void CalvinCELDataAdapter::GetParameters(FusionTagValuePairTypeList& values)
{
ParameterNameValueTypeVector algParams;
calvinCel.GetAlgorithmParameters(algParams);
for (ParameterNameValueTypeIt ii = algParams.begin(); ii!= algParams.end(); ++ii)
{
FusionTagValuePairType ft;
ft.Tag = ii->GetName();
ft.Value = ii->ToString();
ft.DetailedType() = *ii;
values.push_back(ft);
}
}
std::wstring CalvinCELDataAdapter::GetParams()
{
std::wstring params;
ParameterNameValueTypeVector algParams;
calvinCel.GetAlgorithmParameters(algParams);
for (ParameterNameValueTypeIt ii = algParams.begin(); ii!= algParams.end(); ++ii)
{
if (ii != algParams.begin())
params += L";";
params += ii->GetName();
params += L":";
params += ii->ToString();
}
return params;
}
std::wstring CalvinCELDataAdapter::GetAlgorithmParameterTag(int index)
{
ParameterNameValueTypeVector algParams;
calvinCel.GetAlgorithmParameters(algParams);
std::wstring result;
try
{
result = algParams.at(index).GetName();
}
catch(...)
{
}
return result;
}
/*
* Compare the chip summary parameters.
*/
void CHPCompareGCOStoCalvin::CompareChipSummary()
{
TagValuePairTypeList &gparams = gcos.GetHeader().SummaryParameters();
ParameterNameValueTypeVector cparams = calvin.GetChipSums();
CHPCompareUtils::CompareInts((int)gparams.size(), (int)cparams.size(), differences, "chip summary size");
if (gparams.size() != cparams.size())
{
return;
}
int index=0;
for (TagValuePairTypeList::iterator it = gparams.begin(); it!=gparams.end(); ++it)
{
TagValuePairType &gparam = *it;
ParameterNameValueType &cparam = cparams[index++];
CHPCompareUtils::CompareStrings(gparam.Tag, cparam.GetName(), differences, "chip summary name");
CHPCompareUtils::CompareStrings(gparam.Value, cparam.ToString(), differences, "chip summary value");
}
}
ParameterNameValueTypeVector CHPData::GetChipSums()
{
ParameterNameValueTypeVector nvt;
ParameterNameValueTypeIt begin, end;
ParameterNameValueType param;
genericData.Header().GetGenericDataHdr()->GetNameValIterators(begin, end);
while(begin != end)
{
std::wstring key = begin->GetName();
if(key.compare(0, CHIP_SUMMARY_PARAMETER_NAME_PREFIX_S.size(),CHIP_SUMMARY_PARAMETER_NAME_PREFIX_S) == 0)
{
param = *begin;
key.erase(0, CHIP_SUMMARY_PARAMETER_NAME_PREFIX_S.size());
param.SetName(key);
nvt.push_back(param);
}
begin++;
}
return nvt;
}
void DATFileUpdaterTest::CompareParameterNameValueTypeVectors(ParameterNameValueTypeVector& left, ParameterNameValueTypeVector& right)
{
CPPUNIT_ASSERT(left.size() == right.size());
for (ParameterNameValueTypeVector::size_type i = 0; i < left.size(); ++i)
{
CPPUNIT_ASSERT(left[i].GetName() == right[i].GetName());
CPPUNIT_ASSERT(left[i].GetParameterType() == right[i].GetParameterType());
switch(left[i].GetParameterType())
{
case ParameterNameValueType::FloatType:
CPPUNIT_ASSERT(left[i].GetValueFloat() == right[i].GetValueFloat());
break;
case ParameterNameValueType::UInt8Type:
CPPUNIT_ASSERT(left[i].GetValueUInt8() == right[i].GetValueUInt8());
break;
default:
CPPUNIT_ASSERT(0);
break;
}
}
}
int CalvinCELDataAdapter::GetNumberAlgorithmParameters()
{
ParameterNameValueTypeVector algParams;
calvinCel.GetAlgorithmParameters(algParams);
return (int)algParams.size();
}
/*
* 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;
}