int LatexTables::getNumberOfColumns(QDocumentCursor &cur){
QDocumentCursor c(cur);
int result=findNextToken(c,QStringList(),false,true);
if(result!=-2) return -1;
QString line=c.line().text();
int pos=line.indexOf("\\begin");
if(pos>-1){
QStringList values;
LatexParser::resolveCommandOptions(line,pos,values);
return getNumberOfColumns(values);
}
return -1;
}
void FileManager :: printHeader(){
cout << "---------------------Header------------------------------------"<< endl;
cout << "nombre de tabla : "<< getNameOfFile() << endl;
cout << "tamaño archivo : "<< getSizeOfFile() << endl;
cout << "num reg : "<< getNumberOfRegisters() << endl;
cout << "num libres : "<< getNumberOfFreeRegisters() << endl;
cout << "primer reg : "<< getPtrOfFirstRegister() << endl;
cout << "primer libre : "<< getPtrToFirstRegisterFree() << endl;
cout << "ultimo reg : "<< getPtrToLastRegister() << endl;
cout << "tamañoRegistro : "<< getSizeOfRegister() << endl;
cout << "num de columnas : "<< getNumberOfColumns() << endl;
cout << "---------------------end-of-Header------------------------------------"<< endl;
}
/*-------------------------------------------------------------------------------------*/
static int *lengthEachString(int rhspos, int *sizeArrayReturned)
{
int *StringsLength = NULL;
if (VarType(rhspos) == sci_strings)
{
int m = 0, n = 0; /* matrix size */
int mn = 0; /* m*n */
int il = 0;
int ilrd = 0;
int l1 = 0;
int x = 0;
int lw = rhspos + Top - Rhs;
l1 = *Lstk(lw);
il = iadr(l1);
if (*istk(il) < 0)
{
il = iadr(*istk(il + 1));
}
/* get dimensions */
m = getNumberOfLines(il); /* row */
n = getNumberOfColumns(il); /* col */
mn = m * n;
ilrd = il + 4;
StringsLength = (int *)MALLOC(sizeof(int) * mn);
if (StringsLength == NULL)
{
return NULL;
}
*sizeArrayReturned = mn;
for (x = 0; x < mn; x++)
{
StringsLength[x] = (int)(*istk(ilrd + x + 1) - *istk(ilrd + x));
}
}
return StringsLength;
}
RcppModelData::RcppModelData(
ModelType _modelType,
const IntegerVector& _pid,
const NumericVector& _y,
const NumericVector& _z,
const NumericVector& _time,
const NumericVector& dxv, // dense
const IntegerVector& siv, // sparse
const IntegerVector& spv,
const NumericVector& sxv,
const IntegerVector& iiv, // indicator
const IntegerVector& ipv,
bool useTimeAsOffset
) : ModelData(
_modelType,
_pid,
_y,
_z,
_time,
bsccs::make_shared<loggers::RcppProgressLogger>(),
bsccs::make_shared<loggers::RcppErrorHandler>()
) {
if (useTimeAsOffset) {
// offset
// real_vector* r = new real_vector();
RealVectorPtr r = make_shared<RealVector>();
push_back(NULL, r, DENSE);
r->assign(offs.begin(), offs.end()); // TODO Should not be necessary with shared_ptr
setHasOffsetCovariate(true);
getColumn(0).add_label(-1);
}
// Convert dense
int nCovariates = static_cast<int>(dxv.size() / y.size());
for (int i = 0; i < nCovariates; ++i) {
push_back(
static_cast<IntegerVector::iterator>(NULL), static_cast<IntegerVector::iterator>(NULL),
dxv.begin() + i * y.size(), dxv.begin() + (i + 1) * y.size(),
DENSE);
getColumn(getNumberOfColumns() - 1).add_label(getNumberOfColumns() - (getHasOffsetCovariate() ? 1 : 0));
}
// Convert sparse
nCovariates = spv.size() - 1;
for (int i = 0; i < nCovariates; ++i) {
int begin = spv[i];
int end = spv[i + 1];
push_back(
siv.begin() + begin, siv.begin() + end,
sxv.begin() + begin, sxv.begin() + end,
SPARSE);
getColumn(getNumberOfColumns() - 1).add_label(getNumberOfColumns() - (getHasOffsetCovariate() ? 1 : 0));
}
// Convert indicator
nCovariates = ipv.size() - 1;
for (int i = 0; i < nCovariates; ++i) {
int begin = ipv[i];
int end = ipv[i + 1];
push_back(
iiv.begin() + begin, iiv.begin() + end,
static_cast<NumericVector::iterator>(NULL), static_cast<NumericVector::iterator>(NULL),
INDICATOR);
getColumn(getNumberOfColumns() - 1).add_label(getNumberOfColumns() - (getHasOffsetCovariate() ? 1 : 0));
}
this->nRows = y.size();
// Clean out PIDs
std::vector<int>& cpid = getPidVectorRef();
if (cpid.size() == 0) {
for (size_t i = 0; i < nRows; ++i) {
cpid.push_back(i); // TODO These are not necessary; remove.
}
nPatients = nRows;
} else {
int currentCase = 0;
int currentPID = cpid[0];
cpid[0] = currentCase;
for (size_t i = 1; i < pid.size(); ++i) {
int nextPID = cpid[i];
if (nextPID != currentPID) {
currentCase++;
currentPID = nextPID;
}
cpid[i] = currentCase;
}
nPatients = currentCase + 1;
}
}
extern "C" void * haloThread(void * id){
char * HaloID = (char *)id;
cout << "Analyzing halo with ID " << HaloID << endl;
int numberOfParticles, nCols;
double ** positionsArray;
Particle ** particlesArray;
FILE * output;
double radius = 0;
double u;
FILE * positionFile = getPositionFile(HaloID); //make the file path
if (positionFile == NULL)
printf("POSITION FILE NULL\n");
numberOfParticles = getNumberOfRows(positionFile); //count number of particles in file
nCols = getNumberOfColumns(positionFile); //get number of columns in file (3)
particlesArray = new ParticleArray[numberOfParticles]; //make an array of particles
for (int i = 0; i < numberOfParticles; i++){
particlesArray[i] = new Particle(); //each location in the array is a particle (with positions)
}
positionsArray = assembleArray(positionFile,numberOfParticles,nCols);
for (int i = 0; i<numberOfParticles;i++){
particlesArray[i]->position.x = positionsArray[i][0];
particlesArray[i]->position.y = positionsArray[i][1];
particlesArray[i]->position.z = positionsArray[i][2];
free(positionsArray[i]);
}
delete positionsArray;
for(int i = 0; i < numberOfParticles; i++){
for(int j = 0; j < numberOfParticles; j++){
radius = sqrt(sq((particlesArray[i]->position.x)-(particlesArray[j]->position.x))+sq((particlesArray[i]->position.y)-(particlesArray[j]->position.y))+sq((particlesArray[i]->position.z)-(particlesArray[j]->position.z)));
u = radius/EPSILON;
if(u<0.5){
particlesArray[i]->directPotential += GRAVITATIONAL_CONSTANT*PARTICLE_MASS*MASS_MULTIPLIER/EPSILON*(16.0/3.0*sq(u)-48.0/5.0*fourth(u)+32.0/5.0*fifth(u)-14.0/5.0);
}
else if(u<1){
particlesArray[i]->directPotential += GRAVITATIONAL_CONSTANT*PARTICLE_MASS*MASS_MULTIPLIER/EPSILON*(1.0/(15.0*u)+32.0/3.0*sq(u)-16.0*third(u)+48.0/5.0*fourth(u)-32.0/15.0*fifth(u)-16.0/5.0);
}
else{
particlesArray[i]->directPotential += GRAVITATIONAL_CONSTANT*PARTICLE_MASS*MASS_MULTIPLIER/EPSILON*(-1.0/u);
}
}
if(i%100000==0){cout <<HaloID <<" - " <<i <<"th particle's potential calculated" <<endl;}
}
output = makeOutputFileName(HaloID); //make output file
//print output
for(int i = 0; i<numberOfParticles; i++){
fprintf(output,"%f%c\n",particlesArray[i]->directPotential,delimeter);
}
//free memory
for (int i = 0; i < numberOfParticles; i++){
delete particlesArray[i];
}
delete particlesArray;
//close files
fclose(positionFile);
fclose(output);
// Reduce our active threads count.
pthread_mutex_lock(numberOfThreadsMutex);
numberOfThreads--;
pthread_mutex_unlock(numberOfThreadsMutex);
pthread_cond_signal(threadAvailable); // Signal to wake up main.
cout <<"Halo " << HaloID <<" done." <<endl;
}
int main()
{
FILE *myFile1;
FILE *myFile2;
FILE *myFile3;
char *filename="c.txt";
myFile1 = fopen(filename, "r");
if (myFile1 == NULL)
{
printf("Error Reading File\n");
exit (0);
}
printf("all is well \n");
/*get number of lines in the file*/
int r=getNumberOfLines(myFile1);
fclose(myFile1);
myFile2 = fopen(filename, "r");
if (myFile2 == NULL)
{
printf("Error Reading File\n");
exit (0);
}
int c=getNumberOfColumns(myFile2);
fclose(myFile2);
printf("r=%d and c=%d\n",r,c);
char *line=NULL;
char *word=NULL;
int attr;
int i,j;
size_t len = 0;
ssize_t read;
printf("r=%d and c=%d\n",r,c);
myFile3 = fopen(filename, "r");
if (myFile3 == NULL)
{
printf("Error Reading File\n");
exit (0);
}
float *dataset[r];
for (i=0; i<r; i++)
dataset[i] = (float *)malloc(c * sizeof(float));
i=0;
while ((read = getline(&line, &len, myFile3)) != -1) {
j=0;
do{
word=strsep(&line,",");
attr = atoi(word);
dataset[i][j]=(float)attr;
j++;
}while(line!=NULL && word!=NULL);
i++;
}
fclose(myFile3);
printMatrix(dataset, r,c);
freeData(dataset, r,c);
return 0;
}
template<typename X> rawData<X>* C_readDicomDiffData::getUnmosaicData_(unsigned short nb_slice_per_mosa)
{
//returned pointer
rawData<X>* rawDataX = NULL;
if(mImage.GetNumberOfDimensions()!=2) return NULL;
//get number of byte in image buffer
unsigned long buffLen = mImage.GetBufferLength();
//allocate a temporary buffer of buffLen bytes
char* buff = new char[buffLen];
if(buff==NULL) return NULL;
//get image buffer into temporary buffer
if(mImage.GetBuffer(buff))
{
///get subimage dimension
unsigned long subDimX, subDimY, squareDim;
if(sqrt(nb_slice_per_mosa)==floor(sqrt(nb_slice_per_mosa)))
{
squareDim = (unsigned short) floor(sqrt(nb_slice_per_mosa));
}
else
{
squareDim = (unsigned short) floor(sqrt(nb_slice_per_mosa)) + 1;
}
//cout << "before getNumberOfColumns" << endl;
subDimX = getNumberOfColumns()/squareDim;
//cout << "after getNumberOfColumns" << endl;
subDimY = getNumberOfRows()/squareDim;
//cout << "after getNumberOfRows" << endl;
///allocate storage
rawDataX = new rawData<X>(getPixelRepresentation(), 2+1, subDimY, subDimX, nb_slice_per_mosa);
if(rawDataX==NULL)
{
delete buff;
return NULL;
}
if(rawDataX->raw1D==NULL && rawDataX->raw2D==NULL && rawDataX->raw3D==NULL && rawDataX->raw4D==NULL)
{
delete buff;
delete rawDataX;
return NULL;
}
//reorganize buffer into rawData structure
X* bufferX = (X*) buff;
for(unsigned long i=0 ; i<rawDataX->DimX ; i++)
{
for(unsigned long j=0 ; j<rawDataX->DimY ; j++)
{
for(unsigned long k=0 ; k<rawDataX->DimZ ; k++)
{
///store data
rawDataX->raw3D[i][j][k] = bufferX[rawDataX->getIndex3DUnmosaic(i,j,k)];
}
}
}
}
//cout << "before getPixelDimX" << endl;
rawDataX->pixDimX = getPixelDimX();
//cout << "after getPixelDimX" << endl;
rawDataX->pixDimY = getPixelDimY();
rawDataX->pixDimZ = getPixelDimZ(); ///may not be right
rawDataX->pixDimT = 1.0;
delete buff;
return rawDataX;
}
