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some a_func refactoring #4

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86 changes: 84 additions & 2 deletions ch_shrinkwrap/conj_grad_utils.c
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Original file line number Diff line number Diff line change
Expand Up @@ -49,10 +49,11 @@ static PyObject *c_shrinkwrap_a_func(PyObject *self, PyObject *args)
if ((*((int32_t *)PyArray_GETPTR2(v_n, i, 0))) == -1) continue;
for (k=0; k<n_points; ++k)
{
w = *((float *)PyArray_GETPTR2(v_w, i, k));
for (j=0; j<n_dims; ++j)
{
// p_d[k*n_dims+j] += p_f[i*n_dims+j]*(p_w[i*n_points+k]);
w = *((float *)PyArray_GETPTR2(v_w, i, k));

p_d[k*n_dims+j] += p_f[i*n_dims+j]*w;
}
}
Expand Down Expand Up @@ -105,10 +106,11 @@ static PyObject *c_shrinkwrap_ah_func(PyObject *self, PyObject *args)
if ((*((int32_t *)PyArray_GETPTR2(v_n, i, 0))) == -1) continue;
for (k=0; k<n_points; ++k)
{
w = *((float *)PyArray_GETPTR2(v_w, i, k));
for (j=0; j<n_dims; ++j)
{
// p_d[i*n_dims+j] += p_f[k*n_dims+j]*(p_w[i*n_points+k]);
w = *((float *)PyArray_GETPTR2(v_w, i, k));

p_d[i*n_dims+j] += p_f[k*n_dims+j]*w;
}
}
Expand All @@ -118,6 +120,79 @@ static PyObject *c_shrinkwrap_ah_func(PyObject *self, PyObject *args)
return Py_None;
}

void compute_weight_matrix_3D(PyObject* v_f, PyObject* v_n, PyObject* v_points, PyObject* v_dd, int n_verts, int n_points, float shield_sigma)
{
int i, j, k;
float * pt3;
float * pfi;
float * p_f;
float *ds;
float dd_ik, dik, ss2, w;
#define N_DIMS 3 //use a fixed constant to allow loop-unrolling and/or vectorisation

// replace with python/numpy allocation (typically faster as from pre-allocated heap)
//ds = (float *) calloc(n_points, sizeof(float));
ds = (float *) PyMem_Calloc(n_points, sizeof(float));

//initialise to zero
for (k=0; k<n_points; ++k)
{
ds[k] = 0;
}

ss2 = 2*shield_sigma*shield_sigma;

p_f = (float *)PyArray_GETPTR1(v_f, 0);

for (i=0; i<n_verts; ++i)
{
if ((*((float *)PyArray_GETPTR2(v_n, i, 0))) == -1) continue;

pfi = p_f + i*N_DIMS;

for (k=0; k<n_points; ++k)
{
w = 0;
pt3 = (float *)PyArray_GETPTR2(v_points, k, 0);

dd_ik = 0; //*((float *)PyArray_GETPTR2(v_dd, i, k))

for (j=0; j<N_DIMS; ++j)
{
dik = pfi[j] - pt3[j];
dd_ik += dik*dik;
}

// update to point attraction force
if (dd_ik > 0) {
// *((float *)PyArray_GETPTR2(v_dd, i, k)) = (1.0/dik)*exp(-dik/ss2);
//w = expf(-dd_ik/ss2); // use fexp to avoid casts
//dd_ik = (1.0/dd_ik)*w;
dd_ik = (1.0/sqrtf(dd_ik));
*((float *)PyArray_GETPTR2(v_dd, i, k)) = dd_ik;
}

// keep track of sum along n_verts
ds[k] += dd_ik;
}
}

// normalize
for (i=0; i<n_verts; ++i)
{
if ((*((float *)PyArray_GETPTR2(v_n, i, 0))) == -1) continue;
for (k=0; k<n_points; ++k)
{
if (ds[k] == 0) continue;
*((float *)PyArray_GETPTR2(v_dd, i, k)) /= ds[k];
}
}

//free(ds);
PyMem_Free(ds);

}

static PyObject *c_compute_weight_matrix(PyObject *self, PyObject *args)
{
PyObject *v_f = 0, *v_n = 0, *v_points = 0, *v_dd = 0;
Expand Down Expand Up @@ -148,6 +223,13 @@ static PyObject *c_compute_weight_matrix(PyObject *self, PyObject *args)
return NULL;
}

if (n_dims == 3){
// use fixed size code
compute_weight_matrix_3D(v_f, v_n, v_points, v_dd, n_verts, n_points, shield_sigma);
Py_INCREF(Py_None);
return Py_None;
}

p_f = (float *)PyArray_GETPTR1(v_f, 0);

ds = (float *) calloc(n_points, sizeof(float));
Expand Down