/*
* Writing models to resource directory
*/
void LinemodInterface::writeModels(const std::string &resourcePath)
{
const std::vector<std::string> ids = detector->classIds();
const std::string
basePath = resourcePath[resourcePath.size() - 1] == '/' ? resourcePath : resourcePath + '/',
file = "/linemod.yml",
fileGZ = file + ".gz";
std::map<std::string, std::vector<std::string> > baseIds;
for(int i = 0; i < (int)ids.size(); ++i)
{
const std::string
&classId = ids[i],
baseId = classId.substr(0, classId.rfind("_r"));
baseIds[baseId].push_back(classId);
}
std::map<std::string, std::vector<std::string> >::const_iterator
it = baseIds.begin(),
end = baseIds.end();
for(; it != end; ++it)
{
writeModel(basePath + it->first + file, it->second);
writeModel(basePath + it->first + fileGZ, it->second);
}
}
void eeCheck(bool immediately)
{
if (immediately) {
eepromWriteWait();
}
assert(eepromWriteState == EEPROM_IDLE);
if (s_eeDirtyMsk & EE_GENERAL) {
TRACE("eeprom write general");
s_eeDirtyMsk -= EE_GENERAL;
writeGeneralSettings();
if (immediately)
eepromWriteWait();
else
return;
}
if (s_eeDirtyMsk & EE_MODEL) {
TRACE("eeprom write model");
s_eeDirtyMsk -= EE_MODEL;
writeModel(g_eeGeneral.currModel);
if (immediately)
eepromWriteWait();
}
}
void
GeometryExportFile::exportData( ofstream &out )
{
vector<Selectable *>* list;
list = ObjectDB::getInstance()->getSelected();
//list = getMeshes();
// kts for now just edit the last one selected
Entity* entity = NULL;
for(int i=0; i<(int)list->size(); i++)
{
if((*list)[i]->isA(Object::TYPE))
{
entity = (Entity *) (*list)[i];
}
}
if(entity)
writeModel( ( Object * ) ( entity ), out );
else
{
int n = 1;
QString strMessage = "You must select at least ";
QString num;
num.setNum( n );
strMessage += num;
strMessage += " items first";
QMessageBox::information( 0, "World Foundry Geometry Exporter", strMessage );
}
//writeSprite( ( Object * ) ( entity ), out );
}
int main(int argc, char* argv[])
{
boostStruct bst;
char input_file_name[1024], model_file_name[1024];
boost_config(&bst);
parse_command_line(argc, argv, &input_file_name[0], &model_file_name[0], &bst);
read_problem(input_file_name, &bst);
adaBoost(&bst);
writeModel(&bst, model_file_name);
boost_destroy(&bst);
}
void save_solution(const solution_t *solution_curr,
const input_parameters_t *in_para, const int *model){
const protein_t* p_curr;
FILE * pdbfile;
char *file_name;
file_name = Malloc(char, MAX_FILE_NAME);
strcpy(file_name, "monte_carlo_solutions.pdb");
char *fname = path_join_file(in_para->path_local_execute,
file_name);
p_curr = (protein_t*) solution_curr->representation;
if (*model == 1){
pdbfile = open_file(fname, fWRITE);
writeHeader(pdbfile, 0.00, &p_curr->p_topol->numatom);
}else{
pdbfile = open_file(fname, fAPPEND);
}
writeModel(pdbfile, model);
writeATOM(pdbfile, p_curr->p_atoms, &p_curr->p_topol->numatom);
writeEndModel(pdbfile);
fclose(pdbfile);
free(fname);
free(file_name);
}
int main( int argc, char **argv ) {
char *progname = argv[0];
FILE *in , *out;
char opt;
int i;
double startTime;
C = 0;
kernelType = -1;
degree = 0;
sigmaSqr = 0;
binaryFeature = 0;
/* Check command line options */
optarg = NULL;
while (((opt = getopt(argc, argv, OPTSTRING)) != -1)) {
switch(opt) {
case 't':
if ( strcmp(optarg, "0") == 0 ) kernelType = 0;
else if ( strcmp(optarg, "1") == 0 ) kernelType = 1;
else if ( strcmp(optarg, "2") == 0 ) kernelType = 2;
else {
fprintf( stderr, "kernel type is either 0,1 or 2\n");
exit(1);
}
break;
case 'c':
if( sscanf(optarg, "%f", &C) == 0 ) {
fprintf(stderr,"Expect a positive number for C.\n");
exit(1);
} else
C = atof(optarg);
if( C <= 0 ) {
fprintf( stderr, "C has to be > 0\n");
exit(1);
}
break;
case 'd':
if( sscanf(optarg, "%d", °ree) == 0 ) {
fprintf( stderr, "Expect degree to be a positive integer.\n");
exit(1);
} else degree = atoi(optarg);
if ( degree <= 0 ) {
fprintf( stderr, "degree has to be a positive integer.\n");
exit(1);
}
break;
case 'v':
if( sscanf(optarg, "%f", &sigmaSqr) == 0 ) {
fprintf(stderr,"Expect a positive number for variance.\n");
exit(1);
} else sigmaSqr = atof(optarg);
if( sigmaSqr <= 0 ) {
fprintf( stderr, "variance has to be > 0\n");
exit(1);
}
rbfConstant = 1/(2*sigmaSqr);
break;
case 'b':
if( sscanf(optarg, "%d", &binaryFeature) == 0 ) {
fprintf( stderr, "binaryFeature option is either 0 or 1.\n");
exit(1);
} else binaryFeature = atoi(optarg);
if ( binaryFeature != 0 && binaryFeature != 1 ) {
fprintf( stderr, "binaryFeature option is either 0 or 1.\n");
exit(1);
}
break;
case 'h':
useMsg( progname );
exit(1);
break;
default:
useMsg( progname );
exit(1);
break;
}
}
/* Check all necessary parameters are in */
if( kernelType == -1 ) {
fprintf( stderr, "Kernel type has not been specified.\n");
exit(2);
} else if( kernelType == 1 && degree == 0 ) {
fprintf( stderr, "Degree has not been specified.\n");
exit(2);
} else if( kernelType == 2 && sigmaSqr == 0 ){
fprintf( stderr, "Variance has not been specified.\n");
exit(2);
} else if( C == 0 ) C = DEFAULT;
/* Check training file and model file */
printf("INPUT FILE %s\n", argv[argc-2]);
if (( in = fopen( argv[argc-2], "r") ) == NULL ) {
fprintf( stderr, "Can't open %s\n", argv[argc-2] );
exit(2);
}
if (( out = fopen( argv[argc-1], "w") ) == NULL ) {
fprintf( stderr, "Can't open %s\n", argv[argc-1] );
exit(2);
}
printf("smo_learn is preparing to learn. . .\n");
if( ! readFile( in ) ) {
fprintf( stderr, "Error in initializing. Program exits.\n" );
exit (1);
} else fclose( in );
if( !initializeTraining()) {
fprintf( stderr, "Error in initializing data structure. Program exits.\n");
exit(1);
}
printf("Start training . . .\n");
startTime = clock()/CLOCKS_PER_SEC;
startLearn();
printf("Training is completed\n");
/* Print training statistics */
printf("CPU time is %f secs\n", clock()/CLOCKS_PER_SEC-startTime);
printf("Writing training results . . .\n");
writeModel( out );
fclose( out );
printf("Finish writing training results.\n");
printf("no of iteration is %f\n", iteration);
printf("threshold b is %f\n", getb());
if ( kernelType == 0 )
printf("norm of weight vector is %f\n", calculateNorm());
printf("no. of unBound multipliers is %d\n", unBoundSv );
printf("no. of bounded multipliers is %d\n", boundSv );
/* Free memory */
free( target );
free( lambda );
free( nonZeroFeature );
free( error );
free( nonBound );
free( weight );
free( unBoundIndex );
free( nonZeroLambda );
for( i = 0; i <= numExample; i++ ) {
free( example[i] );
}
free( example );
free( errorCache );
return 0;
}
int main(int argc, char *argv[]) {
DIR *dir;
ofstream fout;
char slash = Unix ? '/' : '\\'; // It is '/' or '\' depending on OS
char POS_PATH_BASE[MAX_PATH_LENGTH];
char NEG_PATH_BASE[MAX_PATH_LENGTH];
clock_t tic, toc;
if (argc != 4) {
error("Usage: train [POS_DIR] [NEG_DIR] [OUTPUT_FILE].");
}
if (!(dir = opendir(argv[1]))) {
error("train: [POS_DIR] open failed.");
}
/* Set POS_PATH_BASE to [POS_DIR] and append '/' or '\' */
strcpy(POS_PATH_BASE, argv[1]);
sprintf(POS_PATH_BASE, "%s%c", POS_PATH_BASE, slash);
closedir(dir);
if (!(dir = opendir(argv[2]))) {
error("train: [NEG_DIR] open failed.");
}
/* Set NEG_PATH_BASE to [NEG_DIR] and append '/' or '\' */
strcpy(NEG_PATH_BASE, argv[2]);
sprintf(NEG_PATH_BASE, "%s%c", NEG_PATH_BASE, slash);
closedir(dir);
fout.open(argv[3]);
if (!(fout)) {
error("train: [OUTPUT_FILE] open failed.");
}
/** Command is correct **/
echoOS();
cout << "This program provides cascaded-AdaBoost training.\n" <<
"Please make sure that [POS_DIR] and [NEG_DIR] contain only training image data,\n" <<
" whose size is " << WINDOW_WIDTH << " x " << WINDOW_HEIGHT << ".\n" <<
"Press [Enter] to continue, or ctrl+C/D/Z to exit ...";
getchar();
tic = clock();
/* Use only one large matrix for storing all POS / NEG feature data */
CvMat *POS = NULL, *NEG = NULL;
int N1, N2; /* number of positive / negative images */
int blockCount = 0; /* number of blocks in an image */
/* [1] Feature extraction */
/* First, check for validity of extraction parameters */
assert(!(360 % (BIN_NUM * 2))); // (360 / BIN_NUM / 2) should be an integer */
assert(360 / BIN_NUM == BIN_SIZE);
assert(BIN_SIZE >> 1 == HALF_BIN_SIZE);
cout << "\nStart of feature extraction ...\n";
/* Should pass (CvMat *&) to really create the matrices */
extractAll(POS_PATH_BASE, POS, N1, blockCount);
cout << "Extraction of POS data completed.\n";
#if CHECKNaN
cout << "Check POS matrix for NaN values:" << endl;
if (checkNaN(POS, "POS")) {
error("POS matrix contains NaN values!");
}
else {
cout << "OK!" << endl;
}
#endif
extractAll(NEG_PATH_BASE, NEG, N2, blockCount);
cout << "Extraction of NEG data completed.\n";
#if CHECKNaN
cout << "Check NEG matrix for NaN values:" << endl;
if (checkNaN(NEG, "NEG")) {
error("NEG matrix contains NaN values!");
}
else {
cout << "OK!" << endl;
}
#endif
assert(blockCount > 0);
cout << endl << "# of blocks per image: " << blockCount << ".\n";
#if GETCHAR
getchar();
#endif
/* [2] Cascaded-AdaBoost training */
cout << "Start of cascaded-AdaBoost training ...\n";
srand(time(NULL));
float F_current = 1.0; // current overall false positive rate
int i = 1; // AdaBoost stage counter
int rejectCount = 0; // # of negative images rejected so far
/* Allocate rejection table */
/** Note: All the xxxTable[]'s are of boolean flags **/
bool *rejectTable = new bool[ N2 ];
memset(rejectTable, 0, N2);
bool stop = false; // Stopping flag
vector<AdaStrong> H; // A cascade of AdaBoost strong classifiers
/*** The training algorithm ***/
while (F_current > F_target && !stop) {
/* upper bound for j */
int jEnd = (i == 1) ? (ni + 1) : ni;
for (int j = 1; j <= jEnd; j++) {
/* Learn an A[i,j] stage */
cout << "\nLearning stage A[" << i << "," << j << "]...\n";
if ((stop = learnA(N1, N2, blockCount, rejectCount, rejectTable, POS, NEG, H, F_current))) {
break;
}
cout << "Stage A[" << i << "," << j << "] completed.\n";
#if GETCHAR
getchar();
#endif
}
#if META
if (stop) break;
/* Learn a M[i] stage */
cout << "\nLearning stage M[" << i << "]...\n";
learnM();
cout << "Stage M[" << i << "," << j << "] completed.\n";
#if GETCHAR
getchar();
#endif
#endif
i++;
} // End of loop while (F_current > F_target && !stop)
cout << "The entire training process completed.\nWriting model parameters to " << argv[3] << " ... ";
/* Write model parameters to [OUTPUT_FILE]. See docs/train_format.txt for explanation. */
writeModel(H, fout);
cout << "done!\n";
/* Show running time */
toc = clock();
runningTime(tic, toc);
/* Don't forget to close the file stream */
fout.close();
return 0;
}
int SbmlWriter::write( string filepath,string target )
{
cout << "Sbml Writer: " << filepath << " ---- " << target << endl;
//cout << "use_SBML:" << USE_SBML << endl;
#ifdef USE_SBML
string::size_type loc;
while ( ( loc = filepath.find( "\\" ) ) != string::npos )
{
filepath.replace( loc, 1, "/" );
}
if ( filepath[0]== '~' )
{
cerr << "Error : Replace ~ with absolute path " << endl;
}
string filename = filepath;
string::size_type last_slashpos = filename.find_last_of("/");
filename.erase( 0,last_slashpos + 1 );
vector< string > fileextensions;
fileextensions.push_back( ".xml" );
fileextensions.push_back( ".zip" );
fileextensions.push_back( ".bz2" );
fileextensions.push_back( ".gz" );
vector< string >::iterator i;
for( i = fileextensions.begin(); i != fileextensions.end(); i++ )
{
string::size_type loc = filename.find( *i );
if ( loc != string::npos )
{
int strlen = filename.length();
filename.erase( loc,strlen-loc );
break;
}
}
if ( i == fileextensions.end() && filename.find( "." ) != string::npos )
{
string::size_type loc;
while ( ( loc = filename.find( "." ) ) != string::npos )
{
filename.replace( loc, 1, "_" );
}
}
if ( i == fileextensions.end() )
filepath += ".xml";
cout << " filepath " << filepath << filename << endl;
bool SBMLok = false;
SBMLDocument sbmlDoc(2,4);
createModel(filename,sbmlDoc);
if (SBMLok)
writeModel(&sbmlDoc,filepath);
if( !SBMLok) cerr << "Errors encountered " << endl;
/**
string::size_type loc;
// if blackslash is found then its replaced to '/'
while ((loc = filepath.find("\\")) !=string::npos)
{ filepath.replace(loc,1,"/"); }
if(filepath[0] == '~')
{cerr << "Error : Replace '~' with absolute path" << endl; }
string filename = filepath;
string ::size_type last_slashpos = filename.find_last_of("/");
filename.erase(0,last_slashpos+1);
int strlen = filepath.length();
filepath.erase(last_slashpos+1,strlen);
cout << "\t \t here file path " << filepath << " name " << filename << endl;
//cout << "filepath" << filepath << "filename " << filename;
vector <string> fileextensions;
fileextensions.push_back(".xml");
fileextensions.push_back(".zip");
fileextensions.push_back(".bz2");
fileextensions.push_back(".gz");
vector <string>::iterator i;
// here I need to check for exact file extensions, this peice of code works for any extensions+anything like this xmll
for (i = fileextensions.begin(); i != fileextensions.end(); i++)
{
string::size_type loc = filename.find(*i);
cout << "fileextensions -- " << *i << "loc " << loc << endl;
if(loc != string::npos)
{ int strlen = filename.length();
filename.erase(loc,strlen-loc);
cout << "file " << filename << endl;
break;
}
}
if(i == fileextensions.end())
{
string :: size_type loc = filename.find(".");
if(loc != string::npos)
{ filename.replace(loc,1,"_");
cout <<" %%" << filename << endl;
filename +='.xml';
cout <<" %%%" << filename << endl;
}
else
{ filename+='.xml'; }
}
cout << "$$$" << filepath << " " << filename << endl;
filepath = filepath+filename;
cout << "filepath --- " << filepath << "--filename-- " << filename << endl;
**/
#endif
return 0;
}
int main(int argc, const char *argv[])
{
int N,
M,
T,
maxIters,
seed,
i,
j,
iter,
str_len;
char **alphabet;
double logProb,
newLogProb;
double *pi,
*piBar,
**A,
**Abar,
**B,
**Bbar;
struct stepStruct *step;
FILE *in,
*out;
char s[80];
int wantTraining = 1;
if(argc != 10)
{
fprintf(stderr, "\nUsage: %s N M T maxIters filename alphabet modelfile seed\n\n", argv[0]);
fprintf(stderr, "where N == number of states of the HMM\n");
fprintf(stderr, " M == number of observation symbols\n");
fprintf(stderr, " T == number of observations in the training set\n");
fprintf(stderr, " maxIters == max iterations of re-estimation algorithm\n");
fprintf(stderr, " filename == name of input file\n");
fprintf(stderr, " alphabet == name of file defining the alphabet\n");
fprintf(stderr, " modelfile == name of model output file\n");
fprintf(stderr, " seed == seed value for pseudo-random number generator (PRNG)\n\n");
fprintf(stderr, " wantTraining == to train enter 1, otherwise 0 \n\n");
fprintf(stderr, "For example:\n\n %s 2 10 10000 500 datafile alphabet modelfile 1241\n\n", argv[0]);
fprintf(stderr, "will create a HMM with 2 states and 10 observation symbols,\n");
fprintf(stderr, "will read in the first 10000 observations from `datafile',\n");
fprintf(stderr, "will use the observation symbols defined in file `alphabet', and\n");
fprintf(stderr, "will write the model (pi, A, B) to `modelfile', and\n");
fprintf(stderr, "will seed the PRNG with 1241 and train the HMM with a maximum of 500 iterations.\n\n");
exit(0);
}
N = atoi(argv[1]);
M = atoi(argv[2]);
T = atoi(argv[3]);
maxIters = atoi(argv[4]);
seed = atoi(argv[8]);
wantTraining = atoi(argv[9]);
pi = (double *)malloc(N * sizeof(double));
piBar = (double *)malloc(N * sizeof(double));
A = (double **)malloc(N * sizeof(double*));
Abar =static_cast<double **>(malloc(N * sizeof(double*)));
for (i=0; i<N; ++i)
{
A[i] = static_cast<double *>(malloc(N * sizeof(double)));
Abar[i] = static_cast<double *>(malloc(N * sizeof(double)));
}
B = static_cast<double **>(malloc(N * sizeof(double*)));
Bbar = static_cast<double **>(malloc(N * sizeof(double*)));
for (i=0; i<N; ++i)
{
B[i] = static_cast<double *>(malloc(M * sizeof(double)));
Bbar[i] = static_cast<double *>(malloc(M * sizeof(double)));
}
////////////////////////
// read the data file //
////////////////////////
// allocate memory
printf("allocating %d bytes of memory... ", (T + 1) * sizeof(struct stepStruct));
fflush(stdout);
if((step = static_cast<stepStruct *>(calloc(T + 1, sizeof(struct stepStruct)))) == NULL)
{
fprintf(stderr, "\nUnable to allocate alpha\n\n");
exit(0);
}
for (i=0; i<T+1; ++i)
{
step[i].alpha = static_cast<double *>(malloc(N * sizeof(double)));
step[i].beta = static_cast<double *>(malloc(N * sizeof(double)));
step[i].gamma = static_cast<double *>(malloc(N * sizeof(double)));
step[i].diGamma = static_cast<double **>(malloc(N * sizeof(double*)));
for (j=0; j<N; ++j)
{
step[i].diGamma[j] = static_cast<double *>(malloc(N * sizeof(double)));
}
}
printf("done\n");
// read in the observations from file
printf("GetObservations... ");
fflush(stdout);
in = fopen(argv[5], "r"); // argv[5] = filename
if(in == NULL)
{
fprintf(stderr, "\nError opening file %s\n\n", argv[5]);
exit(0);
}
i = 0;
fgets(s,80,in); // get rid of the first line
while (i < T)
{
fgets(s,80,in);
step[i].obs = atoi(s);
++i;
}
fclose(in);
printf("done\n");
// read in the alphabet from file
printf("GetAlphabet... ");
fflush(stdout);
alphabet = static_cast<char **>(malloc(M * sizeof (char*)));
in = fopen(argv[6], "r"); // argv[6] = alphabet
if(in == NULL)
{
fprintf(stderr, "\nError opening file %s\n\n", argv[6]);
exit(0);
}
i = 0;
fgets(s,80,in); // get rid of the first line
while (i < M)
{
fgets(s,80,in);
str_len = strlen(s);
alphabet[i] = static_cast<char *>(malloc(str_len * sizeof(char)));
strncpy(alphabet[i], s, str_len-1);
alphabet[i][str_len-1] = '\0';
++i;
}
fclose(in);
printf("done\n");
/////////////////////////
// hidden markov model //
/////////////////////////
srand(seed);
// initialize pi[], A[][] and B[][]
initMatrices(pi, A, B, N, M, seed);
// print pi[], A[][] and B[][] transpose
printf("\nN = %d, M = %d, T = %d\n", N, M, T);
printf("initial pi =\n");
printPi(pi, N);
printf("initial A =\n");
printA(A, N);
printf("initial B^T =\n");
printBT(B, N, M, alphabet);
// initialization
iter = 0;
logProb = -1.0;
newLogProb = 0.0;
if (wantTraining) {
// main loop
while((iter < maxIters) && (newLogProb > logProb))
{
printf("\nbegin iteration = %d\n", iter);
logProb = newLogProb;
// alpha (or forward) pass
printf("alpha pass... ");
fflush(stdout);
alphaPass(step, pi, A, B, N, T);
printf("done\n");
// beta (or backwards) pass
printf("beta pass... ");
fflush(stdout);
betaPass(step, pi, A, B, N, T);
printf("done\n");
// compute gamma's and diGamma's
printf("compute gamma's and diGamma's... ");
fflush(stdout);
computeGammas(step, pi, A, B, N, T);
printf("done\n");
// find piBar, reestimate of pi
printf("reestimate pi... ");
fflush(stdout);
reestimatePi(step, piBar, N);
printf("done\n");
// find Abar, reestimate of A
printf("reestimate A... ");
fflush(stdout);
reestimateA(step, Abar, N, T);
printf("done\n");
// find Bbar, reestimate of B
printf("reestimate B... ");
fflush(stdout);
reestimateB(step, Bbar, N, M, T);
printf("done\n");
#ifdef PRINT_REESTIMATES
printf("piBar =\n");
printPi(piBar, N);
printf("Abar =\n");
printA(Abar, N);
printf("Bbar^T = \n");
printBT(Bbar, N, M, alphabet);
#endif // PRINT_REESTIMATES
// assign pi, A and B corresponding "bar" values
for(i = 0; i < N; ++i)
{
pi[i] = piBar[i];
for(j = 0; j < N; ++j)
{
A[i][j] = Abar[i][j];
}
for(j = 0; j < M; ++j)
{
B[i][j] = Bbar[i][j];
}
}// next i
// compute log [P(observations | lambda)], where lambda = (A,B,pi)
newLogProb = 0.0;
for(i = 0; i < T; ++i)
{
newLogProb += log(step[i].c);
}
newLogProb = -newLogProb;
// a little trick so that no initial logProb is required
if(iter == 0)
{
logProb = newLogProb - 1.0;
}
printf("completed iteration = %d, log [P(observation | lambda)] = %f\n",
iter, newLogProb);
++iter;
}// end while
out = fopen(argv[7], "w"); // argv[7] = modelfile
writeModel(pi, A, B, N, M, T, alphabet, out);
fclose(out);
printf("\nT = %d, N = %d, M = %d, iterations = %d\n\n", T, N, M, iter);
printf("final pi =\n");
printPi(pi, N);
printf("\nfinal A =\n");
printA(A, N);
printf("\nfinal B^T =\n");
printBT(B, N, M, alphabet);
printf("\nlog [P(observations | lambda)] = %f\n\n", newLogProb);
} // end of training
else { //want to do testing
out = fopen(argv[7], "r"); // argv[7] = modelfile
readModelFile(pi, A, B, N, M, T, alphabet, out);
// alpha (or forward) pass
printf("alpha pass... ");
fflush(stdout);
alphaPass(step, pi, A, B, N, T);
printf("done\n");
printf("logProb %f\n", computeLogProb(step, T)/T);
// FILE * newFile = fopen("testing.txt", "a");
//writeModel(pi, A, B, N, M, T, alphabet, newFile);
//fclose(newFile);
fclose(out);
} // end of testing
}// end hmm
