bool ChipStreamDataTransform::transformData(PsBoard &board, const DataStore &in, DataStore &out) {
bool needTwoPass = false;
if((InstanceOf(m_ChipStream, SketchQuantNormTran) && board.getOptions()->getOpt("target-sketch").empty()) ||
InstanceOf(m_ChipStream, ArtifactReduction)) {
Verbose::out(1, "Doing two passes.");
needTwoPass = true;
}
/* Send the chip data through the chipstream object. */
int numDataSets = in.getCelDataSetCount();
Verbose::progressBegin(1, ToStr("Processing Chips"), numDataSets, 1, numDataSets);
std::vector<float> data;
for(int chipIx = 0; chipIx < in.getCelDataSetCount(); chipIx++) {
Verbose::progressStep(1);
data.clear();
// Verbose::out(3, "Reading " + m_ChipStream->getDocName() + " for chip: " + ToStr(chipIx));
in.fillInCelData(chipIx, data);
m_ChipStream->newChip(data);
if(!needTwoPass) {
for(int probeIx = 0; probeIx < data.size(); probeIx++) {
data[probeIx] = m_ChipStream->transform(probeIx, chipIx, data[probeIx], board);
}
out.writeColumn(chipIx, in.getCelName(chipIx), data);
}
}
Verbose::progressEnd(1, ToStr("Done."));
if(needTwoPass) {
m_ChipStream->finishedChips();
Verbose::progressBegin(1, ToStr("Processing Stage Two Chips"), numDataSets, 1, numDataSets);
/* Do the chipstream transformation and store the new intensities. */
for(int chipIx = 0; chipIx < in.getCelDataSetCount(); chipIx++) {
Verbose::progressStep(1);
// Verbose::out(3, "Applying " + m_ChipStream->getDocName() + " to chip: " + ToStr(chipIx));
std::vector<float> data;
in.fillInCelData(chipIx, data);
for(int probeIx = 0; probeIx < data.size(); probeIx++) {
data[probeIx] = m_ChipStream->transform(probeIx, chipIx, data[probeIx]);
}
out.writeColumn(chipIx, in.getCelName(chipIx), data);
}
Verbose::progressEnd(1, ToStr("Done."));
}
return true;
}
