void GenericDataTest_FileIndependent::testmethod_DataSet_ByIndex()
{
DataSet* dp = data->DataSet(0,0);
CPPUNIT_ASSERT(0 != dp);
dp->Delete();
dp = data->DataSet(0,1);
CPPUNIT_ASSERT(0 != dp);
dp->Delete();
CPPUNIT_ASSERT_THROW(data->DataSet(1,0), affymetrix_calvin_exceptions::DataGroupNotFoundException);
CPPUNIT_ASSERT_THROW(data->DataSet(0,2), affymetrix_calvin_exceptions::DataSetNotFoundException);
// TODO: Add more asserts to make sure that I am getting back the right data set.
}
void GenericDataTest_FileIndependent::testmethod_DataSet_ByName()
{
GenericData d;
CPPUNIT_ASSERT_THROW(data->DataSet(L"none", dphPI->GetName()), affymetrix_calvin_exceptions::DataGroupNotFoundException);
CPPUNIT_ASSERT_THROW(data->DataSet(L"Default", L"none"), affymetrix_calvin_exceptions::DataSetNotFoundException);
DataSet* dp = data->DataSet(dch->GetName(), dphPI->GetName());
CPPUNIT_ASSERT(0 != dp);
dp->Delete();
dp = data->DataSet(dch->GetName(), dphGrid->GetName());
CPPUNIT_ASSERT(0 != dp);
dp->Delete();
// TODO: Add more asserts to make sure that I am getting back the right data set.
}
void GenericDataTest_MinDPH::DataSetByIndexTest()
{
// Check that a MinDP will be read-in completely before being accessed through GenericData.
DataSet* dp = data->DataSet(0,0);
CPPUNIT_ASSERT(dp);
const DataSetHeader& dph = dp->Header();
CPPUNIT_ASSERT(dph.GetName() == L"acquired data");
CPPUNIT_ASSERT(dph.GetDataStartFilePos() != 0);
CPPUNIT_ASSERT(dph.GetNameValParamCnt() == 2);
CPPUNIT_ASSERT(dph.GetRowSize() == sizeof(u_int16_t));
CPPUNIT_ASSERT(dph.GetDataSize() == sizeof(u_int16_t)*100);
CPPUNIT_ASSERT(dph.GetRowCnt() == 100);
CPPUNIT_ASSERT(dph.GetColumnCnt() == 1);
CPPUNIT_ASSERT(dph.GetDataStartFilePos() == 0x3a0);
// Check the data group name value pairs
ParameterNameValueTypeConstIt nvpBegin, nvpEnd;
dph.GetNameValIterators(nvpBegin, nvpEnd);
CPPUNIT_ASSERT(nvpBegin != nvpEnd);
CPPUNIT_ASSERT(nvpBegin->GetName() == L"Scanner");
CPPUNIT_ASSERT(nvpBegin->GetValueText() == L"M10");
++nvpBegin;
CPPUNIT_ASSERT(nvpBegin != nvpEnd);
CPPUNIT_ASSERT(nvpBegin->GetName() == L"Pixel Size");
CPPUNIT_ASSERT(nvpBegin->GetValueFloat() == 0.051f);
++nvpBegin;
CPPUNIT_ASSERT(nvpBegin == nvpEnd);
// Check the data set columns
CPPUNIT_ASSERT(dph.GetColumnInfo(0).GetColumnType() == UShortColType);
CPPUNIT_ASSERT(dph.GetColumnInfo(0).GetSize() == sizeof(u_int16_t));
dp->Delete();
}
void DataSetTest_GenericData::ColsFromDataSetWithZeroRows()
{
GenericData gd;
GenericFileReader reader;
reader.SetFilename("../data/small_cel_file_with_dataset_of_zero_rows");
reader.ReadHeader(gd);
// Open a DataSet that has 0 rows.
DataSet* ds = gd.DataSet(0,3);
CPPUNIT_ASSERT(ds);
CPPUNIT_ASSERT(ds->Cols() == 2);
CPPUNIT_ASSERT(ds->Rows() == 0);
ds->Delete();
// Open another DataSet that has 0 rows.
ds = gd.DataSet(0,4);
CPPUNIT_ASSERT(ds);
CPPUNIT_ASSERT(ds->Cols() == 2);
CPPUNIT_ASSERT(ds->Rows() == 0);
ds->Delete();
}
void GetRow(int row, RowDataType &d)
{
GenericData data;
GenericFileReader reader;
reader.SetFilename(TEST_FILE);
reader.Open(data);
DataSet *set = data.DataSet(0, 0);
set->Open();
set->GetData(row, 0, d.str);
set->GetData(row, 1, d.wstr);
set->GetData(row, 2, d.b);
set->GetData(row, 3, d.s);
set->GetData(row, 4, d.i);
set->GetData(row, 5, d.ub);
set->GetData(row, 6, d.us);
set->GetData(row, 7, d.ui);
set->GetData(row, 8, d.f);
set->Close();
set->Delete();
}
/*
* Read the file contents into the data object.
*/
void GridControlFileReader::Read(const std::string &fileName, GridControlData& data)
{
// Clear the old data and read the file.
data.Clear();
GenericFileReader reader;
GenericData gdata;
reader.SetFilename(fileName);
reader.ReadHeader(gdata);
// Check the file identifier
if (gdata.FileIdentifier() != GRD_FILE_TYPE_IDENTIFIER)
{
affymetrix_calvin_exceptions::InvalidFileTypeException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
throw e;
}
// Get the header parameters.
ParameterNameValueType param;
gdata.Header().GetGenericDataHdr()->FindNameValParam(GRD_ROWS_PARAMETER_NAME, param);
data.SetRows(param.GetValueInt32());
gdata.Header().GetGenericDataHdr()->FindNameValParam(GRD_COLUMNS_PARAMETER_NAME, param);
data.SetColumns(param.GetValueInt32());
// Get the XY coordinates from the dataSets.
FeatureCoordinate coord;
u_int16_t x;
u_int16_t y;
int nRows;
DataSet *dataSet;
// First the B1 probes.
dataSet = gdata.DataSet(GRD_FILE_COORDINATE_GROUP_NAME, GRD_FILE_B1_SET_NAME);
if (dataSet->Open() == false)
{
affymetrix_calvin_exceptions::DataSetNotOpenException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
throw e;
}
nRows = dataSet->Rows();
data.ResizeB1(nRows);
for (int iRow=0; iRow<nRows; iRow++)
{
dataSet->GetData(iRow, 0, x);
dataSet->GetData(iRow, 1, y);
coord.x = x;
coord.y = y;
data.SetB1(iRow, coord);
}
dataSet->Close();
dataSet->Delete();
// Next the B2 probes.
dataSet = gdata.DataSet(GRD_FILE_COORDINATE_GROUP_NAME, GRD_FILE_B2_SET_NAME);
if (dataSet->Open() == false)
{
affymetrix_calvin_exceptions::DataSetNotOpenException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
throw e;
}
nRows = dataSet->Rows();
data.ResizeB2(nRows);
for (int iRow=0; iRow<nRows; iRow++)
{
dataSet->GetData(iRow, 0, x);
dataSet->GetData(iRow, 1, y);
coord.x = x;
coord.y = y;
data.SetB2(iRow, coord);
}
dataSet->Close();
dataSet->Delete();
// Last the NS probes.
dataSet = gdata.DataSet(GRD_FILE_COORDINATE_GROUP_NAME, GRD_FILE_NS_SET_NAME);
if (dataSet->Open() == false)
{
affymetrix_calvin_exceptions::DataSetNotOpenException e(L"Calvin",L"Default Description, Please Update!",affymetrix_calvin_utilities::DateTime::GetCurrentDateTime().ToString(),std::string(__FILE__),(u_int16_t)__LINE__,0);
throw e;
}
nRows = dataSet->Rows();
data.ResizeNS(nRows);
for (int iRow=0; iRow<nRows; iRow++)
{
dataSet->GetData(iRow, 0, x);
dataSet->GetData(iRow, 1, y);
coord.x = x;
coord.y = y;
data.SetNS(iRow, coord);
}
dataSet->Close();
dataSet->Delete();
}
