void ParseFiles()
{
int offset = outfile.tellp();
for(int i = 0; i < files.size(); i++)
{
ifstream infile(files[i].c_str(), ifstream::binary);
int size = 0;
infile.seekg(0, ios::end);
size = infile.tellg();
infile.seekg(0, ios::beg);
if(size == 0)
continue;
cout << "[+] " << files[i] << " size[" << setw(8) << setfill('0') << size << "]" << endl;
char *data = new char[size];
infile.read(data,size);
outfile.write(data,size);
delete data;
int curOffset = outfile.tellp();
outfile.seekp(8*i);
outfile.write((char*)&offset,4);
outfile.write((char*)&size,4);
outfile.seekp(curOffset);
offset += size;
infile.close();
}
}
static bool writeFile(const wstring &res, ofstream &fs, bkplong pos)
{
static unsigned short magic = 0xFEFF;
//write in Unicode16-LE
if (!fs.good())
return false;
if (pos >= 0)
fs.seekp(pos, ios_base::beg);
else
fs.seekp(pos + 1, ios_base::end);
fs.write((const char *)&magic, 2);
u16string result;
bkplong s = res.size();
bkplong s2 = s * sizeof(wchar_t) / sizeof(char16_t);
result.resize(s2);
#ifdef HAVE_CODECVT
auto& f = use_facet<codecvt<wchar_t, char16_t, mbstate_t>>(locale());
mbstate_t mb = mbstate_t();
char16_t* from_next;
const wchar_t* to_next;
f.out(mb, &res[0], &res[s], to_next, &result[0], &result[s2], from_next);
#else
ucs4toutf16((uint16_t *)&result[0], (uint32_t *)&res[0], s);
#endif
fs.write((const char *)result.c_str(), 2 * result.length());
return true;
}
void CQualLL::CreateFile(ofstream &fp){
char *block;
ifstream fileTemp;
size_t IndexPos = 0, pos_input = 0, end_input = 0, aux = 0, inpos = 1;
if(CQual.length() != 0){
CQual = GZcompressString(CQual);
SaveValue(fileQual, CQual.length());
SaveValue(fileQual, (char *)CQual.c_str(), CQual.length());
CQual = "";
}
fileQual.close();
SaveValue(fp, LOSSLESS);
cds_word Variables[2];
Variables[0] = IndexRate;
Variables[1] = numberOfLines;
SaveValue(fp, Variables, 2);
buffer = init_buffer();
buffer_use = 0;
if(IndexRate > 0){//this will be overwrite at the end
IndexPos = fp.tellp();
IndexLine = new cds_word[1 + (numberOfLines + IndexRate - 1)/IndexRate];
for(cds_word w = 0; w < (1 + (numberOfLines + IndexRate - 1)/IndexRate); w++)
IndexLine[w] = 0;
SaveValue(fp, IndexLine, 1 + ((numberOfLines + IndexRate - 1)/IndexRate));
}
init_qual = fp.tellp();
init_qual += 2 * sizeof(size_t);
SaveValue(fp, init_qual);
SaveValue(fp, end_qual);
fileTemp.open(tmp_name.c_str());
pos_input = fileTemp.tellg();
fileTemp.seekg(0, std::ifstream::end);
end_input = fileTemp.tellg();
fileTemp.seekg(pos_input);
if(IndexRate > 0)
IndexLine[0] = fp.tellp();
while(pos_input < end_input){
aux = LoadValue<size_t>(fileTemp);
block = LoadValue<char>(fileTemp, aux);
pos_input += aux + sizeof(size_t);
SaveValue(fp, block, aux);
if(IndexRate > 0){
IndexLine[inpos] = fp.tellp();
inpos ++;
}
delete [] block;
}
fileTemp.close();
end_qual = fp.tellp();
fp.seekp(IndexPos);
if(IndexRate > 0)
SaveValue(fp, IndexLine, (1 + (numberOfLines + IndexRate - 1)/IndexRate));
delete [] buffer;
fp.seekp(init_qual - sizeof(size_t));
SaveValue(fp, end_qual);
fp.seekp(end_qual);
remove(tmp_name.c_str());
}
size_t dami::getFileSize(ofstream& file)
{
size_t size = 0;
if (file.is_open())
{
streamoff curpos = file.tellp();
file.seekp(0, ios::end);
size = file.tellp();
file.seekp(curpos);
}
return size;
}
void distance(){
if(System::file().doesExist(_outputDir + "/mat_presenceAbsence_jaccard.bin")){
_distanceMatrixJaccard.open((_outputDir + "/mat_presenceAbsence_jaccard.bin").c_str(), ios::binary | ios::in);
_distanceMatrixBrayCurtis.open((_outputDir + "/mat_abundance_braycurtis.bin").c_str(), ios::binary | ios::in);
}
else{
_distanceMatrixJaccard.open((_outputDir + "/mat_presenceAbsence_jaccard.bin").c_str(), ios::binary);
_distanceMatrixBrayCurtis.open((_outputDir + "/mat_abundance_braycurtis.bin").c_str(), ios::binary);
}
bool isSymmetrical = false;
if(_inputFilename1 == _inputFilename2 && _start_i == _start_j){
computeDistanceSymetrical();
isSymmetrical = true;
}
else{
computeDistanceRectangle();
}
for(size_t i=0; i<_threads.size(); i++){
_threads[i]->join();
delete _threads[i];
//cout << i << endl;
}
_progress->finish();
//Fill diagonal with 0
if(isSymmetrical){
for(size_t i=_start_i; i<_start_i+_n_i; i++){
size_t j=i;
u_int64_t pos = i*_nbDataset1*sizeof(DistanceValueType) + (j*sizeof(DistanceValueType));
_distanceMatrixJaccard.seekp(pos);
_distanceMatrixBrayCurtis.seekp(pos);
DistanceValueType nullDist = 0;
_distanceMatrixJaccard.write((const char*)&nullDist, sizeof(nullDist));
_distanceMatrixBrayCurtis.write((const char*)&nullDist, sizeof(nullDist));
}
}
_distanceMatrixJaccard.close();
_distanceMatrixBrayCurtis.close();
//string command = "cp " + string(_inputFilename1+".ids") + " " + _outputDir + "/matrix_infos.ids ";
//cout << command << endl;
//system(command.c_str());
}
/**
* @brief writeHeader Write the header out to a file
* @param file
*/
void writeHeader(ofstream &file)
{
// Write out the header information
file.seekp(0, ios::beg);
file.write((char*)&this->header, sizeof(this->header));
}
int Towers_sm(int disks, int arr1[], int arr2[], int count, bool &ppart, ofstream &fout, ofstream &outfile)
{
int split;
int split_res;
int remaining;
int remaining_res;
int result;
int diskssofar;
int smallest_so_far;
for(diskssofar = 1; diskssofar < count; diskssofar++)
{
arr2[diskssofar - 1] = 2*(diskssofar) - 1;
ppart = true;
}
if(diskssofar >= count)
{
for(int a = diskssofar; a <= disks; a++)
{
//Resetting "smallest_so_far"
smallest_so_far = INT_MAX;
for(split = 1; split < diskssofar; split++)
{
remaining = diskssofar - split;
split_res = arr2[split - 1];
remaining_res = arr1[remaining - 1];
result = 2*(split_res) + remaining_res;
//Only update "smallest_so_far" if "result" is lower
if(result <= smallest_so_far)
smallest_so_far = result;
}
//Setting the used array to "smallest_so_far"
arr1[a-1] = smallest_so_far;
ppart = false;
}
}
cout << "The array is: ";
outfile << "The array is: ";
for (int g = 0; g < disks; g++)
{
cout << arr2[g] << " ";
fout << arr2[g] << " ";
outfile << arr2[g] << " ";
}
cout << endl;
outfile << endl;
//Setting the writting stream cursor back to the beginning
fout.clear();
fout.seekp(0);
return arr2[disks - 1];
}
void Picture::WriteFileHeader(ofstream& fout)const
{
fout.seekp(0);
fout.write(fileHeader.fileType,2);
fout.write((char*)&fileHeader.bfSize,4);
fout.write((char*)&fileHeader.bfReserved1,2);
fout.write((char*)&fileHeader.bfReserved2,2);
fout.write((char*)&fileHeader.bfOffBits,4);
}
//Modify file content function
bool modelA::modifyContFile(ofstream mdfos,unsigned int startPos,unsigned int endPos,string newContent)
{
if(endPos<startPos)
return false;
else
{
//Move ofstream pointer to end position
mdfos.seekp(endPos,ios_base::beg);
//Delete old content
for(int i=0;i<int(endPos-startPos);i++)
mdfos.put(char(8));
//Write new content
mdfos<<newContent<<flush;
//Exit and go to begin
mdfos.clear();
mdfos.seekp(0,ios_base::beg);
}
return true;
}
/**
* @brief writeSample Write a sample out to a file
* @param sample
* @param file
*/
void writeSample(short sample, ofstream &file)
{
// Calculate sample offset
int sampleOffset = 44 + (this->samplesWritten * 2);
// Seek to location of next sample and write
file.seekp(sampleOffset);
file.write((char*)&sample, sizeof(sample));
// Increment number samples written
this->samplesWritten++;
}
// Called from the consumer since this class is a registered MessageListener.
virtual void onMessage( const Message* message ) {
try
{
const TextMessage* textMessage =
dynamic_cast< const TextMessage* >( message );
string text = "";
if( textMessage != NULL ) {
text = textMessage->getText();
const Topic* destination = dynamic_cast<const Topic*>(textMessage->getCMSDestination());
destination->getTopicName();
// Do something with the text, like:
printf("Number of received message is %d\n",numMessage);
printf( "Message Received, messageType: %s, message content: %s\n",destination->getTopicName().c_str(), text.c_str() );
// output message into log file
//open the log file
oFile.open("log_PAS.txt",ios::app);
//move point to the end of the file, append information at the end of the log file
oFile.seekp(0,ios::end);
vector<string> logStr3;
logStr3.push_back("\nMessage Received, messageType: ");
logStr3.push_back(destination->getTopicName().c_str());
logStr3.push_back("\n message content: ");
logStr3.push_back(text.c_str());
logStr3.push_back("\n Number of received Message are : ");
std::stringstream strNum;
strNum << numMessage;
logStr3.push_back(strNum.str());
copy(logStr3.begin(),logStr3.end(),ostream_iterator<string>(oFile));
//close the log file
oFile.close();
numMessage++;
} else {
// Log the error
cerr << "Received a non-text message" << endl;
}
} catch (CMSException& e) {
// Log the error
cerr << "Opps! B exception happened: " << e.getMessage() << endl;
}
}
void MakeImage::WriteSector(ofstream &stream, int sectorNum, char *data) {
int writePos = sectorNum * SECTOR_SIZE;
// get end of file pos
stream.seekp(0, ios::end);
int endPos = stream.tellp();
if(endPos <= writePos) {
do {
stream.put(0);
endPos = stream.tellp();
}
while(endPos <= writePos);
}
stream.seekp(writePos);
stream.seekp(0, ios_base::cur);
stream.write(data, SECTOR_SIZE);
}
void ihexcallback(const uint8_t *ptr, size_t offset, size_t len)
{
//printf("callback: offset %#zx, len %zu\n", offset, len);
// apply the file offset
if (fileoffset > offset) {
fprintf(stderr, "error: offset in hex file out of range of file offset, o %#zx to %#zx\n", offset, fileoffset);
exit(1);
}
offset -= fileoffset;
out.seekp(offset);
out.write((const char *)ptr, len);
}
void Picture::WriteInfoHeader(ofstream& fout) const
{
fout.seekp(14);
fout.write((char*)&infoHeader.biSize,4);
fout.write((char*)&infoHeader.biWidth,4);
fout.write((char*)&infoHeader.biHeight,4);
fout.write((char*)&infoHeader.biPlanes,2);
fout.write((char*)&infoHeader.biBitCount,2);
fout.write((char*)&infoHeader.biCompression,4);
fout.write((char*)&infoHeader.biSizeImage,4);
fout.write((char*)&infoHeader.biXPixelsPerMeter,4);
fout.write((char*)&infoHeader.biYPixelsPerMeter,4);
fout.write((char*)&infoHeader.biClrUsed,4);
fout.write((char*)&infoHeader.biClrImportant,4);
}
//jump to line n in functions
bool MapBuilder::jumpToLine(int n, ifstream &lookFile, ofstream &putFile){
bool newLine = false;
lookFile.seekg(ios_base::beg); //set cursor to the beginning
int counter = 0;
while((n < counter) && (!file.eof())){ //search for n new lines
if(findsNLChar(lookFile)){ //if you find a new line
counter++; //count that
}
}
if(!lookFile.eof()){ //if we got to the end before making n lines
return false; //we never made it
}
putFile.seekp(lookFile.tellg()); //put the putting pointer to where looking pointer is
return true; //successfully got to line n
}
void __stdcall vcamOpenLog(int verbosity, char* message)
{
#ifdef _DEBUG
{
CAutoLock l(&debugLock);
if (numUsers == 0) {
BOOL ok = CreateDirectory(VCAM_DEBUG_DIRNAME, NULL);
if (!ok && GetLastError() == ERROR_ALREADY_EXISTS)
{
ok = TRUE;
}
if (ok) {
try {
debugOut.exceptions(ios::failbit);
debugOut.open(VCAM_DEBUG_FNAME, ios_base::app);
// Truncate log if it's too big
debugOut.seekp(0, ios_base::end);
if (debugOut.tellp() > 1024 * 256) {
debugOut.close();
debugOut.open(VCAM_DEBUG_FNAME, ios_base::trunc);
}
openedOK = TRUE;
}
catch (...)
{
openedOK = FALSE;
}
}
else
{
openedOK = FALSE;
}
if (!openedOK && !showedLogWarning)
{
Msg("Couldn't open multicam log file,\r\nso no logging will be performed");
showedLogWarning = TRUE;
}
}
numUsers++;
}
vcamLog(verbosity, "%s opened log, numUsers = %d", message, numUsers);
#endif
}
int main() {
ifs.open("MTK.txt", ios::in);
ofs.open("DSC.txt", ios::out);
int n; // so dinh
int a[MAX][MAX];
ifs >> n;
for( int i = 1; i<=n; i++ ) {
for( int j = 1; j<=n; j++ ) {
ifs >> a[i][j];
}
}
ifs.close();
int count = 0;
ofs << n << " " << endl << endl << endl;
for( int i = 1; i<=n; i++ ) {
for( int j = i+1; j<=n; j++ ) {
if( a[i][j] ) {
ofs << i << " " << j << endl;
count++;
}
}
}
ofs.seekp(2);
ofs << count;
ofs.close();
ofs.open("DSK.txt", ios::out);
ofs << n << endl;
for( int i = 1; i<=n; i++ ) {
for( int j = 1; j<=n; j++ ) {
if( a[i][j] ) {
ofs << j << " ";
}
}
ofs << endl;
}
ofs.close();
return 0;
}
void write_data_w_pos(ofstream& out_stream, Word* write_data, int pos){
out_stream.seekp(pos);
out_stream.write((char*)&write_data, sizeof(Word));
}
int main(int argc, char** argv)
{
ros::init(argc , argv , "qrcode_multi");
pthread_t thread_getPosition;
pthread_create(&thread_getPosition,NULL,GetPosition,NULL);
sleep(5);
boost::posix_time::ptime now = ros::Time::now().toBoost();
boost::gregorian::date now_date(now.date()); //格林尼治时间
boost::posix_time::time_duration now_time(now.time_of_day().hours(), now.time_of_day().minutes(), now.time_of_day().seconds(), 0);
out.open("/home/peng/robocup/RC2014_SEU-Jolly_Prelim4_qr.csv");
out.seekp(0, ios::end); //每次从文件结尾处输入
out<<"\"qr codes\""<<endl<<"\"1.0\""<<endl<<"\"SEU-Jolly\""<<endl<<"\"China\""<<endl<<"\""<<now_date<<"\""<<endl<<"\""<<now_time<<"\""<<endl<<"\"Prelim4\""<<endl<<endl<<"id,time,text,x,y,z"<<endl;
long imageNo = 0;
string infilename; //存放图片的名字，序列号.bmp,如1.bmp
string infilename1; //存放图片序列号，如1
char ch_imageNo[100];
bool flag_navigation=false;
char ch_subimg[50];
string temp_subimg;
infilename="1.bmp";
Image image;
string directory = "/home/peng/robocup/bmp";
string fullpath;
int fd , watch;
bool isCreated = false;
fd = inotify_init();
char buf[100 * (sizeof(inotify_event) + 0)];
// cout<<"sizeof inotify_event:"<<sizeof(inotify_event)<<endl;
ssize_t length;
try
{
while(1)
{
isCreated = false;
fullpath = directory + "/" + infilename;
watch = inotify_add_watch(fd , directory.c_str() , IN_CREATE |IN_MOVED_TO );
infilename1=infilename.substr(0,infilename.length()-4);
if(access(fullpath.c_str(), F_OK) ==0)
{
//cout<<infilename<<" exists"<<endl;
isCreated = true;
}
while(!isCreated)
{
//cout<<"waiting for "<<infilename<<endl;
length = read(fd , buf , sizeof(buf));
//cout<<"length:"<<length<<endl;
if(length < 0)
break;
inotify_event *event;
for (size_t i = 0; i < static_cast<size_t>(length);i += sizeof(inotify_event) + event->len)
{
event = reinterpret_cast<inotify_event *>(&buf[i]);
if (event->len > 0 && infilename == event->name)
{
//printf("The file %s was created.\n", event->name);
isCreated = true;
break;
}
}
}
//cout<<"reading file.."<<endl;
usleep(200000);
if(isCreated)
image.read(fullpath);
else
break;
//cout<<"finish reading .."<<endl;
// string expected;
// expected = get_expected(infilename);
int gresult = 1;
int hresult = 1;
hresult = test_image_multi_hybrid(image);
if(res==0)
{
cout << "#" <<infilename1 << " " << "hybrid" <<" "<<cell_result<<endl;
for(size_t i = 0; i < cell_results.size(); i++)
{
cout << "#"<<infilename1<<" "<<cell_results[i]<<endl;
}
}
else
{
cout << "#"<<infilename1<<" "<<cell_result<<endl;
}
cell_results.clear(); //清除每次的结果，然后从新开始
if(hresult!=0)
{
cout<<" hybrid failed..."<<endl;
gresult = test_image_multi_global(image);
if(res==0)
{
cout << "#" <<infilename1 << " " << "globle" <<" "<<cell_result<<endl;
for(size_t i = 0; i < cell_results.size(); i++)
{
cout << "#"<<infilename1<<" "<<cell_results[i]<<endl;
}
}
else
{
cout << "#"<<infilename1<<" "<<cell_result<<endl;
}
cell_results.clear(); //清除每次的结果，然后从新开始
if(gresult!=0)
{
cout<<" global failed..."<<endl;
}
}
strcpy(ch_imageNo,infilename1.c_str());
imageNo = atoi(ch_imageNo);
imageNo++;
sprintf(ch_imageNo,"%ld.bmp",imageNo);
infilename=ch_imageNo;
inotify_rm_watch(fd, watch);
if(remove(fullpath.c_str()))
{
cout<<"Could not remove "<<fullpath<<endl;
}
}
}
catch(...)
{
cout<<"error occured"<<endl;
}
out.close();
close(fd);
return 0;
}
int Towers_lg(int disks, int count, int arr2[], int arr3[], bool &ppart, ifstream &infile, ofstream & outfile, ofstream &fout)
{
int even = count%2;
int totres;
int split;
int split_res;
int remaining;
int remaining_res;
int result;
int smallest_so_far;
int disks1;
//Setting in reading stream cursor back to the beginning
infile.clear();
infile.seekg(0);
for(disks1 = 1; disks1 < count; disks1++)
{
arr2[disks1 - 1] = 2*(disks1) - 1;
arr3[disks1 - 1] = 2*(disks1) - 1;
}
//If the number of disks is equal to or less than the number of pegs, then calculate based on 2n-1
if(disks < count)
{
cout << "The array is: ";
outfile << "The array is: ";
if(even == 0)
{
for (int g = 0; g < disks; g++)
{
cout << arr2[g] << " ";
outfile << arr2[g] << " ";
fout << arr2[g] << " ";
}
cout << endl;
outfile << endl;
//Setting the writting stream cursor back to the beginning
fout.clear();
fout.seekp(0);
//Making sure the reading stream is at the beginning of the file
infile.clear();
infile.seekg(0);
ppart = true;
return totres = arr2[disks - 1];
}
else
{
cout << "The array is: ";
outfile << "The array is: ";
for (int r = 0; r < disks; r++)
{
cout << arr3[r] << " ";
outfile << arr3[r] << " ";
fout << arr3[r] << " ";
}
cout << endl;
outfile << endl;
//Setting the writting stream cursor back to the beginning
fout.clear();
fout.seekp(0);
//Making sure the reading stream is at the beginning of the file
infile.clear();
infile.seekg(0);
ppart = true;
return totres = arr3[disks - 1];
}
}
else
{
while(!infile.eof())
{
for(int z = 0; z < disks; z++)
{
infile >> arr2[z];
}
}
//Resetting the reading cursor back to the beginning
infile.clear();
infile.seekg(0);
//Setting the first position in the next array
arr3[0] = 1;
for(int j = 4; j <= count; j++)
{
//Resetting "smallest_so_far"
smallest_so_far = INT_MAX;
for(split = 1; split < disks1; split++)
{
remaining = disks1 - split;
split_res = arr3[split - 1];
remaining_res = arr3[remaining - 1];
result = 2*(split_res) + remaining_res;
//Only update "smallest_so_far" if "result" is lower
if(result <= smallest_so_far)
smallest_so_far = result;
}
//Setting the used array to "smallest_so_far"
arr2[j - 1] = smallest_so_far;
}
cout << "The array is: ";
outfile << "The array is: ";
for (int g = 0; g < disks; g++)
{
cout << arr2[g] << " ";
outfile << arr2[g] << " ";
fout << arr2[g] << " ";
}
cout << endl;
outfile << endl;
//Setting the writting stream cursor back to the beginning
fout.clear();
fout.seekp(0);
//Making sure the reading stream is at the beginning of the file
infile.clear();
infile.seekg(0);
ppart = false;
}
return totres = arr3[disks - 1];
}
int main(int argc, char* argv[]) {
bool quiet = false;
if (argc < 6) {
printf("Usage : rsem-parse-alignments refName imdName statName alignFType('s' for sam, 'b' for bam) alignF [-t Type] [-l fn_list] [-tag tagName] [-q]\n");
exit(-1);
}
strcpy(fn_list, "");
read_type = 0;
if (argc > 6) {
for (int i = 6; i < argc; i++) {
if (!strcmp(argv[i], "-t")) {
read_type = atoi(argv[i + 1]);
}
if (!strcmp(argv[i], "-l")) {
strcpy(fn_list, argv[i + 1]);
}
if (!strcmp(argv[i], "-tag")) {
SamParser::setReadTypeTag(argv[i + 1]);
}
if (!strcmp(argv[i], "-q")) { quiet = true; }
}
}
verbose = !quiet;
sprintf(groupF, "%s.grp", argv[1]);
gi.load(groupF);
sprintf(tiF, "%s.ti", argv[1]);
transcripts.readFrom(tiF);
sprintf(datF, "%s.dat", argv[2]);
sprintf(cntF, "%s.cnt", argv[3]);
init(argv[2], argv[4][0], argv[5]);
hit_out.open(datF);
string firstLine(99, ' ');
firstLine.append(1, '\n'); //May be dangerous!
hit_out<<firstLine;
switch(read_type) {
case 0 : parseIt<SingleRead, SingleHit>(parser); break;
case 1 : parseIt<SingleReadQ, SingleHit>(parser); break;
case 2 : parseIt<PairedEndRead, PairedEndHit>(parser); break;
case 3 : parseIt<PairedEndReadQ, PairedEndHit>(parser); break;
}
hit_out.seekp(0, ios_base::beg);
hit_out<<N[1]<<" "<<nHits<<" "<<read_type;
hit_out.close();
//cntF for statistics of alignments file
ofstream fout(cntF);
fout<<N[0]<<" "<<N[1]<<" "<<N[2]<<" "<<(N[0] + N[1] + N[2])<<endl;
fout<<nUnique<<" "<<nMulti<<" "<<nIsoMulti<<endl;
fout<<nHits<<" "<<read_type<<endl;
fout<<"0\t"<<N[0]<<endl;
for (iter = counter.begin(); iter != counter.end(); iter++) {
fout<<iter->first<<'\t'<<iter->second<<endl;
}
fout<<"Inf\t"<<N[2]<<endl;
fout.close();
release();
if (verbose) { printf("Done!\n"); }
return 0;
}
void fseekp(ofstream &fout, streampos offset, ios_base::seekdir way) {
fout.seekp(offset, way);
}
//Takes a height array height array of variable length and turns it into an STL file
void writeSTLfromArray(){
out.open(savefile.c_str(),ios_base::binary);
uint32_t triangleCount = (width-1)*(height-1)*2; //number of facets in a void-free surface
triangleCount += 4*(width-1); //triangle counts for the walls of the model
triangleCount += 4*(height-1);
triangleCount += 2; //base triangles
float planarScale = 40/width;
float xScale = (float)cos(globalLat);
if(out.good()){
for(int i = 0; i < 80; i++){
out.write("t",1);
}
//write a placeholder number
out.write((char *)&triangleCount,4);
for(int c = 1; c < width; c++){
if((int)hList.at(c)>-50 & (int)hList.at(c-1)>-50 & (int)hList.at(c+width-1)>-50 ){
vertex a = createVertex(c*xScale, 0,hList.at(c));
vertex b = createVertex((c-1)*xScale, 0,hList.at(c-1));
vertex d = createVertex((c-1)*xScale, 1,hList.at(c+width-1));
vertex w = createVertex(c*xScale,0,0); //used in model walls
vertex z = createVertex((c-1)*xScale,0,0);
addTriangle(createTriangle(a,d,b));
addTriangle(createTriangle(b,z,a)); //model walls
addTriangle(createTriangle(w,a,z));
}else{
triangleCount-=3;
}
}
for(int y = 1; y < height-1; y++){
for(int x = 1; x < width; x++){
if((int)hList.at(y*width+x)>-50 & (int)hList.at((y-1)*width+x)>-50 & (int)hList.at(y*width+x-1)>-50 ){
vertex a = createVertex(x*xScale,y,hList.at(y*width+x));
vertex b = createVertex(x*xScale,y-1,hList.at((y-1)*width+x));
vertex c = createVertex((x-1)*xScale,y,hList.at(y*width+x-1));
addTriangle(createTriangle(a,c,b));
}else{
triangleCount--;
}
}
for(int x = 1; x < width; x++){
if((int)hList.at(y*width+x)>-50 & (int)hList.at(y*width+x-1)>-50 & (int)hList.at((y+1)*width+x-1)>-50 ){
vertex a = createVertex(x*xScale,y,hList.at(y*width+x)); //same
vertex b = createVertex((x-1)*xScale,y,hList.at(y*width+x-1));
vertex c = createVertex((x-1)*xScale,y+1,hList.at((y+1)*width+x-1));
addTriangle(createTriangle(a,c,b));
}else{
triangleCount--;
}
}
}
for(int x = 1; x < width; x++){
if((int)hList.at((height-1)*width+x)>-50 & (int)hList.at((height-2)*width+x)>-50 & (int)hList.at((height-1)*width+x-1)>-50){
vertex a = createVertex(x*xScale,height-1,hList.at((height-1)*width+x)); //same
vertex b = createVertex(x*xScale,height-2,hList.at((height-2)*width+x));
vertex c = createVertex((x-1)*xScale,height-1,hList.at((height-1)*width+x-1));
vertex w = createVertex(x*xScale,height-1,0); //used in model walls
vertex z = createVertex((x-1)*xScale,height-1,0);
addTriangle(createTriangle(a,c,b));
addTriangle(createTriangle(c,a,z)); //model walls
addTriangle(createTriangle(w,z,a));
}else{
triangleCount-=3;
}
}
vertex st;
vertex sb;
vertex bt;
vertex bb;
for(int y = 1; y < width; y++){ //adds walls in the y direction for
if((int)hList.at(y*width)>-50 & (int)hList.at((y-1)*width)>-50){
st = createVertex(0,y,hList.at(y*width)); //for x=0 first
sb = createVertex(0,y-1,hList.at((y-1)*width));
bt = createVertex(0,y,0);
bb = createVertex(0,y-1,0);
addTriangle(createTriangle(bb,sb,st));
addTriangle(createTriangle(st,bt,bb));
}else{
triangleCount-=2;
}
if((int)hList.at(y*width+width-1)>-50 & (int)hList.at(y*width-1)>-50){
st = createVertex((width-1)*xScale,y,hList.at(y*width+width-1)); //for x=width next
sb = createVertex((width-1)*xScale,y-1,hList.at(y*width-1));
bt = createVertex((width-1)*xScale,y,0);
bb = createVertex((width-1)*xScale,y-1,0);
addTriangle(createTriangle(sb,bb,st));
addTriangle(createTriangle(bt,st,bb));
}else{
triangleCount-=2;
}
}
vertex origin = createVertex(0,0,0); //create bottom surface
vertex bottomright = createVertex((width-1)*xScale,0,0);
vertex topleft = createVertex(0,height-1,0);
vertex topright = createVertex((width-1)*xScale,height-1,0);
addTriangle(createTriangle(origin,topright,bottomright));
addTriangle(createTriangle(origin,topleft,topright));
//triangleCount-=2;
out.seekp(80);
out.write((char *)&triangleCount,4);
}
cout << triangleCount << "\n";
}
void write_w_pos(ofstream& out, WORD* write_value, const int pos){
out.seekp(pos*sizeof(WORD));
out.write(reinterpret_cast<char*>(write_value), sizeof(WORD));
}
int Logger::lengthFileLog() {
fileLog.seekp(0, ios::end);
int fileLogSize = static_cast<int>(fileLog.tellp());
return fileLogSize;
}
void ImageType::copyHeaderInBinary(ofstream& imageDestination, ifstream& imageSource)
{
imageDestination.seekp(0);
imageSource.seekg(0);
unsigned char line[COMMENT_LENGTH];
imageSource.read((char*)line, 3);
imageDestination.write((char*)line, 3);
if (width < 10)
{
imageSource.read((char*)line, 1);
imageDestination.write((char*)line, 1);
}
else if (width < 100)
{
imageSource.read((char*)line, 2);
imageDestination.write((char*)line, 2);
}
else
{
imageSource.read((char*)line, 3);
imageDestination.write((char*)line, 3);
}
imageSource.read((char*)line, 1);
imageDestination.write((char*)line, 1);
if (height < 10)
{
imageSource.read((char*)line, 1);
imageDestination.write((char*)line, 1);
}
else if (height < 100)
{
imageSource.read((char*)line, 2);
imageDestination.write((char*)line, 2);
}
else
{
imageSource.read((char*)line, 3);
imageDestination.write((char*)line, 3);
}
imageSource.read((char*)line, 1);
imageDestination.write((char*)line, 1);
if (maxValue < 10)
{
imageSource.read((char*)line, 1);
imageDestination.write((char*)line, 1);
}
else if (maxValue < 100)
{
imageSource.read((char*)line, 2);
imageDestination.write((char*)line, 2);
}
else
{
imageSource.read((char*)line, 3);
imageDestination.write((char*)line, 3);
}
imageSource.read((char*)line, 1);
imageDestination.write((char*)line, 1);
}
void CRPSPreMF::CreateFile(ifstream &SamFile, ofstream &fp, int SamOrRps, vector<cds_word>* IndexClusterToLines){
cds_word *index;
size_t index_pos = 0;
getValuesPreSeq(posWin, WINSIZE); // get for last time the values from winSeq
for(cds_word j = 0; j < WINSIZE; j++) //free winSeq
delete [] WinSeq[j];
delete [] WinSeq;
if(tmp_file_string.length() > 0){
fileSeq << tmp_file_string; //write to fileQual (it must exist)
tmp_file_string = "";
}
ClusterIndex[ClusterIndex.size() - 1] = ClusterReads;
if(overlapcluster){ //add extra block if there is at least one read overlap with the next block
ClusterIndex.push_back((cds_word)-1);
if(IndexClusterToLines != NULL)
IndexClusterToLines->push_back(numberOfLines);
ClusterOverlap.push_back(overlapcluster);
}
fileSeq.close();
huffA = new Huffman(occ_notA, 249, true);
huffC = new Huffman(occ_notC, 249, true);
huffG = new Huffman(occ_notG, 249, true);
huffT = new Huffman(occ_notT, 249, true);
SaveValue(fp, ROW);
cout << "ClusterSize: " << ClusterOverlap.size() << endl;
cds_word novacio = 0;
for(cds_word i = 0; i < ClusterIndex.size() ; i++){
if(ClusterIndex[i] != (cds_word)-1)
novacio++;
}
cout << "No vacio: " << novacio << endl;
index = &ClusterIndex[0]; //Index data
if(ClusterIndex.size() != ClusterOverlap.size())
cout << "Error: Number of blocks created is not correct" << endl;
SaveValue(fp, (cds_word)ClusterIndex.size());
index_pos = fp.tellp();
SaveValue(fp, index, ClusterIndex.size());
SaveValue(fp, variableSize);
//if(variableSize){
index = &ClusterOverlap[0];
SaveValue(fp, index, ClusterOverlap.size());
//}
cds_word Variables[6];
Variables[0] = numberOfLinesNR; Variables[1] = numberOfLines; Variables[2] = sizeLine.size();
Variables[3] = preSeqLength; Variables[4] = (cds_word)(RNames.size()); Variables[5] = IndexRate;
SaveValue(fp, Variables, 6);
SaveValue(fp, &sizeLine[0], sizeLine.size());
for(cds_word i = 0; i < RNames.size(); i++){
SaveValue(fp, (cds_word)(RNames[i].length()));
SaveValue(fp, (char *)(RNames[i].c_str()), RNames[i].length());
SaveValue(fp, RNamesCluster[i]);
}
huffA->Save(fp); huffC->Save(fp); huffG->Save(fp); huffT->Save(fp);
init_preseq = fp.tellp();
init_preseq += 3 * sizeof(size_t);
SaveValue(fp, init_preseq);
SaveValue(fp, init_seq);
SaveValue(fp, end_seq);
buffer = init_buffer();
buffer_use = 0;
CompressPressumeSeq(fp, &buffer, &buffer_use);
init_seq = fp.tellp();
//RE-READ SAM FILE AND CREATE NEW FILE
ComputeCSeq(SamFile, fp, SamOrRps);
end_seq = fp.tellp();
fp.seekp(index_pos);
index = &ClusterIndex[0];
SaveValue(fp, index, ClusterIndex.size());
fp.seekp(init_preseq - 2 * sizeof(size_t));
SaveValue(fp, init_seq);
SaveValue(fp, end_seq);
remove(tmp_name.c_str());
fp.seekp(end_seq);
}
