void hgSgdGff3(char *inGff, char *outDir)
/* hgSgdGff3 - Parse out SGD gff3 file into components. */
{
FILE *codingFile = openInDir(outDir, "codingGenes.gff");
FILE *otherFile = openInDir(outDir, "otherFeatures.bed");
FILE *descriptionFile = openInDir(outDir, "descriptions.txt");
FILE *noteFile = openInDir(outDir, "notes.txt");
struct tenFields *tfList = parseTenFields(inGff);
noteIds(tfList, inGff, descriptionFile, noteFile);
saveFeatures(tfList, inGff, codingFile, descriptionFile, otherFile);
carefulClose(&codingFile);
carefulClose(&otherFile);
carefulClose(¬eFile);
}
bool debugSaveFeatures(SPConfig configuration,
LoadedFeatures allFeatures)
{
char curImgName[PATH_BUFFER_LEN] = {0};
SP_CONFIG_MSG configMessage = SP_CONFIG_SUCCESS;
SPPoint * curImageFeatures = NULL;
int curImgNumOfFeats = 0;
sp::ImageProc imageProc = sp::ImageProc(configuration);
int numOfImages = getFeaturesImagesNumber(allFeatures);
/* Try to get the features of all images */
for (int i=0 ; i<numOfImages ; i++)
{
/* Get the path of the index image */
configMessage = spConfigGetImagePath(curImgName, configuration, i);
if (configMessage != SP_CONFIG_SUCCESS)
{
return false;
}
/* Get the features of the image and the number of features */
try {
curImageFeatures = imageProc.getImageFeatures(curImgName, i, &curImgNumOfFeats);
}
catch (...)
{
return false;
}
if (curImageFeatures == NULL)
{
return false;
}
setFeatureArray(allFeatures, i, curImageFeatures);
setFeaturesNumber(allFeatures, i, curImgNumOfFeats);
}
return saveFeatures(configuration, allFeatures);
}
bool
SMF::save()
{
char filename[256];
sprintf( filename, "%s.smf", outPrefix.c_str() );
ofstream smf(filename, ios::binary | ios::out);
if( verbose )printf( "\nINFO: Saving %s.\n", filename );
char magic[] = "spring map file\0";
smf.write( magic, 16 );
int version = 1;
smf.write( (char *)&version, 4);
if( verbose )printf( "\tVersion: %i.\n", version );
int id = rand();
smf.write( (char *)&id, 4);
if( verbose )printf( "\tMapID: %i.\n", id );
int width = this->width * 64;
smf.write( (char *)&width, 4);
if( verbose )printf( "\tWidth: %i.\n", width );
int length = this->length * 64;
smf.write( (char *)&length, 4);
if( verbose )printf( "\tLength: %i.\n", length );
int squareWidth = 8;
smf.write( (char *)&squareWidth, 4);
if( verbose )printf( "\tSquareWidth: %i.\n", squareWidth );
int squareTexels = 8;
smf.write( (char *)&squareTexels, 4);
if( verbose )printf( "\tSquareTexels: %i.\n", squareTexels );
int tileTexels = 32;
smf.write( (char *)&tileTexels, 4);
if( verbose )printf( "\tTileTexels: %i.\n", tileTexels );
float floor = this->floor * 512;
smf.write( (char *)&floor, 4);
if( verbose )printf( "\tMinHeight: %0.2f.\n", floor );
float ceiling = this->ceiling * 512;
smf.write( (char *)&ceiling, 4);
if( verbose )printf( "\tMaxHeight: %0.2f.\n", ceiling );
smf.write( (char *)&heightPtr, 4);
if( verbose )printf( "\tHeightPtr: %i.\n", heightPtr );
smf.write( (char *)&typePtr, 4);
if( verbose )printf( "\tTypePtr: %i.\n", typePtr );
smf.write( (char *)&tilesPtr, 4);
if( verbose )printf( "\tTilesPtr: %i.\n", tilesPtr );
smf.write( (char *)&minimapPtr, 4);
if( verbose )printf( "\tMinimapPtr: %i.\n", minimapPtr );
smf.write( (char *)&metalPtr, 4);
if( verbose )printf( "\tMetalPtr: %i.\n", metalPtr );
smf.write( (char *)&featuresPtr, 4);
if( verbose )printf( "\tFeaturesPtr: %i.\n", featuresPtr );
int nExtraHeaders = extraHeaders.size();
smf.write( (char *)&nExtraHeaders, 4);
if( verbose )printf( "\tExtraHeaders: %i.\n", nExtraHeaders );
if(verbose) printf( " Extra Headers:\n");
for( unsigned int i = 0; i < extraHeaders.size(); ++i ) {
smf.write((char *)extraHeaders[i], extraHeaders[i]->size);
if( verbose ) {
if(extraHeaders[i]->type == 1)
printf("\tGrassPtr: %i.\n",
((SMFEHGrass *)extraHeaders[i])->grassPtr );
else printf( "\t Unknown Header\n");
}
}
smf.close();
saveHeight();
saveType();
saveMinimap();
saveMetal();
for( unsigned int i = 0; i < extraHeaders.size(); ++i ) {
if(extraHeaders[i]->type == 1)saveGrass();
}
saveTilemap();
saveFeatures();
return false;
}
QAction* Graphical_UI::createSaveMenu() {//octomap Menu
QMenu* sm = menuBar()->addMenu(tr("&Save"));
newMenuItem(sm,
"&Save",
SLOT(quickSaveAll()),
"Save all stored point clouds with common coordinate frame to a pcd file",
QKeySequence::Save,
QIcon::fromTheme("document-save"));
newMenuItem(sm,
"Save &Feature Map...",
SLOT(saveFeatures()),
"Save all feature positions and descriptions in a common coordinate frame to a yaml or xml file",
"Ctrl+F",
QIcon::fromTheme("document-save"));
QAction* oa = newMenuItem(sm, "Save Octomap...",
SLOT(saveOctomap()),
"Save computed OctoMap",
"",
QIcon::fromTheme("document-save-as"));
newMenuItem(sm, "&Save as Point Cloud ...",
SLOT(saveAll()),
"Save all stored point clouds with common coordinate frame",
QKeySequence::SaveAs,
QIcon::fromTheme("document-save-as"));
newMenuItem(sm, "&Save Point Cloud Node-Wise...",
SLOT(saveIndividual()),
"Save stored point clouds in individual files",
"Ctrl+N",
QIcon::fromTheme("document-save-all"));
newMenuItem(sm, "Save &G2O Graph...",
SLOT(saveG2OGraphDialog()),
"Save G2O graph (e.g. for use with the g2o viewer or external optimization)",
"",
QIcon::fromTheme("document-save"));
newMenuItem(sm, "Save Clouds to &Bag...",
SLOT(saveBagDialog()),
"Save clouds and transforms to bagfile",
"Ctrl+Shift+B");
newMenuItem(sm, "Save Trajectory &Estimate...",
SLOT(saveTrajectoryDialog()),
"Save trajectory estimate (and ground truth trajectory if available) for external evaluation.",
"Ctrl+E");
sm->addSeparator();
newMenuItem(sm, "&Send Model",
SLOT(sendAll()),
"Send out all stored point clouds with corrected transform",
"Ctrl+M",
QIcon::fromTheme("document-send"));
sm->addSeparator();
newMenuItem(sm, "Save &3D as PDF File...",
SLOT(saveVectorGraphic()),
"Write 3D Scene to a PDF File. Warning: Meant for Pose Graphs not for the clouds or octomaps!",
"",
QIcon::fromTheme("application-pdf"));
newMenuItem(sm, "Save Input &Images to Files...",
SLOT(saveAllImages()),
"Write All images shown in the gui to appropriate files",
"",
QIcon::fromTheme("image-x-generic"));
newMenuItem(sm, "Capture Screencast...",
this,
SLOT(toggleScreencast(bool)),
"Dump Screen as Video",
!ParameterServer::instance()->get<std::string>("screencast_path_prefix").empty());
return oa;
}
int main(int argc, char *argv[])
{
QCoreApplication a(argc, argv);
if (a.arguments().size() < 3) {
qCritical() << "this application requires more arguments!";
return -1;
}
const QString trainDirName = a.arguments().at(1);
const QString testDirName = a.arguments().at(2);
const QString outputName = a.arguments().at(3);
const QString extractorName = a.arguments().at(4);
const QStringList extractorArgs = a.arguments().mid(5);
ExtractorInterface *extractor =
ExtractorFactory::getExtractor(extractorName, extractorArgs);
if (extractor == NULL) {
qCritical() << "failed to initialise extractor" << extractorName;
return -2;
}
QDir trainDir(trainDirName);
QStringList subdirs = QStringList() << "wood" << "straw" << "salt" << "linen";
QList<quint8> labels = QList<quint8>() << 32 << 96 << 160 << 224;
QVector<LabelledData> trainData;
#ifdef HAS_ELAPSED_TIMER
QElapsedTimer extractionTimer;
#else
QTime extractionTimer;
#endif
int threadCount = 1;
#ifdef _OPENMP
#pragma omp parallel
{
#pragma omp single
{
threadCount = omp_get_num_threads();
}
}
#endif
qDebug() << "using" << threadCount << "threads.";
extractionTimer.start();
unsigned int imagesCount = 0;
for (int j = 0; j < subdirs.size(); j++) {
trainDir.cd(subdirs.at(j));
const QFileInfoList fileList = trainDir.entryInfoList(QStringList() << "*.png");
#ifdef HAS_ELAPSED_TIMER
QElapsedTimer extractorTimer;
#else
QTime extractorTimer;
#endif
extractorTimer.start();
for (int i = 0; i < fileList.size(); i++) {
imagesCount++;
const QString filename = fileList.at(i).filePath();
const QImage image(filename);
if (image.format() != QImage::Format_Indexed8) {
qCritical("Image is not greyscale!");
return -1;
}
extractor->preprocess(image);
if (extractor->extracts()) {
unsigned int count = trainData.size();
trainData.resize(trainData.size() + image.width() * image.height());
LabelledData *trainDataPtr = trainData.data();
#pragma omp parallel for
for (int x = 0; x < image.width(); x++) {
for (int y = 0; y < image.height(); y++) {
const QVector<nnreal> res = extractor->extract(image, x, y);
Q_ASSERT(res.size() == extractor->size());
LabelledData li(res, labels.at(j));
const unsigned int idx = count + x * image.height() + y;
trainDataPtr[idx] = li;
}
}
}
const QVector<QVector<nnreal> > ppFeatures = extractor->postprocess(image);
const int ppCount = ppFeatures.size();
if (ppCount > 0) {
const int count = trainData.size();
trainData.resize(trainData.size() + ppFeatures.size());
LabelledData *trainDataPtr = trainData.data();
#pragma omp parallel for
for (int k = 0; k < ppCount; k++) {
Q_ASSERT(ppFeatures.at(k).size() == extractor->size());
LabelledData ld(ppFeatures.at(k), labels.at(j));
trainDataPtr[count + k] = ld;
}
}
qDebug() << fileList.at(i).filePath() << extractorTimer.restart();
}
trainDir.cdUp();
}
const int msecs = extractionTimer.elapsed();
qDebug() << "trainSize:" << trainData.size() << "extraction of "
<< imagesCount << "images took" << msecs << "msecs, average"
<< float(msecs) / imagesCount << "msecs per image";
const QString trainOutFilename(outputName + "_" + extractorName + "_train.out");
QFile trainOutput(trainOutFilename);
if (!trainOutput.open(QIODevice::WriteOnly)) {
qCritical() << "failed to open output file" << trainOutFilename;
return -3;
}
{
#ifdef HAS_ELAPSED_TIMER
QElapsedTimer saveTimer;
#else
QTime saveTimer;
#endif
saveTimer.start();
QDataStream outstream(&trainOutput);
saveFeatures(outstream, extractorName, extractorArgs, extractor->size(), trainData);
int msecs = saveTimer.elapsed();
qDebug() << "saving took" << msecs << "msecs";
}
trainOutput.close();
trainData.clear();
{
QDir testDir(testDirName);
const QFileInfoList dataFileList = testDir.entryInfoList(QStringList() << "test*.png");
const QFileInfoList labelFileList = testDir.entryInfoList(QStringList() << "label*.png");
Q_ASSERT(dataFileList.size() == labelFileList.size());
#ifdef HAS_ELAPSED_TIMER
QElapsedTimer extractorTimer;
#else
QTime extractorTimer;
#endif
extractorTimer.start();
QTextStream out(stdout);
for (int i = 0; i < dataFileList.size(); i++) {
const QImage dataImage(dataFileList.at(i).filePath());
const QImage labelImage(labelFileList.at(i).filePath());
QVector<LabelledData> testData;
extractor->preprocessTest(dataImage, labelImage);
int cnt = 0;
if (extractor->extracts()) {
unsigned int count = testData.size();
testData.resize(dataImage.width() * dataImage.height());
LabelledData *testDataPtr = testData.data();
#pragma omp parallel for
for (int x = 0; x < dataImage.width(); x++) {
#pragma omp critical
{
cnt++;
out << cnt * 100 / dataImage.width() << "%" << '\r';
out.flush();
}
for (int y = 0; y < dataImage.height(); y++) {
const QVector<nnreal> res = extractor->extract(dataImage, x, y);
const quint8 c = labelImage.pixelIndex(x, y);
LabelledData li(res, c);
li.squeeze();
const unsigned int idx = count + x * dataImage.height() + y;
testDataPtr[idx] = li;
}
}
out << endl;
}
const QVector<LabelledData> ppFeatures = extractor->postprocessTest(dataImage, labelImage);
testData << ppFeatures;
qDebug() << dataFileList.at(i).filePath() << extractorTimer.restart();
const QString testOutFilename(outputName + "_" + extractorName + "_test" + QString::number(i) + ".out");
QFile testOutput(testOutFilename);
if (!testOutput.open(QIODevice::WriteOnly)) {
qCritical() << "failed to open output file" << testOutFilename;
return -3;
}
{
#ifdef HAS_ELAPSED_TIMER
QElapsedTimer saveTimer;
#else
QTime saveTimer;
#endif
saveTimer.start();
QDataStream outstream(&testOutput);
saveFeatures(outstream, extractorName, extractorArgs, extractor->size(), testData);
int msecs = saveTimer.elapsed();
qDebug() << "saving took" << msecs << "msecs";
}
testOutput.close();
}
}
delete extractor;
return 0;
}
