//void OccupancyGrid::getVoxelsInBox(const geometry_msgs::Pose &pose, const std::vector<double> &dim, std::vector<btVector3> &voxels)
void OccupancyGrid::getVoxelsInBox(const geometry_msgs::Pose &pose, const std::vector<double> &dim, std::vector<Eigen::Vector3d> &voxels)
{
//btVector3 vin, vout, v(pose.position.x, pose.position.y, pose.position.z);
//btMatrix3x3 m(btQuaternion(pose.orientation.x, pose.orientation.y, pose.orientation.z, pose.orientation.w));
Eigen::Vector3d vin, vout, v(pose.position.x, pose.position.y, pose.position.z);
Eigen::Matrix3d m(Eigen::Quaterniond(pose.orientation.w, pose.orientation.x, pose.orientation.y, pose.orientation.z));
for (double x=0-dim[0]/2.0; x<=dim[0]/2.0; x+=grid_resolution_)
{
for (double y=0-dim[1]/2.0; y<=dim[1]/2.0; y+=grid_resolution_)
{
for (double z=0-dim[2]/2.0; z<=dim[2]/2.0; z+=grid_resolution_)
{
/*
vin.setX(x);
vin.setY(y);
vin.setZ(z);
vout = m*vin;
vout += v;
*/
vin(0) = (x);
vin(1) = (y);
vin(2) = (z);
vout = m*vin;
vout += v;
voxels.push_back(vout);
}
}
}
}
int main() {
VCFInputFile vin("noindex.vcf.gz");
vin.setRangeList("1:0");
int lineNo = 0;
while (vin.readRecord()) {
lineNo ++;
VCFRecord& r = vin.getVCFRecord();
VCFPeople& people = r.getPeople();
VCFIndividual* indv;
printf("%s:%d\t", r.getChrom(), r.getPos());
// e.g.: get TAG from INFO field
// fprintf(stderr, "%s\n", r.getInfoTag("ANNO"));
// e.g.: Loop each (selected) people in the same order as in the VCF
for (int i = 0; i < people.size(); i++) {
indv = people[i];
// get GT index. if you are sure the index will not change, call this function only once!
int GTidx = r.getFormatIndex("GT");
if (GTidx >= 0)
printf("%s ", indv->justGet(0).toStr()); // [0] meaning the first field of each individual
else
fprintf(stderr, "Cannot find GT field!\n");
}
printf("\n");
};
fprintf(stdout, "Total %d VCF records have converted successfully\n", lineNo);
};
main(int argc, char *argv[]) {
node gnd;
node n1("n1");
node n2("n2");
node n3("n3");
node n4("n4");
node n5("n5");
node n6("n6");
vdc vcc("vcc", n6, gnd, 5.0);
vpulse vin("vin", n1, gnd, 0, 5, 2e-9, 2e-9, 2e-9, 10e-9);
r rb1("rb1", n1, n2, 10e3);
r rc1("rc1", n6, n3, 1e3);
qnd q1("q1", n3, n2, gnd);
r rb2("rb2", n3, n4, 10e3);
qnd q2("q2", n5, n4, gnd);
r rc2("rc2", n6, n5, 1e3);
op::monitor = 1;
op();
plot::output = *argv;
plot::add("n1", "n3", "n5");
tran::tsmin = 1.0e-30;
tran::monitor = 1;
tran(0.2e-9, 20.0e-9);
}
bool GFX::project(const vec3 &obj,
const mat4 &modelview_matrix,
const mat4 &projection_matrix,
const int *viewport_matrix,
float *winx, float *winy, float *winz)
{
vec4 vin(obj, 1.0f),
vout;
vout = vin * modelview_matrix;
vin = vout * projection_matrix;
if (!vin->w) return false;
vin->x /= vin->w;
vin->y /= vin->w;
vin->z /= vin->w;
vin->x = vin->x * 0.5f + 0.5f;
vin->y = vin->y * 0.5f + 0.5f;
vin->z = vin->z * 0.5f + 0.5f;
vin->x = vin->x * viewport_matrix[2] + viewport_matrix[0];
vin->y = vin->y * viewport_matrix[3] + viewport_matrix[1];
*winx = vin->x;
*winy = vin->y;
*winz = vin->z;
return true;
}
bool GFX::unproject(const float winx, const float winy, const float winz,
const mat4 &modelview_matrix,
const mat4 &projection_matrix,
const int *viewport_matrix, vec3 &obj)
{
vec4 vin(winx, winy, winz, 1.0f);
for (int i=0; i<2; ++i)
vin[i] = (vin[i] - viewport_matrix[i]) / viewport_matrix[i+2];
for (int i=0; i<3; ++i)
vin[i] = vin[i] * 2.0f - 1.0f;
// Equivalent to operations on vin above. The operations above
// are much more efficient but the operations below give the
// reader better insight into what the code is actually doing
// mathematically.
// TStack l;
//
// l.translate(vec3(-1.0f, -1.0f, -1.0f));
// l.scale(vec3(2.0f, 2.0f, 2.0f));
// l.scale(vec3(1.0f/viewport_matrix[2], 1.0f/viewport_matrix[3], 1.0f));
// l.translate(vec3(-viewport_matrix[0], -viewport_matrix[1], 0.0f));
// vin *= l.back();
vec4 vout = vin / (modelview_matrix * projection_matrix);
return vout->w ? obj=vec3(vout),true : false;
}
void TxToUniv(const CTransaction& tx, const uint256& hashBlock, UniValue& entry, bool include_hex, int serialize_flags)
{
entry.pushKV("txid", tx.GetHash().GetHex());
entry.pushKV("hash", tx.GetWitnessHash().GetHex());
entry.pushKV("version", tx.nVersion);
entry.pushKV("size", (int)::GetSerializeSize(tx, SER_NETWORK, PROTOCOL_VERSION));
entry.pushKV("vsize", (GetTransactionWeight(tx) + WITNESS_SCALE_FACTOR - 1) / WITNESS_SCALE_FACTOR);
entry.pushKV("weight", GetTransactionWeight(tx));
entry.pushKV("locktime", (int64_t)tx.nLockTime);
UniValue vin(UniValue::VARR);
for (unsigned int i = 0; i < tx.vin.size(); i++) {
const CTxIn& txin = tx.vin[i];
UniValue in(UniValue::VOBJ);
if (tx.IsCoinBase())
in.pushKV("coinbase", HexStr(txin.scriptSig.begin(), txin.scriptSig.end()));
else {
in.pushKV("txid", txin.prevout.hash.GetHex());
in.pushKV("vout", (int64_t)txin.prevout.n);
UniValue o(UniValue::VOBJ);
o.pushKV("asm", ScriptToAsmStr(txin.scriptSig, true));
o.pushKV("hex", HexStr(txin.scriptSig.begin(), txin.scriptSig.end()));
in.pushKV("scriptSig", o);
if (!tx.vin[i].scriptWitness.IsNull()) {
UniValue txinwitness(UniValue::VARR);
for (const auto& item : tx.vin[i].scriptWitness.stack) {
txinwitness.push_back(HexStr(item.begin(), item.end()));
}
in.pushKV("txinwitness", txinwitness);
}
}
in.pushKV("sequence", (int64_t)txin.nSequence);
vin.push_back(in);
}
entry.pushKV("vin", vin);
UniValue vout(UniValue::VARR);
for (unsigned int i = 0; i < tx.vout.size(); i++) {
const CTxOut& txout = tx.vout[i];
UniValue out(UniValue::VOBJ);
out.pushKV("value", ValueFromAmount(txout.nValue));
out.pushKV("n", (int64_t)i);
UniValue o(UniValue::VOBJ);
ScriptPubKeyToUniv(txout.scriptPubKey, o, true);
out.pushKV("scriptPubKey", o);
vout.push_back(out);
}
entry.pushKV("vout", vout);
if (!hashBlock.IsNull())
entry.pushKV("blockhash", hashBlock.GetHex());
if (include_hex) {
entry.pushKV("hex", EncodeHexTx(tx, serialize_flags)); // The hex-encoded transaction. Used the name "hex" to be consistent with the verbose output of "getrawtransaction".
}
}
void TxToUniv(const CTransaction &tx, const uint256 &hashBlock,
UniValue &entry) {
entry.pushKV("txid", tx.GetId().GetHex());
entry.pushKV("hash", tx.GetHash().GetHex());
entry.pushKV("version", tx.nVersion);
entry.pushKV("locktime", (int64_t)tx.nLockTime);
UniValue vin(UniValue::VARR);
for (unsigned int i = 0; i < tx.vin.size(); i++) {
const CTxIn &txin = tx.vin[i];
UniValue in(UniValue::VOBJ);
if (tx.IsCoinBase()) {
in.pushKV("coinbase",
HexStr(txin.scriptSig.begin(), txin.scriptSig.end()));
} else {
in.pushKV("txid", txin.prevout.hash.GetHex());
in.pushKV("vout", (int64_t)txin.prevout.n);
UniValue o(UniValue::VOBJ);
o.pushKV("asm", ScriptToAsmStr(txin.scriptSig, true));
o.pushKV("hex",
HexStr(txin.scriptSig.begin(), txin.scriptSig.end()));
in.pushKV("scriptSig", o);
}
in.pushKV("sequence", (int64_t)txin.nSequence);
vin.push_back(in);
}
entry.pushKV("vin", vin);
UniValue vout(UniValue::VARR);
for (unsigned int i = 0; i < tx.vout.size(); i++) {
const CTxOut &txout = tx.vout[i];
UniValue out(UniValue::VOBJ);
UniValue outValue(UniValue::VNUM,
FormatMoney(txout.nValue.GetSatoshis()));
out.pushKV("value", outValue);
out.pushKV("n", (int64_t)i);
UniValue o(UniValue::VOBJ);
ScriptPubKeyToUniv(txout.scriptPubKey, o, true);
out.pushKV("scriptPubKey", o);
vout.push_back(out);
}
entry.pushKV("vout", vout);
if (!hashBlock.IsNull()) {
entry.pushKV("blockhash", hashBlock.GetHex());
}
// the hex-encoded transaction. used the name "hex" to be consistent with
// the verbose output of "getrawtransaction".
entry.pushKV("hex", EncodeHexTx(tx));
}
inline void addvec_simd(F * out, const F in, unsigned int n)
{
const int per_loop = vec<F>::objects_per_cacheline;
vec<F> vin(in);
n /= per_loop;
do
{
detail::addvec<F, per_loop>::mp_iteration(out, vin);
out += per_loop;
}
while (--n);
}
void OccupancyGrid::getOccupiedVoxels(const geometry_msgs::Pose &pose, const std::vector<double> &dim, std::vector<Eigen::Vector3d> &voxels)
{
Eigen::Vector3d vin, vout, v(pose.position.x, pose.position.y, pose.position.z);
Eigen::Matrix3d m(Eigen::Quaterniond(pose.orientation.w, pose.orientation.x, pose.orientation.y, pose.orientation.z));
for (double x=0-dim[0]/2.0; x<=dim[0]/2.0; x+=grid_->getResolution())
{
for (double y=0-dim[1]/2.0; y<=dim[1]/2.0; y+=grid_->getResolution())
{
for (double z=0-dim[2]/2.0; z<=dim[2]/2.0; z+=grid_->getResolution())
{
vin(0) = (x);
vin(1) = (y);
vin(2) = (z);
vout = m*vin;
vout += v;
voxels.push_back(vout);
}
}
}
}
int loadMarkerFromVCF(const std::string& fileName, const std::string& marker,
std::vector<std::string>* rowLabel, Matrix* genotype) {
if (!rowLabel || !genotype) {
// invalid parameter
return -1;
}
Matrix& m = *genotype;
int col = 0;
VCFInputFile vin(fileName);
vin.setRangeList(marker);
while (vin.readRecord()) {
VCFRecord& r = vin.getVCFRecord();
VCFPeople& people = r.getPeople();
VCFIndividual* indv;
m.Dimension(people.size(), col + 1);
int GTidx = r.getFormatIndex("GT");
for (int i = 0; i < (int)people.size(); i++) {
indv = people[i];
// get GT index. if you are sure the index will not change,
// call this function only once!
if (GTidx >= 0) {
// printf("%s ", indv->justGet(0).toStr()); // [0] meaning the first
// field of each individual
m[i][col] = indv->justGet(GTidx).getGenotype();
} else {
logger->error("Cannot find GT field!");
return -1;
}
}
if (col == 0) {
// set-up names
rowLabel->resize(people.size());
for (size_t i = 0; i < people.size(); ++i) {
(*rowLabel)[i] = people[i]->getName();
}
}
std::string colLabel = r.getChrom();
colLabel += ":";
colLabel += r.getPosStr();
m.SetColumnLabel(col, colLabel.c_str());
++col;
}
return 0;
}
void TxToUniv(const CTransaction& tx, const uint256& hashBlock, UniValue& entry)
{
entry.pushKV("txid", tx.GetHash().GetHex());
entry.pushKV("version", tx.nVersion);
entry.pushKV("locktime", (int64_t)tx.nLockTime);
UniValue vin(UniValue::VARR);
BOOST_FOREACH(const CTxIn& txin, tx.vin) {
UniValue in(UniValue::VOBJ);
if (tx.IsCoinBase())
in.pushKV("coinbase", HexStr(txin.scriptSig.begin(), txin.scriptSig.end()));
else {
in.pushKV("txid", txin.prevout.hash.GetHex());
in.pushKV("vout", (int64_t)txin.prevout.n);
UniValue o(UniValue::VOBJ);
o.pushKV("asm", txin.scriptSig.ToString());
o.pushKV("hex", HexStr(txin.scriptSig.begin(), txin.scriptSig.end()));
in.pushKV("scriptSig", o);
}
in.pushKV("sequence", (int64_t)txin.nSequence);
vin.push_back(in);
}
entry.pushKV("vin", vin);
UniValue vout(UniValue::VARR);
for (unsigned int i = 0; i < tx.vout.size(); i++) {
const CTxOut& txout = tx.vout[i];
UniValue out(UniValue::VOBJ);
UniValue outValue(UniValue::VNUM, FormatMoney(txout.nValue));
out.pushKV("value", outValue);
out.pushKV("n", (int64_t)i);
UniValue o(UniValue::VOBJ);
ScriptPubKeyToUniv(txout.scriptPubKey, o, true);
out.pushKV("scriptPubKey", o);
vout.push_back(out);
}
entry.pushKV("vout", vout);
if (hashBlock != 0)
entry.pushKV("blockhash", hashBlock.GetHex());
}
int main(int argc, char *argv[]) {
NODE(gnd);
NODE(in);
NODE(out);
vco vco1("vco1", in, gnd, out, gnd, 1.0, 7.0e6, 30.0e3);
r r1 ("r1", out, gnd, 1.0e6);
vdc vin("vin", in, gnd, 1.0);
op::monitor = 1;
kernel::op();
// plot::output = *argv;
// plot::add("in", "pll_in", "lf_out", "vco_out");
//
// tran::monitor = 1;
// tran::tsmin = 1.0e-21;
// tran(1.0e-7, 300.0e-6, 0.0, 1.0e-9);
}
Vector3 RenderTargetD3D9::project(const Vector3 & v)
{
//world matrix
D3DXMATRIX matWorldD3D ( MappingsD3D9::getMatrix( m_RenderState.m_mtxWorld ) );
//view matrix
xs::Matrix4 matView( m_RenderState.m_mtxView );
matView[2][0] = -matView[2][0];
matView[2][1] = -matView[2][1];
matView[2][2] = -matView[2][2];
matView[2][3] = -matView[2][3];
D3DXMATRIX matViewD3D( MappingsD3D9::getMatrix( matView ) );
//projection matrix
xs::Matrix4 matProj;
convertProjectionMatrix(m_RenderState.m_mtxProjection, matProj, false);
D3DXMATRIX matProjD3D( MappingsD3D9::getMatrix( matProj) );
D3DXVECTOR3 vin(v.x, v.y, v.z);
D3DXVECTOR3 vout;
D3DXVec3Project(&vout, &vin, &m_viewport, &matProjD3D, &matViewD3D, &matWorldD3D);
return Vector3(vout.x, vout.y, vout.z);
}
// -----------------------------------
void OggVorbisSubStream::procHeaders(Channel *ch)
{
unsigned int packPtr=0;
for(int i=0; i<pack.numPackets; i++)
{
MemoryStream vin(&pack.body[packPtr],pack.packetSizes[i]);
packPtr += pack.packetSizes[i];
char id[8];
vin.read(id,7);
id[7]=0;
switch (id[0])
{
case 1: // ident
LOG_CHANNEL("OGG Vorbis Header: Ident (%d bytes)",vin.len);
readIdent(vin,ch->info);
break;
case 3: // comment
{
LOG_CHANNEL("OGG Vorbis Header: Comment (%d bytes)",vin.len);
ChanInfo newInfo = ch->info;
readComment(vin,newInfo);
ch->updateInfo(newInfo);
}
break;
case 5: // setup
LOG_CHANNEL("OGG Vorbis Header: Setup (%d bytes)",vin.len);
//readSetup(vin);
break;
default:
throw StreamException("Unknown Vorbis packet header type");
break;
}
}
}
int main(int argc, char** argv){
time_t currentTime = time(0);
fprintf(stderr, "Analysis started at: %s", ctime(¤tTime));
////////////////////////////////////////////////
BEGIN_PARAMETER_LIST(pl)
ADD_PARAMETER_GROUP(pl, "Input/Output")
ADD_STRING_PARAMETER(pl, inVcf, "--inVcf", "input VCF File")
ADD_STRING_PARAMETER(pl, outVcf, "--outVcf", "output VCF File")
ADD_PARAMETER_GROUP(pl, "Site Filter")
ADD_STRING_PARAMETER(pl, site, "--site", "input site file (.rod file: 0-based position)")
ADD_BOOL_PARAMETER(pl, inverse, "--inverse", "Inverse site")
ADD_STRING_PARAMETER(pl, rangeList, "--rangeList", "Specify some ranges to use, please use chr:begin-end format.")
ADD_STRING_PARAMETER(pl, rangeFile, "--rangeFile", "Specify the file containing ranges, please use chr:begin-end format.")
ADD_BOOL_PARAMETER(pl, snpOnly, "--snpOnly", "Specify only extract SNP site")
END_PARAMETER_LIST(pl)
;
pl.Read(argc, argv);
pl.Status();
if (FLAG_REMAIN_ARG.size() > 0){
fprintf(stderr, "Unparsed arguments: ");
for (unsigned int i = 0; i < FLAG_REMAIN_ARG.size(); i++){
fprintf(stderr, " %s", FLAG_REMAIN_ARG[i].c_str());
}
fprintf(stderr, "\n");
abort();
}
REQUIRE_STRING_PARAMETER(FLAG_inVcf, "Please provide input file using: --inVcf");
REQUIRE_STRING_PARAMETER(FLAG_outVcf, "Please provide output file using: --outVcf");
const char defaultDbSnp[] = "/net/fantasia/home/zhanxw/amd/data/umake-resources/dbSNP/dbsnp_129_b37.rod.map";
if (FLAG_site == "") {
FLAG_site = defaultDbSnp;
fprintf(stderr, "Use default dbsnp: [ %s ]\n", defaultDbSnp);
}
SiteSet snpSet;
snpSet.loadRodFile(FLAG_site);
fprintf(stderr, "%zu dbSNP sites loaded.\n", snpSet.getTotalSite());
const char* fn = FLAG_inVcf.c_str();
VCFInputFile vin(fn);
VCFOutputFile* vout = NULL;
// PlinkOutputFile* pout = NULL;
if (FLAG_outVcf.size() > 0) {
vout = new VCFOutputFile(FLAG_outVcf.c_str());
};
if (vout) vout->writeHeader(vin.getVCFHeader());
// set range filters here
// e.g.
// vin.setRangeList("1:69500-69600");
vin.setRangeList(FLAG_rangeList.c_str());
vin.setRangeFile(FLAG_rangeFile.c_str());
std::string filt;
/// char ref, alt;
bool keep;
int lineNo = 0;
int lineOut = 0;
while (vin.readRecord()){
lineNo ++;
VCFRecord& r = vin.getVCFRecord();
keep = snpSet.isIncluded(r.getChrom(), r.getPos());
if (FLAG_inverse) {
keep = !keep;
}
if (!keep) continue;
if (FLAG_snpOnly) {
if ( strlen(r.getRef()) != 1) continue;
if ( strlen(r.getAlt()) != 1) continue;
if ( r.getAlt()[0] == '.') continue; //deletion e.g. A -> .
}
if (vout) vout->writeRecord(& r);
lineOut ++;
};
delete vout;
fprintf(stdout, "Total %d VCF records have converted successfully\n", lineNo);
fprintf(stdout, "Total %d VCF records have outputted successfully\n", lineOut);
currentTime = time(0);
fprintf(stderr, "Analysis end at: %s", ctime(¤tTime));
return 0;
};
LRESULT CALLBACK WndProc(HWND hWnd, UINT message, WPARAM wParam, LPARAM lParam)
{
int wmId, wmEvent;
PAINTSTRUCT ps;
HDC hdc;
bool flag = true;
FILE* file;
switch (message)
{
case WM_KEYDOWN:
switch (wParam) {
case VK_LEFT:
for(int row = 0; row < 4; ++row){
for(int col = 0; col < 4; ++col){
if (matrix[row][col] == 0 && col < 3 && flag){
matrix[row][col] = matrix[row][col + 1];
matrix[row][col + 1] = 0;
flag = false;
}
}
}
flag = true;
InvalidateRect(hWnd, NULL,true);
break;
case VK_RIGHT:
for(int row = 0; row < 4; ++row){
for(int col = 0; col < 4; ++col){
if (matrix[row][col] == 0 && col > 0 && flag){
matrix[row][col] = matrix[row][col - 1];
matrix[row][col - 1] = 0;
flag = false;
}
}
}
flag = true;
InvalidateRect(hWnd, NULL,true);
break;
case VK_UP:
for(int row = 0; row < 4; ++row){
for(int col = 0; col < 4; ++col){
if (matrix[row][col] == 0 && row < 3 && flag){
matrix[row][col] = matrix[row + 1][col];
matrix[row + 1][col] = 0;
flag = false;
}
}
}
flag = true;
InvalidateRect(hWnd, NULL,true);
break;
case VK_DOWN:
for(int row = 0; row < 4; ++row){
for(int col = 0; col < 4; ++col){
if (matrix[row][col] == 0 && row > 0 && flag){
matrix[row][col] = matrix[row - 1][col];
matrix[row - 1][col] = 0;
flag = false;
}
}
}
flag = true;
InvalidateRect(hWnd, NULL,true);
break;
default:
return DefWindowProc(hWnd, message, wParam, lParam );
break;
}
vin(hWnd);
break;
case WM_LBUTTONDOWN:
{
int xPos = GET_X_LPARAM(lParam);
int yPos = GET_Y_LPARAM(lParam);
for(int row = 0; row < 4; ++row){
for(int col = 0; col < 4; ++col){
if (yPos > row*100+15 && xPos > col*100+15 && yPos < row*100+100 && xPos < col*100+100){
if (matrix[row][col-1] == 0 && col > 0 && flag){
matrix[row][col-1] = matrix[row][col];
matrix[row][col] = 0;
flag = false;
}else if (matrix[row][col+1] == 0 && col < 3 && flag){
matrix[row][col+1] = matrix[row][col];
matrix[row][col] = 0;
flag = false;
}else if (matrix[row-1][col] == 0 && row > 0 && flag){
matrix[row-1][col] = matrix[row][col];
matrix[row][col] = 0;
flag = false;
}else if (matrix[row+1][col] == 0 && row < 3 && flag){
matrix[row+1][col] = matrix[row][col];
matrix[row][col] = 0;
flag = false;
}
}
}
}
flag = true;
InvalidateRect(hWnd, NULL,true);
}
vin(hWnd);
break;
case WM_SIZE:
break;
case WM_COMMAND:
wmId = LOWORD(wParam);
wmEvent = HIWORD(wParam);
// Разобрать выбор в меню:
if (wmId == 10000)
{
for(int i = 0; i < 800; ++i){
v=1;
switch(rand()%(4)){
case 0:
SendMessage(hWnd, WM_KEYDOWN, VK_RIGHT, 1);
UpdateWindow(hWnd);
break;
case 1:
SendMessage(hWnd, WM_KEYDOWN, VK_LEFT, 1);
UpdateWindow(hWnd);
break;
case 2:
SendMessage(hWnd, WM_KEYDOWN, VK_UP, 1);
UpdateWindow(hWnd);
break;
case 3:
SendMessage(hWnd, WM_KEYDOWN, VK_DOWN, 1);
UpdateWindow(hWnd);
break;
}
v=0;
//Sleep(100);
}
MessageBox(hWnd, L"Фсьо, перемішав!", L"", 0);
}else if(wmId == 9000 || wmId == IDM_32773){
file = fopen("save", "w");
for(int row = 0; row < 4; ++row){
for(int col = 0; col < 4; ++col){
if(matrix[row][col] < 10)
fprintf (file, "%d \n", matrix[row][col]);
else
fprintf (file, "%d\n", matrix[row][col]);
}
}
fclose(file);
SetFocus(hWnd);
MessageBox(hWnd,L"Гру успішно збережено", L"Файл записано",NULL);
}else if(wmId == 8000 || wmId == IDM_32772){
file = fopen("save", "a+");
for(int row = 0; row < 4; ++row){
for(int col = 0; col < 4; ++col){
char s[3];
char ss[3];
s[0]=NULL;s[1]=NULL;s[2]=NULL;
fgets(s, 3, file);
fgets(ss, 2, file);
matrix[row][col] = atoi(s);
}
}
fclose(file);
UpdateWindow(hWnd);
InvalidateRect(hWnd, NULL,true);
SetFocus(hWnd);
MessageBox(hWnd,L"Гру відновлено", L"Файл відкрито",NULL);
}else if(wmId == IDM_ABOUT){
DialogBox(hInst, MAKEINTRESOURCE(IDD_ABOUTBOX), hWnd, About);
}else if(wmId == IDM_EXIT){
DestroyWindow(hWnd);
}else{
return DefWindowProc(hWnd, message, wParam, lParam);
}
break;
case WM_PAINT:
hdc = BeginPaint(hWnd, &ps);
Rectangle(hdc, 5,5,425,425);
Rectangle(hdc, 6,6,424,424);
Rectangle(hdc, 7,7,423,423);
for(int row = 0; row < 4; ++row){
for(int col = 0; col < 4; ++col){
if (matrix[row][col] != 0){
paste_picture(hWnd, hdc, row, col, matrix[row][col]);
}
}
}
EndPaint(hWnd, &ps);
break;
case WM_DESTROY:
PostQuitMessage(0);
break;
default:
return DefWindowProc(hWnd, message, wParam, lParam);
}
return 0;
}
int main(int argc, char** argv) {
time_t currentTime = time(0);
fprintf(stderr, "Analysis started at: %s", ctime(¤tTime));
PARSE_PARAMETER(argc, argv);
PARAMETER_STATUS();
REQUIRE_STRING_PARAMETER(FLAG_s, "Please provide input file using: -s");
// load referene
const char* fn = FLAG_s.c_str();
VCFInputFile vin(fn);
StringArray refPeople;
vin.getVCFHeader()->getPeopleName(&refPeople);
VCFInputFile** compareVcfs = new VCFInputFile*[FLAG_REMAIN_ARG.size()];
StringArray comparePeopleNames;
for (unsigned int i = 0; i < FLAG_REMAIN_ARG.size(); i++) {
compareVcfs[i] = new VCFInputFile(FLAG_REMAIN_ARG[i]);
StringArray names;
compareVcfs[i]->getVCFHeader()->getPeopleName(&names);
for (unsigned int j = 0; j < names.size(); j++) {
comparePeopleNames.push_back(names[j]);
};
};
StringArray unionPeopleNames;
StringArray commonNames;
set_union(comparePeopleNames, &unionPeopleNames);
set_intersection(refPeople, unionPeopleNames, &commonNames);
vin.excludeAllPeople();
vin.includePeople(commonNames);
fprintf(stderr, "Total %d samples are included.\n", (int)commonNames.size());
// set range filters here
// e.g.
// vin.setRangeList("1:69500-69600");
vin.setRangeList(FLAG_rangeList.c_str());
vin.setRangeFile(FLAG_rangeFile.c_str());
vin.setSiteFile(FLAG_siteFile.c_str());
AllConcordanceType data;
loadGenotype(vin, &data, Value::REFERENCE);
printf(
"File\t"
"PeopleId\t"
"Overlap\t"
"Std_total\t"
"Input_total\t"
"Std_only\t"
"Input_only\t"
"nonRefConcord_overlap\t"
"Std_variants\t"
"Input_variants\t"
"Std_variants_in_Input\t"
"Ptg_Std_variants_in_Input\t"
"HomR/HomR\tHomR/Het\tHomR/HomA\t"
"Het/HomR\tHet/Het\tHet/HomA\t"
"HomA/HomR\tHomA/Het\tHomA/HomA\n");
for (unsigned int i = 0; i < FLAG_REMAIN_ARG.size(); i++) {
fprintf(stderr, "Process %s ... \n", FLAG_REMAIN_ARG[i].c_str());
compareVcfs[i]->setRangeList(FLAG_rangeList.c_str());
compareVcfs[i]->setRangeFile(FLAG_rangeList.c_str());
compareVcfs[i]->setSiteFile(FLAG_siteFile.c_str());
loadGenotype(*compareVcfs[i], &data, Value::COMPARISON);
StringArray names;
compareVcfs[i]->getVCFHeader()->getPeopleName(&names);
printComparision(*compareVcfs[i], data, names);
clearGenotype(&data);
}
for (unsigned int i = 0; i < FLAG_REMAIN_ARG.size(); i++) {
delete compareVcfs[i];
}
delete[] compareVcfs;
currentTime = time(0);
fprintf(stderr, "Analysis end at: %s", ctime(¤tTime));
return 0;
};
int main(int argc, char** argv) {
time_t currentTime = time(0);
fprintf(stderr, "Analysis started at: %s", ctime(¤tTime));
PARSE_PARAMETER(argc, argv);
PARAMETER_STATUS();
if (FLAG_REMAIN_ARG.size() > 0) {
fprintf(stderr, "Unparsed arguments: ");
for (unsigned int i = 0; i < FLAG_REMAIN_ARG.size(); i++) {
fprintf(stderr, " %s", FLAG_REMAIN_ARG[i].c_str());
}
fprintf(stderr, "\n");
abort();
}
REQUIRE_STRING_PARAMETER(FLAG_inVcf,
"Please provide input file using: --inVcf");
const char* fn = FLAG_inVcf.c_str();
VCFInputFile vin(fn);
// set range filters here
// e.g.
// vin.setRangeList("1:69500-69600");
vin.setRangeList(FLAG_rangeList.c_str());
vin.setRangeFile(FLAG_rangeFile.c_str());
// set people filters here
if (FLAG_peopleIncludeID.size() || FLAG_peopleIncludeFile.size()) {
vin.excludeAllPeople();
vin.includePeople(FLAG_peopleIncludeID.c_str());
vin.includePeopleFromFile(FLAG_peopleIncludeFile.c_str());
}
vin.excludePeople(FLAG_peopleExcludeID.c_str());
vin.excludePeopleFromFile(FLAG_peopleExcludeFile.c_str());
// let's write it out.
if (FLAG_updateId != "") {
int ret = vin.updateId(FLAG_updateId.c_str());
fprintf(stdout, "%d samples have updated id.\n", ret);
}
// load gene ranges
std::map<std::string, std::string> geneRange;
if (FLAG_geneName.size()) {
if (FLAG_geneFile.size() == 0) {
fprintf(stderr, "Have to provide --geneFile to extract by gene.\n");
abort();
}
LineReader lr(FLAG_geneFile);
std::vector<std::string> fd;
while (lr.readLineBySep(&fd, "\t ")) {
if (FLAG_geneName != fd[0]) continue;
fd[2] = chopChr(fd[2]); // chop "chr1" to "1"
if (geneRange.find(fd[0]) == geneRange.end()) {
geneRange[fd[0]] = fd[2] + ":" + fd[4] + "-" + fd[5];
} else {
geneRange[fd[0]] += "," + fd[2] + ":" + fd[4] + "-" + fd[5];
}
};
}
std::string range;
for (std::map<std::string, std::string>::iterator it = geneRange.begin();
it != geneRange.end(); it++) {
if (range.size() > 0) {
range += ",";
}
range += it->second;
};
fprintf(stderr, "range = %s\n", range.c_str());
vin.setRangeList(range.c_str());
Regex regex;
if (FLAG_annoType.size()) {
regex.readPattern(FLAG_annoType);
}
// print header
std::vector<std::string> names;
vin.getVCFHeader()->getPeopleName(&names);
printf("CHROM\tPOS");
for (unsigned int i = 0; i < names.size(); i++) {
printf("\t%s", names[i].c_str());
}
printf("\n");
// real working part
int nonVariantSite = 0;
while (vin.readRecord()) {
VCFRecord& r = vin.getVCFRecord();
VCFPeople& people = r.getPeople();
VCFIndividual* indv;
if (FLAG_variantOnly) {
bool hasVariant = false;
int geno;
int GTidx = r.getFormatIndex("GT");
for (size_t i = 0; i < people.size(); i++) {
indv = people[i];
geno = indv->justGet(GTidx).getGenotype();
if (geno != 0 && geno != MISSING_GENOTYPE) hasVariant = true;
}
if (!hasVariant) {
nonVariantSite++;
continue;
}
}
if (FLAG_annoType.size()) {
bool isMissing = false;
const char* tag = r.getInfoTag("ANNO", &isMissing).toStr();
if (isMissing) continue;
// fprintf(stdout, "ANNO = %s", tag);
bool match = regex.match(tag);
// fprintf(stdout, " %s \t", match ? "match": "noMatch");
// fprintf(stdout, " %s \n", exists ? "exists": "missing");
if (!match) {
continue;
}
}
fprintf(stdout, "%s\t%s", r.getChrom(), r.getPosStr());
for (size_t i = 0; i < people.size(); i++) {
indv = people[i];
fprintf(stdout, "\t%d", indv->justGet(0).getGenotype());
}
fprintf(stdout, "\n");
};
currentTime = time(0);
fprintf(stderr, "Analysis ends at: %s", ctime(¤tTime));
return 0;
};
/* Insert one or more shallow copies of a block (created by DXFBlock as
* Transform Group) into a layer (created by DXFLayer as MaterialGroup) or
* another block.
* \todo
* Could there be a INSERT inside a block referring to another block which has
* not been read yet? We then have to find a solution to enable deferred
* instantiation of INSERT entities :-(
*/
DXFResult DXFInsert::endEntity(void)
{
NodeUnrecPtr ctrafoNodeP = NULL;
// ComponentTransformUnrecPtr ctrafoCoreP = NULL;
TransformUnrecPtr ctrafoCoreP = NULL;
NodeUnrecPtr blockNodeP = NULL;
Node *parentNodeP = getParentNode();
StringToNodePtrMap::iterator itr = _blocksMapP->find(_blockName);
if (itr != _blocksMapP->end() && parentNodeP != NULL)
{
blockNodeP = itr->second;
// TODO: check fetched INSERT Data for consistency!
// Insert multiple times in a grid...
Vec3f offset(0.0, 0.0, 0.0);
for(Int16 column = 0; column < _columnCount; ++ column)
{
offset[0] = column * _columnSpacing;
for(Int16 row = 0; row < _rowCount; ++ row)
{
offset[1] = row * _rowSpacing;
// TODO: find out about DXF insert semantics!
ctrafoNodeP = Node::create();
ctrafoCoreP = Transform::create();
#if 0
beginEditCP(ctrafoCoreP);
#endif
{
if(_blockName == std::string("Rectangular Mullion - 64 x 128 rectangular-V1-Level 1"))
{
std::cout << blockNodeP->getNChildren() << std::endl;
}
OSG::TransformationMatrix<Real32> transMat;
transMat.setIdentity();
transMat.setTranslate(_insertionPoint + offset);
OSG::TransformationMatrix<Real32> rotMat;
rotMat.setIdentity();
OSG::Quaternion rot(OSG::Vec3f(0,0,1),osgDegree2Rad(_rotationAngle));
rotMat.setRotate(rot);
OSG::TransformationMatrix<Real32> scaleMat;
scaleMat.setIdentity();
scaleMat.setScale(_scaleFactor);
OSG::Vec3f vin(-40, 65, 0);
OSG::Vec3f vout;
transMat.mult(rotMat);
transMat.mult(scaleMat);
if(_extrusionDirection[2]<0)
{
transMat[0][0] *= -1.0;
transMat[1][0] *= -1.0;
transMat[2][0] *= -1.0;
transMat[3][0] *= -1.0;
}
ctrafoCoreP->setMatrix(transMat);
}
#if 0
endEditCP(ctrafoCoreP);
#endif
#if 0
beginEditCP(ctrafoNodeP);
#endif
{
ctrafoNodeP->setCore(ctrafoCoreP);
#if 0
ctrafoNodeP->addChild(blockNodeP->clone());
#endif
NodeUnrecPtr pClone = cloneTree(blockNodeP);
ctrafoNodeP->addChild(pClone);
}
#if 0
endEditCP(ctrafoNodeP);
#endif
#if 0
beginEditCP(parentNodeP);
#endif
{
parentNodeP->addChild(ctrafoNodeP);
}
#if 0
endEditCP(parentNodeP);
#endif
}
}
// Warn for details not implemented or assured yet! TODO: better
// implement missing features!
/*if(fabs(_rotationAngle) > Eps)
FWARNING(("DXF Loader: before line %d: "
"DXFInsert does not yet support ROTATION "
"(group code 50). "
"Most likely the graphics are incorrect!\n",
DXFRecord::getLineNumber()
));*/
/*if(_scaleFactor != Vec3f(1.0,1.0,1.0))
FWARNING(("DXF Loader: before line %d: "
"DXFInsert may not interpret SCALING "
"(group codes 41, 42, 43) correctly."
"Graphics may be incorrect!\n",
DXFRecord::getLineNumber()
));*/
if(_columnCount != 1 || _rowCount != 1)
FWARNING(("DXF Loader: before line %d: "
"DXFInsert may not interpret REPEATED INSERTION "
"(group codes 70, 71, 44, 45) correctly."
"Graphics may be incorrect!\n",
DXFRecord::getLineNumber()
));
}
else
{
if(itr == _blocksMapP->end())
FWARNING(("DXF Loader: before line %d (inside %s section): "
"BLOCK '%s' to be inserted not found!\n",
DXFRecord::getLineNumber(),
_parent->getEntityTypeName(),
_blockName.c_str()
));
if(parentNodeP == NULL)
FWARNING(("DXF Loader: before line %d (inside %s section): "
"layer %s to be inserted to not found!\n",
DXFRecord::getLineNumber(),
_parent->getEntityTypeName(),
_layerName.c_str()
));
}
//set back to default value;
_insertionPoint.setNull(),
_scaleFactor[0]=_scaleFactor[1]=_scaleFactor[2]=1.0;
_rotationAngle=0.0;
_columnCount=1;
_rowCount=1;
_columnSpacing=0.0;
_rowSpacing=0.0;
_extrusionDirection[0]=0;
_extrusionDirection[1]=0;
_extrusionDirection[2]=1;
return DXFStateContinue;
}
int main(int argc, char* argv[]) {
{
std::string fn = "all.anno.filtered.extract.bcf.gz";
std::string r = "1:196621007-196716634";
VCFExtractor vin(fn);
vin.setRangeList(r);
printf("Extract two sites\n");
vin.setAnnoType("Nonsynonymous");
while (vin.readRecord()) {
VCFRecord& r = vin.getVCFRecord();
VCFPeople& people = r.getPeople();
VCFIndividual* indv;
printf("%s:%d\n", r.getChrom(), r.getPos());
}
}
if (false) {
// this code demonstrate how to temporarily close stdout
int fd = STDOUT_FILENO;
int dupFd = dup(fileno(stdout));
stdout = fdopen(dupFd, "w");
assert(stdout);
assert(dupFd > 0);
printf("before stdout, fd = %d, dupFd = %d\n", fd, dupFd);
fclose(stdout);
printf("after stdout\n");
return 0;
}
const char* fn = "test.bcf.gz";
{
BCFReader tr(fn);
int n = 0;
std::string line;
while (tr.readLine(&line)) {
// printf("line %d = [ %s ]\n", n, line.c_str());
++n;
}
fprintf(stdout, "Read %d lines\n", n);
assert(n == 14); // without header lines
}
{
BCFReader tr(fn);
tr.addRange("1:196341181-196341254");
int n = 0;
std::string line;
while (tr.readLine(&line)) {
// printf("line %d = [ %s ]\n", n, line.c_str());
++n;
}
fprintf(stdout, "Read %d lines\n", n);
assert(n == 2);
}
{
BCFReader tr(fn);
tr.addRange("1:196341857-196341857");
tr.addRange("1:196341181-196341254");
int n = 0;
std::string line;
while (tr.readLine(&line)) {
// printf("line %d = [ %s ]\n", n, line.c_str());
++n;
}
fprintf(stdout, "Read %d lines\n", n);
// assert ( n == 3) ;
}
{
BCFReader tr(fn);
tr.addRange("2:196341857-196341857");
tr.addRange("2:196341181-196341254");
int n = 0;
std::string line;
while (tr.readLine(&line)) {
printf("line %d = [ %s ]\n", n, line.c_str());
++n;
}
fprintf(stdout, "Read %d lines\n", n);
// assert ( n == 0) ;
}
{
BCFReader tr(fn);
std::string h = tr.getHeader().c_str();
int count = 0;
for (size_t i = 0; i < h.size(); ++i) {
if (h[i] == '\n') count++;
}
fprintf(stdout, "header has %d lines.\n", count);
assert(count == 60);
}
return 0;
}
inline void addvec_simd(F * out, const F in)
{
vec<F> vin(in);
detail::addvec<F, n>::mp_iteration(out, vin);
}
int main(int argc, char** argv){
time_t currentTime = time(0);
fprintf(stderr, "Analysis started at: %s", ctime(¤tTime));
////////////////////////////////////////////////
BEGIN_PARAMETER_LIST(pl)
ADD_PARAMETER_GROUP(pl, "Input/Output")
ADD_STRING_PARAMETER(pl, inVcf, "--inVcf", "input VCF File")
ADD_STRING_PARAMETER(pl, outMerlin, "--outMerlin", "output prefix")
ADD_PARAMETER_GROUP(pl, "People Filter")
ADD_STRING_PARAMETER(pl, peopleIncludeID, "--peopleIncludeID", "give IDs of people that will be included in study")
ADD_STRING_PARAMETER(pl, peopleIncludeFile, "--peopleIncludeFile", "from given file, set IDs of people that will be included in study")
ADD_STRING_PARAMETER(pl, peopleExcludeID, "--peopleExcludeID", "give IDs of people that will be included in study")
ADD_STRING_PARAMETER(pl, peopleExcludeFile, "--peopleExcludeFile", "from given file, set IDs of people that will be included in study")
ADD_PARAMETER_GROUP(pl, "Site Filter")
ADD_STRING_PARAMETER(pl, rangeList, "--rangeList", "Specify some ranges to use, please use chr:begin-end format.")
ADD_STRING_PARAMETER(pl, rangeFile, "--rangeFile", "Specify the file containing ranges, please use chr:begin-end format.")
END_PARAMETER_LIST(pl)
;
pl.Read(argc, argv);
pl.Status();
if (FLAG_REMAIN_ARG.size() > 0){
fprintf(stderr, "Unparsed arguments: ");
for (unsigned int i = 0; i < FLAG_REMAIN_ARG.size(); i++){
fprintf(stderr, " %s", FLAG_REMAIN_ARG[i].c_str());
}
fprintf(stderr, "\n");
abort();
}
REQUIRE_STRING_PARAMETER(FLAG_inVcf, "Please provide input file using: --inVcf");
const char* fn = FLAG_inVcf.c_str();
VCFInputFile vin(fn);
// set range filters here
// e.g.
// vin.setRangeList("1:69500-69600");
vin.setRangeList(FLAG_rangeList.c_str());
vin.setRangeFile(FLAG_rangeFile.c_str());
// set people filters here
if (FLAG_peopleIncludeID.size() || FLAG_peopleIncludeFile.size()) {
vin.excludeAllPeople();
vin.includePeople(FLAG_peopleIncludeID.c_str());
vin.includePeopleFromFile(FLAG_peopleIncludeFile.c_str());
}
vin.excludePeople(FLAG_peopleExcludeID.c_str());
vin.excludePeopleFromFile(FLAG_peopleExcludeFile.c_str());
// let's write it out.
FILE* fMap; // CHROMOSOME MARKER POSITION
FILE* fDat; // A some_disease\n
// T some_trait
// M some_marker
// M another_marker
FILE* fPed; // first 5 column: FID, IID, PID, MID, SEX; then follow Dat file
FILE* fPid; // Person ID file, (extra for Merlin), including all people ID as they are in PED file.
fMap = fopen( (FLAG_outMerlin + ".map").c_str(), "wt");
fDat = fopen( (FLAG_outMerlin + ".dat").c_str(), "wt");
fPed = fopen( (FLAG_outMerlin + ".ped").c_str(), "wt");
fPid = fopen( (FLAG_outMerlin + ".pid").c_str(), "wt");
assert(fMap && fDat && fPed && fPid);
std::string marker; // marker x people
std::vector<std::string> allMarker;
Matrix geno;
fputs("CHROMOSOME\tMARKER\tPOSITION\n", fMap);
while (vin.readRecord()){
VCFRecord& r = vin.getVCFRecord();
VCFPeople& people = r.getPeople();
VCFIndividual* indv;
// write map file
marker = r.getID();
if ( marker == "." ) {
fprintf(fMap, "%s\t%s:%d\t%d\n", r.getChrom(), r.getChrom(), r.getPos(), r.getPos());
fprintf(fDat, "M\t%s:%d\n", r.getChrom(), r.getPos());
} else {
fprintf(fMap, "%s\t%s\t%d\n", r.getChrom(), marker.c_str(), r.getPos());
fprintf(fDat, "M\t%s\n", marker.c_str());
}
allMarker.push_back(marker);
geno.Dimension(allMarker.size(), people.size());
// e.g.: get TAG from INFO field
// fprintf(stderr, "%s\n", r.getInfoTag("ANNO"));
int m = allMarker.size() - 1;
// e.g.: Loop each (selected) people in the same order as in the VCF
for (int i = 0; i < people.size(); i++) {
indv = people[i];
// get GT index. if you are sure the index will not change, call this function only once!
int GTidx = r.getFormatIndex("GT");
if (GTidx >= 0) {
geno[m][i] = (*indv)[GTidx].getGenotype();
}else {
fprintf(stderr, "Cannot find GT field!\n");
abort();
}
}
};
VCFHeader* h = vin.getVCFHeader();
std::vector< std::string> peopleId;
h->getPeopleName(&peopleId);
// dump PED and PID file
for (int p = 0; p < peopleId.size(); p++){
fprintf(fPed, "%s\t%s\t0\t0\t0", peopleId[p].c_str(), peopleId[p].c_str());
for (int m = 0; m < allMarker.size(); m++){
int g = (int)geno[m][p];
switch (g){
case 0:
fputs("\t0/0", fPed);
break;
case 1:
fputs("\t0/1", fPed);
break;
case 2:
fputs("\t1/1", fPed);
break;
default:
fputs("x/x", fPed);
break;
}
}
fputs("\n", fPed);
fprintf(fPid, "%s\n", peopleId[p].c_str());
}
return 0;
};
bool VLFeat::CalculateCommon(int f, bool all, int l) {
string msg = "VLFeat::CalculateCommon("+ToStr(f)+","+ToStr(all)+","+
ToStr(l)+") : ";
// if (!do_fisher && !do_vlad) {
// cerr << msg
// << "either encoding=fisher or encoding=vlad should be specified"
// << endl;
// return false;
// }
if (!gmm && !kmeans) {
cerr << msg << "either gmm=xxx or kmeans=xxx option should be given"
<< endl;
return false;
}
cox::tictac::func tt(tics, "VLFeat::CalculateCommon");
// obs! only some parameters here, should be in ProcessOptionsAndRemove()
// too, also scales and geometry should be made specifiable...
bool normalizeSift = false, renormalize = true, flat_window = true;
size_t step = 3, binsize = 8;
EnsureImage();
int width = Width(true), height = Height(true);
if (FrameVerbose())
cout << msg+"wxh="
<< width << "x" << height << "=" << width*height << endl;
vector<float> rgbcoeff { 0.2989, 0.5870, 0.1140 };
imagedata idata = CurrentFrame();
idata.convert(imagedata::pixeldata_float);
idata.force_one_channel(rgbcoeff);
vector<float> dsift;
size_t descr_size_orig = 0, descr_size_final = 0;
vector<float> scales { 1.0000, 0.7071, 0.5000, 0.3536, 0.2500 };
// vector<float> scales { 1.0000 };
for (size_t i=0; i<scales.size(); i++) {
if (KeyPointVerbose())
cout << "Starting vl_dsift_process() in scale " << scales[i] << endl;
imagedata simg = idata;
if (scales[i]!=1) {
scalinginfo si(simg.width(), simg.height(),
(int)floor(scales[i]*simg.width()+0.5),
(int)floor(scales[i]*simg.height()+0.5));
simg.rescale(si, 1);
}
// VlDsiftFilter *sf = vl_dsift_new(simg.width(), simg.height());
VlDsiftFilter *sf = vl_dsift_new_basic(simg.width(), simg.height(),
step, binsize);
// opts.scales = logspace(log10(1), log10(.25), 5) ;
// void vl_dsift_set_bounds ( VlDsiftFilter * self,
// int minX,
// int minY,
// int maxX,
// int maxY
// );
// VlDsiftDescriptorGeometry geom = { 8, 4, 4, 0, 0 };
// vl_dsift_set_geometry(sf, &geom);
//vl_dsift_set_steps(sf, 3, 3);
//vl_dsift_set_window_size(sf, 8);
vl_dsift_set_flat_window(sf, flat_window); // aka fast in matlab
vector<float> imgvec = simg.get_float();
const float *img_fp = &imgvec[0];
// cout << "IMAGE = " << img_fp[0] << " " << img_fp[1] << " "
// << img_fp[2] << " ... " << img_fp[41] << endl;
vl_dsift_process(sf, img_fp);
// if opts.rootSift // false
// descrs{si} = sqrt(descrs{si}) ;
// end
// if opts.normalizeSift //true
// descrs{si} = snorm(descrs{si}) ;
// end
descr_size_orig = sf->descrSize;
size_t nf = sf->numFrames;
const VlDsiftKeypoint *k = sf->frames;
float *d = sf->descrs;
if (KeyPointVerbose())
cout << " found " << sf->numFrames << " 'frames' in "
<< simg.info() << endl
<< " descriptor dim " << descr_size_orig << endl;
if (PixelVerbose())
for (size_t i=0; i<nf; i++) {
cout << " i=" << i << " x=" << k[i].x << " y=" << k[i].y
<< " s=" << k[i].s << " norm=" << k[i].norm;
if (FullVerbose()) {
cout << " RAW";
for (size_t j=0; j<descr_size_orig; j++)
cout << " " << d[i*descr_size_orig+j];
}
cout << endl;
}
if (normalizeSift) {
for (size_t i=0; i<nf; i++) {
if (PixelVerbose())
cout << " i=" << i << " x=" << k[i].x << " y=" << k[i].y
<< " s=" << k[i].s << " norm=" << k[i].norm;
double mul = 0.0;
for (size_t j=0; j<descr_size_orig; j++)
mul += d[i*descr_size_orig+j]*d[i*descr_size_orig+j];
if (mul)
mul = 1.0/sqrt(mul);
if (FullVerbose())
cout << " NORM";
for (size_t j=0; j<descr_size_orig; j++) {
d[i*descr_size_orig+j] *= mul;
if (FullVerbose())
cout << " " << d[i*descr_size_orig+j];
}
if (PixelVerbose())
cout << endl;
}
}
if (!pca.vector_length()) {
dsift.insert(dsift.end(), d, d+nf*descr_size_orig);
descr_size_final = descr_size_orig;
} else {
for (size_t i=0; i<nf; i++) {
vector<float> vin(d+i*descr_size_orig, d+(i+1)*descr_size_orig);
vector<float> vout = pca.projection_coeff(vin);
dsift.insert(dsift.end(), vout.begin(), vout.end());
}
descr_size_final = pca.base_size();
}
vl_dsift_delete(sf);
}
size_t numdata = dsift.size()/descr_size_final;
const float *datain = &dsift[0];
vector<float> enc((do_fisher?2:1)*descriptor_dim()*nclusters());
float *dataout = &enc[0];
if (do_fisher) {
if (FrameVerbose())
cout << msg << "fisher encoding " << numdata
<< " descriptors of size " << descr_size_orig
<< " => " << descr_size_final
<< " with gmm dimensionality " << descriptor_dim()
<< endl;
if (descr_size_final!=descriptor_dim()) {
cerr << msg << "dimensionality mismatch descr_size_final="
<< descr_size_final << " descriptor_dim()=" << descriptor_dim()
<< endl;
return false;
}
vl_fisher_encode(dataout, VL_TYPE_FLOAT, means(), descriptor_dim(),
nclusters(), covariances(), priors(),
datain, numdata, VL_FISHER_FLAG_IMPROVED) ;
}
if (do_vlad) {
//obs! correct use of pca?
if (FrameVerbose())
cout << msg << "vlad encoding " << numdata
<< " descriptors of size " << descr_size_final << endl;
vector<vl_uint32> indexes(numdata);
vector<float> distances(numdata);
if (kdtree)
vl_kdforest_query_with_array(kdtree, &indexes[0], 1, numdata, &distances[0], datain);
else
vl_kmeans_quantize(kmeans, &indexes[0], &distances[0], datain, numdata);
vector<float> assignments(numdata*nclusters());
for (size_t i=0; i<numdata; i++)
assignments[i * nclusters() + indexes[i]] = 1;
int vlad_flags = VL_VLAD_FLAG_SQUARE_ROOT|VL_VLAD_FLAG_NORMALIZE_COMPONENTS;
vl_vlad_encode(dataout, VL_TYPE_FLOAT, means(), descriptor_dim(),
nclusters(), datain, numdata, &assignments[0],
vlad_flags);
}
if (renormalize) {
if (PixelVerbose())
cout << " RENORM:";
double mul = 0.0;
for (size_t j=0; j<enc.size(); j++)
mul += enc[j]*enc[j];
if (mul)
mul = 1.0/sqrt(mul);
for (size_t j=0; j<enc.size(); j++) {
if (PixelVerbose())
cout << " " << enc[j];
enc[j] *= mul;
if (PixelVerbose())
cout << "->" << enc[j];
}
if (PixelVerbose())
cout << endl;
}
((VectorData*)GetData(0))->setVector(enc);
return true;
}
quint64 Helpers::toQUInt64(const QJsonValue& jv) {
std::string hexStr = jv.toString("0x0").remove(0, 2).toStdString();
BigInt::Vin vin(hexStr, 16);
return vin.toUlong();
}