/* MapPreviewCanvas::showMap
* Adjusts zoom and offset to show the whole map
*******************************************************************/
void MapPreviewCanvas::showMap()
{
// Find extents of map
mep_vertex_t m_min(999999.0, 999999.0);
mep_vertex_t m_max(-999999.0, -999999.0);
for (unsigned a = 0; a < verts.size(); a++)
{
if (verts[a].x < m_min.x)
m_min.x = verts[a].x;
if (verts[a].x > m_max.x)
m_max.x = verts[a].x;
if (verts[a].y < m_min.y)
m_min.y = verts[a].y;
if (verts[a].y > m_max.y)
m_max.y = verts[a].y;
}
// Offset to center of map
double width = m_max.x - m_min.x;
double height = m_max.y - m_min.y;
offset_x = m_min.x + (width * 0.5);
offset_y = m_min.y + (height * 0.5);
// Zoom to fit whole map
double x_scale = ((double)GetClientSize().x) / width;
double y_scale = ((double)GetClientSize().y) / height;
zoom = MIN(x_scale, y_scale);
zoom *= 0.95;
}
// -----------------------------------------------------------------------------
// Adjusts zoom and offset to show the whole map
// -----------------------------------------------------------------------------
void MapPreviewCanvas::showMap()
{
// Find extents of map
Vertex m_min(999999.0, 999999.0);
Vertex m_max(-999999.0, -999999.0);
for (auto& vert : verts_)
{
if (vert.x < m_min.x)
m_min.x = vert.x;
if (vert.x > m_max.x)
m_max.x = vert.x;
if (vert.y < m_min.y)
m_min.y = vert.y;
if (vert.y > m_max.y)
m_max.y = vert.y;
}
// Offset to center of map
double width = m_max.x - m_min.x;
double height = m_max.y - m_min.y;
offset_ = { m_min.x + (width * 0.5), m_min.y + (height * 0.5) };
// Zoom to fit whole map
double x_scale = ((double)GetClientSize().x) / width;
double y_scale = ((double)GetClientSize().y) / height;
zoom_ = std::min<double>(x_scale, y_scale);
zoom_ *= 0.95;
}
CDataContainer CIntTypeInfo::serialize() const
{
CDataContainer serializedData;
if (m_min.isDefined())
serializedData.set("min", m_min());
if (m_max.isDefined())
serializedData.set("max", m_max());
if (m_step.isDefined())
serializedData.set("step", m_step());
return serializedData;
}
//! Get stabilized magnetic field.
//! @param[in] msg magnetic field message.
void
updateField(const IMC::MagneticField& msg)
{
// Insert magnetic field into row matrix.
Math::Matrix mf(1,3);
mf(0) = msg.x;
mf(1) = msg.y;
mf(2) = msg.z;
// Get stabilized magnetic field.
Math::Matrix mf_stab = mf * transpose(m_dcm.toDCM());
// Store maximum and minimum values.
for (unsigned i = 0; i < 3; i++)
{
if (mf_stab(i) > m_max(i))
m_max(i) = mf_stab(i);
if (mf_stab(i) < m_min(i))
m_min(i) = mf_stab(i);
}
}
/*
現在の Depth, Field... を評価する。
*/
static uint Real_GetEval(void) // ret: この局面の評価, 0 は返さない。
{
uint evals[FIELD_W_MAX];
uint ret;
uint index;
if(MaxDepth <= Depth) // ? 探索の上限に達した。-> これ以上先の手は読まない。
return GetCurrEval();
// 現局面で決着 -> これ以上先の手は読まない。
{
uint winner = GetWinner();
if(winner == 1)
return 400000000 + 100 - Depth; // 早い勝利を高く評価
if(winner == 2)
return 1;
}
GetNextEvals(evals);
for(index = 0; index < Field_W; index++)
if(evals[index])
break;
if(index == Field_W) // 次の手が無い -> 引き分け
{
ret = 300000000;
}
else if(Depth % 2) // 相手の手番 -> (自分にとって)最悪手を選ぶ
{
ret = UINTMAX;
for(index = 0; index < Field_W; index++)
if(evals[index])
ret = m_min(ret, evals[index]);
}
else // 自分の手番 -> 最善手を選ぶ
{
ret = 0;
for(index = 0; index < Field_W; index++)
if(evals[index])
ret = m_max(ret, evals[index]);
}
if(ret / 100000000 == 2) // ? 未決着コース
if(IsTaboo())
ret -= 100000000;
return ret;
}
Solution VDSpiral (SpiralParams& sp) {
GradientParams gp;
Matrix<double>& fov = sp.fov;
Matrix<double>& rad = sp.rad;
double k_max, fov_max, dr;
Matrix<double> r, theta;
long n = 0;
assert (numel(rad) >= 2);
assert (isvec(rad) == isvec(fov));
assert (numel(rad) == numel(fov));
k_max = 5.0 / sp.res;
fov_max = m_max(fov);
dr = sp.shots / (fov_max);
n = size(fov,1)*100;
r = linspace<double> (0.0, k_max, n);
Matrix<double> x = k_max*rad;
fov = interp1 (x, fov, r, INTERP::LINEAR);
dr = sp.shots / (1500.0 * fov_max);
n = ceil (k_max/dr);
x = r;
r = linspace<double> (0.0, k_max, n);
fov = interp1 (x, fov, r, INTERP::AKIMA);
theta = cumsum ((2 * PI * dr / sp.shots) * fov);
gp.k = Matrix<double> (numel(r), 3);
for (size_t i = 0; i < numel(r); i++) {
gp.k(i,0) = r[i] * cos (theta[i]);
gp.k(i,1) = r[i] * sin (theta[i]);
}
gp.mgr = sp.mgr;
gp.msr = sp.msr;
gp.dt = sp.dt;
gp.gunits = sp.gunits;
gp.lunits = sp.lunits;
Solution s = ComputeGradient (gp);
return s;
}
/* VTTY thread */
static void *vtty_thread_main(void *arg)
{
vtty_t *vtty;
struct timeval tv;
int fd_max,fd_tcp,res;
fd_set rfds;
int i;
for(;;) {
VTTY_LIST_LOCK();
/* Build the FD set */
FD_ZERO(&rfds);
fd_max = -1;
for(vtty=vtty_list;vtty;vtty=vtty->next) {
switch(vtty->type) {
case VTTY_TYPE_TCP:
for(i=0;i<vtty->fd_count;i++)
if (vtty->fd_array[i] != -1) {
FD_SET(vtty->fd_array[i],&rfds);
if (vtty->fd_array[i] > fd_max)
fd_max = vtty->fd_array[i];
}
fd_tcp = fd_pool_set_fds(&vtty->fd_pool,&rfds);
fd_max = m_max(fd_tcp,fd_max);
break;
default:
if (vtty->fd_array[0] != -1) {
FD_SET(vtty->fd_array[0],&rfds);
fd_max = m_max(vtty->fd_array[0],fd_max);
}
}
}
VTTY_LIST_UNLOCK();
/* Wait for incoming data */
tv.tv_sec = 0;
tv.tv_usec = 50 * 1000; /* 50 ms */
res = select(fd_max+1,&rfds,NULL,NULL,&tv);
if (res == -1) {
if (errno != EINTR) {
perror("vtty_thread: select");
}
continue;
}
/* Examine active FDs and call user handlers */
VTTY_LIST_LOCK();
for(vtty=vtty_list;vtty;vtty=vtty->next) {
switch(vtty->type) {
case VTTY_TYPE_TCP:
/* check incoming connection */
for(i=0;i<vtty->fd_count;i++) {
if (vtty->fd_array[i] == -1)
continue;
if (!FD_ISSET(vtty->fd_array[i],&rfds))
continue;
vtty_tcp_conn_accept(vtty, i);
}
/* check established connection */
fd_pool_check_input(&vtty->fd_pool,&rfds,vtty_tcp_input,vtty);
break;
/* Term, Serial */
default:
if (vtty->fd_array[0] != -1 && FD_ISSET(vtty->fd_array[0],&rfds)) {
vtty_read_and_store(vtty,&vtty->fd_array[0]);
vtty->input_pending = TRUE;
}
}
if (vtty->input_pending) {
if (vtty->read_notifier != NULL)
vtty->read_notifier(vtty);
vtty->input_pending = FALSE;
}
/* Flush any pending output */
if (!vtty->managed_flush)
vtty_flush(vtty);
}
VTTY_LIST_UNLOCK();
}
return NULL;
}
// 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;
}
/* MapPreviewCanvas::createImage
* Draws the map in an image
* TODO: Factorize code with normal draw() and showMap() functions.
* TODO: Find a way to generate an arbitrary-sized image through
* tiled rendering.
*******************************************************************/
void MapPreviewCanvas::createImage(ArchiveEntry& ae, int width, int height)
{
// Find extents of map
mep_vertex_t m_min(999999.0, 999999.0);
mep_vertex_t m_max(-999999.0, -999999.0);
for (unsigned a = 0; a < verts.size(); a++)
{
if (verts[a].x < m_min.x)
m_min.x = verts[a].x;
if (verts[a].x > m_max.x)
m_max.x = verts[a].x;
if (verts[a].y < m_min.y)
m_min.y = verts[a].y;
if (verts[a].y > m_max.y)
m_max.y = verts[a].y;
}
double mapwidth = m_max.x - m_min.x;
double mapheight = m_max.y - m_min.y;
if (width == 0) width = -5;
if (height == 0) height = -5;
if (width < 0)
width = mapwidth / abs(width);
if (height < 0)
height = mapheight / abs(height);
// Setup colours
rgba_t col_save_background = ColourConfiguration::getColour("map_image_background");
rgba_t col_save_line_1s = ColourConfiguration::getColour("map_image_line_1s");
rgba_t col_save_line_2s = ColourConfiguration::getColour("map_image_line_2s");
rgba_t col_save_line_special = ColourConfiguration::getColour("map_image_line_special");
rgba_t col_save_line_macro = ColourConfiguration::getColour("map_image_line_macro");
// Setup OpenGL rigmarole
GLuint texID, fboID;
if (GLEW_ARB_framebuffer_object)
{
glGenTextures(1, &texID);
glBindTexture(GL_TEXTURE_2D, texID);
// We don't use mipmaps, but OpenGL will refuse to attach
// the texture to the framebuffer if they are not present
glTexParameteri(GL_TEXTURE_2D, GL_GENERATE_MIPMAP, GL_TRUE);
glTexImage2D(GL_TEXTURE_2D, 0, GL_RGBA8, width, height, 0, GL_RGBA, GL_UNSIGNED_BYTE, 0);
glBindTexture(GL_TEXTURE_2D, 0);
glGenFramebuffersEXT(1, &fboID);
glBindFramebufferEXT(GL_FRAMEBUFFER_EXT, fboID);
glFramebufferTexture2DEXT(GL_FRAMEBUFFER_EXT, GL_COLOR_ATTACHMENT0_EXT, GL_TEXTURE_2D, texID, 0);
GLenum status = glCheckFramebufferStatusEXT(GL_FRAMEBUFFER_EXT);
}
glViewport(0, 0, width, height);
// Setup the screen projection
glMatrixMode(GL_PROJECTION);
glLoadIdentity();
glOrtho(0, width, 0, height, -1, 1);
glMatrixMode(GL_MODELVIEW);
glLoadIdentity();
// Clear
glClearColor(((double)col_save_background.r)/255.f, ((double)col_save_background.g)/255.f,
((double)col_save_background.b)/255.f, ((double)col_save_background.a)/255.f);
glClear(GL_COLOR_BUFFER_BIT|GL_DEPTH_BUFFER_BIT);
// Translate to inside of pixel (otherwise inaccuracies can occur on certain gl implementations)
if (OpenGL::accuracyTweak())
glTranslatef(0.375f, 0.375f, 0);
// Zoom/offset to show full map
// Offset to center of map
offset_x = m_min.x + (mapwidth * 0.5);
offset_y = m_min.y + (mapheight * 0.5);
// Zoom to fit whole map
double x_scale = ((double)width) / mapwidth;
double y_scale = ((double)height) / mapheight;
zoom = MIN(x_scale, y_scale);
zoom *= 0.95;
// Translate to middle of canvas
glTranslated(width>>1, height>>1, 0);
// Zoom
glScaled(zoom, zoom, 1);
// Translate to offset
glTranslated(-offset_x, -offset_y, 0);
// Setup drawing
glDisable(GL_TEXTURE_2D);
glColor4f(1.0f, 1.0f, 1.0f, 1.0f);
glLineWidth(map_image_thickness);
glEnable(GL_LINE_SMOOTH);
// Draw lines
for (unsigned a = 0; a < lines.size(); a++)
{
mep_line_t line = lines[a];
// Check ends
if (line.v1 >= verts.size() || line.v2 >= verts.size())
continue;
// Get vertices
mep_vertex_t v1 = verts[lines[a].v1];
mep_vertex_t v2 = verts[lines[a].v2];
// Set colour
if (line.special)
OpenGL::setColour(col_save_line_special);
else if (line.macro)
OpenGL::setColour(col_save_line_macro);
else if (line.twosided)
OpenGL::setColour(col_save_line_2s);
else
OpenGL::setColour(col_save_line_1s);
// Draw line
glBegin(GL_LINES);
glVertex2d(v1.x, v1.y);
glVertex2d(v2.x, v2.y);
glEnd();
}
glLineWidth(1.0f);
glDisable(GL_LINE_SMOOTH);
uint8_t* ImageBuffer = new uint8_t[width * height * 4];
glReadPixels(0, 0, width, height, GL_RGBA, GL_UNSIGNED_BYTE, ImageBuffer);
if (GLEW_ARB_framebuffer_object)
{
glBindFramebuffer(GL_FRAMEBUFFER, 0);
glDeleteTextures( 1, &texID );
glDeleteFramebuffersEXT( 1, &fboID );
}
SImage img;
img.setImageData(ImageBuffer, width, height, RGBA);
img.mirror(true);
MemChunk mc;
SIFormat::getFormat("png")->saveImage(img, mc);
ae.importMemChunk(mc);
}