void nucleoliEvaluator(
const TriMesh<float>& nucleusTriMesh,
TriMeshSpatialModel<float>& triMeshSpatialModel,
const string& filename, const string& parentDir,
const string& function, const int& constraints,
DataSet& dataSet, RandomGenerator& randomGenerator)
{
string classif = parentDir;
const string analysisDir = parentDir + "/analysis/";
classif = classif.substr(classif.find_last_of("/\\")+1,classif.length());
//new data
// const DataSet datasetNucleus( analysisDir + filename + "_chromocenters.csv" );
//const DataSet datasetNucleus( analysisDir + filename + "_nucleoli.csv" );
DataSet globalAnalysis( analysisDir + "nuclei_extended.csv" );
const DataSet nucleoliInfo( analysisDir + "nucleoli.csv" );
Vector<string> tempFileNames;
tempFileNames = nucleoliInfo.getValues<string>( nucleoliInfo.variableNames()[0] );
int lastPos, numNucleoli = 0;
for ( int j = 0; j < tempFileNames.getSize(); ++j )
if ( tempFileNames[j] == filename )
{
lastPos = j;
++ numNucleoli;
}
if ( numNucleoli == 0 )
{
EVAL("Nucleus not found");
return;
}
Vertices<float> vertices( 3, numNucleoli, 0, 0 );
int k = 0;
for ( int j = lastPos - numNucleoli + 1 ; j < lastPos + 1; ++j, ++k )
{
vertices[k][0] = nucleoliInfo.getValue<float>( "centroidCoordX", j );
vertices[k][1] = nucleoliInfo.getValue<float>( "centroidCoordY", j );
vertices[k][2] = nucleoliInfo.getValue<float>( "centroidCoordZ", j );
EVAL(vertices[k]);
}
Vector<string> nucleiNames ;
nucleiNames = globalAnalysis.getValues<string>( globalAnalysis.variableNames()[0] );
//unifying datasets
int numCurrentNucleus;
for ( int j = 0; j < nucleiNames.getSize(); ++j )
if ( nucleiNames[j] == filename )
numCurrentNucleus = j;
EVAL (numCurrentNucleus);
//const int numPoints = vertices.getNumVertices();
const int numPatterns = 99;
SpatialModelEvaluator<float,float> modelEvaluator;
modelEvaluator.setModel( triMeshSpatialModel );
modelEvaluator.setNumMonteCarloSamples( numPatterns ); //to check uniformity
modelEvaluator.setPrecision( 0.05 );
SpatialDescriptor<float>* spatialDescriptor;
DataSet saveTest;
//setting function parameters
if ( function == "all" )
{
PRINT("all functions");
SpatialModelCompleteRandomness3D<float> tempTriMeshSpatialModel;
tempTriMeshSpatialModel.setRandomGenerator( randomGenerator );
tempTriMeshSpatialModel.setTriMesh( nucleusTriMesh );
tempTriMeshSpatialModel.initialize();
Vertices<float> evaluationPositions = tempTriMeshSpatialModel.drawSample( 10000 );
//evaluationPositions.save( parentDir + "/" + filename + "_Fpattern-" + ".vx", true); //to check uniformity of the F patterns
SpatialDescriptorFunctionF<float>* spatialDescriptorFunctionF;
spatialDescriptorFunctionF = new SpatialDescriptorFunctionF<float>();
spatialDescriptorFunctionF->setEvaluationPositions( evaluationPositions );
spatialDescriptor = spatialDescriptorFunctionF;
modelEvaluator.addDescriptor( *spatialDescriptor );
spatialDescriptor = new SpatialDescriptorFunctionG<float>();
modelEvaluator.addDescriptor( *spatialDescriptor );
spatialDescriptor = new SpatialDescriptorFunctionH<float>();
modelEvaluator.addDescriptor( *spatialDescriptor );
SpatialDescriptorFunctionB<float>* spatialDescriptorFunctionB;
spatialDescriptorFunctionB = new SpatialDescriptorFunctionB<float>();
spatialDescriptorFunctionB->setTriMesh( nucleusTriMesh );
spatialDescriptor = spatialDescriptorFunctionB;
modelEvaluator.addDescriptor( *spatialDescriptor );
SpatialDescriptorFunctionC<float>* spatialDescriptorFunctionC;
spatialDescriptorFunctionC = new SpatialDescriptorFunctionC<float>();
spatialDescriptorFunctionC->setCenter( nucleusTriMesh.cog() );
spatialDescriptor = spatialDescriptorFunctionC;
modelEvaluator.addDescriptor( *spatialDescriptor );
spatialDescriptor = new SpatialDescriptorFunctionZ<float>();
modelEvaluator.addDescriptor( *spatialDescriptor );
}
else if ( function == "G" )
{
PRINT("G");
spatialDescriptor = new SpatialDescriptorFunctionG<float>();
}
else if ( function == "H" )
{
PRINT("H");
spatialDescriptor = new SpatialDescriptorFunctionH<float>();
}
else if ( function == "B" )
{
PRINT("B");
SpatialDescriptorFunctionB<float>* spatialDescriptorFunctionB;
spatialDescriptorFunctionB = new SpatialDescriptorFunctionB<float>();
spatialDescriptorFunctionB->setTriMesh( nucleusTriMesh );
spatialDescriptor = spatialDescriptorFunctionB;
}
else if ( function == "C" )
{
PRINT("C");
SpatialDescriptorFunctionC<float>* spatialDescriptorFunctionC;
spatialDescriptorFunctionC = new SpatialDescriptorFunctionC<float>();
spatialDescriptorFunctionC->setCenter( nucleusTriMesh.cog() );
spatialDescriptor = spatialDescriptorFunctionC;
}
else if ( function == "Z" )
{
PRINT("Z");
spatialDescriptor = new SpatialDescriptorFunctionZ<float>();
}
else //if ( function == "F" )
{
PRINT("F");
SpatialModelCompleteRandomness3D<float> tempTriMeshSpatialModel;
tempTriMeshSpatialModel.setRandomGenerator( randomGenerator );
tempTriMeshSpatialModel.setTriMesh( nucleusTriMesh );
tempTriMeshSpatialModel.initialize();
Vertices<float> evaluationPositions = tempTriMeshSpatialModel.drawSample( 10000 );
//evaluationPositions.save( parentDir + "/spatial_models/" + filename + "_Fpattern-" + ".vx", true);
SpatialDescriptorFunctionF<float>* spatialDescriptorFunctionF;
spatialDescriptorFunctionF = new SpatialDescriptorFunctionF<float>();
spatialDescriptorFunctionF->setEvaluationPositions( evaluationPositions );
spatialDescriptor = spatialDescriptorFunctionF;
}
//processing data
if ( function != "all" )
{
string newVariable;
switch ( constraints )
{
case 0:
newVariable = ( "SpatialModelCompleteRandomness3D_" + function + "-SDI" );
break;
case 1:
newVariable = ( "SpatialModelHardcoreDistance3D_" + function + "-SDI" );
break;
case 2:
newVariable = ( "spatialModelBorderDistance3D_" + function + "-SDI" );
break;
case 3:
newVariable = ( "SpatialModelBorderHardcoreDistance3D_" + function + "-SDI" );
break;
case 4:
newVariable = ( "SpatialModelMaximalRepulsion3D_" + function + "-SDI" );
break;
}
//globalAnalysis.setValues<float>( newVariable, -1 );
float sdi;
int row;
modelEvaluator.setDescriptor( *spatialDescriptor );
ostringstream iss; //we suppose as much 99 labels
iss << constraints;
DataSet saveTest;
try {
sdi = modelEvaluator.eval( vertices, &saveTest );
EVAL(sdi);
// Vector<float> output = modelEvaluator.evalSDIandMaxDiff( vertices, &saveTest );
// EVAL( output[0] );
// EVAL( output[1] );
saveTest.save( analysisDir + iss.str() + "/" + function + "/" + filename + ".csv", true );
// saveTest.save( analysisDir + iss.str() + "/" + function + "/" + filename + "_random.csv", true );
row = dataSet.size()[0];
dataSet.setValue( "nucleus", row, filename );
dataSet.setValue( "class", row, classif );//classification: mutant, tissue, etc.
dataSet.setValue( "descriptor", row, function );//spatial descriptor
dataSet.setValue( "index", row, sdi );
//dataSet.setValue( "index", row, output[0] );
//dataSet.setValue( "signedMaxDiff", row, output[1] );
globalAnalysis.setValue( newVariable, numCurrentNucleus, sdi );
}
catch( Exception exception ) {
EVAL( exception.getWhat() );
EVAL( exception.getWhere() );
const int row = dataSet.size()[0];
dataSet.setValue( "nucleus", row, filename );
dataSet.setValue( "class", row, classif );//classification: mutant, tissue, etc.
dataSet.setValue( "descriptor", row, function );//spatial descriptor
dataSet.setValue( "index", row, sqrt(-1) );
}
}
else
{
// Vertices<float> vertices ( 3, numPoints, 0, 0 );
// for ( int i = 0; i < numPoints; ++i )
// {
// vertices[i][0] = datasetNucleus.getValue<float>( "centroidCoordX", i );
// vertices[i][1] = datasetNucleus.getValue<float>( "centroidCoordY", i );
// vertices[i][2] = datasetNucleus.getValue<float>( "centroidCoordZ", i );
// EVAL(vertices[i]);
// }
const int row = dataSet.numRows();
vector<float> sdis;
vector<int> ranks;
DataSet saveTest;
// vector<float> maxDiff;
try {
// modelEvaluator.evalSDIandMaxDiff( vertices, pValues, ranks, maxDiff);
modelEvaluator.eval( vertices, sdis, ranks, &saveTest );
EVAL( sdis[0] );
EVAL( sdis[1] );
EVAL( sdis[2] );
EVAL( sdis[3] );
EVAL( sdis[4] );
EVAL( sdis[5] );
string newVariable;
switch ( constraints )
{
case 0: newVariable = "SpatialModelCompleteRandomness3D_";
case 1: newVariable = "SpatialModelHardcoreDistance3D_";
case 2: newVariable = "spatialModelBorderDistance3D_";
case 3: newVariable = "SpatialModelBorderHardcoreDistance3D_";
case 4: newVariable = "SpatialModelMaximalRepulsion3D_";
}
//unifying datasets
for ( int jj = 0; jj < sdis.size(); ++jj )
{
if ( ( sdis[jj] < 0 || sdis[jj] > 1 ) && ( jj = 0 ) )
globalAnalysis.setValue( newVariable + "F-SDI", numCurrentNucleus, sqrt(-1) );
else
globalAnalysis.setValue( newVariable + "F-SDI", numCurrentNucleus, sdis[jj] );
if ( ( sdis[jj] < 0 || sdis[jj] > 1 ) && ( jj = 1 ) )
globalAnalysis.setValue( newVariable + "G-SDI", numCurrentNucleus, sqrt(-1) );
else
globalAnalysis.setValue( newVariable + "G-SDI", numCurrentNucleus, sdis[jj] );
if ( ( sdis[jj] < 0 || sdis[jj] > 1 ) && ( jj = 2 ) )
globalAnalysis.setValue( newVariable + "H-SDI", numCurrentNucleus, sqrt(-1) );
else
globalAnalysis.setValue( newVariable + "H-SDI", numCurrentNucleus, sdis[jj] );
if ( ( sdis[jj] < 0 || sdis[jj] > 1 ) && ( jj = 3 ) )
globalAnalysis.setValue( newVariable + "B-SDI", numCurrentNucleus, sqrt(-1) );
else
globalAnalysis.setValue( newVariable + "B-SDI", numCurrentNucleus, sdis[jj] );
if ( ( sdis[jj] < 0 || sdis[jj] > 1 ) && ( jj = 4 ) )
globalAnalysis.setValue( newVariable + "C-SDI", numCurrentNucleus, sqrt(-1) );
else
globalAnalysis.setValue( newVariable + "C-SDI", numCurrentNucleus, sdis[jj] );
if ( ( sdis[jj] < 0 || sdis[jj] > 1 ) && ( jj = 5 ) )
globalAnalysis.setValue( newVariable + "Z-SDI", numCurrentNucleus, sqrt(-1) );
else
globalAnalysis.setValue( newVariable + "Z-SDI", numCurrentNucleus, sdis[jj] );
}
dataSet.setValue( "nucleus", row, filename );
dataSet.setValue( "class", row, classif );//classification: mutant, tissue, etc.
dataSet.setValue( "F-SDI", row, sdis[0] );
// dataSet.setValue( "F-maxDiff", row, maxDiff[0] );
dataSet.setValue( "G-SDI", row, sdis[1] );
// dataSet.setValue( "G-maxDiff", row, maxDiff[1] );
dataSet.setValue( "H-SDI", row, sdis[2] );
// dataSet.setValue( "H-maxDiff", row, maxDiff[2] );
dataSet.setValue( "B-SDI", row, sdis[3] );
// dataSet.setValue( "B-maxDiff", row, maxDiff[3] );
dataSet.setValue( "C-SDI", row, sdis[4] );
// dataSet.setValue( "C-maxDiff", row, maxDiff[4] );
dataSet.setValue( "Z-SDI", row, sdis[4] );
// dataSet.setValue( "Z-maxDiff", row, maxDiff[5] );
ostringstream iss; //we have 4 constraints
iss << constraints;
saveTest.save( analysisDir + iss.str() + "/" + filename + ".csv", true );
}
catch( Exception exception ) {
EVAL( exception.getWhat() );
EVAL( exception.getWhere() );
const int row = dataSet.size()[0];
dataSet.setValue( "nucleus", row, filename );
dataSet.setValue( "class", row, classif );//classification: mutant, tissue, etc.
dataSet.setValue( "descriptor", row, function );//spatial descriptor
dataSet.setValue( "index", row, sqrt(-1) );
//dataSet.setValue( "index", row, output[0] );
//dataSet.setValue( "signedMaxDiff", row, output[1] );
}
}
globalAnalysis.save( analysisDir + "/" + "nuclei_complete2.csv", true );
}
