void apply(cube<real>& v, real bias) noexcept override
{
real* d = v.data();
size_t n = v.num_elements();
for ( size_t i = 0; i < n; ++i )
d[i] = f_(d[i] + bias);
}
//HELIX ANIMATION
uint8_t animation::helix(cube &c){
float X = 0;
float Y = 0;
float Z = 0;
slow++;
if(slow < 100){
return 0;
}
slow = 0;
c.clearVoxels();
//use my fancy pants sine function
for(uint8_t i = 0; i < 3; i++){
for(uint8_t z = 0; z < 4; z++){
Z = z*52;
X = get_sinA(Z + phase + 18*i);
Y = get_sinA(Z + phase + 90 + 18*i);
X = (X+1)*4;
Y = (Y+1)*4;
c.setVoxel((uint8_t)X, (uint8_t)Y, z);
c.setVoxel((uint8_t)(8-X), (uint8_t)(8-Y), z+4);
}
}
//increment the phase
phase+=18;
if(phase > 360){
phase -= 360;
}
return 1;
}
cube barrel_distort_rgb(const cube &F, double offset_x) {
cube G(F.n_rows, F.n_cols, F.n_slices);
G.slice(0) = barrel_distort(F.slice(0), offset_x);
G.slice(1) = barrel_distort(F.slice(1), offset_x);
G.slice(2) = barrel_distort(F.slice(2), offset_x);
return G;
}
SEXP move_B(const mat& y, cube& B, const mat& kappa_star, const field<mat>& C,
//const field<sp_mat>& C,
mat& gamma, const mat& D, const ucolvec& s, double tau_e)
{
BEGIN_RCPP
// N x T matrix of standardized counts, y
// B = (B_1,...,B_K), where B_k is N x T matrix for iGMRF term k
// N x T matrix, gamma = sum_{k=1^K}(B_k)
// K x T, D, where row k contains T x 1 diagonal elements of Q_k
// sample cluster assignments, s(1), ..., s(N)
// Q = (Q_1,...,Q_K), where Q_k is a T x T de-scaled iGMRF precision matrix
// C = (C_1,...,C_K), where C_k = D_k^-1 * Omega_k,
// where Omega_k is the T x T adjacency matrix for iGMRF term, k
// D is a K x T matrix where row k contains T diagonal elements of Q_k
// K x M matrix, kappa_star records locations for each iGMRF term
int K = B.n_slices;
int N = y.n_rows;
int T = D.n_cols;
colvec bbar_ki(T); bbar_ki.zeros();
rowvec gammatilde_ki(T); gammatilde_ki.zeros();
rowvec ytilde_ki(T); ytilde_ki.zeros();
rowvec d_k(T);
vec zro(T); zro.zeros();
double e_ij, phi_ij, bkij, h_ij;
int k = 0, i = 0, j = 0; /* loop variables */
for( k = 0; k < K; k++ ) /* over iGMRF terms */
{
d_k = D.row(k);
for( i = 0; i < N; i++ ) /* over units */
{
/* take out T x 1, b_ki, to be sampled from gamma */
//gammatilde_ki = gamma.row(i) - B.slice(k).row(i); /* 1 x T */
//ytilde_ki = y.row(i) - gammatilde_ki;
gammatilde_ki = gamma.row(i); /* 1 x T */
// mean of univariate iGMRF, b_kij = 1/d_kj * (omega_kj(-j) * b_ki(-j))
bbar_ki = C(k,0) * B.slice(k).row(i).t(); /* T x 1 */
for( j = 0; j < T; j++ ) /* over time points */
{
gammatilde_ki(j) -= B.slice(k)(i,j);
ytilde_ki(j) = y(i,j) - gammatilde_ki(j);
// mean of univariate iGMRF, b_kij = 1/d_kj * (omega_kj(-j) * b_ki(-j))
B.slice(k)(i,j) = 0;
//bbar_ki(j) = dot( C(k,0).row(j), B.slice(k).row(i) );
e_ij = tau_e*ytilde_ki(j)
+ d_k(j)*kappa_star(k,s(i)) * bbar_ki(j);
phi_ij = tau_e + d_k(j)*kappa_star(k,s(i));
h_ij = (e_ij / phi_ij);
bkij = rnorm( 1, (h_ij), sqrt(1/phi_ij) )[0];
B.slice(k)(i,j) = bkij;
/* put back new sampled values for b_kij */
gammatilde_ki(j) += B.slice(k)(i,j);
} /* end loop j over time points */
/* put back new sampled values for b_ki */
//gamma.row(i) = gammatilde_ki + B.slice(k).row(i);
gamma.row(i) = gammatilde_ki;
} /* end loop i over units */
} /* end loop k over iGMRF terms */
END_RCPP
} /* end function ustep to sample B_1,...,B_K */
inline bool equal(const cube<T>& c1, const cube<T>& c2)
{
if ( c1.n_elem != c2.n_elem )
{
return false;
}
return std::equal(c1.memptr(), c1.memptr() + c1.n_elem, c2.memptr());
}
typename std::enable_if<has_public_member_grad<T>::value>::type
apply_grad(cube<real>& g, const cube<real>& f, const T& fn) noexcept
{
real* gp = g.data();
const real* fp = f.data();
size_t n = g.num_elements();
for ( size_t i = 0; i < n; ++i )
gp[i] *= fn.grad(fp[i]);
}
inline void pairwise_div( cube<T>& a, const cube<T>& b )
{
ZI_ASSERT(a.n_elem==b.n_elem);
T* ap = a.memptr();
const T* bp = b.memptr();
for ( size_t i = 0; i < a.n_elem; ++i )
ap[i] /= bp[i];
}
inline void convolve_constant( cube<T> const & a,
identity_t<T> b,
cube<T> & r) noexcept
{
ZI_ASSERT(size(a)==size(r));
T const * ap = a.data();
T * rp = r.data();
for ( size_t i = 0; i < r.num_elements(); ++i )
rp[i] = ap[i] * b;
}
// REALIZATION OF FUNCTIONS
void rotationMain(int x) {
if (x<=90) {
glutTimerFunc(5,rotationMain,x+1);
animating = true;
Cube.rotateCubesAnim(direction,x);
glutPostRedisplay();
} else {
Cube.rotateCubesAnim(direction,0);
Cube.rotateCubesFace(direction);
animating = false;
glutPostRedisplay();
}
}
inline T convolve_constant_flipped( cube<T> const & a,
cube<T> const & b ) noexcept
{
ZI_ASSERT(size(a)==size(b));
T r = 0;
T const * ap = a.data();
T const * bp = b.data();
for ( size_t i = 0; i < a.num_elements(); ++i )
r += ap[i] * bp[i];
return r;
}
/**********************************************************************
* MSE Class
***********************************************************************/
double MSE::cost(cube pred, cube y){
dbg_assert(y.n_cols == 1 && y.n_slices == 1);
pred.reshape(pred.n_elem,1,1);
y.reshape(y.n_elem,1,1);
double retn = 0.0f;
for(int i=0; i < y.n_elem; i++) {
retn += pow(pred(i,0,0) - y(i,0,0),2);
}
retn /= y.n_elem;
retn *= 0.5f;
//return(retn);
return(0.5 * mean(mean(square(pred.slice(0) - y.slice(0)))));
}
//RANDOM LIGHTS
uint8_t animation::randomExpand(cube &c){
uint16_t count = 0;
uint8_t rX, rY, rZ;
slow++;
if(slow < 20){
return 0;
}
slow = 0;
randomSeed(analogRead(0));
rX = rand()%8+0;
rY = rand()%8+0;
rZ = rand()%8+0;
//find an empty voxel
while(c.getVoxel(rX, rY, rZ) == 1 && dir == 1){
rX = random(0, 8);
rY = random(0, 8);
rZ = random(0, 8);
count++;
if(count > 200){
dir *= -1;
}
}
count = 0;
//find a full voxel
while(c.getVoxel(rX, rY, rZ) == 0 && dir == -1){
rX = random(0, 8);
rY = random(0, 8);
rZ = random(0, 8);
count++;
if(count > 200){
dir *= -1;
}
}
//fill or clear the voxel found
if(dir == 1){
c.setVoxel(rX, rY, rZ);
}else{
c.clearVoxel(rX, rY, rZ);
}
return 1;
}
cube Utils::conv3(cube body, cube kernel)
{
if (body.max() <= 0)
{
return zeros(body.n_rows, body.n_cols, body.n_slices);
}
cube Q(body);
for (int i = 1; i < body.n_slices - 1; i++)
{
Q.slice(i) = conv2(body.slice(i), kernel.slice(1), "same") +
conv2(body.slice(i - 1), kernel.slice(0), "same") +
conv2(body.slice(i + 1), kernel.slice(2), "same");
}
return Q;
}
// performs inplace dropout backward
inline void dropout_backward(cube<real> & g)
{
ZI_ASSERT(mask_);
size_t s = g.num_elements();
for ( size_t i = 0; i < s; ++i )
{
if ( mask_->data()[i] )
g.data()[i] *= scale();
else
g.data()[i] = static_cast<real>(0);
}
// Should we reset mask_ here?
}
//SINGLE PLANE BOUNCING
uint8_t animation::bouncePlane(cube &c, uint8_t axis){
slow++;
if(slow < 200){
return 0;
}
slow = 0;
//the X animation looks the same but actually clears everything in its path
//rather than clear everything at the start, it makes a simple but cool
//transition between some animations
if(axis != 'X'){
c.clearVoxels();
}
switch(axis){
case 'X':
for(uint8_t z = 0; z < Zd; z++){
for(uint8_t y = 0; y < Yd; y++){
for(uint8_t x = 0; x < Xd; x++){
if(x == pos - dir){
c.clearVoxel(x, y, z);
}
c.setVoxel(pos, y, z);
}
}
}
break;
case 'Y':
for(uint8_t x = 0; x < Xd; x++){
for(uint8_t z = 0; z < Zd; z++){
c.setVoxel(x, pos, z);
}
}
break;
case 'Z':
for(uint8_t x = 0; x < Xd; x++){
for(uint8_t y = 0; y < Yd; y++){
c.setVoxel(x, y, pos);
}
}
break;
}
//bounce the pos variable between 0 and 7
bouncePos();
return 1;
}
cube imresize2(const cube &C, uword m, uword n) {
cube F(m, n, C.n_slices);
for (uword k = 0; k < C.n_slices; k++) {
F.slice(k) = imresize2(C.slice(k), m, n);
}
return F;
}
cube noncont_slices(const cube & X, const uvec & index, int r_start, int c_start, int r_stop, int c_stop){
cube Xsub(r_stop-r_start+1, c_stop-c_start+1, index.n_elem);
for(unsigned int i=0; i<index.n_elem; i++){
Xsub.slice(i) = X.slice(index[i]).submat(r_start, c_start, r_stop, c_stop);
}
return Xsub;
}
cube Utils::erode(cube body, cube kernel)
{
int minx, miny, minz, maxx, maxy, maxz;
Utils::bounds(body, minx, miny, minz, maxx, maxy, maxz);
cube result = cube(body);
int size_x = kernel.n_cols / 2;
int size_y = kernel.n_rows / 2;
int size_z = kernel.n_slices / 2;
maxx -= kernel.n_cols;
maxy -= kernel.n_rows;
maxz -= kernel.n_slices;
for (int i = minx; i <= maxx; i++)
{
for (int j = miny; j <= maxy; j++)
{
for (int k = minz; k <= maxz; k++)
{
cube subcube = body.subcube(j, i, k, size(kernel));
subcube -= kernel;
result(j + size_y, i + size_x, k + size_z) = subcube.min() < 0 ? 0 : 1;
}
}
}
return result;
}
cube conv2(const cube &F, const mat &H) {
cube G(F.n_rows, F.n_cols, F.n_slices);
for (uword i = 0; i < F.n_slices; i++) {
G.slice(i) = conv2(F.slice(i), H);
}
return G;
}
inline unique_cube<T> crop_right( const cube<T>& in, const vec3s& s )
{
auto r = pool<T>::get_unique(s);
vec3s b = size(in) - s;
*r = in.subcube(b[0], b[1], b[2], b[0]+s[0]-1, b[1]+s[1]-1, b[2]+s[2]-1);
return r;
}
//! compute (trial)point-to-(model)point Mahalanobis distance
//! @param[in] index index of the points (in trial and model) to be compared
//! @param[in] &trial reference to the trial
//! @param[in] &model reference to the model
//! @param[in] &variance reference to the model variance
//! @return Mahalanobis distance between trial-point and model-point
float Classifier::mahalanobisDist(int index,mat &trial,mat &model,cube &variance)
{
mat difference = trial.col(index) - model.col(index);
mat distance = (difference.t() * (variance.slice(index)).i()) * difference;
return distance(0,0);
}
// Volumetric 2D Convolution
mat conv2d(cube image, cube kernel){
dbg_assert(image.n_rows == image.n_cols);
dbg_assert(kernel.n_rows == kernel.n_cols);
dbg_assert(kernel.n_rows <= image.n_rows);
dbg_assert(kernel.n_slices == image.n_slices);
int kernel_size = kernel.n_rows;
int image_size = image.n_rows;
int result_size = image_size - kernel_size + 1;
mat result = zeros<mat>(result_size, result_size);
for(int row=0; row < result_size; row++){
for(int col=0; col < result_size; col++){
result(row, col) = accu(
image.tube(
row,
col,
row + kernel_size - 1,
col + kernel_size - 1
) % kernel
);
}
}
return(result);
}
void initScene() {
// Clear
glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);
// Set drawing mode
glMatrixMode(GL_MODELVIEW);
// Draw scene
glLoadIdentity();
glTranslatef(0.0f,0.0f,-7.0f);
// Draw lighting
GLfloat ambientColor[] = {0.2f, 0.2f, 0.2f, 1.0f}; //Color (0.2, 0.2, 0.2)
glLightModelfv(GL_LIGHT_MODEL_AMBIENT, ambientColor);
//Add positioned light
GLfloat lightColor0[] = {0.5f, 0.5f, 0.5f, 1.0f}; //Color (0.5, 0.5, 0.5)
GLfloat lightPos0[] = {4.0f, 0.0f, 8.0f, 1.0f}; //Positioned at (4, 0, 8)
glLightfv(GL_LIGHT0, GL_DIFFUSE, lightColor0);
glLightfv(GL_LIGHT0, GL_POSITION, lightPos0);
//Add directed light
GLfloat lightColor1[] = {0.7f, 0.7f, 0.7f, 1.0f}; //Color (0.5, 0.2, 0.2)
//Coming from the direction (-1, 0.5, 0.5)
GLfloat lightPos1[] = {-1.0f, 0.5f, 0.5f, 0.0f};
glLightfv(GL_LIGHT1, GL_DIFFUSE, lightColor1);
glLightfv(GL_LIGHT1, GL_POSITION, lightPos1);
// Draw the cube
Cube.draw(_textureId);
glutSwapBuffers();
}
void connected_cube_list::add( const cube& c )
{
/* check if cube already exists */
auto it = _connected_cubes.find( c );
if ( it != _connected_cubes.end() ) return;
/* find matching cubes */
cube_common_vec_t commons;
int weight = 0;
for ( const auto& other : _cubes )
{
int m = other.match_intersect( c );
if ( m != -1 )
{
commons += std::make_pair( other, (unsigned)m );
weight += c.dimension() - m - 1;
_connected_cubes[other] += std::make_pair( c, (unsigned)m );
cube_weights[other] += other.dimension() - m - 1;
}
}
/* add cube */
_cubes += c;
_connected_cubes[c] = commons;
cube_weights[c] = weight;
}
void lmMean(const cube& wX, const rowvec& vec_beta, mat& mean){
int n = wX.n_slices, P=wX.n_cols;
mean = zeros(n,P);
for(int i=0;i<n;i++){
mean.row(i) = vec_beta* wX.slice(i);
}
}
cube noncont_slices(const cube & X, const uvec & index){
cube Xsub(X.n_rows, X.n_cols, index.n_elem);
for(unsigned int i=0; i<index.n_elem; i++){
Xsub.slice(i) = X.slice(index[i]);
}
return Xsub;
}
inline cube_p<T> convolve_sparse( cube<T> const & a,
cube<T> const & b,
vec3i const & s )
{
if ( s == vec3i::one )
{
return convolve(a,b);
}
vec3i as = size(a);
vec3i bs = size(b);
vec3i rs = size(a) - (size(b) - vec3i::one) * s;
cube_p<T> r = get_cube<T>(rs);
int a_strides[3] = { s[2], as[2]*s[1], as[2]*as[1]*s[0] };
int r_strides[3] = { s[2], rs[2]*s[1], rs[2]*rs[1]*s[0] };
// sparseness
for (int xs=0; xs<s[0]; xs++)
for (int ys=0; ys<s[1]; ys++)
for (int zs=0; zs<s[2]; zs++)
{
vec3i in_size( (as[0]-1)/s[0] + (xs == 0 ? 1 : 0),
(as[1]-1)/s[1] + (ys == 0 ? 1 : 0),
(as[2]-1)/s[2] + (zs == 0 ? 1 : 0) );
const T* in_ptr = &(a[xs][ys][zs]);
T* out_ptr = &((*r)[xs][ys][zs]);
#ifdef ZNN_USE_FLOATS
int status = vslsConvExec( conv_plans.get(in_size, bs),
in_ptr, a_strides,
b.data(), NULL,
out_ptr, r_strides);
#else
int status = vsldConvExec( conv_plans.get(in_size, bs),
in_ptr, a_strides,
b.data(), NULL,
out_ptr, r_strides);
#endif
}
return r;
}
inline void fill_indices(cube<T>& c)
{
T idx = 0;
T* mem = c.memptr();
for ( size_t i = 0; i < c.n_elem; ++i, ++idx )
mem[i] = idx;
}
sseq
compute_szabo_sseq (const cube<Z2> &c)
{
mod_map<Z2> d = c.compute_d (0, 0, 0, 0, 0);
sseq_builder builder (c.khC, d);
return builder.build_sseq ();
}
void white(const mat& y, const mat& y_center, const uvec& sti, const cube& matphi1, const cube& matphi2, mat& wy, mat& wy_center, const uvec& WTIME){
int L=matphi1.n_slices, wT = WTIME.n_elem, t=0;
mat multiply;
if(L==0){wy=y; wy_center = y_center;}
else{
wy = y.rows(WTIME);
wy_center = y_center.rows(WTIME);
for(int wt=0; wt<wT ; wt++){
t = WTIME[wt];
for(int l=0; l<L; l++){
multiply = (sti[t-l-1])?(matphi1.slice(l)):(matphi2.slice(l));
wy.row(wt) -= y.row(t-l-1)*multiply;
wy_center.row(wt) -= y_center.row(t-l-1)*multiply;
}
}
}
}