Correct ugly bug: many algorithmes were using correlation instead of squared correlation

Author: ocommowi

Anima/registration/anatomical-commands/bm_distortion_correction/animaBMDistortionCorrection.cxx

@@ -37,7 +37,7 @@ int main(int argc, const char** argv)
 
     TCLAP::ValueArg<unsigned int> blockTransfoArg("t","in-transform","Transformation computed between blocks (0: direction, 1: direction+scale, 2: direction+scale+skew, default: 2)",false,2,"transformation between blocks",cmd);
     TCLAP::ValueArg<unsigned int> agregatorArg("","agregator","Transformation agregator type (0: Baloo, 1: M-smoother, default: 0)",false,0,"agregator type",cmd);
-    TCLAP::ValueArg<unsigned int> blockMetricArg("","metric","Similarity metric between blocks (0: correlation coefficient, 1: squared correlation coefficient, 2: mean squares, default: 1)",false,1,"similarity metric",cmd);
+    TCLAP::ValueArg<unsigned int> blockMetricArg("","metric","Similarity metric between blocks (0: mean squares, 1: correlation coefficient, 2: squared correlation coefficient, default: 2)",false,2,"similarity metric",cmd);
 
     TCLAP::SwitchArg weightedAgregationArg("w","no-weighted-agregation", "If set, weighted agregation is deactivated", cmd, false);
     TCLAP::ValueArg<double> extrapolationSigmaArg("","fs","Sigma for extrapolation of local pairings (default: 3)",false,3,"extrapolation sigma",cmd);

Anima/registration/anatomical-commands/bm_distortion_correction/animaPyramidalDistortionCorrectionBlockMatchingBridge.h

@@ -9,9 +9,9 @@
 
 enum Metric
 {
-    Correlation = 0,
-    SquaredCorrelation,
-    MeanSquares
+    MeanSquares = 0,
+    Correlation,
+    SquaredCorrelation
 };
 
 enum TransformKind

Anima/registration/anatomical-commands/dense_svf_bm_registration/animaDenseSVFBMRegistration.cxx

@@ -27,7 +27,7 @@ int main(int argc, const char** argv)
 
     TCLAP::ValueArg<unsigned int> blockTransfoArg("t","in-transform","Transformation computed between blocks (0: translation, 1: rigid, 2: affine, 3: directional affine, default: 0)",false,0,"transformation between blocks",cmd);
     TCLAP::ValueArg<unsigned int> directionArg("d","dir","Affine direction for directional transform output (default: 1 = Y axis)",false,1,"direction of directional affine",cmd);
-    TCLAP::ValueArg<unsigned int> blockMetricArg("","metric","Similarity metric between blocks (0: squared correlation coefficient, 1: correlation coefficient, 2: mean squares, default: 0)",false,0,"similarity metric",cmd);
+    TCLAP::ValueArg<unsigned int> blockMetricArg("","metric","Similarity metric between blocks (0: mean squares, 1: correlation coefficient, 2: squared correlation coefficient, default: 2)",false,2,"similarity metric",cmd);
     TCLAP::ValueArg<unsigned int> optimizerArg("","opt","Optimizer for optimal block search (0: Exhaustive, 1: Bobyqa, default: 1)",false,1,"optimizer",cmd);
 
     TCLAP::ValueArg<unsigned int> maxIterationsArg("","mi","Maximum block match iterations (default: 10)",false,10,"maximum iterations",cmd);

Anima/registration/anatomical-commands/dense_svf_bm_registration/animaPyramidalDenseSVFMatchingBridge.h

@@ -73,9 +73,9 @@ class PyramidalDenseSVFMatchingBridge : public itk::ProcessObject
 
     enum Metric
     {
-        SquaredCorrelation = 0,
+        MeanSquares = 0,
         Correlation,
-        MeanSquares
+        SquaredCorrelation
     };
 
     enum Optimizer

Anima/registration/anatomical-commands/eddy_current_correction/animaEddyCurrentCorrection.cxx

@@ -45,7 +45,7 @@ int main(int argc, const char** argv)
     TCLAP::ValueArg<double> stdevThresholdArg("s","stdev","Threshold block standard deviation (default: 5)",false,5,"block minimal standard deviation",cmd);
     TCLAP::ValueArg<double> percentageKeptArg("k","per-kept","Percentage of blocks with the highest variance kept (default: 0.8)",false,0.8,"percentage of blocks kept",cmd);
 
-    TCLAP::ValueArg<unsigned int> blockMetricArg("","metric","Similarity metric between blocks (0: squared correlation coefficient, 1: correlation coefficient, 2: mean squares, default: 0)",false,0,"similarity metric",cmd);
+    TCLAP::ValueArg<unsigned int> blockMetricArg("","metric","Similarity metric between blocks (0: mean squares, 1: correlation coefficient, 2: squared correlation coefficient, default: 2)",false,2,"similarity metric",cmd);
     TCLAP::ValueArg<unsigned int> optimizerArg("","opt","Optimizer for optimal block search (0: Exhaustive, 1: Bobyqa, default: 1)",false,1,"optimizer",cmd);
 
     TCLAP::ValueArg<unsigned int> maxIterationsArg("","mi","Maximum block match iterations (default: 10)",false,10,"maximum iterations",cmd);

Anima/registration/anatomical-commands/pyramidal_bm_registration/animaPyramidalBMRegistration.cxx

@@ -42,7 +42,7 @@ int main(int argc, const char** argv)
 
     TCLAP::ValueArg<unsigned int> blockTransfoArg("t","in-transform","Transformation computed between blocks (0: translation, 1: rigid, 2: affine, 3: directional affine, default: 0)",false,0,"transformation between blocks",cmd);
     TCLAP::ValueArg<unsigned int> directionArg("d","dir","Affine direction for directional transform output (default: 1 = Y axis)",false,1,"direction of directional affine",cmd);
-    TCLAP::ValueArg<unsigned int> blockMetricArg("","metric","Similarity metric between blocks (0: squared correlation coefficient, 1: correlation coefficient, 2: mean squares, default: 0)",false,0,"similarity metric",cmd);
+    TCLAP::ValueArg<unsigned int> blockMetricArg("","metric","Similarity metric between blocks (0: mean squares, 1: correlation coefficient, 2: squared correlation coefficient, default: 2)",false,2,"similarity metric",cmd);
     TCLAP::ValueArg<unsigned int> optimizerArg("","opt","Optimizer for optimal block search (0: Exhaustive, 1: Bobyqa, default: 1)",false,1,"optimizer",cmd);
 
     TCLAP::ValueArg<unsigned int> maxIterationsArg("","mi","Maximum block match iterations (default: 10)",false,10,"maximum iterations",cmd);

Anima/registration/anatomical-commands/pyramidal_bm_registration/animaPyramidalBlockMatchingBridge.h

@@ -74,9 +74,9 @@ class PyramidalBlockMatchingBridge : public itk::ProcessObject
 
     enum Metric
     {
-        SquaredCorrelation = 0,
+        MeanSquares = 0,
         Correlation,
-        MeanSquares
+        SquaredCorrelation
     };
 
     enum Optimizer