CelFileWriter::CelFileWriter(CelFileData &p)
{
p.SetVersion(CurrentCelFileVersion);
writer = new GenericFileWriter(p.GetFileHeader());
intensityPos = 0;
stdDevPos = 0;
pixelPos = 0;
outlierPos = 0;
maskPos = 0;
WriteHeaders();
}
/*
* Get the DAT header from the DAT file header object.
*/
string CELConversionUtilities::GetDatHeader(CelFileData &inFile)
{
std::wstring datHeader;
GenDataHdrVectorIt begin, end;
inFile.GetFileHeader()->GetGenericDataHdr()->GetParentIterators(begin, end);
// Find the DAT generic header
for (GenDataHdrVectorIt ii = begin; ii != end; ++ii)
{
std::string s = ii->GetFileTypeId();
if (ii->GetFileTypeId() == SCAN_ACQUISITION_DATA_TYPE)
{
// found the right header, now look for the parameter
ParameterNameValueType nvt;
if (ii->FindNameValParam(DAT_HEADER_PARAM_NAME, nvt))
{
if (nvt.GetParameterType() == ParameterNameValueType::TextType)
datHeader = nvt.GetValueText();
}
else if (ii->FindNameValParam(PARTIAL_DAT_HEADER_PARAM_NAME, nvt))
{
if (nvt.GetParameterType() == ParameterNameValueType::TextType)
{
std::wstring partialDatHeader = nvt.GetValueText();
u_int16_t min = 0;
u_int16_t max = 0;
// Find the max and min parameters and append to the string.
if (ii->FindNameValParam(MAX_PIXEL_INTENSITY_PARAM_NAME, nvt))
{
if (nvt.GetParameterType() == ParameterNameValueType::UInt16Type)
max = nvt.GetValueUInt16();
}
if (ii->FindNameValParam(MIN_PIXEL_INTENSITY_PARAM_NAME, nvt))
{
if (nvt.GetParameterType() == ParameterNameValueType::UInt16Type)
min = nvt.GetValueUInt16();
}
wchar_t buf[30];
FormatString2(buf, 30, L"[%d..%d]", min, max);
datHeader = buf;
datHeader += partialDatHeader;
}
}
break;
}
}
return StringUtils::ConvertWCSToMBS(datHeader);
}
void CELConversionUtilities::FindAndAddAlgorithmParameter(string name, string defaultValue, CelFileData &inFile, CCELFileData &outFile)
{
ParameterNameValueType nvt;
if (inFile.FindAlgorithmParameter(StringUtils::ConvertMBSToWCS(name), nvt))
{
outFile.AddAlgorithmParameter(name.c_str(), StringUtils::ConvertWCSToMBS(nvt.ToString()).c_str());
}
else
{
outFile.AddAlgorithmParameter(name.c_str(), defaultValue.c_str());
}
}
void CELConversionUtilities::SetCellMargin(CelFileData &inFile, CCELFileData &outFile, int defaultValue)
{
ParameterNameValueType nvt;
if (inFile.FindAlgorithmParameter(L"CellMargin", nvt))
{
if (nvt.GetParameterType() == ParameterNameValueType::Int32Type)
{
outFile.GetHeader().SetMargin(nvt.GetValueInt32());
}
else if(nvt.GetParameterType() == ParameterNameValueType::AsciiType)
{
outFile.GetHeader().SetMargin(atoi(nvt.GetValueAscii().c_str()));
}
}
else
{
outFile.GetHeader().SetMargin(defaultValue);
}
}
/*
* Get the grid from the parameters.
*/
GridCoordinatesType CELConversionUtilities::GetGrid(CelFileData &inFile)
{
GridCoordinatesType grid;
ParameterNameValueType nvt;
grid.lowerleft.x = grid.lowerleft.y = 0;
grid.upperleft.x = grid.upperleft.y = 0;
grid.lowerright.x = grid.lowerright.y = 0;
grid.upperright.x = grid.upperright.y = 0;
if (inFile.FindAlgorithmParameter(GRIDULX_PARAM_NAME, nvt) && nvt.GetParameterType() == ParameterNameValueType::FloatType)
grid.upperleft.x = (int) nvt.GetValueFloat();
if (inFile.FindAlgorithmParameter(GRIDULY_PARAM_NAME, nvt) && nvt.GetParameterType() == ParameterNameValueType::FloatType)
grid.upperleft.y = (int) nvt.GetValueFloat();
if (inFile.FindAlgorithmParameter(GRIDURX_PARAM_NAME, nvt) && nvt.GetParameterType() == ParameterNameValueType::FloatType)
grid.upperright.x = (int) nvt.GetValueFloat();
if (inFile.FindAlgorithmParameter(GRIDURY_PARAM_NAME, nvt) && nvt.GetParameterType() == ParameterNameValueType::FloatType)
grid.upperright.y = (int) nvt.GetValueFloat();
if (inFile.FindAlgorithmParameter(GRIDLRX_PARAM_NAME, nvt) && nvt.GetParameterType() == ParameterNameValueType::FloatType)
grid.lowerright.x = (int) nvt.GetValueFloat();
if (inFile.FindAlgorithmParameter(GRIDLRY_PARAM_NAME, nvt) && nvt.GetParameterType() == ParameterNameValueType::FloatType)
grid.lowerright.y = (int) nvt.GetValueFloat();
if (inFile.FindAlgorithmParameter(GRIDLLX_PARAM_NAME, nvt) && nvt.GetParameterType() == ParameterNameValueType::FloatType)
grid.lowerleft.x = (int) nvt.GetValueFloat();
if (inFile.FindAlgorithmParameter(GRIDLLY_PARAM_NAME, nvt) && nvt.GetParameterType() == ParameterNameValueType::FloatType)
grid.lowerleft.y = (int) nvt.GetValueFloat();
return grid;
}
/*
* 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;
}
void TestFileGenerator::WriteRemaingSmallCelFileWithGridParameters(CelFileData& data)
{
data.SetIntensityCount(25);
data.SetStdDevCount(25);
data.SetPixelCount(25);
data.SetOutlierCount(2);
data.SetMaskCount(3);
data.SetRows(5);
data.SetCols(5);
data.SetArrayType(L"Hg-small");
data.SetLibraryPackageName(L"Hg-small-lib-package");
data.SetMasterFileName(L"Hg-small-master-file");
data.SetAlgorithmName(L"Feature Extraction");
ParameterNameValueType nvt;
nvt.SetName(L"percentile");
nvt.SetValueFloat(0.75f);
data.AddAlgorithmParameter(nvt);
nvt.SetName(L"outlierlow");
nvt.SetValueFloat(1.004f);
data.AddAlgorithmParameter(nvt);
nvt.SetName(L"CellMargin");
nvt.SetValueInt32(2);
data.AddAlgorithmParameter(nvt);
// Add grid
wchar_t* gridParams[] = {L"GridULX", L"GridULY", L"GridURX", L"GridURY", L"GridLRX", L"GridLRY", L"GridLLX", L"GridLLY" };
for (int32_t i = 0; i < 8; ++i)
{
nvt.SetName(gridParams[i]);
nvt.SetValueFloat(2.0f + (float)i);
data.AddAlgorithmParameter(nvt);
}
CelFileWriter* writer = new CelFileWriter(data);
FloatVector vInten;
FloatVector vStdev;
Int16Vector vPixels;
for (int i=0; i<25; ++i)
{
vInten.push_back(100.0f*i);
vStdev.push_back(.5*i);
vPixels.push_back(25);
}
// Do some writing
writer->WriteIntensities(vInten);
writer->WriteStdDevs(vStdev);
writer->WritePixels(vPixels);
// XYCoordVector
XYCoordVector outlier;
XYCoord xy(0,0);
outlier.push_back(xy);
xy.xCoord = 1;
xy.yCoord = 2;
outlier.push_back(xy);
writer->WriteOutlierCoords(outlier);
XYCoordVector masked;
xy.xCoord = 1;
xy.yCoord = 0;
masked.push_back(xy);
xy.xCoord = 2;
xy.yCoord = 1;
masked.push_back(xy);
xy.xCoord = 3;
xy.yCoord = 2;
masked.push_back(xy);
writer->WriteMaskCoords(masked);
delete writer;
}
