BUG: Fix sigma calculation

acsenrafilho · acsenrafilho · commit 090c54dffbe0 · 2018-03-16T13:50:20.000-03:00
The sigma value was changed in order to correctly calculates over foreground area.
In addition, the m_B parameter was changed to m_BackgroundValue
diff --git a/Modules/Features/SampEn2DImageCalculator/itkSampEn2DImageCalculator.h b/Modules/Features/SampEn2DImageCalculator/itkSampEn2DImageCalculator.h
@@ -89,7 +89,7 @@ class SampEn2DImageCalculator:public Object
     itkSetMacro(D, DParameterValueType);
 
     /** Set the B (background value) parameter value. */
-    itkSetMacro(B, BParameterValueType);
+    itkSetMacro(BackgroundValue, BParameterValueType);
 
     /** Get the M parameter value. */
     itkGetMacro(M, MParameterValueType);
@@ -101,7 +101,7 @@ class SampEn2DImageCalculator:public Object
     itkGetMacro(D, DParameterValueType);
 
     /** Get the B parameter value. */
-    itkGetMacro(B, BParameterValueType);
+    itkGetMacro(BackgroundValue, BParameterValueType);
 
     /** Compute the two-dimensional sample entropy value of the input image. */
     void ComputeEntropy(void);
@@ -127,7 +127,7 @@ class SampEn2DImageCalculator:public Object
     MParameterValueType m_M;
     RParameterValueType m_R;
     DParameterValueType m_D;
-    BParameterValueType m_B;
+    BParameterValueType m_BackgroundValue;
     ImageConstPointer   m_Image;
 
     /** Test to check the M, R, D and B parameters values */
diff --git a/Modules/Features/SampEn2DImageCalculator/itkSampEn2DImageCalculator.hxx b/Modules/Features/SampEn2DImageCalculator/itkSampEn2DImageCalculator.hxx
@@ -36,7 +36,7 @@ SampEn2DImageCalculator< TInputImage >
     m_M = 1;
     m_R = 0.10;
     m_D = 1;
-    m_B = 0.0;
+    m_BackgroundValue = 0.0;
     m_RegionSetByUser = false;
 }
 
@@ -58,31 +58,41 @@ SampEn2DImageCalculator< TInputImage >
     typename ImageType::SizeType radius;
     radius.Fill(static_cast<int>(m_M));
 
-    typedef itk::StatisticsImageFilter<ImageType> StatisticsImageFilterType;
-    typename StatisticsImageFilterType::Pointer statisticsImageFilter = StatisticsImageFilterType::New();
-    statisticsImageFilter->SetInput(m_Image);
-    statisticsImageFilter->Update();
-
-    DoublePixelType tolerance = m_R*statisticsImageFilter->GetSigma();
-
     typename ImageType::SizeType size = m_Region.GetSize();
 
-//        clock_t begin, end;
-//        begin=clock();
-
     m_Nx = size[0]; //ncols
     m_Ny = size[1]; //nrows
 
     double image_matrix[m_Nx*m_Ny];
+    double sigma = 0.0, mean = 0.0;
+    unsigned int N = 0;
 
     ConstRegionIteratorType    copyIt(m_Image, m_Region);
     copyIt.GoToBegin();
     int count=0;
     while (!copyIt.IsAtEnd()) {
         image_matrix[count++]=copyIt.Get();
+
+        if (copyIt.Get()!=m_BackgroundValue) {
+            N++;
+            mean+=copyIt.Get();
+        }
         ++copyIt;
     }
+    mean/=N;
 
+    //Calculating stantard deviation only in the foreground area
+    copyIt.GoToBegin();
+    while (!copyIt.IsAtEnd()) {
+        if (copyIt.Get()!=m_BackgroundValue) {
+            sigma+=pow(copyIt.Get()-mean,2.0);
+        }
+        ++copyIt;
+    }
+    sigma/=(N-1);
+    sigma=sqrt(sigma);
+
+    DoublePixelType tolerance = m_R*sigma;
 
     //Limit indexes for cols and rows
     int xLim = m_Nx - m_M*m_D; 
@@ -153,7 +163,7 @@ SampEn2DImageCalculator< TInputImage >
             //check if it is a valid pattern
             valid = true;
             for (k=0; k < nmm1; k++) {
-                if(image_matrix[ki+kdmm1[k]]==bv) {
+                if(image_matrix[ki+kdmm1[k]]==m_BackgroundValue) {
                     valid = false;
                     break; 
                 }
@@ -167,14 +177,10 @@ SampEn2DImageCalculator< TInputImage >
                     jlim = (j*m_Nx)+xLim; //set limit index in current row for moving pattern
 
                     while (kj < jlim ) { //go across columns
-                        //for debug
-                        //printf("(%d) ",kj); 
-                        
-
                         //pattern matching for m using tolerance
                         for (k=0; k < nm; k++) {
                             v = image_matrix[kj+kdm[k]];
-                            if(v != bv) {//if it is not a background pixel
+                            if(v != m_BackgroundValue) {//if it is not a background pixel
                                 d = fabs(image_matrix[ki+kdm[k]] - v);
                                 if (d >= tolerance) {
                                     d = -1.0; //it is not a similar pattern
@@ -192,7 +198,7 @@ SampEn2DImageCalculator< TInputImage >
                             //pattern matching for m+1 using tolerance
                             for (kk=0; kk < nm1; kk++) {
                                 v = image_matrix[kj+kdm1[kk]];
-                                if(v != bv) {//if it is not a background pixel
+                                if(v != m_BackgroundValue) {//if it is not a background pixel
                                     d = fabs(image_matrix[ki+kdm1[kk]] - v);
                                     if (d >= tolerance) {
                                         d = -1.0; //it is not a similar pattern
@@ -207,7 +213,7 @@ SampEn2DImageCalculator< TInputImage >
                             if (valid) { // is pattern valid so far?
                                 //check remaining pixels
                                 while(++kk < nm1) { 
-                                    if(image_matrix[kj+kdm1[kk]] == bv) //if it is a background pixel
+                                    if(image_matrix[kj+kdm1[kk]] == m_BackgroundValue) //if it is a background pixel
                                       valid = false; //it is not a valid pattern
                                 }
                                 
@@ -233,13 +239,8 @@ SampEn2DImageCalculator< TInputImage >
             }// if valid pattern
             
             ki++;
-        } //while ki    
-        //for debug
-        //printf("\n");
-        
+        } //while ki            
     } //for i
-    //for debug
-    //printf("%d \n %d \n %f \n %f \n",Cim,Cim1,den,bv);
      
     /* outputs: probabilities */
     Cm = ((static_cast<double>(Cim)/(den-1.0))/den)*2.0;
@@ -250,182 +251,6 @@ SampEn2DImageCalculator< TInputImage >
     free(kdmm1);
 
     m_Entropy = static_cast<double>(-1)*std::log(static_cast<double>(Cm1)/static_cast<double>(Cm));
-
-
-/*- - - - - - - - - -*/
-// //Limit indexes for cols and rows
-//     int xLim = m_Nx - m_M*m_D; 
-//     int yLim = m_Ny - m_M*m_D; 
-    
-//     // Total number of valid patterns (for both m and m+1)
-//     double den=0; 
-   
-//     //Counters of similar patterns for m and m+1
-//     unsigned int B, A;  // for each template pattern   
-//     unsigned long long Cim=0, Cim1=0;  //sum over all template patters
-
-//     //Probabilities of patterns ocurrence for m and m+1
-//     double Cm, Cm1; 
-    
-    
-//     int i, j; //col's running indexes 
-//     int ilim, jlim; // limits for pattern's indexes
-        
-//     //Pre-allocating indexes shift for patterns matching and validation
-//     int nm = m_M*m_M;
-//     int nm1 = 2*m_M+1;
-//     int nmm1 = nm+nm1;
-    
-//     int *kdm, *kdm1, *kdmm1; //arrays with shift indexes for m and m+1 matching and validation
-//     if ((kdm = (int *) calloc(nm, sizeof(int))) == NULL) exit(1);
-//     if ((kdm1 = (int *) calloc(nm1, sizeof(int))) == NULL) exit(1);
-//     if ((kdmm1 = (int *) calloc(nmm1, sizeof(int))) == NULL) exit(1);
-    
-//     int kk;  
-//     int k=0; 
-//     for (i = 0; i < m_M ; i++){
-//         kk = m_Ny * i * m_D;
-//         for (j = 0; j < m_M ; j++ ){
-//             kdm[k] = kk + j*m_D;
-//             kdmm1[k] = kdm[k];
-//             k++;
-//         }
-//     }
-//     k=0;
-//     for (j = 0; j <= m_M; j++) {  // Compares column m+1      
-//         kdm1[k] = (m_Ny*m_M +j) * m_D;
-//         kdmm1[k+nm] = kdm1[k];
-//         k++;
-//     }
-//     for (i = 0; i < m_M; i++) {  // Compares row m+1
-//         kdm1[k] = (m_Ny*i + m_M) * m_D;
-//         kdmm1[k+nm] = kdm1[k];
-//         k++;
-//     }
-//     //End pre-allocating
-    
-//     int ki, kj; //pattern's indexes
-//     double d; //differences during pattern matching
-//     bool valid; //valid pattern (has no background)
-//     double v;   //a moving pattern pixel value
-    
-//     /* Starts running */
-//     for(i=0; i<xLim; i++) { //for each column
-//         ilim = (i*m_Ny)+yLim; //set limit index for template pattern
-        
-//         ki = i*m_Ny; //ki is the template pattern
-        
-//         while (ki < ilim) {
-//             B = 0;
-//             A = 0;
-          
-//             //check if it is a valid pattern
-//             valid = true;
-//             for (k=0; k < nmm1; k++) {
-//                 if(image_matrix[ki+kdmm1[k]]==bv) {
-//                     valid = false;
-//                     break; 
-//                 }
-//             }
-            
-//             if(valid) {//if it is a valid pattern (has no background)
-
-//                 kj = ki+1; //kj is the moving pattern
-
-//                 for(j=i; j<xLim; j++) { //for each column
-//                     jlim = (j*m_Ny)+yLim; //set limit index for moving pattern
-
-//                     while (kj < jlim ) {
-//                         //for debug
-//                         //printf("(%d) ",kj); 
-                        
-
-//                         //pattern matching for m with tolerance r
-//                         for (k=0; k < nm; k++) {
-//                             v = image_matrix[kj+kdm[k]];
-//                             if(v != bv) {//if it is not a background pixel
-//                                 d = fabs(image_matrix[ki+kdm[k]] - v);
-//                                 if (d >= r) {
-//                                     d = -1.0; //it is not a similar pattern
-//                                     break;
-//                                 }
-//                             } else {
-//                                 d = -1.0; //it is not a valid pattern
-//                                 break;
-//                             }
-//                         }
-
-//                         // is pattern valid and similar for m?
-//                         if (d != -1.0) { 
-//                             valid=true;
-//                             //pattern matching for m+1 with tolerance r
-//                             for (kk=0; kk < nm1; kk++) {
-//                                 v = image_matrix[kj+kdm1[kk]];
-//                                 if(v != bv) {//if it is not a background pixel
-//                                     d = fabs(image_matrix[ki+kdm1[kk]] - v);
-//                                     if (d >= r) {
-//                                         d = -1.0; //it is not a similar pattern
-//                                         break;
-//                                     }
-//                                 } else {
-//                                     valid = false; //it is not a valid pattern
-//                                     break;
-//                                 }
-//                             }
-
-//                             if (valid) { // is pattern valid so far?
-//                                 //check remaining pixels
-//                                 while(++kk < nm1) { 
-//                                     if(image_matrix[kj+kdm1[kk]] == bv) //if it is a background pixel
-//                                       valid = false; //it is not a valid pattern
-//                                 }
-                                
-//                                 // is pattern valid?
-//                                 if (valid) {
-//                                     B++; //increment m counter
-//                                     if (d != -1.0) // is pattern similar for m+1?
-//                                         A++; //increment m+1 counter
-//                                 }
-//                             }
-//                         }// if valid and similar for m
-
-//                         kj++;
-//                     }//while kj
-
-//                     kj= (j+1)*m_Ny;
-//                 }//for j
-
-//                 Cim += B;
-//                 Cim1 += A;
-
-//                 den++;
-//             }// if valid pattern
-            
-//             ki++;
-//         } //while ki    
-//         //for debug
-//         //printf("\n");
-        
-//     } //for i
-//     //for debug
-//     //printf("%d \n %d \n %f \n %f \n",Cim,Cim1,den,bv);
-     
-//     /* outputs: probabilities */
-//     Cm = ((Cim/(den-1))/den)*2;
-//     Cm1 = ((Cim1/(den-1))/den)*2;
-    
-//     free(kdm);
-//     free(kdm1);
-//     free(kdmm1);
-
-//     m_Entropy = static_cast<double>(-1)*std::log(static_cast<double>(Cm1)/static_cast<double>(Cm));
-/*- - - - - - - - - -*/
-    
-
-//        end=clock();
-//        double time = (double)(end-begin)/CLOCKS_PER_SEC;
-//        cout<<"time "<<time<<endl;
-
 }
 
 
@@ -472,10 +297,10 @@ SampEn2DImageCalculator< TInputImage >
     }
 
 //TODO -- B must be double
-    // if (m_B < 0)
+    // if (m_BackgroundValue < 0)
     // {
     //     itkWarningMacro( << "Wrong value for B parameters: "
-    //                      << m_B << std::endl
+    //                      << m_BackgroundValue << std::endl
     //                      << "B must be a float point positive value.");
     // }
 }
