void dumpCurrentContext(std::ostream &os)
{
JSONWriter json(os);
#ifndef NDEBUG
GLint old_bindings[NUM_BINDINGS];
for (unsigned i = 0; i < NUM_BINDINGS; ++i) {
old_bindings[i] = 0;
glGetIntegerv(bindings[i], &old_bindings[i]);
}
#endif
dumpParameters(json);
dumpShaders(json);
dumpTextures(json);
dumpFramebuffer(json);
#ifndef NDEBUG
for (unsigned i = 0; i < NUM_BINDINGS; ++i) {
GLint new_binding = 0;
glGetIntegerv(bindings[i], &new_binding);
if (new_binding != old_bindings[i]) {
std::cerr << "warning: " << enumToString(bindings[i]) << " was clobbered\n";
}
}
#endif
}
void
dumpDevice(std::ostream &os, ID3D11DeviceContext *pDeviceContext)
{
JSONWriter json(os);
dumpParameters(json, pDeviceContext);
dumpShaders(json, pDeviceContext);
// TODO: dump constant buffers
json.beginMember("uniforms");
json.beginObject();
json.endObject();
json.endMember(); // uniforms
// TODO: dump stream-out buffer, vertex buffer
json.beginMember("buffers");
json.beginObject();
json.endObject();
json.endMember(); // buffers
dumpTextures(json, pDeviceContext);
dumpFramebuffer(json, pDeviceContext);
}
void
dumpDevice(StateWriter &writer, ID3D10Device *pDevice)
{
dumpParameters(writer, pDevice);
dumpShaders(writer, pDevice);
dumpTextures(writer, pDevice);
dumpFramebuffer(writer, pDevice);
}
void dumpCurrentContext(std::ostream &os)
{
JSONWriter json(os);
#ifndef NDEBUG
GLint old_bindings[NUM_BINDINGS];
for (unsigned i = 0; i < NUM_BINDINGS; ++i) {
old_bindings[i] = 0;
glGetIntegerv(bindings[i], &old_bindings[i]);
}
#endif
Context context;
/* Temporarily disable messages, as dumpParameters blindlessly tries to
* get state, regardless the respective extension is supported or not.
*/
GLDEBUGPROC prevDebugCallbackFunction = 0;
void *prevDebugCallbackUserParam = 0;
if (context.KHR_debug) {
glGetPointerv(GL_DEBUG_CALLBACK_FUNCTION, (GLvoid **) &prevDebugCallbackFunction);
glGetPointerv(GL_DEBUG_CALLBACK_USER_PARAM, &prevDebugCallbackUserParam);
glDebugMessageCallback(NULL, NULL);
}
dumpParameters(json, context);
// Use our own debug-message callback.
if (context.KHR_debug) {
glDebugMessageCallback(debugMessageCallback, NULL);
}
dumpShadersUniforms(json, context);
dumpTextures(json, context);
dumpFramebuffer(json, context);
#ifndef NDEBUG
for (unsigned i = 0; i < NUM_BINDINGS; ++i) {
GLint new_binding = 0;
glGetIntegerv(bindings[i], &new_binding);
if (new_binding != old_bindings[i]) {
std::cerr << "warning: " << enumToString(bindings[i]) << " was clobbered\n";
}
}
#endif
// Restore debug message callback
if (context.KHR_debug) {
glDebugMessageCallback(prevDebugCallbackFunction, prevDebugCallbackUserParam);
}
}
int Docking::outputScores(const string& outputFile, const string& header, vector <pair<double, ScoreConfiguration> > scores) const
{
/*PdbFile ligandPDB;
PdbFile receptorPDB;*/
FILE *fp = fopen(outputFile.c_str(), "wt");
//FILE *fpPDB = 0;
if (fp == 0)
{
// can't open file
return -1;
}
/*if (ligandPath_!="" && receptorPath_!="" && radiiPath_!="")
{
fpPDB = fopen((outputFile + ".pdb").c_str(), "w");
if (fpPDB == NULL)
return -1;
}
if (ligandPath_!="" && receptorPath_!="" && radiiPath_!="")
{
ligandPDB.Init((char *) ligandPath_.c_str());
if (!ligandPDB.LoadAtmtypenumbers((char *) radiiPath_.c_str()))
return -1;
ligandPDB.UseUnitedRadius();
ligandPDB.Import();
receptorPDB.Init((char *) receptorPath_.c_str());
if (!receptorPDB.LoadAtmtypenumbers((char *) radiiPath_.c_str()))
return -1;
receptorPDB.UseUnitedRadius();
receptorPDB.Import();
}*/
fprintf(fp, "%s", header.c_str());
dumpParameters(fp);
sort(scores.begin(), scores.end(), greater < pair<double, ScoreConfiguration> >());
//fprintf(fp, "# rank score R beta1 gamma1 alpha2 beta2 gamma2\n");
fprintf(fp, "# rank score R Rec_beta1 Rec_gamma1 Lig_alpha2 Lig_beta2 Lig_gamma2\n");
for (unsigned int i = 0; i < scores.size(); ++i)
{
//fprintf(fp, "%d %lf %lf %lf %lf %lf %lf %lf\n", i+1, scores[i].first, scores[i].second.R, scores[i].second.beta1, scores[i].second.gamma1, scores[i].second.alpha, scores[i].second.beta2, scores[i].second.gamma2);
fprintf(fp, "%d %E %lf %lf %lf %lf %lf %lf\n", i+1, scores[i].first, scores[i].second.R, scores[i].second.beta1, scores[i].second.gamma1, scores[i].second.alpha, scores[i].second.beta2, scores[i].second.gamma2 );
/*if (ligandPath_!="" && receptorPath_!="" && radiiPath_!="")
{
fprintf (fpPDB, "MODEL %d\n", i);
receptorPDB.WriteTransformedAtoms(fpPDB, 'R', scores[i].second.R, 0.0f, scores[i].second.beta1, scores[i].second.gamma1);
fprintf (fpPDB, "TER\n");
ligandPDB.WriteTransformedAtoms(fpPDB, 'L', 0.0f, scores[i].second.alpha, scores[i].second.beta2, scores[i].second.gamma2);
fprintf (fpPDB, "TER\n");
fprintf (fpPDB, "ENDMDL\n");
}*/
}
fclose(fp);
/*if (ligandPath_!="" && receptorPath_!="" && radiiPath_!="")
fclose(fpPDB);*/
return 0;
}
int main(int argc, char* argv[]) {
// parses the command line arguments
std::string filename="";
eClassifierType cType=RBF;
std::string cParam="";
eKernelType kType=Linear;
std::string kScalar="";
std::string vParam="";
int width=400;
int height=400;
lti::dpoint ur(-1,-1);
lti::dpoint ll(1,1);
bool ok;
for (int i=1; i<argc; i++) {
if (*argv[i] == '-') {
switch (argv[i][1]) {
// dump parametes?
case 'd':
dumpParameters();
exit(0);
break;
// print help
case '-':
if (strcasecmp(&argv[i][2],"help")==0) {
printHelp();
exit(0);
} else {
std::cerr << "Unknown option "<<argv[i]<<std::endl;
}
break;
// classifier
case 'c':
if (i < argc-1) {
++i;
if (strcasecmp(argv[i],"rbf") == 0) {
cType=RBF;
} else if (strcasecmp(argv[i],"mlp") == 0) {
cType=MLP;
} else if (strcasecmp(argv[i],"svm") == 0) {
cType=SVM;
} else if (strcasecmp(argv[i],"knn") == 0) {
cType=KNN;
} else {
std::cerr << "Warning: Classifier " << argv[i]
<< " is not supported, using RBF instead\n";
}
} else {
std::cerr << "Missing argument to -c\n";
}
break;
// classifier parameters
case 'p':
if (i < argc-1) {
cParam=argv[++i];
} else {
std::cerr << "Missing argument to -p\n";
}
break;
// kernel
case 'k':
if (i < argc-1) {
++i;
if (strcasecmp(argv[i],"linear") == 0) {
kType=Linear;
} else if (strcasecmp(argv[i],"polynomial") == 0) {
kType=Polynomial;
} else if (strcasecmp(argv[i],"radial") == 0) {
kType=Radial;
} else if (strcasecmp(argv[i],"sigmoid") == 0) {
kType=Sigmoid;
} else {
std::cerr << "Warning: Kernel " << argv[i]
<< " is not supported using Linear\n";
}
} else {
std::cerr << "Missing argument to -k\n";
}
break;
// kernel parameter
case 's':
if (i < argc-1) {
kScalar=argv[++i];
} else {
std::cerr << "Missing argument to -s\n";
}
break;
// visualizer parameters
case 'v':
if (i < argc-1) {
vParam=argv[++i];
} else {
std::cerr << "Missing argument to -v\n";
}
break;
// image width
case 'w':
if (i < argc-1) {
width=atoi(argv[++i]);
} else {
std::cerr << "Missing argument to -w\n";
}
break;
// image height
case 'h':
if (i < argc-1) {
height=atoi(argv[++i]);
} else {
std::cerr << "Missing argument to -h\n";
}
break;
// range
case 'r':
ok = i < argc-1;
if (ok) {
ll.x=atof(&argv[++i][1]);
}
ok = ok && i < argc-1;
if (ok) {
ll.y=atof(argv[++i]);
}
ok = ok && i < argc-1;
if (ok) {
ur.x=atof(argv[++i]);
}
ok = ok && i < argc-1;
if (ok) {
++i;
int itmp;
itmp=strlen(argv[i]);
char stmp[itmp-1];
strncpy(stmp,argv[i],itmp-2);
ur.y=atof(stmp);
}
if (!ok) {
std::cerr << "Missing argument to -r or argument incomplete\n";
}
break;
// unknown option
default:
std::cerr << "Warning: Unknown option -" << argv[i][1] << std::endl;
break;
}
} else {
filename=argv[i];
if (i<argc-1) {
std::cerr << "filename must be last argument, ignoring the rest.\n";
break;
}
}
}
if (filename.length() == 0) {
std::cerr << "You need to give a file name.\n";
printHelp();
exit(1);
}
lti::supervisedInstanceClassifier* classifier=0;
if (!initClassifier(classifier, cType, cParam, kType, kScalar)) {
std::cerr << "Could not initialize classifier\n";
exit(1);
}
if (classifier==0) {
std::cerr << "Classifier not initialized\n";
exit(1);
}
lti::dmatrix data;
lti::ivector ids;
if (!getData(filename,data,ids)) {
std::string msg="Could not read data from file " + filename;
std::cerr << msg << std::endl;
exit(1);
}
if (!classifier->train(data,ids)) {
std::cerr << "Could not train classifier on given data\n";
std::cerr << classifier->getStatusString() << std::endl;
exit(1);
}
lti::classifier2DVisualizer::parameters vizParam;
if (!initVisualizerParam(vizParam, vParam, width, height, ll, ur)) {
std::cerr << "Could not initialize visualizer\n";
exit(1);
}
_my_viz.setParameters(vizParam);
lti::image img(width,height);
if (!_my_viz.apply(*classifier,data,img,ids)) {
std::cerr << "Error visualizing the classification result\n";
}
_my_viewer.show(img);
_my_viewer.waitButtonPressed();
_my_viewer.hide();
lti::passiveWait(10000);
delete classifier;
classifier=0;
lti::gtkServer::shutdown();
}
