/*
* Copy the file contents.
*/
bool CELConversionUtilities::Copy(CelFileData &inFile, CCELFileData &outFile, CELFileConversionOptions *options)
{
// Set the dimensions
outFile.SetDimensions(inFile.GetRows(), inFile.GetCols());
// Set the intensities, stdv and pixels
FloatVector values;
int n = inFile.GetNumCells();
inFile.GetIntensities(0, n, values);
for (int i=0; i<n; i++)
{
outFile.SetIntensity(i, values[i]);
}
values.clear();
inFile.GetStdev(0, n, values);
for (int i=0; i<n; i++)
{
outFile.SetStdv(i, values[i]);
}
Int16Vector pixels;
inFile.GetNumPixels(0, n, pixels);
for (int i=0; i<n; i++)
{
outFile.SetPixels(i, pixels[i]);
}
// Set the outliers and masks.
XYCoordVector xy;
inFile.GetOutlierCoords(xy);
n = (int) xy.size();
for (int i=0; i<n; i++)
{
outFile.SetOutlier(xy[i].xCoord, xy[i].yCoord, true);
}
xy.clear();
inFile.GetMaskedCoords(xy);
n = (int) xy.size();
for (int i=0; i<n; i++)
{
outFile.SetMask(xy[i].xCoord, xy[i].yCoord, true);
}
// Set the header.
outFile.SetGridCorners(GetGrid(inFile));
if((options != NULL)&&(options->m_ChipType != NULL))
{
outFile.SetChipType(options->m_ChipType);
}
else
{
outFile.SetChipType(StringUtils::ConvertWCSToMBS(inFile.GetArrayType()).c_str());
}
// Make sure the algorithm name is "Percentile" so it can import into GCOS.
outFile.SetAlgorithmName("Percentile");
//outFile.SetAlgorithmName(StringUtils::ConvertWCSToMBS(inFile.GetAlgorithmName()).c_str());
// Add the first four algorithm parameters required by GCOS.
FindAndAddAlgorithmParameter("Percentile", "75", inFile, outFile);
FindAndAddAlgorithmParameter("CellMargin", "2", inFile, outFile);
FindAndAddAlgorithmParameter("OutlierHigh", "1.500", inFile, outFile);
FindAndAddAlgorithmParameter("OutlierLow", "1.004", inFile, outFile);
// Set the CellMargin
SetCellMargin(inFile, outFile, 2);
ParameterNameValueTypeVector algParams;
inFile.GetAlgorithmParameters(algParams);
n = (int) algParams.size();
string tag;
string value;
for (int i=0; i<n; i++)
{
tag = StringUtils::ConvertWCSToMBS(algParams[i].GetName());
value = StringUtils::ConvertWCSToMBS(algParams[i].ToString());
// Filter the first four required GCOS algorithm parameters.
if (tag == "Percentile" || tag == "CellMargin" || tag == "OutlierHigh" || tag == "OutlierLow")
{
continue;
}
// Don't include the grid parameters added by the converter.
if (tag.length() > strlen("Grid") && strncmp(tag.c_str(), "Grid", strlen("Grid")) == 0)
continue;
// Add the parameter;
outFile.AddAlgorithmParameter(tag.c_str(), value.c_str());
}
if((options != NULL)&&(options->m_DATFileName != NULL))
{
std::string datHeader = CELFileConversionOptions::newDatName(GetDatHeader(inFile).c_str(), options->m_DATFileName);
if(datHeader == "")
{
return false;
}
else
{
outFile.GetHeader().SetDatHeader(datHeader.c_str());
}
}
else
{
outFile.GetHeader().SetDatHeader(GetDatHeader(inFile).c_str());
}
outFile.GetHeader().SetHeader(outFile.GetHeader().GetHeader().c_str());
return true;
}
