nsresult txXSLTNumber::createNumber(Expr* aValueExpr, txPattern* aCountPattern,
txPattern* aFromPattern, LevelType aLevel,
Expr* aGroupSize, Expr* aGroupSeparator,
Expr* aFormat, txIEvalContext* aContext,
nsAString& aResult)
{
aResult.Truncate();
nsresult rv = NS_OK;
// Parse format
txList counters;
nsAutoString head, tail;
rv = getCounters(aGroupSize, aGroupSeparator, aFormat, aContext, counters,
head, tail);
NS_ENSURE_SUCCESS(rv, rv);
// Create list of values to format
txList values;
nsAutoString valueString;
rv = getValueList(aValueExpr, aCountPattern, aFromPattern, aLevel,
aContext, values, valueString);
NS_ENSURE_SUCCESS(rv, rv);
if (!valueString.IsEmpty()) {
aResult = valueString;
return NS_OK;
}
// Create resulting string
aResult = head;
bool first = true;
txListIterator valueIter(&values);
txListIterator counterIter(&counters);
valueIter.resetToEnd();
int32_t value;
txFormattedCounter* counter = 0;
while ((value = NS_PTR_TO_INT32(valueIter.previous()))) {
if (counterIter.hasNext()) {
counter = (txFormattedCounter*)counterIter.next();
}
if (!first) {
aResult.Append(counter->mSeparator);
}
counter->appendNumber(value, aResult);
first = false;
}
aResult.Append(tail);
txListIterator iter(&counters);
while (iter.hasNext()) {
delete (txFormattedCounter*)iter.next();
}
return NS_OK;
}
void
CalculateLargestDiameter(itk::Image<TPixel, VImageDimension>* mask, mitk::Image::Pointer valueImage, mitk::GIFVolumetricStatistics::FeatureListType & featureList, std::string prefix)
{
typedef itk::Image<double, VImageDimension> ValueImageType;
typename ValueImageType::Pointer itkValueImage = ValueImageType::New();
mitk::CastToItkImage(valueImage, itkValueImage);
typedef itk::Image<TPixel, VImageDimension> ImageType;
typedef typename ImageType::PointType PointType;
typename ImageType::SizeType radius;
for (int i=0; i < (int)VImageDimension; ++i)
radius[i] = 1;
itk::NeighborhoodIterator<ImageType> iterator(radius, mask, mask->GetRequestedRegion());
itk::NeighborhoodIterator<ValueImageType> valueIter(radius, itkValueImage, itkValueImage->GetRequestedRegion());
std::vector<PointType> borderPoints;
unsigned int maskDimensionX = mask->GetLargestPossibleRegion().GetSize()[0];
unsigned int maskDimensionY = mask->GetLargestPossibleRegion().GetSize()[1];
unsigned int maskDimensionZ = mask->GetLargestPossibleRegion().GetSize()[2];
double maskVoxelSpacingX = mask->GetSpacing()[0];
double maskVoxelSpacingY = mask->GetSpacing()[1];
double maskVoxelSpacingZ = mask->GetSpacing()[2];
int maskMinimumX = maskDimensionX;
int maskMaximumX = 0;
int maskMinimumY = maskDimensionY;
int maskMaximumY = 0;
int maskMinimumZ = maskDimensionZ;
int maskMaximumZ = 0;
//
// Calculate surface in different directions
//
double surface = 0;
std::vector<double> directionSurface;
for (int i = 0; i < (int)(iterator.Size()); ++i)
{
auto offset = iterator.GetOffset(i);
double deltaS = 1;
int nonZeros = 0;
for (unsigned int j = 0; j < VImageDimension; ++j)
{
if (offset[j] != 0 && nonZeros == 0)
{
for (unsigned int k = 0; k < VImageDimension; ++k)
{
if (k != j)
deltaS *= mask->GetSpacing()[k];
}
nonZeros++;
}
else if (offset[j] != 0)
{
deltaS = 0;
}
}
if (nonZeros < 1)
deltaS = 0;
directionSurface.push_back(deltaS);
}
//
// Prepare calulation of Centre of mass shift
//
PointType normalCenter(0);
PointType normalCenterUncorrected(0);
PointType weightedCenter(0);
PointType currentPoint;
int numberOfPoints = 0;
int numberOfPointsUncorrected = 0;
double sumOfPoints = 0;
while(!iterator.IsAtEnd())
{
if (iterator.GetCenterPixel() == 0)
{
++iterator;
++valueIter;
continue;
}
maskMinimumX = (maskMinimumX > iterator.GetIndex()[0]) ? iterator.GetIndex()[0] : maskMinimumX;
maskMaximumX = (maskMaximumX < iterator.GetIndex()[0]) ? iterator.GetIndex()[0] : maskMaximumX;
maskMinimumY = (maskMinimumY > iterator.GetIndex()[1]) ? iterator.GetIndex()[1] : maskMinimumY;
maskMaximumY = (maskMaximumY < iterator.GetIndex()[1]) ? iterator.GetIndex()[1] : maskMaximumY;
maskMinimumZ = (maskMinimumZ > iterator.GetIndex()[2]) ? iterator.GetIndex()[2] : maskMinimumZ;
maskMaximumZ = (maskMaximumZ < iterator.GetIndex()[2]) ? iterator.GetIndex()[2] : maskMaximumZ;
mask->TransformIndexToPhysicalPoint(iterator.GetIndex(), currentPoint);
normalCenterUncorrected += currentPoint.GetVectorFromOrigin();
++numberOfPointsUncorrected;
double intensityValue = valueIter.GetCenterPixel();
if (intensityValue == intensityValue)
{
normalCenter += currentPoint.GetVectorFromOrigin();
weightedCenter += currentPoint.GetVectorFromOrigin() * intensityValue;
sumOfPoints += intensityValue;
++numberOfPoints;
}
bool border = false;
for (int i = 0; i < (int)(iterator.Size()); ++i)
{
if (iterator.GetPixel(i) == 0 || ( ! iterator.IndexInBounds(i)))
{
border = true;
surface += directionSurface[i];
//break;
}
}
if (border)
{
auto centerIndex = iterator.GetIndex();
PointType centerPoint;
mask->TransformIndexToPhysicalPoint(centerIndex, centerPoint );
borderPoints.push_back(centerPoint);
}
++iterator;
++valueIter;
}
auto normalCenterVector = normalCenter.GetVectorFromOrigin() / numberOfPoints;
auto normalCenterVectorUncorrected = normalCenter.GetVectorFromOrigin() / numberOfPointsUncorrected;
auto weightedCenterVector = weightedCenter.GetVectorFromOrigin() / sumOfPoints;
auto differenceOfCentersUncorrected = (normalCenterVectorUncorrected - weightedCenterVector).GetNorm();
auto differenceOfCenters = (normalCenterVector - weightedCenterVector).GetNorm();
double longestDiameter = 0;
unsigned long numberOfBorderPoints = borderPoints.size();
for (int i = 0; i < (int)numberOfBorderPoints; ++i)
{
auto point = borderPoints[i];
for (int j = i; j < (int)numberOfBorderPoints; ++j)
{
double newDiameter=point.EuclideanDistanceTo(borderPoints[j]);
if (newDiameter > longestDiameter)
longestDiameter = newDiameter;
}
}
double boundingBoxVolume = maskVoxelSpacingX* (maskMaximumX - maskMinimumX) * maskVoxelSpacingY* (maskMaximumY - maskMinimumY) * maskVoxelSpacingZ* (maskMaximumZ - maskMinimumZ);
featureList.push_back(std::make_pair(prefix + "Maximum 3D diameter", longestDiameter));
featureList.push_back(std::make_pair(prefix + "Surface (voxel based)", surface));
featureList.push_back(std::make_pair(prefix + "Centre of mass shift", differenceOfCenters));
featureList.push_back(std::make_pair(prefix + "Centre of mass shift (uncorrected)", differenceOfCentersUncorrected));
featureList.push_back(std::make_pair(prefix + "Bounding Box Volume", boundingBoxVolume));
}
