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spot_viewer.cc
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#include <gvars3/instances.h>
#include <gvars3/GUI_readline.h>
#include <gvars3/GStringUtil.h>
#include <cvd/timer.h>
#include <cvd/image_io.h>
#include <cvd/image_interpolate.h>
#include <cvd/glwindow.h>
#include <cvd/draw.h>
#include <cvd/convolution.h>
#include <cvd/morphology.h>
#include <cvd/vector_image_ref.h>
#include <cvd/gl_helpers.h>
#include <TooN/TooN.h>
#include <algorithm>
#include <cstdlib>
#include <cerrno>
#include <tag/printf.h>
#undef make_tuple
#include <tr1/tuple>
#include "cxxgplot.h"
#include "debug.h"
#include "storm_imagery.h"
using namespace CVD;
using namespace TooN;
using namespace GVars3;
using namespace std;
using namespace std::tr1;
map<string, map<string, string> > watch;
void next_show(void*, string , string )
{
GV3::get<int>("show")++;
}
void prev_show(void*, string , string )
{
GV3::get<int>("show")--;
}
void watch_var(void*, string comm, string d)
{
vector<string> vs = ChopAndUnquoteString(d);
string w_class="";
if(vs.size() != 1 && vs.size() != 2)
{
cerr << "Error: " << comm << " takes 1 or 2 arguments: " << comm << " gvar [class]\n";
return;
}
if(vs.size() == 2)
w_class = vs[1];
GV3::get<int>(w_class + ".force", 0, 1);
watch[w_class][vs[0]] = GV3::get_var(vs[0]);
watch[w_class][w_class + ".force"]="0";
}
vector<vector<Vector<4> > > spots, spots2;
void print_current(void*, string comm, string d)
{
vector<string> vs = ChopAndUnquoteString(d);
if(vs.size() != 0)
{
cerr << "Error: " << comm << " takes no arguments\n";
return;
}
int n = GV3::get<int>("show", spots.size()-1, 1);
n = max(0, min(n, (int)spots.size()-1));
for(unsigned int i=0; i < spots[n].size(); i++)
cout << spots[n][i] << endl;
}
bool watch_update(const string& w_class="")
{
bool changes=0;
//GV3::get<bool>("");
for(map<string, string>::iterator i=watch[w_class].begin(); i != watch[w_class].end(); i++)
{
string s = GV3::get_var(i->first);
if(s != watch[w_class][i->first])
{
changes=1;
watch[w_class][i->first] = s;
}
}
GV3::get<int>(w_class + ".force", 0, 1) = 0;
watch[w_class][w_class + ".force"]="0";
return changes;
}
Image<float> average_image(const vector<Image<float> >& ims)
{
assert_same_size(ims);
Image<float> r(ims[0].size(), 0);
for(unsigned int i=0; i < ims.size(); i++)
transform(r.begin(), r.end(), ims[i].begin(), r.begin(), plus<float>());
transform(r.begin(), r.end(), r.begin(), bind2nd(multiplies<float>(), 1./ims.size()));
return r;
}
Image<byte> scale_to_bytes(const Image<float>& im, const double mult=1)
{
float lo = *min_element(im.begin(), im.end());
float hi = *max_element(im.begin(), im.end());
Image<byte> out(im.size());
for(int r=0; r < out.size().y-0; r++)
for(int c=0; c < out.size().x-0; c++)
out[r][c] = (int)min(255., floor( mult* ( (im[r][c]-lo)*255/(hi-lo))));
return out;
}
void glDrawCross(const Vector<2>& p, float size=3.0)
{
glVertex(p + makeVector(0, size));
glVertex(p + makeVector(0, -size));
glVertex(p + makeVector( size, 0));
glVertex(p + makeVector(-size, 0));
}
double get_zoom(ImageRef imsize, ImageRef winsize, double scale)
{
ImageRef newsize = winsize;
ImageRef size=imsize;
float old_r = (float)imsize.x / imsize.y;
float new_r = (float)newsize.x / newsize.y;
double zoom;
if(new_r > old_r) //Then use the y axis
zoom = newsize.y / (float)size.y;
else
zoom = newsize.x / (float)size.x;
return zoom * pow(10, scale/10);;
}
double set_GL_zoom_size(ImageRef imsize, ImageRef winsize, double scale)
{
ImageRef newsize = winsize;
glViewport(0, 0, newsize.x, newsize.y);
glMatrixMode(GL_PROJECTION);
glLoadIdentity();
double zoom = get_zoom(imsize, winsize, scale);
glOrtho(-.5/zoom, (newsize.x-1.5)/zoom, (newsize.y-1.5)/zoom, -.5/zoom, -1 , 1);
glPixelZoom(zoom,-zoom);
glRasterPos2f(0, 0);
return zoom;
}
Rgba<byte> hot2(double d, double gutter)
{
d = max(0., min(d, 0.99999999));
if(d < gutter)
return Rgba<byte>(255, 0, 255, (int)floor(d*255 * (1./gutter)));
else if(d < 1./3.)
{
//d sits between gutter and 1/3
//Scale to 0--1
double s = (d - gutter)/(1./3 - gutter);
return Rgba<byte>(255, 0, (int)floor((1-s)*255), 255);
}
else if(d < 2./3.)
return Rgba<byte>(255, (int)floor((d-1./3.)*255*3), 0, 255);
else
return Rgba<byte>(255, 255, (int)floor((d-1./3.)*255*3), 255);
}
Rgba<byte> hot(double d, bool opaque)
{
d = max(0., min(d, 0.99999999));
if(d < 1./3.)
if(opaque)
return Rgba<byte>((int)floor(d * 255*3), 0, 0, 255);
else
return Rgba<byte>(255, 0, 0, (int)floor(d*255*3));
else if(d < 2./3.)
return Rgba<byte>(255, (int)floor((d-1./3.)*255*3), 0, 255);
else
return Rgba<byte>(255, 255, (int)floor((d-1./3.)*255*3), 255);
}
Rgba<byte> gray(double d)
{
d = max(0., min(d, 0.99999999));
int i = floor(d*255);
return Rgba<byte>(i,i,i,i);
}
Rgba<byte> green(double d)
{
d = max(0., min(d, 0.99999999));
int i = floor(d*255);
return Rgba<byte>(0,i,0,255);
}
Rgba<byte> magenta(double d)
{
d = max(0., min(d, 0.99999999));
int r = floor(d*255/1.5);
int g = floor(d*255/1.3);
int b = floor(d*255);
return Rgba<byte>(r,g,b,255);
}
Rgba<byte> lightblue(double d)
{
d = max(0., min(d, 0.99999999));
int i = floor(d*255);
return Rgba<byte>(i,0,i,255);
}
Rgba<byte> red(double d)
{
d = max(0., min(d, 0.99999999));
int i = floor(d*255);
return Rgba<byte>(i,0,0,255);
}
pair<Image<Rgba<byte> >, Image<float> > make_hot_map(ImageRef size, const vector<Vector<4> >& spots, bool use_brightness, bool use_max_intensity, double max_brightness, double sigma, double colorscale, double glow_power, int zoom)
{
Image<float> density(size*zoom);
density.fill(0);
for(unsigned int i=0; i < spots.size(); i++)
{
double alpha=1;
if(use_brightness)
{
double brightness;
if(use_max_intensity)
brightness = spots[i][0] / (spots[i][1]*sqrt(2*M_PI));
else
brightness = spots[i][0] / sqrt(2*M_PI);
alpha = min(1.0, brightness / max_brightness);
}
density[ir_rounded((spots[i].slice<2,2>() + Ones*.5)*zoom)] += alpha;
}
convolveGaussian(density, zoom * sigma);
double mul = colorscale/ *max_element(density.begin(), density.end());
Image<Rgba<byte> > out(density.size());
for(int r=0; r < out.size().y; r++)
for(int c=0; c < out.size().x; c++)
out[r][c] = hot(pow(density[r][c] * mul, glow_power), 0);
return make_pair(out, density);
}
//Turbo-bodge: ripped shamelessly from make_simulations.cc
vector<Vector<4> > some_simulated_spots(ImageRef size)
{
vector<Vector<4> > spot_parameters;
int num_spots = GV3::get<int>("simulations.spots", 0, -1);
double spot_max_brightness = GV3::get<double>("simulations.max_brightness", 0, -1);
double spot_fwhm = GV3::get<double>("simulations.fwhm", 0, -1);
double spot_sigma = spot_fwhm / ( 2 * sqrt(2 * log(2)));
double spot_brightness = spot_max_brightness * spot_sigma * sqrt(2*M_PI);
double spot_spacing = GV3::get<double>("simulations.spacing", 0, -1);
for(int s=0; s < num_spots; s++)
{
double xpos = size.x / 2.0 + (s - (num_spots-1)/2.0) * spot_spacing;
spot_parameters.push_back(makeVector(spot_brightness, spot_sigma, xpos, size.y/2.0));
}
return spot_parameters;
}
vector<pair<Vector<2>, Vector<2> > > get_normal_points(const vector<Vector<4> >& spots, vector<Vector<2> > linescan_coords, double normal_width)
{
vector<pair<Vector<2>, Vector<2> > > data;
if(linescan_coords.size() == 2)
{
Vector<2> line = linescan_coords[1] - linescan_coords[0];
Vector<2> line_vec = line / norm_sq(line);
Vector<2> norm_vec = unit(Matrix<2>(Data(0, 1, -1, 0)) * line);
double w = normal_width;
for(unsigned int i=0; i < spots.size(); i++)
{
Vector<2> d = spots[i].slice<2,2>() - linescan_coords[0];
if(d*line_vec > 0 && d* line_vec < 1 && std::abs(d*norm_vec) < w)
data.push_back(make_pair(spots[i].slice<2,2>(),makeVector(d*line_vec, d*norm_vec) ));
}
}
return data;
}
vector<Vector<4> > get_normal_points2(const vector<Vector<4> >& spots, vector<Vector<2> > linescan_coords, double normal_width)
{
vector<Vector<4> > data;
if(linescan_coords.size() == 2)
{
Vector<2> line = linescan_coords[1] - linescan_coords[0];
Vector<2> line_vec = line / norm_sq(line);
Vector<2> norm_vec = unit(Matrix<2>(Data(0, 1, -1, 0)) * line);
double w = normal_width;
for(unsigned int i=0; i < spots.size(); i++)
{
Vector<2> d = spots[i].slice<2,2>() - linescan_coords[0];
if(d*line_vec > 0 && d* line_vec < 1 && std::abs(d*norm_vec) < w)
data.push_back(spots[i]);
}
}
return data;
}
double scaling(const Vector<4>& spot, int use_brightness, int use_max_intensity, double max_brightness)
{
double alpha=1;
if(use_brightness)
{
double brightness;
if(use_max_intensity)
brightness = spot[0] / (spot[1]*sqrt(2*M_PI));
else
brightness = spot[0] / sqrt(2*M_PI);
alpha = min(1.0, brightness / max_brightness);
}
return alpha;
}
void do_linescan(const string& prefix, cplot::Plotter& linescan, const vector<Vector<4> >& spots, vector<Vector<2> > linescan_coords, vector<string>& text)
{
double max_brightness = GV3::get<double>(prefix + ".max_brightness", 1, 1);
int use_brightness = GV3::get<int>(prefix + ".use_brightness", 0, 1);
int use_max_intensity = GV3::get<int>(prefix + ".use_max_intensity", 0, 1);
double sig = GV3::get<float>(prefix + ".glow_sigma");
double xoff = GV3::get<float>(prefix + ".xoff");
double yoff = GV3::get<float>(prefix + ".yoff");
int npoints = GV3::get<int>("linescan.points", 1000, 1);
double pixel_size_in_nm = GV3::get<double>("pixel_size_in_nm");
linescan.newline("line title \" " + prefix + " linescan\"");
Vector<2> off = makeVector(xoff, yoff);
linescan_coords[0] -= off;
linescan_coords[1] -= off;
vector<Vector<4> > n_pts = get_normal_points2(spots, linescan_coords, sig * 4);
double maxval=-1e99;
int maxpos = -1;
vector< Vector<2> > scan;
for(int n=0; n < npoints; n++)
{
double p = n * 1.0 /(npoints-1);
Vector<2> pos = (linescan_coords[0] * (1-p) + p*linescan_coords[1]);
double sum=0;
for(unsigned int i=0; i < n_pts.size(); i++)
sum += exp(-(norm_sq(pos - n_pts[i].slice<2,2>()) / (2*sig*sig))) * scaling(n_pts[i], use_brightness, use_max_intensity, max_brightness);
sum /= sqrt(2*M_PI*sig*sig);
scan.push_back(makeVector(p * norm(linescan_coords[1] - linescan_coords[0])*pixel_size_in_nm, sum));
//linescan.addpt(scan.back());
if(scan.back()[1] > maxval)
{
maxval = scan.back()[1];
maxpos = n;
}
//if(save)
// fo << p * norm(linescan_coords[1] - linescan_coords[0]) << " " << sum << endl;
}
text.resize(npoints);
const bool nz = GV3::get<int>(prefix + ".linescan.normalize", 0, 1);
for(int n=0; n < npoints; n++)
{
Vector<2> p = scan[n];
if(nz)
p[1] /= maxval;
ostringstream os;
if(text[n] == "")
os << p[0];
os << " " << scan[n][1]/maxval;
text[n] += os.str();
linescan.addpt(p);
}
}
void dynamic_zoom(const ImageRef win_size, const vector<Vector<4> >& spots, const double scale, const Vector<2> offset, Image<float>& density, Image<Rgba<byte> >& hotmap, string prefix="")
{
//Oh! The humanity!
if(prefix != "")
prefix += ".";
double max_brightness = GV3::get<double>(prefix + "max_brightness", 1, 1);
int use_brightness = GV3::get<int>(prefix + "use_brightness", 0, 1);
int use_max_intensity = GV3::get<int>(prefix + "use_max_intensity", 0, 1);
//This one is really display related and doesn't need to vary with prefix
int extra_zoom = GV3::get<int>("dynamic_zoom.zoom", 4, 1);
density.resize(win_size * extra_zoom);
float xoff = GV3::get<float>(prefix + "xoff")+.5;
float yoff = GV3::get<float>(prefix + "yoff")+.5;
float glow_sigma = GV3::get<float>(prefix + "glow_sigma");
float glow_power = GV3::get<float>(prefix + "glow_power");
float glow_transparency = GV3::get<float>(prefix + "glow_transparency", 1, 1);
float gutter = GV3::get<float>(prefix + "glow.ohot.gutter", .1, 1);
string cmap = GV3::get<string>(prefix + "glow_map", "hot", 1);
//Find which pixes in the original image are viewable
//cout << "Top left:\n";
//cout << -offset << endl;
//cout << -offset + vec(win.size()) / scale << endl;
density.fill(0);
for(unsigned int i=0; i < spots.size(); i++)
{
double alpha= scaling(spots[i], use_brightness, use_max_intensity, max_brightness);
ImageRef pos = ir_rounded((spots[i].slice<2,2>() + makeVector(xoff, yoff) + offset)*scale);
if(density.in_image(pos))
density[pos] += alpha;
}
//This one is really display related and doesn't need to vary with prefix
double sigma = max(scale*extra_zoom*glow_sigma, GV3::get<double>("dynamic_zoom.min_sigma"));
convolveGaussian(density, sigma);
double mul;
if(GV3::get<int>(prefix + "dynamic_zoom.use_fixed_scale"))
mul = GV3::get<float>(prefix + "dynamic_zoom.fixed_scale");
else
mul = GV3::get<float>(prefix + "glow_scale")/ *max_element(density.begin(), density.end());
if(GV3::get<bool>(prefix + "dynamic_zoom.scale_by_number", 0, 1))
mul /= spots.size();
hotmap.resize(density.size());
Image<Rgba<byte> > out=hotmap;
double gp = glow_power;
if(cmap == "ohot")
for(int r=0; r < out.size().y; r++)
for(int c=0; c < out.size().x; c++)
{
//out[r][c] = Rgba<byte>(r%255, c%255, ((r+c)%2)*255, 128) ; //hot(pow(density[r][c] * mul, gp), 0);
out[r][c] = hot2(pow(density[r][c] * mul, gp), gutter);
out[r][c].alpha *= glow_transparency;
//out[r][c].alpha = min(out[r][c].alpha*1.0f, glow_transparency*255);
}
else if(cmap == "gray" || cmap == "grey")
for(int r=0; r < out.size().y; r++)
for(int c=0; c < out.size().x; c++)
{
out[r][c] = gray(pow(density[r][c] * mul, gp));
out[r][c].alpha *= glow_transparency;
}
else if(cmap == "green")
for(int r=0; r < out.size().y; r++)
for(int c=0; c < out.size().x; c++)
{
out[r][c] = green(pow(density[r][c] * mul, gp));
out[r][c].alpha *= glow_transparency;
}
else if(cmap == "red")
for(int r=0; r < out.size().y; r++)
for(int c=0; c < out.size().x; c++)
{
out[r][c] = red(pow(density[r][c] * mul, gp));
out[r][c].alpha *= glow_transparency;
}
else if(cmap == "magenta")
for(int r=0; r < out.size().y; r++)
for(int c=0; c < out.size().x; c++)
{
out[r][c] = magenta(pow(density[r][c] * mul, gp));
out[r][c].alpha *= glow_transparency;
}
else if(cmap == "lightblue")
for(int r=0; r < out.size().y; r++)
for(int c=0; c < out.size().x; c++)
{
out[r][c] = lightblue(pow(density[r][c] * mul, gp));
out[r][c].alpha *= glow_transparency;
}
else
for(int r=0; r < out.size().y; r++)
for(int c=0; c < out.size().x; c++)
{
//out[r][c] = Rgba<byte>(r%255, c%255, ((r+c)%2)*255, 128) ; //hot(pow(density[r][c] * mul, gp), 0);
out[r][c] = hot(pow(density[r][c] * mul, gp), 0);
out[r][c].alpha *= glow_transparency;
//out[r][c].alpha = min(out[r][c].alpha*1.0f, glow_transparency*255);
}
//Perform atrificial pixellization
int px = GV3::get<int>(prefix + "pixelate.size");
if(px > 1)
for(int r=0; r < out.size().y-px; r+= px)
for(int c=0; c < out.size().x-px; c+=px)
{
Rgba<int> s(0,0,0,0);
for(int rr=0; rr < px; rr++)
for(int cc=0; cc < px; cc++)
s += out[r+rr][c+cc];
s/=(px*px);
for(int rr=0; rr < px; rr++)
for(int cc=0; cc < px; cc++)
out[r+rr][c+cc] = s;
}
//Now draw a density scale
if(GV3::get<int>(prefix+"density_scale", 1))
{
int width=floor(GV3::get<double>(prefix + "density_scale.width", .7) * win_size.x + .5);
int height=floor(GV3::get<double>(prefix + "density_scale.height", .7) * win_size.y + .5);
int xs=floor(GV3::get<double>(prefix + "density_scale.x", .1) * win_size.x + .5);
int ys=floor(GV3::get<double>(prefix + "density_scale.y", .8) * win_size.y + .5);
xs = max(0, min(xs, out.size().x-1));
ys = max(0, min(ys, out.size().y-1));
width = max(0, min(width+xs, out.size().x-1)-xs);
height = max(0, min(height+ys, out.size().y-1)-ys);
double dmax = *max_element(density.begin(), density.end());
for(int x=0; x < width; x++)
{
float d = dmax * x/(width-1);
Rgba<byte> col;
if(cmap == "ohot")
col = hot2(pow(d * mul, gp), gutter);
else if(cmap == "gray" || cmap == "grey")
col = gray(pow(d * mul, gp));
else if(cmap == "green")
col = green(pow(d * mul, gp));
else if(cmap == "red")
col = red(pow(d * mul, gp));
else if(cmap == "lightblue")
col = lightblue(pow(d * mul, gp));
else if(cmap == "magenta")
col = magenta(pow(d * mul, gp));
else
col = hot(pow(d * mul, gp), 0);
col.red = (col.red*col.alpha)/255;
col.green = (col.green*col.alpha)/255;
col.blue = (col.blue*col.alpha)/255;
col.alpha=255;
for(int y=0; y < height; y++)
out[y+ys][x+xs] = col;
}
Vector<4> border = GV3::get<Vector<4> >(prefix+"density_scale.border.color", Zeros);
Rgba<byte> c(border[0], border[1], border[2], border[3]);
int bw = GV3::get<int>(prefix+"density_scale.border.width");
bw = min(bw, min(width, height));
for(int x=0; x < width; x++)
for(int b=0; b < bw; b++)
{
out[ys+b][xs+x] = c;
out[ys+height-b-1][xs+x] = c;
}
for(int y=0; y < height; y++)
for(int b=0; b < bw; b++)
{
out[ys+y][xs+b] = c;
out[ys+y][xs+width-1-b] = c;
}
}
}
Rgb<byte> composite(const Rgba<byte>& fg, const Rgb<byte>& bg)
{
return Rgb<byte>((bg.red * (255 - fg.alpha) + fg.red * fg.alpha)/255,
(bg.green * (255 - fg.alpha) + fg.green * fg.alpha)/255,
(bg.blue * (255 - fg.alpha) + fg.blue * fg.alpha)/255);
}
void dump_video(const ImageRef win_size, const vector<vector<Vector<4> > >& spots, const double scale, const Vector<2> offset, bool transparent, const Image<byte>& mean, double pixel_size, const vector<Image<byte> >& all_images)
{
int video_number = ++GV3::get<int>("video_number", -1, 0);
string stub = GV3::get<string>("video_stub");
string dstub = GV3::get<string>("dump.density_stub");
Image<float> density;
Image<Rgba<byte> > hotmap;
Image<Rgb<byte> > output;
int scalebar = GV3::get<int>("scalebar", 1, 1);
double scale_width = GV3::get<float>("scalebar.width", 6, 1);
Vector<2> scale_pos = GV3::get<Vector<2> >("scalebar.pos");
double scale_size = GV3::get<double>("scalebar.scale", 100, 1);
bool also_wf = GV3::get<int>("dump.separate_widefield", 0, 1);
bool use_mean = GV3::get<int>("use_mean", 1, 1);
bool save_density = GV3::get<int>("dump.save_density", 0, 1);
glDisable(GL_BLEND);
for(unsigned int i=0; i < spots.size(); i++)
{
dynamic_zoom(win_size, spots[i], scale, offset, density, hotmap);
SubImage<Rgb<byte> > hotmap2(0, ImageRef_zero, 0), wf_part(0, ImageRef_zero, 0);
if(also_wf)
{
output.resize(hotmap.size().dot_times(ImageRef(2,1)));
hotmap2 = output.sub_image(ImageRef(hotmap.size().x, 0), hotmap.size());
wf_part = output.sub_image(ImageRef(0, 0), hotmap.size());
}
else
{
output.resize(hotmap.size());
hotmap2 = output;
wf_part = output;
}
unsigned int img = min(max(0, (int)i), (int)(all_images.size()-1));
for(int r=0; r < hotmap.size().y; r++)
for(int c=0; c < hotmap.size().x; c++)
{
//.5 for the pixel offset, then .5 to round properly. Oh yeah
int xc = (int)floor(-offset[0] + c/scale);
int yc = (int)floor(-offset[1] + r/scale);
Rgb<byte> wf(0,0,0), bg(0,0,0);
if((transparent||also_wf) && mean.in_image(ImageRef(xc, yc)))
{
int val;
if(use_mean)
val = mean[yc][xc];
else
val = all_images[img][yc][xc];
wf.red = val;
wf.green = val;
wf.blue = val;
}
if(transparent)
bg = wf;
//hotmap2[r][c].red = (hotmap[r][c].red * (1+ 2*hotmap[r][c].alpha))/510;
//hotmap2[r][c].green = (hotmap[r][c].green * (1+ 2*hotmap[r][c].alpha))/510;
//hotmap2[r][c].blue = (hotmap[r][c].blue * (1+ 2*hotmap[r][c].alpha))/510;
hotmap2[r][c] = composite(hotmap[r][c], bg);
if(also_wf)
wf_part[r][c] = wf;
}
//Now draw the scale bar
if(scalebar)
{
int npix = (int)floor(scale_size *scale / pixel_size + .5);
ImageRef pos = ir_rounded(scale_pos.as_diagonal() * vec(win_size));
ImageRef tl = pos;
tl.y -= scale_width/2;
ImageRef sz = ImageRef(npix, scale_width);
if(hotmap2.in_image(tl) && hotmap2.in_image(tl + sz))
hotmap2.sub_image(tl, sz).fill(Rgb<byte>(255,255,255));
else
cerr << "Warning: scale bar outside image\n";
}
img_save(output, sPrintf(stub, video_number, i));
if(save_density)
img_save(density, sPrintf(dstub, video_number, i));
}
}
template<class C>
int make_image_list(const BasicImage<C>& mean)
{
GLuint draw_image = glGenLists(1);
vector<Vector<2> > linescan_coords;
glNewList(draw_image, GL_COMPILE);
glEnable(GL_TEXTURE_RECTANGLE_NV);
glTexEnvf(GL_TEXTURE_ENV, GL_TEXTURE_ENV_MODE, GL_REPLACE);
glTexParameterf( GL_TEXTURE_RECTANGLE_NV, GL_TEXTURE_MIN_FILTER, GL_NEAREST );
glTexParameterf( GL_TEXTURE_RECTANGLE_NV, GL_TEXTURE_MAG_FILTER, GL_NEAREST );
glPixelStorei(GL_UNPACK_ALIGNMENT,1);
glTexImage2D(mean, 0, GL_TEXTURE_RECTANGLE_NV);
glBegin(GL_QUADS);
glTexCoord2i(0, 0);
glVertex2i(0,0);
glTexCoord2i(mean.size().x, 0);
glVertex2i(mean.size().x,0);
glTexCoord2i(mean.size().x,mean.size().y);
glVertex2i(mean.size().x,mean.size().y);
glTexCoord2i(0, mean.size().y);
glVertex2i(0, mean.size().y);
glEnd ();
glDisable(GL_TEXTURE_RECTANGLE_NV);
glEndList();
return draw_image;
}
Image<Rgba<byte> > mask_to_image(const Image<bool>& mask)
{
Vector<4> v = GV3::get<Vector<4> >("mask.color");
Image<Rgba<byte> > ret(mask.size());
Rgba<byte> c(v[0], v[1], v[2], v[3]);
for(int y=0; y < ret.size().y; y++)
for(int x=0; x < ret.size().x; x++)
if(mask[y][x])
ret[y][x] = c;
else
ret[y][x] = Rgba<byte>(0,0,0,0);
return ret;
}
vector<vector<Vector<4> > > read_spots(string name, const SubImage<bool>& mask, int f = -1)
{
vector<vector<Vector<4> > > spots;
string sfn = GV3::get<string>(name, "", f);
if(sfn == "")
return spots;
ifstream sf;
sf.open(sfn.c_str());
int err = errno;
if(!sf.good())
{
cerr << "ERROR: failed to open " << sfn << ": " <<strerror(err) << endl;
exit(1);
}
//Read in the spots
for(int l=0;;l++)
{
string line;
getline(sf, line);
if(line == "")
break;
istringstream ln(line);
string dummy;
ln >> dummy;
if(dummy != "[")
{
cerr << "Bad line " << l << ". Expected \"[\" : " << line << endl;
break;
}
vector<Vector<4> > vv;
copy(istream_iterator<Vector<4> >(ln), istream_iterator<Vector<4> >(), back_inserter(vv));
if(mask.size().area())
{
vector<Vector<4> > vv2;
for(unsigned int i=0; i < vv.size(); i++)
{
ImageRef p = ir_rounded(vv[i].slice<2,2>());
if(mask.in_image(p) && mask[p])
vv2.push_back(vv[i]);
}
vv = vv2;
}
cout << "Line " << l << " has " << vv.size() << " spots\n";
spots.push_back(vv);
}
return spots;
}
void draw_a_dynamic_density_image(const BasicImage<Rgba<byte> >& hotmap, const Vector<2>& hm, const Vector<2>& offset)
{
glEnable(GL_BLEND);
glEnable(GL_TEXTURE_RECTANGLE_NV);
glTexEnvf(GL_TEXTURE_ENV, GL_TEXTURE_ENV_MODE, GL_REPLACE);
glTexParameterf( GL_TEXTURE_RECTANGLE_NV, GL_TEXTURE_MIN_FILTER, GL_NEAREST );
glTexParameterf( GL_TEXTURE_RECTANGLE_NV, GL_TEXTURE_MAG_FILTER, GL_NEAREST );
glPixelStorei(GL_UNPACK_ALIGNMENT,1);
glTexImage2D(hotmap, 0, GL_TEXTURE_RECTANGLE_NV);
glBegin(GL_QUADS);
glTexCoord2i(0, 0);
glVertex(-offset + DiagonalMatrix<2>(makeVector(0,0)) * hm);
glTexCoord2i(hotmap.size().x, 0);
glVertex(-offset + DiagonalMatrix<2>(makeVector(1,0)) * hm);
glTexCoord2i(hotmap.size().x,hotmap.size().y);
glVertex(-offset + DiagonalMatrix<2>(makeVector(1,1)) * hm);
glTexCoord2i(0, hotmap.size().y);
glVertex(-offset + DiagonalMatrix<2>(makeVector(0,1)) * hm);
glEnd ();
glDisable(GL_TEXTURE_RECTANGLE_NV);
glDisable(GL_BLEND);
}
class Macro
{
public:
Macro()
:fn("macro", "", 1)
{}
void process()
{
//Check ic the file is open
//If not, then attempt to open it.
if(!f.is_open())
{
if(*fn != "")
{
f.open(fn->c_str());
if(!f.is_open())
cerr << "Error: could not open file \"" << *fn << "\" : " << strerror(errno) << endl;
}
}
if(!f.is_open())
return;
for(;;)
{
string line;
getline(f, line);
if(!f.good())
{
f.close();
return;
}
else if(line == "BREAK")
return;
else if(line == "END")
{
f.close();
*fn="";
return;
}
else
GUI.ParseLine(line);
}
}
private:
ifstream f;
gvar3<string> fn;
};
int main(int argc, char** argv)
{
cplot::Plotter linescan;
GUI.RegisterCommand("watch", watch_var);
GUI.RegisterCommand("next", next_show);
GUI.RegisterCommand("prev", prev_show);
GUI.RegisterCommand("dump", print_current);
GUI.LoadFile("spot_viewer.cfg");
int lastarg = GUI.parseArguments(argc, argv);
if(lastarg >= argc)
{
cerr << "Specify the images to load\n";
exit(1);
}
Image<bool> mask;
if(GV3::get<string>("mask_spots", "", 1) != "")
{
mask = img_load(GV3::get<string>("mask_spots", "", 1));
Image<bool>mask2=morphology(mask, getDisc(GV3::get<float>("mask.dilate", 0, 1)), Morphology::Dilate<bool>());
mask = mask2;
}
spots = read_spots("spots", mask);
spots2 = read_spots("spots2", mask, 1);
//Load the raw data, and then load the spot parameters.
vector<string> files(argv + lastarg, argv + argc);
vector<Image<float> > ims = load_and_preprocess_images(files);
vector<Image<byte> > all_images;
for(unsigned int i=0; i < ims.size(); i++)
all_images.push_back(scale_to_bytes(ims[i]));
Image<byte> mean = scale_to_bytes(average_image(ims));
Image<float> av = average_image(ims);
cout << (int)*max_element(av.begin(), av.end()) << endl;
readline_in_current_thread line("> ");
GLWindow win(mean.size());
glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA);
glEnable(GL_LINE_SMOOTH);