def main():
"""
NAME
plot_map_pts.py
DESCRIPTION
plots points on map
SYNTAX
plot_map_pts.py [command line options]
OPTIONS
-h prints help and quits
-sym [ro, bs, g^, r., b-, etc.] [1,5,10] symbol and size for points
colors are r=red,b=blue,g=green, etc.
symbols are '.' for points, ^, for triangle, s for square, etc.
-, for lines, -- for dotted lines, see matplotlib online documentation for plot()
-eye ELAT ELON [specify eyeball location]
-etp put on topography
-cmap color map [default is jet]
-f FILE, specify input file
-o color ocean blue/land green (default is not)
-res [c,l,i,h] specify resolution (crude, low, intermediate, high]
-fmt [pdf,eps, png] specify output format (default is pdf)
-R don't plot details of rivers
-B don't plot national/state boundaries, etc.
-pad [LAT LON] pad bounding box by LAT/LON (default is not)
-grd SPACE specify grid spacing
-sav save plot and quit
-prj PROJ, specify one of the supported projections:
pc = Plate Carree
aea = Albers Equal Area
aeqd = Azimuthal Equidistant
lcc = Lambert Conformal
lcyl = Lambert Cylindrical
merc = Mercator
mill = Miller Cylindrical
moll = Mollweide [default]
ortho = Orthographic
robin = Robinson
sinu = Sinusoidal
stere = Stereographic
tmerc = Transverse Mercator
utm = UTM
laea = Lambert Azimuthal Equal Area
geos = Geostationary
npstere = North-Polar Stereographic
spstere = South-Polar Stereographic
Special codes for MagIC formatted input files:
-n
-l
INPUTS
space or tab delimited LON LAT data
OR:
standard MagIC formatted er_sites or pmag_results table
DEFAULTS
res: c
prj: mollweide; lcc for MagIC format files
ELAT,ELON = 0,0
pad LAT,LON=0,0
NB: high resolution or lines can be very slow
"""
dir_path='.'
plot=0
ocean=0
res='c'
proj='moll'
Lats,Lons=[],[]
fmt='pdf'
sym='ro'
symsize=5
fancy=0
rivers,boundaries,ocean=1,1,0
latmin,latmax,lonmin,lonmax,lat_0,lon_0=-90,90,0.,360.,0.,0.
padlat,padlon,gridspace=0,0,30
lat_0,lon_0="",""
basemap=1
prn_name,prn_loc,names,locs=0,0,[],[]
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
if '-res' in sys.argv:
ind = sys.argv.index('-res')
res=sys.argv[ind+1]
if res!= 'c' and res!='l':
print('this resolution will take a while - be patient')
if '-etp' in sys.argv:
fancy=1
print ('-W- plotting will require patience!')
if '-ctp' in sys.argv: basemap=0
if '-sav' in sys.argv: plot=1
if '-R' in sys.argv:rivers=0
if '-B' in sys.argv:boundaries=0
if '-o' in sys.argv:ocean=1
if '-cmap' in sys.argv:
ind = sys.argv.index('-cmap')
cmap=float(sys.argv[ind+1])
else:
cmap='jet'
if '-grd' in sys.argv:
ind = sys.argv.index('-grd')
gridspace=float(sys.argv[ind+1])
if '-eye' in sys.argv:
ind = sys.argv.index('-eye')
lat_0=float(sys.argv[ind+1])
lon_0=float(sys.argv[ind+2])
if '-sym' in sys.argv:
ind = sys.argv.index('-sym')
sym=sys.argv[ind+1]
symsize=int(sys.argv[ind+2])
if '-pad' in sys.argv:
ind = sys.argv.index('-pad')
padlat=float(sys.argv[ind+1])
padlon=float(sys.argv[ind+2])
if '-f' in sys.argv:
ind = sys.argv.index('-f')
file=dir_path+'/'+sys.argv[ind+1]
header=open(file,'r').readlines()[0].split('\t')
if 'tab' in header[0]:
proj='lcc'
if 'sites' in header[1]:
latkey='lat'
lonkey='lon'
namekey='site'
lockey=''
else:
print('file type not supported')
print(main.__doc__)
sys.exit()
Sites,file_type=pmag.magic_read(file)
Lats=pmag.get_dictkey(Sites,latkey,'f')
Lons=pmag.get_dictkey(Sites,lonkey,'f')
if prn_name==1:names=pmag.get_dictkey(Sites,namekey,'')
if prn_loc==1:names=pmag.get_dictkey(Sites,lockey,'')
else:
ptdata=numpy.loadtxt(file)
Lons=ptdata.transpose()[0]
Lats=ptdata.transpose()[1]
latmin=numpy.min(Lats)-padlat
lonmin=numpy.min(Lons)-padlon
latmax=numpy.max(Lats)+padlat
lonmax=numpy.max(Lons)+padlon
if lon_0=="":
lon_0=0.5*(lonmin+lonmax)
lat_0=0.5*(latmin+latmax)
else:
print("input file must be specified")
sys.exit()
if '-prj' in sys.argv:
ind = sys.argv.index('-prj')
proj=sys.argv[ind+1]
FIG={'map':1}
pmagplotlib.plot_init(FIG['map'],6,6)
cnt=0
Opts={'latmin':latmin,'latmax':latmax,'lonmin':lonmin,'lonmax':lonmax,'lat_0':lat_0,'lon_0':lon_0,'proj':proj,'sym':sym,'symsize':3,'pltgrid':1,'res':res,'boundinglat':0.,'padlon':padlon,'padlat':padlat,'gridspace':gridspace,'cmap':cmap}
Opts['details']={}
Opts['details']['coasts']=1
Opts['details']['rivers']=rivers
Opts['details']['states']=boundaries
Opts['details']['countries']=boundaries
Opts['details']['ocean']=ocean
Opts['details']['fancy']=fancy
if len(names)>0:Opts['names']=names
if len(locs)>0:Opts['loc_name']=locs
if proj=='merc':
Opts['latmin']=-70
Opts['latmax']=70
Opts['lonmin']=-180
Opts['lonmax']=180
print('please wait to draw points')
Opts['sym']=sym
Opts['symsize']=symsize
if basemap:
pmagplotlib.plot_map(FIG['map'],Lats,Lons,Opts)
else:
pmagplotlib.plot_map(FIG['map'],Lats,Lons,Opts)
files={}
titles={}
titles['map']='PT Map'
for key in list(FIG.keys()):
files[key]='map_pts'+'.'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
FIG = pmagplotlib.add_borders(FIG,titles,black,purple)
pmagplotlib.save_plots(FIG,files)
if plot==1:
pmagplotlib.save_plots(FIG,files)
else:
pmagplotlib.draw_figs(FIG)
ans=input(" S[a]ve to save plot, Return to quit: ")
if ans=="a": pmagplotlib.save_plots(FIG,files)
def main():
"""
NAME
vgpmap_magic.py
DESCRIPTION
makes a map of vgps and a95/dp,dm for site means in a pmag_results table
SYNTAX
vgpmap_magic.py [command line options]
OPTIONS
-h prints help and quits
-eye ELAT ELON [specify eyeball location], default is 90., 0.
-f FILE pmag_results format file, [default is pmag_results.txt]
-res [c,l,i,h] specify resolution (crude, low, intermediate, high]
-etp plot the etopo20 topographpy data (requires high resolution data set)
-prj PROJ, specify one of the following:
ortho = orthographic
lcc = lambert conformal
moll = molweide
merc = mercator
-sym SYM SIZE: choose a symbol and size, examples:
ro 5 : small red circles
bs 10 : intermediate blue squares
g^ 20 : large green triangles
-ell plot dp/dm or a95 ellipses
-rev RSYM RSIZE : flip reverse poles to normal antipode
-S: plot antipodes of all poles
-age : plot the ages next to the poles
-crd [g,t] : choose coordinate system, default is to plot all site VGPs
-fmt [pdf, png, eps...] specify output format, default is pdf
-sav save and quit
DEFAULTS
FILE: pmag_results.txt
res: c
prj: ortho
ELAT,ELON = 0,0
SYM SIZE: ro 8
RSYM RSIZE: g^ 8
"""
dir_path = '.'
res, ages = 'c', 0
plot = 0
proj = 'ortho'
results_file = 'pmag_results.txt'
ell, flip = 0, 0
lat_0, lon_0 = 90., 0.
fmt = 'pdf'
sym, size = 'ro', 8
rsym, rsize = 'g^', 8
anti = 0
fancy = 0
coord = ""
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind+1]
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-S' in sys.argv:
anti = 1
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt = sys.argv[ind+1]
if '-sav' in sys.argv:
plot = 1
if '-res' in sys.argv:
ind = sys.argv.index('-res')
res = sys.argv[ind+1]
if '-etp' in sys.argv:
fancy = 1
if '-prj' in sys.argv:
ind = sys.argv.index('-prj')
proj = sys.argv[ind+1]
if '-rev' in sys.argv:
flip = 1
ind = sys.argv.index('-rev')
rsym = (sys.argv[ind+1])
rsize = int(sys.argv[ind+2])
if '-sym' in sys.argv:
ind = sys.argv.index('-sym')
sym = (sys.argv[ind+1])
size = int(sys.argv[ind+2])
if '-eye' in sys.argv:
ind = sys.argv.index('-eye')
lat_0 = float(sys.argv[ind+1])
lon_0 = float(sys.argv[ind+2])
if '-ell' in sys.argv:
ell = 1
if '-age' in sys.argv:
ages = 1
if '-f' in sys.argv:
ind = sys.argv.index('-f')
results_file = sys.argv[ind+1]
if '-crd' in sys.argv:
ind = sys.argv.index('-crd')
crd = sys.argv[ind+1]
if crd == 'g':
coord = '0'
if crd == 't':
coord = '100'
results_file = dir_path+'/'+results_file
data, file_type = pmag.magic_read(results_file)
if file_type != 'pmag_results':
print("bad results file")
sys.exit()
FIG = {'map': 1}
pmagplotlib.plot_init(FIG['map'], 6, 6)
# read in er_sites file
lats, lons, dp, dm, a95 = [], [], [], [], []
Pars = []
dates, rlats, rlons = [], [], []
if 'data_type' in data[0].keys():
# get all site level data
Results = pmag.get_dictitem(data, 'data_type', 'i', 'T')
else:
Results = data
# get all non-blank latitudes
Results = pmag.get_dictitem(Results, 'vgp_lat', '', 'F')
# get all non-blank longitudes
Results = pmag.get_dictitem(Results, 'vgp_lon', '', 'F')
if coord != "":
# get specified coordinate system
Results = pmag.get_dictitem(Results, 'tilt_correction', coord, 'T')
location = ""
for rec in Results:
if rec['er_location_names'] not in location:
location = location+':'+rec['er_location_names']
if 'average_age' in rec.keys() and rec['average_age'] != "" and ages == 1:
dates.append(rec['average_age'])
lat = float(rec['vgp_lat'])
lon = float(rec['vgp_lon'])
if flip == 0:
lats.append(lat)
lons.append(lon)
elif flip == 1:
if lat < 0:
rlats.append(-lat)
lon = lon+180.
if lon > 360:
lon = lon-360.
rlons.append(lon)
else:
lats.append(lat)
lons.append(lon)
elif anti == 1:
lats.append(-lat)
lon = lon+180.
if lon > 360:
lon = lon-360.
lons.append(lon)
ppars = []
ppars.append(lon)
ppars.append(lat)
ell1, ell2 = "", ""
if 'vgp_dm' in rec.keys() and rec['vgp_dm'] != "":
ell1 = float(rec['vgp_dm'])
if 'vgp_dp' in rec.keys() and rec['vgp_dp'] != "":
ell2 = float(rec['vgp_dp'])
if 'vgp_alpha95' in rec.keys() and rec['vgp_alpha95'] != "":
ell1, ell2 = float(rec['vgp_alpha95']), float(rec['vgp_alpha95'])
if ell1 != "" and ell2 != "":
ppars = []
ppars.append(lons[-1])
ppars.append(lats[-1])
ppars.append(ell1)
ppars.append(lons[-1])
isign = abs(lats[-1])/lats[-1]
ppars.append(lats[-1]-isign*90.)
ppars.append(ell2)
ppars.append(lons[-1]+90.)
ppars.append(0.)
Pars.append(ppars)
location = location.strip(':')
Opts = {'latmin': -90, 'latmax': 90, 'lonmin': 0., 'lonmax': 360., 'lat_0': lat_0, 'lon_0': lon_0,
'proj': proj, 'sym': 'bs', 'symsize': 3, 'pltgrid': 0, 'res': res, 'boundinglat': 0.}
Opts['details'] = {'coasts': 1, 'rivers': 0, 'states': 0,
'countries': 0, 'ocean': 1, 'fancy': fancy}
# make the base map with a blue triangle at the pole`
pmagplotlib.plot_map(FIG['map'], [90.], [0.], Opts)
Opts['pltgrid'] = -1
Opts['sym'] = sym
Opts['symsize'] = size
if len(dates) > 0:
Opts['names'] = dates
if len(lats) > 0:
# add the lats and lons of the poles
pmagplotlib.plot_map(FIG['map'], lats, lons, Opts)
Opts['names'] = []
if len(rlats) > 0:
Opts['sym'] = rsym
Opts['symsize'] = rsize
# add the lats and lons of the poles
pmagplotlib.plot_map(FIG['map'], rlats, rlons, Opts)
if plot == 0:
pmagplotlib.draw_figs(FIG)
if ell == 1: # add ellipses if desired.
Opts['details'] = {'coasts': 0, 'rivers': 0,
'states': 0, 'countries': 0, 'ocean': 0}
Opts['pltgrid'] = -1 # turn off meridian replotting
Opts['symsize'] = 2
Opts['sym'] = 'g-'
for ppars in Pars:
if ppars[2] != 0:
PTS = pmagplotlib.plot_ell(FIG['map'], ppars, 'g.', 0, 0)
elats, elons = [], []
for pt in PTS:
elons.append(pt[0])
elats.append(pt[1])
# make the base map with a blue triangle at the pole`
pmagplotlib.plot_map(FIG['map'], elats, elons, Opts)
if plot == 0:
pmagplotlib.draw_figs(FIG)
files = {}
for key in FIG.keys():
if pmagplotlib.isServer: # use server plot naming convention
files[key] = 'LO:_'+location+'_VGP_map.'+fmt
else: # use more readable plot naming convention
files[key] = '{}_VGP_map.{}'.format(
location.replace(' ', '_'), fmt)
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles = {}
titles['eq'] = 'LO:_'+location+'_VGP_map'
FIG = pmagplotlib.add_borders(FIG, titles, black, purple)
pmagplotlib.save_plots(FIG, files)
elif plot == 0:
pmagplotlib.draw_figs(FIG)
ans = input(" S[a]ve to save plot, Return to quit: ")
if ans == "a":
pmagplotlib.save_plots(FIG, files)
else:
print("Good bye")
sys.exit()
else:
pmagplotlib.save_plots(FIG, files)
def main():
"""
NAME
plot_geomagia.py
DESCRIPTION
makes a map and VADM plot of geomagia download file
SYNTAX
plot_geomagia.py [command line options]
OPTIONS
-h prints help message and quits
-f FILE, specify geomagia download file
-res [c,l,i,h] specify resolution (crude,low,intermediate,high)
-etp plot the etopo20 topographic mesh
-pad [LAT LON] pad bounding box by LAT/LON (default is [.5 .5] degrees)
-grd SPACE specify grid spacing
-prj [lcc] , specify projection (lcc=lambert conic conformable), default is mercator
-o color ocean blue/land green (default is not)
-d plot details of rivers, boundaries, etc.
-sav save plot and quit quietly
-fmt [png,svg,eps,jpg,pdf] specify format for output, default is pdf
DEFAULTS
resolution: intermediate
saved images are in pdf
"""
dir_path='.'
names,res,proj,locs,padlon,padlat,fancy,gridspace,details=[],'l','lcc','',0,0,0,15,1
Age_bounds=[-5000,2000]
Lat_bounds=[20,45]
Lon_bounds=[15,55]
fmt='pdf'
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-f' in sys.argv:
ind = sys.argv.index('-f')
sites_file=sys.argv[ind+1]
if '-res' in sys.argv:
ind = sys.argv.index('-res')
res=sys.argv[ind+1]
if '-etp' in sys.argv:fancy=1
if '-o' in sys.argv:ocean=1
if '-d' in sys.argv:details=1
if '-prj' in sys.argv:
ind = sys.argv.index('-prj')
proj=sys.argv[ind+1]
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt=sys.argv[ind+1]
verbose=pmagplotlib.verbose
if '-sav' in sys.argv:
verbose=0
if '-pad' in sys.argv:
ind = sys.argv.index('-pad')
padlat=float(sys.argv[ind+1])
padlon=float(sys.argv[ind+2])
if '-grd' in sys.argv:
ind = sys.argv.index('-grd')
gridspace=float(sys.argv[ind+1])
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
sites_file=dir_path+'/'+sites_file
geo_in=open(sites_file,'r').readlines()
Age,AgeErr,Vadm,VadmErr,slats,slons=[],[],[],[],[],[]
for line in geo_in[2:]: # skip top two rows`
rec=line.split()
if float(rec[0])>Age_bounds[0] and float(rec[0])<Age_bounds[1] \
and float(rec[12])>Lat_bounds[0] and float(rec[12]) < Lat_bounds[1]\
and float(rec[13])>Lon_bounds[0] and float(rec[13])<Lon_bounds[1]:
Age.append(float(rec[0]))
AgeErr.append(float(rec[1]))
Vadm.append(10.*float(rec[6]))
VadmErr.append(10.*float(rec[7]))
slats.append(float(rec[12]))
slons.append(float(rec[13]))
FIGS={'map':1,'vadms':2}
pmagplotlib.plot_init(FIGS['map'],6,6)
pmagplotlib.plot_init(FIGS['vadms'],6,6)
Opts={'res':res,'proj':proj,'loc_name':locs,'padlon':padlon,'padlat':padlat,'latmin':numpy.min(slats)-padlat,'latmax':numpy.max(slats)+padlat,'lonmin':numpy.min(slons)-padlon,'lonmax':numpy.max(slons)+padlon,'sym':'ro','boundinglat':0.,'pltgrid':1}
Opts['lon_0']=int(0.5*(numpy.min(slons)+numpy.max(slons)))
Opts['lat_0']=int(0.5*(numpy.min(slats)+numpy.max(slats)))
Opts['gridspace']=gridspace
if details==1:
Opts['details']={'coasts':1,'rivers':0,'states':1,'countries':1,'ocean':1}
else:
Opts['details']={'coasts':1,'rivers':0,'states':0,'countries':0,'ocean':1}
Opts['details']['fancy']=fancy
pmagplotlib.plot_map(FIGS['map'],slats,slons,Opts)
pmagplotlib.plot_xy(FIGS['vadms'],Age,Vadm,sym='bo',xlab='Age (Years CE)',ylab=r'VADM (ZAm$^2$)')
if verbose:pmagplotlib.draw_figs(FIGS)
files={}
for key in list(FIGS.keys()):
files[key]=key+'.'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles={}
titles['map']='Map'
titles['vadms']='VADMs'
FIG = pmagplotlib.add_borders(FIGS,titles,black,purple)
pmagplotlib.save_plots(FIGS,files)
elif verbose:
ans=input(" S[a]ve to save plot, Return to quit: ")
if ans=="a":
pmagplotlib.save_plots(FIGS,files)
else:
pmagplotlib.save_plots(FIGS,files)
def main():
"""
NAME
vgpmap_magic.py
DESCRIPTION
makes a map of vgps and a95/dp,dm for site means in a pmag_results table
SYNTAX
vgpmap_magic.py [command line options]
OPTIONS
-h prints help and quits
-eye ELAT ELON [specify eyeball location], default is 90., 0.
-f FILE pmag_results format file, [default is pmag_results.txt]
-res [c,l,i,h] specify resolution (crude, low, intermediate, high]
-etp plot the etopo20 topographpy data (requires high resolution data set)
-prj PROJ, specify one of the following:
ortho = orthographic
lcc = lambert conformal
moll = molweide
merc = mercator
-sym SYM SIZE: choose a symbol and size, examples:
ro 5 : small red circles
bs 10 : intermediate blue squares
g^ 20 : large green triangles
-ell plot dp/dm or a95 ellipses
-rev RSYM RSIZE : flip reverse poles to normal antipode
-S: plot antipodes of all poles
-age : plot the ages next to the poles
-crd [g,t] : choose coordinate system, default is to plot all site VGPs
-fmt [pdf, png, eps...] specify output format, default is pdf
-sav save and quit
DEFAULTS
FILE: pmag_results.txt
res: c
prj: ortho
ELAT,ELON = 0,0
SYM SIZE: ro 8
RSYM RSIZE: g^ 8
"""
dir_path = '.'
res, ages = 'c', 0
plot = 0
proj = 'ortho'
results_file = 'pmag_results.txt'
ell, flip = 0, 0
lat_0, lon_0 = 90., 0.
fmt = 'pdf'
sym, size = 'ro', 8
rsym, rsize = 'g^', 8
anti = 0
fancy = 0
coord = ""
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-S' in sys.argv:
anti = 1
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt = sys.argv[ind + 1]
if '-sav' in sys.argv:
plot = 1
if '-res' in sys.argv:
ind = sys.argv.index('-res')
res = sys.argv[ind + 1]
if '-etp' in sys.argv:
fancy = 1
if '-prj' in sys.argv:
ind = sys.argv.index('-prj')
proj = sys.argv[ind + 1]
if '-rev' in sys.argv:
flip = 1
ind = sys.argv.index('-rev')
rsym = (sys.argv[ind + 1])
rsize = int(sys.argv[ind + 2])
if '-sym' in sys.argv:
ind = sys.argv.index('-sym')
sym = (sys.argv[ind + 1])
size = int(sys.argv[ind + 2])
if '-eye' in sys.argv:
ind = sys.argv.index('-eye')
lat_0 = float(sys.argv[ind + 1])
lon_0 = float(sys.argv[ind + 2])
if '-ell' in sys.argv:
ell = 1
if '-age' in sys.argv:
ages = 1
if '-f' in sys.argv:
ind = sys.argv.index('-f')
results_file = sys.argv[ind + 1]
if '-crd' in sys.argv:
ind = sys.argv.index('-crd')
crd = sys.argv[ind + 1]
if crd == 'g':
coord = '0'
if crd == 't':
coord = '100'
results_file = dir_path + '/' + results_file
data, file_type = pmag.magic_read(results_file)
if file_type != 'pmag_results':
print("bad results file")
sys.exit()
FIG = {'map': 1}
pmagplotlib.plot_init(FIG['map'], 6, 6)
# read in er_sites file
lats, lons, dp, dm, a95 = [], [], [], [], []
Pars = []
dates, rlats, rlons = [], [], []
if 'data_type' in data[0].keys():
# get all site level data
Results = pmag.get_dictitem(data, 'data_type', 'i', 'T')
else:
Results = data
# get all non-blank latitudes
Results = pmag.get_dictitem(Results, 'vgp_lat', '', 'F')
# get all non-blank longitudes
Results = pmag.get_dictitem(Results, 'vgp_lon', '', 'F')
if coord != "":
# get specified coordinate system
Results = pmag.get_dictitem(Results, 'tilt_correction', coord, 'T')
location = ""
for rec in Results:
if rec['er_location_names'] not in location:
location = location + ':' + rec['er_location_names']
if 'average_age' in rec.keys(
) and rec['average_age'] != "" and ages == 1:
dates.append(rec['average_age'])
lat = float(rec['vgp_lat'])
lon = float(rec['vgp_lon'])
if flip == 0:
lats.append(lat)
lons.append(lon)
elif flip == 1:
if lat < 0:
rlats.append(-lat)
lon = lon + 180.
if lon > 360:
lon = lon - 360.
rlons.append(lon)
else:
lats.append(lat)
lons.append(lon)
elif anti == 1:
lats.append(-lat)
lon = lon + 180.
if lon > 360:
lon = lon - 360.
lons.append(lon)
ppars = []
ppars.append(lon)
ppars.append(lat)
ell1, ell2 = "", ""
if 'vgp_dm' in rec.keys() and rec['vgp_dm'] != "":
ell1 = float(rec['vgp_dm'])
if 'vgp_dp' in rec.keys() and rec['vgp_dp'] != "":
ell2 = float(rec['vgp_dp'])
if 'vgp_alpha95' in rec.keys() and rec['vgp_alpha95'] != "":
ell1, ell2 = float(rec['vgp_alpha95']), float(rec['vgp_alpha95'])
if ell1 != "" and ell2 != "":
ppars = []
ppars.append(lons[-1])
ppars.append(lats[-1])
ppars.append(ell1)
ppars.append(lons[-1])
isign = abs(lats[-1]) / lats[-1]
ppars.append(lats[-1] - isign * 90.)
ppars.append(ell2)
ppars.append(lons[-1] + 90.)
ppars.append(0.)
Pars.append(ppars)
location = location.strip(':')
Opts = {
'latmin': -90,
'latmax': 90,
'lonmin': 0.,
'lonmax': 360.,
'lat_0': lat_0,
'lon_0': lon_0,
'proj': proj,
'sym': 'bs',
'symsize': 3,
'pltgrid': 0,
'res': res,
'boundinglat': 0.
}
Opts['details'] = {
'coasts': 1,
'rivers': 0,
'states': 0,
'countries': 0,
'ocean': 1,
'fancy': fancy
}
# make the base map with a blue triangle at the pole`
pmagplotlib.plot_map(FIG['map'], [90.], [0.], Opts)
Opts['pltgrid'] = -1
Opts['sym'] = sym
Opts['symsize'] = size
if len(dates) > 0:
Opts['names'] = dates
if len(lats) > 0:
# add the lats and lons of the poles
pmagplotlib.plot_map(FIG['map'], lats, lons, Opts)
Opts['names'] = []
if len(rlats) > 0:
Opts['sym'] = rsym
Opts['symsize'] = rsize
# add the lats and lons of the poles
pmagplotlib.plot_map(FIG['map'], rlats, rlons, Opts)
if plot == 0:
pmagplotlib.draw_figs(FIG)
if ell == 1: # add ellipses if desired.
Opts['details'] = {
'coasts': 0,
'rivers': 0,
'states': 0,
'countries': 0,
'ocean': 0
}
Opts['pltgrid'] = -1 # turn off meridian replotting
Opts['symsize'] = 2
Opts['sym'] = 'g-'
for ppars in Pars:
if ppars[2] != 0:
PTS = pmagplotlib.plot_ell(FIG['map'], ppars, 'g.', 0, 0)
elats, elons = [], []
for pt in PTS:
elons.append(pt[0])
elats.append(pt[1])
# make the base map with a blue triangle at the pole`
pmagplotlib.plot_map(FIG['map'], elats, elons, Opts)
if plot == 0:
pmagplotlib.draw_figs(FIG)
files = {}
for key in FIG.keys():
if pmagplotlib.isServer: # use server plot naming convention
files[key] = 'LO:_' + location + '_VGP_map.' + fmt
else: # use more readable plot naming convention
files[key] = '{}_VGP_map.{}'.format(location.replace(' ', '_'),
fmt)
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles = {}
titles['eq'] = 'LO:_' + location + '_VGP_map'
FIG = pmagplotlib.add_borders(FIG, titles, black, purple)
pmagplotlib.save_plots(FIG, files)
elif plot == 0:
pmagplotlib.draw_figs(FIG)
ans = input(" S[a]ve to save plot, Return to quit: ")
if ans == "a":
pmagplotlib.save_plots(FIG, files)
else:
print("Good bye")
sys.exit()
else:
pmagplotlib.save_plots(FIG, files)
def main():
"""
NAME
basemap_magic.py
NB: this program no longer maintained - use plot_map_pts.py for greater functionality
DESCRIPTION
makes a map of locations in er_sites.txt
SYNTAX
basemap_magic.py [command line options]
OPTIONS
-h prints help message and quits
-f SFILE, specify er_sites.txt or pmag_results.txt format file
-res [c,l,i,h] specify resolution (crude,low,intermediate,high)
-etp plot the etopo20 topographic mesh
-pad [LAT LON] pad bounding box by LAT/LON (default is [.5 .5] degrees)
-grd SPACE specify grid spacing
-prj [lcc] , specify projection (lcc=lambert conic conformable), default is mercator
-n print site names (default is not)
-l print location names (default is not)
-o color ocean blue/land green (default is not)
-R don't plot details of rivers
-B don't plot national/state boundaries, etc.
-sav save plot and quit quietly
-fmt [png,svg,eps,jpg,pdf] specify format for output, default is pdf
DEFAULTS
SFILE: 'er_sites.txt'
resolution: intermediate
saved images are in pdf
"""
dir_path = '.'
sites_file = 'er_sites.txt'
ocean = 0
res = 'i'
proj = 'merc'
prn_name = 0
prn_loc = 0
fancy = 0
rivers, boundaries = 0, 0
padlon, padlat, gridspace, details = .5, .5, .5, 1
fmt = 'pdf'
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-f' in sys.argv:
ind = sys.argv.index('-f')
sites_file = sys.argv[ind+1]
if '-res' in sys.argv:
ind = sys.argv.index('-res')
res = sys.argv[ind+1]
if '-etp' in sys.argv:
fancy = 1
if '-n' in sys.argv:
prn_name = 1
if '-l' in sys.argv:
prn_loc = 1
if '-o' in sys.argv:
ocean = 1
if '-R' in sys.argv:
rivers = 0
if '-B' in sys.argv:
boundaries = 0
if '-prj' in sys.argv:
ind = sys.argv.index('-prj')
proj = sys.argv[ind+1]
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt = sys.argv[ind+1]
verbose = pmagplotlib.verbose
if '-sav' in sys.argv:
verbose = 0
if '-pad' in sys.argv:
ind = sys.argv.index('-pad')
padlat = float(sys.argv[ind+1])
padlon = float(sys.argv[ind+2])
if '-grd' in sys.argv:
ind = sys.argv.index('-grd')
gridspace = float(sys.argv[ind+1])
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind+1]
sites_file = dir_path+'/'+sites_file
location = ""
FIG = {'map': 1}
pmagplotlib.plot_init(FIG['map'], 6, 6)
# read in er_sites file
Sites, file_type = pmag.magic_read(sites_file)
if 'results' in file_type:
latkey = 'average_lat'
lonkey = 'average_lon'
namekey = 'pmag_result_name'
lockey = 'er_location_names'
else:
latkey = 'site_lat'
lonkey = 'site_lon'
namekey = 'er_site_name'
lockey = 'er_location_name'
lats, lons = [], []
slats, slons = [], []
names, locs = [], []
for site in Sites:
if prn_loc == 1 and location == "":
location = site['er_location_name']
lats.append(float(site[latkey]))
l = float(site[lonkey])
if l < 0:
l = l+360. # make positive
lons.append(l)
if prn_name == 1:
names.append(site[namekey])
if prn_loc == 1:
locs.append(site[lockey])
for lat in lats:
slats.append(lat)
for lon in lons:
slons.append(lon)
Opts = {'res': res, 'proj': proj, 'loc_name': locs, 'padlon': padlon, 'padlat': padlat, 'latmin': numpy.min(slats)-padlat, 'latmax': numpy.max(
slats)+padlat, 'lonmin': numpy.min(slons)-padlon, 'lonmax': numpy.max(slons)+padlon, 'sym': 'ro', 'boundinglat': 0., 'pltgrid': 1.}
Opts['lon_0'] = 0.5*(numpy.min(slons)+numpy.max(slons))
Opts['lat_0'] = 0.5*(numpy.min(slats)+numpy.max(slats))
Opts['names'] = names
Opts['gridspace'] = gridspace
Opts['details'] = {'coasts': 1, 'rivers': 1,
'states': 1, 'countries': 1, 'ocean': 0}
if ocean == 1:
Opts['details']['ocean'] = 1
if rivers == 1:
Opts['details']['rivers'] = 0
if boundaries == 1:
Opts['details']['states'] = 0
Opts['details']['countries'] = 0
Opts['details']['fancy'] = fancy
pmagplotlib.plot_map(FIG['map'], lats, lons, Opts)
if verbose:
pmagplotlib.draw_figs(FIG)
files = {}
for key in list(FIG.keys()):
files[key] = 'Site_map'+'.'+fmt
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles = {}
titles['map'] = 'Site Map'
FIG = pmagplotlib.add_borders(FIG, titles, black, purple)
pmagplotlib.save_plots(FIG, files)
elif verbose:
ans = input(" S[a]ve to save plot, Return to quit: ")
if ans == "a":
pmagplotlib.save_plots(FIG, files)
else:
pmagplotlib.save_plots(FIG, files)
def main():
"""
NAME
polemap_magic.py
DESCRIPTION
makes a map of paleomagnetic poles and a95/dp,dm for pole in a locations table
SYNTAX
polemap_magic.py [command line options]
OPTIONS
-h prints help and quits
-eye ELAT ELON [specify eyeball location], default is 90., 0.
-f FILE location format file, [default is locations.txt]
-res [c,l,i,h] specify resolution (crude, low, intermediate, high]
-etp plot the etopo20 topographpy data (requires high resolution data set)
-prj PROJ, specify one of the following:
ortho = orthographic
lcc = lambert conformal
moll = molweide
merc = mercator
-sym SYM SIZE: choose a symbol and size, examples:
ro 5 : small red circles
bs 10 : intermediate blue squares
g^ 20 : large green triangles
-ell plot dp/dm or a95 ellipses
-rev RSYM RSIZE : flip reverse poles to normal antipode
-S: plot antipodes of all poles
-age : plot the ages next to the poles
-crd [g,t] : choose coordinate system, default is to plot all location poles
-fmt [pdf, png, eps...] specify output format, default is pdf
-sav save and quit
DEFAULTS
FILE: locations.txt
res: c
prj: ortho
ELAT,ELON = 0,0
SYM SIZE: ro 8
RSYM RSIZE: g^ 8
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
dir_path = pmag.get_named_arg("-WD", ".")
# plot: default is 0, if -sav in sys.argv should be 1
plot = pmag.get_flag_arg_from_sys("-sav", true=1, false=0)
fmt = pmag.get_named_arg("-fmt", "pdf")
res = pmag.get_named_arg("-res", "c")
proj = pmag.get_named_arg("-prj", "ortho")
anti = pmag.get_flag_arg_from_sys("-S", true=1, false=0)
fancy = pmag.get_flag_arg_from_sys("-etp", true=1, false=0)
ell = pmag.get_flag_arg_from_sys("-ell", true=1, false=0)
ages = pmag.get_flag_arg_from_sys("-age", true=1, false=0)
if '-rev' in sys.argv:
flip = 1
ind = sys.argv.index('-rev')
rsym = (sys.argv[ind + 1])
rsize = int(sys.argv[ind + 2])
else:
flip, rsym, rsize = 0, "g^", 8
if '-sym' in sys.argv:
ind = sys.argv.index('-sym')
sym = (sys.argv[ind + 1])
size = int(sys.argv[ind + 2])
else:
sym, size = 'ro', 8
if '-eye' in sys.argv:
ind = sys.argv.index('-eye')
lat_0 = float(sys.argv[ind + 1])
lon_0 = float(sys.argv[ind + 2])
else:
lat_0, lon_0 = 90., 0.
crd = pmag.get_named_arg("-crd", "")
coord_dict = {'g': 0, 't': 100}
coord = coord_dict[crd] if crd else ""
results_file = pmag.get_named_arg("-f", "locations.txt")
con = cb.Contribution(dir_path, single_file=results_file)
if not list(con.tables.keys()):
print("-W - Couldn't read in data")
return False, "Couldn't read in data"
FIG = {'map': 1}
pmagplotlib.plot_init(FIG['map'], 6, 6)
# read in location file
lats, lons = [], []
Pars = []
dates, rlats, rlons = [], [], []
polarities = []
pole_container = con.tables['locations']
pole_df = pole_container.df
# use individual results
if not pmagplotlib.isServer:
if 'result_type' in pole_df.columns:
pole_df = pole_df[pole_df['result_type'] == 'a']
if 'pole_lat' not in pole_df.columns or 'pole_lon' not in pole_df.columns:
print(
"-W- pole_lat and pole_lon are required columns to run polemap_magic.py"
)
return False, "pole_lat and pole_lon are required columns to run polemap_magic.py"
# use records with pole_lat and pole_lon
cond1, cond2 = pole_df['pole_lat'].notnull(), pole_df['pole_lon'].notnull()
Results = pole_df[cond1 & cond2]
# use tilt correction
if coord and 'dir_tilt_correction' in Results.columns:
Results = Results[Results['dir_tilt_correction'] == coord]
# get location name and average ages
loc_list = Results['location'].values
locations = ":".join(Results['location'].unique())
if 'age' not in Results.columns and 'age_low' in Results.columns and 'age_high' in Results.columns:
Results['age'] = Results['age_low']+0.5 * \
(Results['age_high']-Results['age_low'])
if 'age' in Results.columns and ages == 1:
dates = Results['age'].unique()
if not any(Results.index):
print("-W- No poles could be plotted")
return False, "No poles could be plotted"
# go through rows and extract data
for ind, row in Results.iterrows():
lat, lon = float(row['pole_lat']), float(row['pole_lon'])
if 'dir_polarity' in row:
polarities.append(row['dir_polarity'])
if anti == 1:
lats.append(-lat)
lon = lon + 180.
if lon > 360:
lon = lon - 360.
lons.append(lon)
elif flip == 0:
lats.append(lat)
lons.append(lon)
elif flip == 1:
if lat < 0:
rlats.append(-lat)
lon = lon + 180.
if lon > 360:
lon = lon - 360
rlons.append(lon)
else:
lats.append(lat)
lons.append(lon)
ppars = []
ppars.append(lon)
ppars.append(lat)
ell1, ell2 = "", ""
if 'pole_dm' in list(row.keys()) and row['pole_dm']:
ell1 = float(row['pole_dm'])
if 'pole_dp' in list(row.keys()) and row['pole_dp']:
ell2 = float(row['pole_dp'])
if 'pole_alpha95' in list(row.keys()) and row['pole_alpha95']:
ell1, ell2 = float(row['pole_alpha95']), float(row['pole_alpha95'])
if ell1 and ell2:
ppars = []
ppars.append(lons[-1])
ppars.append(lats[-1])
ppars.append(ell1)
ppars.append(lons[-1])
isign = abs(lats[-1]) / lats[-1]
ppars.append(lats[-1] - isign * 90.)
ppars.append(ell2)
ppars.append(lons[-1] + 90.)
ppars.append(0.)
Pars.append(ppars)
locations = locations.strip(':')
Opts = {
'latmin': -90,
'latmax': 90,
'lonmin': 0.,
'lonmax': 360.,
'lat_0': lat_0,
'lon_0': lon_0,
'proj': proj,
'sym': 'bs',
'symsize': 3,
'pltgrid': 0,
'res': res,
'boundinglat': 0.
}
Opts['details'] = {
'coasts': 1,
'rivers': 0,
'states': 0,
'countries': 0,
'ocean': 1,
'fancy': fancy
}
base_Opts = Opts.copy()
# make the base map with a blue triangle at the pole
pmagplotlib.plot_map(FIG['map'], [90.], [0.], Opts)
Opts['pltgrid'] = -1
Opts['sym'] = sym
Opts['symsize'] = size
if len(dates) > 0:
Opts['names'] = dates
if len(lats) > 0:
# add the lats and lons of the poles
pmagplotlib.plot_map(FIG['map'], lats, lons, Opts)
Opts['names'] = []
titles = {}
files = {}
if pmagplotlib.isServer:
# plot each indvidual pole for the server
for ind in range(len(lats)):
lat = lats[ind]
lon = lons[ind]
polarity = ""
if 'polarites' in locals():
polarity = polarities[ind]
polarity = "_" + polarity if polarity else ""
location = loc_list[ind]
FIG["map_{}".format(ind)] = ind + 2
pmagplotlib.plot_init(FIG['map'], 6, 6)
# if with baseOpts, lat/lon don't show
# if with Opts, grid lines don't show
pmagplotlib.plot_map(ind + 2, [90], [0.], base_Opts)
pmagplotlib.plot_map(ind + 2, [lat], [lon], Opts)
titles["map_{}".format(ind)] = location
files["map_{}".format(ind)] = "LO:_{}{}_TY:_POLE_map_.{}".format(
location, polarity, fmt)
# truncate location names so that ultra long filenames are not created
if len(locations) > 50:
locations = locations[:50]
if pmagplotlib.isServer:
# use server plot naming convention
if 'contribution' in con.tables:
# try to get contribution id
con_id = con.tables['contribution'].df.iloc[0].id
files['map'] = 'MC:_{}_TY:_POLE_map.{}'.format(con_id, fmt)
else:
# no contribution id available
files['map'] = 'LO:_' + locations + '_TY:_POLE_map.' + fmt
else:
# use readable naming convention for non-database use
files['map'] = '{}_POLE_map.{}'.format(locations, fmt)
#
if len(rlats) > 0:
Opts['sym'] = rsym
Opts['symsize'] = rsize
# add the lats and lons of the poles
pmagplotlib.plot_map(FIG['map'], rlats, rlons, Opts)
if plot == 0 and not set_env.IS_WIN:
pmagplotlib.draw_figs(FIG)
if ell == 1: # add ellipses if desired.
Opts['details'] = {
'coasts': 0,
'rivers': 0,
'states': 0,
'countries': 0,
'ocean': 0,
'fancy': fancy
}
Opts['pltgrid'] = -1 # turn off meridian replotting
Opts['symsize'] = 2
Opts['sym'] = 'g-'
for ppars in Pars:
if ppars[2] != 0:
PTS = pmagplotlib.plot_ell(FIG['map'], ppars, 'g.', 0, 0)
elats, elons = [], []
for pt in PTS:
elons.append(pt[0])
elats.append(pt[1])
# make the base map with a blue triangle at the pole
pmagplotlib.plot_map(FIG['map'], elats, elons, Opts)
if plot == 0 and not set_env.IS_WIN:
pmagplotlib.draw_figs(FIG)
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles['map'] = 'LO:_' + locations + '_POLE_map'
if 'contribution' in con.tables:
con_id = con.tables['contribution'].df.iloc[0].id
titles['map'] = "MagIC contribution {} all locations".format(
con_id)
FIG = pmagplotlib.add_borders(FIG, titles, black, purple)
pmagplotlib.save_plots(FIG, files)
elif plot == 0:
pmagplotlib.draw_figs(FIG)
ans = input(" S[a]ve to save plot, Return to quit: ")
if ans == "a":
pmagplotlib.save_plots(FIG, files)
else:
print("Good bye")
else:
pmagplotlib.save_plots(FIG, files)
return True, files
def main():
"""
NAME
vgpmap_magic.py
DESCRIPTION
makes a map of vgps and a95/dp,dm for site means in a sites table
SYNTAX
vgpmap_magic.py [command line options]
OPTIONS
-h prints help and quits
-eye ELAT ELON [specify eyeball location], default is 90., 0.
-f FILE sites format file, [default is sites.txt]
-res [c,l,i,h] specify resolution (crude, low, intermediate, high]
-etp plot the etopo20 topographpy data (requires high resolution data set)
-prj PROJ, specify one of the following:
ortho = orthographic
lcc = lambert conformal
moll = molweide
merc = mercator
-sym SYM SIZE: choose a symbol and size, examples:
ro 5 : small red circles
bs 10 : intermediate blue squares
g^ 20 : large green triangles
-ell plot dp/dm or a95 ellipses
-rev RSYM RSIZE : flip reverse poles to normal antipode
-S: plot antipodes of all poles
-age : plot the ages next to the poles
-crd [g,t] : choose coordinate system, default is to plot all site VGPs
-fmt [pdf, png, eps...] specify output format, default is pdf
-sav save and quit
DEFAULTS
FILE: sites.txt
res: c
prj: ortho
ELAT,ELON = 0,0
SYM SIZE: ro 8
RSYM RSIZE: g^ 8
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
dir_path = pmag.get_named_arg("-WD", ".")
# plot: default is 0, if -sav in sys.argv should be 1
plot = pmag.get_flag_arg_from_sys("-sav", true=1, false=0)
fmt = pmag.get_named_arg("-fmt", "pdf")
res = pmag.get_named_arg("-res", "c")
proj = pmag.get_named_arg("-prj", "ortho")
anti = pmag.get_flag_arg_from_sys("-S", true=1, false=0)
fancy = pmag.get_flag_arg_from_sys("-etp", true=1, false=0)
ell = pmag.get_flag_arg_from_sys("-ell", true=1, false=0)
ages = pmag.get_flag_arg_from_sys("-age", true=1, false=0)
if '-rev' in sys.argv:
flip = 1
ind = sys.argv.index('-rev')
rsym = (sys.argv[ind + 1])
rsize = int(sys.argv[ind + 2])
else:
flip, rsym, rsize = 0, "g^", 8
if '-sym' in sys.argv:
ind = sys.argv.index('-sym')
sym = (sys.argv[ind + 1])
size = int(sys.argv[ind + 2])
else:
sym, size = 'ro', 8
if '-eye' in sys.argv:
ind = sys.argv.index('-eye')
lat_0 = float(sys.argv[ind + 1])
lon_0 = float(sys.argv[ind + 2])
else:
lat_0, lon_0 = 90., 0.
crd = pmag.get_named_arg("-crd", "")
coord_dict = {'g': 0, 't': 100}
coord = coord_dict[crd] if crd else ""
results_file = pmag.get_named_arg("-f", "sites.txt")
con = cb.Contribution(dir_path, single_file=results_file)
if not list(con.tables.keys()):
print("-W - Couldn't read in data")
return
FIG = {'map': 1}
pmagplotlib.plot_init(FIG['map'], 6, 6)
# read in er_sites file
lats, lons = [], []
Pars = []
dates, rlats, rlons = [], [], []
site_container = con.tables['sites']
site_df = site_container.df
# use individual results
if 'result_type' in site_df.columns:
site_df = site_df[site_df['result_type'] == 'i']
# use records with vgp_lat and vgp_lon
if 'vgp_lat' in site_df.columns and 'vgp_lon' in site_df.columns:
cond1, cond2 = site_df['vgp_lat'].notnull(
), site_df['vgp_lon'].notnull()
else:
print('nothing to plot')
sys.exit()
Results = site_df[cond1 & cond2]
# use tilt correction
if coord and 'dir_tilt_correction' in Results.columns:
Results = Results[Results['dir_tilt_correction'] == coord]
# get location name and average ages
location = ":".join(Results['location'].unique())
if 'age' in Results.columns and ages == 1:
dates = Results['age'].unique()
# go through rows and extract data
for ind, row in Results.iterrows():
lat, lon = float(row['vgp_lat']), float(row['vgp_lon'])
if anti == 1:
lats.append(-lat)
lon = lon + 180.
if lon > 360:
lon = lon - 360.
lons.append(lon)
elif flip == 0:
lats.append(lat)
lons.append(lon)
elif flip == 1:
if lat < 0:
rlats.append(-lat)
lon = lon + 180.
if lon > 360:
lon = lon - 360
rlons.append(lon)
else:
lats.append(lat)
lons.append(lon)
ppars = []
ppars.append(lon)
ppars.append(lat)
ell1, ell2 = "", ""
if 'vgp_dm' in list(row.keys()) and row['vgp_dm']:
ell1 = float(row['vgp_dm'])
if 'vgp_dp' in list(row.keys()) and row['vgp_dp']:
ell2 = float(row['vgp_dp'])
if 'vgp_alpha95' in list(row.keys()) and row['vgp_alpha95'].notnull():
ell1, ell2 = float(row['vgp_alpha95']), float(row['vgp_alpha95'])
if ell1 and ell2:
ppars = []
ppars.append(lons[-1])
ppars.append(lats[-1])
ppars.append(ell1)
ppars.append(lons[-1])
isign = abs(lats[-1]) / lats[-1]
ppars.append(lats[-1] - isign * 90.)
ppars.append(ell2)
ppars.append(lons[-1] + 90.)
ppars.append(0.)
Pars.append(ppars)
location = location.strip(':')
Opts = {
'latmin': -90,
'latmax': 90,
'lonmin': 0.,
'lonmax': 360.,
'lat_0': lat_0,
'lon_0': lon_0,
'proj': proj,
'sym': 'bs',
'symsize': 3,
'pltgrid': 0,
'res': res,
'boundinglat': 0.
}
Opts['details'] = {
'coasts': 1,
'rivers': 0,
'states': 0,
'countries': 0,
'ocean': 1,
'fancy': fancy
}
# make the base map with a blue triangle at the pole
pmagplotlib.plot_map(FIG['map'], [90.], [0.], Opts)
Opts['pltgrid'] = -1
Opts['sym'] = sym
Opts['symsize'] = size
if len(dates) > 0:
Opts['names'] = dates
if len(lats) > 0:
# add the lats and lons of the poles
pmagplotlib.plot_map(FIG['map'], lats, lons, Opts)
Opts['names'] = []
if len(rlats) > 0:
Opts['sym'] = rsym
Opts['symsize'] = rsize
# add the lats and lons of the poles
pmagplotlib.plot_map(FIG['map'], rlats, rlons, Opts)
if plot == 0 and not set_env.IS_WIN:
pmagplotlib.draw_figs(FIG)
if ell == 1: # add ellipses if desired.
Opts['details'] = {
'coasts': 0,
'rivers': 0,
'states': 0,
'countries': 0,
'ocean': 0,
'fancy': fancy
}
Opts['pltgrid'] = -1 # turn off meridian replotting
Opts['symsize'] = 2
Opts['sym'] = 'g-'
for ppars in Pars:
if ppars[2] != 0:
PTS = pmagplotlib.plot_ell(FIG['map'], ppars, 'g.', 0, 0)
elats, elons = [], []
for pt in PTS:
elons.append(pt[0])
elats.append(pt[1])
# make the base map with a blue triangle at the pole
pmagplotlib.plot_map(FIG['map'], elats, elons, Opts)
if plot == 0 and not set_env.IS_WIN:
pmagplotlib.draw_figs(FIG)
files = {}
for key in list(FIG.keys()):
if pmagplotlib.isServer: # use server plot naming convention
files[key] = 'LO:_' + location + '_VGP_map.' + fmt
else: # use more readable naming convention
files[key] = '{}_VGP_map.{}'.format(location, fmt)
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles = {}
titles['map'] = 'LO:_' + location + '_VGP_map'
FIG = pmagplotlib.add_borders(FIG, titles, black, purple)
pmagplotlib.save_plots(FIG, files)
elif plot == 0:
pmagplotlib.draw_figs(FIG)
ans = input(" S[a]ve to save plot, Return to quit: ")
if ans == "a":
pmagplotlib.save_plots(FIG, files)
else:
print("Good bye")
sys.exit()
else:
pmagplotlib.save_plots(FIG, files)
def main():
"""
NAME
vgpmap_magic.py
DESCRIPTION
makes a map of vgps and a95/dp,dm for site means in a sites table
SYNTAX
vgpmap_magic.py [command line options]
OPTIONS
-h prints help and quits
-eye ELAT ELON [specify eyeball location], default is 90., 0.
-f FILE sites format file, [default is sites.txt]
-res [c,l,i,h] specify resolution (crude, low, intermediate, high]
-etp plot the etopo20 topographpy data (requires high resolution data set)
-prj PROJ, specify one of the following:
ortho = orthographic
lcc = lambert conformal
moll = molweide
merc = mercator
-sym SYM SIZE: choose a symbol and size, examples:
ro 5 : small red circles
bs 10 : intermediate blue squares
g^ 20 : large green triangles
-ell plot dp/dm or a95 ellipses
-rev RSYM RSIZE : flip reverse poles to normal antipode
-S: plot antipodes of all poles
-age : plot the ages next to the poles
-crd [g,t] : choose coordinate system, default is to plot all site VGPs
-fmt [pdf, png, eps...] specify output format, default is pdf
-sav save and quit
DEFAULTS
FILE: sites.txt
res: c
prj: ortho
ELAT,ELON = 0,0
SYM SIZE: ro 8
RSYM RSIZE: g^ 8
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
dir_path = pmag.get_named_arg("-WD", ".")
# plot: default is 0, if -sav in sys.argv should be 1
plot = pmag.get_flag_arg_from_sys("-sav", true=1, false=0)
fmt = pmag.get_named_arg("-fmt", "pdf")
res = pmag.get_named_arg("-res", "c")
proj = pmag.get_named_arg("-prj", "ortho")
anti = pmag.get_flag_arg_from_sys("-S", true=1, false=0)
fancy = pmag.get_flag_arg_from_sys("-etp", true=1, false=0)
ell = pmag.get_flag_arg_from_sys("-ell", true=1, false=0)
ages = pmag.get_flag_arg_from_sys("-age", true=1, false=0)
if '-rev' in sys.argv:
flip = 1
ind = sys.argv.index('-rev')
rsym = (sys.argv[ind + 1])
rsize = int(sys.argv[ind + 2])
else:
flip, rsym, rsize = 0, "g^", 8
if '-sym' in sys.argv:
ind = sys.argv.index('-sym')
sym = (sys.argv[ind + 1])
size = int(sys.argv[ind + 2])
else:
sym, size = 'ro', 8
if '-eye' in sys.argv:
ind = sys.argv.index('-eye')
lat_0 = float(sys.argv[ind + 1])
lon_0 = float(sys.argv[ind + 2])
else:
lat_0, lon_0 = 90., 0.
crd = pmag.get_named_arg("-crd", "")
coord_dict = {'g': 0, 't': 100}
coord = coord_dict[crd] if crd else ""
results_file = pmag.get_named_arg("-f", "sites.txt")
con = cb.Contribution(dir_path, single_file=results_file)
if not list(con.tables.keys()):
print("-W - Couldn't read in data")
return
FIG = {'map': 1}
pmagplotlib.plot_init(FIG['map'], 6, 6)
# read in er_sites file
lats, lons = [], []
Pars = []
dates, rlats, rlons = [], [], []
site_container = con.tables['sites']
site_df = site_container.df
# use records with vgp_lat and vgp_lon
if 'vgp_lat' in site_df.columns and 'vgp_lon' in site_df.columns:
cond1, cond2 = site_df['vgp_lat'].notnull(), site_df['vgp_lon'].notnull()
else:
print ('nothing to plot')
sys.exit()
Results = site_df[cond1 & cond2]
# use tilt correction
if coord and 'dir_tilt_correction' in Results.columns:
Results = Results[Results['dir_tilt_correction'] == coord]
# get location name and average ages
locs = Results['location'].unique()
if len(locs):
location = ":".join(Results['location'].unique())
else:
location = ""
if 'age' in Results.columns and ages == 1:
dates = Results['age'].unique()
# go through rows and extract data
for ind, row in Results.iterrows():
lat, lon = float(row['vgp_lat']), float(row['vgp_lon'])
if anti == 1:
lats.append(-lat)
lon = lon + 180.
if lon > 360:
lon = lon - 360.
lons.append(lon)
elif flip == 0:
lats.append(lat)
lons.append(lon)
elif flip == 1:
if lat < 0:
rlats.append(-lat)
lon = lon + 180.
if lon > 360:
lon = lon - 360
rlons.append(lon)
else:
lats.append(lat)
lons.append(lon)
ppars = []
ppars.append(lon)
ppars.append(lat)
ell1, ell2 = "", ""
if 'vgp_dm' in list(row.keys()) and row['vgp_dm']:
ell1 = float(row['vgp_dm'])
if 'vgp_dp' in list(row.keys()) and row['vgp_dp']:
ell2 = float(row['vgp_dp'])
if 'vgp_alpha95' in list(row.keys()) and (row['vgp_alpha95'] or row['vgp_alpha95'] == 0):
ell1, ell2 = float(row['vgp_alpha95']), float(row['vgp_alpha95'])
if ell1 and ell2:
ppars = []
ppars.append(lons[-1])
ppars.append(lats[-1])
ppars.append(ell1)
ppars.append(lons[-1])
try:
isign = abs(lats[-1]) / lats[-1]
except ZeroDivisionError:
isign = 1
ppars.append(lats[-1] - isign * 90.)
ppars.append(ell2)
ppars.append(lons[-1] + 90.)
ppars.append(0.)
Pars.append(ppars)
location = location.strip(':')
Opts = {'latmin': -90, 'latmax': 90, 'lonmin': 0., 'lonmax': 360.,
'lat_0': lat_0, 'lon_0': lon_0, 'proj': proj, 'sym': 'bs',
'symsize': 3, 'pltgrid': 0, 'res': res, 'boundinglat': 0.}
Opts['details'] = {'coasts': 1, 'rivers': 0, 'states': 0,
'countries': 0, 'ocean': 1, 'fancy': fancy}
# make the base map with a blue triangle at the pole
pmagplotlib.plot_map(FIG['map'], [90.], [0.], Opts)
Opts['pltgrid'] = -1
Opts['sym'] = sym
Opts['symsize'] = size
if len(dates) > 0:
Opts['names'] = dates
if len(lats) > 0:
# add the lats and lons of the poles
pmagplotlib.plot_map(FIG['map'], lats, lons, Opts)
Opts['names'] = []
if len(rlats) > 0:
Opts['sym'] = rsym
Opts['symsize'] = rsize
# add the lats and lons of the poles
pmagplotlib.plot_map(FIG['map'], rlats, rlons, Opts)
if plot == 0 and not set_env.IS_WIN:
pmagplotlib.draw_figs(FIG)
if ell == 1: # add ellipses if desired.
Opts['details'] = {'coasts': 0, 'rivers': 0, 'states': 0,
'countries': 0, 'ocean': 0, 'fancy': fancy}
Opts['pltgrid'] = -1 # turn off meridian replotting
Opts['symsize'] = 2
Opts['sym'] = 'g-'
for ppars in Pars:
if ppars[2] != 0:
PTS = pmagplotlib.plot_ell(FIG['map'], ppars, 'g.', 0, 0)
elats, elons = [], []
for pt in PTS:
elons.append(pt[0])
elats.append(pt[1])
# make the base map with a blue triangle at the pole
pmagplotlib.plot_map(FIG['map'], elats, elons, Opts)
if plot == 0 and not set_env.IS_WIN:
pmagplotlib.draw_figs(FIG)
files = {}
for key in list(FIG.keys()):
if pmagplotlib.isServer: # use server plot naming convention
files[key] = 'LO:_' + location + '_TY:_VGP_map.' + fmt
else: # use more readable naming convention
files[key] = '{}_VGP_map.{}'.format(location, fmt)
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles = {}
titles['map'] = location + ' VGP map'
FIG = pmagplotlib.add_borders(FIG, titles, black, purple)
pmagplotlib.save_plots(FIG, files)
elif plot == 0:
pmagplotlib.draw_figs(FIG)
ans = input(" S[a]ve to save plot, Return to quit: ")
if ans == "a":
pmagplotlib.save_plots(FIG, files)
else:
print("Good bye")
sys.exit()
else:
pmagplotlib.save_plots(FIG, files)
def main():
"""
NAME
cont_rot.py
DESCRIPTION
rotates continental fragments according to specified Euler pole
SYNTAX
cont_rot.py [command line options]
OPTIONS
-h prints help and quits
-con [af, congo, kala, aus, balt, eur, ind, sam, ant, grn, lau, nam, gond] , specify colon delimited list of continents to be displayed, e.g., af, af:aus], etc
-age use finite rotations of Torsvik et al. 2008 for specific age (5 Ma increments <325Ma)
rotates to paleomagnetic reference frame
available conts: [congo kala aus eur ind sam ant grn nam]
-sac include rotation of south african craton to pmag reference
-sym [ro, bs, g^, r., b-, etc.] [1,5,10] symbol and size for continent
colors are r=red,b=blue,g=green, etc.
symbols are '.' for points, ^, for triangle, s for square, etc.
-, for lines, -- for dotted lines, see matplotlib online documentation for plot()
-eye ELAT ELON [specify eyeball location]
-pfr PLAT PLON OMEGA [specify pole of finite rotation lat,lon and degrees]
-ffr FFILE, specifies series of finite rotations
vector in tab delimited file
-sr treat poles as sequential rotations
-fpp PFILE, specifies series of paleopoles from which
euler poles can be calculated: vector in tab delimited file
-pt LAT LON, specify a point to rotate along with continent
-fpt PTFILE, specifies file with a series of points to be plotted
-res [c,l,i,h] specify resolution (crude, low, intermediate, high]
-fmt [png,jpg,svg,pdf] format for saved figure - pdf is default
-sav saves plots and quits
-prj PROJ, specify one of the supported projections: (see basemap.py online documentation)
aeqd = Azimuthal Equidistant
poly = Polyconic
gnom = Gnomonic
moll = Mollweide
tmerc = Transverse Mercator
nplaea = North-Polar Lambert Azimuthal
mill = Miller Cylindrical
merc = Mercator
stere = Stereographic
npstere = North-Polar Stereographic
geos = Geostationary
laea = Lambert Azimuthal Equal Area
sinu = Sinusoidal
spstere = South-Polar Stereographic
lcc = Lambert Conformal
npaeqd = North-Polar Azimuthal Equidistant
eqdc = Equidistant Conic
cyl = Cylindrical Equidistant
omerc = Oblique Mercator
aea = Albers Equal Area
spaeqd = South-Polar Azimuthal Equidistant
ortho = Orthographic
cass= Cassini-Soldner
splaea = South-Polar Lambert Azimuthal
robin = Robinson
DEFAULTS
con: nam
res: c
prj: mollweide
ELAT,ELON = 0,0
NB: high resolution or lines can be very slow
"""
dir_path = '.'
ocean = 0
res = 'c'
proj = 'moll'
euler_file = ''
Conts = []
Poles = []
PTS = []
lat_0, lon_0 = 0., 0.
fmt = 'pdf'
sym = 'r.'
symsize = 5
plot = 0
SEQ, age, SAC = 0, 0, 0
rconts = [
'af', 'congo', 'kala', 'aus', 'eur', 'ind', 'sam', 'ant', 'grn', 'nam'
]
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-fmt' in sys.argv:
ind = sys.argv.index('-fmt')
fmt = sys.argv[ind + 1]
if '-con' in sys.argv:
ind = sys.argv.index('-con')
Conts = sys.argv[ind + 1].split(':')
if '-age' in sys.argv:
ind = sys.argv.index('-age')
age = int(sys.argv[ind + 1])
if age % 5 != 0 and age > 320:
print(main.__doc__)
print('age must be multiple of 5 less than 325')
sys.exit()
import pmagpy.frp as frp
if '-res' in sys.argv:
ind = sys.argv.index('-res')
res = sys.argv[ind + 1]
if res != 'c' and res != 'l':
print('this resolution will take a while - be patient')
if '-prj' in sys.argv:
ind = sys.argv.index('-prj')
proj = sys.argv[ind + 1]
if '-sav' in sys.argv:
plot = 1
if '-eye' in sys.argv:
ind = sys.argv.index('-eye')
lat_0 = float(sys.argv[ind + 1])
lon_0 = float(sys.argv[ind + 2])
if '-pt' in sys.argv:
ind = sys.argv.index('-pt')
pt_lat = float(sys.argv[ind + 1])
pt_lon = float(sys.argv[ind + 2])
PTS.append([pt_lat, pt_lon])
if '-sym' in sys.argv:
ind = sys.argv.index('-sym')
sym = sys.argv[ind + 1]
symsize = int(sys.argv[ind + 2])
# if '-rsym' in sys.argv:
# ind = sys.argv.index('-rsym')
# rsym=sys.argv[ind+1]
# rsymsize=int(sys.argv[ind+2])
if '-sr' in sys.argv:
SEQ = 1
if '-sac' in sys.argv:
SAC = 1
if '-pfr' in sys.argv:
ind = sys.argv.index('-pfr')
Poles.append([
float(sys.argv[ind + 1]),
float(sys.argv[ind + 2]),
float(sys.argv[ind + 3])
])
elif '-ffr' in sys.argv:
ind = sys.argv.index('-ffr')
file = dir_path + '/' + sys.argv[ind + 1]
f = open(file, 'r')
edata = f.readlines()
for line in edata:
rec = line.split()
Poles.append([float(rec[0]), float(rec[1]), float(rec[2])])
elif '-fpp' in sys.argv:
ind = sys.argv.index('-fpp')
file = dir_path + '/' + sys.argv[ind + 1]
f = open(file, 'r')
pdata = f.readlines()
for line in pdata:
rec = line.split()
# transform paleopole to Euler pole taking shortest route
Poles.append([0., float(rec[1]) - 90., 90. - float(rec[0])])
if '-fpt' in sys.argv:
ind = sys.argv.index('-fpt')
file = dir_path + '/' + sys.argv[ind + 1]
f = open(file, 'r')
ptdata = f.readlines()
for line in ptdata:
rec = line.split()
PTS.append([float(rec[0]), float(rec[1])])
FIG = {'map': 1}
pmagplotlib.plot_init(FIG['map'], 6, 6)
# read in er_sites file
if res == 'c':
skip = 8
if res == 'l':
skip = 5
if res == 'i':
skip = 2
if res == 'h':
skip = 1
cnt = 0
Opts = {
'latmin': -90,
'latmax': 90,
'lonmin': 0.,
'lonmax': 360.,
'lat_0': lat_0,
'lon_0': lon_0,
'proj': proj,
'sym': sym,
'symsize': 3,
'pltgrid': 0,
'res': res,
'boundinglat': 0.
}
if proj == 'merc':
Opts['latmin'] = -70
Opts['latmax'] = 70
Opts['lonmin'] = -180
Opts['lonmax'] = 180
pmagplotlib.plot_map(FIG['map'], [], [], Opts) # plot the basemap
Opts['pltgrid'] = -1 # turn off replotting of gridlines
if '-pt' in sys.argv:
Opts['sym'] = sym
Opts['symsize'] = symsize
pmagplotlib.plot_map(FIG['map'], [pt_lat], [pt_lon], Opts)
if plot == 0 and not IS_WIN:
pmagplotlib.draw_figs(FIG)
for cont in Conts:
Opts['sym'] = sym
lats, lons = [], []
if age != 0:
Poles = []
rcont = cont
if rcont not in rconts:
print(main.__doc__)
print(rcont)
print('continents must be one of following: ')
print(rconts)
sys.exit()
if rcont == 'congo':
rcont = 'nwaf'
if rcont == 'kala':
rcont = 'neaf'
if rcont == 'sam':
rcont = 'sac'
if rcont == 'ant':
rcont = 'eant'
if rcont != 'af':
Poles.append(frp.get_pole(rcont, age))
else:
Poles.append([0, 0, 0])
if SAC == 1:
Poles.append(frp.get_pole('saf', age))
SEQ = 1
if Poles[-1] == 'NONE':
print('continent does not exist for rotation, try again ')
sys.exit()
data = continents.get_continent(cont + '.asc')
for line in data:
if float(line[0]) == 0 and float(line[1]) == 0:
line[
0] = '100.' # change stupid 0,0s to delimeters with lat=100
if float(line[0]) > 90:
lats.append(float(line[0]))
lons.append(float(line[1]))
elif cnt % skip == 0:
lats.append(float(line[0]))
lons.append(float(line[1]))
cnt += 1
if len(lats) > 0 and len(Poles) == 0:
pmagplotlib.plot_map(FIG['map'], lats, lons, Opts)
if plot == 0 and not IS_WIN:
pmagplotlib.draw_figs(FIG)
newlats, newlons = [], []
for lat in lats:
newlats.append(lat)
for lon in lons:
newlons.append(lon)
Opts['pltgrid'] = -1 # turns off replotting of meridians and parallels
for pole in Poles:
Rlats, Rlons = pmag.pt_rot(pole, newlats, newlons)
Opts['sym'] = sym
Opts['symsize'] = 3
if SEQ == 0:
pmagplotlib.plot_map(FIG['map'], Rlats, Rlons, Opts)
elif pole == Poles[
-1]: # plot only last pole for sequential rotations
pmagplotlib.plot_map(FIG['map'], Rlats, Rlons, Opts)
if plot == 0 and not IS_WIN:
pmagplotlib.draw_figs(FIG)
if SEQ == 1: # treat poles as sequential rotations
newlats, newlons = [], []
for lat in Rlats:
newlats.append(lat)
for lon in Rlons:
newlons.append(lon)
for pt in PTS:
pt_lat = pt[0]
pt_lon = pt[1]
Opts['sym'] = 'r*'
Opts['symsize'] = 5
pmagplotlib.plot_map(FIG['map'], [pt[0]], [pt[1]], Opts)
if plot == 0 and not IS_WIN:
pmagplotlib.draw_figs(FIG)
Opts['pltgrid'] = -1 # turns off replotting of meridians and parallels
for pole in Poles:
Opts['sym'] = sym
Opts['symsize'] = symsize
Rlats, Rlons = pmag.pt_rot(pole, [pt_lat], [pt_lon])
print(Rlats, Rlons)
pmagplotlib.plot_map(FIG['map'], Rlats, Rlons, Opts)
if plot == 0 and not IS_WIN:
pmagplotlib.draw_figs(FIG)
Opts['sym'] = 'g^'
Opts['symsize'] = 5
pmagplotlib.plot_map(FIG['map'], [pole[0]], [pole[1]], Opts)
if plot == 0 and not IS_WIN:
pmagplotlib.draw_figs(FIG)
files = {}
for key in list(FIG.keys()):
files[key] = 'Cont_rot' + '.' + fmt
if plot == 0 and not IS_WIN:
pmagplotlib.draw_figs(FIG)
if plot == 1:
pmagplotlib.save_plots(FIG, files)
sys.exit()
if pmagplotlib.isServer:
black = '#000000'
purple = '#800080'
titles = {}
titles['eq'] = 'Site Map'
FIG = pmagplotlib.add_borders(FIG, titles, black, purple)
pmagplotlib.save_plots(FIG, files)
else:
pmagplotlib.draw_figs(FIG)
ans = pmagplotlib.save_or_quit()
if ans == "a":
pmagplotlib.save_plots(FIG, files)