/** Reads from the file getting in order: an unused integer, on the next line the number of
* spectra in the group and next one or more lines the spectra numbers, (format in GroupDetectors.h)
* @param specs2index :: a map that links spectra numbers to indexes
* @param File :: the input stream that is linked to the file
* @param lineNum :: the last line read in the file, is updated by this function
* @param unUsedSpec :: list of spectra that haven't yet been included in a group
* @throw invalid_argument if there is any problem with the file
*/
void GroupDetectors2::readFile(spec2index_map &specs2index, std::ifstream &File, size_t &lineNum, std::vector<int64_t> &unUsedSpec)
{
// used in writing the spectra to the outData map. The groups are just labelled incrementally from 1
int spectrumNo = 1;
// go through the rest of the file reading in lists of spectra number to group
while ( File )
{
std::string thisLine;
do
{
std::getline( File, thisLine ), lineNum ++;
// we haven't started reading a new group and so if the file ends here it is OK
if ( ! File ) return;
}
while( readInt(thisLine) == EMPTY_LINE && File );
// the number of spectra that will be combined in the group
int numberOfSpectra = EMPTY_LINE;
do
{
if ( ! File ) throw std::invalid_argument("Premature end of file, expecting an integer with the number of spectra in the group");
std::getline( File, thisLine ), lineNum ++;
numberOfSpectra = readInt(thisLine);
}
while( numberOfSpectra == EMPTY_LINE );
// the value of this map is the list of spectra numbers that will be combined into a group
m_GroupSpecInds[spectrumNo].reserve(numberOfSpectra);
do
{
if ( ! File ) throw std::invalid_argument("Premature end of file, found number of spectra specification but no spectra list");
std::getline( File, thisLine ), lineNum ++;
// the spectra numbers that will be included in the group
readSpectraIndexes(
thisLine, specs2index, m_GroupSpecInds[spectrumNo], unUsedSpec);
}
while (static_cast<int>(m_GroupSpecInds[spectrumNo].size()) < numberOfSpectra);
if ( static_cast<int>(m_GroupSpecInds[spectrumNo].size()) != numberOfSpectra )
{// it makes no sense to continue reading the file, we'll stop here
throw std::invalid_argument(std::string("Bad number of spectra specification or spectra list near line number ") + boost::lexical_cast<std::string>(lineNum));
}
// make regular progress reports and check for a cancellastion notification
if ( (m_GroupSpecInds.size() % INTERVAL) == 1 )
{
fileReadProg( m_GroupSpecInds.size(), specs2index.size() );
}
spectrumNo++;
}
}
