GVN::Value * GVN::getValue(const OpValue::Kind kind, const GVN::Value & LV, const GVN::Value & RV)
{
OpValue ov(kind, LV.value, RV.value);
switch (kind)
{
case OpValue::PLUS:
return getValue([](const MultivariatePolynomial & LMP, const MultivariatePolynomial & RMP)
{
return LMP + RMP;
}, LV, RV, ov);
case OpValue::MINUS:
return getValue([](const MultivariatePolynomial & LMP, const MultivariatePolynomial & RMP)
{
return LMP - RMP;
}, LV, RV, ov);
case OpValue::TIMES:
case OpValue::DOTTIMES:
return getValue([](const MultivariatePolynomial & LMP, const MultivariatePolynomial & RMP)
{
return LMP * RMP;
}, LV, RV, ov);
case OpValue::RDIV:
case OpValue::DOTRDIV:
return getValue([](const MultivariatePolynomial & LMP, const MultivariatePolynomial & RMP)
{
return LMP / RMP;
}, LV, RV, ov);
case OpValue::POWER:
case OpValue::DOTPOWER:
return getValue([](const MultivariatePolynomial & LMP, const MultivariatePolynomial & RMP)
{
return LMP ^ RMP;
}, LV, RV, ov);
default:
return getValue([](const MultivariatePolynomial & LMP, const MultivariatePolynomial & RMP)
{
return MultivariatePolynomial::getInvalid();
}, LV, RV, ov);
}
}
OrderVector ListVector::getOrderVector(map<string,int>* orderMap = NULL) {
try {
if(orderMap == NULL) {
OrderVector ov;
for(int i=0; i<data.size(); i++) {
int binSize = m->getNumNames(data[i]);
for(int j=0; j<binSize; j++) {
ov.push_back(i);
}
}
random_shuffle(ov.begin(), ov.end());
ov.setLabel(label);
ov.getNumBins();
return ov;
}
else {
OrderVector ov(numSeqs);
for(int i=0; i<data.size(); i++) {
string listOTU = data[i];
int length = listOTU.size();
string seqName="";
for(int j=0; j<length; j++) {
if(listOTU[j] != ',') {
seqName += listOTU[j];
}
else {
if(orderMap->count(seqName) == 0) {
m->mothurOut(seqName + " not found, check *.names file\n");
exit(1);
}
ov.set((*orderMap)[seqName], i);
seqName = "";
}
}
if(orderMap->count(seqName) == 0) {
m->mothurOut(seqName + " not found, check *.names file\n");
exit(1);
}
ov.set((*orderMap)[seqName], i);
}
ov.setLabel(label);
ov.getNumBins();
return ov;
}
}
catch(exception& e) {
m->errorOut(e, "ListVector", "getOrderVector");
exit(1);
}
}
std::ostream& operator << (std::ostream& ostr, const value_t& v)
{
stream_output_visitor ov(ostr);
boost::apply_visitor(ov, v);
return ostr;
}
void Uniform::setColorElement(const omega::Color& value, uint index)
{
osg::Vec4 ov(value[0], value[1], value[2], value[3]);
myOsgUniform->setElement(index, ov);
}
void Uniform::setVector3fElement(const omega::Vector3f& value, uint index)
{
osg::Vec3 ov(value[0], value[1], value[2]);
myOsgUniform->setElement(index, ov);
}
void Uniform::setColor(const omega::Color& value)
{
osg::Vec4 ov(value[0], value[1], value[2], value[3]);
myOsgUniform->set(ov);
}
void Uniform::setVector3f(const omega::Vector3f& value)
{
osg::Vec3 ov(value[0], value[1], value[2]);
myOsgUniform->set(ov);
}
void Uniform::setVector2f(const omega::Vector2f& value)
{
osg::Vec2 ov(value[0], value[1]);
myOsgUniform->set(ov);
}
bool wxvbamApp::OnInit()
{
// use consistent names for config
SetAppName(_("vbam"));
#if (wxMAJOR_VERSION >= 3)
SetAppDisplayName(_T("VisualBoyAdvance-M"));
#endif
// load system default locale, if available
locale.Init();
locale.AddCatalog(_T("wxvbam"));
// make built-in xrc file available
// this has to be done before parent OnInit() so xrc dump works
wxFileSystem::AddHandler(new wxMemoryFSHandler);
wxFileSystem::AddHandler(new wxArchiveFSHandler);
wxMemoryFSHandler::AddFileWithMimeType(wxT("wxvbam.xrs"), builtin_xrs, sizeof(builtin_xrs), wxT("application/zip"));
if (!wxApp::OnInit())
return false;
// prepare for loading xrc files
wxXmlResource* xr = wxXmlResource::Get();
// note: if linking statically, next 2 pull in lot of unused code
// maybe in future if not wxSHARED, load only builtin-needed handlers
xr->InitAllHandlers();
wxInitAllImageHandlers();
get_config_path(config_path);
// first, load override xrcs
// this can only override entire root nodes
// 2.9 has LoadAllFiles(), but this is 2.8, so we'll do it manually
wxString cwd = wxGetCwd();
for (int i = 0; i < config_path.size(); i++)
if (wxDirExists(config_path[i]) && wxSetWorkingDirectory(config_path[i]))
{
// *.xr[cs] doesn't work (double the number of scans)
// 2.9 gives errors for no files found, so manual precheck needed
// (yet another double the number of scans)
if (!wxFindFirstFile(wxT("*.xrc")).empty())
xr->Load(wxT("*.xrc"));
if (!wxFindFirstFile(wxT("*.xrs")).empty())
xr->Load(wxT("*.xrs"));
}
wxFileName xrcDir(GetConfigurationPath() + wxT("//xrc"), wxEmptyString);
if (xrcDir.DirExists() && wxSetWorkingDirectory(xrcDir.GetFullPath()) && !wxFindFirstFile(wxT("*.xrc")).empty())
{
xr->Load(wxT("*.xrc"));
}
else
{
// finally, load built-in xrc
xr->Load(wxT("memory:wxvbam.xrs"));
}
wxSetWorkingDirectory(cwd);
// set up config file
// this needs to be in a subdir to support other config as well
// but subdir flag behaves differently 2.8 vs. 2.9. Oh well.
// NOTE: this does not support XDG (freedesktop.org) paths
#if defined(__WXMSW__) || defined(__APPLE__)
wxFileName vbamconf(GetConfigurationPath(), _T("vbam.ini"));
cfg = new wxFileConfig(wxT("vbam"), wxEmptyString,
vbamconf.GetFullPath(),
wxEmptyString, wxCONFIG_USE_LOCAL_FILE);
#else
cfg = new wxFileConfig(wxEmptyString, wxEmptyString, wxEmptyString,
wxEmptyString,
// style =
wxCONFIG_USE_GLOBAL_FILE | wxCONFIG_USE_LOCAL_FILE |
wxCONFIG_USE_SUBDIR);
#endif
// set global config for e.g. Windows font mapping
wxFileConfig::Set(cfg);
// yet another bug/deficiency in wxConfig: dirs are not created if needed
// since a default config is always written, dirs are always needed
// Can't figure out statically if using wxFileConfig w/o duplicating wx's
// logic, so do it at run-time
// wxFileConfig *f = wxDynamicCast(cfg, wxFileConfig);
// wxConfigBase does not derive from wxObject!!! so no wxDynamicCast
wxFileConfig* fc = dynamic_cast<wxFileConfig*>(cfg);
if (fc)
{
wxFileName s(wxFileConfig::GetLocalFileName(GetAppName()));
// at least up to 2.8.12, GetLocalFileName returns the dir if
// SUBDIR is specified instead of actual file name
// and SUBDIR only affects UNIX
#if defined(__UNIX__) && !wxCHECK_VERSION(2,9,0)
s.AppendDir(s.GetFullName());
#endif
// only the path part gets created
// note that 0777 is default (assumes umask will do og-w)
s.Mkdir(0777, wxPATH_MKDIR_FULL);
s = wxFileName::DirName(GetConfigurationPath());
s.Mkdir(0777, wxPATH_MKDIR_FULL);
}
load_opts();
// process command-line options
for (int i = 0; i < pending_optset.size(); i++)
{
wxString p = pending_optset[i];
size_t eqat = p.find(wxT('='));
p[eqat] = 0;
opt_set(p.c_str(), p.c_str() + eqat + 1);
}
pending_optset.clear();
wxFileName vba_over(GetConfigurationPath(), wxT("vba-over.ini"));
wxFileName rdb(GetConfigurationPath(), wxT("Nintendo - Game Boy Advance*.dat"));
wxFileName scene_rdb(GetConfigurationPath(), wxT("Nintendo - Game Boy Advance (Scene)*.dat"));
wxFileName nointro_rdb(GetConfigurationPath(), wxT("Official No-Intro Nintendo Gameboy Advance Number (Date).xml"));
wxString f = wxFindFirstFile(nointro_rdb.GetFullPath(), wxFILE);
if (!f.empty() && wxFileName(f).IsFileReadable())
rom_database_nointro = f;
f = wxFindFirstFile(scene_rdb.GetFullPath(), wxFILE);
if (!f.empty() && wxFileName(f).IsFileReadable())
rom_database_scene = f;
f = wxFindFirstFile(rdb.GetFullPath(), wxFILE);
while (!f.empty())
{
if (f == rom_database_scene.GetFullPath())
{
f = wxFindNextFile();
}
else if (wxFileName(f).IsFileReadable())
{
rom_database = f;
break;
}
}
// load vba-over.ini
// rather than dealing with wxConfig's broken search path, just use
// the same one that the xrc overrides use
// this also allows us to override a group at a time, add commments, and
// add the file from which the group came
wxMemoryInputStream mis(builtin_over, sizeof(builtin_over));
overrides = new wxFileConfig(mis);
wxRegEx cmtre;
// not the most efficient thing to do: read entire file into a string
// just to parse the comments out
wxString bovs((const char*)builtin_over, wxConvUTF8, sizeof(builtin_over));
bool cont;
wxString s;
long grp_idx;
#define CMT_RE_START wxT("(^|[\n\r])# ?([^\n\r]*)(\r?\n|\r)\\[")
for (cont = overrides->GetFirstGroup(s, grp_idx); cont;
cont = overrides->GetNextGroup(s, grp_idx))
{
// apparently even MacOSX sometimes uses the old \r by itself
wxString cmt(CMT_RE_START);
cmt += s + wxT("\\]");
if (cmtre.Compile(cmt) && cmtre.Matches(bovs))
cmt = cmtre.GetMatch(bovs, 2);
else
cmt = wxEmptyString;
overrides->Write(s + wxT("/comment"), cmt);
}
if (vba_over.FileExists())
{
wxStringOutputStream sos;
wxFileInputStream fis(vba_over.GetFullPath());
// not the most efficient thing to do: read entire file into a string
// just to parse the comments out
fis.Read(sos);
// rather than assuming the file is seekable, use the string we just
// read as an input stream
wxStringInputStream sis(sos.GetString());
wxFileConfig ov(sis);
for (cont = ov.GetFirstGroup(s, grp_idx); cont;
cont = ov.GetNextGroup(s, grp_idx))
{
overrides->DeleteGroup(s);
overrides->SetPath(s);
ov.SetPath(s);
overrides->Write(wxT("path"), GetConfigurationPath());
// apparently even MacOSX sometimes uses \r by itself
wxString cmt(CMT_RE_START);
cmt += s + wxT("\\]");
if (cmtre.Compile(cmt) && cmtre.Matches(sos.GetString()))
cmt = cmtre.GetMatch(sos.GetString(), 2);
else
cmt = wxEmptyString;
overrides->Write(wxT("comment"), cmt);
long ent_idx;
for (cont = ov.GetFirstEntry(s, ent_idx); cont;
cont = ov.GetNextEntry(s, ent_idx))
overrides->Write(s, ov.Read(s, wxEmptyString));
ov.SetPath(wxT("/"));
overrides->SetPath(wxT("/"));
}
}
// create the main window
frame = wxDynamicCast(xr->LoadFrame(NULL, wxT("MainFrame")), MainFrame);
if (!frame)
{
wxLogError(_("Could not create main window"));
return false;
}
// Create() cannot be overridden easily
if (!frame->BindControls())
return false;
frame->Show(true);
return true;
}
void
L1Graph::L1Minimization(SpMatrix<float>& alpha,std::vector<int>& neighborhood)
{
//neighborhood contains cidx
int p_num=index_->size();
int f_dim=(*features_)[0].size();
Matrix<float> X(f_dim, p_num - 1);
//construct matrix X
std::map<int,int> map_gl; //map between global and local point index
for(int j = 0, k = 0; j < p_num; j++) { //cols
int id=(*index_)[j];
if(id==cidx_) {
continue;
}
Util::StdVector2MatrixCol((*features_)[id], X, k);
map_gl.insert(make_pair<int,int>(k,id));
++k;
}
//TODO:dont use I
//construct I
// Matrix<float> I(f_dim,f_dim);
// I.eye();
// Util::Matrix2File(I,"I.txt");
// Matrix<float> B(f_dim, f_dim + p_num - 1);
// X.merge(I, B);
// Util::Matrix2File(B,"B.txt");
//clean
// X.clear();
// I.clear();
//using lasso
Matrix<float> x; //x=Ba
Util::StdVector2Matrix((*features_)[cidx_], x);
float lambda = 0.01; //lambda
int L = (*features_)[0].size(); //max non-zero number
// int L = 20; //max non-zero number
SpMatrix<float> all;
//TODO:debug in matlab
ofstream fout("f.txt");
for (int i = 0; i < x.m(); i++) {
for (int j = 0; j < x.n(); j++) {
fout<<x(i,j)<<" ";
}
fout<<std::endl;
}
fout.close();
ofstream dout("d.txt");
for (int i = 0; i < X.m(); i++) {
for (int j = 0; j < X.n(); j++) {
dout<<X(i,j)<<" ";
}
dout<<std::endl;
}
dout.close();
lasso2<float>(x, X, all, L, lambda , 0 , PENALTY , true); //TODO:X->B
Util::SubSpMatrix(all,alpha,p_num-1);
// all.print("all");
// alpha.print("alpha");
// getchar();
Matrix<float> tmp;
X.mult(alpha,tmp);
x.add(tmp,-1);
std::cout<<(0.5*x.normFsq())<<" "<<(lambda*alpha.asum())<<" "<<(0.5*x.normFsq())/(lambda*alpha.asum())<<std::endl;
//save for vis
std::vector<int> mk;
std::vector<float> mv;
for(int ii = 0; ii < alpha.n(); ++ii) {
//TODO:calls for pB and pE are not consist
for(int j = alpha.pB(ii); j < alpha.pE()[ii]; ++j) {
//<i,j>->all.v(j)
mk.push_back(map_gl[j]);
mv.push_back(alpha.v(j));
neighborhood.push_back(map_gl[j]);
}
}
std::string namev = "debug/" + boost::lexical_cast<std::string>(cidx_) + ".xyznq";
ofstream ov(namev.c_str());
for(int ii = 0; ii < cloud_->size(); ++ii) {
if(ii == cidx_) {
ov << cloud_->points[ii].x << " " << cloud_->points[ii].y << " " << cloud_->points[ii].z << " 0 0 0 1" << std::endl;
} else {
std::vector<int>::iterator it = find(mk.begin(), mk.end(), ii);
if(it != mk.end()) {
int dis = std::distance(mk.begin(), it);
ov << cloud_->points[ii].x << " " << cloud_->points[ii].y << " " << cloud_->points[ii].z << " 0 0 0 " << mv[dis] << std::endl;
// ov << cloud_->points[ii].x <<" " << cloud_->points[ii].y << " " << cloud_->points[ii].z << " 0 0 0 0" << std::endl;
} else {
ov << cloud_->points[ii].x << " " << cloud_->points[ii].y << " " << cloud_->points[ii].z << " 0 0 0 -1" << std::endl;
}
}
}
ov.close();
return ;
} /* ----- end of method L1Graph::L1Minimization ----- */
ExecStatus
Weights<View>::propagate(Space& home, const ModEventDelta&) {
ModEvent me = ME_SET_NONE;
if (!x.assigned()) {
// Collect the weights of the elements in the unknown set in an array
int size = elements.size();
Region r(home);
int* currentWeights = r.alloc<int>(size);
UnknownRanges<View> ur(x);
Iter::Ranges::ToValues<UnknownRanges<View> > urv(ur);
for (int i=0; i<size; i++) {
if (!urv() || elements[i]<urv.val()) {
currentWeights[i] = 0;
} else {
assert(elements[i] == urv.val());
currentWeights[i] = weights[i];
++urv;
}
}
// Sort the weights of the unknown elements
IntLess il;
Support::quicksort<int>(currentWeights, size, il);
// The maximum number of elements that can still be added to x
int delta = static_cast<int>(std::min(x.unknownSize(), x.cardMax() - x.glbSize()));
// The weight of the elements already in x
GlbRanges<View> glb(x);
int glbWeight = weightI<GlbRanges<View> >(elements, weights, glb);
// Compute the weight of the current lower bound of x, plus at most
// delta-1 further elements with smallest negative weights. This weight
// determines which elements in the upper bound cannot possibly be
// added to x (those whose weight would exceed the capacity even if
// all other elements are minimal)
int lowWeight = glbWeight;
for (int i=0; i<delta-1; i++) {
if (currentWeights[i] >= 0)
break;
lowWeight+=currentWeights[i];
}
// Compute the lowest possible weight of x. If there is another element
// with negative weight left, then add its weight to lowWeight.
// Otherwise lowWeight is already the lowest possible weight.
int lowestWeight = lowWeight;
if (delta>0 && currentWeights[delta-1]<0)
lowestWeight+=currentWeights[delta-1];
// If after including the minimal number of required elements,
// no more element with negative weight is available, then
// a tighter lower bound can be computed.
if ( (x.cardMin() - x.glbSize() > 0 &&
currentWeights[x.cardMin() - x.glbSize() - 1] >= 0) ||
currentWeights[0] >= 0 ) {
int lowestPosWeight = glbWeight;
for (unsigned int i=0; i<x.cardMin() - x.glbSize(); i++) {
lowestPosWeight += currentWeights[i];
}
lowestWeight = std::max(lowestWeight, lowestPosWeight);
}
// Compute the highest possible weight of x as the weight of the lower
// bound plus the weight of the delta heaviest elements still in the
// upper bound.
int highestWeight = glbWeight;
for (int i=0; i<delta; i++) {
if (currentWeights[size-i-1]<=0)
break;
highestWeight += currentWeights[size-i-1];
}
// Prune the weight using the computed bounds
GECODE_ME_CHECK(y.gq(home, lowestWeight));
GECODE_ME_CHECK(y.lq(home, highestWeight));
// Exclude all elements that are too heavy from the set x.
// Elements are too heavy if their weight alone already
// exceeds the remaining capacity
int remainingCapacity = y.max()-lowWeight;
UnknownRanges<View> ur2(x);
Iter::Ranges::ToValues<UnknownRanges<View> > urv2(ur2);
OverweightValues<Iter::Ranges::ToValues<UnknownRanges<View> > >
ov(remainingCapacity, elements, weights, urv2);
Iter::Values::ToRanges<OverweightValues<
Iter::Ranges::ToValues<UnknownRanges<View> > > > ovr(ov);
me = x.excludeI(home, ovr);
GECODE_ME_CHECK(me);
}
if (x.assigned()) {
// If x is assigned, just compute its weight and assign y.
GlbRanges<View> glb(x);
int w =
weightI<GlbRanges<View> >(elements, weights, glb);
GECODE_ME_CHECK(y.eq(home, w));
return home.ES_SUBSUMED(*this);
}
return me_modified(me) ? ES_NOFIX : ES_FIX;
}
