diff --git a/Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFFirstOrderNumericStatistics.cpp b/Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFFirstOrderNumericStatistics.cpp index 661da77654..38f3a7ad77 100644 --- a/Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFFirstOrderNumericStatistics.cpp +++ b/Modules/Classification/CLUtilities/src/GlobalImageFeatures/mitkGIFFirstOrderNumericStatistics.cpp @@ -1,358 +1,357 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include // MITK #include #include #include // ITK #include #include #include // STL #include struct FirstOrderNumericParameterStruct { mitk::IntensityQuantifier::Pointer quantifier; double MinimumIntensity; double MaximumIntensity; int Bins; std::string prefix; }; template void CalculateFirstOrderStatistics(itk::Image* itkImage, mitk::Image::Pointer mask, mitk::GIFFirstOrderNumericStatistics::FeatureListType & featureList, FirstOrderNumericParameterStruct params) { typedef itk::Image ImageType; typedef itk::Image MaskType; typename MaskType::Pointer maskImage = MaskType::New(); mitk::CastToItkImage(mask, maskImage); // // Calculate the Volume of Voxel (Maximum to the 3th order) // double voxelVolume = 1; for (unsigned int i = 0; i < std::min(3, VImageDimension); ++i) voxelVolume *= itkImage->GetSpacing()[i]; // // Calculate the Hypervolume of Voxel // double voxelSpace = 1; for (unsigned int i = 0; i < VImageDimension; ++i) voxelSpace *= itkImage->GetSpacing()[i]; unsigned int numberOfBins = params.quantifier->GetBins(); std::vector histogram; histogram.resize(numberOfBins, 0); double minimum = std::numeric_limits::max(); double maximum = std::numeric_limits::lowest(); double absoluteMinimum = std::numeric_limits::max(); double absoluteMaximum = std::numeric_limits::lowest(); double sum = 0; double sumTwo= 0; double sumThree = 0; unsigned int numberOfVoxels = 0; itk::ImageRegionIterator imageIter(itkImage, itkImage->GetLargestPossibleRegion()); itk::ImageRegionIterator maskIter(maskImage, maskImage->GetLargestPossibleRegion()); while (!imageIter.IsAtEnd()) { double value = imageIter.Get(); absoluteMinimum = std::min(minimum, value); absoluteMaximum = std::max(maximum, value); if (maskIter.Get() > 0) { minimum = std::min(minimum, value); maximum = std::max(maximum, value); sum += value; sumTwo += value * value; sumThree += value * value*value; histogram[params.quantifier->IntensityToIndex(value)] += 1; ++numberOfVoxels; } ++maskIter; ++imageIter; } // // Histogram based calculations // unsigned int passedValues = 0; double doubleNoOfVoxes = numberOfVoxels; double median = 0; double lastIntensityWithValues = params.quantifier->IndexToMeanIntensity(0); std::size_t modeIdx = 0; - double modeValue = 0; double entropy = 0; double uniformity = 0; std::vector percentiles; percentiles.resize(20, 0); for (std::size_t idx = 0; idx < histogram.size(); ++idx) { unsigned int actualValues = histogram[idx]; for (std::size_t percentileIdx = 0; percentileIdx < percentiles.size(); ++percentileIdx) { double threshold = doubleNoOfVoxes * (percentileIdx + 1) *1.0 / (percentiles.size()); if ((passedValues < threshold) & ((passedValues + actualValues) >= threshold)) { // Lower Bound if (passedValues == std::floor(threshold)) { percentiles[percentileIdx] = 0.5*(lastIntensityWithValues + params.quantifier->IndexToMeanIntensity(idx)); } else { percentiles[percentileIdx] = params.quantifier->IndexToMeanIntensity(idx); } } } if ((passedValues < doubleNoOfVoxes * 0.5) & ((passedValues + actualValues) >= doubleNoOfVoxes * 0.5)) { // Lower Bound if (passedValues == std::floor(doubleNoOfVoxes * 0.5)) { median = 0.5*(lastIntensityWithValues + params.quantifier->IndexToMeanIntensity(idx)); } else { median = params.quantifier->IndexToMeanIntensity(idx); } } if (actualValues > histogram[modeIdx]) { modeIdx = idx; } if (actualValues > 0) { lastIntensityWithValues = params.quantifier->IndexToMeanIntensity(idx); double currentProbability = actualValues / (1.0 *numberOfVoxels); uniformity += currentProbability * currentProbability; entropy += currentProbability * std::log(currentProbability) / std::log(2); } passedValues += actualValues; } double p10 = percentiles[1]; double p25idx = params.quantifier->IntensityToIndex(percentiles[4]); double p75idx = params.quantifier->IntensityToIndex(percentiles[14]); double p90 = percentiles[17]; double mean = sum / (numberOfVoxels); double variance = sumTwo / (numberOfVoxels) - (mean*mean); double energy = sumTwo; double rootMeanSquare = std::sqrt(sumTwo / numberOfVoxels); double sumAbsoluteDistanceToMean = 0; double sumAbsoluteDistanceToMedian = 0; double sumRobust = 0; double sumRobustSquare = 0; double sumRobustAbsolulteDistanceToMean = 0; double sumValueMinusMean = 0; double sumValueMinusMeanThree = 0; double sumValueMinusMeanFour = 0; unsigned int numberOfRobustVoxel = 0; maskIter.GoToBegin(); imageIter.GoToBegin(); while (!imageIter.IsAtEnd()) { if (maskIter.Get() > 0) { double value = imageIter.Get(); double valueMinusMean = value - mean; sumAbsoluteDistanceToMean += std::abs(valueMinusMean); sumAbsoluteDistanceToMedian += std::abs(value - median); sumValueMinusMean += valueMinusMean; sumValueMinusMeanThree += valueMinusMean * valueMinusMean * valueMinusMean; sumValueMinusMeanFour += valueMinusMean * valueMinusMean * valueMinusMean * valueMinusMean; if ((p10 <= value) & (value <= p90)) { sumRobust += value; sumRobustSquare += value * value; ++numberOfRobustVoxel; } } ++maskIter; ++imageIter; } double robustMean = sumRobust / numberOfRobustVoxel; double robustVariance = sumRobustSquare / numberOfRobustVoxel - (robustMean * robustMean); maskIter.GoToBegin(); imageIter.GoToBegin(); while (!imageIter.IsAtEnd()) { if (maskIter.Get() > 0) { double value = imageIter.Get(); if ((p10 <= value) & (value <= p90)) { sumRobustAbsolulteDistanceToMean += std::abs(value - robustMean); } } ++maskIter; ++imageIter; } double meanAbsoluteDeviation = sumAbsoluteDistanceToMean / numberOfVoxels; double medianAbsoluteDeviation = sumAbsoluteDistanceToMedian / numberOfVoxels; double robustMeanAbsoluteDeviation = sumRobustAbsolulteDistanceToMean / numberOfRobustVoxel; double skewness = sumValueMinusMeanThree / numberOfVoxels / variance / std::sqrt(variance); double kurtosis = sumValueMinusMeanFour / numberOfVoxels / variance / variance; double interquantileRange = p75idx - p25idx; double coefficientOfVariation = std::sqrt(variance) / mean; double quantileCoefficientOfDispersion = (p75idx - p25idx) / (p75idx + p25idx + 2); double coveredImageRange = (maximum - minimum)/ (absoluteMaximum - absoluteMinimum) ; featureList.push_back(std::make_pair(params.prefix + "Mean", mean)); featureList.push_back(std::make_pair(params.prefix + "Variance", variance)); featureList.push_back(std::make_pair(params.prefix + "Skewness", skewness)); featureList.push_back(std::make_pair(params.prefix + "Excess kurtosis", kurtosis-3)); featureList.push_back(std::make_pair(params.prefix + "Median", median)); featureList.push_back(std::make_pair(params.prefix + "Minimum", minimum)); featureList.push_back(std::make_pair(params.prefix + "05th Percentile", percentiles[0])); featureList.push_back(std::make_pair(params.prefix + "10th Percentile", percentiles[1])); featureList.push_back(std::make_pair(params.prefix + "15th Percentile", percentiles[2])); featureList.push_back(std::make_pair(params.prefix + "20th Percentile", percentiles[3])); featureList.push_back(std::make_pair(params.prefix + "25th Percentile", percentiles[4])); featureList.push_back(std::make_pair(params.prefix + "30th Percentile", percentiles[5])); featureList.push_back(std::make_pair(params.prefix + "35th Percentile", percentiles[6])); featureList.push_back(std::make_pair(params.prefix + "40th Percentile", percentiles[7])); featureList.push_back(std::make_pair(params.prefix + "45th Percentile", percentiles[8])); featureList.push_back(std::make_pair(params.prefix + "50th Percentile", percentiles[9])); featureList.push_back(std::make_pair(params.prefix + "55th Percentile", percentiles[10])); featureList.push_back(std::make_pair(params.prefix + "60th Percentile", percentiles[11])); featureList.push_back(std::make_pair(params.prefix + "65th Percentile", percentiles[12])); featureList.push_back(std::make_pair(params.prefix + "70th Percentile", percentiles[13])); featureList.push_back(std::make_pair(params.prefix + "75th Percentile", percentiles[14])); featureList.push_back(std::make_pair(params.prefix + "80th Percentile", percentiles[15])); featureList.push_back(std::make_pair(params.prefix + "85th Percentile", percentiles[16])); featureList.push_back(std::make_pair(params.prefix + "90th Percentile", percentiles[17])); featureList.push_back(std::make_pair(params.prefix + "95th Percentile", percentiles[18])); featureList.push_back(std::make_pair(params.prefix + "Maximum", maximum)); featureList.push_back(std::make_pair(params.prefix + "Interquantile range", interquantileRange)); featureList.push_back(std::make_pair(params.prefix + "Range", maximum-minimum)); featureList.push_back(std::make_pair(params.prefix + "Mean absolute deviation", meanAbsoluteDeviation)); featureList.push_back(std::make_pair(params.prefix + "Robust mean absolute deviation", robustMeanAbsoluteDeviation)); featureList.push_back(std::make_pair(params.prefix + "Median absolute deviation", medianAbsoluteDeviation)); featureList.push_back(std::make_pair(params.prefix + "Coefficient of variation", coefficientOfVariation)); featureList.push_back(std::make_pair(params.prefix + "Quantile coefficient of dispersion", quantileCoefficientOfDispersion)); featureList.push_back(std::make_pair(params.prefix + "Energy", energy)); featureList.push_back(std::make_pair(params.prefix + "Root mean square", rootMeanSquare)); featureList.push_back(std::make_pair(params.prefix + "Standard Deviation", std::sqrt(variance))); featureList.push_back(std::make_pair(params.prefix + "Kurtosis", kurtosis)); featureList.push_back(std::make_pair(params.prefix + "Robust mean", robustMean)); featureList.push_back(std::make_pair(params.prefix + "Robust variance", robustVariance)); featureList.push_back(std::make_pair(params.prefix + "Covered image intensity range", coveredImageRange)); featureList.push_back(std::make_pair(params.prefix + "Mode index", modeIdx)); featureList.push_back(std::make_pair(params.prefix + "Mode value", params.quantifier->IndexToMeanIntensity(modeIdx))); featureList.push_back(std::make_pair(params.prefix + "Mode probability", histogram[modeIdx] / (1.0*numberOfVoxels))); featureList.push_back(std::make_pair(params.prefix + "Entropy", entropy)); featureList.push_back(std::make_pair(params.prefix + "Uniformtiy", uniformity)); featureList.push_back(std::make_pair(params.prefix + "Number of voxels", numberOfVoxels)); featureList.push_back(std::make_pair(params.prefix + "Sum of voxels", sum)); featureList.push_back(std::make_pair(params.prefix + "Voxel space", voxelSpace)); featureList.push_back(std::make_pair(params.prefix + "Voxel volume", voxelVolume)); featureList.push_back(std::make_pair(params.prefix + "Image Dimension", VImageDimension)); return; } mitk::GIFFirstOrderNumericStatistics::GIFFirstOrderNumericStatistics() { SetShortName("fon"); SetLongName("first-order-numeric"); SetFeatureClassName("First Order Numeric"); } mitk::GIFFirstOrderNumericStatistics::FeatureListType mitk::GIFFirstOrderNumericStatistics::CalculateFeatures(const Image::Pointer & image, const Image::Pointer &mask) { InitializeQuantifier(image, mask); FeatureListType featureList; FirstOrderNumericParameterStruct params; params.quantifier = GetQuantifier(); params.MinimumIntensity = GetQuantifier()->GetMinimum(); params.MaximumIntensity = GetQuantifier()->GetMaximum(); params.Bins = GetQuantifier()->GetBins(); params.prefix = FeatureDescriptionPrefix(); AccessByItk_3(image, CalculateFirstOrderStatistics, mask, featureList, params); return featureList; } mitk::GIFFirstOrderNumericStatistics::FeatureNameListType mitk::GIFFirstOrderNumericStatistics::GetFeatureNames() { FeatureNameListType featureList; return featureList; } void mitk::GIFFirstOrderNumericStatistics::AddArguments(mitkCommandLineParser &parser) { std::string name = GetOptionPrefix(); parser.addArgument(GetLongName(), name, mitkCommandLineParser::Bool, "Use First Order Statistic (Numeric)", "calculates First Order Statistic (Numeric)", us::Any()); AddQuantifierArguments(parser); } void mitk::GIFFirstOrderNumericStatistics::CalculateFeaturesUsingParameters(const Image::Pointer & feature, const Image::Pointer &, const Image::Pointer &maskNoNAN, FeatureListType &featureList) { auto parsedArgs = GetParameter(); if (parsedArgs.count(GetLongName())) { InitializeQuantifierFromParameters(feature, maskNoNAN); MITK_INFO << "Start calculating first order features ...."; auto localResults = this->CalculateFeatures(feature, maskNoNAN); featureList.insert(featureList.end(), localResults.begin(), localResults.end()); MITK_INFO << "Finished calculating first order features...."; } } std::string mitk::GIFFirstOrderNumericStatistics::GetCurrentFeatureEncoding() { return QuantifierParameterString(); } \ No newline at end of file