void testAdaBoost(int colorspace) {
ImageLoader loaderTrue("c:\\Images\\true", colorspace);
ImageLoader loaderFalse("c:\\Images\\false", colorspace);
ImageLoader loaderTest("c:\\Images\\test", colorspace);
vector< Image* > slikeTrue = loaderTrue.loadNextImages();
vector< Image* > slikeFalse= loaderFalse.loadNextImages();
Feature::loadBaseFeatures("bftest.txt");
int tmpChans[] = {0, 1, 2};
vector< int > channels(tmpChans, tmpChans + 3 ); //kanali nad kojima ce se raditi
vector < Feature > tmp = Feature::generateAll( 20, 20, 3, 1.25, channels );
writeFeatures( tmp );
AdaBoost boost;
vector< Feature > level = boost.startTraining( slikeTrue, slikeFalse, tmp, 20);
cout << "IZABRANI FEATURE-i" << endl; writeFeatures( level );
vector< Image * > testSlike = loaderTest.loadNextImages();
//testSlike[0]->showImageOverlappedWithFeature( level[1], true );
testSlike[0]->evaluirajLevel( level );
//for(int i=0; i<testSlike.size(); i++) {
// testSlike[i]->evaluirajLevel( level );
//}
}
void genePredWriteToGtf(struct genePred *gp, char *source,
struct hash *dupeHash, FILE *f)
/* Write out genePredName to GTF file. */
{
int i;
char *name = findUniqueName(dupeHash, gp->name);
char *geneName = gp->name2;
char *chrom = gp->chrom;
char strand = gp->strand[0];
int *frames = (gp->optFields & genePredExonFramesFld) ? gp->exonFrames : calcFrames(gp);
struct codonCoords firstCodon = findFirstCodon(gp, frames);
struct codonCoords lastCodon = findLastCodon(gp, frames);
// figure out bounds of CDS and UTR regions, moving stop codon to outside of
// CDS.
int firstUtrEnd = gp->cdsStart, lastUtrStart = gp->cdsEnd;
int cdsStart = gp->cdsStart, cdsEnd = gp->cdsEnd;
if ((strand == '+') && codonComplete(&lastCodon))
cdsEnd = movePos(gp, lastUtrStart, -3);
if ((strand == '-') && codonComplete(&firstCodon))
cdsStart = movePos(gp, cdsStart, 3);
if (addComments)
fprintf(f, "###\n# %s %s:%d-%d (%s) CDS: %d-%d\n#\n",
gp->name, gp->chrom, gp->txStart, gp->txEnd,
gp->strand, gp->cdsStart, gp->cdsEnd);
for (i=0; i<gp->exonCount; ++i)
{
writeGtfLine(f, source, name, geneName, chrom, strand, "exon",
gp->exonStarts[i], gp->exonEnds[i], i, -1);
if (cdsStart < cdsEnd)
writeFeatures(gp, i, source, name, chrom, strand, geneName,
firstUtrEnd, cdsStart, cdsEnd, lastUtrStart,
frames[i], f);
}
if (gp->strand[0] == '+')
{
if (codonComplete(&firstCodon))
writeCodon(f, source, name, geneName, chrom, strand, "start_codon",
&firstCodon);
if (codonComplete(&lastCodon))
writeCodon(f, source, name, geneName, chrom, strand, "stop_codon",
&lastCodon);
}
else
{
if (codonComplete(&lastCodon))
writeCodon(f, source, name, geneName, chrom, strand, "start_codon",
&lastCodon);
if (codonComplete(&firstCodon))
writeCodon(f, source, name, geneName, chrom, strand, "stop_codon",
&firstCodon);
}
if (!(gp->optFields & genePredExonFramesFld))
freeMem(frames);
}
void ParticleSorterMpi::run()
{
int total_nr_images = MDin.numberOfObjects();
features.resize(total_nr_images, NR_FEATURES);
// Each node does part of the work
long int my_first_image, my_last_image, my_nr_images;
divide_equally(total_nr_images, node->size, node->rank, my_first_image, my_last_image);
my_nr_images = my_last_image - my_first_image + 1;
int barstep;
if (verb > 0)
{
std::cout << "Calculating sorting features for all input particles..." << std::endl;
init_progress_bar(my_nr_images);
barstep = XMIPP_MAX(1, my_nr_images/ 60);
}
long int ipart = 0;
FOR_ALL_OBJECTS_IN_METADATA_TABLE(MDin)
{
if (ipart >= my_first_image && ipart <= my_last_image)
{
if (verb > 0 && ipart % barstep == 0)
progress_bar(ipart);
calculateFeaturesOneParticle(ipart);
}
ipart++;
}
if (verb > 0)
progress_bar(my_nr_images);
// Combine results from all nodes
MultidimArray<double> allnodes_features;
allnodes_features.resize(features);
MPI_Allreduce(MULTIDIM_ARRAY(features), MULTIDIM_ARRAY(allnodes_features), MULTIDIM_SIZE(features), MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
features = allnodes_features;
// Only the master writes out files
if (verb > 0)
{
normaliseFeatures();
writeFeatures();
}
}
void CascadeWriter::writeCascade()
{
xml.writeStartElement("cascade");
xml.writeTextElement("stageType", m_cascadeObj.stageType());
xml.writeTextElement("featureType", m_cascadeObj.featureType());
xml.writeTextElement("height", QString::number(m_cascadeObj.height()));
xml.writeTextElement("width", QString::number(m_cascadeObj.width()));
writeStageParams();
writeFeatureParams();
xml.writeTextElement("stageNum", QString::number(m_cascadeObj.stageNum()));
writeStages();
writeFeatures();
xml.writeEndElement();
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void AbaqusSurfaceMeshWriter::execute()
{
int32_t err = 0;
setErrorCondition(err);
dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer sm = getDataContainerArray()->getDataContainer(getSurfaceMeshFaceLabelsArrayPath().getDataContainerName());
// Make sure any directory path is also available as the user may have just typed
// in a path without actually creating the full path
QFileInfo fi(getOutputFile());
QDir parentPath = fi.path();
if(!parentPath.mkpath("."))
{
QString ss = QObject::tr("Error creating parent path '%1'").arg(parentPath.absolutePath());
setErrorCondition(-8005);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
TriangleGeom::Pointer triangleGeom = sm->getGeometryAs<TriangleGeom>();
// Store all the unique Spins
std::set<int32_t> uniqueSpins;
for (int64_t i = 0; i < triangleGeom->getNumberOfTris(); i++)
{
uniqueSpins.insert(m_SurfaceMeshFaceLabels[i * 2]);
uniqueSpins.insert(m_SurfaceMeshFaceLabels[i * 2 + 1]);
}
FILE* f = fopen(m_OutputFile.toLatin1().data(), "wb");
ScopedFileMonitor fileMonitor(f);
err = writeHeader(f, triangleGeom->getNumberOfVertices(), triangleGeom->getNumberOfTris(), uniqueSpins.size() - 1);
if(err < 0)
{
QString ss = QObject::tr("Error writing header for file '%1'").arg(m_OutputFile);
setErrorCondition(-8001);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
err = writeNodes(f);
if(err < 0)
{
QString ss = QObject::tr("Error writing nodes for file '%1'").arg(m_OutputFile);
setErrorCondition(-8002);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
err = writeTriangles(f);
if(err < 0)
{
QString ss = QObject::tr("Error writing triangles for file '%1'").arg(m_OutputFile);
setErrorCondition(-8003);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
err = writeFeatures(f);
if(err < 0)
{
QString ss = QObject::tr("Error writing Features for file '%1'").arg(m_OutputFile);
setErrorCondition(-8004);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
notifyStatusMessage(getHumanLabel(), "Complete");
}
