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#include <hdf/HDFPulseDataFile.hpp>
DSLength HDFPulseDataFile::GetAllReadLengths(std::vector<DNALength> &readLengths)
{
nReads = static_cast<UInt>(zmwReader.numEventArray.arrayLength);
readLengths.resize(nReads);
zmwReader.numEventArray.Read(0, nReads, &readLengths[0]);
return readLengths.size();
}
void HDFPulseDataFile::CheckMemoryAllocation(long allocSize, long allocLimit, const char *fieldName)
{
if (allocSize > allocLimit) {
if (fieldName == NULL) {
std::cout << "Allocating too large of memory" << std::endl;
} else {
std::cout << "Allocate size " << allocSize << " > allocate limit " << allocLimit
<< std::endl;
std::cout << "ERROR! Reading the dataset " << fieldName << " will use too much memory."
<< std::endl;
std::cout << "The pls/bas file is too large, exiting." << std::endl;
}
std::exit(EXIT_FAILURE);
}
}
HDFPulseDataFile::HDFPulseDataFile()
{
pulseDataGroupName = "PulseData";
nReads = 0;
useScanData = false;
closeFileOnExit = false;
maxAllocNElements = INT_MAX;
preparedForRandomAccess = false;
rootGroupPtr = NULL;
}
void HDFPulseDataFile::PrepareForRandomAccess()
{
std::vector<DNALength> offset_;
GetAllReadLengths(offset_);
// type of read length of a single read : DNALength
// type of total read length of all reads in plx.h5: DSLength
eventOffset.assign(offset_.begin(), offset_.end());
DSLength curOffset = 0;
for (size_t i = 0; i < eventOffset.size(); i++) {
DSLength curLength = eventOffset[i];
eventOffset[i] = curOffset;
curOffset = curOffset + curLength;
}
nReads = static_cast<UInt>(eventOffset.size());
preparedForRandomAccess = true;
}
int HDFPulseDataFile::OpenHDFFile(std::string fileName, const H5::FileAccPropList &fileAccPropList)
{
try {
H5::FileAccPropList propList = fileAccPropList;
H5::Exception::dontPrint();
hdfBasFile.openFile(fileName.c_str(), H5F_ACC_RDONLY, propList);
} catch (H5::Exception &e) {
std::cout << "ERROR, could not open hdf file" << fileName << ", exiting." << std::endl;
std::exit(EXIT_FAILURE);
}
closeFileOnExit = true;
return 1;
}
//
// All pulse data files contain the "PulseData" group name.
//
//
int HDFPulseDataFile::InitializePulseDataFile(std::string fileName,
const H5::FileAccPropList &fileAccPropList)
{
if (OpenHDFFile(fileName, fileAccPropList) == 0) return 0;
return 1;
}
int HDFPulseDataFile::Initialize(std::string fileName, const H5::FileAccPropList &fileAccPropList)
{
if (InitializePulseDataFile(fileName, fileAccPropList) == 0) {
return 0;
}
//
// The pulse group is contained directly below the root group.
//
if (rootGroup.Initialize(hdfBasFile, "/") == 0) {
return 0;
}
rootGroupPtr = &rootGroup;
return Initialize();
}
//
// Initialize inside another open group.
//
int HDFPulseDataFile::Initialize(HDFGroup *rootGroupP)
{
rootGroupPtr = rootGroupP;
return Initialize();
}
//
// Initialize all fields
//
int HDFPulseDataFile::Initialize()
{
preparedForRandomAccess = false;
if (InitializePulseGroup() == 0) return 0;
if (rootGroupPtr->ContainsObject("ScanData")) {
if (scanDataReader.Initialize(rootGroupPtr) == 0) {
return 0;
} else {
useScanData = true;
}
}
return 1;
}
int HDFPulseDataFile::InitializePulseGroup()
{
if (pulseDataGroup.Initialize(rootGroupPtr->group, pulseDataGroupName) == 0) return 0;
return 1;
}
size_t HDFPulseDataFile::GetAllHoleNumbers(std::vector<unsigned int> &holeNumbers)
{
CheckMemoryAllocation(zmwReader.holeNumberArray.arrayLength, maxAllocNElements,
"HoleNumbers (base)");
holeNumbers.resize(nReads);
zmwReader.holeNumberArray.Read(0, nReads, &holeNumbers[0]);
return holeNumbers.size();
}
void HDFPulseDataFile::Close()
{
if (useScanData) {
scanDataReader.Close();
}
pulseDataGroup.Close();
if (rootGroupPtr == &rootGroup) {
rootGroup.Close();
}
/*
std::cout << "there are " << hdfBasFile.getObjCount(H5F_OBJ_FILE) << " open files upon closing." <<std::endl;
std::cout << "there are " << hdfBasFile.getObjCount(H5F_OBJ_DATASET) << " open datasets upon closing." <<std::endl;
std::cout << "there are " << hdfBasFile.getObjCount(H5F_OBJ_GROUP) << " open groups upon closing." <<std::endl;
std::cout << "there are " << hdfBasFile.getObjCount(H5F_OBJ_DATATYPE) << " open datatypes upon closing." <<std::endl;
std::cout << "there are " << hdfBasFile.getObjCount(H5F_OBJ_ATTR) << " open attributes upon closing." <<std::endl;
*/
if (closeFileOnExit) {
hdfBasFile.close();
}
}
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