BSONObj qgmMerge( const BSONObj &left, const BSONObj &right )
{
PD_TRACE_ENTRY( SDB__QGMMERGE ) ;
BSONObj obj ;
BSONObjBuilder builder ;
try
{
BSONObjIterator itr1( left ) ;
while ( itr1.more() )
{
builder.append( itr1.next() ) ;
}
BSONObjIterator itr2( right ) ;
while ( itr2.more() )
{
builder.append( itr2.next() ) ;
}
obj = builder.obj() ;
}
catch ( std::exception &e )
{
PD_LOG( PDERROR, "unexpected err happened:%s",
e.what() ) ;
}
PD_TRACE_EXIT( SDB__QGMMERGE ) ;
return obj ;
}
void VolumeProcess::SetInput(ImageType::Pointer inImage)
{
m_inputImage = inImage;
//m_outputImage = inImage; //THIS IS NOT CORRECT IT WILL CAUSE INPUT IMAGE TO CHANGE
//Init the output image to the input image:
m_outputImage = ImageType::New();
m_outputImage->SetRegions( m_inputImage->GetLargestPossibleRegion() );
m_outputImage->Allocate();
m_outputImage->FillBuffer(0);
itk::ImageRegionIterator< ImageType > itr1( m_inputImage, m_inputImage->GetLargestPossibleRegion() );
itk::ImageRegionIterator< ImageType > itr2( m_outputImage, m_outputImage->GetLargestPossibleRegion() );
for(itr1.GoToBegin(), itr2.GoToBegin() ; !itr1.IsAtEnd(); ++itr1, ++itr2)
{
itr2.Set( itr1.Get() );
}
}
//This function removes all objects that are <= minObjSize from the foreground.
//The foreground remains grayscale after this filter
void Preprocess::RemoveConnectedComponents(int minObjSize)
{
typedef itk::Image< unsigned short, 3 > ShortImageType;
typedef itk::ConnectedComponentImageFilter< ImageType3D, ShortImageType > CCFilterType;
typedef itk::RelabelComponentImageFilter< ShortImageType, ShortImageType > RelabelType;
CCFilterType::Pointer ccfilter = CCFilterType::New();
RelabelType::Pointer relabel = RelabelType::New();
ccfilter->SetInput( myImg );
ccfilter->FullyConnectedOn();
relabel->SetInput( ccfilter->GetOutput() );
relabel->SetMinimumObjectSize( minObjSize );
relabel->InPlaceOn();
try
{
relabel->Update();
}
catch( itk::ExceptionObject & excep )
{
std::cerr << "Relabel: exception caught !" << std::endl;
std::cerr << excep << std::endl;
return;
}
unsigned short initNumObjects = ccfilter->GetObjectCount();
unsigned short finalNumObjects = relabel->GetNumberOfObjects();
unsigned short removedNumObjects = initNumObjects - finalNumObjects;
std::cout << "Removed " << removedNumObjects << " of " << initNumObjects << " objects...";
ShortImageType::Pointer ccImage = relabel->GetOutput();
//Use connected component image as a mask:
itk::ImageRegionIterator< ShortImageType > itr1( ccImage, ccImage->GetLargestPossibleRegion() );
itk::ImageRegionIterator< ImageType3D > itr2( myImg, myImg->GetLargestPossibleRegion() );
for(itr1.GoToBegin(), itr2.GoToBegin() ; !itr1.IsAtEnd(); ++itr1, ++itr2)
{
if(itr1.Get() == 0)
{
itr2.Set( 0 );
}
}
}
//This function removes all objects that are <= minObjSize from the foreground.
//The foreground remains grayscale after this filter
bool VolumeProcess::MaskSmallConnComp(int minObjSize)
{
typedef itk::Image< unsigned short, Dimension > ShortImageType;
typedef itk::ConnectedComponentImageFilter< ImageType, ShortImageType > CCFilterType;
typedef itk::RelabelComponentImageFilter< ShortImageType, ShortImageType > RelabelType;
CCFilterType::Pointer ccfilter = CCFilterType::New();
RelabelType::Pointer relabel = RelabelType::New();
ccfilter->SetInput (m_outputImage);
ccfilter->FullyConnectedOn();
relabel->SetInput( ccfilter->GetOutput() );
relabel->SetMinimumObjectSize( minObjSize );
relabel->InPlaceOn();
try
{
relabel->Update();
}
catch( itk::ExceptionObject & excep )
{
std::cerr << "Relabel: exception caught !" << std::endl;
std::cerr << excep << std::endl;
return false;
}
unsigned short numObjects = relabel->GetNumberOfObjects();
if(debug)
std::cerr << "Connected components = " << numObjects << std::endl;
ShortImageType::Pointer ccImage = relabel->GetOutput();
//Use connected component image as a mask:
itk::ImageRegionIterator< ShortImageType > itr1( ccImage, ccImage->GetLargestPossibleRegion() );
itk::ImageRegionIterator< ImageType > itr2( m_outputImage, m_outputImage->GetLargestPossibleRegion() );
for(itr1.GoToBegin(), itr2.GoToBegin() ; !itr1.IsAtEnd(); ++itr1, ++itr2)
{
if(itr1.Get() == 0)
{
itr2.Set( 0 );
}
}
return true;
}
bool VolumeProcess:: RunFillingZeroOnBouandary(int Bx,int By,int Bz)
{
ImageType::Pointer tempImg = ImageType::New();
tempImg->SetRegions( m_outputImage->GetLargestPossibleRegion() );
tempImg->Allocate();
tempImg->FillBuffer(0);
ImageType::RegionType fullRegion = m_outputImage->GetBufferedRegion();
int numColumns = fullRegion.GetSize(0);
int numRows = fullRegion.GetSize(1);
int numStacks = fullRegion.GetSize(2);
int i, j,k;
itk::ImageRegionIteratorWithIndex< ImageType > itr( m_outputImage, fullRegion );
for(itr.GoToBegin(); !itr.IsAtEnd(); ++itr)
{
ImageType::IndexType index = itr.GetIndex();
ImageType::PixelType pix = m_outputImage->GetPixel(index);
i = index[0];
j = index[1];
k = index[2];
if (i < Bx || i > numColumns -Bx || j < By || j > numRows-By ||k <Bz ||k > numStacks-Bz )
tempImg->SetPixel(itr.GetIndex(), 0);
else
tempImg->SetPixel(itr.GetIndex(), pix);
}
//Copy temp img back to image
itk::ImageRegionIterator< ImageType > itr1( tempImg, tempImg->GetLargestPossibleRegion());
itk::ImageRegionIterator< ImageType > itr2( m_outputImage, m_outputImage->GetLargestPossibleRegion());
for(itr1.GoToBegin(), itr2.GoToBegin() ; !itr1.IsAtEnd(); ++itr1, ++itr2)
{
itr2.Set( itr1.Get() );
}
if(debug)
std::cerr << "RunFillingZero Done" << std::endl;
return true;
}
int main(int argc, char* argv[])
{
std::vector<std::string> args;
bool appendMode = false;
int retval = 0;
for (int i = 0; i < argc; i++)
{
if (strcmp(argv[i], "-a") == 0)
appendMode = true;
else
args.push_back(argv[i]);
}
if ((args.size() < 3) || (args.size() > 4))
{
std::cout << "Usage: processEventLog [-a] <path> <out> [tz-offset-hours]" << std::endl;
return 1;
}
try
{
boost::filesystem::path path(args[1]);
if (!boost::filesystem::exists(path))
{
std::cout << args[1] << " does not exist." << std::endl;
return 2;
}
if (!appendMode && !boost::filesystem::is_directory(path))
{
std::cout << args[1] << " must be a directory." << std::endl;
return 3;
}
std::ofstream out(args[2].c_str(), appendMode ? std::ofstream::app : std::ofstream::trunc );
if (!out.is_open())
{
std::cout << "failed to open output file " << args[2] << std::endl;
return 4;
}
int hrsOffset = 0;
if (args.size() > 3)
hrsOffset = atoi(args[3].c_str());
result_t results;
if (!appendMode)
{
boost::filesystem::directory_iterator end_itr; // default construction yields past-the-end
for ( boost::filesystem::directory_iterator itr( path );
itr != end_itr;
++itr )
{
if ( boost::filesystem::is_directory(itr->status()) )
{
for ( boost::filesystem::directory_iterator itr2( *itr );
itr2 != end_itr;
++itr2 )
{
if (!boost::filesystem::is_regular_file(*itr2))
continue;
processFile(itr2->path(), hrsOffset, results);
}
}
}
out << "DATE\t" << "TIME\t" << "relay" << '\t' << "target"
<< '\t' << "inside" << '\t' << "humidity" << '\t' << "coded\t"
<< "FILE" << std::endl;
}
else
processFile(path, hrsOffset, results);
boost::posix_time::time_facet *facet =
new boost::posix_time::time_facet("%Y/%m/%d %H:%M:%S");
std::ostringstream date_ss;
date_ss.imbue(std::locale(date_ss.getloc(), facet));
for (
result_t::const_iterator resItor = results.begin();
resItor != results.end();
resItor++)
{
date_ss.str("");
date_ss << resItor->first;
const Event &e = resItor->second;
out << date_ss.str() << "\t" <<
e.relay() << '\t' <<
e.target() << '\t' <<
e.temperature() << '\t' <<
e.humidity() << '\t' <<
e.relayCoded() << '\t' <<
e.filename() <<
std::endl;
int insideTemp = (int)(e.temperature() + 0.5);
if ((insideTemp >= 45) && (insideTemp <= 90))
retval = insideTemp;
}
}
catch (const std::exception &e)
{
std::cout << "Didn't work because " << e.what() << std::endl;
}
return retval;
}
int
fix_omap(int argc, char **argv)
{
typedef boost::filesystem3::directory_iterator directory_iterator;
// Get file paths
if(argc < 4)
throw std::runtime_error("Path to second occluded oMap directory is required as third arg\n");
if(argc < 3)
throw std::runtime_error("Path to occluded oMap directory is required as second arg\n");
if(argc < 2)
throw std::runtime_error("Path to oMap directory is required as first arg\n");
std::string dir_omap(argv[1]);
std::string dir_omap_occ(argv[2]);
std::string dir_omap_occ_2(argv[3]);
for (directory_iterator itr(dir_omap); itr!=directory_iterator(); ++itr)
{
// Get first txt file
std::string curr_ext(itr->path().extension().string());
if( curr_ext.compare(".txt") == 0 )
{
std::string curr_stem( itr->path().stem().string() );
std::string curr_name( itr->path().filename().string() );
for (directory_iterator itr2(dir_omap_occ); itr2!=directory_iterator(); ++itr2)
{
std::string curr_occ_name( itr2->path().filename().string() );
if( curr_occ_name.compare(curr_name) == 0)
{
for (directory_iterator itr3(dir_omap_occ_2); itr3!=directory_iterator(); ++itr3)
{
std::string curr_occ_2_name( itr3->path().filename().string() );
if( curr_occ_2_name.compare(curr_name) == 0)
{
std::cout << curr_occ_name << std::endl;
// Open files
std::ifstream f1, f2, f3;
std::ofstream f4;
io_utils::open_in_file( f1, itr->path().string() );
io_utils::open_in_file( f2, itr2->path().string() );
io_utils::open_in_file( f3, itr3->path().string() );
io_utils::open_out_file( f4, "./" + curr_stem + "_combined.txt" );
if( !f1 )
throw std::runtime_error("Cannot open oMap file " + curr_stem + "\n");
if( !f2 )
throw std::runtime_error("Cannot open occ file " + curr_stem + "\n");
if( !f2 )
throw std::runtime_error("Cannot open occ2 file " + curr_stem + "\n");
if( !f4 )
throw std::runtime_error("Cannot open out file...\n");
// Combine them
int cntr = 0;
int vp1 = -1, vp2 = -1, vp3 = -1;
std::string st1, st2, st3;
double sc1, sc2, sc3;
while( (f1 >> vp1) && (f1 >> st1) && (f1 >> sc1) )
{
if( vp1 == cntr )
f4 << vp1 << " " << st1 << " " << sc1 << std::endl;
else
{
if(vp2 != -1)
{
f4 << vp2 << " " << st2 << " " << sc2 << std::endl;
}
while( (f2 >> vp2) && (f2 >> st2) && (f2 >> sc2) )
{
if(vp2 == cntr)
f4 << vp2 << " " << st2 << " " << sc2 << std::endl;
else
{
if(vp3 != -1)
{
f4 << vp3 << " " << st3 << " " << sc3 << std::endl;
}
while( (f3 >> vp3) && (f3 >> st3) && (f3 >> sc3) )
{
if(vp3 == cntr)
f4 << vp3 << " " << st3 << " " << sc3 << std::endl;
else
break;
}
break;
}
}
f4 << vp1 << " " << st1 << " " << sc1 << std::endl;
++cntr;
}
}
f4 << vp2 << " " << st2 << " " << sc2 << std::endl;
while( (f2 >> vp2) && (f2 >> st2) && (f2 >> sc2) )
{
f4 << vp2 << " " << st2 << " " << sc2 << std::endl;
}
f4 << vp3 << " " << st3 << " " << sc3 << std::endl;
while( (f3 >> vp3) && (f3 >> st3) && (f3 >> sc3) )
{
f4 << vp3 << " " << st3 << " " << sc3 << std::endl;
}
// close the files
f1.close();
f2.close();
f3.close();
f4.close();
}
}
}
}
}
bool VolumeProcess::DialateImage(int iterations)
{
int border = 2;
ImageType::Pointer tempImg = ImageType::New();
tempImg->SetRegions( m_outputImage->GetLargestPossibleRegion() );
tempImg->Allocate();
tempImg->FillBuffer(0);
ImageType::RegionType fullRegion = m_outputImage->GetBufferedRegion();
ImageType::RegionType borderRegion;
borderRegion.SetIndex(0, fullRegion.GetIndex(0)+border);
borderRegion.SetIndex(1, fullRegion.GetIndex(1)+border);
borderRegion.SetIndex(2, fullRegion.GetIndex(2)+border);
borderRegion.SetSize(0, fullRegion.GetSize(0)-(2*border));
borderRegion.SetSize(1, fullRegion.GetSize(1)-(2*border));
borderRegion.SetSize(2, fullRegion.GetSize(2)-(2*border));
itk::ImageRegionIteratorWithIndex< ImageType > itr( m_outputImage, borderRegion );
while(iterations > 0)
{
for(itr.GoToBegin(); !itr.IsAtEnd(); ++itr)
{
double blockMax = itr.Get();
for(int k=-1; k<=1; k++)
{
for(int j=-1; j<=1; j++)
{
for(int i=-1; i<=1; i++)
{
ImageType::IndexType index = itr.GetIndex();
index[0] += i;
index[1] += j;
index[2] += k;
ImageType::PixelType pix = m_outputImage->GetPixel(index);
if((double)pix > blockMax)
{
blockMax = (double)pix;
}
}
}
}
// Keep the peak of the original intensity
if (blockMax == itr.Get() && blockMax != 0)
{
blockMax = blockMax + 1;
}
tempImg->SetPixel(itr.GetIndex(), blockMax);
}
//Copy temp img back to image for next dialation
itk::ImageRegionIterator< ImageType > itr1( tempImg, tempImg->GetLargestPossibleRegion() );
itk::ImageRegionIterator< ImageType > itr2( m_outputImage, m_outputImage->GetLargestPossibleRegion() );
for(itr1.GoToBegin(), itr2.GoToBegin() ; !itr1.IsAtEnd(); ++itr1, ++itr2)
{
itr2.Set( itr1.Get() );
}
iterations--;
}
if(debug)
std::cerr << "Dialation Done" << std::endl;
return true;
}
