_sample_name'] = samp
PmagSampRec['er_location_name'] = SampI[0]["er_location_name"]
PmagSampRec["er_citation_names"] = "This study"
PmagSampRec["er_analyst_mail_names"] = user
if agefile != "":
PmagSampRec = pmag.get_age(PmagSampRec, "er_site_name",
"sample_inferred_", AgeNFO,
DefaultAge)
site_height = pmag.get_dictitem(height_nfo, 'er_site_name',
PmagSampRec['er_site_name'],
'T')
if len(site_height) > 0:
PmagSampRec["sample_height"] = site_height[0][
'site_height'] # add in height if available
PmagSampRec['er_specimen_names'] = pmag.get_list(
SampI, 'er_specimen_name')
PmagSampRec['magic_method_codes'] = pmag.get_list(
SampI, 'magic_method_codes')
if nocrit != 1: # apply criteria!
kill = pmag.grade(PmagSampRec, accept, 'sample_int')
if len(kill) == 0:
PmagSampRec['pmag_criteria_codes'] = "ACCEPT"
SampInts.append(PmagSampRec)
PmagSamps.append(PmagSampRec)
else:
PmagSampRec = {} # sample rejected
else: # no criteria
SampInts.append(PmagSampRec)
PmagSamps.append(PmagSampRec)
PmagSampRec['pmag_criteria_codes'] = ""
if vgps == 1 and get_model_lat != 0 and PmagSampRec != {}: #
if get_model_lat == 1: # use sample latitude
PmagResRec = pmag.getsampVDM(PmagSampRec, SampNFO)
del (PmagResRec['model_lat']
) # get rid of the model lat key
elif get_model_lat == 2: # use model latitude
PmagResRec = pmag.getsampVDM(PmagSampRec, ModelLats)
if PmagResRec != {}:
PmagResRec['magic_method_codes'] = PmagResRec[
'magic_method_codes'] + ":IE-MLAT"
if PmagResRec != {}:
PmagResRec['er_specimen_names'] = PmagSampRec[
'er_specimen_names']
PmagResRec['er_sample_names'] = PmagSampRec[
'er_sample_name']
PmagResRec['pmag_criteria_codes'] = 'ACCEPT'
PmagResRec['average_int_sigma_perc'] = PmagSampRec[
'sample_int_sigma_perc']
PmagResRec['average_int_sigma'] = PmagSampRec[
'sample_int_sigma']
PmagResRec['average_int_n'] = PmagSampRec[
'sample_int_n']
PmagResRec['vadm_n'] = PmagSampRec['sample_int_n']
PmagResRec['data_type'] = 'i'
PmagResults.append(PmagResRec)
if len(PmagSamps) > 0:
TmpSamps, keylist = pmag.fillkeys(
PmagSamps) # fill in missing keys from different types of records
pmag.magic_write(sampout, TmpSamps,
'pmag_samples') # save in sample output file
print ' sample averages written to ', sampout
#
#create site averages from specimens or samples as specified
#
for site in sites:
if Daverage == 0:
key, dirlist = 'specimen', SpecDirs # if specimen averages at site level desired
if Daverage == 1:
key, dirlist = 'sample', SampDirs # if sample averages at site level desired
tmp = pmag.get_dictitem(dirlist, 'er_site_name', site,
'T') # get all the sites with directions
tmp1 = pmag.get_dictitem(
tmp, key + '_tilt_correction', coords[-1],
'T') # use only the last coordinate if Caverage==0
sd = pmag.get_dictitem(
SiteNFO, 'er_site_name', site,
'T') # fish out site information (lat/lon, etc.)
if len(sd) > 0:
sitedat = sd[0]
if Caverage == 0: # do component wise averaging
for comp in Comps:
siteD = pmag.get_dictitem(tmp1, key + '_comp_name', comp,
'T') # get all components comp
if len(
siteD
) > 0: # there are some for this site and component name
PmagSiteRec = pmag.lnpbykey(
siteD, 'site', key) # get an average for this site
PmagSiteRec[
'site_comp_name'] = comp # decorate the site record
PmagSiteRec["er_location_name"] = siteD[0][
'er_location_name']
PmagSiteRec["er_site_name"] = siteD[0]['er_site_name']
PmagSiteRec['site_tilt_correction'] = coords[-1]
PmagSiteRec['site_comp_name'] = pmag.get_list(
siteD, key + '_comp_name')
if Daverage == 1:
PmagSiteRec['er_sample_names'] = pmag.get_list(
siteD, 'er_sample_name')
else:
PmagSiteRec['er_specimen_names'] = pmag.get_list(
siteD, 'er_specimen_name')
# determine the demagnetization code (DC3,4 or 5) for this site
AFnum = len(
pmag.get_dictitem(siteD, 'magic_method_codes',
'LP-DIR-AF', 'has'))
Tnum = len(
pmag.get_dictitem(siteD, 'magic_method_codes',
'LP-DIR-T', 'has'))
DC = 3
if AFnum > 0: DC += 1
if Tnum > 0: DC += 1
PmagSiteRec['magic_method_codes'] = pmag.get_list(
siteD,
'magic_method_codes') + ':' + 'LP-DC' + str(DC)
PmagSiteRec['magic_method_codes'].strip(":")
if plotsites == 1:
print PmagSiteRec['er_site_name']
pmagplotlib.plotSITE(EQ['eqarea'], PmagSiteRec,
siteD,
key) # plot and list the data
pmagplotlib.drawFIGS(EQ)
PmagSites.append(PmagSiteRec)
else: # last component only
siteD = tmp1[:] # get the last orientation system specified
if len(siteD) > 0: # there are some
PmagSiteRec = pmag.lnpbykey(
siteD, 'site', key) # get the average for this site
PmagSiteRec["er_location_name"] = siteD[0][
'er_location_name'] # decorate the record
PmagSiteRec["er_site_name"] = siteD[0]['er_site_name']
PmagSiteRec['site_comp_name'] = comp
PmagSiteRec['site_tilt_correction'] = coords[-1]
PmagSiteRec['site_comp_name'] = pmag.get_list(
siteD, key + '_comp_name')
PmagSiteRec['er_specimen_names'] = pmag.get_list(
siteD, 'er_specimen_name')
PmagSiteRec['er_sample_names'] = pmag.get_list(
siteD, 'er_sample_name')
AFnum = len(
pmag.get_dictitem(siteD, 'magic_method_codes',
'LP-DIR-AF', 'has'))
Tnum = len(
pmag.get_dictitem(siteD, 'magic_method_codes',
'LP-DIR-T', 'has'))
DC = 3
if AFnum > 0: DC += 1
if Tnum > 0: DC += 1
PmagSiteRec['magic_method_codes'] = pmag.get_list(
siteD, 'magic_method_codes') + ':' + 'LP-DC' + str(DC)
PmagSiteRec['magic_method_codes'].strip(":")
if Daverage == 0:
PmagSiteRec['site_comp_name'] = pmag.get_list(
siteD, key + '_comp_name')
if plotsites == 1:
pmagplotlib.plotSITE(EQ['eqarea'], PmagSiteRec, siteD,
key)
pmagplotlib.drawFIGS(EQ)
PmagSites.append(PmagSiteRec)
else:
print 'site information not found in er_sites for site, ', site, ' site will be skipped'
for PmagSiteRec in PmagSites: # now decorate each dictionary some more, and calculate VGPs etc. for results table
PmagSiteRec["er_citation_names"] = "This study"
PmagSiteRec["er_analyst_mail_names"] = user
PmagSiteRec['magic_software_packages'] = version_num
if agefile != "":
PmagSiteRec = pmag.get_age(PmagSiteRec, "er_site_name",
"site_inferred_", AgeNFO, DefaultAge)
PmagSiteRec['pmag_criteria_codes'] = 'ACCEPT'
if 'site_n_lines' in PmagSiteRec.keys(
) and 'site_n_planes' in PmagSiteRec.keys() and PmagSiteRec[
'site_n_lines'] != "" and PmagSiteRec['site_n_planes'] != "":
if int(PmagSiteRec["site_n_planes"]) > 0:
PmagSiteRec["magic_method_codes"] = PmagSiteRec[
'magic_method_codes'] + ":DE-FM-LP"
elif int(PmagSiteRec["site_n_lines"]) > 2:
PmagSiteRec["magic_method_codes"] = PmagSiteRec[
'magic_method_codes'] + ":DE-FM"
kill = pmag.grade(PmagSiteRec, accept, 'site_dir')
if len(kill) == 0:
PmagResRec = {
} # set up dictionary for the pmag_results table entry
PmagResRec['data_type'] = 'i' # decorate it a bit
PmagResRec['magic_software_packages'] = version_num
PmagSiteRec[
'site_description'] = 'Site direction included in results table'
PmagResRec['pmag_criteria_codes'] = 'ACCEPT'
dec = float(PmagSiteRec["site_dec"])
inc = float(PmagSiteRec["site_inc"])
if 'site_alpha95' in PmagSiteRec.keys(
) and PmagSiteRec['site_alpha95'] != "":
a95 = float(PmagSiteRec["site_alpha95"])
else:
a95 = 180.
sitedat = pmag.get_dictitem(
SiteNFO, 'er_site_name', PmagSiteRec['er_site_name'],
'T')[0] # fish out site information (lat/lon, etc.)
lat = float(sitedat['site_lat'])
lon = float(sitedat['site_lon'])
plong, plat, dp, dm = pmag.dia_vgp(
dec, inc, a95, lat, lon) # get the VGP for this site
if PmagSiteRec['site_tilt_correction'] == '-1':
C = ' (spec coord) '
if PmagSiteRec['site_tilt_correction'] == '0':
C = ' (geog. coord) '
if PmagSiteRec['site_tilt_correction'] == '100':
C = ' (strat. coord) '
PmagResRec["pmag_result_name"] = "VGP Site: " + PmagSiteRec[
"er_site_name"] # decorate some more
PmagResRec[
"result_description"] = "Site VGP, coord system = " + str(
coord) + ' component: ' + comp
PmagResRec['er_site_names'] = PmagSiteRec['er_site_name']
PmagResRec['pmag_criteria_codes'] = 'ACCEPT'
PmagResRec['er_citation_names'] = 'This study'
PmagResRec['er_analyst_mail_names'] = user
PmagResRec["er_location_names"] = PmagSiteRec[
"er_location_name"]
if Daverage == 1:
PmagResRec["er_sample_names"] = PmagSiteRec[
"er_sample_names"]
else:
PmagResRec["er_specimen_names"] = PmagSiteRec[
"er_specimen_names"]
PmagResRec["tilt_correction"] = PmagSiteRec[
'site_tilt_correction']
PmagResRec["pole_comp_name"] = PmagSiteRec['site_comp_name']
PmagResRec["average_dec"] = PmagSiteRec["site_dec"]
PmagResRec["average_inc"] = PmagSiteRec["site_inc"]
PmagResRec["average_alpha95"] = PmagSiteRec["site_alpha95"]
PmagResRec["average_n"] = PmagSiteRec["site_n"]
PmagResRec["average_n_lines"] = PmagSiteRec["site_n_lines"]
PmagResRec["average_n_planes"] = PmagSiteRec["site_n_planes"]
PmagResRec["vgp_n"] = PmagSiteRec["site_n"]
PmagResRec["average_k"] = PmagSiteRec["site_k"]
PmagResRec["average_r"] = PmagSiteRec["site_r"]
PmagResRec["average_lat"] = '%10.4f ' % (lat)
PmagResRec["average_lon"] = '%10.4f ' % (lon)
if agefile != "":
PmagResRec = pmag.get_age(PmagResRec, "er_site_names",
"average_", AgeNFO, DefaultAge)
site_height = pmag.get_dictitem(height_nfo, 'er_site_name',
site, 'T')
if len(site_height) > 0:
PmagResRec["average_height"] = site_height[0][
'site_height']
PmagResRec["vgp_lat"] = '%7.1f ' % (plat)
PmagResRec["vgp_lon"] = '%7.1f ' % (plong)
PmagResRec["vgp_dp"] = '%7.1f ' % (dp)
PmagResRec["vgp_dm"] = '%7.1f ' % (dm)
PmagResRec["magic_method_codes"] = PmagSiteRec[
"magic_method_codes"]
if PmagSiteRec['site_tilt_correction'] == '0':
PmagSiteRec['magic_method_codes'] = PmagSiteRec[
'magic_method_codes'] + ":DA-DIR-GEO"
if PmagSiteRec['site_tilt_correction'] == '100':
PmagSiteRec['magic_method_codes'] = PmagSiteRec[
'magic_method_codes'] + ":DA-DIR-TILT"
PmagSiteRec['site_polarity'] = ""
if polarity == 1: # assign polarity based on angle of pole lat to spin axis - may want to re-think this sometime
angle = pmag.angle([0, 0], [0, (90 - plat)])
if angle <= 55.: PmagSiteRec["site_polarity"] = 'n'
if angle > 55. and angle < 125.:
PmagSiteRec["site_polarity"] = 't'
if angle >= 125.: PmagSiteRec["site_polarity"] = 'r'
PmagResults.append(PmagResRec)
if polarity == 1:
crecs = pmag.get_dictitem(PmagSites, 'site_tilt_correction', '100',
'T') # find the tilt corrected data
if len(crecs) < 2:
crecs = pmag.get_dictitem(
PmagSites, 'site_tilt_correction', '0',
'T') # if there aren't any, find the geographic corrected data
if len(crecs) > 2: # if there are some,
comp = pmag.get_list(
crecs,
'site_comp_name').split(':')[0] # find the first component
crecs = pmag.get_dictitem(
crecs, 'site_comp_name', comp,
'T') # fish out all of the first component
precs = []
for rec in crecs:
precs.append({
'dec': rec['site_dec'],
'inc': rec['site_inc'],
'name': rec['er_site_name'],
'loc': rec['er_location_name']
})
polpars = pmag.fisher_by_pol(
precs) # calculate average by polarity
for mode in polpars.keys(
): # hunt through all the modes (normal=A, reverse=B, all=ALL)
PolRes = {}
PolRes['er_citation_names'] = 'This study'
PolRes[
"pmag_result_name"] = "Polarity Average: Polarity " + mode #
PolRes["data_type"] = "a"
PolRes["average_dec"] = '%7.1f' % (polpars[mode]['dec'])
PolRes["average_inc"] = '%7.1f' % (polpars[mode]['inc'])
PolRes["average_n"] = '%i' % (polpars[mode]['n'])
PolRes["average_r"] = '%5.4f' % (polpars[mode]['r'])
PolRes["average_k"] = '%6.0f' % (polpars[mode]['k'])
PolRes["average_alpha95"] = '%7.1f' % (
polpars[mode]['alpha95'])
PolRes['er_site_names'] = polpars[mode]['sites']
PolRes['er_location_names'] = polpars[mode]['locs']
PolRes['magic_software_packages'] = version_num
PmagResults.append(PolRes)
if noInt != 1 and nositeints != 1:
for site in sites: # now do intensities for each site
if plotsites == 1: print site
if Iaverage == 0:
key, intlist = 'specimen', SpecInts # if using specimen level data
if Iaverage == 1:
key, intlist = 'sample', PmagSamps # if using sample level data
Ints = pmag.get_dictitem(
intlist, 'er_site_name', site,
'T') # get all the intensities for this site
if len(Ints) > 0: # there are some
PmagSiteRec = pmag.average_int(
Ints, key,
'site') # get average intensity stuff for site table
PmagResRec = pmag.average_int(
Ints, key,
'average') # get average intensity stuff for results table
if plotsites == 1: # if site by site examination requested - print this site out to the screen
for rec in Ints:
print rec['er_' + key + '_name'], ' %7.1f' % (
1e6 * float(rec[key + '_int']))
if len(Ints) > 1:
print 'Average: ', '%7.1f' % (1e6 * float(
PmagResRec['average_int'])), 'N: ', len(Ints)
print 'Sigma: ', '%7.1f' % (
1e6 * float(PmagResRec['average_int_sigma'])
), 'Sigma %: ', PmagResRec['average_int_sigma_perc']
raw_input('Press any key to continue\n')
er_location_name = Ints[0]["er_location_name"]
PmagSiteRec[
"er_location_name"] = er_location_name # decorate the records
PmagSiteRec["er_citation_names"] = "This study"
PmagResRec["er_location_names"] = er_location_name
PmagResRec["er_citation_names"] = "This study"
PmagSiteRec["er_analyst_mail_names"] = user
PmagResRec["er_analyst_mail_names"] = user
PmagResRec["data_type"] = 'i'
if Iaverage == 0:
PmagSiteRec['er_specimen_names'] = pmag.get_list(
Ints, 'er_specimen_name') # list of all specimens used
PmagResRec['er_specimen_names'] = pmag.get_list(
Ints, 'er_specimen_name')
PmagSiteRec['er_sample_names'] = pmag.get_list(
Ints, 'er_sample_name') # list of all samples used
PmagResRec['er_sample_names'] = pmag.get_list(
Ints, 'er_sample_name')
PmagSiteRec['er_site_name'] = site
PmagResRec['er_site_names'] = site
PmagSiteRec['magic_method_codes'] = pmag.get_list(
Ints, 'magic_method_codes')
PmagResRec['magic_method_codes'] = pmag.get_list(
Ints, 'magic_method_codes')
kill = pmag.grade(PmagSiteRec, accept, 'site_int')
if nocrit == 1 or len(kill) == 0:
b, sig = float(PmagResRec['average_int']), ""
if (PmagResRec['average_int_sigma']) != "":
sig = float(PmagResRec['average_int_sigma'])
sdir = pmag.get_dictitem(PmagResults, 'er_site_names',
site,
'T') # fish out site direction
if len(sdir) > 0 and sdir[-1][
'average_inc'] != "": # get the VDM for this record using last average inclination (hope it is the right one!)
inc = float(sdir[0]['average_inc']) #
mlat = pmag.magnetic_lat(
inc) # get magnetic latitude using dipole formula
PmagResRec["vdm"] = '%8.3e ' % (pmag.b_vdm(
b, mlat)) # get VDM with magnetic latitude
PmagResRec["vdm_n"] = PmagResRec['average_int_n']
if 'average_int_sigma' in PmagResRec.keys(
) and PmagResRec['average_int_sigma'] != "":
vdm_sig = pmag.b_vdm(
float(PmagResRec['average_int_sigma']), mlat)
PmagResRec["vdm_sigma"] = '%8.3e ' % (vdm_sig)
else:
PmagResRec["vdm_sigma"] = ""
mlat = "" # define a model latitude
if get_model_lat == 1: # use present site latitude
mlats = pmag.get_dictitem(SiteNFO, 'er_site_name',
site, 'T')
if len(mlats) > 0: mlat = mlats[0]['site_lat']
elif get_model_lat == 2: # use a model latitude from some plate reconstruction model (or something)
mlats = pmag.get_dictitem(ModelLats, 'er_site_name',
site, 'T')
if len(mlats) > 0:
PmagResRec['model_lat'] = mlats[0][
'site_model_lat']
mlat = PmagResRec['model_lat']
if mlat != "":
PmagResRec["vadm"] = '%8.3e ' % (
pmag.b_vdm(b, float(mlat))
) # get the VADM using the desired latitude
if sig != "":
vdm_sig = pmag.b_vdm(
float(PmagResRec['average_int_sigma']),
float(mlat))
PmagResRec["vadm_sigma"] = '%8.3e ' % (vdm_sig)
PmagResRec["vadm_n"] = PmagResRec['average_int_n']
else:
PmagResRec["vadm_sigma"] = ""
sitedat = pmag.get_dictitem(
SiteNFO, 'er_site_name', PmagSiteRec['er_site_name'],
'T') # fish out site information (lat/lon, etc.)
if len(sitedat) > 0:
sitedat = sitedat[0]
PmagResRec['average_lat'] = sitedat['site_lat']
PmagResRec['average_lon'] = sitedat['site_lon']
else:
PmagResRec['average_lon'] = 'UNKNOWN'
PmagResRec['average_lon'] = 'UNKNOWN'
PmagResRec['magic_software_packages'] = version_num
PmagResRec["pmag_result_name"] = "V[A]DM: Site " + site
PmagResRec["result_description"] = "V[A]DM of site"
PmagResRec["pmag_criteria_codes"] = "ACCEPT"
if agefile != "":
PmagResRec = pmag.get_age(PmagResRec, "er_site_names",
"average_", AgeNFO,
DefaultAge)
site_height = pmag.get_dictitem(height_nfo, 'er_site_name',
site, 'T')
if len(site_height) > 0:
PmagResRec["average_height"] = site_height[0][
'site_height']
PmagSites.append(PmagSiteRec)
PmagResults.append(PmagResRec)
if len(PmagSites) > 0:
Tmp, keylist = pmag.fillkeys(PmagSites)
pmag.magic_write(siteout, Tmp, 'pmag_sites')
print ' sites written to ', siteout
else:
print "No Site level table"
if len(PmagResults) > 0:
TmpRes, keylist = pmag.fillkeys(PmagResults)
pmag.magic_write(resout, TmpRes, 'pmag_results')
print ' results written to ', resout
else:
print "No Results level table"
def main():
"""
NAME
eqarea_magic.py
DESCRIPTION
makes equal area projections from declination/inclination data
SYNTAX
eqarea_magic.py [command line options]
INPUT
takes magic formatted pmag_results, pmag_sites, pmag_samples or pmag_specimens
OPTIONS
-h prints help message and quits
-f FILE: specify input magic format file from magic,default='pmag_results.txt'
supported types=[magic_measurements,pmag_specimens, pmag_samples, pmag_sites, pmag_results, magic_web]
-obj OBJ: specify level of plot [all, sit, sam, spc], default is all
-crd [s,g,t]: specify coordinate system, [s]pecimen, [g]eographic, [t]ilt adjusted
default is geographic
-fmt [svg,png,jpg] format for output plots
-ell [F,K,B,Be,Bv] plot Fisher, Kent, Bingham, Bootstrap ellipses or Boostrap eigenvectors
-c plot as colour contour
NOTE
all: entire file; sit: site; sam: sample; spc: specimen
"""
FIG={} # plot dictionary
FIG['eq']=1 # eqarea is figure 1
in_file,plot_key,coord,crd='pmag_results.txt','all',"-1",'g'
fmt,dist,mode='svg','F',1
plotE,contour=0,0
dir_path='.'
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]
pmagplotlib.plot_init(FIG['eq'],5,5)
if '-f' in sys.argv:
ind=sys.argv.index("-f")
in_file=dir_path+"/"+sys.argv[ind+1]
if '-obj' in sys.argv:
ind=sys.argv.index('-obj')
plot_by=sys.argv[ind+1]
if plot_by=='all':plot_key='all'
if plot_by=='sit':plot_key='er_site_name'
if plot_by=='sam':plot_key='er_sample_name'
if plot_by=='spc':plot_key='er_specimen_name'
if '-c' in sys.argv: contour=1
if '-ell' in sys.argv:
plotE=1
ind=sys.argv.index('-ell')
ell_type=sys.argv[ind+1]
if ell_type=='F':dist='F'
if ell_type=='K':dist='K'
if ell_type=='B':dist='B'
if ell_type=='Be':dist='BE'
if ell_type=='Bv':
dist='BV'
FIG['bdirs']=2
pmagplotlib.plot_init(FIG['bdirs'],5,5)
if '-crd' in sys.argv:
ind=sys.argv.index("-crd")
coord=sys.argv[ind+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]
Dec_keys=['site_dec','sample_dec','specimen_dec','measurement_dec','average_dec']
Inc_keys=['site_inc','sample_inc','specimen_inc','measurement_inc','average_inc']
Tilt_keys=['tilt_correction','site_tilt_correction','sample_tilt_correction','specimen_tilt_correction']
Dir_type_keys=['','site_direction_type','sample_direction_type','specimen_direction_type']
Name_keys=['er_specimen_name','er_sample_name','er_site_name','pmag_result_name']
data,file_type=pmag.magic_read(in_file)
if file_type=='pmag_results' and plot_key!="all":plot_key=plot_key+'s' # need plural for results table
if pmagplotlib.verbose:
print len(data),' records read from ',in_file
#
#
# find desired dec,inc data:
#
dir_type_key=''
#
# get plotlist if not plotting all records
#
plotlist=[]
if plot_key!="all":
for rec in data:
if rec[plot_key] not in plotlist:
plotlist.append(rec[plot_key])
plotlist.sort()
else:
plotlist.append('Whole file')
for plot in plotlist:
DIblock=[]
GCblock=[]
SLblock,SPblock=[],[]
tilt_key=""
mode=1
for rec in data: # find what data are available
if plot_key=='all' or rec[plot_key]==plot:
if plot_key!="all":
title=rec[plot_key]
else:
title=plot
if coord=='-1':title=title+' Specimen Coordinates'
if coord=='0':title=title+' Geographic Coordinates'
if coord=='100':title=title+' Tilt corrected Coordinates'
dec_key,inc_key,tilt_key,name_key,k="","","","",0
while dec_key=="" and k<len(Dec_keys):
if Dec_keys[k] in rec.keys() and rec[Dec_keys[k]]!="" and Inc_keys[k] in rec.keys() and rec[Inc_keys[k]]!="":
dec_key,inc_key =Dec_keys[k],Inc_keys[k]
k+=1
k=0
while tilt_key=="" and k<len(Tilt_keys):
if Tilt_keys[k] in rec.keys():tilt_key=Tilt_keys[k]
k+=1
k=0
while name_key=="" and k<len(Name_keys):
if Name_keys[k] in rec.keys():name_key=Name_keys[k]
k+=1
k=1
while dir_type_key=="" and k<len(Dir_type_keys):
if Dir_type_keys[k] in rec.keys():dir_type_key=Dir_type_keys[k]
k+=1
if dec_key!="":break
if tilt_key=="":tilt_key='-1'
if dir_type_key=="":dir_type_key='direction_type'
for rec in data: # pick out the data
if (plot_key=='all' or rec[plot_key]==plot) and rec[dec_key].strip()!="" and rec[inc_key].strip()!="":
if dir_type_key not in rec.keys() or rec[dir_type_key]=="":rec[dir_type_key]='l'
if tilt_key not in rec.keys():rec[tilt_key]='-1' # assume specimen coordinates unless otherwise specified
if coord=='-1':
DIblock.append([float(rec[dec_key]),float(rec[inc_key])])
SLblock.append([rec[name_key],rec['magic_method_codes']])
elif rec[tilt_key]==coord and rec[dir_type_key]=='l' and rec[dec_key]!="" and rec[inc_key]!="":
if rec[tilt_key]==coord and rec[dir_type_key]=='l' and rec[dec_key]!="" and rec[inc_key]!="":
DIblock.append([float(rec[dec_key]),float(rec[inc_key])])
SLblock.append([rec[name_key],rec['magic_method_codes']])
elif rec[tilt_key]==coord and rec[dir_type_key]!='l' and rec[dec_key]!="" and rec[inc_key]!="":
GCblock.append([float(rec[dec_key]),float(rec[inc_key])])
SPblock.append([rec[name_key],rec['magic_method_codes']])
if len(DIblock)==0 and len(GCblock)==0:
if pmagplotlib.verbose: print "no records for plotting"
sys.exit()
if pmagplotlib.verbose:
for k in range(len(SLblock)):
print '%s %s %7.1f %7.1f'%(SLblock[k][0],SLblock[k][1],DIblock[k][0],DIblock[k][1])
for k in range(len(SPblock)):
print '%s %s %7.1f %7.1f'%(SPblock[k][0],SPblock[k][1],GCblock[k][0],GCblock[k][1])
if len(DIblock)>0:
if contour==0:
pmagplotlib.plotEQ(FIG['eq'],DIblock,title)
else:
pmagplotlib.plotEQcont(FIG['eq'],DIblock)
else: pmagplotlib.plotNET(FIG['eq'])
if len(GCblock)>0:
for rec in GCblock: pmagplotlib.plotC(FIG['eq'],rec,90.,'g')
if plotE==1:
ppars=pmag.doprinc(DIblock) # get principal directions
nDIs,rDIs,npars,rpars=[],[],[],[]
for rec in DIblock:
angle=pmag.angle([rec[0],rec[1]],[ppars['dec'],ppars['inc']])
if angle>90.:
rDIs.append(rec)
else:
nDIs.append(rec)
if dist=='B': # do on whole dataset
etitle="Bingham confidence ellipse"
bpars=pmag.dobingham(DIblock)
for key in bpars.keys():
if key!='n' and pmagplotlib.verbose:print " ",key, '%7.1f'%(bpars[key])
if key=='n' and pmagplotlib.verbose:print " ",key, ' %i'%(bpars[key])
npars.append(bpars['dec'])
npars.append(bpars['inc'])
npars.append(bpars['Zeta'])
npars.append(bpars['Zdec'])
npars.append(bpars['Zinc'])
npars.append(bpars['Eta'])
npars.append(bpars['Edec'])
npars.append(bpars['Einc'])
if dist=='F':
etitle="Fisher confidence cone"
if len(nDIs)>2:
fpars=pmag.fisher_mean(nDIs)
for key in fpars.keys():
if key!='n' and pmagplotlib.verbose:print " ",key, '%7.1f'%(fpars[key])
if key=='n' and pmagplotlib.verbose:print " ",key, ' %i'%(fpars[key])
mode+=1
npars.append(fpars['dec'])
npars.append(fpars['inc'])
npars.append(fpars['alpha95']) # Beta
npars.append(fpars['dec'])
isign=abs(fpars['inc'])/fpars['inc']
npars.append(fpars['inc']-isign*90.) #Beta inc
npars.append(fpars['alpha95']) # gamma
npars.append(fpars['dec']+90.) # Beta dec
npars.append(0.) #Beta inc
if len(rDIs)>2:
fpars=pmag.fisher_mean(rDIs)
if pmagplotlib.verbose:print "mode ",mode
for key in fpars.keys():
if key!='n' and pmagplotlib.verbose:print " ",key, '%7.1f'%(fpars[key])
if key=='n' and pmagplotlib.verbose:print " ",key, ' %i'%(fpars[key])
mode+=1
rpars.append(fpars['dec'])
rpars.append(fpars['inc'])
rpars.append(fpars['alpha95']) # Beta
rpars.append(fpars['dec'])
isign=abs(fpars['inc'])/fpars['inc']
rpars.append(fpars['inc']-isign*90.) #Beta inc
rpars.append(fpars['alpha95']) # gamma
rpars.append(fpars['dec']+90.) # Beta dec
rpars.append(0.) #Beta inc
if dist=='K':
etitle="Kent confidence ellipse"
if len(nDIs)>3:
kpars=pmag.dokent(nDIs,len(nDIs))
if pmagplotlib.verbose:print "mode ",mode
for key in kpars.keys():
if key!='n' and pmagplotlib.verbose:print " ",key, '%7.1f'%(kpars[key])
if key=='n' and pmagplotlib.verbose:print " ",key, ' %i'%(kpars[key])
mode+=1
npars.append(kpars['dec'])
npars.append(kpars['inc'])
npars.append(kpars['Zeta'])
npars.append(kpars['Zdec'])
npars.append(kpars['Zinc'])
npars.append(kpars['Eta'])
npars.append(kpars['Edec'])
npars.append(kpars['Einc'])
if len(rDIs)>3:
kpars=pmag.dokent(rDIs,len(rDIs))
if pmagplotlib.verbose:print "mode ",mode
for key in kpars.keys():
if key!='n' and pmagplotlib.verbose:print " ",key, '%7.1f'%(kpars[key])
if key=='n' and pmagplotlib.verbose:print " ",key, ' %i'%(kpars[key])
mode+=1
rpars.append(kpars['dec'])
rpars.append(kpars['inc'])
rpars.append(kpars['Zeta'])
rpars.append(kpars['Zdec'])
rpars.append(kpars['Zinc'])
rpars.append(kpars['Eta'])
rpars.append(kpars['Edec'])
rpars.append(kpars['Einc'])
else: # assume bootstrap
if dist=='BE':
if len(nDIs)>5:
BnDIs=pmag.di_boot(nDIs)
Bkpars=pmag.dokent(BnDIs,1.)
if pmagplotlib.verbose:print "mode ",mode
for key in Bkpars.keys():
if key!='n' and pmagplotlib.verbose:print " ",key, '%7.1f'%(Bkpars[key])
if key=='n' and pmagplotlib.verbose:print " ",key, ' %i'%(Bkpars[key])
mode+=1
npars.append(Bkpars['dec'])
npars.append(Bkpars['inc'])
npars.append(Bkpars['Zeta'])
npars.append(Bkpars['Zdec'])
npars.append(Bkpars['Zinc'])
npars.append(Bkpars['Eta'])
npars.append(Bkpars['Edec'])
npars.append(Bkpars['Einc'])
if len(rDIs)>5:
BrDIs=pmag.di_boot(rDIs)
Bkpars=pmag.dokent(BrDIs,1.)
if pmagplotlib.verbose:print "mode ",mode
for key in Bkpars.keys():
if key!='n' and pmagplotlib.verbose:print " ",key, '%7.1f'%(Bkpars[key])
if key=='n' and pmagplotlib.verbose:print " ",key, ' %i'%(Bkpars[key])
mode+=1
rpars.append(Bkpars['dec'])
rpars.append(Bkpars['inc'])
rpars.append(Bkpars['Zeta'])
rpars.append(Bkpars['Zdec'])
rpars.append(Bkpars['Zinc'])
rpars.append(Bkpars['Eta'])
rpars.append(Bkpars['Edec'])
rpars.append(Bkpars['Einc'])
etitle="Bootstrapped confidence ellipse"
elif dist=='BV':
if len(nDIs)>5:
BnDIs=pmag.di_boot(nDIs)
pmagplotlib.plotEQ(FIG['bdirs'],BnDIs,'Bootstrapped Eigenvectors')
if len(rDIs)>5:
BrDIs=pmag.di_boot(rDIs)
if len(nDIs)>5: # plot on existing plots
pmagplotlib.plotDI(FIG['bdirs'],BrDIs)
else:
pmagplotlib.plotEQ(FIG['bdirs'],BrDIs,'Bootstrapped Eigenvectors')
if dist=='B':
if len(nDIs)> 3 or len(rDIs)>3: pmagplotlib.plotCONF(FIG['eq'],etitle,[],npars,0)
elif len(nDIs)>3 and dist!='BV':
pmagplotlib.plotCONF(FIG['eq'],etitle,[],npars,0)
if len(rDIs)>3:
pmagplotlib.plotCONF(FIG['eq'],etitle,[],rpars,0)
elif len(rDIs)>3 and dist!='BV':
pmagplotlib.plotCONF(FIG['eq'],etitle,[],rpars,0)
pmagplotlib.drawFIGS(FIG)
#
files={}
for key in FIG.keys():
files[key]=title.replace(" ","_")+'_'+'eqarea'+'.'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['eq']='Equal Area Plot'
FIG = pmagplotlib.addBorders(FIG,titles,black,purple)
pmagplotlib.saveP(FIG,files)
else:
ans=raw_input(" S[a]ve to save plot, [q]uit, Return to continue: ")
if ans=="q": sys.exit()
if ans=="a":
pmagplotlib.saveP(FIG,files)
def main():
"""
NAME
specimens_results_magic.py
DESCRIPTION
combines pmag_specimens.txt file with age, location, acceptance criteria and
outputs pmag_results table along with other MagIC tables necessary for uploading to the database
SYNTAX
specimens_results_magic.py [command line options]
OPTIONS
-h prints help message and quits
-usr USER: identify user, default is ""
-f: specimen input magic_measurements format file, default is "magic_measurements.txt"
-fsp: specimen input pmag_specimens format file, default is "pmag_specimens.txt"
-fsm: sample input er_samples format file, default is "er_samples.txt"
-fsi: specimen input er_sites format file, default is "er_sites.txt"
-fla: specify a file with paleolatitudes for calculating VADMs, default is not to calculate VADMS
format is: site_name paleolatitude (space delimited file)
-fa AGES: specify er_ages format file with age information
-crd [s,g,t,b]: specify coordinate system
(s, specimen, g geographic, t, tilt corrected, b, geographic and tilt corrected)
Default is to assume geographic
NB: only the tilt corrected data will appear on the results table, if both g and t are selected.
-cor [AC:CR:NL]: colon delimited list of required data adjustments for all specimens
included in intensity calculations (anisotropy, cooling rate, non-linear TRM)
unless specified, corrections will not be applied
-pri [TRM:ARM] colon delimited list of priorities for anisotropy correction (-cor must also be set to include AC). default is TRM, then ARM
-age MIN MAX UNITS: specify age boundaries and units
-exc: use exiting selection criteria (in pmag_criteria.txt file), default is default criteria
-C: no acceptance criteria
-aD: average directions per sample, default is NOT
-aI: average multiple specimen intensities per sample, default is by site
-aC: average all components together, default is NOT
-pol: calculate polarity averages
-sam: save sample level vgps and v[a]dms, default is by site
-xSi: skip the site level intensity calculation
-p: plot directions and look at intensities by site, default is NOT
-fmt: specify output for saved images, default is svg (only if -p set)
-lat: use present latitude for calculating VADMs, default is not to calculate VADMs
-xD: skip directions
-xI: skip intensities
OUPUT
writes pmag_samples, pmag_sites, pmag_results tables
"""
# set defaults
Comps=[] # list of components
version_num=pmag.get_version()
args=sys.argv
DefaultAge=["none"]
skipdirs,coord,excrit,custom,vgps,average,Iaverage,plotsites,opt=1,0,0,0,0,0,0,0,0
get_model_lat=0 # this skips VADM calculation altogether, when get_model_lat=1, uses present day
fmt='svg'
dir_path="."
model_lat_file=""
Caverage=0
infile='pmag_specimens.txt'
measfile="magic_measurements.txt"
sampfile="er_samples.txt"
sitefile="er_sites.txt"
agefile="er_ages.txt"
specout="er_specimens.txt"
sampout="pmag_samples.txt"
siteout="pmag_sites.txt"
resout="pmag_results.txt"
critout="pmag_criteria.txt"
instout="magic_instruments.txt"
sigcutoff,OBJ="",""
noDir,noInt=0,0
polarity=0
coords=['0']
Dcrit,Icrit,nocrit=0,0,0
corrections=[]
nocorrection=['DA-NL','DA-AC','DA-CR']
priorities=['DA-AC-ARM','DA-AC-TRM'] # priorities for anisotropy correction
# get command line stuff
if "-h" in args:
print main.__doc__
sys.exit()
if '-WD' in args:
ind=args.index("-WD")
dir_path=args[ind+1]
if '-cor' in args:
ind=args.index('-cor')
cors=args[ind+1].split(':') # list of required data adjustments
for cor in cors:
nocorrection.remove('DA-'+cor)
corrections.append('DA-'+cor)
if '-pri' in args:
ind=args.index('-pri')
priorities=args[ind+1].split(':') # list of required data adjustments
for p in priorities:
p='DA-AC-'+p
if '-f' in args:
ind=args.index("-f")
measfile=args[ind+1]
if '-fsp' in args:
ind=args.index("-fsp")
infile=args[ind+1]
if '-fsi' in args:
ind=args.index("-fsi")
sitefile=args[ind+1]
if "-crd" in args:
ind=args.index("-crd")
coord=args[ind+1]
if coord=='s':coords=['-1']
if coord=='g':coords=['0']
if coord=='t':coords=['100']
if coord=='b':coords=['0','100']
if "-usr" in args:
ind=args.index("-usr")
user=sys.argv[ind+1]
else: user=""
if "-C" in args: Dcrit,Icrit,nocrit=1,1,1 # no selection criteria
if "-sam" in args: vgps=1 # save sample level VGPS/VADMs
if "-xSi" in args:
nositeints=1 # skip site level intensity
else:
nositeints=0
if "-age" in args:
ind=args.index("-age")
DefaultAge[0]=args[ind+1]
DefaultAge.append(args[ind+2])
DefaultAge.append(args[ind+3])
Daverage,Iaverage,Caverage=0,0,0
if "-aD" in args: Daverage=1 # average by sample directions
if "-aI" in args: Iaverage=1 # average by sample intensities
if "-aC" in args: Caverage=1 # average all components together ??? why???
if "-pol" in args: polarity=1 # calculate averages by polarity
if '-xD' in args:noDir=1
if '-xI' in args:
noInt=1
elif "-fla" in args:
if '-lat' in args:
print "you should set a paleolatitude file OR use present day lat - not both"
sys.exit()
ind=args.index("-fla")
model_lat_file=dir_path+'/'+args[ind+1]
get_model_lat=2
mlat=open(model_lat_file,'rU')
ModelLats=[]
for line in mlat.readlines():
ModelLat={}
tmp=line.split()
ModelLat["er_site_name"]=tmp[0]
ModelLat["site_model_lat"]=tmp[1]
ModelLat["er_sample_name"]=tmp[0]
ModelLat["sample_lat"]=tmp[1]
ModelLats.append(ModelLat)
get_model_lat=2
elif '-lat' in args:
get_model_lat=1
if "-p" in args:
plotsites=1
if "-fmt" in args:
ind=args.index("-fmt")
fmt=args[ind+1]
if noDir==0: # plot by site - set up plot window
import pmagplotlib
EQ={}
EQ['eqarea']=1
pmagplotlib.plot_init(EQ['eqarea'],5,5) # define figure 1 as equal area projection
pmagplotlib.plotNET(EQ['eqarea']) # I don't know why this has to be here, but otherwise the first plot never plots...
pmagplotlib.drawFIGS(EQ)
if '-WD' in args:
infile=dir_path+'/'+infile
measfile=dir_path+'/'+measfile
instout=dir_path+'/'+instout
sampfile=dir_path+'/'+sampfile
sitefile=dir_path+'/'+sitefile
agefile=dir_path+'/'+agefile
specout=dir_path+'/'+specout
sampout=dir_path+'/'+sampout
siteout=dir_path+'/'+siteout
resout=dir_path+'/'+resout
critout=dir_path+'/'+critout
if "-exc" in args: # use existing pmag_criteria file
if "-C" in args:
print 'you can not use both existing and no criteria - choose either -exc OR -C OR neither (for default)'
sys.exit()
crit_data,file_type=pmag.magic_read(critout)
print "Acceptance criteria read in from ", critout
else : # use default criteria (if nocrit set, then get really loose criteria as default)
crit_data=pmag.default_criteria(nocrit)
if nocrit==0:
print "Acceptance criteria are defaults"
else:
print "No acceptance criteria used "
accept={}
for critrec in crit_data:
for key in critrec.keys():
if 'sample_int_sigma_uT' in critrec.keys():
critrec['sample_int_sigma']='%10.3e'%(eval(critrec['sample_int_sigma_uT'])*1e-6)
if key not in accept.keys() and critrec[key]!='':
accept[key]=critrec[key]
#
#
if "-exc" not in args and "-C" not in args:
print "args",args
pmag.magic_write(critout,[accept],'pmag_criteria')
print "\n Pmag Criteria stored in ",critout,'\n'
#
# now we're done slow dancing
#
SiteNFO,file_type=pmag.magic_read(sitefile) # read in site data - has the lats and lons
SampNFO,file_type=pmag.magic_read(sampfile) # read in site data - has the lats and lons
height_nfo=pmag.get_dictitem(SiteNFO,'site_height','','F') # find all the sites with height info.
if agefile !="":AgeNFO,file_type=pmag.magic_read(agefile) # read in the age information
Data,file_type=pmag.magic_read(infile) # read in specimen interpretations
IntData=pmag.get_dictitem(Data,'specimen_int','','F') # retrieve specimens with intensity data
comment,orient="",[]
samples,sites=[],[]
for rec in Data: # run through the data filling in missing keys and finding all components, coordinates available
# fill in missing fields, collect unique sample and site names
if 'er_sample_name' not in rec.keys():
rec['er_sample_name']=""
elif rec['er_sample_name'] not in samples:
samples.append(rec['er_sample_name'])
if 'er_site_name' not in rec.keys():
rec['er_site_name']=""
elif rec['er_site_name'] not in sites:
sites.append(rec['er_site_name'])
if 'specimen_int' not in rec.keys():rec['specimen_int']=''
if 'specimen_comp_name' not in rec.keys() or rec['specimen_comp_name']=="":rec['specimen_comp_name']='A'
if rec['specimen_comp_name'] not in Comps:Comps.append(rec['specimen_comp_name'])
rec['specimen_tilt_correction']=rec['specimen_tilt_correction'].strip('\n')
if "specimen_tilt_correction" not in rec.keys(): rec["specimen_tilt_correction"]="-1" # assume sample coordinates
if rec["specimen_tilt_correction"] not in orient: orient.append(rec["specimen_tilt_correction"]) # collect available coordinate systems
if "specimen_direction_type" not in rec.keys(): rec["specimen_direction_type"]='l' # assume direction is line - not plane
if "specimen_dec" not in rec.keys(): rec["specimen_direction_type"]='' # if no declination, set direction type to blank
if "specimen_n" not in rec.keys(): rec["specimen_n"]='' # put in n
if "specimen_alpha95" not in rec.keys(): rec["specimen_alpha95"]='' # put in alpha95
if "magic_method_codes" not in rec.keys(): rec["magic_method_codes"]=''
#
# start parsing data into SpecDirs, SpecPlanes, SpecInts
SpecInts,SpecDirs,SpecPlanes=[],[],[]
samples.sort() # get sorted list of samples and sites
sites.sort()
if noInt==0: # don't skip intensities
IntData=pmag.get_dictitem(Data,'specimen_int','','F') # retrieve specimens with intensity data
if nocrit==0: # use selection criteria
for rec in IntData: # do selection criteria
kill=pmag.grade(rec,accept,'specimen_int')
if len(kill)==0: SpecInts.append(rec) # intensity record to be included in sample, site calculations
else:
SpecInts=IntData[:] # take everything - no selection criteria
# check for required data adjustments
if len(corrections)>0 and len(SpecInts)>0:
for cor in corrections:
SpecInts=pmag.get_dictitem(SpecInts,'magic_method_codes',cor,'has') # only take specimens with the required corrections
if len(nocorrection)>0 and len(SpecInts)>0:
for cor in nocorrection:
SpecInts=pmag.get_dictitem(SpecInts,'magic_method_codes',cor,'not') # exclude the corrections not specified for inclusion
# take top priority specimen of its name in remaining specimens (only one per customer)
PrioritySpecInts=[]
specimens=pmag.get_specs(SpecInts) # get list of uniq specimen names
for spec in specimens:
ThisSpecRecs=pmag.get_dictitem(SpecInts,'er_specimen_name',spec,'T') # all the records for this specimen
if len(ThisSpecRecs)==1:
PrioritySpecInts.append(ThisSpecRecs[0])
elif len(ThisSpecRecs)>1: # more than one
prec=[]
for p in priorities:
ThisSpecRecs=pmag.get_dictitem(SpecInts,'magic_method_codes',p,'has') # all the records for this specimen
if len(ThisSpecRecs)>0:prec.append(ThisSpecRecs[0])
PrioritySpecInts.append(prec[0]) # take the best one
SpecInts=PrioritySpecInts # this has the first specimen record
if noDir==0: # don't skip directions
AllDirs=pmag.get_dictitem(Data,'specimen_direction_type','','F') # retrieve specimens with directed lines and planes
Ns=pmag.get_dictitem(AllDirs,'specimen_n','','F') # get all specimens with specimen_n information
if nocrit!=1: # use selection criteria
for rec in Ns: # look through everything with specimen_n for "good" data
kill=pmag.grade(rec,accept,'specimen_dir')
if len(kill)==0: # nothing killed it
SpecDirs.append(rec)
else: # no criteria
SpecDirs=AllDirs[:] # take them all
# SpecDirs is now the list of all specimen directions (lines and planes) that pass muster
#
PmagSamps,SampDirs=[],[] # list of all sample data and list of those that pass the DE-SAMP criteria
PmagSites,PmagResults=[],[] # list of all site data and selected results
SampInts=[]
for samp in samples: # run through the sample names
if Daverage==1: # average by sample if desired
SampDir=pmag.get_dictitem(SpecDirs,'er_sample_name',samp,'T') # get all the directional data for this sample
if len(SampDir)>0: # there are some directions
for coord in coords: # step through desired coordinate systems
CoordDir=pmag.get_dictitem(SampDir,'specimen_tilt_correction',coord,'T') # get all the directions for this sample
if len(CoordDir)>0: # there are some with this coordinate system
if Caverage==0: # look component by component
for comp in Comps:
CompDir=pmag.get_dictitem(CoordDir,'specimen_comp_name',comp,'T') # get all directions from this component
if len(CompDir)>0: # there are some
PmagSampRec=pmag.lnpbykey(CompDir,'sample','specimen') # get a sample average from all specimens
PmagSampRec["er_location_name"]=CompDir[0]['er_location_name'] # decorate the sample record
PmagSampRec["er_site_name"]=CompDir[0]['er_site_name']
PmagSampRec["er_sample_name"]=samp
PmagSampRec["er_citation_names"]="This study"
PmagSampRec["er_analyst_mail_names"]=user
PmagSampRec['magic_software_packages']=version_num
if nocrit!=1:PmagSampRec['pmag_criteria_codes']="ACCEPT"
if agefile != "": PmagSampRec= pmag.get_age(PmagSampRec,"er_site_name","sample_inferred_",AgeNFO,DefaultAge)
site_height=pmag.get_dictitem(height_nfo,'er_site_name',PmagSampRec['er_site_name'],'T')
if len(site_height)>0:PmagSampRec["sample_height"]=site_height[0]['site_height'] # add in height if available
PmagSampRec['sample_comp_name']=comp
PmagSampRec['sample_tilt_correction']=coord
PmagSampRec['er_specimen_names']= pmag.get_list(CompDir,'er_specimen_name') # get a list of the specimen names used
PmagSampRec['magic_method_codes']= pmag.get_list(CompDir,'magic_method_codes') # get a list of the methods used
if nocrit!=1: # apply selection criteria
kill=pmag.grade(PmagSampRec,accept,'sample_dir')
else:
kill=[]
if len(kill)==0:
SampDirs.append(PmagSampRec)
if vgps==1: # if sample level VGP info desired, do that now
PmagResRec=pmag.getsampVGP(PmagSampRec,SiteNFO)
if PmagResRec!="":PmagResults.append(PmagResRec)
PmagSamps.append(PmagSampRec)
if Caverage==1: # average all components together basically same as above
PmagSampRec=pmag.lnpbykey(CoordDir,'sample','specimen')
PmagSampRec["er_location_name"]=CoordDir[0]['er_location_name']
PmagSampRec["er_site_name"]=CoordDir[0]['er_site_name']
PmagSampRec["er_sample_name"]=samp
PmagSampRec["er_citation_names"]="This study"
PmagSampRec["er_analyst_mail_names"]=user
PmagSampRec['magic_software_packages']=version_num
if nocrit!=1:PmagSampRec['pmag_criteria_codes']=""
if agefile != "": PmagSampRec= pmag.get_age(PmagSampRec,"er_site_name","sample_inferred_",AgeNFO,DefaultAge)
site_height=pmag.get_dictitem(height_nfo,'er_site_name',site,'T')
if len(site_height)>0:PmagSampRec["sample_height"]=site_height[0]['site_height'] # add in height if available
PmagSampRec['sample_tilt_correction']=coord
PmagSampRec['sample_comp_name']= pmag.get_list(CoordDir,'specimen_comp_name') # get components used
PmagSampRec['er_specimen_names']= pmag.get_list(CoordDir,'er_specimen_name') # get specimne names averaged
PmagSampRec['magic_method_codes']= pmag.get_list(CoordDir,'magic_method_codes') # assemble method codes
if nocrit!=1: # apply selection criteria
kill=pmag.grade(PmagSampRec,accept,'sample_dir')
if len(kill)==0: # passes the mustard
SampDirs.append(PmagSampRec)
if vgps==1:
PmagResRec=pmag.getsampVGP(PmagSampRec,SiteNFO)
if PmagResRec!="":PmagResults.append(PmagResRec)
else: # take everything
SampDirs.append(PmagSampRec)
if vgps==1:
PmagResRec=pmag.getsampVGP(PmagSampRec,SiteNFO)
if PmagResRec!="":PmagResults.append(PmagResRec)
PmagSamps.append(PmagSampRec)
if Iaverage==1: # average by sample if desired
SampI=pmag.get_dictitem(SpecInts,'er_sample_name',samp,'T') # get all the intensity data for this sample
if len(SampI)>0: # there are some
PmagSampRec=pmag.average_int(SampI,'specimen','sample') # get average intensity stuff
PmagSampRec["sample_description"]="sample intensity" # decorate sample record
PmagSampRec["sample_direction_type"]=""
PmagSampRec['er_site_name']=SampI[0]["er_site_name"]
PmagSampRec['er_sample_name']=samp
PmagSampRec['er_location_name']=SampI[0]["er_location_name"]
PmagSampRec["er_citation_names"]="This study"
PmagSampRec["er_analyst_mail_names"]=user
if agefile != "": PmagSampRec=pmag.get_age(PmagSampRec,"er_site_name","sample_inferred_", AgeNFO,DefaultAge)
site_height=pmag.get_dictitem(height_nfo,'er_site_name',PmagSampRec['er_site_name'],'T')
if len(site_height)>0:PmagSampRec["sample_height"]=site_height[0]['site_height'] # add in height if available
PmagSampRec['er_specimen_names']= pmag.get_list(SampI,'er_specimen_name')
PmagSampRec['magic_method_codes']= pmag.get_list(SampI,'magic_method_codes')
if nocrit!=1: # apply criteria!
kill=pmag.grade(PmagSampRec,accept,'sample_int')
if len(kill)==0:
PmagSampRec['pmag_criteria_codes']="ACCEPT"
SampInts.append(PmagSampRec)
PmagSamps.append(PmagSampRec)
else:PmagSampRec={} # sample rejected
else: # no criteria
SampInts.append(PmagSampRec)
PmagSamps.append(PmagSampRec)
PmagSampRec['pmag_criteria_codes']=""
if vgps==1 and get_model_lat!=0 and PmagSampRec!={}: #
if get_model_lat==1: # use sample latitude
PmagResRec=pmag.getsampVDM(PmagSampRec,SampNFO)
del(PmagResRec['model_lat']) # get rid of the model lat key
elif get_model_lat==2: # use model latitude
PmagResRec=pmag.getsampVDM(PmagSampRec,ModelLats)
if PmagResRec!={}:PmagResRec['magic_method_codes']=PmagResRec['magic_method_codes']+":IE-MLAT"
if PmagResRec!={}:
PmagResRec['er_specimen_names']=PmagSampRec['er_specimen_names']
PmagResRec['er_sample_names']=PmagSampRec['er_sample_name']
PmagResRec['pmag_criteria_codes']='ACCEPT'
PmagResRec['average_int_sigma_perc']=PmagSampRec['sample_int_sigma_perc']
PmagResRec['average_int_sigma']=PmagSampRec['sample_int_sigma']
PmagResRec['average_int_n']=PmagSampRec['sample_int_n']
PmagResRec['vadm_n']=PmagSampRec['sample_int_n']
PmagResRec['data_type']='i'
PmagResults.append(PmagResRec)
if len(PmagSamps)>0:
TmpSamps,keylist=pmag.fillkeys(PmagSamps) # fill in missing keys from different types of records
pmag.magic_write(sampout,TmpSamps,'pmag_samples') # save in sample output file
print ' sample averages written to ',sampout
#
#create site averages from specimens or samples as specified
#
for site in sites:
if Daverage==0: key,dirlist='specimen',SpecDirs # if specimen averages at site level desired
if Daverage==1: key,dirlist='sample',SampDirs # if sample averages at site level desired
tmp=pmag.get_dictitem(dirlist,'er_site_name',site,'T') # get all the sites with directions
tmp1=pmag.get_dictitem(tmp,key+'_tilt_correction',coords[-1],'T') # use only the last coordinate if Caverage==0
sd=pmag.get_dictitem(SiteNFO,'er_site_name',site,'T') # fish out site information (lat/lon, etc.)
if len(sd)>0:
sitedat=sd[0]
if Caverage==0: # do component wise averaging
for comp in Comps:
siteD=pmag.get_dictitem(tmp1,key+'_comp_name',comp,'T') # get all components comp
if len(siteD)>0: # there are some for this site and component name
PmagSiteRec=pmag.lnpbykey(siteD,'site',key) # get an average for this site
PmagSiteRec['site_comp_name']=comp # decorate the site record
PmagSiteRec["er_location_name"]=siteD[0]['er_location_name']
PmagSiteRec["er_site_name"]=siteD[0]['er_site_name']
PmagSiteRec['site_tilt_correction']=coords[-1]
PmagSiteRec['site_comp_name']= pmag.get_list(siteD,key+'_comp_name')
if Daverage==1:
PmagSiteRec['er_sample_names']= pmag.get_list(siteD,'er_sample_name')
else:
PmagSiteRec['er_specimen_names']= pmag.get_list(siteD,'er_specimen_name')
# determine the demagnetization code (DC3,4 or 5) for this site
AFnum=len(pmag.get_dictitem(siteD,'magic_method_codes','LP-DIR-AF','has'))
Tnum=len(pmag.get_dictitem(siteD,'magic_method_codes','LP-DIR-T','has'))
DC=3
if AFnum>0:DC+=1
if Tnum>0:DC+=1
PmagSiteRec['magic_method_codes']= pmag.get_list(siteD,'magic_method_codes')+':'+ 'LP-DC'+str(DC)
PmagSiteRec['magic_method_codes'].strip(":")
if plotsites==1:
print PmagSiteRec['er_site_name']
pmagplotlib.plotSITE(EQ['eqarea'],PmagSiteRec,siteD,key) # plot and list the data
pmagplotlib.drawFIGS(EQ)
PmagSites.append(PmagSiteRec)
else: # last component only
siteD=tmp1[:] # get the last orientation system specified
if len(siteD)>0: # there are some
PmagSiteRec=pmag.lnpbykey(siteD,'site',key) # get the average for this site
PmagSiteRec["er_location_name"]=siteD[0]['er_location_name'] # decorate the record
PmagSiteRec["er_site_name"]=siteD[0]['er_site_name']
PmagSiteRec['site_comp_name']=comp
PmagSiteRec['site_tilt_correction']=coords[-1]
PmagSiteRec['site_comp_name']= pmag.get_list(siteD,key+'_comp_name')
PmagSiteRec['er_specimen_names']= pmag.get_list(siteD,'er_specimen_name')
PmagSiteRec['er_sample_names']= pmag.get_list(siteD,'er_sample_name')
AFnum=len(pmag.get_dictitem(siteD,'magic_method_codes','LP-DIR-AF','has'))
Tnum=len(pmag.get_dictitem(siteD,'magic_method_codes','LP-DIR-T','has'))
DC=3
if AFnum>0:DC+=1
if Tnum>0:DC+=1
PmagSiteRec['magic_method_codes']= pmag.get_list(siteD,'magic_method_codes')+':'+ 'LP-DC'+str(DC)
PmagSiteRec['magic_method_codes'].strip(":")
if Daverage==0:PmagSiteRec['site_comp_name']= pmag.get_list(siteD,key+'_comp_name')
if plotsites==1:
pmagplotlib.plotSITE(EQ['eqarea'],PmagSiteRec,siteD,key)
pmagplotlib.drawFIGS(EQ)
PmagSites.append(PmagSiteRec)
else:
print 'site information not found in er_sites for site, ',site,' site will be skipped'
for PmagSiteRec in PmagSites: # now decorate each dictionary some more, and calculate VGPs etc. for results table
PmagSiteRec["er_citation_names"]="This study"
PmagSiteRec["er_analyst_mail_names"]=user
PmagSiteRec['magic_software_packages']=version_num
if agefile != "": PmagSiteRec= pmag.get_age(PmagSiteRec,"er_site_name","site_inferred_",AgeNFO,DefaultAge)
PmagSiteRec['pmag_criteria_codes']='ACCEPT'
if 'site_n_lines' in PmagSiteRec.keys() and 'site_n_planes' in PmagSiteRec.keys() and PmagSiteRec['site_n_lines']!="" and PmagSiteRec['site_n_planes']!="":
if int(PmagSiteRec["site_n_planes"])>0:
PmagSiteRec["magic_method_codes"]=PmagSiteRec['magic_method_codes']+":DE-FM-LP"
elif int(PmagSiteRec["site_n_lines"])>2:
PmagSiteRec["magic_method_codes"]=PmagSiteRec['magic_method_codes']+":DE-FM"
kill=pmag.grade(PmagSiteRec,accept,'site_dir')
if len(kill)==0:
PmagResRec={} # set up dictionary for the pmag_results table entry
PmagResRec['data_type']='i' # decorate it a bit
PmagResRec['magic_software_packages']=version_num
PmagSiteRec['site_description']='Site direction included in results table'
PmagResRec['pmag_criteria_codes']='ACCEPT'
dec=float(PmagSiteRec["site_dec"])
inc=float(PmagSiteRec["site_inc"])
if 'site_alpha95' in PmagSiteRec.keys() and PmagSiteRec['site_alpha95']!="":
a95=float(PmagSiteRec["site_alpha95"])
else:a95=180.
sitedat=pmag.get_dictitem(SiteNFO,'er_site_name',PmagSiteRec['er_site_name'],'T')[0] # fish out site information (lat/lon, etc.)
lat=float(sitedat['site_lat'])
lon=float(sitedat['site_lon'])
plong,plat,dp,dm=pmag.dia_vgp(dec,inc,a95,lat,lon) # get the VGP for this site
if PmagSiteRec['site_tilt_correction']=='-1':C=' (spec coord) '
if PmagSiteRec['site_tilt_correction']=='0':C=' (geog. coord) '
if PmagSiteRec['site_tilt_correction']=='100':C=' (strat. coord) '
PmagResRec["pmag_result_name"]="VGP Site: "+PmagSiteRec["er_site_name"] # decorate some more
PmagResRec["result_description"]="Site VGP, coord system = "+str(coord)+' component: '+comp
PmagResRec['er_site_names']=PmagSiteRec['er_site_name']
PmagResRec['pmag_criteria_codes']='ACCEPT'
PmagResRec['er_citation_names']='This study'
PmagResRec['er_analyst_mail_names']=user
PmagResRec["er_location_names"]=PmagSiteRec["er_location_name"]
if Daverage==1:
PmagResRec["er_sample_names"]=PmagSiteRec["er_sample_names"]
else:
PmagResRec["er_specimen_names"]=PmagSiteRec["er_specimen_names"]
PmagResRec["tilt_correction"]=PmagSiteRec['site_tilt_correction']
PmagResRec["pole_comp_name"]=PmagSiteRec['site_comp_name']
PmagResRec["average_dec"]=PmagSiteRec["site_dec"]
PmagResRec["average_inc"]=PmagSiteRec["site_inc"]
PmagResRec["average_alpha95"]=PmagSiteRec["site_alpha95"]
PmagResRec["average_n"]=PmagSiteRec["site_n"]
PmagResRec["average_n_lines"]=PmagSiteRec["site_n_lines"]
PmagResRec["average_n_planes"]=PmagSiteRec["site_n_planes"]
PmagResRec["vgp_n"]=PmagSiteRec["site_n"]
PmagResRec["average_k"]=PmagSiteRec["site_k"]
PmagResRec["average_r"]=PmagSiteRec["site_r"]
PmagResRec["average_lat"]='%10.4f ' %(lat)
PmagResRec["average_lon"]='%10.4f ' %(lon)
if agefile != "": PmagResRec= pmag.get_age(PmagResRec,"er_site_names","average_",AgeNFO,DefaultAge)
site_height=pmag.get_dictitem(height_nfo,'er_site_name',site,'T')
if len(site_height)>0:PmagResRec["average_height"]=site_height[0]['site_height']
PmagResRec["vgp_lat"]='%7.1f ' % (plat)
PmagResRec["vgp_lon"]='%7.1f ' % (plong)
PmagResRec["vgp_dp"]='%7.1f ' % (dp)
PmagResRec["vgp_dm"]='%7.1f ' % (dm)
PmagResRec["magic_method_codes"]= PmagSiteRec["magic_method_codes"]
if PmagSiteRec['site_tilt_correction']=='0':PmagSiteRec['magic_method_codes']=PmagSiteRec['magic_method_codes']+":DA-DIR-GEO"
if PmagSiteRec['site_tilt_correction']=='100':PmagSiteRec['magic_method_codes']=PmagSiteRec['magic_method_codes']+":DA-DIR-TILT"
PmagSiteRec['site_polarity']=""
if polarity==1: # assign polarity based on angle of pole lat to spin axis - may want to re-think this sometime
angle=pmag.angle([0,0],[0,(90-plat)])
if angle <= 55.: PmagSiteRec["site_polarity"]='n'
if angle > 55. and angle < 125.: PmagSiteRec["site_polarity"]='t'
if angle >= 125.: PmagSiteRec["site_polarity"]='r'
PmagResults.append(PmagResRec)
if noInt!=1 and nositeints!=1:
for site in sites: # now do intensities for each site
if plotsites==1:print site
if Iaverage==0: key,intlist='specimen',SpecInts # if using specimen level data
if Iaverage==1: key,intlist='sample',PmagSamps # if using sample level data
Ints=pmag.get_dictitem(intlist,'er_site_name',site,'T') # get all the intensities for this site
if len(Ints)>0: # there are some
PmagSiteRec=pmag.average_int(Ints,key,'site') # get average intensity stuff for site table
PmagResRec=pmag.average_int(Ints,key,'average') # get average intensity stuff for results table
if plotsites==1: # if site by site examination requested - print this site out to the screen
for rec in Ints:print rec['er_'+key+'_name'],' %7.1f'%(1e6*float(rec[key+'_int']))
if len(Ints)>1:
print 'Average: ','%7.1f'%(1e6*float(PmagResRec['average_int'])),'N: ',len(Ints)
print 'Sigma: ','%7.1f'%(1e6*float(PmagResRec['average_int_sigma'])),'Sigma %: ',PmagResRec['average_int_sigma_perc']
raw_input('Press any key to continue\n')
er_location_name=Ints[0]["er_location_name"]
PmagSiteRec["er_location_name"]=er_location_name # decorate the records
PmagSiteRec["er_citation_names"]="This study"
PmagResRec["er_location_names"]=er_location_name
PmagResRec["er_citation_names"]="This study"
PmagSiteRec["er_analyst_mail_names"]=user
PmagResRec["er_analyst_mail_names"]=user
PmagResRec["data_type"]='i'
if Iaverage==0:
PmagSiteRec['er_specimen_names']= pmag.get_list(Ints,'er_specimen_name') # list of all specimens used
PmagResRec['er_specimen_names']= pmag.get_list(Ints,'er_specimen_name')
PmagSiteRec['er_sample_names']= pmag.get_list(Ints,'er_sample_name') # list of all samples used
PmagResRec['er_sample_names']= pmag.get_list(Ints,'er_sample_name')
PmagSiteRec['er_site_name']= site
PmagResRec['er_site_names']= site
PmagSiteRec['magic_method_codes']= pmag.get_list(Ints,'magic_method_codes')
PmagResRec['magic_method_codes']= pmag.get_list(Ints,'magic_method_codes')
kill=pmag.grade(PmagSiteRec,accept,'site_int')
if nocrit==1 or len(kill)==0:
b,sig=float(PmagResRec['average_int']),""
if(PmagResRec['average_int_sigma'])!="":sig=float(PmagResRec['average_int_sigma'])
sdir=pmag.get_dictitem(PmagResults,'er_site_names',site,'T') # fish out site direction
if len(sdir)>0 and sdir[-1]['average_inc']!="": # get the VDM for this record using last average inclination (hope it is the right one!)
inc=float(sdir[0]['average_inc']) #
mlat=pmag.magnetic_lat(inc) # get magnetic latitude using dipole formula
PmagResRec["vdm"]='%8.3e '% (pmag.b_vdm(b,mlat)) # get VDM with magnetic latitude
PmagResRec["vdm_n"]=PmagResRec['average_int_n']
if 'average_int_sigma' in PmagResRec.keys() and PmagResRec['average_int_sigma']!="":
vdm_sig=pmag.b_vdm(float(PmagResRec['average_int_sigma']),mlat)
PmagResRec["vdm_sigma"]='%8.3e '% (vdm_sig)
else:
PmagResRec["vdm_sigma"]=""
mlat="" # define a model latitude
if get_model_lat==1: # use present site latitude
mlats=pmag.get_dictitem(SiteNFO,'er_site_name',site,'T')
if len(mlats)>0: mlat=mlats[0]['site_lat']
elif get_model_lat==2: # use a model latitude from some plate reconstruction model (or something)
mlats=pmag.get_dictitem(ModelLats,'er_site_name',site,'T')
if len(mlats)>0: PmagResRec['model_lat']=mlats[0]['site_model_lat']
mlat=PmagResRec['model_lat']
if mlat!="":
PmagResRec["vadm"]='%8.3e '% (pmag.b_vdm(b,float(mlat))) # get the VADM using the desired latitude
if sig!="":
vdm_sig=pmag.b_vdm(float(PmagResRec['average_int_sigma']),float(mlat))
PmagResRec["vadm_sigma"]='%8.3e '% (vdm_sig)
PmagResRec["vadm_n"]=PmagResRec['average_int_n']
else:
PmagResRec["vadm_sigma"]=""
sitedat=pmag.get_dictitem(SiteNFO,'er_site_name',PmagSiteRec['er_site_name'],'T') # fish out site information (lat/lon, etc.)
if len(sitedat)>0:
sitedat=sitedat[0]
PmagResRec['average_lat']=sitedat['site_lat']
PmagResRec['average_lon']=sitedat['site_lon']
else:
PmagResRec['average_lon']='UNKNOWN'
PmagResRec['average_lon']='UNKNOWN'
PmagResRec['magic_software_packages']=version_num
PmagResRec["pmag_result_name"]="V[A]DM: Site "+site
PmagResRec["result_description"]="V[A]DM of site"
PmagResRec["pmag_criteria_codes"]="ACCEPT"
if agefile != "": PmagResRec= pmag.get_age(PmagResRec,"er_site_names","average_",AgeNFO,DefaultAge)
site_height=pmag.get_dictitem(height_nfo,'er_site_name',site,'T')
if len(site_height)>0:PmagResRec["average_height"]=site_height[0]['site_height']
PmagSites.append(PmagSiteRec)
PmagResults.append(PmagResRec)
if len(PmagSites)>0:
Tmp,keylist=pmag.fillkeys(PmagSites)
pmag.magic_write(siteout,Tmp,'pmag_sites')
print ' sites written to ',siteout
else: print "No Site level table"
if len(PmagResults)>0:
TmpRes,keylist=pmag.fillkeys(PmagResults)
pmag.magic_write(resout,TmpRes,'pmag_results')
print ' results written to ',resout
else: print "No Results level table"
def main():
"""
NAME
pyscu_draw.py
DESCRIPTION
plot the data calculated in pyscu_calc.py
INPUT
ouput files from pyscu_calc.py
SYNTAX
pyscu_draw.py [-h] [command line options]
OPTIONS
-h, plots help message and quits
-f AFILE, specify file for input
this is the main file output from the pyscu_calc.py program
the other files have to been placed in the same folder
-F RFILE, specify file for output
-A, plot the A/N matrix
-s [s/i/n], plot the SCI solutions, the intersections, or none.
-fmt [svg, jpg, eps, pdf] format for output images.
-i interactive entry of the remagnetization direction
DEFAULTS
-f, AFILE: SCdata_main.txt
-F, RFILE: out
DON'T plot the A/N matrix
-s, DON'T plot the SCI solutions or the intersections
-fmt, save as svg
get de remagnetization direction from SCdata_Ref.txt
"""
print ('\nThis program uses the PmagPy and pySCu softwares utilities\n\tTauxe et al. 2016, G3, http://dx.doi.org/10.1002/2016GC006307\n\tCalvín et al. 2017, C&G, http://dx.doi.org/10.1016/j.cageo.2017.07.002')
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]
else: infile='SCdata_main.txt'
if '-F' in sys.argv:
ind=sys.argv.index('-F')
outfile=sys.argv[ind+1]
else: outfile=infile[:-9]
if '-A' in sys.argv:
preA='y'
else: preA='n'
if '-s' in sys.argv:
ind=sys.argv.index('-s')
preS=sys.argv[ind+1]
else: preS='n'
if '-fmt' in sys.argv:
ind=sys.argv.index('-fmt')
fmt='.'+sys.argv[ind+1]
else: fmt='.svg'
if '-i' in sys.argv:
iRef='true'
print('\nInput the Kent parameters (separated by spaces) of the remagnetization direction:')
ref_input = input("\nDec Inc Eta Dec_Eta Inc_Eta Zeta Dec_Zeta Inc_Zeta: An example...\n329.9 39.5 10.5 155.1 50.4 4.9 62.3 2.6\n").split(' ')
ref=[]
for dato in ref_input:
ref.append(float(dato))
else: iRef='false'
infile_m=infile[:-8]+'mat.txt'
infile_ref=infile[:-8]+'Ref.txt'
infile_inter=infile[:-8]+'inter.txt'
infile_sci=infile[:-8]+'SCIs.txt'
if path.exists(infile_ref): Ref='true'
else: Ref='false'
if path.exists(infile_m): matrix='true'
else: matrix='false'
if path.exists(infile_inter): inter='true'
else: inter='false'
if path.exists(infile_sci): SCIs='true'
else: SCIs='false'
if Ref=='false' and iRef=='false':
print("\nTake care, I don't found the file", infile_ref, " whit the reference direction")
if matrix=='false' and preA=='y':
print("\nTake care, I don't found the file", infile_m, ' whit the A/N matriz data')
if inter=='false' and preS=='i':
print("\nTake care, I don't found the file", infile_inter, ' whit the intersections directions')
if SCIs=='false' and preS=='s':
print("\nTake care, I don't found the file", infile_sci, ' whit the SCIs directions')
out_name_bbc=outfile+'_bbc'+fmt
out_name_bfd=outfile+'_bfd'+fmt
out_name_atbc=outfile+'_atbc'+fmt
out_name_mat=outfile+'_mat'+fmt
print('\nPlease, wait a moment')
print('\nPlots will be saved as', out_name_bbc, ', ', out_name_bfd, '...\n')
#Saving the data in different list
site,sc,geo,tilt,bfd=scu.getInFile_main(infile) #main file
n=len(site)
if Ref=='true' and iRef=='false': #reference direction
reader=csv.reader(open(infile_ref), delimiter=' ')
dat_Ref=list(reader)
ref=[float(dat_Ref[1][1]),float(dat_Ref[1][2]),float(dat_Ref[1][3]),float(dat_Ref[1][5]),
float(dat_Ref[1][6]),float(dat_Ref[1][4]),float(dat_Ref[1][7]),float(dat_Ref[1][8]),float(dat_Ref[1][11])]
if inter=='true' and preS=='i': #intersections directions
reader=csv.reader(open(infile_inter), delimiter=' ')
dat_inter_h=list(reader)
dat_inter=dat_inter_h[1:]
if SCIs=='true' and preS=='s': #intersections directions
reader=csv.reader(open(infile_sci), delimiter=' ')
dat_SCIs_h=list(reader)
dat_SCIs=dat_SCIs_h[1:]
if matrix=='true' and preA=='y': #A/n values
X,Y,Z,minA,maxA=scu.getInFile_mat(infile_m)
#Drawing...
plt.figure(num=1,figsize=(6,7),facecolor='white')
#Plotting the BBC directions, the SCs and the reference
pmagpl.plotNET(1)
pylab.figtext(.02, .045, 'pySCu v3.1')
plt.text(0.85, 0.7, 'BBC', fontsize = 13)
plt.scatter(0.8, 0.74, color='r',marker='s',s=30)
plt.text(0.70, 0.85, 'n='+str(n), fontsize = 13)
for dato in sc: #The SCs
scu.smallcirc(dato,1)
for dato in geo: #The BBC directions
scu.plot_di_mean(dato[0],dato[1],dato[2],color='r',marker='s',markersize=8,label='Geo',legend='no',zorder=3)
#You can change the marker (+, ., o, *, p, s, x, D, h, ^), the color (b, g, r, c, m, y, k, w) or the size as you prefere
if Ref=='true': #The reference
scu.plotCONF(ref)
plt.text(0.51, -1.05, 'Reference', fontsize = 13)
plt.scatter(0.45, -1, color='m',marker='*',s=100)
plt.title('Before Bedding Correction',fontsize=15)
plt.savefig(out_name_bbc)
#Plotting the ATBC directions, the SCs and the reference
plt.figure(num=2,figsize=(6,7),facecolor='white')
pmagpl.plotNET(2)
pylab.figtext(.02, .045, 'pySCu v3.1')
plt.text(0.85, 0.7, 'ATBC', fontsize = 13)
plt.scatter(0.8, 0.745, color='g',marker='^',s=40)
plt.text(0.70, 0.85, 'n='+str(n), fontsize = 13)
plt.title('After total bedding correction',fontsize=15)
for dato in sc:
scu.smallcirc(dato,1)
if Ref=='true':
scu.plotCONF(ref)
plt.text(0.51, -1.05, 'Reference', fontsize = 13)
plt.scatter(0.45, -1, color='m',marker='*',s=100)
for dato in tilt:
scu.plot_di_mean(dato[0],dato[1],dato[2],color='g',marker='^',markersize=9,label='Tilt',legend='no',zorder=3)
plt.savefig(out_name_atbc)
#Plotting the BFD directions, the SCs and the reference
plt.figure(num=3,figsize=(6,7),facecolor='white')
pmagpl.plotNET(3)
pylab.figtext(.02, .045, 'pySCu v3.1')
plt.text(0.85, 0.7, 'BFD', fontsize = 13)
plt.scatter(0.8, 0.74, color='b',marker='o',s=30)
plt.text(0.70, 0.85, 'n='+str(n), fontsize = 13)
plt.title('After partial bedding correction',fontsize=15)
for dato in sc:
scu.smallcirc(dato,1)
for dato in bfd:
scu.plot_di_mean(dato[0],dato[1],dato[2],color='b',marker='o',markersize=5,label='BFD',legend='no',zorder=3)
if Ref=='true': #Ploting the reference and the leyend
scu.plotCONF(ref)
plt.text(0.51, -1.05, 'Reference', fontsize = 13)
plt.scatter(0.45, -1, color='m',marker='*',s=100)
plt.savefig(out_name_bfd)
#Plotting the A/n contour plot and/or the intersections
if (preA=='y' and matrix=='true') or (preS=='i' and inter=='true') or (preS=='s' and SCIs=='true'):
plt.figure(num=4,figsize=(9.5,9.5),facecolor='white')
pmagpl.plotNET(4)
pylab.figtext(.02, .045, 'pySCu v3.1')
fig4='true'
else: fig4='false'
if preA=='y' and matrix=='true': #plotting the A/n contour plot
max_z=max(Z)
max_z_s=max_z+(5-max_z%5)+0.1
min_z=min(Z)
min_z_s=min_z-(min_z%5)
levels5 = np.arange(min_z_s,max_z_s, 5)
levels1 = np.arange(min_z_s,max_z_s, 1)
CS=plt.tricontourf(X, Y, Z, vmin=min_z,vmax=max_z, cmap = 'Blues', levels=levels1) #Other colormaps (as 'rainbow') are possibles. Change 'Blues' for the choosed colormap
cbar=plt.colorbar(CS, orientation='horizontal',pad=0.05)
CS2=plt.tricontour(X,Y,Z, colors='k',linewidths = .5, levels=levels5)
#plt.clabel(CS2,levels=levels5, inline=1, fmt='%1.0f', fontsize=10)
cbar.ax.set_xlabel('A/n value'+' ('+str(round(minA,1))+'-'+str(round(maxA,1))+')')
#cbar.add_lines(CS2)
plt.axis((-1.35,1.35,-1.35,1.35))
else:
for dato in sc:
scu.smallcirc(dato,1)
if preS=='i' and inter=='true': #plotting the intersections
text_i='SCs intersec. (n='+str(len(dat_inter))+')'
plt.text(-0.3, -1.2, text_i, fontsize = 12)
plt.scatter(-0.38, -1.12, color='k',marker='.',s=50)
for dato in dat_inter:
scu.plot_di_mean(float(dato[0]),float(dato[1]),0.,color='k',marker='.',markersize=1,label='Intersections',legend='no')
if preS=='s' and SCIs=='true': #plotting the SCIs
text_s='SCIs solutions (n='+str(len(dat_SCIs))+')'
plt.text(-0.3, -1.2, text_s, fontsize = 12)
plt.scatter(-0.38, -1.12, color='k',marker='.',s=50)
for dato in dat_SCIs:
scu.plot_di_mean(float(dato[0]),float(dato[1]),0.,color='k',marker='.',markersize=1,label='SCIs',legend='no')
if fig4=='true' and Ref=='true': #Plotting the reference and the leyend
scu.plotCONF(ref)
plt.text(0.6, 0.83, 'Reference', fontsize = 13)
plt.scatter(0.93, 0.73, color='m',marker='*',s=100)
text_rat='mr/mp='+str(ref[8])+';'
plt.text(-1.37, -1.2, text_rat, fontsize = 12)
plt.title('A/n matriz',fontsize=15)
if fig4=='true':
plt.savefig(out_name_mat)
plt.show()
