Strip trailing spaces and convert tabs to spaces

ukf/NrrdData.cc

@@ -113,7 +113,7 @@ void NrrdData::Interp3Signal(const vec3_t& pos,
     signal[i] /= w_sum;
 
     // Push into second spot.
-    signal[i + _num_gradients]  = signal[i];  // Duplicate the signals
+    signal[i + _num_gradients]  = signal[i]; // Duplicate the signals
     }
 
 }
@@ -419,7 +419,7 @@ bool NrrdData::LoadSignal(Nrrd* input_nrrd, const bool normalizedDWIData)
   else
     {
     this->_data_nrrd = nrrdNew();
-    dwiNormalize(input_nrrd, _data_nrrd);   // Do preprocessing on the data
+    dwiNormalize(input_nrrd, _data_nrrd); // Do preprocessing on the data
     }
 
   // After normalization, the first axis of the nrrd data is the list, namely the gradient axis
@@ -493,7 +493,7 @@ bool NrrdData::LoadSignal(Nrrd* input_nrrd, const bool normalizedDWIData)
   nrrdSpacingCalculate(this->_data_nrrd, 1, &spacing1, space_dir);
   nrrdSpacingCalculate(this->_data_nrrd, 2, &spacing2, space_dir);
   nrrdSpacingCalculate(this->_data_nrrd, 3, &spacing3, space_dir);
-  _voxel << spacing3, spacing2, spacing1;  // NOTE that the _voxel here is in reverse axis order!
+  _voxel << spacing3, spacing2, spacing1; // NOTE that the _voxel here is in reverse axis order!
 
   // make sure something computable is in spacing.
   for(unsigned int i = 0; i < this->_data_nrrd->dim; ++i)
@@ -569,8 +569,8 @@ bool NrrdData::LoadSignal(Nrrd* input_nrrd, const bool normalizedDWIData)
 
   R(0, 0) *=  vox_x_inv;
   R(1, 0) *=  vox_x_inv;
-  R(2, 0) *=  vox_x_inv;  // R(0,0), R(1,0), R(2,0) is a unit vector, and is just the normalized spacedirection of axis
-                          // 1
+  R(2, 0) *=  vox_x_inv; // R(0,0), R(1,0), R(2,0) is a unit vector, and is just the normalized spacedirection of axis
+                         // 1
   R(0, 1) *=  vox_y_inv;
   R(1, 1) *=  vox_y_inv;
   R(2, 1) *=  vox_y_inv;

ukf/cli.cc

@@ -80,11 +80,11 @@ int ukf_parse_cli(int argc, char** argv, UKFSettings& s)
   // HANDLE ERRORNOUS INPUT
   if (dwiFile.empty() || maskFile.empty() || tracts.empty()) {
     std::cout << "Error! Must indicate DWI data, mask and tracts output files!" << std::endl << std::endl ;
-    return 1 ;  //This is to indicate that the module returns with error
+    return 1 ; //This is to indicate that the module returns with error
   }
 
   if (numTensor == 1) {
-    tractsWithSecondTensor.clear() ;  //Reassure the string is empty
+    tractsWithSecondTensor.clear() ; //Reassure the string is empty
   }
 
   if (l_maxHalfFiberLength <= 0) {
@@ -137,7 +137,7 @@ int ukf_parse_cli(int argc, char** argv, UKFSettings& s)
 
   if (l_seedingThreshold == 0.0) {
     ukf_setAndTell(l_seedingThreshold, FULL_BRAIN_MEAN_SIGNAL_MIN,
-               "seedingThreshold");  // Used to default to 2 times the FA threshold.
+               "seedingThreshold"); // Used to default to 2 times the FA threshold.
   } else {
     ukf_tell(l_seedingThreshold, "seedingThreshold");
   }
@@ -156,12 +156,12 @@ int ukf_parse_cli(int argc, char** argv, UKFSettings& s)
       else
         ukf_setAndTell(l_Qm, 0.001, "Qm");
     } else if (numTensor == 1) {
-        ukf_setAndTell(l_Qm, 0.005, "Qm");//l_Qm = 0.0015;
+        ukf_setAndTell(l_Qm, 0.005, "Qm"); //l_Qm = 0.0015;
     } else {
       if (fullTensorModel) {
-        ukf_setAndTell(l_Qm, 0.002, "Qm");//l_Qm = 0.002;
+        ukf_setAndTell(l_Qm, 0.002, "Qm"); //l_Qm = 0.002;
       } else {
-        ukf_setAndTell(l_Qm, 0.001, "Qm");//l_Qm = 0.001; was 0.003, changed to 0.001 for new Interp3Signal
+        ukf_setAndTell(l_Qm, 0.001, "Qm"); //l_Qm = 0.001; was 0.003, changed to 0.001 for new Interp3Signal
       }
     }
   } else {
@@ -178,11 +178,11 @@ int ukf_parse_cli(int argc, char** argv, UKFSettings& s)
   else {
     if (l_Ql == 0.0) {
       if (numTensor == 1) {
-        ukf_setAndTell(l_Ql, 300.0, "Ql");//l_Ql = 25.0;
+        ukf_setAndTell(l_Ql, 300.0, "Ql"); //l_Ql = 25.0;
       } else if (numTensor == 2) {
-        ukf_setAndTell(l_Ql, 50.0, "Ql");//was l_Ql = 100.0; for old Interp3Signal
+        ukf_setAndTell(l_Ql, 50.0, "Ql"); //was l_Ql = 100.0; for old Interp3Signal
       } else if (numTensor == 3) {
-        ukf_setAndTell(l_Ql, 100.0, "Ql");//l_Ql = 150.0;
+        ukf_setAndTell(l_Ql, 100.0, "Ql"); //l_Ql = 150.0;
       }
     } else {
         ukf_tell(l_Ql, "Ql");
@@ -192,12 +192,12 @@ int ukf_parse_cli(int argc, char** argv, UKFSettings& s)
 
   if (l_Rs == 0.0) {
     if (numTensor == 1) {
-      ukf_setAndTell(l_Rs, 0.01, "Rs");//l_Rs = 0.02;
+      ukf_setAndTell(l_Rs, 0.01, "Rs"); //l_Rs = 0.02;
     } else {
       if (fullTensorModel) {
-        ukf_setAndTell(l_Rs, 0.01, "Rs");// = 0.01;
+        ukf_setAndTell(l_Rs, 0.01, "Rs"); // = 0.01;
       } else {
-        ukf_setAndTell(l_Rs, 0.02, "Rs");//was l_Rs = 0.015;for old Interp3Signal
+        ukf_setAndTell(l_Rs, 0.02, "Rs"); //was l_Rs = 0.015;for old Interp3Signal
       }
     }
   } else {

ukf/dwi_normalize.cc

@@ -45,7 +45,7 @@ void dwiNormalize(const Nrrd *raw, Nrrd *& normalized)
     throw;
     }
 
-  nrrdKeyValueClear(normalized);  // Force to erase the key/value pairs
+  nrrdKeyValueClear(normalized); // Force to erase the key/value pairs
 
   // Process the key/value pairs. Identify the non-zero gradients, namely the non-zero B values
   std::vector<std::pair<std::string, std::string> > keyValuePairsOfRaw;
@@ -149,7 +149,7 @@ void dwiNormalize(const Nrrd *raw, Nrrd *& normalized)
   // Compute the permutation
   std::vector<unsigned int> permutation(DATA_DIMENSION);
   unsigned int              permuteCounter = 0;
-  permutation[0] = static_cast<unsigned int>(listAxis);     // Shift the list axis to the fastest axis
+  permutation[0] = static_cast<unsigned int>(listAxis); // Shift the list axis to the fastest axis
   for( int i = 1; i < DATA_DIMENSION; i++ )
     {
     if( permuteCounter == static_cast<unsigned int>(listAxis) )
@@ -272,7 +272,7 @@ void dwiNormalize(const Nrrd *raw, Nrrd *& normalized)
   if( normalized->content != NULL )
     {
     free( normalized->content );
-    normalized->content = NULL;   // Get rid of the content field
+    normalized->content = NULL; // Get rid of the content field
     }
   // Add the key/value pairs back to the normalized data
   int totalGradientCounter = 0;

ukf/filter_Full1T_FW.h

@@ -34,15 +34,15 @@ class Full1T_FW : public FilterModel
 
     // Setting the constraints according to D'*x >= -d
     _D(6, 0) = -1;
-    _d(0) = 1;  // w <= 1
+    _d(0) = 1; // w <= 1
     _D(6, 1) = 1;
-    _d(1) = 0;  // w >= 0
+    _d(1) = 0; // w >= 0
     _D(3, 2) = 1;
-    _d(2) = 0;  // l1 >= 0
+    _d(2) = 0; // l1 >= 0
     _D(4, 3) = 1;
-    _d(3) = 0;  // l2 >= 0
+    _d(3) = 0; // l2 >= 0
     _D(5, 4) = 1;
-    _d(4) = 0;  // l3 >= 0
+    _d(4) = 0; // l3 >= 0
 
   }
 

ukf/filter_Full2T_FW.h

@@ -35,21 +35,21 @@ class Full2T_FW : public FilterModel
 
     // Setting the constraints according to D'*x >= -d
     _D(12, 0) = -1;
-    _d(0) = 1;  // w <= 1
+    _d(0) = 1; // w <= 1
     _D(12, 1) = 1;
-    _d(1) = 0;  // w >= 0
+    _d(1) = 0; // w >= 0
     _D(3, 2)  = 1;
-    _d(2) = 0;  // l11 >= 0
+    _d(2) = 0; // l11 >= 0
     _D(4, 3)  = 1;
-    _d(3) = 0;  // l21 >= 0
+    _d(3) = 0; // l21 >= 0
     _D(5, 4)  = 1;
-    _d(4) = 0;  // l31 >= 0
+    _d(4) = 0; // l31 >= 0
     _D(9, 5)  = 1;
-    _d(5) = 0;  // l12 >= 0
+    _d(5) = 0; // l12 >= 0
     _D(10, 6) = 1;
-    _d(6) = 0;  // l22 >= 0
+    _d(6) = 0; // l22 >= 0
     _D(11, 7) = 1;
-    _d(7) = 0;  // l32 >= 0
+    _d(7) = 0; // l32 >= 0
   }
 
   virtual ~Full2T_FW()

ukf/filter_NODDI1F.h

@@ -26,17 +26,17 @@ class NODDI1F : public FilterModel
 
     // Setting the constraints according to D'*x >= -d
     _D(5, 0) = -1;
-    _d(0) = 1;  // Viso <= 1
+    _d(0) = 1; // Viso <= 1
     _D(5, 1) = 1;
-    _d(1) = 0;  // Viso >= 0
+    _d(1) = 0; // Viso >= 0
 
     _D(3, 2) = 1;
-    _d(2) = 0;  // Vic >= 0
+    _d(2) = 0; // Vic >= 0
     _D(3, 3) = -1;
-    _d(3) = 1;  // Vic <= 1
+    _d(3) = 1; // Vic <= 1
 
     _D(4, 4) = 1;
-    _d(4) = 0;  // kappa >= 0
+    _d(4) = 0; // kappa >= 0
 
   }
 

ukf/filter_NODDI2F.h

@@ -25,25 +25,25 @@ class NODDI2F : public FilterModel
 
     // Setting the constraints according to D'*x >= -d
     _D(10, 0) = -1;
-    _d(0) = 1;  // Viso <= 1
+    _d(0) = 1; // Viso <= 1
     _D(10, 1) = 1;
-    _d(1) = 0;  // Viso >= 0
+    _d(1) = 0; // Viso >= 0
 
     _D(3, 2) = 1;
-    _d(2) = 0;  // Vic >= 0
+    _d(2) = 0; // Vic >= 0
     _D(3, 3) = -1;
-    _d(3) = 1;  // Vic <= 1
+    _d(3) = 1; // Vic <= 1
 
     _D(4, 4) = 1;
-    _d(4) = 0;  // kappa >= 0
+    _d(4) = 0; // kappa >= 0
 
     _D(8, 5) = 1;
-    _d(5) = 0;  // Vic >= 0
+    _d(5) = 0; // Vic >= 0
     _D(8, 6) = -1;
-    _d(6) = 1;  // Vic <= 1
+    _d(6) = 1; // Vic <= 1
 
     _D(9, 7) = 1;
-    _d(7) = 0;  // kappa >= 0
+    _d(7) = 0; // kappa >= 0
 
   }
 

ukf/filter_Simple1T_FW.h

@@ -34,13 +34,13 @@ class Simple1T_FW : public FilterModel
 
     // Setting the constraints according to D'*x >= -d
     _D(5, 0) = -1;
-    _d(0) = 1;  // w <= 1
+    _d(0) = 1; // w <= 1
     _D(5, 1) = 1;
-    _d(1) = 0;  // w >= 0
+    _d(1) = 0; // w >= 0
     _D(3, 2) = 1;
-    _d(2) = 0;  // l1 >= 0
+    _d(2) = 0; // l1 >= 0
     _D(4, 3) = 1;
-    _d(3) = 0;  // l2 >= 0
+    _d(3) = 0; // l2 >= 0
 
   }
 

ukf/filter_Simple2T_FW.h

@@ -34,17 +34,17 @@ class Simple2T_FW : public FilterModel
 
     // Setting the constraints according to D'*x >= -d
     _D(10, 0) = -1;
-    _d(0) = 1;  // w <= 1
+    _d(0) = 1; // w <= 1
     _D(10, 1) = 1;
-    _d(1) = 0;  // w >= 0
+    _d(1) = 0; // w >= 0
     _D(3, 2)  = 1;
-    _d(2) = 0;  // l11 >= 0
+    _d(2) = 0; // l11 >= 0
     _D(4, 3)  = 1;
-    _d(3) = 0;  // l21 >= 0
+    _d(3) = 0; // l21 >= 0
     _D(8, 4)  = 1;
-    _d(4) = 0;  // l12 >= 0
+    _d(4) = 0; // l12 >= 0
     _D(9, 5)  = 1;
-    _d(5) = 0;  // l22 >= 0
+    _d(5) = 0; // l22 >= 0
   }
 
   virtual ~Simple2T_FW()