def test_speed(self):
mod_name = 'list_speed'+self.compiler
mod_name = unique_mod(test_dir,mod_name)
mod = ext_tools.ext_module(mod_name)
a = range(1000000);
code = """
int v, sum = 0;
for(int i = 0; i < a.len(); i++)
{
v = a[i];
if (v % 2)
sum += v;
else
sum -= v;
}
return_val = sum;
"""
with_cxx = ext_tools.ext_function('with_cxx',code,['a'])
mod.add_function(with_cxx)
code = """
int vv, sum = 0;
PyObject *v;
for(int i = 0; i < a.len(); i++)
{
v = PyList_GetItem(py_a,i);
//didn't set error here -- just speed test
vv = py_to_int(v,"list item");
if (vv % 2)
sum += vv;
else
sum -= vv;
}
return_val = sum;
"""
no_checking = ext_tools.ext_function('no_checking',code,['a'])
mod.add_function(no_checking)
mod.compile(location = test_dir, compiler = self.compiler)
exec 'from ' + mod_name + ' import with_cxx, no_checking'
import time
t1 = time.time()
sum1 = with_cxx(a)
t2 = time.time()
print 'speed test for list access'
print 'compiler:', self.compiler
print 'scxx:', t2 - t1
t1 = time.time()
sum2 = no_checking(a)
t2 = time.time()
print 'C, no checking:', t2 - t1
sum3 = 0
t1 = time.time()
for i in a:
if i % 2:
sum3 += i
else:
sum3 -= i
t2 = time.time()
print 'python:', t2 - t1
assert_( sum1 == sum2 and sum1 == sum3)
def gseidel(mod):
# ****gseidel****
code="""
int numpoints=Ny[0];
double x0;
for (int i=0; i<n; ++i) {
for (int j=0; j<numpoints; ++j) {
x0=0;
for (int k=0; k<j; ++k) {
x0+=A(j,k)*x(k);
};
for (int k=j+1; k<numpoints; ++k) {
x0+=A(j,k)*x(k);
};
x0=(1-om)*x(j)+om*(y(j)-x0);
x(j)=x0>0.0 ? x0 : 0;
}
}
"""
n=1 #eigenwert nr
om=1.0 # relaxation parameter
A=zeros((2,2),'d') #psf-Matrix
x=zeros((2),'d') #damas-ergebnis
y=zeros((2),'d') #beamf-ergebnis
func = ext_tools.ext_function('gseidel',code,['A','y','x','n','om'],type_converters=converters.blitz)
mod.add_function(func)
# ****gseidel1****
# with relaxation parameter = 1
code="""
int numpoints=Ny[0];
float x0;
for (int i=0; i<n; ++i) {
for (int j=0; j<numpoints; ++j) {
x0=0;
for (int k=0; k<j; ++k) {
x0+=A(j,k)*x(k);
};
for (int k=j+1; k<numpoints; ++k) {
x0+=A(j,k)*x(k);
};
x0=(y(j)-x0);
x(j)=x0>0.0 ? x0 : 0;
}
}
"""
n=1 #eigenwert nr
om=1.0 # relaxation parameter
A=zeros((2,2),'f') #psf-Matrix
x=zeros((2),'f') #damas-ergebnis
y=zeros((2),'f') #beamf-ergebnis
func = ext_tools.ext_function('gseidel1',code,['A','y','x','n'],type_converters=converters.blitz)
mod.add_function(func)
def add_state2tensor1(mod):
# example data for type definitions
X = np.empty((5,1), dtype='float64', order='F')
y = np.empty(3)
code = """
// unpack
double m_norm = 1e-10;
for (int i = 0; i < 3; ++i) {
double x = m[i] = X[i];
m_norm += x * x;
}
// normalize
m_norm = sqrt(m_norm);
for (int i = 0; i < 3; ++i)
m[i] /= m_norm;
// flip orientation?
if (m[0]*y[0] + m[1]*y[1] + m[2]*y[2] < 0) {
for (int i = 0; i < 3; ++i)
m[i] = -m[i];
}
// lambda (clamped)
*l1 = max(X[3], 100);
*l2 = max(X[4], 100);
"""
m = np.empty((3,1))
l1 = np.empty(1);
l2 = np.empty(1);
fn = et.ext_function('c_state2tensor1', code, ['X', 'y', 'm', 'l1', 'l2'])
mod.add_function(fn)
def transfer(mod):
# **** matrix of vectors with transfer Functions ****
# mit vorberechneten Abstaenden
# ohne diag removal
code="""
int numpoints = Nrtm[0];
int nc = Nrtm[1];
int numfreq = Nkj[0];
float expon, kj_freq, r0, factor, ri;
for (int i_freq=0; i_freq<numfreq; ++i_freq) {
kj_freq = (kj(i_freq)).imag();
for (int t=0; t<numpoints; ++t) {
r0 = rt0(t);
for (int i=0; i<nc; ++i) {
ri = rtm(t,i);
factor = r0/ri;
expon = kj_freq * ( r0 - ri );
h(i_freq,t,i) = factor*(std::complex<float>(cosf(expon),sinf(expon)));
}
}
}
"""
h=zeros((2,2,2),'D') #ausgabe, spaeter t+i vertauschen t->spalten, i->zeilen
rtm=zeros((2,2),'d') # Abstaende Mics Gridpts
rt0=zeros((2),'d') # Abstaende Gridpts Arraycenter
kj=zeros((2),'D') # wellenzahl * j
func = ext_tools.ext_function('transfer',code,['h','rt0','rtm','kj'],
type_converters=converters.blitz)
mod.add_function(func)
def faverage(mod):
# **** faverage *****
code="""
std::complex<double> temp;
int nf=Ncsm[0];
int nc=Ncsm[1];
int f,i,j;
#pragma omp parallel private(f,i,j,temp) shared(csm,nc,nf,ft)
{
#pragma omp for schedule(auto) nowait
for (f=0; f<nf; ++f) {
for (i=0; i<nc; ++i) {
temp=conj(ft(f,i));
for (j=0; j<nc; ++j) {
csm(f,i,j)+=temp * ft(f,j);
}
}
}
}
"""
#type declarations
csm=zeros((2,2,2),'D') # cross spectral matrix
ft=zeros((2,2),'D') # fourier spectra of all channels
func = ext_tools.ext_function('faverage',code,['csm','ft'],type_converters=converters.blitz)
mod.add_function(func)
def add_model_2tensor_f(mod):
# typedefs
X = np.empty((10,1), dtype='float64', order='F')
m = X.shape[1]
code = """
for (int i = 0; i < m; ++i) {
double *o1 = X, *o2 = X + 5;
// unpack and normalize orientations
vec_t m1 = make_vec(o1[0], o1[1], o1[2]); m1 = m1 / norm(m1);
vec_t m2 = make_vec(o2[0], o2[1], o2[2]); m2 = m2 / norm(m2);
double l11 = o1[3], l12 = o1[4];
double l21 = o2[3], l22 = o2[4];
// ensure: lambda >= L
double L = 100;
if (l11 < L) l11 = L;
if (l12 < L) l12 = L;
if (l21 < L) l21 = L;
if (l22 < L) l22 = L;
// write back
vec2mem(m1, o1); vec2mem(m2, o2);
o1[3] = l11; o2[3] = l21;
o1[4] = l12; o2[4] = l22;
// prepare for next
X += 10;
}
"""
fn = et.ext_function('c_model_2tensor_f', code, ['X', 'm'])
mod.add_function(fn)
def build_math():
""" Builds an extension module with fibonacci calculators.
"""
mod = ext_tools.ext_module('math_ext')
time = 0.435 # this is effectively a type declaration
e_code = """
#include "math.h"
#include "spike_prop.h"
#define DECAY 7
inline double e(double time){
double asrf=0;
if (time > 0){
//spike response function
asrf = (time * pow(M_E, (1 - time * 0.142857143))) * 0.142857143;
}
return asrf;
}
"""
ext_code = """
return_val = e(time);
"""
e_ = ext_tools.ext_function('e', ext_code, ['time'])
e_.customize.add_support_code(e_code)
mod.add_function(e_)
mod.compile()
def add_model_1tensor_f(mod):
# example data for type definitions
X = np.empty((5,1), dtype='float64', order='F')
m = X.shape[1]
code = """
for (int i = 0; i < m; ++i) {
// normalize
double m_norm = 1e-16;
for (int i = 0; i < 3; ++i) {
double x = X[i];
m_norm += x * x;
}
m_norm = sqrt(m_norm);
for (int i = 0; i < 3; ++i)
X[i] /= m_norm;
// lambda (clamped)
X[3] = max(X[3], 100);
X[4] = max(X[4], 100);
// prepare for next
X += 5;
}
"""
fn = et.ext_function('c_model_1tensor_f', code, ['X', 'm'])
mod.add_function(fn)
def add_function(self,name, code, *varlist):
for t in varlist:
assert(type(t) == tuple)
assert(len(t) == 2)
assert(type(t[0]) == str)
args = [n for n, v in varlist]
vardict = dict(varlist)
self.extension.add_function(ext_tools.ext_function(name, code, args, local_dict = vardict))
def add_function(_module, _func):
_arg_names = []
if "arg_names" in _func:
_arg_names = _func["arg_names"]
intersection = set(locals()) & set(_func["arg_names"])
if intersection:
raise ValueError("The following argument-names collide with Python locals(): %s" % list(intersection))
locals().update(dict(zip(_arg_names, _func["arg_instances"])))
_module.add_function(ext_tools.ext_function(_func["name"], _func["code"], _arg_names))
def _create_python_code(mod, modname, cppcode):
# param variable size
p = {}
pip = py_init_param
pip_global = py_init_global_param
py_notify = Filter().notify_output_observers
image = np.zeros((1, 1), dtype=np.uint8)
image_original = np.zeros((1, 1), dtype=np.uint8)
dct_global_param = {}
# help
func = ext_tools.ext_function('help_' + modname, help_code(), [])
mod.add_function(func)
# __init__
func = ext_tools.ext_function('init_' + modname, init_code("void init()" in cppcode), ['p', 'pip', 'py_notify', 'dct_global_param', 'pip_global'])
func.customize.add_support_code(params_code())
func.customize.add_support_code(notify_code())
mod.add_function(func)
# configure
if "void configure()" in cppcode:
has_configure = True
func = ext_tools.ext_function('config_' + modname, config_code(), [])
func.customize.add_support_code(params_code())
func.customize.add_support_code(cppcode)
func.customize.add_support_code(notify_code())
mod.add_function(func)
else:
has_configure = False
# destroy
if "void destroy()" in cppcode:
has_destroy = True
func = ext_tools.ext_function('destroy_' + modname, destroy_code(), [])
mod.add_function(func)
else:
has_destroy = False
# set original image
func = ext_tools.ext_function('set_original_image_' + modname, set_original_image_code(), ['image_original'])
mod.add_function(func)
# set global params
func = ext_tools.ext_function('set_global_params_' + modname, set_global_params_code(), ['dct_global_param'])
mod.add_function(func)
# execute
# Get the size of parameter
func = ext_tools.ext_function('exec_' + modname, execute_code(), ['image'])
func.customize.add_support_code(params_code())
func.customize.add_support_code(cppcode)
func.customize.add_support_code(notify_code())
mod.add_function(func)
def add_interp3signal(mod):
S = np.empty((100, 100, 100, 52), dtype='float32', order='F')
p = np.empty(3)
v = np.empty(3)
sigma = 0.
code = """
#line 0 "interp3signal"
double w_sum = 1e-16;
double px = p[0], py = p[1], pz = p[2];
double vx = v[0], vy = v[1], vz = v[2];
for (int i = 0; i < 2*n; ++i)
s[i] = 0;
for (int zz = -1; zz <= 1; ++zz) {
int z = round(pz) + zz;
if (z < 0 || nz <= z) continue;
double dz = (z - pz)*vz, dzz = dz*dz;
for (int yy = -1; yy <= 1; ++yy) {
int y = round(py) + yy;
if (y < 0 || ny <= y) continue;
double dy = (y - py)*vy, dyy = dy*dy;
for (int xx = -1; xx <= 1; ++xx) {
int x = round(px) + xx;
if (x < 0 || nx <= x) continue;
double dx = (x - px)*vx, dxx = dx*dx;
double w = exp( -(dxx + dyy + dzz)/sigma );
for (int i = 0; i < n; ++i)
s[i] += w * S[(nz*ny*x + nz*y + z)*n + i];
w_sum += w;
}
}
}
w_sum *= 2; // double each occurance
for (int i = 0; i < n; ++i) {
s[i ] /= w_sum;
s[i+n] = s[i]; // push into second spot
}
"""
nx, ny, nz, n = S.shape
s = np.empty((2 * n, ), dtype='float32') # preallocate output (doubled)
fn = et.ext_function('c_interp3signal', code,
['s', 'S', 'p', 'v', 'sigma', 'nx', 'ny', 'nz', 'n'])
mod.add_function(fn)
def add_interp3signal(mod):
S = np.empty((100,100,100,52), dtype='float32', order='F')
p = np.empty(3)
v = np.empty(3)
sigma = 0.
code = """
#line 0 "interp3signal"
double w_sum = 1e-16;
double px = p[0], py = p[1], pz = p[2];
double vx = v[0], vy = v[1], vz = v[2];
for (int i = 0; i < 2*n; ++i)
s[i] = 0;
for (int zz = -1; zz <= 1; ++zz) {
int z = round(pz) + zz;
if (z < 0 || nz <= z) continue;
double dz = (z - pz)*vz, dzz = dz*dz;
for (int yy = -1; yy <= 1; ++yy) {
int y = round(py) + yy;
if (y < 0 || ny <= y) continue;
double dy = (y - py)*vy, dyy = dy*dy;
for (int xx = -1; xx <= 1; ++xx) {
int x = round(px) + xx;
if (x < 0 || nx <= x) continue;
double dx = (x - px)*vx, dxx = dx*dx;
double w = exp( -(dxx + dyy + dzz)/sigma );
for (int i = 0; i < n; ++i)
s[i] += w * S[(nz*ny*x + nz*y + z)*n + i];
w_sum += w;
}
}
}
w_sum *= 2; // double each occurance
for (int i = 0; i < n; ++i) {
s[i ] /= w_sum;
s[i+n] = s[i]; // push into second spot
}
"""
nx,ny,nz,n = S.shape
s = np.empty((2*n,), dtype='float32') # preallocate output (doubled)
fn = et.ext_function('c_interp3signal', code, ['s','S', 'p', 'v', 'sigma', 'nx','ny','nz','n'])
mod.add_function(fn)
def test_string_and_int(self):
# decalaring variables
a = 2;b = 'string'
# declare module
mod = ext_tools.ext_module('ext_string_and_int')
code = """
a=b.length();
return_val = PyInt_FromLong(a);
"""
test = ext_tools.ext_function('test',code,['a','b'])
mod.add_function(test)
mod.compile(location = build_dir)
import ext_string_and_int
c = ext_string_and_int.test(a,b)
assert_(c == len(b))
def __call__(self,func):
name = func.__name__
code = func.__doc__
if code == None:
code = func()
import inspect
(args,_,_,defaults) = inspect.getargspec(func)
(file,line) = inspect.getframeinfo(inspect.currentframe().f_back)[0:2]
code = ('#line %d "%s"\n'%(line,file))+code
defaults = [] if defaults==None else defaults
if len(args) != len(defaults):
raise Exception("The %s function must have default values for all arguments"%name)
vardict = dict(zip(args,defaults))
self.extension.add_function(ext_tools.ext_function(name, code, args, local_dict = vardict))
return func
def __call__(self,func):
name = func.__name__
code = func.__doc__
if code == None:
code = func()
import inspect
(args,_,_,defaults) = inspect.getargspec(func)
(file,line) = inspect.getframeinfo(inspect.currentframe().f_back)[0:2]
code = ('#line %d "%s"\n'%(line,file))+code
defaults = [] if defaults==None else defaults
if len(args) != len(defaults):
raise Exception("The %s function must have default values for all arguments"%name)
vardict = dict(list(zip(args,defaults)))
self.extension.add_function(ext_tools.ext_function(name, code, args, local_dict = vardict))
return func
def test_string_and_int(self):
# decalaring variables
a = 2;b = 'string'
# declare module
mod = ext_tools.ext_module('ext_string_and_int')
code = """
a=b.length();
return_val = PyInt_FromLong(a);
"""
test = ext_tools.ext_function('test',code,['a','b'])
mod.add_function(test)
mod.compile(location = build_dir)
import ext_string_and_int
c = ext_string_and_int.test(a,b)
assert(c == len(b))
def test_complex_return(self):
mod_name = sys._getframe().f_code.co_name + self.compiler
mod_name = unique_mod(test_dir,mod_name)
mod = ext_tools.ext_module(mod_name)
a = 1.+1j
code = """
a= a + std::complex<double>(2.,2.);
return_val = PyComplex_FromDoubles(a.real(),a.imag());
"""
test = ext_tools.ext_function('test',code,['a'])
mod.add_function(test)
mod.compile(location=test_dir, compiler=self.compiler)
exec('from ' + mod_name + ' import test')
b = 1.+1j
c = test(b)
assert_(c == 3.+3j)
def test_return(self):
mod_name = 'string_return' + self.compiler
mod_name = unique_mod(test_dir, mod_name)
mod = ext_tools.ext_module(mod_name)
a = 'string'
code = """
a= std::string("hello");
return_val = PyString_FromString(a.c_str());
"""
test = ext_tools.ext_function('test', code, ['a'])
mod.add_function(test)
mod.compile(location=test_dir, compiler=self.compiler)
exec('from ' + mod_name + ' import test')
b = 'bub'
c = test(b)
assert_(c == 'hello')
def test_return(self):
mod_name = 'string_return'+self.compiler
mod_name = unique_mod(test_dir,mod_name)
mod = ext_tools.ext_module(mod_name)
a = 'string'
code = """
a= std::string("hello");
return_val = PyString_FromString(a.c_str());
"""
test = ext_tools.ext_function('test',code,['a'])
mod.add_function(test)
mod.compile(location = test_dir, compiler = self.compiler)
exec 'from ' + mod_name + ' import test'
b='bub'
c = test(b)
assert_( c == 'hello')
def test_complex_return(self):
mod_name = sys._getframe().f_code.co_name + self.compiler
mod_name = unique_mod(test_dir, mod_name)
mod = ext_tools.ext_module(mod_name)
a = 1. + 1j
code = """
a= a + std::complex<double>(2.,2.);
return_val = PyComplex_FromDoubles(a.real(),a.imag());
"""
test = ext_tools.ext_function('test', code, ['a'])
mod.add_function(test)
mod.compile(location=test_dir, compiler=self.compiler)
exec('from ' + mod_name + ' import test')
b = 1. + 1j
c = test(b)
assert_(c == 3. + 3j)
def test_float_return(self):
mod_name = sys._getframe().f_code.co_name + self.compiler
mod_name = unique_mod(test_dir, mod_name)
mod = ext_tools.ext_module(mod_name)
a = 1.
code = """
a=a+2.;
return_val = PyFloat_FromDouble(a);
"""
test = ext_tools.ext_function('test', code, ['a'])
mod.add_function(test)
mod.compile(location=test_dir, compiler=self.compiler)
exec('from ' + mod_name + ' import test')
b = 1.
c = test(b)
assert_(c == 3.)
def test_float_return(self):
mod_name = sys._getframe().f_code.co_name + self.compiler
mod_name = unique_mod(test_dir,mod_name)
mod = ext_tools.ext_module(mod_name)
a = 1.
code = """
a=a+2.;
return_val = PyFloat_FromDouble(a);
"""
test = ext_tools.ext_function('test',code,['a'])
mod.add_function(test)
mod.compile(location = test_dir, compiler = self.compiler)
exec 'from ' + mod_name + ' import test'
b=1.
c = test(b)
assert_( c == 3.)
def add_model_2tensor_h(mod):
# typedefs
X = np.empty((10, 1), dtype='float64', order='F')
u = np.empty((102, 3), dtype='float64', order='F')
b = 900.0
n = u.shape[0]
m = X.shape[1]
s = np.empty((n, m), order='F')
code = """
for (int i = 0; i < m; ++i) {
double *o1 = X, *o2 = X + 5;
// unpack and normalize orientations
vec_t m1 = make_vec(o1[0], o1[1], o1[2]); m1 /= norm(m1);
double l11 = o1[3], l12 = o1[4];
vec_t m2 = make_vec(o2[0], o2[1], o2[2]); m2 /= norm(m2);
double l21 = o2[3], l22 = o2[4];
// ensure: lambda >= L
double L = 100;
if (l11 < L) l11 = L;
if (l12 < L) l12 = L;
if (l21 < L) l21 = L;
if (l22 < L) l22 = L;
// flip if necessary
if (m1._[0] < 0) m1 = -m1;
if (m2._[0] < 0) m2 = -m2;
// calculate diffusion matrix
mat_t D1 = diffusion(m1, l11, l12);
mat_t D2 = diffusion(m2, l21, l22);
// reconstruct signal
for (int i = 0; i < n; ++i, ++s) {
vec_t u_ = make_vec(u[3*i], u[3*i+1], u[3*i+2]);
*s = (exp(-b*dot(u_,D1*u_)) + exp(-b*dot(u_,D2*u_)))/2;
}
// prepare for next
X += 10;
}
"""
fn = et.ext_function('c_model_2tensor_h', code,
['s', 'X', 'u', 'b', 'n', 'm'])
mod.add_function(fn)
def __compile_weave_func(self):
"""
Fast version of the integrand function f() in moment().
We write all functions called in f() in C-code and
compile it once during runtime. See scipy.weave for info.
NOTE: remove TEM_wqslit_weave.so if C-code is changed
"""
from scipy.weave import ext_tools
mod = ext_tools.ext_module('TEM_wqslit_weave')
# create module TEM_wqslit_weave
r = a = b = x1 = x2 = y1 = y2 = q = qE = q0 = dqx = dqy = n = 1.
# declaration of variable type
# translated C-code for arc_segment() and arc_in_box()
code = """
double arc_segment(double r, double a, double b) {
if (r<a) return 0;
else if (r*r>a*a+b*b) return r*asin(b/r);
else return r*acos(a/r);
};
double arc_in_box(double r, double x1, double y1, double x2, double y2) {
double x, y;
if (x1<0 && x2<0) { x1=-x1; x2=-x2;};
if (y1<0 && y2<0) { y1=-y1; y2=-y2;};
if (x1>x2) {x=x1; x1=x2; x2=x;};
if (y1>y2) {y=y1; y1=y2; y2=y;};
if (x1*x2<0) return arc_in_box(r, 0, y1, -x1, y2) + arc_in_box( r, 0, y1, x2, y2);
if (y1<0) return arc_in_box(r, x1, 0, x2, y2) - arc_in_box( r, x1, 0, x2,-y1);
if (y1>0) return arc_in_box(r, x1, 0, x2, y2) + arc_in_box( r, x1, 0, x2, y1);
return arc_segment(r,x1,y2) - arc_segment(r,x2,y2);
};
"""
# translated C-code for integrand in moment(), skips p(), weight_q()
main = "return_val = pow(q,n) / (q*q + qE*qE) * 2 \
* arc_in_box(q, q0-dqx/2., 0, q0+dqx/2., dqy/2.);"
# compile module
func = ext_tools.ext_function('f', main,
['q', 'qE', 'n', 'q0', 'dqx', 'dqy'])
func.customize.add_support_code(code)
mod.add_function(func)
mod.compile()
def test_return(self):
mod_name = 'list_return'+self.compiler
mod_name = unique_mod(test_dir,mod_name)
mod = ext_tools.ext_module(mod_name)
a = [1]
code = """
a=py::list();
a.append("hello");
return_val = a;
"""
test = ext_tools.ext_function('test',code,['a'])
mod.add_function(test)
mod.compile(location = test_dir, compiler = self.compiler)
exec 'from ' + mod_name + ' import test'
b=[1,2]
c = test(b)
assert_( c == ['hello'])
def test_string_and_int(self):
# decalaring variables
a = 2
b = "string"
# declare module
mod = ext_tools.ext_module("ext_string_and_int")
code = """
a=b.length();
return_val = PyInt_FromLong(a);
"""
test = ext_tools.ext_function("test", code, ["a", "b"])
mod.add_function(test)
mod.compile(location=build_dir)
import ext_string_and_int
c = ext_string_and_int.test(a, b)
assert_(c == len(b))
def test_return(self):
mod_name = 'dict_return'+self.compiler
mod_name = unique_mod(test_dir,mod_name)
mod = ext_tools.ext_module(mod_name)
a = {'z':1}
code = """
a=py::dict();
a["hello"] = 5;
return_val = a;
"""
test = ext_tools.ext_function('test',code,['a'])
mod.add_function(test)
mod.compile(location = test_dir, compiler = self.compiler)
exec 'from ' + mod_name + ' import test'
b = {'z':2}
c = test(b)
assert_( c['hello'] == 5)
def test_return(self):
mod_name = 'list_return' + self.compiler
mod_name = unique_mod(test_dir, mod_name)
mod = ext_tools.ext_module(mod_name)
a = [1]
code = """
a=py::list();
a.append("hello");
return_val = a;
"""
test = ext_tools.ext_function('test', code, ['a'])
mod.add_function(test)
mod.compile(location=test_dir, compiler=self.compiler)
exec('from ' + mod_name + ' import test')
b = [1, 2]
c = test(b)
assert_(c == ['hello'])
def add_model_2tensor_h(mod):
# typedefs
X = np.empty((10,1), dtype='float64', order='F')
u = np.empty((102,3), dtype='float64', order='F')
b = 900.0
n = u.shape[0]
m = X.shape[1]
s = np.empty((n,m), order='F')
code = """
for (int i = 0; i < m; ++i) {
double *o1 = X, *o2 = X + 5;
// unpack and normalize orientations
vec_t m1 = make_vec(o1[0], o1[1], o1[2]); m1 /= norm(m1);
double l11 = o1[3], l12 = o1[4];
vec_t m2 = make_vec(o2[0], o2[1], o2[2]); m2 /= norm(m2);
double l21 = o2[3], l22 = o2[4];
// ensure: lambda >= L
double L = 100;
if (l11 < L) l11 = L;
if (l12 < L) l12 = L;
if (l21 < L) l21 = L;
if (l22 < L) l22 = L;
// flip if necessary
if (m1._[0] < 0) m1 = -m1;
if (m2._[0] < 0) m2 = -m2;
// calculate diffusion matrix
mat_t D1 = diffusion(m1, l11, l12);
mat_t D2 = diffusion(m2, l21, l22);
// reconstruct signal
for (int i = 0; i < n; ++i, ++s) {
vec_t u_ = make_vec(u[3*i], u[3*i+1], u[3*i+2]);
*s = (exp(-b*dot(u_,D1*u_)) + exp(-b*dot(u_,D2*u_)))/2;
}
// prepare for next
X += 10;
}
"""
fn = et.ext_function('c_model_2tensor_h', code, ['s', 'X', 'u', 'b', 'n', 'm'])
mod.add_function(fn)
def r_beam_psf4(mod):
# ****r_beam_psf4**** (siehe Sarradj2012, Variante IV 'true location')
# mit vorberechneten Abstaenden
# ohne diag removal
code = """
std::complex<float> term2;
int numpoints_grid = Nrtm[0];
int numpoints = Nrsm[0];
int nc = Nrtm[1];
float term1, expon, kj_freq;
float r0, rsi, rti;
kj_freq = kj.imag();
for (int t=0; t<numpoints_grid; ++t) {
for (int s=0; s<numpoints; ++s) {
term1 = 0;
term2 = 0;
for (int i=0; i<nc; ++i) {
rsi = rsm(s,i);
rti = rtm(t,i);
term1 += 1/(rti*rti);
expon = kj_freq * (rti-rsi);
term2 += (std::complex<float>(cosf(expon),sinf(expon))) / (rsi*rti);
}
r0 = rs0(s);
h(t,s) = r0*r0 / (nc*term1*term1) * (term2*conj(term2)).real();
}
}
"""
h = zeros((2, 2), 'd') #ausgabe
rtm = zeros((2, 2), 'd') # Abstaende Mics Gridpts
rsm = zeros((2, 2), 'd') # Abstaende Mics Deconv.pts
rs0 = zeros((2), 'd') # Abstaende Gridpts Arraycenter
rt0 = zeros((2),
'd') # Abstaende Deconv.pts Arraycenter -- not needed here
dummy = zeros((2), 'D') # to declare complex128, alt.: kj=1.2+0.3j
kj = dummy[0] # wellenzahl * j
func = ext_tools.ext_function('r_beam_psf4',
code,
['h', 'rt0', 'rs0', 'rtm', 'rsm', 'kj'],
type_converters=converters.blitz)
mod.add_function(func)
def test_int_return(self):
mod_name = sys._getframe().f_code.co_name + self.compiler
mod_name = unique_mod(test_dir, mod_name)
mod = ext_tools.ext_module(mod_name)
a = 1
code = """
a=a+2;
return_val = PyInt_FromLong(a);
"""
test = ext_tools.ext_function('test', code, ['a'])
mod.add_function(test)
mod.compile(location=test_dir, compiler=self.compiler)
exec 'from ' + mod_name + ' import test'
b = 1
c = test(b)
assert (c == 3)
def test_return(self):
mod_name = 'dict_return' + self.compiler
mod_name = unique_mod(test_dir, mod_name)
mod = ext_tools.ext_module(mod_name)
a = {'z': 1}
code = """
a=py::dict();
a["hello"] = 5;
return_val = a;
"""
test = ext_tools.ext_function('test', code, ['a'])
mod.add_function(test)
mod.compile(location=test_dir, compiler=self.compiler)
exec('from ' + mod_name + ' import test')
b = {'z': 2}
c = test(b)
assert_(c['hello'] == 5)
def r_beam_psf(mod):
# ****r_beam_psf****
# mit vorberechneten Abstaenden
# ohne diag removal
code = """
std::complex<float> temp1,kjj;
int numpoints=Nrm[0];
int nc=Nrm[1];
int numfreq=Nkj[0];
float temp2;
float r00,rmm,r0m,rs;
for (int i=0; i<numfreq; ++i) {
kjj=kj(i);//.imag();
for (int j=0; j<numpoints; ++j) {
for (int p=0; p<numpoints; ++p) {
rs=0;
r00=r0(p);
temp1=0.0;
for (int ii=0; ii<nc; ++ii) {
rmm=rm(p,ii);
rs+=1.0/(rmm*rmm);
r0m=rm(j,ii);
temp2=(kjj*(r00+r0m-rmm)).imag();
e(ii)=(std::complex<double>(cosf(temp2),sinf(temp2)))*(1.0/(rmm*r0m));
}
rs*=r00/nc;
temp1=0.0;
for (int ii=0; ii<nc; ++ii) {
temp1+=e(ii);
}
h(i,j,p)=(temp1*conj(temp1)).real()/(rs*rs);
}
}
}
"""
e = zeros((2), 'D') #hilfsvektor
f = zeros((2), 'D') #hilfsvektor
h = zeros((2, 2, 2), 'd') #ausgabe
rm = zeros((2, 2), 'd')
r0 = zeros((2), 'd')
kj = zeros((2), 'D') # wellenzahl * j
func = ext_tools.ext_function('r_beam_psf',
code, ['e', 'f', 'h', 'r0', 'rm', 'kj'],
type_converters=converters.blitz)
mod.add_function(func)
def test_return(self):
mod_name = 'tuple_return'+self.compiler
mod_name = unique_mod(test_dir,mod_name)
mod = ext_tools.ext_module(mod_name)
a = (1,)
code = """
a=py::tuple(2);
a[0] = "hello";
a.set_item(1,py::None);
return_val = a;
"""
test = ext_tools.ext_function('test',code,['a'])
mod.add_function(test)
mod.compile(location = test_dir, compiler = self.compiler)
exec 'from ' + mod_name + ' import test'
b=(1,2)
c = test(b)
assert_( c == ('hello',None))
def test_return(self):
mod_name = 'tuple_return' + self.compiler
mod_name = unique_mod(test_dir, mod_name)
mod = ext_tools.ext_module(mod_name)
a = (1, )
code = """
a=py::tuple(2);
a[0] = "hello";
a.set_item(1,py::None);
return_val = a;
"""
test = ext_tools.ext_function('test', code, ['a'])
mod.add_function(test)
mod.compile(location=test_dir, compiler=self.compiler)
exec('from ' + mod_name + ' import test')
b = (1, 2)
c = test(b)
assert_(c == ('hello', None))
def build_ex1():
ext = ext_tools.ext_module('_ex1')
# Type declarations - define a sequence and a function
seq = []
func = string.upper
code = """
py::tuple args(1);
py::list result(seq.length());
for(int i = 0; i < seq.length();i++)
{
args[0] = seq[i];
result[i] = func.call(args);
}
return_val = result;
"""
func = ext_tools.ext_function('my_map', code, ['func', 'seq'])
ext.add_function(func)
ext.compile()
def add_s2ga(mod):
s = np.empty((102,1), dtype='float64')
n = s.shape[0]
code = """
#line 0 "s2ga"
double mu = 0, mu_sq = 0;
for (int i = 0; i < n; ++i, ++s) {
mu += *s;
mu_sq += *s * *s;
}
mu /= n;
mu_sq /= n;
double ga = sqrt(mu_sq - mu*mu) / sqrt(mu_sq);
return_val = ga;
"""
fn = et.ext_function('c_s2ga', code, ['s', 'n'])
mod.add_function(fn)
def add_s2ga(mod):
s = np.empty((102, 1), dtype='float64')
n = s.shape[0]
code = """
#line 0 "s2ga"
double mu = 0, mu_sq = 0;
for (int i = 0; i < n; ++i, ++s) {
mu += *s;
mu_sq += *s * *s;
}
mu /= n;
mu_sq /= n;
double ga = sqrt(mu_sq - mu*mu) / sqrt(mu_sq);
return_val = ga;
"""
fn = et.ext_function('c_s2ga', code, ['s', 'n'])
mod.add_function(fn)
def __compile_weave_func(self):
"""
Fast version of the integrand function f() in moment().
We write all functions called in f() in C-code and
compile it once during runtime. See scipy.weave for info.
NOTE: remove TEM_wqslit_weave.so if C-code is changed
"""
from scipy.weave import ext_tools;
mod = ext_tools.ext_module('TEM_wqslit_weave'); # create module TEM_wqslit_weave
r=a=b=x1=x2=y1=y2=q=qE=q0=dqx=dqy=n=1.; # declaration of variable type
# translated C-code for arc_segment() and arc_in_box()
code="""
double arc_segment(double r, double a, double b) {
if (r<a) return 0;
else if (r*r>a*a+b*b) return r*asin(b/r);
else return r*acos(a/r);
};
double arc_in_box(double r, double x1, double y1, double x2, double y2) {
double x, y;
if (x1<0 && x2<0) { x1=-x1; x2=-x2;};
if (y1<0 && y2<0) { y1=-y1; y2=-y2;};
if (x1>x2) {x=x1; x1=x2; x2=x;};
if (y1>y2) {y=y1; y1=y2; y2=y;};
if (x1*x2<0) return arc_in_box(r, 0, y1, -x1, y2) + arc_in_box( r, 0, y1, x2, y2);
if (y1<0) return arc_in_box(r, x1, 0, x2, y2) - arc_in_box( r, x1, 0, x2,-y1);
if (y1>0) return arc_in_box(r, x1, 0, x2, y2) + arc_in_box( r, x1, 0, x2, y1);
return arc_segment(r,x1,y2) - arc_segment(r,x2,y2);
};
"""
# translated C-code for integrand in moment(), skips p(), weight_q()
main = "return_val = pow(q,n) / (q*q + qE*qE) * 2 \
* arc_in_box(q, q0-dqx/2., 0, q0+dqx/2., dqy/2.);"
# compile module
func = ext_tools.ext_function('f',main,['q','qE','n','q0','dqx','dqy']);
func.customize.add_support_code(code);
mod.add_function(func);
mod.compile();
def r_beam_psf3(mod):
# ****r_beam_psf3**** (siehe Sarradj2012, Variante III 'true level')
# mit vorberechneten Abstaenden
# ohne diag removal
code="""
std::complex<float> term2;
int numpoints_grid = Nrtm[0];
int numpoints = Nrsm[0];
int nc = Nrtm[1];
float term1, expon, kj_freq;
float r0, rsi, rti;
kj_freq = kj.imag();
for (int t=0; t<numpoints_grid; ++t) {
for (int s=0; s<numpoints; ++s) {
term1 = 0;
term2 = 0;
for (int i=0; i<nc; ++i) {
rsi = rsm(s,i);
rti = rtm(t,i);
term1 += 1/(rti*rti);
expon = kj_freq * (rti-rsi);
term2 += (std::complex<float>(cosf(expon),sinf(expon))) / (rsi*rti);
}
r0 = rs0(s)/rt0(t);
h(t,s) = r0*r0 / (term1*term1) * (term2*conj(term2)).real();
}
}
"""
h=zeros((2,2),'d') #ausgabe
rtm=zeros((2,2),'d') # Abstaende Mics Gridpts
rsm=zeros((2,2),'d') # Abstaende Mics Deconv.pts
rt0=zeros((2),'d') # Abstaende Deconv.pts Arraycenter
rs0=zeros((2),'d') # Abstaende Gridpts Arraycenter
dummy=zeros((2),'D') # to declare complex128, alt.: kj=1.2+0.3j
kj=dummy[0] # wellenzahl * j
func = ext_tools.ext_function('r_beam_psf3',code,['h','rt0','rs0','rtm','rsm','kj'],type_converters=converters.blitz)
mod.add_function(func)
def r_beam_psf(mod):
# ****r_beam_psf****
# mit vorberechneten Abstaenden
# ohne diag removal
code="""
std::complex<float> temp1,kjj;
int numpoints=Nrm[0];
int nc=Nrm[1];
int numfreq=Nkj[0];
float temp2;
float r00,rmm,r0m,rs;
for (int i=0; i<numfreq; ++i) {
kjj=kj(i);//.imag();
for (int j=0; j<numpoints; ++j) {
for (int p=0; p<numpoints; ++p) {
rs=0;
r00=r0(p);
temp1=0.0;
for (int ii=0; ii<nc; ++ii) {
rmm=rm(p,ii);
rs+=1.0/(rmm*rmm);
r0m=rm(j,ii);
temp2=(kjj*(r00+r0m-rmm)).imag();
e(ii)=(std::complex<double>(cosf(temp2),sinf(temp2)))*(1.0/(rmm*r0m));
}
rs*=r00/nc;
temp1=0.0;
for (int ii=0; ii<nc; ++ii) {
temp1+=e(ii);
}
h(i,j,p)=(temp1*conj(temp1)).real()/(rs*rs);
}
}
}
"""
e=zeros((2),'D') #hilfsvektor
f=zeros((2),'D') #hilfsvektor
h=zeros((2,2,2),'d') #ausgabe
rm=zeros((2,2),'d')
r0=zeros((2),'d')
kj=zeros((2),'D') # wellenzahl * j
func = ext_tools.ext_function('r_beam_psf',code,['e','f','h','r0','rm','kj'],type_converters=converters.blitz)
mod.add_function(func)
def build_ramp_ext():
mod = ext_tools.ext_module('ramp_ext')
# type declarations
result = array([0],float64)
start,end = 0.,0.
code = """
const int size = Nresult[0];
const double step = (end-start)/(size-1);
double val = start;
for (int i = 0; i < size; i++)
{
result[i] = val;
val += step;
}
"""
func = ext_tools.ext_function('Ramp',code,['result','start','end'])
mod.add_function(func)
mod.compile(compiler='gcc')
def test_return_tuple(self):
# decalaring variables
a = 2
# declare module
mod = ext_tools.ext_module('ext_return_tuple')
var_specs = ext_tools.assign_variable_types(['a'],locals())
code = """
int b;
b = a + 1;
py::tuple returned(2);
returned[0] = a;
returned[1] = b;
return_val = returned;
"""
test = ext_tools.ext_function('test',code,['a'])
mod.add_function(test)
mod.compile(location = build_dir)
import ext_return_tuple
c,d = ext_return_tuple.test(a)
assert_(c==a and d == a+1)
def test_return_tuple(self):
# decalaring variables
a = 2
# declare module
mod = ext_tools.ext_module('ext_return_tuple')
var_specs = ext_tools.assign_variable_types(['a'],locals())
code = """
int b;
b = a + 1;
py::tuple returned(2);
returned[0] = a;
returned[1] = b;
return_val = returned;
"""
test = ext_tools.ext_function('test',code,['a'])
mod.add_function(test)
mod.compile(location=build_dir)
import ext_return_tuple
c,d = ext_return_tuple.test(a)
assert_(c == a and d == a+1)
def add_model_1tensor_h(mod):
# typedefs
X = np.empty((5, 1), dtype='float64', order='F')
u = np.empty((102, 3), dtype='float64', order='F')
b = 900.0
n = u.shape[0]
m = X.shape[1]
s = np.empty((n, m), order='F')
code = """
for (int i = 0; i < m; ++i) {
// unpack and normalize orientations
vec_t m1 = make_vec(X[0], X[1], X[2]); m1 /= norm(m1);
double l11 = X[3], l12 = X[4];
// ensure: lambda >= L
double L = 100;
if (l11 < L) l11 = L;
if (l12 < L) l12 = L;
// flip if necessary
if (m1._[0] < 0) m1 = -m1;
// calculate diffusion matrix
mat_t D = diffusion(m1, l11, l12);
// reconstruct signal
for (int i = 0; i < n; ++i, ++s) {
vec_t u_ = make_vec(u[3*i], u[3*i+1], u[3*i+2]);
*s = exp(-b*dot(u_,D*u_));
}
// prepare for next
X += 5;
}
"""
fn = et.ext_function('c_model_1tensor_h', code,
['s', 'X', 'u', 'b', 'n', 'm'])
mod.add_function(fn)
def add_interp3scalar(mod):
M = np.empty((100, 100, 100), dtype='uint16', order='F')
p = np.empty(3)
v = np.empty(3)
sigma = 0.
code = """
#line 0 "interp3scalar"
double s = 0, w_sum = 1e-16;
double px = p[0], py = p[1], pz = p[2];
double vx = v[0], vy = v[1], vz = v[2];
for (int zz = -1; zz <= 1; zz++) {
int z = round(pz) + zz;
if (z < 0 || nz <= z) continue;
double dz = (z - pz)*vz, dzz = dz*dz;
for (int yy = -1; yy <= 1; yy++) {
int y = round(py) + yy;
if (y < 0 || ny <= y) continue;
double dy = (y - py)*vy, dyy = dy*dy;
for (int xx = -1; xx <= 1; xx++) {
int x = round(px) + xx;
if (x < 0 || nx <= x) continue;
double dx = (x - px)*vx, dxx = dx*dx;
float w = exp( -(dxx + dyy + dzz)/sigma );
float d = M[nz*ny*x + nz*y + z];
s += w * d;
w_sum += w;
}
}
}
return_val = s / w_sum;
"""
nx, ny, nz = M.shape
fn = et.ext_function('c_interp3scalar', code,
['M', 'p', 'v', 'sigma', 'nx', 'ny', 'nz'])
mod.add_function(fn)
def add_interp3scalar(mod):
M = np.empty((100,100,100), dtype='uint16', order='F')
p = np.empty(3)
v = np.empty(3)
sigma = 0.
code = """
#line 0 "interp3scalar"
double s = 0, w_sum = 1e-16;
double px = p[0], py = p[1], pz = p[2];
double vx = v[0], vy = v[1], vz = v[2];
for (int zz = -1; zz <= 1; zz++) {
int z = round(pz) + zz;
if (z < 0 || nz <= z) continue;
double dz = (z - pz)*vz, dzz = dz*dz;
for (int yy = -1; yy <= 1; yy++) {
int y = round(py) + yy;
if (y < 0 || ny <= y) continue;
double dy = (y - py)*vy, dyy = dy*dy;
for (int xx = -1; xx <= 1; xx++) {
int x = round(px) + xx;
if (x < 0 || nx <= x) continue;
double dx = (x - px)*vx, dxx = dx*dx;
float w = exp( -(dxx + dyy + dzz)/sigma );
float d = M[nz*ny*x + nz*y + z];
s += w * d;
w_sum += w;
}
}
}
return_val = s / w_sum;
"""
nx,ny,nz = M.shape
fn = et.ext_function('c_interp3scalar', code, ['M', 'p', 'v', 'sigma', 'nx','ny','nz'])
mod.add_function(fn)
def test_float_var_in(self):
mod_name = sys._getframe().f_code.co_name + self.compiler
mod_name = unique_mod(test_dir, mod_name)
mod = ext_tools.ext_module(mod_name)
a = 1.
code = "a=2.;"
test = ext_tools.ext_function('test', code, ['a'])
mod.add_function(test)
mod.compile(location=test_dir, compiler=self.compiler)
exec 'from ' + mod_name + ' import test'
b = 1.
test(b)
try:
b = 1.
test(b)
except TypeError:
pass
try:
b = 'abc'
test(b)
except TypeError:
pass
def test_var_in(self):
mod_name = 'dict_var_in' + self.compiler
mod_name = unique_mod(test_dir, mod_name)
mod = ext_tools.ext_module(mod_name)
a = {'z': 1}
code = 'a=py::dict();' # This just checks to make sure the type is correct
test = ext_tools.ext_function('test', code, ['a'])
mod.add_function(test)
mod.compile(location=test_dir, compiler=self.compiler)
exec('from ' + mod_name + ' import test')
b = {'y': 2}
test(b)
try:
b = 1.
test(b)
except TypeError:
pass
try:
b = 'string'
test(b)
except TypeError:
pass
def test_var_in(self):
mod_name = 'tuple_var_in' + self.compiler
mod_name = unique_mod(test_dir, mod_name)
mod = ext_tools.ext_module(mod_name)
a = (1, )
code = 'a=py::tuple();'
test = ext_tools.ext_function('test', code, ['a'])
mod.add_function(test)
mod.compile(location=test_dir, compiler=self.compiler)
exec('from ' + mod_name + ' import test')
b = (1, 2)
test(b)
try:
b = 1.
test(b)
except TypeError:
pass
try:
b = 'string'
test(b)
except TypeError:
pass
def test_var_in(self):
mod_name = 'int_var_in' + self.compiler
mod_name = unique_mod(test_dir, mod_name)
mod = ext_tools.ext_module(mod_name)
a = 1
code = "a=2;"
test = ext_tools.ext_function('test', code, ['a'])
mod.add_function(test)
mod.compile(location=test_dir, compiler=self.compiler)
exec('from ' + mod_name + ' import test')
b = 1
test(b)
try:
b = 1.
test(b)
except TypeError:
pass
try:
b = 'abc'
test(b)
except TypeError:
pass
def test_complex_var_in(self):
mod_name = sys._getframe().f_code.co_name + self.compiler
mod_name = unique_mod(test_dir, mod_name)
mod = ext_tools.ext_module(mod_name)
a = 1. + 1j
code = "a=std::complex<double>(2.,2.);"
test = ext_tools.ext_function('test', code, ['a'])
mod.add_function(test)
mod.compile(location=test_dir, compiler=self.compiler)
exec('from ' + mod_name + ' import test')
b = 1. + 1j
test(b)
try:
b = 1.
test(b)
except TypeError:
pass
try:
b = 'abc'
test(b)
except TypeError:
pass
def test_var_in(self):
mod_name = 'string_var_in' + self.compiler
mod_name = unique_mod(test_dir, mod_name)
mod = ext_tools.ext_module(mod_name)
a = 'string'
code = 'a=std::string("hello");'
test = ext_tools.ext_function('test', code, ['a'])
mod.add_function(test)
mod.compile(location=test_dir, compiler=self.compiler)
exec('from ' + mod_name + ' import test')
b = 'bub'
test(b)
try:
b = 1.
test(b)
except TypeError:
pass
try:
b = 1
test(b)
except TypeError:
pass
def buildBoundedThinPlateLibrary():
from scipy.weave import ext_tools
thinPlate2D_code = r"""
#line 8 "_bounded_thinPlate.py"
//void thinPlate2D_mat(double* C,double R, int cmin=0, int cmax=-1, int symm=0)
if (cmax==-1)
cmax=Nc[1];
if (symm)
{
for(int j=cmin;j<cmax;j++)
{
C2(j,j)=1.;
for(int i=0;i<j-1;i++)
{
C2(i,j)=thinPlate2D(C2(i,j),R);
}
}
} else {
for(int j=cmin;j<cmax;j++)
{
C2(j,j)=1.;
for(int i=0;i<Nc[0];i++)
{
C2(i,j)=thinPlate2D(C2(i,j),R);
}
}
}
"""
thinPlate3D_code = thinPlate2D_code.replace('2D', '3D')
thinPlate_support_code = r"""
#line 39 "_bounded_thinPlate.py"
double thinPlate2D(double d, double R)
{
double t;
if (d == 0.0)
t = 1.0;
else {
if (d < R){
const double d2 = d*d;
const double R2 = R*R;
t = (2*d2*log(d)-(1+2*log(R))*d2+R2)/R2;
}else{
t = 0.0e0 ;
}
}
return t;
}
double thinPlate3D(double d,double R)
{
double t;
if (d == 0.)
t = 1.0e0;
else {
if (d < R) {
const double d2 = d*d;
const double d3 = fabs(d)*d2;
const double R2 = R*R;
const double R3 = fabs(R)*R2;
t = (2*d3-3*R*d2+R3)/R3;
}else{
t = 0.0e0;
}
}
return t;
}
"""
innerProduct_thinPlate3D_normalized_code = r"""
#line 83 "_bounded_thinPlate.py"
//innerProduct_thinPlate3D_normalized(C,Q,R,symm)
if (R < Q) {
const double a = Q;
Q = R;
R = a;
}
double Rs[10];
double Qs[10];
Rs[0] = R;
Qs[0] = Q;
int i;
for( i=0;i<9;i++ ){
Rs[i+1] = Rs[i] * R;
Qs[i+1] = Qs[i] * Q;
}
if (symm) {
for (int j=0;j<Nc[1];i++)
{
int i;
for (i=0; i<j; i++){
C2(i,j) = covIntegralThinPlateR3Normalized( C2(i,j), Q, R, Qs, Rs);
C2(j,i) = C2(i,j);
}
}
}else{
for(int j=0; j<Nc[1]; j++)
{
int i;
for(i=0;i<Nc[0]; i++)
{
C2(i,j) = covIntegralThinPlateR3Normalized( C2(i,j), Q, R, Qs, Rs);
}
}
}
"""
innerProduct_thinPlate3D_normalized_support_code = r"""
#line 115 "_bounded_thinPlate.py"
double covIntTPR3NwLTRminusQ (double w, double Q, double R, const double* Qs, const double* Rs);
double covIntTP3NRminusQLTw ( double w, double Q, double R, const double* Qs, const double* Rs);
double covIntTP3NwGTR ( double w, double Q, double R, const double* Qs, const double* Rs);
double covIntegralThinPlateR3Normalized( double w, double Q, double R, const double* Qs, const double* Rs)
{
double aux;
if ( Q > R ) {
aux = R;
R = Q;
Q = aux;
}
if ( w == 0 ) {
return acos( -1.0e0 ) * double(Qs[3]) * double(84 * Rs[3] - 81 *R * Qs[2] + 35 * Qs[3]) / double(Rs[3]) / 0.315e3;
}else if ( w <= (R-Q) ) {
return covIntTPR3NwLTRminusQ(w,Q,R,Qs,Rs);
}else if ( ( (R-Q) < w ) && ( w <= R) ) {
return covIntTP3NRminusQLTw(w,Q,R,Qs,Rs);
}else if ( w > R ) {
return covIntTP3NwGTR(w,Q,R,Qs,Rs);
}
return 0;
}
double covIntTPR3NwLTRminusQ (double w, double Q, double R, const double* Qs, const double* Rs)
{
if ( w <= Q ) {
return acos( -1.0e0 ) * double(-405 * Qs[8] * R - 1260 * Qs[6] * R * pow(w,2) + 420 * Qs[6] * Rs[3] + 15 * Q * pow(w,8) + 175 * Qs[9] + 900 * Qs[7] * pow(w,2) + 378* Qs[5] * pow(w,4) - 60 * Qs[3] * pow(w,6) - 4 * pow(w,9)) / double(Qs[3]) / double(Rs[3]) / 0.1575e4;
}else{
return acos( -1.0e0 ) * double(Qs[3]) * double(-135 * Qs[2] * w * R - 420 * pow(w,3) * R + 140 * w * Rs[3] + 180 * Qs[2] * pow(w,2) + 280 * pow(w,4) + 8 * Qs[4]) / double(w) / double(Rs[3]) / 0.525e3;
}
}
double covIntTP3NRminusQLTw ( double w, double Q, double R, const double* Qs, const double* Rs)
{
if ( w <= Q ) {
return -0.40e1 / 0.525e3 * M_PI *(pow(w,10) / 0.2e1 + (-0.5e1 / 0.8e1 * R - 0.5e1 / 0.8e1 * Q) * pow(w,9) - 0.135e3 / 0.64e2 * pow(w,8) * R * Q + (0.5e1 / 0.2e1 * Rs[3] + 0.5e1 / 0.2e1 * Qs[3]) * pow(w,7) + 0.105e3 / 0.16e2 * Q * R * (Rs[2] + Qs[2]) * pow(w,6) + (-0.63e2 / 0.4e1 * Qs[5] - 0.63e2 / 0.4e1 * Rs[5]) * pow(w,5) + (-0.945e3 / 0.32e2 * Q * Rs[5] - 0.175e3/ 0.16e2 * Qs[3] * Rs[3] - 0.945e3 / 0.32e2 * Qs[5] * R + 0.35e2 * Rs[6] + 0.35e2 * Qs[6]) * pow(w,4) + (0.105e3 / 0.2e1 * Rs[6] * Q - 0.75e2 / 0.2e1 * Rs[7] + 0.105e3 / 0.2e1 * Qs[6] * R - 0.75e2 / 0.2e1 * Qs[7]) * pow(w,3) + 0.45e2 / 0.2e1 * pow(( Q - R ),4)* (Qs[4] + 0.17e2 / 0.8e1 * Qs[3] * R + 0.5e1 / 0.2e1 * Qs[2] *Rs[2] + 0.17e2 / 0.8e1 * Q * Rs[3] + Rs[4]) * pow(w,2) + (0.135e3 / 0.8e1 * Rs[8] * Q - 0.175e3 / 0.24e2 * Qs[9] - 0.35e2 /0.2e1* Qs[6] * Rs[3] - 0.175e3 / 0.24e2 * Rs[9] - 0.35e2 / 0.2e1 *Rs[6] * Qs[3] + 0.135e3 / 0.8e1 * Qs[8] * R)*w + pow(( Q - R ),6) * (Qs[4] + 0.209e3 / 0.64e2 * Qs[3] * R + 0.147e3 / 0.32e2 * Qs[2] * Rs[2] + 0.209e3 / 0.64e2 * Q * Rs[3] + Rs[4])) / Qs[3] / w / Rs[3] ;
}else{
return M_PI * (0.192e3 * pow(Q,10) - 0.192e3 * pow(R,10) - 0.32e2 * pow(w,10) + 0.8100e4 * pow(w,2) * Qs[7] * R - 0.10080e5 * pow(w,3) * Qs[6] * R + 0.8100e4 * Q * pow(w,2) * Rs[7] - 0.3780e4 * pow(w,2) * Qs[5] * Rs[3] + 0.3360e4 * Rs[6] * Qs[3] * w - 0.3240e4 * w * Qs[8] * R - 0.900e3 * Qs[7] * Rs[3] + 0.480e3 * pow(w,7) * Qs[3] + 0.405e3 * pow(w,8) * R * Q - 0.3780e4 * Qs[3] * pow(w,2) * Rs[5] - 0.1260e4 * pow(w,6) * Qs[3] * R + 0.5670e4 * Q * pow(w,4) * Rs[5] + 0.5670e4 * pow(w,4) * Qs[5] * R - 0.3240e4 * Rs[8] * Q * w + 0.3360e4 * w * Qs[6] * Rs[3] + 0.2100e4 * pow(w,4) * Qs[3] * Rs[3] - 0.1260e4 * pow(w,6) * Q * Rs[3] - 0.10080e5 * pow(w,3) * Rs[6] * Q + 0.525e3 * Qs[9] * R - 0.480e3 * pow(w,7) * Rs[3] + 0.120e3 * pow(w,9) * R - 0.120e3 * pow(w,9) * Q - 0.1400e4 * w * Qs[9] + 0.4320e4 * pow(w,2) * Qs[8] - 0.7200e4 * pow(w,3) * Qs[7] + 0.6720e4 * pow(w,4) * Qs[6] + 0.525e3 * Q * Rs[9] + 0.1134e4 * Qs[5] * Rs[5] - 0.900e3 * Qs[3] * Rs[7] + 0.7200e4 * pow(w,3) * Rs[7] + 0.1400e4 * w * Rs[9] - 0.6720e4 * pow(w,4) * Rs[6] + 0.3024e4 * pow(w,5) * Rs[5] - 0.4320e4 * pow(w,2) * Rs[8] - 0.3024e4 * pow(w,5) * Qs[5]) / Qs[3] / w / Rs[3] / 0.25200e5;
}
}
double covIntTP3NwGTR ( double w, double Q, double R, const double* Qs, const double* Rs)
{
if ( w <= R+Q ) {
return 0.4e1 / 0.525e3 * acos( -1.0e0 ) * pow((R + Q - w),6) * (pow(w,4) / 0.6e1 + (0.3e1 / 0.8e1 * Q + 0.3e1 / 0.8e1 * R) * pow(w,3) + (0.103e3 / 0.64e2 * Q * R - Qs[2] / 0.4e1 - Rs[2] / 0.4e1) * pow(w,2) - 0.31e2 / 0.24e2 * (Rs[2] - 0.247e3 / 0.124e3 * Q * R + Qs[2]) * (R + Q) * w + Rs[4] - 0.209e3 / 0.64e2 * Qs[3] * R + 0.147e3 / 0.32e2 * Qs[2] * Rs[2] + Qs[4] -0.209e3 / 0.64e2 * Q * Rs[3]) / Qs[3] / w / Rs[3];
}else{
return 0;
}
}
"""
import numpy
c = numpy.eye(5, dtype=float)
R = 1.
Q = 1.
cmin = 1
cmax = 1
symm = 1
thinPlateArguments = ['c', 'R', 'cmin', 'cmax', 'symm']
innerProductArguments = ['c', 'R', 'Q', 'symm']
mod = ext_tools.ext_module('_bounded_thinPlate_lib')
mod.add_function(
ext_tools.ext_function('thinPlate2D_mat', thinPlate2D_code,
thinPlateArguments))
mod.add_function(
ext_tools.ext_function('thinPlate3D_mat', thinPlate3D_code,
thinPlateArguments))
mod.add_function(
ext_tools.ext_function('innerProduct_thinPlate3D_normalized',
innerProduct_thinPlate3D_normalized_code,
innerProductArguments))
mod.customize.add_support_code(thinPlate_support_code)
mod.customize.add_support_code(
innerProduct_thinPlate3D_normalized_support_code)
# mod.customize.add_extra_compile_arg('-O3')
# mod.customize.add_extra_link_arg('-O3')
mod.compile()
def compile_cpp_filters():
"""
This method finds and compile every c++ filters
If a c++ file changed, the file must be recompiled in a new .so file
"""
BUILD_DIR = 'build'
RELOAD_DIR = os.path.join('build', 'reload')
if not os.path.exists(BUILD_DIR):
os.mkdir(BUILD_DIR)
if not os.path.exists(RELOAD_DIR):
os.mkdir(RELOAD_DIR)
if len(g.cppfiles) == 0:
for f in os.listdir(RELOAD_DIR):
os.remove(os.path.join(RELOAD_DIR, f))
image = np.zeros((1,1), dtype=np.uint8)
params = {}
def ext_code():
"""
Return the code that calls a c++ filter
"""
return """
cv::Mat mat(Nimage[0], Nimage[1], CV_8UC(3), image);
cv::Mat ret = execute(mat);
if (mat.data != ret.data) {
ret.copyTo(mat);
}
"""
def init_code():
"""
This method returns the code to initialize the parameters
"""
return """
params = p;
py_init_param = pip;
init();
"""
def params_code():
"""
Support code to declare parameters in the C++ filters
It assumes a method py_init_param received as a parameter from
the python side to create the parameters in the python object.
"""
return """
py::dict params;
py::object py_init_param;
void init_param(const char* name, int min, int max, int def_val) {
py::tuple args(4);
args[0] = name;
args[1] = min;
args[2] = max;
args[3] = def_val;
py_init_param.call(args);
}
long ParameterAsInt(const char* name, int min, int max, int def_val) {
if(!params.has_key(name)) {
init_param(name, min, max, def_val);
}
py::object o = params.get(name);
return PyInt_AsLong(o.mcall("get_current_value"));
}
bool ParameterAsBool(const char* name, int min, int max, int def_val) {
if(!params.has_key(name)) {
init_param(name, min, max, def_val);
}
return PyInt_AsLong(params.get(name).mcall("get_current_value"));
}
"""
def help_code():
"""
Return the code that returns the help string from a c++ file
"""
return """
#ifdef DOCSTRING
return_val = DOCSTRING;
#else
return_val = "";
#endif
"""
def config_code():
"""
Code to reconfigure the filter
"""
return """
configure();
"""
def create_execute(cppfunc):
"""
Create and return an "execute" method for the dynamically
created class that wraps the c++ filters
"""
def execute(self, image):
cppfunc(image)
return image
return execute
def create_configure(cppfunc):
"""
"""
def configure(self):
cppfunc()
return configure
def create_init(cppfunc, params):
"""
"""
def __init__(self):
self.params = {}
cppfunc(self.params, self.py_init_param)
return __init__
def py_init_param(self, name, min, max, def_val):
param = Parameter(name, min, max, def_val)
self.params[name] = param
setattr(self, name, param)
dirname = os.path.dirname(__file__)
for f in os.listdir(dirname):
if not f.endswith(".cpp"):
continue
filename, _ = os.path.splitext(f)
cppcode = open(os.path.join(dirname, f)).read()
#Verify if there are changes in the c++ code file. If there are
#changes, add a timestamp to the filter .so file name to force a
#reimportation of the new filter.
if g.cppfiles.has_key(filename):
if cppcode != g.cppfiles[filename]:
g.cpptimestamps[filename] = str(int(time.time()))
g.cppfiles[filename] = cppcode
if g.cpptimestamps.has_key(filename):
modname = filename + g.cpptimestamps[filename]
else:
modname = filename
#Compile filters
#The included files are found in the .cpp file
mod = ext_tools.ext_module(modname)
[mod.customize.add_header(line.replace('#include ', ''))
for line in cppcode.split('\n')
if line.startswith('#include')]
mod.customize.add_header("<Python.h>")
mod.customize.add_extra_link_arg("`pkg-config --cflags --libs opencv python`")
mod.customize.add_extra_link_arg("-L/usr/local/cuda/lib64")
func = ext_tools.ext_function('exec_' + filename, ext_code(),['image'])
func.customize.add_support_code(params_code())
func.customize.add_support_code(cppcode)
mod.add_function(func)
helpfunc = ext_tools.ext_function('help_' + filename, help_code(), [])
mod.add_function(helpfunc)
p = params
pip = py_init_param
initfunc = ext_tools.ext_function('init_' + filename, init_code(), ['p', 'pip'])
initfunc.customize.add_support_code(params_code())
#initfunc.customize.add_support_code(cppcode)
mod.add_function(initfunc)
configfunc = ext_tools.ext_function('config_' + filename, config_code(), [])
configfunc.customize.add_support_code(params_code())
configfunc.customize.add_support_code(cppcode)
mod.add_function(configfunc)
try:
if g.cpptimestamps.has_key(filename):
#Reloaded modules are saved in the reload folder for easy cleanup
mod.compile(RELOAD_DIR)
else:
mod.compile(BUILD_DIR)
cppmodule = __import__(modname)
params = {}
clazz = type(filename, (object,),
{'__init__' : create_init(
getattr(cppmodule, 'init_' + filename), params),
'configure' : create_configure(
getattr(cppmodule, 'config_' + filename)),
'execute' : create_execute(
getattr(cppmodule, 'exec_' + filename)),
'py_init_param' : py_init_param,
'__doc__' : getattr(cppmodule, 'help_' + filename)()})
setattr(sys.modules[__name__], filename, clazz)
del clazz
except Exception as e:
sys.stderr.write(str(e) + '\n')
sys.stderr.write(traceback.format_exc() + "\n")
