// Computes specificity of the model by comparing random samples of the model with the test mashes.
float specificity(Logger& logger, StatisticalModelType::Pointer model, const MeshDataList& testMeshes, unsigned numberOfSamples) {
// draw a number of samples and compute its distance to the closest training dataset
double accumulatedDistToClosestTrainingShape = 0;
for (unsigned i = 0; i < numberOfSamples; i++) {
MeshType::Pointer sample = model->DrawSample();
double minDist = std::numeric_limits<double>::max();
for (MeshDataList::const_iterator it = testMeshes.begin(); it != testMeshes.end(); ++it) {
MeshType::Pointer testMesh = it->first;
// before we compute the distances between the meshes, we normalize the scale by scaling them
// to optimally match the mean. This makes sure that models that include scale and those that have them normalized
// ar etreated the same.
MeshType::Pointer sampledScaledToMean = normalizeScale(sample, model->DrawMean());
MeshType::Pointer testScaledToMean = normalizeScale(testMesh, model->DrawMean());
double dist = computeAverageDistance(testScaledToMean, sampledScaledToMean, ConfigParameters::numSamplingPointsSpecificity);
logger.Get(logINFO) << "distance " << dist << std::endl;
if (dist < minDist) {
minDist = dist;
}
}
logger.Get(logINFO) << "closest distance for sample " << i << ": " << minDist << std::endl;
accumulatedDistToClosestTrainingShape += minDist;
}
double avgDist = accumulatedDistToClosestTrainingShape / numberOfSamples;
logger.Get(logINFO) << "average distance " << avgDist << std::endl;
return avgDist;
}
ImageDataList getImagesInDir (Logger& logger, std::string dirname)
{
ImageDataList images;
itk::Directory::Pointer directory = itk::Directory::New();
directory->Load(dirname.c_str());
for (unsigned i = 0; i < directory->GetNumberOfFiles(); i++) {
std::string filename(directory->GetFile(i));
if (filename.find(".vtk") != std::string::npos || filename.find(".mha") != std::string::npos) {
std::string fullpath = std::string(dirname) +"/" + filename;
logger.Get(logINFO) << "reading image " << fullpath << std::endl;
BinaryImageType::Pointer image = readBinaryImage(fullpath);
images.push_back(std::make_pair(image, fullpath));
}
}
return images;
}
