/*!
* Initialize phi
*/
void ActiveContourSeed::initializePhi(int protobuf_idx, Protobuf *proto) {
// set resolution
phi_->setResolution(p_->res_x, p_->res_y, p_->res_z);
// initialize image
phi_->resize(_dimx_Rel, _dimy_Rel, _dimz_Rel);
// get cell centers, previous sparse segmentation from protobuf file
Array1D<int> xAbs(cb), yAbs(cb), zAbs(cb);
proto->getSparseSegmentationCoordinates("full", protobuf_idx, &xAbs, &yAbs,
&zAbs);
// if previous sparse segmentation is empty, then initialize phi from single point
if (xAbs.size() == 0) {
for (int x = 0; x < _dimx_Rel; x++) {
for (int y = 0; y < _dimy_Rel; y++) {
for (int z = 0; z < _dimz_Rel; z++) {
float xRadial = (float) (x - _hszX);
float yRadial = (float) (y - _hszY);
float zRadial = (float) (z - _hszZ);
(*phi_)(x, y, z) = sqrtf(
xRadial * xRadial + yRadial * yRadial + zRadial
* zRadial) - p_->r;
}
}
}
// otherwise, initialize phi using distance transform on previous segmentation
} else {
// get previous binary segmentation, store in phi
for (int p = 0; p < xAbs.size(); p++) {
int xRel, yRel, zRel;
absToRel(xRel, yRel, zRel, xAbs(p), yAbs(p), zAbs(p));
(*phi_)(xRel, yRel, zRel) = 1;
}
// get perimeter segmentation and store in phi. Store original segmentation in temp
Image3D<float> temp(*phi_);
perim(phi_, 1);
// calculate distance transform
bwdist(phi_);
// Make distances negative inside the segmentation
for (int x = 0; x < _dimx_Rel; x++) {
for (int y = 0; y < _dimy_Rel; y++) {
for (int z = 0; z < _dimz_Rel; z++) {
if (temp(x, y, z) > float(BWTHRESH)) {
(*phi_)(x, y, z) = -(*phi_)(x, y, z);
}
}
}
}
}
updateFullSeg(phi_);
}
CChartDataList AFR::toChartData(unsigned interalParts) const {
CChartDataList result;
if (interalParts & Real) {
CDimensionArray* xRe(new CDimensionArray(static_cast<int>(this->size())));
CDimensionArray* yRe(new CDimensionArray(static_cast<int>(this->size())));
double* xReIt(xRe->data());
double* yReIt(yRe->data());
for (AFR::const_iterator it(this->begin()); it != this->end(); ++it, ++xReIt, ++yReIt) {
*xReIt = it->frequency;
*yReIt = it->amplitude.real();
}
xRe->updateRange();
yRe->updateRange();
CChartData re;
re.push_back(xRe);
re.push_back(yRe);
result << re;
}
if (interalParts & Imaginary) {
CDimensionArray* xIm(new CDimensionArray(static_cast<int>(this->size())));
CDimensionArray* yIm(new CDimensionArray(static_cast<int>(this->size())));
double* xImIt(xIm->data());
double* yImIt(yIm->data());
for (AFR::const_iterator it(this->begin()); it != this->end(); ++it, ++xImIt, ++yImIt) {
*xImIt= it->frequency;
*yImIt = it->amplitude.imag();
}
xIm->updateRange();
yIm->updateRange();
CChartData im;
im.push_back(xIm);
im.push_back(yIm);
result << im;
}
if (interalParts & Amplitude) {
CDimensionArray* xAbs(new CDimensionArray(static_cast<int>(this->size())));
CDimensionArray* yAbs(new CDimensionArray(static_cast<int>(this->size())));
double* xAbsIt(xAbs->data());
double* yAbsIt(yAbs->data());
for (AFR::const_iterator it(this->begin()); it != this->end(); ++it, ++xAbsIt, ++yAbsIt) {
*xAbsIt = it->frequency;
*yAbsIt = abs(it->amplitude);
}
xAbs->updateRange();
yAbs->updateRange();
CChartData abs;
abs.push_back(xAbs);
abs.push_back(yAbs);
result << abs;
}
return result;
}