// Returns pair distance between two particles (including periodic images).
void LAMMPS_Data::pair_distances(int step, int i, int j, Histogram &h) const {
auto dump = _dump[step];
const Coord &ri = dump.scaled_coordinates[i];
const Coord &rj = dump.scaled_coordinates[j];
double dx = dump.dx*fabs(ri.x-rj.x);
double dy = dump.dy*fabs(ri.y-rj.y);
double dz = dump.dz*fabs(ri.z-rj.z);
double dx2[] = {dx, dx-dump.dx};
double dy2[] = {dy, dy-dump.dy};
double dz2[] = {dz, dz-dump.dz};
for (int a=0; a<2; ++a) {
dx2[a] *= dx2[a];
dy2[a] *= dy2[a];
dz2[a] *= dz2[a];
}
for (int a=0; a<2; ++a) {
for (int b=0; b<2; ++b)
for (int c=0; c<2; ++c)
h.add(sqrt(dx2[a] + dy2[b] + dz2[c]));
}
}
Template::Template(QString path){
width = -2;
height = -2;
for (int i = 0; i < TEMPLATES_COUNT; i++){
QString file = path + QString::number(i) + ".png";
cv::Mat im = cv::imread(file.toStdString());
cvtColor(im, images[i], CV_RGB2GRAY);
if (width == -2){
width = images[i].cols;
}
else if (images[i].cols != width){
qDebug() << "Error : all templates must be the same size";
}
if (height == -2){
height = images[i].rows;
}
else if (images[i].rows != height){
qDebug() << "Error : all templates must be the same size";
}
std::vector<std::vector<cv::Point> > templateContours;
std::vector<cv::Vec4i> hierarchy;
findContours(images[i].clone(), templateContours, hierarchy, CV_RETR_TREE, CV_CHAIN_APPROX_SIMPLE, cv::Point(0, 0));
if (templateContours.size() == 0){
qDebug() << "Error, template doesn't have a contour";
}
else {
cv::Moments imageMoments = moments(templateContours[0], false);
massCenters[i] = cv::Point2f(imageMoments.m10/imageMoments.m00 , imageMoments.m01/imageMoments.m00);
}
cv::Mat firstHalf = cv::Mat(images[i].clone(), cv::Rect(0, 0, images[i].cols/2, images[i].rows));
cv::Mat secondHalf = cv::Mat(images[i].clone(), cv::Rect(images[i].cols/2, 0, images[i].cols/2, images[i].rows));
halfMassCenters[i][0] = getMassCenterFromImage(firstHalf);
halfMassCenters[i][1] = getMassCenterFromImage(secondHalf);
cv::Mat firstHalfHori = cv::Mat(images[i].clone(), cv::Rect(0, 0, images[i].cols, images[i].rows/2));
cv::Mat secondHalfHori = cv::Mat(images[i].clone(), cv::Rect(0, images[i].rows/2, images[i].cols, images[i].rows/2));
halfMassCentersHori[i][0] = getMassCenterFromImage(firstHalfHori);
halfMassCentersHori[i][1] = getMassCenterFromImage(secondHalfHori);
Histogram* hori = new Histogram(width);
Histogram* verti = new Histogram(height);
for (int x = 0; x < images[i].cols; x++){
for (int y = 0; y < images[i].rows; y++){
hori->add(x, images[i].at<uchar>(y, x)/255.0);
verti->add(y ,images[i].at<uchar>(y, x)/255.0);
}
}
histoHori[i] = hori;
histoVerti[i] = verti;
}
}