From c1b964b56f8d21c8e8ce0bd4ce53016de1a6137e Mon Sep 17 00:00:00 2001
From: Manuel Grizonnet <manuel.grizonnet@gmail.com>
Date: Fri, 25 Jun 2010 16:14:51 +0200
Subject: [PATCH] ENH:add MEAN texture in advanced texture coefficients
computation
---
...rixAdvancedTextureCoefficientsCalculator.h | 7 +++--
...xAdvancedTextureCoefficientsCalculator.txx | 11 ++++----
.../otbScalarImageToAdvancedTexturesFilter.h | 3 +++
...otbScalarImageToAdvancedTexturesFilter.txx | 26 ++++++++++++++++---
Testing/Code/FeatureExtraction/CMakeLists.txt | 4 ++-
...xAdvancedTextureCoefficientsCalculator.cxx | 12 ++++++++-
...otbScalarImageToAdvancedTexturesFilter.cxx | 6 +++++
7 files changed, 56 insertions(+), 13 deletions(-)
diff --git a/Code/FeatureExtraction/otbGreyLevelCooccurrenceMatrixAdvancedTextureCoefficientsCalculator.h b/Code/FeatureExtraction/otbGreyLevelCooccurrenceMatrixAdvancedTextureCoefficientsCalculator.h
index 5b313456a2..b40d274d40 100644
--- a/Code/FeatureExtraction/otbGreyLevelCooccurrenceMatrixAdvancedTextureCoefficientsCalculator.h
+++ b/Code/FeatureExtraction/otbGreyLevelCooccurrenceMatrixAdvancedTextureCoefficientsCalculator.h
@@ -34,6 +34,8 @@ namespace otb {
* The features calculated are as follows (where \f$ g(i, j) \f$ is the element in
* cell i, j of a a normalized GLCM):
*
+ * "Mean" \f$ = \sum_{i,j}i g(i,j) \f$
+ *
* "Sum of squares: Variance" \f$ = f_4 = \sum_{i,j}(i -mu)^2 g(i,j) \f$
*
* "Sum average" \f$ = f_6 = -\sum_{i}i g_{x+y}(i)
@@ -117,6 +119,7 @@ public:
itkSetObjectMacro( Histogram, HistogramType );
itkGetObjectMacro( Histogram, HistogramType );
+ itkGetMacro(Mean, double);
itkGetMacro(Variance, double);
itkGetMacro(SumAverage, double);
itkGetMacro(SumVariance, double);
@@ -142,8 +145,8 @@ private:
HistogramPointer m_Histogram;
void NormalizeHistogram(void);
- void ComputeMean( double &pixelMean );
- double m_Variance, m_SumAverage, m_SumVariance,m_SumEntropy, m_DifferenceEntropy,
+ void ComputeMean();
+ double m_Mean, m_Variance, m_SumAverage, m_SumVariance,m_SumEntropy, m_DifferenceEntropy,
m_DifferenceVariance, m_IC1, m_IC2;
double ComputePS ( long unsigned int k );
diff --git a/Code/FeatureExtraction/otbGreyLevelCooccurrenceMatrixAdvancedTextureCoefficientsCalculator.txx b/Code/FeatureExtraction/otbGreyLevelCooccurrenceMatrixAdvancedTextureCoefficientsCalculator.txx
index 22bf0c22c4..c75af60b05 100644
--- a/Code/FeatureExtraction/otbGreyLevelCooccurrenceMatrixAdvancedTextureCoefficientsCalculator.txx
+++ b/Code/FeatureExtraction/otbGreyLevelCooccurrenceMatrixAdvancedTextureCoefficientsCalculator.txx
@@ -41,7 +41,7 @@ NormalizeHistogram( void )
template< class THistogram >
void
GreyLevelCooccurrenceMatrixAdvancedTextureCoefficientsCalculator< THistogram >::
-ComputeMean( double &pixelMean )
+ComputeMean( )
{
// This function takes two passes through the histogram and two passes through
// an array of the same length as a histogram axis. This could probably be
@@ -49,7 +49,7 @@ ComputeMean( double &pixelMean )
typedef typename HistogramType::Iterator HistogramIterator;
// Initialize everything
- pixelMean = 0;
+ m_Mean = 0;
// Ok, now do the first pass through the histogram to get the marginal sums
// and compute the pixel mean
@@ -58,7 +58,7 @@ ComputeMean( double &pixelMean )
{
MeasurementType frequency = hit.GetFrequency();
IndexType index = m_Histogram->GetIndex(hit.GetInstanceIdentifier());
- pixelMean += index[0] * frequency;
+ m_Mean += index[0] * frequency;
}
}
@@ -80,8 +80,7 @@ Compute ()
}
// Now get the pixel mean.
- double pixelMean;
- this->ComputeMean( pixelMean );
+ this->ComputeMean();
m_SumAverage = 0;
m_SumEntropy = 0;
@@ -151,7 +150,7 @@ Compute ()
IndexType index = m_Histogram->GetIndex(hit.GetInstanceIdentifier());
- m_Variance += ( (index[0] - pixelMean) * (index[0] - pixelMean) ) * frequency;
+ m_Variance += ( (index[0] - m_Mean) * (index[0] - m_Mean) ) * frequency;
Entropy -= (frequency > 0.0001) ? frequency * vcl_log(frequency) / log2 : 0;
double pipj = m_Histogram->GetFrequency (index[0] , 0) * m_Histogram->GetFrequency (index[1] , 1);
diff --git a/Code/FeatureExtraction/otbScalarImageToAdvancedTexturesFilter.h b/Code/FeatureExtraction/otbScalarImageToAdvancedTexturesFilter.h
index 46ad156c82..2f54b1bec8 100644
--- a/Code/FeatureExtraction/otbScalarImageToAdvancedTexturesFilter.h
+++ b/Code/FeatureExtraction/otbScalarImageToAdvancedTexturesFilter.h
@@ -91,6 +91,9 @@ public:
/** Get the input image maximum */
itkGetMacro(InputImageMaximum,InputPixelType);
+ /** Get the mean output image */
+ OutputImageType * GetMeanOutput();
+
/** Get the variance output image */
OutputImageType * GetVarianceOutput();
diff --git a/Code/FeatureExtraction/otbScalarImageToAdvancedTexturesFilter.txx b/Code/FeatureExtraction/otbScalarImageToAdvancedTexturesFilter.txx
index 0849ce9b13..f58cbed03d 100644
--- a/Code/FeatureExtraction/otbScalarImageToAdvancedTexturesFilter.txx
+++ b/Code/FeatureExtraction/otbScalarImageToAdvancedTexturesFilter.txx
@@ -33,10 +33,10 @@ ScalarImageToAdvancedTexturesFilter<TInputImage,TOutputImage>
m_InputImageMinimum(0),
m_InputImageMaximum(256)
{
- // There are 8 outputs corresponding to the 8 textures indices
- this->SetNumberOfOutputs(8);
+ // There are 9 outputs corresponding to the 8 textures indices
+ this->SetNumberOfOutputs(9);
- // Create the 8 outputs
+ // Create the 9 outputs
this->SetNthOutput(0,OutputImageType::New());
this->SetNthOutput(1,OutputImageType::New());
this->SetNthOutput(2,OutputImageType::New());
@@ -45,6 +45,7 @@ ScalarImageToAdvancedTexturesFilter<TInputImage,TOutputImage>
this->SetNthOutput(5,OutputImageType::New());
this->SetNthOutput(6,OutputImageType::New());
this->SetNthOutput(7,OutputImageType::New());
+ this->SetNthOutput(8,OutputImageType::New());
}
template <class TInputImage,class TOutputImage>
@@ -156,6 +157,19 @@ ScalarImageToAdvancedTexturesFilter<TInputImage,TOutputImage>
return static_cast<OutputImageType *>(this->GetOutput(7));
}
+template <class TInputImage,class TOutputImage>
+typename ScalarImageToAdvancedTexturesFilter<TInputImage,TOutputImage>
+::OutputImageType *
+ScalarImageToAdvancedTexturesFilter<TInputImage,TOutputImage>
+::GetMeanOutput()
+{
+ if(this->GetNumberOfOutputs()<1)
+ {
+ return 0;
+ }
+ return static_cast<OutputImageType *>(this->GetOutput(8));
+}
+
template <class TInputImage,class TOutputImage>
void
ScalarImageToAdvancedTexturesFilter<TInputImage,TOutputImage>
@@ -221,6 +235,7 @@ ScalarImageToAdvancedTexturesFilter<TInputImage,TOutputImage>
{
// Retrieve the input and output pointers
InputImagePointerType inputPtr = const_cast<InputImageType *>(this->GetInput());
+ OutputImagePointerType meanPtr = this->GetMeanOutput();
OutputImagePointerType variancePtr = this->GetVarianceOutput();
OutputImagePointerType sumAveragePtr = this->GetSumAverageOutput();
OutputImagePointerType sumVariancePtr = this->GetSumVarianceOutput();
@@ -232,6 +247,7 @@ ScalarImageToAdvancedTexturesFilter<TInputImage,TOutputImage>
// Build output iterators
itk::ImageRegionIteratorWithIndex<OutputImageType> varianceIt(variancePtr,outputRegionForThread);
+ itk::ImageRegionIterator<OutputImageType> meanIt(meanPtr,outputRegionForThread);
itk::ImageRegionIterator<OutputImageType> sumAverageIt(sumAveragePtr,outputRegionForThread);
itk::ImageRegionIterator<OutputImageType> sumVarianceIt(sumVariancePtr,outputRegionForThread);
itk::ImageRegionIterator<OutputImageType> sumEntropytIt(sumEntropytPtr,outputRegionForThread);
@@ -242,6 +258,7 @@ ScalarImageToAdvancedTexturesFilter<TInputImage,TOutputImage>
// Go to begin
varianceIt.GoToBegin();
+ meanIt.GoToBegin();
sumAverageIt.GoToBegin();
sumVarianceIt.GoToBegin();
sumEntropytIt.GoToBegin();
@@ -265,6 +282,7 @@ ScalarImageToAdvancedTexturesFilter<TInputImage,TOutputImage>
// Iterate on outputs to compute textures
while(!varianceIt.IsAtEnd()
+ &&!meanIt.IsAtEnd()
&&!sumAverageIt.IsAtEnd()
&&!sumVarianceIt.IsAtEnd()
&&!sumEntropytIt.IsAtEnd()
@@ -302,6 +320,7 @@ ScalarImageToAdvancedTexturesFilter<TInputImage,TOutputImage>
// Fill outputs
varianceIt.Set(texturesCalculator->GetVariance());
+ meanIt.Set(texturesCalculator->GetMean());
sumAverageIt.Set(texturesCalculator->GetSumAverage());
sumVarianceIt.Set(texturesCalculator->GetSumVariance());
sumEntropytIt.Set(texturesCalculator->GetSumEntropy());
@@ -315,6 +334,7 @@ ScalarImageToAdvancedTexturesFilter<TInputImage,TOutputImage>
// Increment iterators
++varianceIt;
+ ++meanIt;
++sumAverageIt;
++sumVarianceIt;
++sumEntropytIt;
diff --git a/Testing/Code/FeatureExtraction/CMakeLists.txt b/Testing/Code/FeatureExtraction/CMakeLists.txt
index fb6b1a2336..07e398aee7 100644
--- a/Testing/Code/FeatureExtraction/CMakeLists.txt
+++ b/Testing/Code/FeatureExtraction/CMakeLists.txt
@@ -1817,9 +1817,11 @@ ADD_TEST(feTuScalarImageToAdvancedTexturesFilterNew ${FEATUREEXTRACTION_TESTS15}
)
ADD_TEST(feTvScalarImageToAdvancedTexturesFilter ${FEATUREEXTRACTION_TESTS15}
- --compare-n-images ${EPSILON_8} 8
+ --compare-n-images ${EPSILON_8} 9
${BASELINE}/feTvScalarImageToAdvancedTexturesFilterOutputVariance.tif
${TEMP}/feTvScalarImageToAdvancedTexturesFilterOutputVariance.tif
+ ${BASELINE}/feTvScalarImageToAdvancedTexturesFilterOutputMean.tif
+ ${TEMP}/feTvScalarImageToAdvancedTexturesFilterOutputMean.tif
${BASELINE}/feTvScalarImageToAdvancedTexturesFilterOutputSumAverage.tif
${TEMP}/feTvScalarImageToAdvancedTexturesFilterOutputSumAverage.tif
${BASELINE}/feTvScalarImageToAdvancedTexturesFilterOutputSumVariance.tif
diff --git a/Testing/Code/FeatureExtraction/otbGreyLevelCooccurrenceMatrixAdvancedTextureCoefficientsCalculator.cxx b/Testing/Code/FeatureExtraction/otbGreyLevelCooccurrenceMatrixAdvancedTextureCoefficientsCalculator.cxx
index 14e101c86c..604953efaf 100644
--- a/Testing/Code/FeatureExtraction/otbGreyLevelCooccurrenceMatrixAdvancedTextureCoefficientsCalculator.cxx
+++ b/Testing/Code/FeatureExtraction/otbGreyLevelCooccurrenceMatrixAdvancedTextureCoefficientsCalculator.cxx
@@ -79,6 +79,7 @@ int otbGreyLevelCooccurrenceMatrixAdvancedTextureCoefficientsCalculator(int argc
glcmCalc->Compute();
double trueVariance = 7.6475;
+ double trueMean = 3.95;
double trueSumAverage = 0;
double trueSumVariance = 0;
double trueSumEntropy = 0;
@@ -88,6 +89,7 @@ int otbGreyLevelCooccurrenceMatrixAdvancedTextureCoefficientsCalculator(int argc
double trueIC2 = 0.908663;
double variance = glcmCalc->GetVariance();
+ double mean = glcmCalc->GetMean();
double sumAverage = glcmCalc->GetSumAverage();
double sumVariance = glcmCalc->GetSumVariance();
double sumEntropy = glcmCalc->GetSumEntropy();
@@ -105,7 +107,15 @@ int otbGreyLevelCooccurrenceMatrixAdvancedTextureCoefficientsCalculator(int argc
<< variance << std::endl;
passed = false;
}
-
+
+ if( vnl_math_abs(mean - trueMean) > 0.001 )
+ {
+ std::cerr << "Error:" << std::endl;
+ std::cerr << "Mean calculated wrong. Expected: " << trueMean << ", got: "
+ << mean << std::endl;
+ passed = false;
+ }
+
if( vnl_math_abs(sumAverage - trueSumAverage) > 0.001 )
{
std::cerr << "Error:" << std::endl;
diff --git a/Testing/Code/FeatureExtraction/otbScalarImageToAdvancedTexturesFilter.cxx b/Testing/Code/FeatureExtraction/otbScalarImageToAdvancedTexturesFilter.cxx
index 369b6a3ae7..a435e0f25d 100644
--- a/Testing/Code/FeatureExtraction/otbScalarImageToAdvancedTexturesFilter.cxx
+++ b/Testing/Code/FeatureExtraction/otbScalarImageToAdvancedTexturesFilter.cxx
@@ -88,6 +88,12 @@ int otbScalarImageToAdvancedTexturesFilter(int argc, char * argv[])
oss<<outprefix<<"Variance.tif";
writer->SetInput(filter->GetVarianceOutput());
writer->SetFileName(oss.str());
+ writer->Update();
+
+ oss.str("");
+ oss<<outprefix<<"Mean.tif";
+ writer->SetInput(filter->GetMeanOutput());
+ writer->SetFileName(oss.str());
writer->Update();
oss.str("");
--
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