int main(int argc, char **argv) {
struct arguments args;
args.theta_file = "";
args.phi_file = "";
args.scale_file = "";
args.cube_name = "";
args.neuron_name = "";
args.output_name = "output";
args.min_width = 0;
args.renderScale = 1;
argp_parse(&argp, argc, argv, 0, 0, &args);
printf("The arguments are:\n cube_name: %s\n neuron_name: %s\n"
" output_name: %s\n theta_file: %s\n phi_file: %s\n scale_name: %s\n"
" min_width: %f\n renderScale = %f\n",
args.cube_name.c_str(), args.neuron_name.c_str(), args.output_name.c_str(),
args.theta_file.c_str(), args.phi_file.c_str(), args.scale_file.c_str(),
args.min_width, args.renderScale);
// exit(0);
Neuron* neuron = new Neuron(args.neuron_name);
Cube<uchar, ulong>* orig = new Cube<uchar,ulong>(args.cube_name);
Cube<uchar,ulong>* rendered = orig->create_blank_cube_uchar(args.output_name);
Cube<float, double>* theta = NULL;
Cube<float, double>* phi = NULL;
Cube<float, double>* scale = NULL;
if(args.theta_file != "")
theta = orig->create_blank_cube(args.theta_file);
if(args.phi_file != "")
phi = orig->create_blank_cube(args.phi_file);
if(args.scale_file != "")
scale = orig->create_blank_cube(args.scale_file);
neuron->renderInCube(rendered, theta, phi, scale, args.min_width, args.renderScale);
// rendered->put_all(255);
// neuron->renderSegmentInCube(neuron->dendrites[0],rendered, theta, phi, scale, args.min_width, args.renderScale);
}
