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#include <hdf/HDFRegionTableReader.hpp>
#include <cassert>
int HDFRegionTableReader::Initialize(std::string ®ionTableFileName,
const H5::FileAccPropList &fileAccPropList)
{
/*
* Initialize access to the HDF file.
*/
try {
regionTableFile.Open(regionTableFileName.c_str(), H5F_ACC_RDONLY, fileAccPropList);
} catch (H5::Exception &e) {
std::cout << e.getDetailMsg() << std::endl;
return 0;
}
if (pulseDataGroup.Initialize(regionTableFile.rootGroup, "PulseData") == 0) {
return 0;
}
if (pulseDataGroup.ContainsObject("Regions") == 0) {
fileContainsRegionTable = false;
return 0;
} else {
fileContainsRegionTable = true;
}
if (regions.Initialize(pulseDataGroup, "Regions") == 0) {
return 0;
}
if (columnNames.Initialize(regions, "ColumnNames") == 0) {
return 0;
}
if (regionTypes.Initialize(regions, "RegionTypes") == 0) {
return 0;
}
if (regionDescriptions.Initialize(regions, "RegionDescriptions") == 0) {
return 0;
}
if (regionSources.Initialize(regions, "RegionSources") == 0) {
return 0;
}
nRows = regions.GetNRows();
isInitialized_ = true;
curRow = 0;
return 1;
}
bool HDFRegionTableReader::IsInitialized(void) const { return isInitialized_; }
bool HDFRegionTableReader::HasRegionTable(void) const
{
assert(IsInitialized() && "HDFRegionTable is not initialize!");
return fileContainsRegionTable;
}
int HDFRegionTableReader::GetNext(RegionAnnotation &annotation)
{
assert(IsInitialized() && "HDFRegionTable is not initialize!");
//
// Bail with no-op if this is the last row.
//
if (fileContainsRegionTable == false) {
return 0;
}
if (curRow == nRows) {
return 0;
}
regions.Read(curRow, curRow + 1, annotation.row);
++curRow;
return 1;
}
void HDFRegionTableReader::Close()
{
isInitialized_ = false;
fileContainsRegionTable = false;
columnNames.Close();
regionTypes.Close();
regionDescriptions.Close();
regionSources.Close();
pulseDataGroup.Close();
regions.Close();
regionTableFile.Close();
}
// Note that (1) there is NO GUARANTEE that region annotations in hdf5
// `Regions` dataset be sorted in any order, so we cannot iterate over
// `Regions` in order to traverse zmws in order.
// (2) region table of a million zmws is approximately 5M.
void HDFRegionTableReader::ReadTable(RegionTable &table)
{
assert(IsInitialized() && "HDFRegionTable is not initialize!");
table.Reset();
if (fileContainsRegionTable) {
// Read attributes.
std::vector<std::string> names, types, descs, sources;
if (columnNames.IsInitialized()) columnNames.Read(names);
if (regionTypes.IsInitialized())
regionTypes.Read(types);
else {
std::cout << "ERROR MUST HAVE REGIONTYPES" << std::endl;
std::exit(EXIT_FAILURE);
}
if (regionDescriptions.IsInitialized()) regionDescriptions.Read(descs);
if (regionSources.IsInitialized()) regionSources.Read(sources);
// Read region annotations
std::vector<RegionAnnotation> ras;
ras.resize(nRows);
assert(curRow == 0);
for (; curRow < nRows; curRow++) {
regions.Read(curRow, curRow + 1, ras[curRow].row);
}
// Reconstruct table
table.ConstructTable(ras, types);
table.ColumnNames(names);
table.RegionDescriptions(descs);
table.RegionSources(sources);
}
}
void HDFRegionTableReader::GetMinMaxHoleNumber(UInt &minHole, UInt &maxHole)
{
assert(IsInitialized() && "HDFRegionTable is not initialize!");
// Hole numbers may not be sorted ascendingly, so do not
// return the first and last hole numbers as the min and max.
UInt saveCurRow = curRow;
curRow = 0;
bool init = false;
RegionAnnotation annotation;
while (GetNext(annotation) == 1) {
UInt curHole = annotation.GetHoleNumber();
if (not init) {
minHole = maxHole = curHole;
init = true;
} else {
minHole = (minHole > curHole) ? (curHole) : (minHole);
maxHole = (maxHole < curHole) ? (curHole) : (maxHole);
}
}
curRow = saveCurRow;
}
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