//Return the mean of the values in a vector
double mean(VEC * in)
{
double sum = 0.0;
int i;
for(i = 0; i < in->dim; i++)
sum+=v_get_val(in, i);
return sum/(double)in->dim;
}
// Returns the sum of all of the elements in the specified vector
double sum_v(VEC *vector) {
if (vector == NULL) return 0.0;
int i;
double sum = 0.0;
for (i = 0; i < vector->dim; i++)
sum += v_get_val(vector, i);
return sum;
}
//Return the standard deviation of the values in a vector
double std_dev(VEC * in)
{
double m = mean(in), sum =0.0;
int i;
for(i = 0; i < in->dim; i++)
{
double temp = v_get_val(in, i) - m;
sum+=temp*temp;
}
return sqrt(sum/(double)in->dim);
}
// Main
int main(int argc, char ** argv) {
// Choose the best GPU in case there are multiple available
choose_GPU();
// Keep track of the start time of the program
long long program_start_time = get_time();
if (argc !=3){
fprintf(stderr, "usage: %s <input file> <number of frames to process>", argv[0]);
exit(1);
}
// Let the user specify the number of frames to process
int num_frames = atoi(argv[2]);
// Open video file
char *video_file_name = argv[1];
avi_t *cell_file = AVI_open_input_file(video_file_name, 1);
if (cell_file == NULL) {
AVI_print_error("Error with AVI_open_input_file");
return -1;
}
int i, j, *crow, *ccol, pair_counter = 0, x_result_len = 0, Iter = 20, ns = 4, k_count = 0, n;
MAT *cellx, *celly, *A;
double *GICOV_spots, *t, *G, *x_result, *y_result, *V, *QAX_CENTERS, *QAY_CENTERS;
double threshold = 1.8, radius = 10.0, delta = 3.0, dt = 0.01, b = 5.0;
// Extract a cropped version of the first frame from the video file
MAT *image_chopped = get_frame(cell_file, 0, 1, 0);
printf("Detecting cells in frame 0\n");
// Get gradient matrices in x and y directions
MAT *grad_x = gradient_x(image_chopped);
MAT *grad_y = gradient_y(image_chopped);
// Allocate for gicov_mem and strel
gicov_mem = (float*) malloc(sizeof(float) * grad_x->m * grad_y->n);
strel = (float*) malloc(sizeof(float) * strel_m * strel_n);
m_free(image_chopped);
int grad_m = grad_x->m;
int grad_n = grad_y->n;
#pragma acc data create(sin_angle,cos_angle,theta,tX,tY) \
create(gicov_mem[0:grad_x->m*grad_y->n])
{
// Precomputed constants on GPU
compute_constants();
// Get GICOV matrices corresponding to image gradients
long long GICOV_start_time = get_time();
MAT *gicov = GICOV(grad_x, grad_y);
long long GICOV_end_time = get_time();
// Dilate the GICOV matrices
long long dilate_start_time = get_time();
MAT *img_dilated = dilate(gicov);
long long dilate_end_time = get_time();
} /* end acc data */
// Find possible matches for cell centers based on GICOV and record the rows/columns in which they are found
pair_counter = 0;
crow = (int *) malloc(gicov->m * gicov->n * sizeof(int));
ccol = (int *) malloc(gicov->m * gicov->n * sizeof(int));
for(i = 0; i < gicov->m; i++) {
for(j = 0; j < gicov->n; j++) {
if(!double_eq(m_get_val(gicov,i,j), 0.0) && double_eq(m_get_val(img_dilated,i,j), m_get_val(gicov,i,j)))
{
crow[pair_counter]=i;
ccol[pair_counter]=j;
pair_counter++;
}
}
}
GICOV_spots = (double *) malloc(sizeof(double) * pair_counter);
for(i = 0; i < pair_counter; i++)
GICOV_spots[i] = sqrt(m_get_val(gicov, crow[i], ccol[i]));
G = (double *) calloc(pair_counter, sizeof(double));
x_result = (double *) calloc(pair_counter, sizeof(double));
y_result = (double *) calloc(pair_counter, sizeof(double));
x_result_len = 0;
for (i = 0; i < pair_counter; i++) {
if ((crow[i] > 29) && (crow[i] < BOTTOM - TOP + 39)) {
x_result[x_result_len] = ccol[i];
y_result[x_result_len] = crow[i] - 40;
G[x_result_len] = GICOV_spots[i];
x_result_len++;
}
}
// Make an array t which holds each "time step" for the possible cells
t = (double *) malloc(sizeof(double) * 36);
for (i = 0; i < 36; i++) {
t[i] = (double)i * 2.0 * PI / 36.0;
}
// Store cell boundaries (as simple circles) for all cells
cellx = m_get(x_result_len, 36);
celly = m_get(x_result_len, 36);
for(i = 0; i < x_result_len; i++) {
for(j = 0; j < 36; j++) {
m_set_val(cellx, i, j, x_result[i] + radius * cos(t[j]));
m_set_val(celly, i, j, y_result[i] + radius * sin(t[j]));
}
}
A = TMatrix(9,4);
V = (double *) malloc(sizeof(double) * pair_counter);
QAX_CENTERS = (double * )malloc(sizeof(double) * pair_counter);
QAY_CENTERS = (double *) malloc(sizeof(double) * pair_counter);
memset(V, 0, sizeof(double) * pair_counter);
memset(QAX_CENTERS, 0, sizeof(double) * pair_counter);
memset(QAY_CENTERS, 0, sizeof(double) * pair_counter);
// For all possible results, find the ones that are feasibly leukocytes and store their centers
k_count = 0;
for (n = 0; n < x_result_len; n++) {
if ((G[n] < -1 * threshold) || G[n] > threshold) {
MAT * x, *y;
VEC * x_row, * y_row;
x = m_get(1, 36);
y = m_get(1, 36);
x_row = v_get(36);
y_row = v_get(36);
// Get current values of possible cells from cellx/celly matrices
x_row = get_row(cellx, n, x_row);
y_row = get_row(celly, n, y_row);
uniformseg(x_row, y_row, x, y);
// Make sure that the possible leukocytes are not too close to the edge of the frame
if ((m_min(x) > b) && (m_min(y) > b) && (m_max(x) < cell_file->width - b) && (m_max(y) < cell_file->height - b)) {
MAT * Cx, * Cy, *Cy_temp, * Ix1, * Iy1;
VEC *Xs, *Ys, *W, *Nx, *Ny, *X, *Y;
Cx = m_get(1, 36);
Cy = m_get(1, 36);
Cx = mmtr_mlt(A, x, Cx);
Cy = mmtr_mlt(A, y, Cy);
Cy_temp = m_get(Cy->m, Cy->n);
for (i = 0; i < 9; i++)
m_set_val(Cy, i, 0, m_get_val(Cy, i, 0) + 40.0);
// Iteratively refine the snake/spline
for (i = 0; i < Iter; i++) {
int typeofcell;
if(G[n] > 0.0) typeofcell = 0;
else typeofcell = 1;
splineenergyform01(Cx, Cy, grad_x, grad_y, ns, delta, 2.0 * dt, typeofcell);
}
X = getsampling(Cx, ns);
for (i = 0; i < Cy->m; i++)
m_set_val(Cy_temp, i, 0, m_get_val(Cy, i, 0) - 40.0);
Y = getsampling(Cy_temp, ns);
Ix1 = linear_interp2(grad_x, X, Y);
Iy1 = linear_interp2(grad_x, X, Y);
Xs = getfdriv(Cx, ns);
Ys = getfdriv(Cy, ns);
Nx = v_get(Ys->dim);
for (i = 0; i < Ys->dim; i++)
v_set_val(Nx, i, v_get_val(Ys, i) / sqrt(v_get_val(Xs, i)*v_get_val(Xs, i) + v_get_val(Ys, i)*v_get_val(Ys, i)));
Ny = v_get(Xs->dim);
for (i = 0; i < Xs->dim; i++)
v_set_val(Ny, i, -1.0 * v_get_val(Xs, i) / sqrt(v_get_val(Xs, i)*v_get_val(Xs, i) + v_get_val(Ys, i)*v_get_val(Ys, i)));
W = v_get(Nx->dim);
for (i = 0; i < Nx->dim; i++)
v_set_val(W, i, m_get_val(Ix1, 0, i) * v_get_val(Nx, i) + m_get_val(Iy1, 0, i) * v_get_val(Ny, i));
V[n] = mean(W) / std_dev(W);
// Find the cell centers by computing the means of X and Y values for all snaxels of the spline contour
QAX_CENTERS[k_count] = mean(X);
QAY_CENTERS[k_count] = mean(Y) + TOP;
k_count++;
// Free memory
v_free(W);
v_free(Ny);
v_free(Nx);
v_free(Ys);
v_free(Xs);
m_free(Iy1);
m_free(Ix1);
v_free(Y);
v_free(X);
m_free(Cy_temp);
m_free(Cy);
m_free(Cx);
}
// Free memory
v_free(y_row);
v_free(x_row);
m_free(y);
m_free(x);
}
}
// Free memory
free(gicov_mem);
free(strel);
free(V);
free(ccol);
free(crow);
free(GICOV_spots);
free(t);
free(G);
free(x_result);
free(y_result);
m_free(A);
m_free(celly);
m_free(cellx);
m_free(img_dilated);
m_free(gicov);
m_free(grad_y);
m_free(grad_x);
// Report the total number of cells detected
printf("Cells detected: %d\n\n", k_count);
// Report the breakdown of the detection runtime
printf("Detection runtime\n");
printf("-----------------\n");
printf("GICOV computation: %.5f seconds\n", ((float) (GICOV_end_time - GICOV_start_time)) / (1000*1000));
printf(" GICOV dilation: %.5f seconds\n", ((float) (dilate_end_time - dilate_start_time)) / (1000*1000));
printf(" Total: %.5f seconds\n", ((float) (get_time() - program_start_time)) / (1000*1000));
// Now that the cells have been detected in the first frame,
// track the ellipses through subsequent frames
if (num_frames > 1) printf("\nTracking cells across %d frames\n", num_frames);
else printf("\nTracking cells across 1 frame\n");
long long tracking_start_time = get_time();
int num_snaxels = 20;
ellipsetrack(cell_file, QAX_CENTERS, QAY_CENTERS, k_count, radius, num_snaxels, num_frames);
printf(" Total: %.5f seconds\n", ((float) (get_time() - tracking_start_time)) / (float) (1000*1000*num_frames));
// Report total program execution time
printf("\nTotal application run time: %.5f seconds\n", ((float) (get_time() - program_start_time)) / (1000*1000));
return 0;
}
void ellipseevolve(MAT *f, double *xc0, double *yc0, double *r0, double *t, int Np, double Er, double Ey) {
/*
% ELLIPSEEVOLVE evolves a parametric snake according
% to some energy constraints.
%
% INPUTS:
% f............potential surface
% xc0,yc0......initial center position
% r0,t.........initial radii & angle vectors (with Np elements each)
% Np...........number of snaxel points per snake
% Er...........expected radius
% Ey...........expected y position
%
% OUTPUTS
% xc0,yc0.......final center position
% r0...........final radii
%
% Matlab code written by: DREW GILLIAM (based on work by GANG DONG /
% NILANJAN RAY)
% Ported to C by: MICHAEL BOYER
*/
// Constants
double deltax = 0.2;
double deltay = 0.2;
double deltar = 0.2;
double converge = 0.1;
double lambdaedge = 1;
double lambdasize = 0.2;
double lambdapath = 0.05;
int iterations = 1000; // maximum number of iterations
int i, j;
// Initialize variables
double xc = *xc0;
double yc = *yc0;
double *r = (double *) malloc(sizeof(double) * Np);
for (i = 0; i < Np; i++) r[i] = r0[i];
// Compute the x- and y-gradients of the MGVF matrix
MAT *fx = gradient_x(f);
MAT *fy = gradient_y(f);
// Normalize the gradients
int fh = f->m, fw = f->n;
for (i = 0; i < fh; i++) {
for (j = 0; j < fw; j++) {
double temp_x = m_get_val(fx, i, j);
double temp_y = m_get_val(fy, i, j);
double fmag = sqrt((temp_x * temp_x) + (temp_y * temp_y));
m_set_val(fx, i, j, temp_x / fmag);
m_set_val(fy, i, j, temp_y / fmag);
}
}
double *r_old = (double *) malloc(sizeof(double) * Np);
VEC *x = v_get(Np);
VEC *y = v_get(Np);
// Evolve the snake
int iter = 0;
double snakediff = 1.0;
while (iter < iterations && snakediff > converge) {
// Save the values from the previous iteration
double xc_old = xc, yc_old = yc;
for (i = 0; i < Np; i++) {
r_old[i] = r[i];
}
// Compute the locations of the snaxels
for (i = 0; i < Np; i++) {
v_set_val(x, i, xc + r[i] * cos(t[i]));
v_set_val(y, i, yc + r[i] * sin(t[i]));
}
// See if any of the points in the snake are off the edge of the image
double min_x = v_get_val(x, 0), max_x = v_get_val(x, 0);
double min_y = v_get_val(y, 0), max_y = v_get_val(y, 0);
for (i = 1; i < Np; i++) {
double x_i = v_get_val(x, i);
if (x_i < min_x) min_x = x_i;
else if (x_i > max_x) max_x = x_i;
double y_i = v_get_val(y, i);
if (y_i < min_y) min_y = y_i;
else if (y_i > max_y) max_y = y_i;
}
if (min_x < 0.0 || max_x > (double) fw - 1.0 || min_y < 0 || max_y > (double) fh - 1.0) break;
// Compute the length of the snake
double L = 0.0;
for (i = 0; i < Np - 1; i++) {
double diff_x = v_get_val(x, i + 1) - v_get_val(x, i);
double diff_y = v_get_val(y, i + 1) - v_get_val(y, i);
L += sqrt((diff_x * diff_x) + (diff_y * diff_y));
}
double diff_x = v_get_val(x, 0) - v_get_val(x, Np - 1);
double diff_y = v_get_val(y, 0) - v_get_val(y, Np - 1);
L += sqrt((diff_x * diff_x) + (diff_y * diff_y));
// Compute the potential surface at each snaxel
MAT *vf = linear_interp2(f, x, y);
MAT *vfx = linear_interp2(fx, x, y);
MAT *vfy = linear_interp2(fy, x, y);
// Compute the average potential surface around the snake
double vfmean = sum_m(vf ) / L;
double vfxmean = sum_m(vfx) / L;
double vfymean = sum_m(vfy) / L;
// Compute the radial potential surface
int m = vf->m, n = vf->n;
MAT *vfr = m_get(m, n);
for (i = 0; i < n; i++) {
double vf_val = m_get_val(vf, 0, i);
double vfx_val = m_get_val(vfx, 0, i);
double vfy_val = m_get_val(vfy, 0, i);
double x_val = v_get_val(x, i);
double y_val = v_get_val(y, i);
double new_val = (vf_val + vfx_val * (x_val - xc) + vfy_val * (y_val - yc) - vfmean) / L;
m_set_val(vfr, 0, i, new_val);
}
// Update the snake center and snaxels
xc = xc + (deltax * lambdaedge * vfxmean);
yc = (yc + (deltay * lambdaedge * vfymean) + (deltay * lambdapath * Ey)) / (1.0 + deltay * lambdapath);
double r_diff = 0.0;
for (i = 0; i < Np; i++) {
r[i] = (r[i] + (deltar * lambdaedge * m_get_val(vfr, 0, i)) + (deltar * lambdasize * Er)) /
(1.0 + deltar * lambdasize);
r_diff += fabs(r[i] - r_old[i]);
}
// Test for convergence
snakediff = fabs(xc - xc_old) + fabs(yc - yc_old) + r_diff;
// Free temporary matrices
m_free(vf);
m_free(vfx);
m_free(vfy);
m_free(vfr);
iter++;
}
// Set the return values
*xc0 = xc;
*yc0 = yc;
for (i = 0; i < Np; i++)
r0[i] = r[i];
// Free memory
free(r);
free(r_old);
v_free( x);
v_free( y);
m_free(fx);
m_free(fy);
}