double
vpHomography::computeRotation(unsigned int nbpoint,
vpPoint *c1P,
vpPoint *c2P,
vpHomogeneousMatrix &c2Mc1,
int userobust
)
{
vpColVector e(2) ;
double r_1 = -1 ;
vpColVector p2(3) ;
vpColVector p1(3) ;
vpColVector Hp2(3) ;
vpColVector Hp1(3) ;
vpMatrix H2(2,3) ;
vpColVector e2(2) ;
vpMatrix H1(2,3) ;
vpColVector e1(2) ;
int only_1 = 0 ;
int only_2 = 0 ;
int iter = 0 ;
unsigned int n=0 ;
for (unsigned int i=0 ; i < nbpoint ; i++) {
// if ((c2P[i].get_x() !=-1) && (c1P[i].get_x() !=-1))
if ( (std::fabs(c2P[i].get_x() + 1) > std::fabs(vpMath::maximum(c2P[i].get_x(), 1.)))
&&
(std::fabs(c1P[i].get_x() + 1) > std::fabs(vpMath::maximum(c1P[i].get_x(), 1.))) )
{
n++ ;
}
}
if ((only_1==1) || (only_2==1)) ; else n *=2 ;
vpRobust robust(n);
vpColVector res(n) ;
vpColVector w(n) ;
w =1 ;
robust.setThreshold(0.0000) ;
vpMatrix W(2*n,2*n) ;
W = 0 ;
vpMatrix c2Rc1(3,3) ;
double r =0 ;
while (vpMath::equal(r_1,r,threshold_rotation) == false )
{
r_1 =r ;
// compute current position
//Change frame (current)
for (unsigned int i=0 ; i < 3 ; i++)
for (unsigned int j=0 ; j < 3 ; j++)
c2Rc1[i][j] = c2Mc1[i][j] ;
vpMatrix L(2,3), Lp ;
int k =0 ;
for (unsigned int i=0 ; i < nbpoint ; i++) {
//if ((c2P[i].get_x() !=-1) && (c1P[i].get_x() !=-1))
if ( (std::fabs(c2P[i].get_x() + 1) > std::fabs(vpMath::maximum(c2P[i].get_x(), 1.)))
&&
(std::fabs(c1P[i].get_x() + 1) > std::fabs(vpMath::maximum(c1P[i].get_x(), 1.))) )
{
p2[0] = c2P[i].get_x() ;
p2[1] = c2P[i].get_y() ;
p2[2] = 1.0 ;
p1[0] = c1P[i].get_x() ;
p1[1] = c1P[i].get_y() ;
p1[2] = 1.0 ;
Hp2 = c2Rc1.t()*p2 ; // p2 = Hp1
Hp1 = c2Rc1*p1 ; // p1 = Hp2
Hp2 /= Hp2[2] ; // normalisation
Hp1 /= Hp1[2] ;
// set up the interaction matrix
double x = Hp2[0] ;
double y = Hp2[1] ;
H2[0][0] = x*y ; H2[0][1] = -(1+x*x) ; H2[0][2] = y ;
H2[1][0] = 1+y*y ; H2[1][1] = -x*y ; H2[1][2] = -x ;
H2 *=-1 ;
H2 = H2*c2Rc1.t() ;
// Set up the error vector
e2[0] = Hp2[0] - c1P[i].get_x() ;
e2[1] = Hp2[1] - c1P[i].get_y() ;
// set up the interaction matrix
x = Hp1[0] ;
y = Hp1[1] ;
H1[0][0] = x*y ; H1[0][1] = -(1+x*x) ; H1[0][2] = y ;
H1[1][0] = 1+y*y ; H1[1][1] = -x*y ; H1[1][2] = -x ;
// Set up the error vector
e1[0] = Hp1[0] - c2P[i].get_x() ;
e1[1] = Hp1[1] - c2P[i].get_y() ;
if (only_2==1)
{
if (k == 0) { L = H2 ; e = e2 ; }
else
{
L = vpMatrix::stackMatrices(L,H2) ;
e = vpMatrix::stackMatrices(e,e2) ;
}
}
else
if (only_1==1)
{
if (k == 0) { L = H1 ; e= e1 ; }
else
{
L = vpMatrix::stackMatrices(L,H1) ;
e = vpMatrix::stackMatrices(e,e1) ;
}
}
else
{
if (k == 0) {L = H2 ; e = e2 ; }
else
{
L = vpMatrix::stackMatrices(L,H2) ;
e = vpMatrix::stackMatrices(e,e2) ;
}
L = vpMatrix::stackMatrices(L,H1) ;
e = vpMatrix::stackMatrices(e,e1) ;
}
k++ ;
}
}
if (userobust)
{
robust.setIteration(0);
for (unsigned int k=0 ; k < n ; k++)
{
res[k] = vpMath::sqr(e[2*k]) + vpMath::sqr(e[2*k+1]) ;
}
robust.MEstimator(vpRobust::TUKEY, res, w);
// compute the pseudo inverse of the interaction matrix
for (unsigned int k=0 ; k < n ; k++)
{
W[2*k][2*k] = w[k] ;
W[2*k+1][2*k+1] = w[k] ;
}
}
else
{
for (unsigned int k=0 ; k < 2*n ; k++) W[k][k] = 1 ;
}
// CreateDiagonalMatrix(w, W) ;
(L).pseudoInverse(Lp, 1e-6) ;
// Compute the camera velocity
vpColVector c2Rc1, v(6) ;
c2Rc1 = -2*Lp*W*e ;
for (unsigned int i=0 ; i < 3 ; i++) v[i+3] = c2Rc1[i] ;
// only for simulation
updatePoseRotation(c2Rc1, c2Mc1) ;
r =e.sumSquare() ;
if ((W*e).sumSquare() < 1e-10) break ;
if (iter>25) break ;
iter++ ; // std::cout << iter <<" e=" <<(e).sumSquare() <<" e=" <<(W*e).sumSquare() <<std::endl ;
}
// std::cout << c2Mc1 <<std::endl ;
return (W*e).sumSquare() ;
}
///////////////////////////////////////////////////////////////////////////
// Drawing Firework ///////////////////////////////////////////////////////
///////////////////////////////////////////////////////////////////////////
void DrawFirework(int no)
{
/* to display
* each firework particle
* You should calculate and display the trail of each
* particle here
*/
int i, j, k, u;
float interpolated_pt[2];
float Color[4];
for (i=0; i< fire[no].total_no; i++)
{
// if the paticle is still "alive"
if (!fire[no].particle[i].death)
{
glLineWidth(1.5);
glBegin(GL_LINE_STRIP); // for each paticle, generate its spline curve
Color[0] = fire[no].particle[i].col[0];
Color[1] = fire[no].particle[i].col[1];
Color[2] = fire[no].particle[i].col[2];
Color[3] = fire[no].particle[i].col[3];
for (k=0; k<3; k++)
Color[k] = 1.0;
// print the initial position
glColor4fv(Color);
glVertex2fv(fire[no].init_pos);
// interpolation
for (u=1; u<=10; u++)
{
for (j=0; j<2; j++)
// using the Hermite Spline Interpolation technique to find the interpolated points
interpolated_pt[j] = fire[no].init_pos[j]*H0(u/10.0)+
fire[no].particle[i].pos[j]*H1(u/10.0)+
fire[no].particle[i].init_vel[j]*fire[no].t*H2(u/10.0)+
fire[no].particle[i].vel[j]*fire[no].t*H3(u/10.0);
// print the interpolated points
for (k=0; k<3; k++)
Color[k] = (1-fire[no].particle[i].col[k])*0.49 + fire[no].particle[i].col[k];
glColor4fv(Color);
glVertex2fv(interpolated_pt);
}
// print the current point
for (k=0; k<3; k++)
Color[k] = (1-fire[no].particle[i].col[k])*0.4 + fire[no].particle[i].col[k];
glColor4fv(Color);
glVertex2fv(fire[no].particle[i].pos);
glEnd();
}
}
}
void FindMaximum2::Fit(ColumnVector& Theta, int n_it)
{
Tracer tr("FindMaximum2::Fit");
enum State {Start, Restart, Continue, Interpolate, Extrapolate,
Fail, Convergence};
State TheState = Start;
Real z,w,x,x2,g,l1,l2,l3,d1,d2=0,d3;
ColumnVector Theta1, Theta2, Theta3;
int np = Theta.Nrows();
ColumnVector H1(np), H3, HP(np), K, K1(np);
bool oorg, conv;
int counter = 0;
Theta1 = Theta; HP = 0.0; g = 0.0;
// This is really a set of gotos and labels, but they do not work
// correctly in AT&T C++ and Sun 4.01 C++.
for(;;)
{
switch (TheState)
{
case Start:
tr.ReName("FindMaximum2::Fit/Start");
Value(Theta1, true, l1, oorg);
if (oorg) Throw(ProgramException("invalid starting value\n"));
case Restart:
tr.ReName("FindMaximum2::Fit/ReStart");
conv = NextPoint(H1, d1);
if (conv) { TheState = Convergence; break; }
if (counter++ > n_it) { TheState = Fail; break; }
z = 1.0 / sqrt(d1);
H3 = H1 * z; K = (H3 - HP) * g; HP = H3;
g = 0.0; // de-activate to use curved projection
if (g==0.0) K1 = 0.0; else K1 = K * 0.2 + K1 * 0.6;
// (K - K1) * alpha + K1 * (1 - alpha)
// = K * alpha + K1 * (1 - 2 * alpha)
K = K1 * d1; g = z;
case Continue:
tr.ReName("FindMaximum2::Fit/Continue");
Theta2 = Theta1 + H1 + K;
Value(Theta2, false, l2, oorg);
if (counter++ > n_it) { TheState = Fail; break; }
if (oorg)
{
H1 *= 0.5; K *= 0.25; d1 *= 0.5; g *= 2.0;
TheState = Continue; break;
}
d2 = LastDerivative(H1 + K * 2.0);
case Interpolate:
tr.ReName("FindMaximum2::Fit/Interpolate");
z = d1 + d2 - 3.0 * (l2 - l1);
w = z * z - d1 * d2;
if (w < 0.0) { TheState = Extrapolate; break; }
w = z + sqrt(w);
if (1.5 * w + d1 < 0.0)
{ TheState = Extrapolate; break; }
if (d2 > 0.0 && l2 > l1 && w > 0.0)
{ TheState = Extrapolate; break; }
x = d1 / (w + d1); x2 = x * x; g /= x;
Theta3 = Theta1 + H1 * x + K * x2;
Value(Theta3, true, l3, oorg);
if (counter++ > n_it) { TheState = Fail; break; }
if (oorg)
{
if (x <= 1.0)
{ x *= 0.5; x2 = x*x; g *= 2.0; d1 *= x; H1 *= x; K *= x2; }
else
{
x = 0.5 * (x-1.0); x2 = x*x; Theta1 = Theta2;
H1 = (H1 + K * 2.0) * x;
K *= x2; g = 0.0; d1 = x * d2; l1 = l2;
}
TheState = Continue; break;
}
if (l3 >= l1 && l3 >= l2)
{ Theta1 = Theta3; l1 = l3; TheState = Restart; break; }
d3 = LastDerivative(H1 + K * 2.0);
if (l1 > l2)
{ H1 *= x; K *= x2; Theta2 = Theta3; d1 *= x; d2 = d3*x; }
else
{
Theta1 = Theta2; Theta2 = Theta3;
x -= 1.0; x2 = x*x; g = 0.0; H1 = (H1 + K * 2.0) * x;
K *= x2; l1 = l2; l2 = l3; d1 = x*d2; d2 = x*d3;
if (d1 <= 0.0) { TheState = Start; break; }
}
TheState = Interpolate; break;
case Extrapolate:
tr.ReName("FindMaximum2::Fit/Extrapolate");
Theta1 = Theta2; g = 0.0; K *= 4.0; H1 = (H1 * 2.0 + K);
d1 = 2.0 * d2; l1 = l2;
TheState = Continue; break;
case Fail:
Throw(ConvergenceException(Theta));
case Convergence:
Theta = Theta1; return;
}
}
}
/*****************************************************************************
* Help:
*****************************************************************************/
static void Help( x264_param_t *defaults, int b_longhelp )
{
#define H0 printf
#define H1 if(b_longhelp) printf
H0( "x264 core:%d%s\n"
"Syntax: x264 [options] -o outfile infile [widthxheight]\n"
"\n"
"Infile can be raw YUV 4:2:0 (in which case resolution is required),\n"
" or YUV4MPEG 4:2:0 (*.y4m),\n"
" or AVI or Avisynth if compiled with AVIS support (%s).\n"
"Outfile type is selected by filename:\n"
" .264 -> Raw bytestream\n"
" .mkv -> Matroska\n"
" .mp4 -> MP4 if compiled with GPAC support (%s)\n"
"\n"
"Options:\n"
"\n"
" -h, --help List the more commonly used options\n"
" --longhelp List all options\n"
"\n",
X264_BUILD, X264_VERSION,
#ifdef AVIS_INPUT
"yes",
#else
"no",
#endif
#ifdef MP4_OUTPUT
"yes"
#else
"no"
#endif
);
H0( "Frame-type options:\n" );
H0( "\n" );
H0( " -I, --keyint <integer> Maximum GOP size [%d]\n", defaults->i_keyint_max );
H1( " -i, --min-keyint <integer> Minimum GOP size [%d]\n", defaults->i_keyint_min );
H1( " --scenecut <integer> How aggressively to insert extra I-frames [%d]\n", defaults->i_scenecut_threshold );
H1( " --pre-scenecut Faster, less precise scenecut detection.\n"
" Required and implied by multi-threading.\n" );
H0( " -b, --bframes <integer> Number of B-frames between I and P [%d]\n", defaults->i_bframe );
H1( " --b-adapt Adaptive B-frame decision method [%d]\n"
" Higher values may lower threading efficiency.\n"
" - 0: Disabled\n"
" - 1: Fast\n"
" - 2: Optimal (slow with high --bframes)\n", defaults->i_bframe_adaptive );
H1( " --b-bias <integer> Influences how often B-frames are used [%d]\n", defaults->i_bframe_bias );
H0( " --b-pyramid Keep some B-frames as references\n" );
H0( " --no-cabac Disable CABAC\n" );
H0( " -r, --ref <integer> Number of reference frames [%d]\n", defaults->i_frame_reference );
H1( " --no-deblock Disable loop filter\n" );
H0( " -f, --deblock <alpha:beta> Loop filter AlphaC0 and Beta parameters [%d:%d]\n",
defaults->i_deblocking_filter_alphac0, defaults->i_deblocking_filter_beta );
H0( " --interlaced Enable pure-interlaced mode\n" );
H0( "\n" );
H0( "Ratecontrol:\n" );
H0( "\n" );
H0( " -q, --qp <integer> Set QP (0=lossless) [%d]\n", defaults->rc.i_qp_constant );
H0( " -B, --bitrate <integer> Set bitrate (kbit/s)\n" );
H0( " --crf <float> Quality-based VBR (nominal QP)\n" );
H1( " --vbv-maxrate <integer> Max local bitrate (kbit/s) [%d]\n", defaults->rc.i_vbv_max_bitrate );
H0( " --vbv-bufsize <integer> Enable CBR and set size of the VBV buffer (kbit) [%d]\n", defaults->rc.i_vbv_buffer_size );
H1( " --vbv-init <float> Initial VBV buffer occupancy [%.1f]\n", defaults->rc.f_vbv_buffer_init );
H1( " --qpmin <integer> Set min QP [%d]\n", defaults->rc.i_qp_min );
H1( " --qpmax <integer> Set max QP [%d]\n", defaults->rc.i_qp_max );
H1( " --qpstep <integer> Set max QP step [%d]\n", defaults->rc.i_qp_step );
H0( " --ratetol <float> Allowed variance of average bitrate [%.1f]\n", defaults->rc.f_rate_tolerance );
H0( " --ipratio <float> QP factor between I and P [%.2f]\n", defaults->rc.f_ip_factor );
H0( " --pbratio <float> QP factor between P and B [%.2f]\n", defaults->rc.f_pb_factor );
H1( " --chroma-qp-offset <integer> QP difference between chroma and luma [%d]\n", defaults->analyse.i_chroma_qp_offset );
H1( " --aq-mode <integer> AQ method [%d]\n"
" - 0: Disabled\n"
" - 1: Variance AQ (complexity mask)\n", defaults->rc.i_aq_mode );
H0( " --aq-strength <float> Reduces blocking and blurring in flat and\n"
" textured areas. [%.1f]\n"
" - 0.5: weak AQ\n"
" - 1.5: strong AQ\n", defaults->rc.f_aq_strength );
H0( "\n" );
H0( " -p, --pass <1|2|3> Enable multipass ratecontrol\n"
" - 1: First pass, creates stats file\n"
" - 2: Last pass, does not overwrite stats file\n"
" - 3: Nth pass, overwrites stats file\n" );
H0( " --stats <string> Filename for 2 pass stats [\"%s\"]\n", defaults->rc.psz_stat_out );
H0( " --qcomp <float> QP curve compression: 0.0 => CBR, 1.0 => CQP [%.2f]\n", defaults->rc.f_qcompress );
H1( " --cplxblur <float> Reduce fluctuations in QP (before curve compression) [%.1f]\n", defaults->rc.f_complexity_blur );
H1( " --qblur <float> Reduce fluctuations in QP (after curve compression) [%.1f]\n", defaults->rc.f_qblur );
H0( " --zones <zone0>/<zone1>/... Tweak the bitrate of some regions of the video\n" );
H1( " Each zone is of the form\n"
" <start frame>,<end frame>,<option>\n"
" where <option> is either\n"
" q=<integer> (force QP)\n"
" or b=<float> (bitrate multiplier)\n" );
H1( " --qpfile <string> Force frametypes and QPs for some or all frames\n"
" Format of each line: framenumber frametype QP\n"
" QP of -1 lets x264 choose. Frametypes: I,i,P,B,b.\n" );
H0( "\n" );
H0( "Analysis:\n" );
H0( "\n" );
H0( " -A, --partitions <string> Partitions to consider [\"p8x8,b8x8,i8x8,i4x4\"]\n"
" - p8x8, p4x4, b8x8, i8x8, i4x4\n"
" - none, all\n"
" (p4x4 requires p8x8. i8x8 requires --8x8dct.)\n" );
H0( " --direct <string> Direct MV prediction mode [\"%s\"]\n"
" - none, spatial, temporal, auto\n",
strtable_lookup( x264_direct_pred_names, defaults->analyse.i_direct_mv_pred ) );
H0( " -w, --weightb Weighted prediction for B-frames\n" );
H0( " --me <string> Integer pixel motion estimation method [\"%s\"]\n",
strtable_lookup( x264_motion_est_names, defaults->analyse.i_me_method ) );
H1( " - dia: diamond search, radius 1 (fast)\n"
" - hex: hexagonal search, radius 2\n"
" - umh: uneven multi-hexagon search\n"
" - esa: exhaustive search\n"
" - tesa: hadamard exhaustive search (slow)\n" );
else H0( " - dia, hex, umh\n" );
int main(void){
std::cout << " ---- Programa de Tests de la pseudoinverse de Mansard ----" << std::endl;
unsigned int nq = 10;
unsigned int nx1 = 7;
Eigen::MatrixXd H1(Eigen::MatrixXd::Zero(nx1,nx1));
H1(0,0) = 0;
H1(1,1) = 0.2;
H1(2,2) = 0;
H1(3,3) = 0.5;
H1(4,4) = 0;
H1(5,5) = 0;
H1(6,6) = 0.7;
std::vector<unsigned int> active_joints;
for (unsigned int i=0; i<nx1; ++i) if (H1(i,i)) active_joints.push_back(i);
unsigned int n_active_joints = active_joints.size();
std::cout << "n_active_joints: " << n_active_joints << std::endl;
// Initialize pseudoinverse to zero
Eigen::MatrixXd pJ1(Eigen::MatrixXd::Zero(nq,nx1));
// // Per cada grup de 'i' elements
// for (unsigned int i=1; i<=n_active_joints; ++i){
// std::vector<bool> v(n_active_joints);
// std::fill(v.begin(), v.begin() + i, true);
// do {
// Eigen::MatrixXd J_sum(Eigen::MatrixXd::Zero(nx1,nq));
// double h_prod = 1.0;
// for (int j = 0; j < n_active_joints; ++j) {
// unsigned int qi = active_joints[j];
// if (v[j]) {
//// std::cout << j << " ";
// std::cout << qi << " ";
// J_sum(qi,qi+3) = 1.0;
// h_prod *= H1(qi,qi);
// }
// else h_prod *= 1.0 - H1(qi,qi);
// }
// std::cout << "\n";
//// std::cout << " - P h: " << h_prod << "\n";
// std::cout << " J_sum: " << "\n" << J_sum << "\n";
// Eigen::MatrixXd pJ_sum(pinv(J_sum,0.00001));
// std::cout << " h_prod * pJ_sum: " << "\n" << h_prod * pJ_sum << "\n";
// pJ1 = pJ1 + h_prod * pJ_sum;
// std::cout << " pJ1: " << "\n" << pJ1 << "\n";
// } while (std::prev_permutation(v.begin(), v.end()));
// std::cout << "-----\n";
// }
// std::cout << " pJ1: " << "\n" << pJ1 << "\n";
// Per cada grup de 'i' elements
pJ1 = Eigen::MatrixXd::Zero(nq,nx1);
for (unsigned int i=1; i<=n_active_joints; ++i){
std::vector<bool> v(n_active_joints);
std::fill(v.begin(), v.begin() + i, true);
do {
Eigen::MatrixXd J_sum(Eigen::MatrixXd::Zero(nx1,nq));
double h_prod = 1.0;
for (unsigned int j = 0; j < n_active_joints; ++j) {
unsigned int qi = active_joints[j];
if (v[j]) {
J_sum(qi,qi+3) = 1.0;
h_prod *= H1(qi,qi);
}
else
h_prod *= 1.0 - H1(qi,qi);
}
pJ1 = pJ1 + h_prod * pinv(J_sum,0.00001);
} while (std::prev_permutation(v.begin(), v.end()));
}
std::cout << " pJ1: " << "\n" << pJ1 << "\n";
// Eigen::MatrixXd m_id(Eigen::MatrixXd::Identity(6,6));
// m_id(1,1) = 0.2;
// m_id(4,4) = -3;
// Eigen::VectorXi TS(3);
// TS(0) = 2;
// TS(1) = 3;
// TS(2) = 1;
// Eigen::VectorXd H(3);
// H(0) = 0.1;
// H(1) = 0.6;
// H(2) = 0.4;
// std::cout << " cinv: " << "\n" << cinv(m_id,TS,H) << "\n";
double tol = 0.0000001;
Eigen::MatrixXd m_id(Eigen::MatrixXd::Identity(nx1,nx1));
Eigen::VectorXi TS(nx1);
for (unsigned int i=0; i<nx1; ++i) TS(i) = 1.0;
Eigen::VectorXd H(nx1);
H(0) = 0;
H(1) = 0.2;
H(2) = 0;
H(3) = 0.5;
H(4) = 0;
H(5) = 0;
H(6) = 0.7;
std::cout << "cinv: " << "\n" << cinv(m_id,TS,H) << "\n";
Eigen::MatrixXd lH(nx1,nx1);
lH(0,0) = 0;
lH(1,1) = 0.2;
lH(2,2) = 0;
lH(3,3) = 0.5;
lH(4,4) = 0;
lH(5,5) = 0;
lH(6,6) = 0.7;
std::cout << "cinv: " << "\n" << cinv(m_id,TS,lH) << "\n";
std::cout << "left cinv: " << "\n" << left_cinv(m_id,TS,lH) << "\n";
std::cout << "right cinv: " << "\n" << right_cinv(m_id,TS,lH) << "\n";
return 0;
}
Big PFC::hash_to_group(char *ID)
{
Big m=H1(ID);
return m%(*ord);
}
void tSecureStream::m_setupClient(const tRSA& rsa, string appGreeting)
{
// This block is protected by constant timing in case
// there is a man-in-the-middle who is causing the client
// connection to fail over-and-over and analysing the time
// it takes for the client to re-start the connection.
// This block prevents info from being leaked about the
// particular pre_secret that is being used by the current
// connection attempt.
vector<u8> rand_c, pre_secret, enc;
{
tConstTimeBlock ctb(&gClientInitTimingHistory);
// Generate the client random vector.
rand_c = s_genRand(kRandVectLen);
// Generate the pre-secret random vector.
pre_secret = s_genRand(kPreSecretLen);
// Encrypt the pre-secret under the server's RSA public key.
enc = rsa.encrypt(pre_secret);
}
// Send all this to the server.
pack(m_internal_writable, kLibrhoGreeting);
pack(m_internal_writable, appGreeting);
pack(m_internal_writable, rand_c);
pack(m_internal_writable, enc);
s_flush(m_internal_writable);
// Read the greeting from the server.
// We don't care if timing info is leaked here
// because 'kSuccessfulGreeting' is not a secret.
string greetingResponse;
try {
unpack(m_internal_readable, greetingResponse,
(u32)(std::max(kSuccessfulGreeting.length(), kFailedGreeting.length())));
} catch (ebObject& e) {
throw eRuntimeError("The secure server didn't reply with its greeting.");
}
if (greetingResponse != kSuccessfulGreeting)
throw eRuntimeError("The secure server sent a failure greeting.");
// Read the random server bytes.
// Again, we don't care about leaking timing info here.
vector<u8> rand_s;
try {
unpack(m_internal_readable, rand_s, kRandVectLen);
} catch (ebObject& e) {
throw eRuntimeError("The secure server sent a random vector of the wrong length.");
}
if (rand_s.size() != kRandVectLen)
throw eRuntimeError("The secure server sent a random vector of the wrong length.");
// Another const timing block.
vector<u8> secret, fPrime, g;
{
tConstTimeBlock ctb(&gClientProcessResponseTimingHistory);
// Calculated the shared secret (from the pre-secret).
secret = H1(pre_secret, rand_c, rand_s);
// Calculate the correct response from the server.
fPrime = H2(secret, rand_c, rand_s);
// Calculate the proof-of-client.
g = H3(secret, rand_c, rand_s);
}
// Read the proof-of-server hash.
vector<u8> f;
try {
unpack(m_internal_readable, f, (u32)fPrime.size());
} catch (ebObject& e) {
throw eRuntimeError("The secure server failed to verify itself.");
}
if (!s_constTimeIsEqual(f, fPrime))
throw eRuntimeError("The secure server failed to verify itself.");
// Send the proof-of-client. (That is, prove we are not just replaying some other connection.)
pack(m_internal_writable, g);
s_flush(m_internal_writable);
// Setup secure streams with the server.
vector<u8> ksw = H4(pre_secret, secret, rand_c, rand_s); // <-- the Key for the Server Writer
vector<u8> kcw = H5(pre_secret, secret, rand_c, rand_s); // <-- the Key for the Client Writer
m_readable = new tReadableAES(m_internal_readable, kOpModeCBC,
&ksw[0], s_toKeyLen(ksw.size()));
m_writable = new tWritableAES(m_internal_writable, kOpModeCBC,
&kcw[0], s_toKeyLen(kcw.size()));
}
static int get_hash_1(int index)
{
H1(crypt_out[index]);
}
// Fonction d'intérpolation Hermite
void SolveTCB ( float t, int *x, int *y, int *z)
{
// Déclaration des Keyframes utilisés
Key *NextKey, *NextNextKey, *CurKey, *PrevKey;
// Varaible d'incrémentation
int i;
// Taille du tableau de Keyframe
const int NumKeys = ((double)sizeof(TabKey))/((double)sizeof(Key));
const int NumKeysMinusOne = NumKeys-1;
// Boucle de parcours des Keyframes
//..
for(i = 0; i < NumKeys;i++)
{
NextKey = &TabKey[i];
if (t<NextKey->t){
if(i==0) {
CurKey = &TabKey[NumKeysMinusOne];
PrevKey = &TabKey[NumKeysMinusOne-1];
NextNextKey = &TabKey[1];
}
else if(i==1){
CurKey = &TabKey[0];
PrevKey = &TabKey[NumKeysMinusOne];
NextNextKey = &TabKey[2];
}
else if(i==NumKeysMinusOne){
CurKey = &TabKey[i-1];
PrevKey = &TabKey[i-2];
NextNextKey = &TabKey[0];
}
else {
CurKey = &TabKey[i-1];
PrevKey = &TabKey[i-2];
NextNextKey = &TabKey[i+1];
}
// calcul tangents
//curent
float u = ((t-CurKey->t) / (NextKey->t - CurKey->t));
float ctx,cty,ctz;
float ntx,nty,ntz;
ctx = Tn(CurKey->tension,CurKey->bias,CurKey->continuity,PrevKey->pos.x,CurKey->pos.x);
cty = Tn(CurKey->tension,CurKey->bias,CurKey->continuity,PrevKey->pos.y,CurKey->pos.y);
ctz = Tn(CurKey->tension,CurKey->bias,CurKey->continuity,PrevKey->pos.z,CurKey->pos.z);
//printf("ctx -- > %lf \n",ctx);
//next
ntx = Tn1(CurKey->tension,CurKey->bias,CurKey->continuity,PrevKey->pos.x,CurKey->pos.x,NextKey->pos.x,NextNextKey->pos.x);
nty = Tn1(CurKey->tension,CurKey->bias,CurKey->continuity,PrevKey->pos.y,CurKey->pos.y,NextKey->pos.y,NextNextKey->pos.y);
ntz = Tn1(CurKey->tension,CurKey->bias,CurKey->continuity,PrevKey->pos.z,CurKey->pos.z,NextKey->pos.z,NextNextKey->pos.z);
//printf(" ntx -- > %lf \n",ntx);
// mise a jour des positions
*x = (int) (H0(u)*CurKey->pos.x + H1(u)*NextKey->pos.x + H2(u)*ctx + H3(u)*ntx);
*y = (int) (H0(u)*CurKey->pos.y + H1(u)*NextKey->pos.y + H2(u)*cty + H3(u)*nty);
*z = (int) (H0(u)*CurKey->pos.z + H1(u)*NextKey->pos.z + H2(u)*ctz + H3(u)*ntz);
printf("\n%lf\n",( CurKey->pos.x ));
printf("\n%lf, %lf\n",H1(t),( NextKey->pos.x ));
printf("\n%lf\n",( H2(t)*CurKey->tension ));
printf("\n%lf\n",( H3(t)*NextKey->tension ));
//printf(" time -> %f X -- > %d \n",t,*x);
//printf(" H0(t) = %f , H1(t) = %f , H2(t) = %f , H3(t) = %f \n",H0(t),H1(t),H2(t),H3(t));
//if(*x < (-8000) || *x > 8000)
//exit(0);
//break;
return;
}
}
time = 0;
return;
}
int main(int argc, char* argv[])
{
bool verb,fsrf,snap,expl,dabc,sout,uses;
int jsnap,ntsnap,jdata;
char *atype;
#ifdef _OPENMP
int ompnth=1;
#endif
/* I/O files */
sf_file Fwav=NULL; /* wavelet */
sf_file Fsou=NULL; /* sources */
sf_file Frec=NULL; /* receivers */
sf_file Fvel=NULL; /* velocity */
sf_file Fang=NULL; /* angles */
sf_file Fdat=NULL; /* data */
sf_file Fwfl=NULL; /* wavefield */
/* cube axes */
sf_axis at,az,ax;
sf_axis as,ar;
int nt,nz,nx,ns,nr,nb;
int it,iz,ix;
float dt,dz,dx,dt2;
/* FDM structure */
fdm2d fdm=NULL;
abcone2d abc=NULL;
sponge spo=NULL;
/* I/O arrays */
float *ww=NULL; /* wavelet */
pt2d *ss=NULL; /* sources */
pt2d *rr=NULL; /* receivers */
float *dd=NULL; /* data */
float **tt=NULL;
float **vp=NULL; /* velocity */
float **vpn=NULL;
float **vpz=NULL;
float **vpx=NULL;
float **vsz=NULL;
float **tht=NULL,**sit=NULL,**cot=NULL;
float st,ct;
float **pm=NULL,**po=NULL,**pp=NULL,**pa=NULL,**pt=NULL; /* main wavefield */
float **qm=NULL,**qo=NULL,**qp=NULL,**qa=NULL,**qt=NULL; /* auxiliary wavefield */
float **sf=NULL; /* "stress" field */
/* linear inteppolation weights/indices */
lint2d cs,cr;
/* FD operator size */
float cox,cax,cbx,c1x,c2x;
float coz,caz,cbz,c1z,c2z;
/* wavefield cut params */
sf_axis acz=NULL,acx=NULL;
int nqz,nqx;
float oqz,oqx;
float dqz,dqx;
float **pc=NULL;
float H1p,H2p,H1q,H2q;
/*------------------------------------------------------------*/
/* init RSF */
sf_init(argc,argv);
/* select anisotropy model */
if (NULL == (atype = sf_getstring("atype"))) atype = "i";
switch(atype[0]) {
case 't':
sf_warning("TTI model");
break;
case 'v':
sf_warning("VTI model");
break;
case 'i':
default:
sf_warning("ISO model");
break;
}
/*------------------------------------------------------------*/
/* OMP parameters */
#ifdef _OPENMP
ompnth=omp_init();
#endif
/*------------------------------------------------------------*/
/*------------------------------------------------------------*/
if(! sf_getbool("verb",&verb)) verb=false; /* verbosity */
if(! sf_getbool("snap",&snap)) snap=false; /* wavefield snapshots */
if(! sf_getbool("free",&fsrf)) fsrf=false; /* free surface */
if(! sf_getbool("expl",&expl)) expl=false; /* "exploding reflector" */
if(! sf_getbool("dabc",&dabc)) dabc=false; /* absorbing BC */
if(! sf_getbool("sout",&sout)) sout=false; /* stress output */
if(! sf_getbool("uses",&uses)) uses=false; /* use vsz */
/*------------------------------------------------------------*/
/*------------------------------------------------------------*/
/* I/O files */
Fwav = sf_input ("in" ); /* wavelet */
Fvel = sf_input ("vel"); /* velocity */
Fsou = sf_input ("sou"); /* sources */
Frec = sf_input ("rec"); /* receivers */
Fang = sf_input ("ang"); /* angles */
Fwfl = sf_output("wfl"); /* wavefield */
Fdat = sf_output("out"); /* data */
/*------------------------------------------------------------*/
/* axes */
at = sf_iaxa(Fwav,2); sf_setlabel(at,"t"); if(verb) sf_raxa(at); /* time */
az = sf_iaxa(Fvel,1); sf_setlabel(az,"z"); if(verb) sf_raxa(az); /* depth */
ax = sf_iaxa(Fvel,2); sf_setlabel(ax,"x"); if(verb) sf_raxa(ax); /* space */
as = sf_iaxa(Fsou,2); sf_setlabel(as,"s"); if(verb) sf_raxa(as); /* sources */
ar = sf_iaxa(Frec,2); sf_setlabel(ar,"r"); if(verb) sf_raxa(ar); /* receivers */
nt = sf_n(at); dt = sf_d(at);
nz = sf_n(az); dz = sf_d(az);
nx = sf_n(ax); dx = sf_d(ax);
ns = sf_n(as);
nr = sf_n(ar);
/*------------------------------------------------------------*/
/*------------------------------------------------------------*/
/* other execution parameters */
if(! sf_getint("jdata",&jdata)) jdata=1;
if(snap) { /* save wavefield every *jsnap* time steps */
if(! sf_getint("jsnap",&jsnap)) jsnap=nt;
}
/*------------------------------------------------------------*/
/*------------------------------------------------------------*/
/* setup output data header */
sf_oaxa(Fdat,ar,1);
sf_setn(at,nt/jdata);
sf_setd(at,dt*jdata);
sf_oaxa(Fdat,at,2);
/* setup output wavefield header */
if(snap) {
if(!sf_getint ("nqz",&nqz)) nqz=sf_n(az);
if(!sf_getint ("nqx",&nqx)) nqx=sf_n(ax);
if(!sf_getfloat("oqz",&oqz)) oqz=sf_o(az);
if(!sf_getfloat("oqx",&oqx)) oqx=sf_o(ax);
dqz=sf_d(az);
dqx=sf_d(ax);
acz = sf_maxa(nqz,oqz,dqz); sf_raxa(acz);
acx = sf_maxa(nqx,oqx,dqx); sf_raxa(acx);
/* check if the imaging window fits in the wavefield domain */
pc=sf_floatalloc2(sf_n(acz),sf_n(acx));
ntsnap=0;
for(it=0; it<nt; it++) {
if(it%jsnap==0) ntsnap++;
}
sf_setn(at, ntsnap);
sf_setd(at,dt*jsnap);
if(verb) sf_raxa(at);
sf_oaxa(Fwfl,acz,1);
sf_oaxa(Fwfl,acx,2);
sf_oaxa(Fwfl,at, 3);
}
/*------------------------------------------------------------*/
/* expand domain for FD operators and ABC */
if( !sf_getint("nb",&nb) || nb<NOP) nb=NOP;
fdm=fdutil_init(verb,fsrf,az,ax,nb,1);
sf_setn(az,fdm->nzpad); sf_seto(az,fdm->ozpad); if(verb) sf_raxa(az);
sf_setn(ax,fdm->nxpad); sf_seto(ax,fdm->oxpad); if(verb) sf_raxa(ax);
/*------------------------------------------------------------*/
if(expl) {
ww = sf_floatalloc( 1);
} else {
ww = sf_floatalloc(ns);
}
dd = sf_floatalloc(nr);
/*------------------------------------------------------------*/
/* setup source/receiver coordinates */
ss = (pt2d*) sf_alloc(ns,sizeof(*ss));
rr = (pt2d*) sf_alloc(nr,sizeof(*rr));
pt2dread1(Fsou,ss,ns,2); /* read (x,z) coordinates */
pt2dread1(Frec,rr,nr,2); /* read (x,z) coordinates */
cs = lint2d_make(ns,ss,fdm);
cr = lint2d_make(nr,rr,fdm);
/*------------------------------------------------------------*/
/* setup FD coefficients */
cox = C0 / (dx*dx);
cax = CA / (dx*dx);
cbx = CB / (dx*dx);
c1x = C1 / dx;
c2x = C2 / dx;
coz = C0 / (dz*dz);
caz = CA / (dz*dz);
cbz = CB / (dz*dz);
c1z = C1 / dz;
c2z = C2 / dz;
/* precompute dt^2*/
dt2 = dt*dt;
/*------------------------------------------------------------*/
tt = sf_floatalloc2(nz,nx);
/*------------------------------------------------------------*/
/* input velocity */
vp =sf_floatalloc2(fdm->nzpad,fdm->nxpad);
vpz =sf_floatalloc2(fdm->nzpad,fdm->nxpad);
sf_floatread(tt[0],nz*nx,Fvel );
expand(tt,vpz,fdm); /* VPz */
for (ix=0; ix<fdm->nxpad; ix++) {
for(iz=0; iz<fdm->nzpad; iz++) {
vp [ix][iz] = vpz[ix][iz];
vpz[ix][iz] = vpz[ix][iz] * vpz[ix][iz];
}
}
if(fsrf) { /* free surface */
for (ix=0; ix<fdm->nxpad; ix++) {
for(iz=0; iz<fdm->nb; iz++) {
vpz[ix][iz]=0;
}
}
}
if(atype[0] != 'i') {
vpn =sf_floatalloc2(fdm->nzpad,fdm->nxpad);
sf_floatread(tt[0],nz*nx,Fvel );
expand(tt,vpn,fdm); /* VPn */
vpx =sf_floatalloc2(fdm->nzpad,fdm->nxpad);
sf_floatread(tt[0],nz*nx,Fvel );
expand(tt,vpx,fdm); /* VPx */
for (ix=0; ix<fdm->nxpad; ix++) {
for(iz=0; iz<fdm->nzpad; iz++) {
vpn[ix][iz] = vpn[ix][iz] * vpn[ix][iz];
vpx[ix][iz] = vpx[ix][iz] * vpx[ix][iz];
}
}
if(fsrf) { /* free surface */
for (ix=0; ix<fdm->nxpad; ix++) {
for(iz=0; iz<fdm->nb; iz++) {
vpn[ix][iz]=0;
vpx[ix][iz]=0;
}
}
}
if(uses) {
vsz =sf_floatalloc2(fdm->nzpad,fdm->nxpad);
sf_floatread(tt[0],nz*nx,Fvel );
expand(tt,vsz,fdm); /* VSz */
for (ix=0; ix<fdm->nxpad; ix++) {
for(iz=0; iz<fdm->nzpad; iz++) {
vsz[ix][iz] = vsz[ix][iz] * vsz[ix][iz];
}
}
}
}
/*------------------------------------------------------------*/
if( atype[0]=='t') {
/* input tilt angle */
tht =sf_floatalloc2(fdm->nzpad,fdm->nxpad);
sit =sf_floatalloc2(fdm->nzpad,fdm->nxpad);
cot =sf_floatalloc2(fdm->nzpad,fdm->nxpad);
sf_floatread(tt[0],nz*nx,Fang);
expand(tt,tht,fdm);
for (ix=0; ix<fdm->nxpad; ix++) {
for(iz=0; iz<fdm->nzpad; iz++) {
tht[ix][iz] *= SF_PI/180.;
sit[ix][iz] = sinf(tht[ix][iz]);
cot[ix][iz] = cosf(tht[ix][iz]);
}
}
free(*tht); free(tht);
}
/*------------------------------------------------------------*/
free(*tt); free(tt);
/*------------------------------------------------------------*/
/*------------------------------------------------------------*/
/* allocate wavefield arrays */
pm=sf_floatalloc2(fdm->nzpad,fdm->nxpad);
po=sf_floatalloc2(fdm->nzpad,fdm->nxpad);
pp=sf_floatalloc2(fdm->nzpad,fdm->nxpad);
pa=sf_floatalloc2(fdm->nzpad,fdm->nxpad);
for (ix=0; ix<fdm->nxpad; ix++) {
for(iz=0; iz<fdm->nzpad; iz++) {
pm[ix][iz]=0;
po[ix][iz]=0;
pp[ix][iz]=0;
pa[ix][iz]=0;
}
}
if(atype[0] != 'i') {
qm=sf_floatalloc2(fdm->nzpad,fdm->nxpad);
qo=sf_floatalloc2(fdm->nzpad,fdm->nxpad);
qp=sf_floatalloc2(fdm->nzpad,fdm->nxpad);
qa=sf_floatalloc2(fdm->nzpad,fdm->nxpad);
for (ix=0; ix<fdm->nxpad; ix++) {
for(iz=0; iz<fdm->nzpad; iz++) {
qm[ix][iz]=0;
qo[ix][iz]=0;
qp[ix][iz]=0;
qa[ix][iz]=0;
}
}
if(sout) sf=sf_floatalloc2(fdm->nzpad,fdm->nxpad);
}
/*------------------------------------------------------------*/
if(dabc) {
abc = abcone2d_make(NOP,dt,vp,fsrf,fdm); /* one-way */
spo = sponge_make(fdm->nb); /* sponge */
}
/*------------------------------------------------------------*/
/*
* MAIN LOOP
*/
/*------------------------------------------------------------*/
if(verb) fprintf(stderr,"\n");
for (it=0; it<nt; it++) {
if(verb) fprintf(stderr,"\b\b\b\b\b%d",it);
/* compute acceleration */
switch(atype[0]) {
case 't':
if(uses) {
#ifdef _OPENMP
#pragma omp parallel for \
schedule(dynamic,fdm->ompchunk) \
private(ix,iz,H1p,H2p,H1q,H2q,st,ct) \
shared(fdm,pa,po,qa,qo, \
cox,cax,cbx,c1x,c2x, \
coz,caz,cbz,c1z,c2z, \
vpn,vpz,vpx,vsz, \
sit,cot)
#endif
for (ix=NOP; ix<fdm->nxpad-NOP; ix++) {
for(iz=NOP; iz<fdm->nzpad-NOP; iz++) {
st=sit[ix][iz];
ct=cot[ix][iz];
H1p = H1(po,ix,iz, \
st,ct, \
cox,cax,cbx,c1x,c2x, \
coz,caz,cbz,c1z,c2z);
H2p = H2(po,ix,iz, \
st,ct, \
cox,cax,cbx,c1x,c2x, \
coz,caz,cbz,c1z,c2z);
H1q = H1(qo,ix,iz, \
st,ct, \
cox,cax,cbx,c1x,c2x, \
coz,caz,cbz,c1z,c2z);
H2q = H2(qo,ix,iz, \
st,ct, \
cox,cax,cbx,c1x,c2x, \
coz,caz,cbz,c1z,c2z);
/* p - main field */
pa[ix][iz] =
H1p * vsz[ix][iz] +
H2p * vpx[ix][iz] +
H1q * vpz[ix][iz] -
H1q * vsz[ix][iz];
/* q - auxiliary field */
qa[ix][iz] =
H2p * vpn[ix][iz] -
H2p * vsz[ix][iz] +
H1q * vpz[ix][iz] +
H2q * vsz[ix][iz];
}
}
} else {
#ifdef _OPENMP
#pragma omp parallel for \
schedule(dynamic,fdm->ompchunk) \
private(ix,iz,H2p,H1q,st,ct) \
shared(fdm,pa,po,qa,qo, \
cox,cax,cbx,c1x,c2x, \
coz,caz,cbz,c1z,c2z, \
vpn,vpz,vpx, \
sit,cot)
#endif
for (ix=NOP; ix<fdm->nxpad-NOP; ix++) {
for(iz=NOP; iz<fdm->nzpad-NOP; iz++) {
st=sit[ix][iz];
ct=cot[ix][iz];
H2p = H2(po,ix,iz, \
st,ct, \
cox,cax,cbx,c1x,c2x, \
coz,caz,cbz,c1z,c2z);
H1q = H1(qo,ix,iz, \
st,ct, \
cox,cax,cbx,c1x,c2x, \
coz,caz,cbz,c1z,c2z);
/* p - main field */
pa[ix][iz] =
H2p * vpx[ix][iz] +
H1q * vpz[ix][iz];
/* q - auxiliary field */
qa[ix][iz] =
H2p * vpn[ix][iz] +
H1q * vpz[ix][iz];
}
}
}
break;
case 'v':
if(uses) {
#ifdef _OPENMP
#pragma omp parallel for \
schedule(dynamic,fdm->ompchunk) \
private(ix,iz,H1p,H2p,H1q,H2q) \
shared(fdm,pa,po,qa,qo, \
cox,cax,cbx, \
coz,caz,cbz, \
vpn,vpz,vpx,vsz)
#endif
for (ix=NOP; ix<fdm->nxpad-NOP; ix++) {
for(iz=NOP; iz<fdm->nzpad-NOP; iz++) {
H1p = Dzz(po,ix,iz,coz,caz,cbz);
H1q = Dzz(qo,ix,iz,coz,caz,cbz);
H2p = Dxx(po,ix,iz,cox,cax,cbx);
H2q = Dxx(qo,ix,iz,cox,cax,cbx);
/* p - main field */
pa[ix][iz] =
H1p * vsz[ix][iz] +
H2p * vpx[ix][iz] +
H1q * vpz[ix][iz] -
H1q * vsz[ix][iz];
/* q - auxiliary field */
qa[ix][iz] =
H2p * vpn[ix][iz] -
H2p * vsz[ix][iz] +
H1q * vpz[ix][iz] +
H2q * vsz[ix][iz];
}
}
} else {
#ifdef _OPENMP
#pragma omp parallel for \
schedule(dynamic,fdm->ompchunk) \
private(ix,iz,H2p,H1q) \
shared(fdm,pa,po,qa,qo, \
cox,cax,cbx, \
coz,caz,cbz, \
vpn,vpx,vpz)
#endif
for (ix=NOP; ix<fdm->nxpad-NOP; ix++) {
for(iz=NOP; iz<fdm->nzpad-NOP; iz++) {
H1q = Dzz(qo,ix,iz,coz,caz,cbz);
H2p = Dxx(po,ix,iz,cox,cax,cbx);
/* p - main field */
pa[ix][iz] =
H2p * vpx[ix][iz] +
H1q * vpz[ix][iz];
/* q - auxiliary field */
qa[ix][iz] =
H2p * vpn[ix][iz] +
H1q * vpz[ix][iz];
}
}
}
break;
case 'i':
default:
#ifdef _OPENMP
#pragma omp parallel for \
schedule(dynamic,fdm->ompchunk) \
private(ix,iz) \
shared(fdm,pa,po, \
cox,cax,cbx, \
coz,caz,cbz, \
vpz)
#endif
for (ix=NOP; ix<fdm->nxpad-NOP; ix++) {
for(iz=NOP; iz<fdm->nzpad-NOP; iz++) {
pa[ix][iz] = ( Dxx(po,ix,iz,cox,cax,cbx) +
Dzz(po,ix,iz,coz,caz,cbz) ) * vpz[ix][iz];
}
}
break;
}
/* inject acceleration source */
if(expl) {
sf_floatread(ww, 1,Fwav);
; lint2d_inject1(pa,ww[0],cs);
if(atype[0] != 'i') lint2d_inject1(qa,ww[0],cs);
} else {
sf_floatread(ww,ns,Fwav);
; lint2d_inject(pa,ww,cs);
if(atype[0] != 'i') lint2d_inject(qa,ww,cs);
}
/* step forward in time */
#ifdef _OPENMP
#pragma omp parallel for \
schedule(dynamic,fdm->ompchunk) \
private(ix,iz) \
shared(fdm,pa,po,pm,pp,dt2)
#endif
for (ix=0; ix<fdm->nxpad; ix++) {
for(iz=0; iz<fdm->nzpad; iz++) {
pp[ix][iz] = 2*po[ix][iz]
- pm[ix][iz]
+ pa[ix][iz] * dt2;
}
}
/* circulate wavefield arrays */
pt=pm;
pm=po;
po=pp;
pp=pt;
if(atype[0] != 'i') {
#ifdef _OPENMP
#pragma omp parallel for \
schedule(dynamic,fdm->ompchunk) \
private(ix,iz) \
shared(fdm,qa,qo,qm,qp,dt2)
#endif
for (ix=0; ix<fdm->nxpad; ix++) {
for(iz=0; iz<fdm->nzpad; iz++) {
qp[ix][iz] = 2*qo[ix][iz]
- qm[ix][iz]
+ qa[ix][iz] * dt2;
}
}
/* circulate wavefield arrays */
qt=qm;
qm=qo;
qo=qp;
qp=qt;
}
/* one-way abc apply */
if(dabc) {
abcone2d_apply(po,pm,NOP,abc,fdm);
sponge2d_apply(pm,spo,fdm);
sponge2d_apply(po,spo,fdm);
if(atype[0] != 'i') {
abcone2d_apply(qo,qm,NOP,abc,fdm);
sponge2d_apply(qm,spo,fdm);
sponge2d_apply(qo,spo,fdm);
}
}
/* compute stress */
if(sout && (atype[0] != 'i')) {
#ifdef _OPENMP
#pragma omp parallel for \
schedule(dynamic,fdm->ompchunk) \
private(ix,iz) \
shared(fdm,po,qo,sf)
#endif
for (ix=0; ix<fdm->nxpad; ix++) {
for(iz=0; iz<fdm->nzpad; iz++) {
sf[ix][iz] = po[ix][iz] + qo[ix][iz];
}
}
}
/* extract data at receivers */
if(sout && (atype[0] != 'i')) {lint2d_extract(sf,dd,cr);
} else { lint2d_extract(po,dd,cr);}
if(it%jdata==0) sf_floatwrite(dd,nr,Fdat);
/* extract wavefield in the "box" */
if(snap && it%jsnap==0) {
if(sout && (atype[0] != 'i')) {cut2d(sf,pc,fdm,acz,acx);
} else { cut2d(po,pc,fdm,acz,acx);}
sf_floatwrite(pc[0],sf_n(acz)*sf_n(acx),Fwfl);
}
}
if(verb) fprintf(stderr,"\n");
/*------------------------------------------------------------*/
/* deallocate arrays */
free(*pm); free(pm);
free(*pp); free(pp);
free(*po); free(po);
free(*pa); free(pa);
free(*pc); free(pc);
free(*vp); free(vp);
free(*vpz); free(vpz);
if(atype[0] != 'i') {
free(*qm); free(qm);
free(*qp); free(qp);
free(*qo); free(qo);
free(*qa); free(qa);
free(*vpn); free(vpn);
free(*vpx); free(vpx);
if(uses){ free(*vsz); free(vsz); }
if(sout){ free(*sf); free(sf); }
}
if(atype[0] == 't') {
free(*sit); free(sit);
free(*cot); free(cot);
}
free(ww);
free(ss);
free(rr);
free(dd);
/*------------------------------------------------------------*/
exit (0);
}
static int binary_hash_1(void *binary)
{
H1((char *)binary);
}
void Tower::hanoiStart()
{
H1(0, 3, counter);
}
void Tower::H2(int source, int dest, int & counter)
{
//source = 3, dest = 1
move(source, dest, counter);
H1(dest + 1, source, counter);
}
static int get_hash_1(int index)
{
H1(buffer[index].out);
}
double
vpHomography::computeDisplacement(unsigned int nbpoint,
vpPoint *c1P,
vpPoint *c2P,
vpPlane *oN,
vpHomogeneousMatrix &c2Mc1,
vpHomogeneousMatrix &c1Mo,
int userobust
)
{
vpColVector e(2) ;
double r_1 = -1 ;
vpColVector p2(3) ;
vpColVector p1(3) ;
vpColVector Hp2(3) ;
vpColVector Hp1(3) ;
vpMatrix H2(2,6) ;
vpColVector e2(2) ;
vpMatrix H1(2,6) ;
vpColVector e1(2) ;
int only_1 = 1 ;
int only_2 = 0 ;
int iter = 0 ;
unsigned int i ;
unsigned int n=0 ;
n = nbpoint ;
if ((only_1==1) || (only_2==1)) ; else n *=2 ;
vpRobust robust(n);
vpColVector res(n) ;
vpColVector w(n) ;
w =1 ;
robust.setThreshold(0.0000) ;
vpMatrix W(2*n,2*n) ;
W = 0 ;
vpColVector N1(3), N2(3) ;
double d1, d2 ;
double r =1e10 ;
iter =0 ;
while (vpMath::equal(r_1,r,threshold_displacement) == false )
{
r_1 =r ;
// compute current position
//Change frame (current)
vpHomogeneousMatrix c1Mc2, c2Mo ;
vpRotationMatrix c1Rc2, c2Rc1 ;
vpTranslationVector c1Tc2, c2Tc1 ;
c1Mc2 = c2Mc1.inverse() ;
c2Mc1.extract(c2Rc1) ;
c2Mc1.extract(c2Tc1) ;
c2Mc1.extract(c1Rc2) ;
c1Mc2.extract(c1Tc2) ;
c2Mo = c2Mc1*c1Mo ;
vpMatrix L(2,3), Lp ;
int k =0 ;
for (i=0 ; i < nbpoint ; i++)
{
getPlaneInfo(oN[i], c1Mo, N1, d1) ;
getPlaneInfo(oN[i], c2Mo, N2, d2) ;
p2[0] = c2P[i].get_x() ;
p2[1] = c2P[i].get_y() ;
p2[2] = 1.0 ;
p1[0] = c1P[i].get_x() ;
p1[1] = c1P[i].get_y() ;
p1[2] = 1.0 ;
vpMatrix H(3,3) ;
Hp2 = ((vpMatrix)c1Rc2 + ((vpMatrix)c1Tc2*N2.t())/d2)*p2 ; // p2 = Hp1
Hp1 = ((vpMatrix)c2Rc1 + ((vpMatrix)c2Tc1*N1.t())/d1)*p1 ; // p1 = Hp2
Hp2 /= Hp2[2] ; // normalisation
Hp1 /= Hp1[2] ;
// set up the interaction matrix
double x = Hp2[0] ;
double y = Hp2[1] ;
double Z1 ;
Z1 = (N1[0]*x+N1[1]*y+N1[2])/d1 ; // 1/z
H2[0][0] = -Z1 ; H2[0][1] = 0 ; H2[0][2] = x*Z1 ;
H2[1][0] = 0 ; H2[1][1] = -Z1 ; H2[1][2] = y*Z1 ;
H2[0][3] = x*y ; H2[0][4] = -(1+x*x) ; H2[0][5] = y ;
H2[1][3] = 1+y*y ; H2[1][4] = -x*y ; H2[1][5] = -x ;
H2 *=-1 ;
vpMatrix c1CFc2(6,6) ;
{
vpMatrix sTR = c1Tc2.skew()*(vpMatrix)c1Rc2 ;
for (unsigned int k=0 ; k < 3 ; k++)
for (unsigned int l=0 ; l<3 ; l++)
{
c1CFc2[k][l] = c1Rc2[k][l] ;
c1CFc2[k+3][l+3] = c1Rc2[k][l] ;
c1CFc2[k][l+3] = sTR[k][l] ;
}
}
H2 = H2*c1CFc2 ;
// Set up the error vector
e2[0] = Hp2[0] - c1P[i].get_x() ;
e2[1] = Hp2[1] - c1P[i].get_y() ;
x = Hp1[0] ;
y = Hp1[1] ;
Z1 = (N2[0]*x+N2[1]*y+N2[2])/d2 ; // 1/z
H1[0][0] = -Z1 ; H1[0][1] = 0 ; H1[0][2] = x*Z1 ;
H1[1][0] = 0 ; H1[1][1] = -Z1 ; H1[1][2] = y*Z1;
H1[0][3] = x*y ; H1[0][4] = -(1+x*x) ; H1[0][5] = y ;
H1[1][3] = 1+y*y ; H1[1][4] = -x*y ; H1[1][5] = -x ;
// Set up the error vector
e1[0] = Hp1[0] - c2P[i].get_x() ;
e1[1] = Hp1[1] - c2P[i].get_y() ;
if (only_2==1)
{
if (k == 0) { L = H2 ; e = e2 ; }
else
{
L = vpMatrix::stackMatrices(L,H2) ;
e = vpMatrix::stackMatrices(e,e2) ;
}
}
else
if (only_1==1)
{
if (k == 0) { L = H1 ; e= e1 ; }
else
{
L = vpMatrix::stackMatrices(L,H1) ;
e = vpMatrix::stackMatrices(e,e1) ;
}
}
else
{
if (k == 0) {L = H2 ; e = e2 ; }
else
{
L = vpMatrix::stackMatrices(L,H2) ;
e = vpMatrix::stackMatrices(e,e2) ;
}
L = vpMatrix::stackMatrices(L,H1) ;
e = vpMatrix::stackMatrices(e,e1) ;
}
k++ ;
}
if (userobust)
{
robust.setIteration(0);
for (unsigned int k=0 ; k < n ; k++)
{
res[k] = vpMath::sqr(e[2*k]) + vpMath::sqr(e[2*k+1]) ;
}
robust.MEstimator(vpRobust::TUKEY, res, w);
// compute the pseudo inverse of the interaction matrix
for (unsigned int k=0 ; k < n ; k++)
{
W[2*k][2*k] = w[k] ;
W[2*k+1][2*k+1] = w[k] ;
}
}
else
{
for (unsigned int k=0 ; k < 2*n ; k++) W[k][k] = 1 ;
}
(W*L).pseudoInverse(Lp, 1e-16) ;
// Compute the camera velocity
vpColVector c2Tcc1 ;
c2Tcc1 = -1*Lp*W*e ;
// only for simulation
c2Mc1 = vpExponentialMap::direct(c2Tcc1).inverse()*c2Mc1 ; ;
// UpdatePose2(c2Tcc1, c2Mc1) ;
r =(W*e).sumSquare() ;
if (r < 1e-15) {break ; }
if (iter>1000){break ; }
if (r>r_1) { break ; }
iter++ ;
}
return (W*e).sumSquare() ;
}
Big PFC::hash_to_group(char *ID)
{
Big m=H1(ID);
Big o=pow((Big)2,2*S);
return m%o;
}
void PFC::hash_and_map(G1& w,char *ID)
{
Big x0=H1(ID);
while (!w.g.set(x0,x0)) x0+=1;
w.g*=*cof;
}
Molecule C6H6()
{
int nAtoms = 12;
// These are in Angstrom
Eigen::Vector3d C1(5.274, 1.999, -8.568);
Eigen::Vector3d C2(6.627, 2.018, -8.209);
Eigen::Vector3d C3(7.366, 0.829, -8.202);
Eigen::Vector3d C4(6.752, -0.379, -8.554);
Eigen::Vector3d C5(5.399, -0.398, -8.912);
Eigen::Vector3d C6(4.660, 0.791, -8.919);
Eigen::Vector3d H1(4.704, 2.916, -8.573);
Eigen::Vector3d H2(7.101, 2.950, -7.938);
Eigen::Vector3d H3(8.410, 0.844, -7.926);
Eigen::Vector3d H4(7.322, -1.296, -8.548);
Eigen::Vector3d H5(4.925, -1.330, -9.183);
Eigen::Vector3d H6(3.616, 0.776, -9.196);
// Scale
C1 /= convertBohrToAngstrom;
C2 /= convertBohrToAngstrom;
C3 /= convertBohrToAngstrom;
C4 /= convertBohrToAngstrom;
C5 /= convertBohrToAngstrom;
C6 /= convertBohrToAngstrom;
H1 /= convertBohrToAngstrom;
H2 /= convertBohrToAngstrom;
H3 /= convertBohrToAngstrom;
H4 /= convertBohrToAngstrom;
H5 /= convertBohrToAngstrom;
H6 /= convertBohrToAngstrom;
Eigen::MatrixXd geom(3, nAtoms);
geom.col(0) = C1.transpose();
geom.col(1) = C2.transpose();
geom.col(2) = C3.transpose();
geom.col(3) = C4.transpose();
geom.col(4) = C5.transpose();
geom.col(5) = C6.transpose();
geom.col(6) = H1.transpose();
geom.col(7) = H2.transpose();
geom.col(8) = H3.transpose();
geom.col(9) = H4.transpose();
geom.col(10) = H5.transpose();
geom.col(11) = H6.transpose();
Eigen::VectorXd charges(12), masses(12);
charges << 6.0, 6.0, 6.0, 6.0, 6.0, 6.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0;
masses << 12.00, 12.0, 12.0, 12.0, 12.0, 12.0, 1.0078250, 1.0078250, 1.0078250,
1.0078250, 1.0078250, 1.0078250;
double radiusC = 1.70 / convertBohrToAngstrom;
double radiusH = 1.20 / convertBohrToAngstrom;
std::vector<Atom> atoms;
atoms.push_back( Atom("Carbon", "C", charges(0), masses(0), radiusC, C1, 1.0) );
atoms.push_back( Atom("Carbon", "C", charges(1), masses(1), radiusC, C2, 1.0) );
atoms.push_back( Atom("Carbon", "C", charges(2), masses(2), radiusC, C3, 1.0) );
atoms.push_back( Atom("Carbon", "C", charges(3), masses(3), radiusC, C4, 1.0) );
atoms.push_back( Atom("Carbon", "C", charges(4), masses(4), radiusC, C5, 1.0) );
atoms.push_back( Atom("Carbon", "C", charges(5), masses(5), radiusC, C6, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(6), masses(6), radiusH, H1, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(7), masses(7), radiusH, H2, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(8), masses(8), radiusH, H3, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(9), masses(9), radiusH, H4, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(10), masses(10), radiusH, H5, 1.0) );
atoms.push_back( Atom("Hydrogen", "H", charges(11), masses(11), radiusH, H6, 1.0) );
std::vector<Sphere> spheres;
Sphere sph1(C1, radiusC);
Sphere sph2(C2, radiusC);
Sphere sph3(C3, radiusC);
Sphere sph4(C4, radiusC);
Sphere sph5(C5, radiusC);
Sphere sph6(C6, radiusC);
Sphere sph7(H1, radiusH);
Sphere sph8(H2, radiusH);
Sphere sph9(H3, radiusH);
Sphere sph10(H4, radiusH);
Sphere sph11(H5, radiusH);
Sphere sph12(H6, radiusH);
spheres.push_back(sph1);
spheres.push_back(sph2);
spheres.push_back(sph3);
spheres.push_back(sph4);
spheres.push_back(sph5);
spheres.push_back(sph6);
spheres.push_back(sph7);
spheres.push_back(sph8);
spheres.push_back(sph9);
spheres.push_back(sph10);
spheres.push_back(sph11);
spheres.push_back(sph12);
// D2h as generated by Oxy, Oxz, Oyz
Symmetry pGroup = buildGroup(0, 0, 0, 0);
return Molecule(nAtoms, charges, masses, geom, atoms, spheres, pGroup);
};
BamX::BamX(pars & Params1) // optional constructor
{
// parameters
Params=Params1;
Nread=0;
Npair=0;
Nproper=0;
Nout=0;
LFlow=INT_MIN;
LFhigh=INT_MAX;
region.limit=false;
IlluminizeBam=0;
outFragTailBam=false;
outInterChromBam=false;
outUniqueMultipleBam=false;
outUniquePartialBam=false;
outUniqueUnmappedBam=false;
outAllPairsBam=false;
outReadPairPosBam=false;
//output file
//samfile_t *fp;
bam_header_t *bam_header;
string s = Params.getInput();
BamUtil bam1(s);
Bam = bam1;
string filename=extractfilename(s);
// parameters
string fragPosFile = Params.getString("ReadPairPosFile");
string r = Params.getString("ChromRegion");
int maxReads = Params.getInt("MaxReads");
Qmin = Params.getInt("Qmin");
LRmin = Params.getInt("MinReadLength");
maxmismatchPC=Params.getDouble("FractionMaxMisMatches");
FragLengthWindow=Params.getInt("FragmentLengthWindow");
int cmd_MateMode=Params.getInt("ReadPairSenseConfig");
string ReferenceFastaFile=Params.getString("ReferenceFastaFile");
FragmentTailPercent=Params.getDouble("FragmentTailPercent");
IlluminizeBam=Params.getInt("Illuminize")>0;
outputDirectory=Params.getString("OutputDirectory");
int minLR=Params.getInt("MinReadLength");
int SplitBracketMin=Params.getInt("SplitBracketMin");
int SplitBaseQmin=Params.getInt("SplitBaseQmin");
string StatFile=Params.getString("StatFile");
if (StatFile.size()>0) {
hists H1(StatFile);
hist HLF=H1.h["LF"];
hist HLR=H1.h["LR"];
Params.setHist("LF",HLF);
Params.setHist("LR",HLR);
H1.h.clear(); // free some memory
if (FragmentTailPercent>0) {
LFlow=int(HLF.p2xTrim(FragmentTailPercent/100.));
LFhigh=int(HLF.p2xTrim(1-FragmentTailPercent/100.));
}
}
int dbg = Params.getInt("Dbg");
time(&tprev);
if (ReferenceFastaFile.size()>0) {
FastaObj RF1(ReferenceFastaFile, "");
Reference=RF1;
RF1.seq.clear(); // free some memory
}
bam_header= Bam.fp->header;
string bamheadertext = bam_header->text;
ReadGroup = extractBamTag(bamheadertext,"@RG");
outAllPairsBam=(r.size()>0);
if (!outAllPairsBam) {
outFragTailBam=true; //FragmentTailPercent>=0;
outInterChromBam=true;
outUniqueMultipleBam=true;
outUniquePartialBam=true;
outUniqueUnmappedBam=true;
}
// output Bams
outputBam.clear();
/*
// test BamHeaderContainer
vector<BamHeaderContainer> x;
string sv=SpannerVersion;
string q="@PG\tID:FragmentTail\tPN:SpannerX\tVN"+sv+"\tCL:"+Params.getCmdLine();
while (true) {
string outfile=outputDirectory+"/"+filename+".fragtail.bam";
q=q+"\n@PG\tID:FragmentTail\tPN:SpannerX\tVN"+sv+"\tCL:"+Params.getCmdLine();
BamHeaderContainer x1( bam_header, q);
x.push_back(x1);
bam_header_t* h1=x[x.size()-1].header();
cout<< h1->text << endl;
}
cout << x.size() << endl;
*/
samfile_t *fpFT=0;
samfile_t *fpIC=0;
samfile_t *fpUM=0;
samfile_t *fpUP=0;
samfile_t *fpUZ=0;
samfile_t *fpAP=0;
samfile_t *fpWP=0;
//region
if (r.size()>0) {
int r1,r2,r3;
C_region r0(r);
region=r0;
string bamRegion=region.region;
size_t k=bamRegion.find("chr");
if (k!=string::npos) {
bamRegion=bamRegion.substr(3);
}
if ( bam_parse_region(bam_header, bamRegion.c_str(), &r1, &r2, &r3)==0) {
region.limit=true;
region.anchor=r1;
region.start=r2;
region.end=r3;
} else {
cerr << "region not found\t" << r << endl;
exit(111);
}
}
//fragPosFile
if (fragPosFile.size()>0) {
FragmentPosFileObj fp(fragPosFile);
if (fp.fragmentPosList.size()>0) {
FragPos=fp;
} else {
cerr << "Read Pair Pos file not found\t" << fragPosFile << endl;
exit(112);
}
outFragTailBam=false;
outInterChromBam=false;
outUniqueMultipleBam=false;
outUniquePartialBam=false;
outUniqueUnmappedBam=false;
outReadPairPosBam=true;
}
if (outAllPairsBam) {
string outfile=outputDirectory+"/"+filename+"."+r+".bam";
string sv=SpannerVersion;
string q="@PG\tID:Region\tPN:SpannerX\tVN"+sv+"\tCL:"+Params.getCmdLine();
outputBam["AP"]=BamHeaderContainer(bam_header,q);
bam_header_t* h1=outputBam["AP"].header();
if ((fpAP = samopen(outfile.c_str(), "wb", h1)) == 0) {
fprintf(stderr, "samopen: Fail to open output BAM file %s\n", filename.c_str());
exit(160);
}
}
if (outFragTailBam) {
string outfile=outputDirectory+"/"+filename+".fragtail.bam";
string sv=SpannerVersion;
string q="@PG\tID:FragmentTail\tPN:SpannerX\tVN"+sv+"\tCL:"+Params.getCmdLine();
outputBam["FT"]=BamHeaderContainer(bam_header,q);
bam_header_t* h1=outputBam["FT"].header();
if ((fpFT = samopen(outfile.c_str(), "wb", h1)) == 0) {
fprintf(stderr, "samopen: Fail to open output BAM file %s\n", filename.c_str());
exit(161);
}
}
if (outInterChromBam) {
string outfile=outputDirectory+"/"+filename+".interchrom.bam";
string sv=SpannerVersion;
string q="@PG\tID:InterChromPairs\tPN:SpannerX\tVN"+sv+"\tCL:"+Params.getCmdLine();
outputBam["IC"]=BamHeaderContainer(bam_header,q);
bam_header_t* h1=outputBam["IC"].header();
if ((fpIC = samopen(outfile.c_str(), "wb", h1)) == 0) {
fprintf(stderr, "samopen: Fail to open output BAM file %s\n", filename.c_str());
exit(162);
}
}
if (outUniqueMultipleBam) {
string outfile=outputDirectory+"/"+filename+".uMult.bam";
string sv=SpannerVersion;
string q="@PG\tID:uniqMultiplyMappedPairs\tPN:SpannerX\tVN"+sv+"\tCL:"+Params.getCmdLine();
outputBam["UM"]=BamHeaderContainer(bam_header,q);
bam_header_t* h1=outputBam["IUM"].header();
if ((fpUM = samopen(outfile.c_str(), "wb", h1)) == 0) {
fprintf(stderr, "samopen: Fail to open output BAM file %s\n", filename.c_str());
exit(163);
}
}
if (outUniquePartialBam) {
string outfile=outputDirectory+"/"+filename+".uPart.bam";
string sv=SpannerVersion;
string q="@PG\tID:uniqPartiallyMappedPairs\tPN:SpannerX\tVN"+sv+"\tCL:"+Params.getCmdLine();
outputBam["UP"]=BamHeaderContainer(bam_header,q);
bam_header_t* h1=outputBam["UP"].header();
if ((fpUP = samopen(outfile.c_str(), "wb", h1)) == 0) {
fprintf(stderr, "samopen: Fail to open output BAM file %s\n", filename.c_str());
exit(164);
}
}
if (outUniqueUnmappedBam) {
string outfile=outputDirectory+"/"+filename+".uUnmapped.bam";
string sv=SpannerVersion;
string q="@PG\tID:uniqUnMappedPairs\tPN:SpannerX\tVN"+sv+"\tCL:"+Params.getCmdLine();
outputBam["UZ"]=BamHeaderContainer(bam_header,q);
bam_header_t* h1=outputBam["UZ"].header();
if ((fpUZ = samopen(outfile.c_str(), "wb", h1)) == 0) {
fprintf(stderr, "samopen: Fail to open output BAM file %s\n", filename.c_str());
exit(165);
}
}
if (outReadPairPosBam) {
string outfile=outputDirectory+"/"+filename+".weirdpairs.bam";
string sv=SpannerVersion;
string q="@PG\tID:weirdpairs\tPN:SpannerX\tVN"+sv+"\tCL:"+Params.getCmdLine();
outputBam["WP"]=BamHeaderContainer(bam_header,q);
bam_header_t* h1=outputBam["WP"].header();
if ((fpWP = samopen(outfile.c_str(), "wb", h1)) == 0) {
fprintf(stderr, "samopen: Fail to open output BAM file %s\n", filename.c_str());
exit(165);
}
}
cout << ReadGroup << endl << endl;
//extractMateMode();
if (cmd_MateMode>=0) MateMode=cmd_MateMode;
BamContainerPair bampair;
bool more = true;
while (more)
{
bampair=Bam.getNextBamPair();
// skip if neither end within region
more=(bampair.BamEnd.size()>1);
Npair++;
if (Npair>=maxReads) break;
//
if ( (dbg!=0)&&(elapsedtime()>float(dbg))) {
time(&tprev);
cout << " pairs:" << Npair << "\toutput:" << Nout;
cout << "\tchr:" << bampair.BamEnd[0].b.core.tid+1;
cout << "\tpos:" << bampair.BamEnd[0].b.core.pos;
cout << endl;
}
if (!more) continue;
if (region.limit) {
bool overlap = false;
for (int e=0; e<=1; e++) {
int a1=bampair.BamEnd[e].b.core.tid;
int p1=bampair.BamEnd[e].b.core.pos;
int p2=p1+bampair.BamEnd[e].len;
overlap=region.overlap(a1,p1,p2);
if (overlap) break;
}
if (!overlap) continue;
}
bampair.Illuminize(IlluminizeBam);
bampair.calcFragmentLengths();
more=(bampair.BamEnd[1].packeddata.size()>1);
//if (bampair.BamEnd[0].b.core.tid==bampair.BamEnd[1].b.core.tid)
// cout<< bampair << endl;
bool bothmap = ((bampair.BamEnd[0].b.core.flag&BAM_FUNMAP)==0)&&((bampair.BamEnd[0].b.core.flag&BAM_FMUNMAP)==0);
if (outAllPairsBam) {
Nout++;
int s1=samwrite(fpAP, &(bampair.BamEnd[0].b));
int s2=samwrite(fpAP, &(bampair.BamEnd[1].b));
if ((s1*s2)>0) {
continue;
} else {
cerr << "bad write to pairs.bam" << endl;
exit(150);
}
}
if (outReadPairPosBam) {
int ichr1=bampair.BamEnd[0].b.core.tid+1;
int istd1=bampair.BamEnd[0].sense=='+'? 0: 1;
int ista1=bampair.BamEnd[0].b.core.pos+1;
int iq1=bampair.BamEnd[0].q;
int ichr2=bampair.BamEnd[1].b.core.tid+1;
int istd2=bampair.BamEnd[1].sense=='+'? 0: 1;
int ista2=bampair.BamEnd[1].b.core.pos+1;
int iq2=bampair.BamEnd[1].q;
FragmentPosObj fp1(0,ichr1,istd1,ista1,0,ichr2,istd2,ista2,0,iq1, iq2,0);
/*
if ((fp1.chr1==10)&&(fp1.start1>=89687801)&&(fp1.end1<=89700722)) {
cout << "read "<< fp1 << endl;
}
*/
if (FragPos.find(fp1)) {
Nout++;
int s1=samwrite(fpWP, &(bampair.BamEnd[0].b));
int s2=samwrite(fpWP, &(bampair.BamEnd[1].b));
if ((s1*s2)>0) {
continue;
} else {
cerr << "bad write to weirdpairs.bam" << endl;
exit(156);
}
}
}
bool ok[2];
for (int e=0; e<2; e++) {
uint8_t* bq=bam1_qual(&(bampair.BamEnd[e].b));
int LR=bampair.BamEnd[0].b.core.l_qseq;
double bok=0;
for (int ib=0; ib<LR; ib++) {
if (bq[ib]>SplitBaseQmin) {
bok++;
}
}
ok[e]=(bok>LRmin);
}
if (! (ok[0]&ok[1]) )
continue;
if ( (outFragTailBam) & ((bampair.BamEnd[0].q>=Qmin)|(bampair.BamEnd[1].q>=Qmin)) ) {
bool FT=(bampair.FragmentLength>LFhigh)|((bampair.FragmentLength<LFlow)&(bampair.FragmentLength>INT_MIN))&bothmap;
if (FT && (fpFT!=0)) {
Nout++;
int s1=samwrite(fpFT, &(bampair.BamEnd[0].b));
int s2=samwrite(fpFT, &(bampair.BamEnd[1].b));
//if (outputBam["FT"].write(&(bampair.BamEnd[0].b),&(bampair.BamEnd[1].b))) {
if ((s1*s2)>0) {
continue;
} else {
cerr << "bad write to fragtail.bam" << endl;
exit(151);
}
}
}
if ((outInterChromBam) & ((bampair.BamEnd[0].q>=Qmin)&(bampair.BamEnd[1].q>=Qmin))) {
bool IC=(bampair.BamEnd[0].b.core.tid!=bampair.BamEnd[1].b.core.tid)&&bothmap;
if (IC && (fpIC!=0)) {
Nout++;
int s1=samwrite(fpIC, &(bampair.BamEnd[0].b));
int s2=samwrite(fpIC, &(bampair.BamEnd[1].b));
if ((s1*s2)>0) {
continue;
} else {
cerr << "bad write to interchrom.bam" << endl;
exit(152);
}
}
}
if ((outUniqueMultipleBam) & ((bampair.BamEnd[0].q>=Qmin)|(bampair.BamEnd[1].q>=Qmin))){
int im=bampair.BamEnd[0].nmap>1? 0: 1;
int iu=bampair.BamEnd[0].q>=Qmin? 0: 1;
bool UM=(bampair.BamEnd[iu].nmap>1)&&(iu!=im)&&bothmap;
if (UM && (fpUM!=0)) {
Nout++;
int s1=samwrite(fpUM, &(bampair.BamEnd[0].b));
int s2=samwrite(fpUM, &(bampair.BamEnd[1].b));
if ((s1*s2)>0) {
continue;
} else {
cerr << "bad write to uMult.bam" << endl;
exit(153);
}
}
}
if ( (outUniquePartialBam) && ((bampair.BamEnd[0].q>=Qmin)|(bampair.BamEnd[1].q>=Qmin)) && bothmap) {
int c0=bampair.BamEnd[0].clip[0]+bampair.BamEnd[0].clip[1];
int LR=bampair.BamEnd[0].b.core.l_qseq;
bool split0=((LR-c0)>SplitBracketMin)&(c0>SplitBracketMin);
int ib0=0;
if ((split0)&(bampair.BamEnd[0].clip[0]>SplitBracketMin)) {
ib0=bampair.BamEnd[0].clip[0];
} else if ((split0)&(bampair.BamEnd[0].clip[1]>SplitBracketMin) ) {
ib0=LR-bampair.BamEnd[0].clip[1];
}
split0=split0&(ib0>0);
if (split0) {
uint8_t* bq=bam1_qual(&(bampair.BamEnd[0].b));
for (int ib=(ib0-SplitBracketMin); ib<(ib0+SplitBracketMin); ib++) {
if (bq[ib]<SplitBaseQmin) {
split0=false;
break;
}
}
}
int c1=bampair.BamEnd[1].clip[0]+bampair.BamEnd[1].clip[1];
LR=bampair.BamEnd[1].b.core.l_qseq;
bool split1=((LR-c0)>SplitBracketMin)&(c1>SplitBracketMin);;
int ib1=0;
if ((split1)&(bampair.BamEnd[1].clip[0]>SplitBracketMin)) {
ib1=bampair.BamEnd[1].clip[0];
} else if ((split1)&(bampair.BamEnd[1].clip[1]>SplitBracketMin) ) {
ib1=LR-bampair.BamEnd[1].clip[1];
}
split1=split1&(ib1>0);
if (split1) {
uint8_t* bq=bam1_qual(&(bampair.BamEnd[1].b));
for (int ib=(ib1-SplitBracketMin); ib<(ib1+SplitBracketMin); ib++) {
if (bq[ib]<SplitBaseQmin) {
split1=false;
break;
}
}
}
bool UP=(split0|split1)&((c1+c0)>minLR);
if (UP && (fpUP!=0)) {
Nout++;
int s1=samwrite(fpUP, &(bampair.BamEnd[0].b));
int s2=samwrite(fpUP, &(bampair.BamEnd[1].b));
if ((s1*s2)>0) {
continue;
} else {
cerr << "bad write to uPart.bam" << endl;
exit(154);
}
}
}
if ( (outUniqueUnmappedBam) & ((bampair.BamEnd[0].q>=Qmin)|(bampair.BamEnd[1].q>=Qmin)) ) {
bool z0=((bampair.BamEnd[0].b.core.flag&BAM_FUNMAP)>0);
bool z1=((bampair.BamEnd[1].b.core.flag&BAM_FUNMAP)>0);
uint8_t* bq=bam1_qual(&(bampair.BamEnd[0].b));
for (int nb,ib=0; ib<bampair.BamEnd[0].b.core.l_qseq; ib++) {
if (bq[ib]<SplitBaseQmin) {
nb++;
}
}
bool UZ=(z0|z1)&(!(z1&z0));
if (UZ && (fpUZ!=0)) {
Nout++;
int s1=samwrite(fpUZ, &(bampair.BamEnd[0].b));
int s2=samwrite(fpUZ, &(bampair.BamEnd[1].b));
if ((s1*s2)>0) {
continue;
} else {
cerr << "bad write to uUnmapped.bam" << endl;
exit(155);
}
}
}
//cout<< bampair.Orientation << "\t"<< bampair.FragmentLength << "\t" <<bampair.BamEnd[1].b.core.pos << endl;
}
if (outReadPairPosBam) {
samclose(fpWP);
} else {
if (outAllPairsBam) {
samclose(fpAP);
} else {
samclose(fpFT);
samclose(fpIC);
samclose(fpUP);
samclose(fpUM);
samclose(fpUZ);
}
}
/*
for (ioutputBam=outputBam.begin(); ioutputBam!=outputBam.end(); ioutputBam++) {
(*ioutputBam).second.close();
}
if (FragmentTailPercent>0)
outputBam["FT"].close();
*/
samclose(Bam.fp);
}
void tSecureStream::m_setupServer(const tRSA& rsa, string appGreeting)
{
// Read the greeting (part 1) from the client.
// Note: The following DOES leak timing information, but we don't
// care because 'kLibrhoGreeting' isn't a secret.
string receivedLibrhoGreeting;
try {
unpack(m_internal_readable, receivedLibrhoGreeting, (u32)kLibrhoGreeting.size());
} catch (ebObject& e) {
s_failConnection(m_internal_writable, "The secure client did not greet me properly.");
}
if (receivedLibrhoGreeting != kLibrhoGreeting)
s_failConnection(m_internal_writable, "The secure client did not greet me properly.");
// Read the greeting (part 2) from the client.
// Note: The following DOES leak timing information, but we don't
// care because 'appGreeting' isn't a secret.
string receivedAppGreeting;
try {
unpack(m_internal_readable, receivedAppGreeting, (u32)appGreeting.size());
} catch (ebObject& e) {
s_failConnection(m_internal_writable, "The secure client requested a different application.");
}
if (receivedAppGreeting != appGreeting)
s_failConnection(m_internal_writable, "The secure client requested a different application.");
// Read the client's random bytes.
// Again, we don't care about the leaked info here because the correct
// random vector length is not a secret.
vector<u8> rand_c;
try {
unpack(m_internal_readable, rand_c, kRandVectLen);
} catch (ebObject& e) {
s_failConnection(m_internal_writable, "The secure client sent a random byte vector of the wrong length.");
}
if (rand_c.size() != kRandVectLen)
s_failConnection(m_internal_writable, "The secure client sent a random byte vector of the wrong length.");
// Read the encrypted pre-secret from the client.
// (No info is leaked by this section.)
vector<u8> enc;
try {
unpack(m_internal_readable, enc, rsa.maxMessageLength()+5);
} catch (ebObject& e) {
s_failConnection(m_internal_writable, "The secure client failed to send an encrypted pre-secret.");
}
// Now that the server has read everything from the client, it
// will do some calculations.
// We will protect this section with a const time block to
// protect against timing side-channel attacks.
vector<u8> pre_secret, rand_s, secret, f, gPrime;
{
// This object is constructed in this code block, and it
// will be destructed when this block ends. The d'tor of
// this class calls sleep() in order to enforce consistent
// timing of the execution of this block.
tConstTimeBlock ctb(&gServerProcessGreetingTimingHistory);
// Decrypt the pre-secret and make sure it looks okay.
pre_secret = rsa.decrypt(enc);
if (pre_secret.size() != kPreSecretLen)
s_failConnection(m_internal_writable, "The secure client gave a pre-secret that is the wrong length.");
// Generate the server random byte vector.
rand_s = s_genRand(kRandVectLen);
// Calculated the shared secret (from the pre-secret).
secret = H1(pre_secret, rand_c, rand_s);
// Calculate the proof-of-server hash. (The convinces the client that we are the actual server.)
f = H2(secret, rand_c, rand_s);
// Calculate what the client correct response would be.
gPrime = H3(secret, rand_c, rand_s);
}
// Write back to the client all this stuff.
pack(m_internal_writable, kSuccessfulGreeting);
pack(m_internal_writable, rand_s);
pack(m_internal_writable, f);
s_flush(m_internal_writable);
// Have the client prove that it is a real client, not a reply attack.
vector<u8> g;
try {
unpack(m_internal_readable, g, (u32)gPrime.size());
} catch (ebObject& e) {
throw eRuntimeError("The secure client failed to show proof that it is real.");
}
if (!s_constTimeIsEqual(g, gPrime))
throw eRuntimeError("The secure client failed to show proof that it is real.");
// Setup secure streams with the client.
vector<u8> ksw = H4(pre_secret, secret, rand_c, rand_s); // <-- the Key for the Server Writer
vector<u8> kcw = H5(pre_secret, secret, rand_c, rand_s); // <-- the Key for the Client Writer
m_readable = new tReadableAES(m_internal_readable, kOpModeCBC,
&kcw[0], s_toKeyLen(kcw.size()));
m_writable = new tWritableAES(m_internal_writable, kOpModeCBC,
&ksw[0], s_toKeyLen(ksw.size()));
}