//--------------------------------------------------------------------------------------------------------
//
// Private: ReadExperimentalData
//
//--------------------------------------------------------------------------------------------------------
Bool ReconstructionSetup::ReadExperimentalData( CSimulationData & oExpData, bool bServerMode )
{
const vector< SIntRange > & vFileRangeList = oExpSetup.GetFileRangeList();
const vector< SRange > & vOmegaRangeList = oExpSetup.GetOmegaRangeList();
const vector< CDetector > & vDetectorList = oExpSetup.GetDetectorList();
RUNTIME_ASSERT( vFileRangeList.size() == vDetectorList.size() && vDetectorList.size() > 0,
"ERROR: File range not specified for some detector(s) \n" );
//
// TODO: This needs to be more robust
//
oExpData.Initialize( vOmegaRangeList.size(), vDetectorList.size(),
vDetectorList[0].GetNumCols(), vDetectorList[0].GetNumRows() );
for ( Size_Type nDetector = 0; nDetector < vFileRangeList.size(); nDetector ++ )
{
Size_Type nNumFile = vFileRangeList[ nDetector ].nHigh - vFileRangeList[ nDetector ].nLow + 1;
RUNTIME_ASSERT( nNumFile == vOmegaRangeList.size(),
"ERROR: Number of files does not match specified number of omega inteval\n");
// Using -- openmp -- TODO - limit number of threads?
#pragma omp parallel for
for ( Int nFileNum = vFileRangeList[nDetector].nLow;
nFileNum <= vFileRangeList[nDetector].nHigh; nFileNum ++ )
{
Int nCurrentFileIndex = nFileNum - vFileRangeList[nDetector].nLow;
stringstream ssFilename;
ssFilename << InputParameters().InFileBasename
<< InitFileIO::NumToSuffix( nFileNum, InputParameters().InFileSerialLength )
<< "." << InputParameters().InFileExt << nDetector + oExpSetup.GetBCDetectorOffset();
Bool bSuccess = false;
switch( InputParameters().InFileType )
{
case eASCII:
bSuccess= oExpData.mImageMap[ nCurrentFileIndex ][ nDetector ].ReadCXDMSimulationDataFile( ssFilename.str() );
break;
case eBin:
bSuccess= oExpData.mImageMap[ nCurrentFileIndex ][ nDetector ].ReadCXDMSimulationUFFFile( ssFilename.str(), bServerMode );
break;
case eTif:
RUNTIME_ASSERT( 0, "Error: Tif input format not yet supported\n" );
break;
default:
RUNTIME_ASSERT( 0, "Error: Input File Type Not Recognized" );
}
DEBUG_ALERT( 0, ssFilename.str() + "\n" );
RUNTIME_ASSERT( bSuccess, "Error! Input data files cannot be read, please check file format and location\n" + ssFilename.str() );
}
}
return true;
}
//---------------------------------------------------------
//
// Public:
// Read
//
//
//---------------------------------------------------------
// MIC file format
//
// line 1: a0, the fundamental lattice constant for the triangular mesh
//
// others:
//
// columns 1 -3: xyz location of left vertex of a triangle
// column 4: 1/2 for triangle type -- 1 for upward pointing or 2 for downward
// pointing
// column 5: generation number -- triangle side length = a0/(2^generation),
// generation = 0,1,2,...
// column 6: 0/1 for phase -- 0 mean it wasn't (or hasn't yet) fitted to an
// orientation, 1 means it was
// columns 7 -9: Eulers in degrees
// column 10: confidence parameter: fraction of simulated Bragg peaks that hit
// experimental peaks
//---------------------------------------------------------
bool CMic::ReadEffient( const string &filename )
{
vector< vector<string> > vsTokens;
if( !ReadFileToBuf(filename))
{
return false;
}
std::ifstream InputStream;
if( !InputStream.open( filename ) )
return false;
std::string Tokens = " \t\n";
// GeneralLib::Tokenize( vsTokens, string( pBuffer, nBufferSize ), " \t\n");
// we expect side length for the first line
if(vsTokens[0].size() > 1){
cerr << "[CMic::ReadMicFile] Incorrect Mic File Format " << filename << endl;
exit(0);
}
// fInitialSideLength = atof(vsTokens[0][0].c_str());
// for( Size_Type i = 1; i < vsTokens.size(); i ++){
while()
{
if(vsTokens[i].size() < 9 )
{
cerr << "[CMic::ReadMicFile] Error: Incorrect number of columns, line: "
<< i << filename << endl;
}
else
{
DEBUG_ALERT( vsTokens[i].size() >= 10, "CMic::Read: Warning! Old format MIC file with only 9 columns\n" );
SVoxel v;
v.nGeneration = atoi( vsTokens[i][4].c_str() );
v.fSideLength = fInitialSideLength / pow( 2, v.nGeneration ) ;
v.nPhase = atoi( vsTokens[i][5].c_str() );
Float fX, fY, fZ;
fX = atof( vsTokens[i][0].c_str() );
fY = atof( vsTokens[i][1].c_str() );
fZ = atof( vsTokens[i][2].c_str() );
if ( atoi( vsTokens[i][3].c_str() ) == UP )
{
// Winding order, counter clockwise
v.pVertex[0].Set( fX, fY, fZ );
v.pVertex[1].Set( fX + v.fSideLength, fY, fZ );
v.pVertex[2].Set( fX + v.fSideLength / (Float) 2.0 , fY + v.fSideLength / (Float) 2.0 * sqrt( (Float) 3.0 ) , fZ);
v.bVoxelPointsUp = true;
}
else
{
// Winding order, counter clockwise
v.pVertex[0].Set( fX, fY, fZ );
v.pVertex[1].Set( fX + v.fSideLength / (Float) 2.0 , fY - v.fSideLength / (Float) 2.0 * sqrt( (Float) 3.0 ) , fZ);
v.pVertex[2].Set( fX + v.fSideLength, fY, fZ );
v.bVoxelPointsUp = false;
}
SVector3 oOrientation;
oOrientation.Set( DEGREE_TO_RADIAN( atof(vsTokens[i][6].c_str()) ),
DEGREE_TO_RADIAN( atof(vsTokens[i][7].c_str()) ),
DEGREE_TO_RADIAN( atof(vsTokens[i][8].c_str()) ) );
// note that orientation matrix assigned here - the choice of active vs. passive
// transform is made by the file format
v.oOrientMatrix.BuildActiveEulerMatrix( oOrientation.m_fX,
oOrientation.m_fY,
oOrientation.m_fZ );
if( vsTokens[i].size() > 9 )
v.fConfidence = atof( vsTokens[i][9].c_str() );
else
v.fConfidence = 0;
if( vsTokens[i].size() == 19 ) // Defining our strain tensor to be ( I)
{
v.fCost = atof( vsTokens[i][10].c_str() );
v.fPixelOverlapRatio = atof( vsTokens[i][11].c_str() );
v.oDeformation.m[0][0] = atof( vsTokens[i][13].c_str() );
v.oDeformation.m[1][1] = atof( vsTokens[i][14].c_str() );
v.oDeformation.m[2][2] = atof( vsTokens[i][15].c_str() );
v.oDeformation.m[0][1] = v.oDeformation.m[1][0] = atof( vsTokens[i][16].c_str() );
v.oDeformation.m[1][2] = v.oDeformation.m[2][1] = atof( vsTokens[i][17].c_str() );
v.oDeformation.m[0][2] = v.oDeformation.m[2][0] = atof( vsTokens[i][18].c_str() );
}
else
{
v.oDeformation.SetIdentity();
}
oVoxelList.push_back(v);
}
}
ClearBuffer(); // clear buffer after use
return true;
}