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octave.py
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octave.py
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r"""
Interface to GNU Octave
GNU Octave is a free software (GPL) MATLAB-like program with numerical
routines for integrating, solving systems of equations, special
functions, and solving (numerically) differential equations. Please see
http://octave.org/ for more details.
The commands in this section only work if you have the optional
"octave" interpreter installed and available in your PATH. It's not
necessary to install any special Sage packages.
EXAMPLES::
sage: octave.eval('2+2') # optional - octave
'ans = 4'
sage: a = octave(10) # optional - octave
sage: a**10 # optional - octave
1e+10
LOG: - creation (William Stein) - ? (David Joyner, 2005-12-18) -
Examples (David Joyner, 2005-01-03)
Computation of Special Functions
--------------------------------
Octave implements computation of the following special functions
(see the maxima and gp interfaces for even more special
functions)::
airy
Airy functions of the first and second kind, and their derivatives.
airy(0,x) = Ai(x), airy(1,x) = Ai'(x), airy(2,x) = Bi(x), airy(3,x) = Bi'(x)
besselj
Bessel functions of the first kind.
bessely
Bessel functions of the second kind.
besseli
Modified Bessel functions of the first kind.
besselk
Modified Bessel functions of the second kind.
besselh
Compute Hankel functions of the first (k = 1) or second (k = 2) kind.
beta
The Beta function,
beta (a, b) = gamma (a) * gamma (b) / gamma (a + b).
betainc
The incomplete Beta function,
erf
The error function,
erfinv
The inverse of the error function.
gamma
The Gamma function,
gammainc
The incomplete gamma function,
For example,
::
sage: octave("airy(3,2)") # optional - octave
4.10068
sage: octave("beta(2,2)") # optional - octave
0.166667
sage: octave("betainc(0.2,2,2)") # optional - octave
0.104
sage: octave("besselh(0,2)") # optional - octave
(0.223891,0.510376)
sage: octave("besselh(0,1)") # optional - octave
(0.765198,0.088257)
sage: octave("besseli(1,2)") # optional - octave
1.59064
sage: octave("besselj(1,2)") # optional - octave
0.576725
sage: octave("besselk(1,2)") # optional - octave
0.139866
sage: octave("erf(0)") # optional - octave
0
sage: octave("erf(1)") # optional - octave
0.842701
sage: octave("erfinv(0.842)") # optional - octave
0.998315
sage: octave("gamma(1.5)") # optional - octave
0.886227
sage: octave("gammainc(1.5,1)") # optional - octave
0.77687
The Octave interface reads in even very long input (using files) in
a robust manner::
sage: t = '"%s"'%10^10000 # ten thousand character string.
sage: a = octave.eval(t + ';') # optional - octave, < 1/100th of a second
sage: a = octave(t) # optional - octave
Note that actually reading ``a`` back out takes forever. This *must*
be fixed as soon as possible, see :trac:`940`.
Tutorial
--------
EXAMPLES::
sage: octave('4+10') # optional - octave
14
sage: octave('date') # optional - octave; random output
18-Oct-2007
sage: octave('5*10 + 6') # optional - octave
56
sage: octave('(6+6)/3') # optional - octave
4
sage: octave('9')^2 # optional - octave
81
sage: a = octave(10); b = octave(20); c = octave(30) # optional - octave
sage: avg = (a+b+c)/3 # optional - octave
sage: avg # optional - octave
20
sage: parent(avg) # optional - octave
Octave
::
sage: my_scalar = octave('3.1415') # optional - octave
sage: my_scalar # optional - octave
3.1415
sage: my_vector1 = octave('[1,5,7]') # optional - octave
sage: my_vector1 # optional - octave
1 5 7
sage: my_vector2 = octave('[1;5;7]') # optional - octave
sage: my_vector2 # optional - octave
1
5
7
sage: my_vector1 * my_vector2 # optional - octave
75
"""
#*****************************************************************************
# Copyright (C) 2005 William Stein <wstein@gmail.com>
#
# Distributed under the terms of the GNU General Public License (GPL)
#
# This code is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
#
# The full text of the GPL is available at:
#
# http://www.gnu.org/licenses/
#*****************************************************************************
import os
from sage.interfaces.expect import Expect, ExpectElement
from pexpect import EOF
from sage.misc.misc import verbose
class Octave(Expect):
r"""
Interface to the Octave interpreter.
EXAMPLES::
sage: octave.eval("a = [ 1, 1, 2; 3, 5, 8; 13, 21, 33 ]") # optional - octave
'a =\n\n 1 1 2\n 3 5 8\n 13 21 33\n\n'
sage: octave.eval("b = [ 1; 3; 13]") # optional - octave
'b =\n\n 1\n 3\n 13\n\n'
sage: octave.eval("c=a \\ b") # solves linear equation: a*c = b # optional - octave; random output
'c =\n\n 1\n 7.21645e-16\n -7.21645e-16\n\n'
sage: octave.eval("c") # optional - octave; random output
'c =\n\n 1\n 7.21645e-16\n -7.21645e-16\n\n'
"""
def __init__(self, maxread=100, script_subdirectory=None, logfile=None, server=None, server_tmpdir=None,
seed=None):
"""
EXAMPLES::
sage: octave == loads(dumps(octave))
True
"""
Expect.__init__(self,
name = 'octave',
# We want the prompt sequence to be unique to avoid confusion with syntax error messages containing >>>
prompt = 'octave\:\d+> ',
# We don't want any pagination of output
command = "sage-native-execute octave --no-line-editing --silent --eval 'PS2(PS1());more off' --persist",
maxread = maxread,
server = server,
server_tmpdir = server_tmpdir,
script_subdirectory = script_subdirectory,
restart_on_ctrlc = False,
verbose_start = False,
logfile = logfile,
eval_using_file_cutoff=100)
self._seed = seed
def set_seed(self, seed=None):
"""
Sets the seed for the random number generator
for this octave interpreter.
EXAMPLES::
sage: o = Octave() # optional - octave
sage: o.set_seed(1) # optional - octave
1
sage: [o.rand() for i in range(5)] # optional - octave
[ 0.134364, 0.847434, 0.763775, 0.255069, 0.495435]
"""
if seed is None:
seed = self.rand_seed()
self.eval("rand('state',%d)" % seed)
self._seed = seed
return seed
def __reduce__(self):
"""
EXAMPLES::
sage: octave.__reduce__()
(<function reduce_load_Octave at 0x...>, ())
"""
return reduce_load_Octave, tuple([])
def _read_in_file_command(self, filename):
"""
EXAMPLES::
sage: filename = tmp_filename()
sage: octave._read_in_file_command(filename)
'source("...");'
"""
return 'source("%s");'%filename
def _quit_string(self):
"""
EXAMPLES::
sage: octave._quit_string()
'quit;'
"""
return 'quit;'
def _install_hints(self):
"""
Returns hints on how to install Octave.
EXAMPLES::
sage: print octave._install_hints()
You must get ...
"""
return """
You must get the program "octave" in order to use Octave
from Sage. You can read all about Octave at
http://www.gnu.org/software/octave/
LINUX / WINDOWS (colinux):
Do apt-get install octave as root on your machine
(or, in Windows, in the colinux console).
OS X:
* This website has links to binaries for OS X PowerPC
and OS X Intel builds of the latest version of Octave:
http://hpc.sourceforge.net/
Once you get the tarball from there, go to the / directory
and type
tar zxvf octave-intel-bin.tar.gz
to extract it to usr/local/... Make sure /usr/local/bin
is in your PATH. Then type "octave" and verify that
octave starts up.
* Darwin ports and fink have Octave as well.
"""
def _eval_line(self, line, reformat=True, allow_use_file=False,
wait_for_prompt=True, restart_if_needed=False):
"""
EXAMPLES::
sage: print octave._eval_line('2+2') #optional - octave
ans = 4
"""
if not wait_for_prompt:
return Expect._eval_line(self, line)
if line == '':
return ''
if self._expect is None:
self._start()
if allow_use_file and len(line)>3000:
return self._eval_line_using_file(line)
try:
E = self._expect
verbose("in = '%s'"%line,level=3)
E.sendline(line)
E.expect(self._prompt)
out = E.before
verbose("out = '%s'"%out,level=3)
except EOF:
if self._quit_string() in line:
return ''
except KeyboardInterrupt:
self._keyboard_interrupt()
if reformat:
if '>>> ' in out and 'syntax error' in out:
raise SyntaxError(out)
out = "\n".join(out.splitlines()[1:])
return out
def _keyboard_interrupt(self):
print "CntrlC: Interrupting %s..."%self
if self._restart_on_ctrlc:
try:
self._expect.close(force=1)
except pexpect.ExceptionPexpect as msg:
raise pexpect.ExceptionPexpect( "THIS IS A BUG -- PLEASE REPORT. This should never happen.\n" + msg)
self._start()
raise KeyboardInterrupt("Restarting %s (WARNING: all variables defined in previous session are now invalid)"%self)
else:
self._expect.send('\003') # control-c
#self._expect.expect(self._prompt)
#self._expect.expect(self._prompt)
raise KeyboardInterrupt("Ctrl-c pressed while running %s"%self)
def quit(self, verbose=False):
"""
EXAMPLES::
sage: o = Octave()
sage: o._start() # optional - octave
sage: o.quit(True) # optional - octave
Exiting spawned Octave process.
"""
# Don't bother, since it just hangs in some cases, and it
# isn't necessary, since octave behaves well with respect
# to signals.
if not self._expect is None:
if verbose:
print "Exiting spawned %s process." % self
return
def _start(self):
"""
Starts the Octave process.
EXAMPLES::
sage: o = Octave() # optional - octave
sage: o.is_running() # optional - octave
False
sage: o._start() # optional - octave
sage: o.is_running() # optional - octave
True
"""
Expect._start(self)
self.eval("page_screen_output=0;")
self.eval("format none;")
# set random seed
self.set_seed(self._seed)
def _equality_symbol(self):
"""
EXAMPLES::
sage: octave('0 == 1') # optional - octave
0
sage: octave('1 == 1') # optional - octave
1
"""
return '=='
def _true_symbol(self):
"""
EXAMPLES::
sage: octave('1 == 1') # optional - octave
1
"""
return '1'
def _false_symbol(self):
"""
EXAMPLES::
sage: octave('0 == 1') # optional - octave
0
"""
return '0'
def set(self, var, value):
"""
Set the variable ``var`` to the given ``value``.
EXAMPLES::
sage: octave.set('x', '2') # optional - octave
sage: octave.get('x') # optional - octave
' 2'
"""
cmd = '%s=%s;'%(var,value)
out = self.eval(cmd)
if out.find(">>> ") and (out.find("error") != -1 or out.find("Error") != -1):
raise TypeError("Error executing code in Octave\nCODE:\n\t%s\nOctave ERROR:\n\t%s"%(cmd, out))
def get(self, var):
"""
Get the value of the variable ``var``.
EXAMPLES::
sage: octave.set('x', '2') # optional - octave
sage: octave.get('x') # optional - octave
' 2'
"""
s = self.eval('%s'%var)
i = s.find('=')
return s[i+1:]
def clear(self, var):
"""
Clear the variable named var.
EXAMPLES::
sage: octave.set('x', '2') # optional - octave
sage: octave.clear('x') # optional - octave
sage: octave.get('x') # optional - octave
"error: 'x' undefined near line ... column 1"
"""
self.eval('clear %s'%var)
def console(self):
"""
Spawn a new Octave command-line session.
This requires that the optional octave program be installed and in
your PATH, but no optional Sage packages need be installed.
EXAMPLES::
sage: octave_console() # not tested
GNU Octave, version 2.1.73 (i386-apple-darwin8.5.3).
Copyright (C) 2006 John W. Eaton.
...
octave:1> 2+3
ans = 5
octave:2> [ctl-d]
Pressing ctrl-d exits the octave console and returns you to Sage.
octave, like Sage, remembers its history from one session to
another.
"""
octave_console()
def version(self):
"""
Return the version of Octave.
OUTPUT: string
EXAMPLES::
sage: octave.version() # optional - octave; random output depending on version
'2.1.73'
"""
return octave_version()
def solve_linear_system(self, A, b):
r"""
Use octave to compute a solution x to A\*x = b, as a list.
INPUT:
- ``A`` -- mxn matrix A with entries in `\QQ` or `\RR`
- ``b`` -- m-vector b entries in `\QQ` or `\RR` (resp)
OUTPUT: A list x (if it exists) which solves M\*x = b
EXAMPLES::
sage: M33 = MatrixSpace(QQ,3,3)
sage: A = M33([1,2,3,4,5,6,7,8,0])
sage: V3 = VectorSpace(QQ,3)
sage: b = V3([1,2,3])
sage: octave.solve_linear_system(A,b) # optional - octave (and output is slightly random in low order bits)
[-0.33333299999999999, 0.66666700000000001, -3.5236600000000002e-18]
AUTHORS:
- David Joyner and William Stein
"""
m = A.nrows()
if m != len(b):
raise ValueError("dimensions of A and b must be compatible")
from sage.matrix.all import MatrixSpace
from sage.rings.all import QQ
MS = MatrixSpace(QQ,m,1)
b = MS(list(b)) # converted b to a "column vector"
sA = self.sage2octave_matrix_string(A)
sb = self.sage2octave_matrix_string(b)
self.eval("a = " + sA )
self.eval("b = " + sb )
soln = octave.eval("c = a \\ b")
soln = soln.replace("\n\n ","[")
soln = soln.replace("\n\n","]")
soln = soln.replace("\n",",")
sol = soln[3:]
return eval(sol)
def sage2octave_matrix_string(self, A):
"""
Return an octave matrix from a Sage matrix.
INPUT: A Sage matrix with entries in the rationals or reals.
OUTPUT: A string that evaluates to an Octave matrix.
EXAMPLES::
sage: M33 = MatrixSpace(QQ,3,3)
sage: A = M33([1,2,3,4,5,6,7,8,0])
sage: octave.sage2octave_matrix_string(A) # optional - octave
'[1, 2, 3; 4, 5, 6; 7, 8, 0]'
AUTHORS:
- David Joyner and William Stein
"""
return str(A.rows()).replace('), (', '; ').replace('(', '').replace(')','')
def de_system_plot(self, f, ics, trange):
r"""
Plots (using octave's interface to gnuplot) the solution to a
`2\times 2` system of differential equations.
INPUT:
- ``f`` - a pair of strings representing the
differential equations; The independent variable must be called x
and the dependent variable must be called y.
- ``ics`` - a pair [x0,y0] such that x(t0) = x0, y(t0)
= y0
- ``trange`` - a pair [t0,t1]
OUTPUT: a gnuplot window appears
EXAMPLES::
sage: octave.de_system_plot(['x+y','x-y'], [1,-1], [0,2]) # not tested -- does this actually work (on OS X it fails for me -- William Stein, 2007-10)
This should yield the two plots `(t,x(t)), (t,y(t))` on the
same graph (the `t`-axis is the horizontal axis) of the
system of ODEs
.. math::
x' = x+y, x(0) = 1;\qquad y' = x-y, y(0) = -1, \quad\text{for}\quad 0 < t < 2.
"""
eqn1 = f[0].replace('x','x(1)').replace('y','x(2)')
eqn2 = f[1].replace('x','x(1)').replace('y','x(2)')
fcn = "function xdot = f(x,t) xdot(1) = %s; xdot(2) = %s; endfunction"%(eqn1, eqn2)
self.eval(fcn)
x0_eqn = "x0 = [%s; %s]"%(ics[0], ics[1])
self.eval(x0_eqn)
t_eqn = "t = linspace(%s, %s, 200)'"%(trange[0], trange[1])
self.eval(t_eqn)
x_eqn = 'x = lsode("f",x0,t);'
self.eval(x_eqn)
self.eval("plot(t,x)")
def _object_class(self):
"""
EXAMPLES::
sage: octave._object_class()
<class 'sage.interfaces.octave.OctaveElement'>
"""
return OctaveElement
octave_functions = set()
def to_complex(octave_string, R):
r"""
Helper function to convert octave complex number
TESTS::
sage: from sage.interfaces.octave import to_complex
sage: to_complex('(0,1)', CDF)
1.0*I
sage: to_complex('(1.3231,-0.2)', CDF)
1.3231 - 0.2*I
"""
real, imag = octave_string.strip('() ').split(',')
return R(float(real), float(imag))
class OctaveElement(ExpectElement):
def _get_sage_ring(self):
r"""
TESTS::
sage: octave('1')._get_sage_ring() # optional - octave
Real Double Field
sage: octave('I')._get_sage_ring() # optional - octave
Complex Double Field
sage: octave('[]')._get_sage_ring() # optional - octave
Real Double Field
"""
if self.isinteger():
import sage.rings.integer_ring
return sage.rings.integer_ring.ZZ
elif self.isreal():
import sage.rings.real_double
return sage.rings.real_double.RDF
elif self.iscomplex():
import sage.rings.complex_double
return sage.rings.complex_double.CDF
else:
raise TypeError("no Sage ring associated to this element.")
def __nonzero__(self):
r"""
Test whether this element is nonzero.
EXAMPLES::
sage: bool(octave('0')) # optional - octave
False
sage: bool(octave('[]')) # optional - octave
False
sage: bool(octave('[0,0]')) # optional - octave
False
sage: bool(octave('[0,0,0;0,0,0]')) # optional - octave
False
sage: bool(octave('0.1')) # optional - octave
True
sage: bool(octave('[0,1,0]')) # optional - octave
True
sage: bool(octave('[0,0,-0.1;0,0,0]')) # optional - octave
True
"""
return str(self) != ' [](0x0)' and any(x != '0' for x in str(self).split())
def _matrix_(self, R=None):
r"""
Return Sage matrix from this octave element.
EXAMPLES::
sage: A = octave('[1,2;3,4.5]') # optional - octave
sage: matrix(A) # optional - octave
[1.0 2.0]
[3.0 4.5]
sage: _.base_ring() # optional - octave
Real Double Field
sage: A = octave('[I,1;-1,0]') # optional - octave
sage: matrix(A) # optional - octave
[1.0*I 1.0]
[ -1.0 0.0]
sage: _.base_ring() # optional - octave
Complex Double Field
sage: A = octave('[1,2;3,4]') # optional - octave
sage: matrix(ZZ, A) # optional - octave
[1 2]
[3 4]
sage: A = octave('[1,2;3,4.5]') # optional - octave
sage: matrix(RR, A) # optional - octave
[1.00000000000000 2.00000000000000]
[3.00000000000000 4.50000000000000]
"""
oc = self.parent()
if not self.ismatrix():
raise TypeError('not an octave matrix')
if R is None:
R = self._get_sage_ring()
s = str(self).strip('\n ')
w = [u.strip().split(' ') for u in s.split('\n')]
nrows = len(w)
ncols = len(w[0])
if self.iscomplex():
w = [[to_complex(x,R) for x in row] for row in w]
from sage.matrix.all import MatrixSpace
s = str(self).strip()
v = s.split('\n ')
nrows = len(v)
if nrows == 0:
return MatrixSpace(R,0,0)(0)
ncols = len(v[0].split())
M = MatrixSpace(R, nrows, ncols)
v = sum([[x for x in w.split()] for w in v], [])
return M(v)
def _vector_(self, R=None):
r"""
Return Sage vector from this octave element.
EXAMPLES::
sage: A = octave('[1,2,3,4]') # optional - octave
sage: vector(ZZ, A) # optional - octave
(1, 2, 3, 4)
sage: A = octave('[1,2.3,4.5]') # optional - octave
sage: vector(A) # optional - octave
(1.0, 2.3, 4.5)
sage: A = octave('[1,I]') # optional - octave
sage: vector(A) # optional - octave
(1.0, 1.0*I)
"""
oc = self.parent()
if not self.isvector():
raise TypeError('not an octave vector')
if R is None:
R = self._get_sage_ring()
s = str(self).strip('\n ')
w = s.strip().split(' ')
nrows = len(w)
if self.iscomplex():
w = [to_complex(x, R) for x in w]
from sage.modules.free_module import FreeModule
return FreeModule(R, nrows)(w)
def _scalar_(self):
"""
Return Sage scalar from this octave element.
EXAMPLES::
sage: A = octave('2833') # optional - octave
sage: As = A.sage(); As # optional - octave
2833.0
sage: As.parent() # optional - octave
Real Double Field
sage: B = sqrt(A) # optional - octave
sage: Bs = B.sage(); Bs # optional - octave
53.2259
sage: Bs.parent() # optional - octave
Real Double Field
sage: C = sqrt(-A) # optional - octave
sage: Cs = C.sage(); Cs # optional - octave
53.2259*I
sage: Cs.parent() # optional - octave
Complex Double Field
"""
if not self.isscalar():
raise TypeError("not an octave scalar")
R = self._get_sage_ring()
if self.iscomplex():
return to_complex(str(self), R)
else:
return R(str(self))
def _sage_(self):
"""
Try to parse the octave object and return a sage object.
EXAMPLES::
sage: A = octave('2833') # optional - octave
sage: A.sage() # optional - octave
2833.0
sage: B = sqrt(A) # optional - octave
sage: B.sage() # optional - octave
53.2259
sage: C = sqrt(-A) # optional - octave
sage: C.sage() # optional - octave
53.2259*I
sage: A = octave('[1,2,3,4]') # optional - octave
sage: A.sage() # optional - octave
(1.0, 2.0, 3.0, 4.0)
sage: A = octave('[1,2.3,4.5]') # optional - octave
sage: A.sage() # optional - octave
(1.0, 2.3, 4.5)
sage: A = octave('[1,2.3+I,4.5]') # optional - octave
sage: A.sage() # optional - octave
(1.0, 2.3 + 1.0*I, 4.5)
"""
if self.isscalar():
return self._scalar_()
elif self.isvector():
return self._vector_()
elif self.ismatrix():
return self._matrix_()
else:
raise NotImplementedError('octave type is not recognized')
# An instance
octave = Octave()
def reduce_load_Octave():
"""
EXAMPLES::
sage: from sage.interfaces.octave import reduce_load_Octave
sage: reduce_load_Octave()
Octave
"""
return octave
def octave_console():
"""
Spawn a new Octave command-line session.
This requires that the optional octave program be installed and in
your PATH, but no optional Sage packages need be installed.
EXAMPLES::
sage: octave_console() # not tested
GNU Octave, version 2.1.73 (i386-apple-darwin8.5.3).
Copyright (C) 2006 John W. Eaton.
...
octave:1> 2+3
ans = 5
octave:2> [ctl-d]
Pressing ctrl-d exits the octave console and returns you to Sage.
octave, like Sage, remembers its history from one session to
another.
"""
os.system('octave')
def octave_version():
"""
Return the version of Octave installed.
EXAMPLES::
sage: octave_version() # optional - octave; and output is random
'2.9.12'
"""
return str(octave('version')).strip()