def main(args):
system = args.input
print('Solving system in file %s' % system)
a = xppy.run(system, verbose=True)
desc = a.getDesc()
data = a.getRawData()
tvec = a[:, desc['time']]
if not args.no_subplots:
ax = plt.subplot(111)
i = 0
for k in desc:
if type(desc[k]) == int:
if k in ['t', 'time']:
continue
if args.no_subplots:
ax = plt.subplot(data.shape[1] - 1, 1, i + 1)
i += 1
ax.plot(tvec, data[:, desc[k]], label=k)
ax.legend()
outfile = args.output or '%s.png' % args.input
plt.savefig(outfile)
print('Saved to %s' % outfile)
def main( args ):
system = args.input
print( 'Solving system in file %s' % system )
a = xppy.run( system, verbose = True )
desc = a.getDesc( )
data = a.getRawData( )
tvec = a[:,desc['time']]
if not args.no_subplots:
ax = plt.subplot(111)
i = 0
for k in desc:
if type(desc[k]) == int:
if k in [ 't', 'time' ]:
continue
if args.no_subplots:
ax = plt.subplot( data.shape[1] - 1, 1, i + 1 )
i += 1
ax.plot( tvec, data[:,desc[k]], label = k )
ax.legend( )
outfile = args.output or '%s.png' % args.input
plt.savefig( outfile )
print( 'Saved to %s' % outfile )
def run( self ):
"""
"""
# init the xppy object
xppy.createTmp( self.ode )
# run it
self.out = xppy.run( )
# omit first time axis in self.dim
nx, ny = self.out.getRawData().shape
self.tmax = nx - 1 # total number of steps/iterations
self.dim = ny - 1
def run_file(): squareBurst=xppy.run(odefile) return squareBurst
# coding: utf-8
import xppy
xppy.set_cmd('/PATH_TO_XPPAUT/')
subHopf = xppy.run('SOME_ODE_FILE.ode')
subHopf.getDesc()
sHData = subHopf.getRawData()
sHData.shape
from xppy.utils import plot
plot.plotLC(subHopf.getRawData())
plot.pl.show()
import xppy
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
#ode_file = 'lorenz96.ode'; color='b'
#ode_file = 'lorenz96v2.ode'; color='r'
# Lorenz 84
ode_file = 'lorenz84.ode'; color='b'
# init the xppy object
xppy.createTmp( ode_file )
# run it
out = xppy.run( )# ode_file )
# equivalent to xpp continue
pars = xppy.parse.readOdePars(ode_file, False, True, False)
ts = list( out[0] )
xs = list( out[1] )
ys = list( out[2] )
zs = list( out[3] )
# first, 3d
fig = plt.figure( 1 )
ax = fig.gca(projection='3d')
ax.plot( xs, ys, zs, color=color, marker='o' )#, lw=3, alpha=0.8)
ax.set_xlabel("X")
ax.set_ylabel("Y")
ax.set_zlabel("Z")
"""
This file demonstrates how to modify an ode file and plot the output.
"""
from shutil import copyfile
import os
import matplotlib.pyplot as plt
import xppy
# run ode file, collect data (see ex1.py)
out1 = xppy.run('simple.ode')
dat1 = out1.getRawData()
desc1 = out1.getDesc()
t1 = dat1[:,desc1['t']]
u1 = dat1[:,desc1['u']]
v1 = dat1[:,desc1['v']]
# this feature is unimplemented, but you can hack around it.
# get this list by running
# readOdePars(ode_file)
# modify the entry you want.
# Let's change q from 1 to 10.
# and u from .2 to -.2
inputdat = [['par', 'q', '10'],
['init', 'u', '-.2'],
['init', 'v', '.5'],
['@', 'dt', '.01'],
['@', 'total', '100']]
import xppy
import pylab
import numpy
ode_file = 'Lab5.ode'
plot_ext = 'ps'
pylab.cla()
for vp0 in [ -60, -50, -30, -10, 0 ]:
xppy.createTmp(ode_file)
params = [
['par', 'g_ampa', 0.000],
['par', 'g_nmda', 0.038],
['par', 'g_gaba', 0.000],
['par', 'g_gabb', 0.000],
['par', 'g_dep', 0.000],
['par', 'mg', 1],
['par', 'ip', 35],
['par', 'vp0', vp0],
['@', 'total', 1000],
]
xppy.changeOde(params)
o = xppy.run()
pylab.plot(o['vpost'], o['i_nmda'], '-', label='NMDA')
pylab.show()
# coding: utf-8
import xppy
xppy.set_cmd('/PATH_TO_XPPAUT/')
subHopf=xppy.run('SOME_ODE_FILE.ode')
subHopf.getDesc()
sHData=subHopf.getRawData()
sHData.shape
from xppy.utils import plot
plot.plotLC(subHopf.getRawData())
plot.pl.show()