/*---------------------------------------------------------------------------
* FindBipResponder()
*---------------------------------------------------------------------------
*
* Synopsis: Return the BIP Responder channel given the ObexServerApp pointer.
*
* Return: BipObexClient* or BipObexServer*
*/
void *FindBipResponder(void *app)
{
I8 i;
/* Go through the BIP server array. */
for (i = 0; i < BIP_NUM_RESPONDERS; i++) {
if (BIP(responder)[i] && &BIP(responder)[i]->primary.sApp == app) {
return &(BIP(responder)[i]->primary);
}
}
return 0;
}
/*---------------------------------------------------------------------------
* FindBipInitiator()
*---------------------------------------------------------------------------
*
* Synopsis: Return the BIP Initiator channel given the ObexClientApp pointer.
*
* Return: BipObexClient* or BipObexServer*
*/
void *FindBipInitiator(void *app)
{
I8 i;
/* Go through the BIP client array. */
for (i = 0; i < BIP_NUM_INITIATORS; i++) {
if (BIP(initiator)[i] && &BIP(initiator)[i]->primary.cApp == app) {
return &(BIP(initiator)[i]->primary);
}
}
return 0;
}
//Color one blob for one thread
void ColorBlob( cv::Mat BinImPad, std::vector< std::pair<int,int> > *indices,
const int &start, const int &end, unsigned char ¤t_index, unsigned char &replace_ind ){
//Check the 8-connected neighborhood and set them if they are within bounds
std::pair<int,int> CI = indices->back();
indices->pop_back();
if( (CI.second-1)>=start ){//Bounds checking for current thread
for( int i=-1; i<2; ++i ) if( BIP((CI.first+i),(CI.second-1)) ==replace_ind ){
BIP( (CI.first+i),(CI.second-1) ) = current_index;
std::pair<int,int> PushInd( (CI.first+i),(CI.second-1) );
indices->push_back( PushInd );
}
}
if( (CI.second+1)<end ){//Bounds checking for next thread
for( int i=-1; i<2; ++i ) if( BIP((CI.first+i),(CI.second+1)) ==replace_ind ){
BIP( (CI.first+i),(CI.second+1) ) = current_index;
std::pair<int,int> PushInd( (CI.first+i),(CI.second+1) );
indices->push_back( PushInd );
}
}
if( BIP((CI.first-1),(CI.second))==replace_ind ){
BIP( (CI.first-1),(CI.second) ) = current_index;
std::pair<int,int> PushInd( (CI.first-1),(CI.second) );
indices->push_back( PushInd );
}
if( BIP((CI.first+1),(CI.second))==replace_ind ){
BIP( (CI.first+1),(CI.second) ) = current_index;
std::pair<int,int> PushInd( (CI.first+1),(CI.second) );
indices->push_back( PushInd );
}
if(!indices->empty()){
ColorBlob( BinImPad, indices, start, end, current_index, replace_ind );
}
}
/*---------------------------------------------------------------------------
* BipAppCallBack()
*---------------------------------------------------------------------------
*
* Synopsis: Call the application with the specified event.
*
* Return:
*/
void BipAppCallBack(BipCallbackParms *parms, U16 status, BipEvent event)
{
BipCallback callback = 0; /* Application callback function */
parms->status = status;
parms->event = event;
parms->channel = parms->obex.client->channel;
switch (parms->channel) {
#if BIP_NUM_INITIATORS > 0
case BIPCH_INITIATOR_PRIMARY:
case BIPCH_INITIATOR_SECONDARY:
callback = BIP(initiatorCallback);
break;
#endif
#if BIP_NUM_RESPONDERS > 0
case BIPCH_RESPONDER_PRIMARY:
case BIPCH_RESPONDER_SECONDARY:
callback = BIP(responderCallback);
break;
#endif
default:
break;
}
/* Copy the channel data pointer into parms */
switch (parms->channel) {
case BIPCH_INITIATOR_PRIMARY:
case BIPCH_RESPONDER_SECONDARY:
parms->data = parms->obex.client->data;
break;
case BIPCH_INITIATOR_SECONDARY:
case BIPCH_RESPONDER_PRIMARY:
parms->data = &parms->obex.server->request;
break;
default:
break;
}
Assert(callback);
callback(parms);
}
//Computes the area and the centroid for a given label
bool GetStats(cv::Mat LabelIm, int i, int j, cv::Mat BinImPad, std::vector<int> &one_stat){
//Seed with the first pixel
std::pair<int,int> seed(i,j);
std::vector< std::pair<int,int> > indices, queueue;
indices.push_back(seed); queueue.push_back(seed);
BIP(i,j) = 0;
double x_men = 0, y_men = 0; //centroid
//Find indices of all pixels with the same label
while( !queueue.empty() ){
std::pair<int, int> index = queueue.back();
queueue.pop_back();
//Check 8-neighborhood
for( int k=-1; k<2; ++k )
for( int l=-1; l<2; ++l )
if( (k==0) && (l==0) ) continue;
else{
if( BIP( (index.first+k),(index.second+l) ) ){
std::pair<int,int> sed( (index.first+k),(index.second+l) );
queueue.push_back( sed );
indices.push_back( sed );
LabelIm.at<unsigned char>( sed.first, sed.second ) = BIP( sed.first,sed.second );
BIP( sed.first, sed.second ) = 0;
x_men += sed.first;
y_men += sed.second;
}
}
}
x_men = round(x_men/((double)indices.size()));
y_men = round(y_men/((double)indices.size()));
one_stat[1] = indices.size();
one_stat[2] = (int)x_men;
one_stat[3] = (int)y_men;
if( (indices.size())>=15 ){ return true; }
else{
std::vector< std::pair<int,int> >::iterator it;
for( it=indices.begin() ; it < indices.end(); ++it )
LabelIm.at<unsigned char>(it->first, it->second) = 0;
return false;
}
}
//This function binarizes the nuclei in an image and colors connected components
void computebin(cv::Mat src, cv::Mat BinImPad, cv::Mat BinIm ){
//Get Image Dimensions
int thresh = GetThresh(src);
int nthreads, tid;
#pragma omp parallel private(tid,nthreads)
{
tid = omp_get_thread_num();
nthreads = omp_get_num_threads();
int start, end;
start = tid*(rows/nthreads);
end = (tid+1)*(rows/nthreads);
if( tid == (nthreads-1) ) end = rows;
for( int j=start; j<rows; ++j )
for( int i=0; i<cols; ++i )
if( src.at<unsigned char>(i,j) > thresh ){
BinIm.at<unsigned char>(i,j) = 0;
BIP((i+1),(j+1)) = 0;
}
else{
BinIm.at<unsigned char>(i,j) = 255;
BIP((i+1),(j+1)) = UCHAR_MAX;
}
}
//Set the borders of the padded image
for( int i=0; i<(cols+2); ++i ){
BIP(i,0) = 0;
BIP(i,(rows+1)) = 0;
}
for( int i=1; i<(rows+2); ++i ){
BIP(0,i) = 0;
BIP((cols+1),i) = 0;
}
if(write_files){
std::string out_str1 = "binary_" + file_open;
cv::imwrite(out_str1.c_str(),BinIm);
}
std::cout<<"The threshold is: "<<thresh<<std::endl;
}
int main(int argc, char *argv[])
{
{
libmaus2::lz::LineSplittingGzipOutputStream LSG("gzsplit",4,17);
for ( uint64_t i = 0; i < 17; ++i )
LSG << "line_" << i << "\n";
}
{
libmaus2::lz::LineSplittingGzipOutputStream LSG("nogzsplit",4,17);
}
testGzip();
testlz4();
#if 0
maskBamDuplicateFlag(std::cin,std::cout);
return 0;
#endif
#if 0
{
libmaus2::lz::BgzfInflateDeflateParallel BIDP(std::cin,std::cout,Z_DEFAULT_COMPRESSION,32,128);
libmaus2::autoarray::AutoArray<char> B(64*1024,false);
int r;
uint64_t t = 0;
uint64_t last = std::numeric_limits<uint64_t>::max();
uint64_t lcnt = 0;
uint64_t const mod = 64*1024*1024;
libmaus2::timing::RealTimeClock rtc; rtc.start();
libmaus2::timing::RealTimeClock lrtc; lrtc.start();
while ( (r = BIDP.read(B.begin(),B.size())) )
{
BIDP.write(B.begin(),r);
lcnt += r;
t += r;
if ( t/mod != last/mod )
{
if ( isatty(STDERR_FILENO) )
std::cerr
<< "\r" << std::string(60,' ') << "\r";
std::cerr
<< rtc.formatTime(rtc.getElapsedSeconds()) << " " << t/(1024*1024) << "MB, " << (lcnt/lrtc.getElapsedSeconds())/(1024.0*1024.0) << "MB/s";
if ( isatty(STDERR_FILENO) )
std::cerr << std::flush;
else
std::cerr << std::endl;
lrtc.start();
last = t;
lcnt = 0;
}
}
if ( isatty(STDERR_FILENO) )
std::cerr
<< "\r" << std::string(60,' ') << "\r";
std::cerr
<< rtc.formatTime(rtc.getElapsedSeconds()) << " " << t/(1024*1024) << "MB, " << (t/rtc.getElapsedSeconds())/(1024.0*1024.0) << "MB/s";
std::cerr << std::endl;
return 0;
}
#endif
#if 0
{
::libmaus2::lz::BgzfDeflateParallel BDP(std::cout,32,128,Z_DEFAULT_COMPRESSION);
while ( std::cin )
{
libmaus2::autoarray::AutoArray<char> B(16384);
std::cin.read(B.begin(),B.size());
int64_t const r = std::cin.gcount();
BDP.write(B.begin(),r);
}
BDP.flush();
std::cout.flush();
}
return 0;
#endif
#if 0
{
try
{
libmaus2::lz::BgzfInflateParallel BIP(std::cin /* ,4,16 */);
uint64_t c = 0;
uint64_t b = 0;
uint64_t d = 0;
libmaus2::timing::RealTimeClock rtc; rtc.start();
libmaus2::autoarray::AutoArray<uint8_t> adata(64*1024,false);
while ( (d=BIP.read(reinterpret_cast<char *>(adata.begin()),adata.size())) != 0 )
{
b += d;
if ( ++c % (16*1024) == 0 )
{
std::cerr << c << "\t" << b/(1024.0*1024.0*1024.0) << "\t" << static_cast<double>(b)/(1024.0*1024.0*rtc.getElapsedSeconds()) << " MB/s" << std::endl;
}
}
std::cerr << c << "\t" << b/(1024.0*1024.0*1024.0) << "\t" << static_cast<double>(b)/(1024.0*1024.0*rtc.getElapsedSeconds()) << " MB/s" << std::endl;
std::cerr << "decoded " << b << " bytes in " << rtc.getElapsedSeconds() << " seconds." << std::endl;
}
catch(std::exception const & ex)
{
std::cerr << ex.what() << std::endl;
return EXIT_FAILURE;
}
}
return 0;
#endif
std::cerr << "Testing random data on bgzf...";
testBgzfRandom();
std::cerr << "done." << std::endl;
std::cerr << "Testing mono...";
testBgzfMono();
std::cerr << "done." << std::endl;
::libmaus2::lz::BgzfDeflate<std::ostream> bdefl(std::cout);
char const * str = "Hello, world.\n";
bdefl.write(reinterpret_cast<char const *>(str),strlen(str));
bdefl.flush();
bdefl.write(reinterpret_cast<char const *>(str),strlen(str));
bdefl.flush();
bdefl.addEOFBlock();
return 0;
::libmaus2::lz::BgzfInflateStream SW(std::cin);
::libmaus2::autoarray::AutoArray<char> BB(200,false);
while ( SW.read(BB.begin(),BB.size()) )
{
}
if ( argc < 2 )
return EXIT_FAILURE;
return 0;
#if 0
::libmaus2::lz::GzipHeader GZH(argv[1]);
return 0;
#endif
std::ostringstream ostr;
::libmaus2::autoarray::AutoArray<uint8_t> message = ::libmaus2::util::GetFileSize::readFile(argv[1]);
std::cerr << "Deflating message of length " << message.size() << "...";
::libmaus2::lz::Deflate DEFL(ostr);
DEFL.write ( reinterpret_cast<char const *>(message.begin()), message.size() );
DEFL.flush();
std::cerr << "done." << std::endl;
std::cerr << "Checking output...";
std::istringstream istr(ostr.str());
::libmaus2::lz::Inflate INFL(istr);
int c;
uint64_t i = 0;
while ( (c=INFL.get()) >= 0 )
{
assert ( c == message[i] );
i++;
}
std::cerr << "done." << std::endl;
// std::cerr << "Message size " << message.size() << std::endl;
std::string testfilename = "test";
::libmaus2::lz::BlockDeflate BD(testfilename);
BD.write ( message.begin(), message.size() );
BD.flush();
uint64_t const decpos = message.size() / 3;
::libmaus2::lz::BlockInflate BI(testfilename,decpos);
::libmaus2::autoarray::AutoArray<uint8_t> dmessage (message.size(),false);
uint64_t const red = BI.read(dmessage.begin()+decpos,dmessage.size());
assert ( red == dmessage.size()-decpos );
std::cerr << "(";
for ( uint64_t i = decpos; i < message.size(); ++i )
assert ( message[i] == dmessage[i] );
std::cerr << ")\n";
std::string shortmes1("123456789");
std::string shortmes2("AA");
std::string shortmes3("BB");
std::string shortmes4("CC");
std::string textfile1("test1");
std::string textfile2("test2");
std::string textfile3("test3");
std::string textfile4("test4");
::libmaus2::lz::BlockDeflate BD1(textfile1);
BD1.write ( reinterpret_cast<uint8_t const *>(shortmes1.c_str()), shortmes1.size() );
BD1.flush();
::libmaus2::lz::BlockDeflate BD2(textfile2);
BD2.write ( reinterpret_cast<uint8_t const *>(shortmes2.c_str()), shortmes2.size() );
BD2.flush();
::libmaus2::lz::BlockDeflate BD3(textfile3);
BD3.write ( reinterpret_cast<uint8_t const *>(shortmes3.c_str()), shortmes3.size() );
BD3.flush();
::libmaus2::lz::BlockDeflate BD4(textfile4);
BD4.write ( reinterpret_cast<uint8_t const *>(shortmes4.c_str()), shortmes4.size() );
BD4.flush();
std::vector < std::string > filenames;
filenames.push_back(textfile1);
filenames.push_back(textfile2);
filenames.push_back(textfile3);
filenames.push_back(textfile4);
for ( uint64_t j = 0; j <= 15; ++j )
{
::libmaus2::lz::ConcatBlockInflate CBI(filenames,j);
for ( uint64_t i = 0; i < j; ++i )
std::cerr << ' ';
for ( uint64_t i = 0; i < CBI.n-j; ++i )
std::cerr << (char)CBI.get();
std::cerr << std::endl;
}
return 0;
}
void computeLabels(cv::Mat src, cv::Mat BinImPad){
cv::Mat LabelIm = cvCreateMat(cols,rows,src.type());
for( int j=0; j<rows; ++j )
for( int i=0; i<cols; ++i ) LabelIm.at<unsigned char>(i,j)=0;
int nthreads, tid;
//omp_set_num_threads(4);
bool redo_coloring = true;
#pragma omp parallel private(tid,nthreads)
{
//Color blob recursively as soon as a pixel in FG is found
tid = omp_get_thread_num();
nthreads = omp_get_num_threads();
int end1;
unsigned char start_index, label_index;
label_index = UCHAR_MAX * tid / nthreads;
++label_index; start_index = label_index;
const int start = tid*(rows/nthreads) + 1;
end1 = (tid+1)*(rows/nthreads) + 1;
if( tid==(nthreads-1) ) ++end1; ++end1;
const int end = end1;
for( int j=start; j<end; ++j )
for( int i=1; i<=cols; ++i ){
if( BIP(i,j)==UCHAR_MAX ){
std::vector< std::pair<int,int> > indices;
std::pair<int,int> one_index; one_index.first = i; one_index.second = j;
indices.push_back(one_index);
BIP(i,j) = label_index;
unsigned char temp = UCHAR_MAX;
ColorBlob( BinImPad, &indices, start, end, label_index, temp );
++label_index;
}
}
#pragma omp barrier
//Re-color blob if the previous thread has assigned it
//to a different color
if( tid==0 && write_files ){
std::string out_str1 = "label_intermediate.png";
cv::imwrite(out_str1.c_str(),BinImPad);
}
while( redo_coloring ){
#pragma omp barrier
if( tid == 0 ) redo_coloring = false;
for( int i=1; i<=cols; ++i ){
if( (BIP((i-1),(start-1)) && BIP(i,start)) &&
(BIP((i-1),(start-1))!=BIP(i,start)) ){
redo_coloring = true;
unsigned char lund=BIP(i,start);
BIP(i,start)=BIP((i-1),(start-1));
std::pair<int,int> one_index; one_index.first = i; one_index.second = start;
std::vector< std::pair<int,int> > indices;
indices.push_back(one_index);
unsigned char temp = BIP(i,start);
ColorBlob( BinImPad, &indices, start, end, temp, lund );
}
else if( (BIP(i,(start-1)) && BIP(i,start)) &&
(BIP(i,(start-1))!=BIP(i,start)) ){
redo_coloring = true;
unsigned char lund=BIP(i,start);
BIP(i,start)=BIP(i,(start-1));
std::pair<int,int> one_index; one_index.first = i; one_index.second = start;
std::vector< std::pair<int,int> > indices;
indices.push_back(one_index);
unsigned char temp = BIP(i,start);
ColorBlob( BinImPad, &indices, start, end, temp, lund );
}
else if( BIP((i+1),(start-1)) && BIP(i,start) &&
(BIP((i+1),(start-1))!=BIP(i,start)) ){
redo_coloring = true;
unsigned char lund=BIP(i,start);
BIP(i,start)=BIP((i+1),(start-1));
std::pair<int,int> one_index; one_index.first = i; one_index.second = start;
std::vector< std::pair<int,int> > indices;
indices.push_back(one_index);
unsigned char temp = BIP(i,start);
ColorBlob( BinImPad, &indices, start, end, temp, lund );
}
}
#pragma omp barrier
if( tid==0 && write_files ){
std::string out_str1 = "label_intermediate1.png";
cv::imwrite(out_str1.c_str(),BinImPad);
}
}
}
//Output the centroids and areas
std::vector< std::vector<int> > statistics;
for( int j=1; j<=rows; ++j )
for( int i=1; i<=cols; ++i )
if( ((int)BIP(i,j))>0){
std::vector<int> one_stat(4);
one_stat[0] = BIP(i,j);
bool bigEnough = GetStats(LabelIm,i,j,BinImPad,one_stat);
if(bigEnough) statistics.push_back( one_stat );
//else std::cout<<one_stat[0]<<"\t"<<one_stat[1]<<"\t"<<one_stat[2]<<"\t"<<one_stat[3]<<"\n";
}
std::string out_str1 = "label_final.png";
cv::imwrite(out_str1.c_str(),LabelIm);
out_str1 = "binary_" + file_open;
IplImage *img = cvLoadImage(out_str1.c_str(), CV_LOAD_IMAGE_COLOR);
CvFont font;
cvInitFont(&font, CV_FONT_HERSHEY_SIMPLEX, 0.3, 0.3, 0, 1);
std::vector< std::vector<int> >::iterator it; int i=1;
for( it=statistics.begin() ; it < statistics.end(); ++it ){
std::stringstream ss;
ss<<i<<","<<it->at(1);++i;
std::string sss=ss.str();
cvPutText(img, sss.c_str(), cvPoint((it->at(3)),(it->at(2))), &font, cvScalar(255, 255, 100, 0));
cvCircle(img, cvPoint((it->at(3)),(it->at(2))), 3, cvScalar(0,255,0), 1);
}
cvShowImage("Binary Image", img);
out_str1 = "final.png";
cvSaveImage(out_str1.c_str(),img);
return;
}