void
TolerantEditDistance::extractCells() {
if (_groundTruth->size() != _reconstruction->size())
BOOST_THROW_EXCEPTION(SizeMismatchError() << error_message("ground truth and reconstruction have different size") << STACK_TRACE);
if (_groundTruth->height() != _reconstruction->height() || _groundTruth->width() != _reconstruction->width())
BOOST_THROW_EXCEPTION(SizeMismatchError() << error_message("ground truth and reconstruction have different size") << STACK_TRACE);
_depth = _groundTruth->size();
_width = _groundTruth->width();
_height = _groundTruth->height();
LOG_ALL(tedlog) << "extracting cells in " << _width << "x" << _height << "x" << _depth << " volume" << std::endl;
vigra::MultiArray<3, std::pair<float, float> > gtAndRec(vigra::Shape3(_width, _height, _depth));
vigra::MultiArray<3, unsigned int> cellIds(vigra::Shape3(_width, _height, _depth));
// prepare gt and rec image
for (unsigned int z = 0; z < _depth; z++) {
boost::shared_ptr<Image> gt = (*_groundTruth)[z];
boost::shared_ptr<Image> rec = (*_reconstruction)[z];
for (unsigned int x = 0; x < _width; x++)
for (unsigned int y = 0; y < _height; y++) {
float gtLabel = (*gt)(x, y);
float recLabel = (*rec)(x, y);
gtAndRec(x, y, z) = std::make_pair(gtLabel, recLabel);
}
}
// find connected components in gt and rec image
cellIds = 0;
_numCells = vigra::labelMultiArray(gtAndRec, cellIds);
LOG_DEBUG(tedlog) << "found " << _numCells << " cells" << std::endl;
// let tolerance function extract cells from that
_toleranceFunction->extractCells(
_numCells,
cellIds,
*_reconstruction,
*_groundTruth);
LOG_ALL(tedlog)
<< "found "
<< _toleranceFunction->getGroundTruthLabels().size()
<< " ground truth labels and "
<< _toleranceFunction->getReconstructionLabels().size()
<< " reconstruction labels"
<< std::endl;
}
void
VariationOfInformation::updateOutputs() {
// set output
if (!_errors)
_errors = new VariationOfInformationErrors();
if (_headerOnly)
return;
if (_reconstruction->size() != _groundTruth->size())
BOOST_THROW_EXCEPTION(SizeMismatchError() << error_message("image stacks have different size") << STACK_TRACE);
// count label occurences
_p1.clear();
_p2.clear();
_p12.clear();
ImageStack::const_iterator i1 = _reconstruction->begin();
ImageStack::const_iterator i2 = _groundTruth->begin();
unsigned int n = 0;
for (; i1 != _reconstruction->end(); i1++, i2++) {
if ((*i1)->size() != (*i2)->size())
BOOST_THROW_EXCEPTION(SizeMismatchError() << error_message("images have different size") << STACK_TRACE);
n += (*i1)->size();
Image::iterator j1 = (*i1)->begin();
Image::iterator j2 = (*i2)->begin();
for (; j1 != (*i1)->end(); j1++, j2++) {
if (_ignoreBackground && *j2 == 0) {
n--;
continue;
}
_p1[*j1]++;
_p2[*j2]++;
_p12[std::make_pair(*j1, *j2)]++;
}
}
// normalize
for (typename LabelProb::iterator i = _p1.begin(); i != _p1.end(); i++)
i->second /= n;
for (typename LabelProb::iterator i = _p2.begin(); i != _p2.end(); i++)
i->second /= n;
for (typename JointLabelProb::iterator i = _p12.begin(); i != _p12.end(); i++)
i->second /= n;
// compute information
// H(stack 1)
double H1 = 0.0;
// H(stack 2)
double H2 = 0.0;
double I = 0.0;
for(typename LabelProb::const_iterator i = _p1.begin(); i != _p1.end(); i++)
H1 -= i->second * std::log2(i->second);
for(typename LabelProb::const_iterator i = _p2.begin(); i != _p2.end(); i++)
H2 -= i->second * std::log2(i->second);
for(typename JointLabelProb::const_iterator i = _p12.begin(); i != _p12.end(); i++) {
const float j = i->first.first;
const float k = i->first.second;
const double pjk = i->second;
const double pj = _p1[j];
const double pk = _p2[k];
I += pjk * std::log2( pjk / (pj*pk) );
}
// H(stack 1, stack2)
double H12 = H1 + H2 - I;
// We compare stack1 (reconstruction) to stack2 (groundtruth). Thus, the
// split entropy represents the number of splits of regions in stack2 in
// stack1, and the merge entropy the number of merges of regions in stack2
// in stack1.
//
// H(stack 1|stack 2) = H(stack 1, stack 2) - H(stack 2)
// (i.e., if I know the ground truth label, how much bits do I need to
// infer the reconstructino label?)
_errors->setSplitEntropy(H12 - H2);
// H(stack 2|stack 1) = H(stack 1, stack 2) - H(stack 1)
// (i.e., if I know the reconstruction label, how much bits do I need to
// infer the groundtruth label?)
_errors->setMergeEntropy(H12 - H1);
LOG_DEBUG(variationofinformationlog)
<< "sum of conditional entropies is " << _errors->getEntropy()
<< ", which should be equal to " << (H1 + H2 - 2.0*I) << std::endl;
}
void
VariationOfInformation::updateOutputs() {
if (_stack1->size() != _stack2->size())
BOOST_THROW_EXCEPTION(SizeMismatchError() << error_message("image stacks have different size") << STACK_TRACE);
// count label occurences
_p1.clear();
_p2.clear();
_p12.clear();
ImageStack::const_iterator i1 = _stack1->begin();
ImageStack::const_iterator i2 = _stack2->begin();
unsigned int n = 0;
for (; i1 != _stack1->end(); i1++, i2++) {
if ((*i1)->size() != (*i2)->size())
BOOST_THROW_EXCEPTION(SizeMismatchError() << error_message("images have different size") << STACK_TRACE);
n += (*i1)->size();
Image::iterator j1 = (*i1)->begin();
Image::iterator j2 = (*i2)->begin();
for (; j1 != (*i1)->end(); j1++, j2++) {
_p1[*j1]++;
_p2[*j2]++;
_p12[std::make_pair(*j1, *j2)]++;
}
}
// normalize
for (typename LabelProb::iterator i = _p1.begin(); i != _p1.end(); i++)
i->second /= n;
for (typename LabelProb::iterator i = _p2.begin(); i != _p2.end(); i++)
i->second /= n;
for (typename JointLabelProb::iterator i = _p12.begin(); i != _p12.end(); i++)
i->second /= n;
// compute information
double H0 = 0.0;
double H1 = 0.0;
double I = 0.0;
for(typename LabelProb::const_iterator i = _p1.begin(); i != _p1.end(); i++)
H0 -= i->second * std::log(i->second);
for(typename LabelProb::const_iterator i = _p2.begin(); i != _p2.end(); i++)
H1 -= i->second * std::log(i->second);
for(typename JointLabelProb::const_iterator i = _p12.begin(); i != _p12.end(); i++) {
const float j = i->first.first;
const float k = i->first.second;
const double pjk = i->second;
const double pj = _p1[j];
const double pk = _p2[k];
I += pjk * std::log( pjk / (pj*pk) );
}
// set output
*_variationOfInformation = H0 + H1 - 2.0 * I;
// dump to output (useful for redirection into file)
LOG_USER(variationofinformationlog) << "# VOI" << std::endl;
LOG_USER(variationofinformationlog) << (*_variationOfInformation) << std::endl;
}
