clitkTransformLandmarks

- can now transform using a matrix (file) and/or spacing (cmd line)

diff --git a/tools/clitkTransformLandmarks.cxx b/tools/clitkTransformLandmarks.cxx
index ea84d18674c8712845468accfffb6707d6a28913..86745a419363ad9d97194b0e9ccdf921c39ee39e 100644 (file)
--- a/tools/clitkTransformLandmarks.cxx
+++ b/tools/clitkTransformLandmarks.cxx
@@ -36,6 +36,7 @@ void write_points_txt(const std::string& fileName, const PointArrayType& points,
 void read_points_pts(const std::string& fileName, PointArrayType& points);
 void write_points_pts(const std::string& fileName, const PointArrayType& points);
 
+void apply_spacing(const PointArrayType& input, const double* spacing, PointArrayType& output);
 void transform_points(const PointArrayType& input, const MatrixType& matrix, PointArrayType& output);
 
 
@@ -46,8 +47,6 @@ int main(int argc, char** argv)
   GGO(clitkTransformLandmarks, args_info);
   verbose = args_info.verbose_flag;
 
-  MatrixType matrix = clitk::ReadMatrix3D(args_info.matrix_arg);
-
   TxtDataArrayType data;
   PointArrayType inputPoints;
   if (strcmp(args_info.type_arg, "txt") == 0) {
@@ -58,13 +57,29 @@ int main(int argc, char** argv)
   }
   
   PointArrayType outputPoints;
-  transform_points(inputPoints, matrix, outputPoints);
+  PointArrayType spacingPoints;
+  PointArrayType* workingInputPoints = &inputPoints;
+  PointArrayType* workingOutputPoints = &outputPoints;
+  if (args_info.spacing_given) {
+    if (verbose) std::cout << "Processing spacing..." << std::endl;
+    
+    apply_spacing(*workingInputPoints, args_info.spacing_arg, spacingPoints);
+    workingInputPoints = &spacingPoints;
+    workingOutputPoints = &spacingPoints;
+  }
+
+  MatrixType matrix;
+  if (args_info.matrix_given) {
+    matrix = clitk::ReadMatrix3D(args_info.matrix_arg);
+    transform_points(*workingInputPoints, matrix, outputPoints);
+    workingOutputPoints = &outputPoints;
+  }
 
   if (strcmp(args_info.type_arg, "txt") == 0) {
-    write_points_txt(args_info.output_arg, outputPoints, data);
+    write_points_txt(args_info.output_arg, *workingOutputPoints, data);
   }
   else {
-    write_points_pts(args_info.output_arg, outputPoints);
+    write_points_pts(args_info.output_arg, *workingOutputPoints);
   }
   
   return 0;
@@ -74,14 +89,14 @@ void read_points_txt(const std::string& fileName, PointArrayType& points, TxtDat
 {
   std::ifstream landmarksFile(fileName.c_str());
   if (landmarksFile.fail()) {
-    std::cout << "ERROR: could not open '" << fileName << "'" << std::endl;
+    std::cerr << "ERROR: could not open '" << fileName << "'" << std::endl;
     exit(-2);
   }
   
   std::string line;
   std::getline(landmarksFile, line);
   if (line.find("LANDMARKS") == std::string::npos) {
-    std::cout << "ERROR: invalid landmarks file '" << fileName << "'" << std::endl;
+    std::cerr << "ERROR: invalid landmarks file '" << fileName << "'" << std::endl;
     exit(-3);
   }
   
@@ -119,14 +134,14 @@ void read_points_pts(const std::string& fileName, PointArrayType& points)
 {
   std::ifstream landmarksFile(fileName.c_str());
   if (landmarksFile.fail()) {
-    std::cout << "ERROR: could not open '" << fileName << "'" << std::endl;
+    std::cerr << "ERROR: could not open '" << fileName << "'" << std::endl;
     exit(-2);
   }
   
   std::string line;
   std::getline(landmarksFile, line);
   if (line.find("#X") != 0) {
-    std::cout << "ERROR: invalid landmarks file '" << fileName << "'" << std::endl;
+    std::cerr << "ERROR: invalid landmarks file '" << fileName << "'" << std::endl;
     exit(-3);
   }
   
@@ -156,6 +171,22 @@ void write_points_pts(const std::string& fileName, const PointArrayType& points)
     landmarksFile << points[i][0] << "\t" << points[i][1] << "\t" << points[i][2] << "\t" << std::endl;
 }
 
+void apply_spacing(const PointArrayType& input, const double* spacing, PointArrayType& output)
+{
+  PointType out;
+  out.Fill(1);
+  
+  for (size_t i = 0; i < input.size(); i++) {
+    out[0] = input[i][0] * spacing[0];
+    out[1] = input[i][1] * spacing[1];
+    out[2] = input[i][2] * spacing[2];
+    if (verbose){
+      std::cout << "output " << out << std::endl;
+    }
+    output.push_back(out);
+  }
+}
+
 void transform_points(const PointArrayType& input, const MatrixType& matrix, PointArrayType& output)
 {
   for (size_t i = 0; i < input.size(); i++) {

diff --git a/tools/clitkTransformLandmarks.ggo b/tools/clitkTransformLandmarks.ggo
index 71186ef19eec14c84b3a8f35af5e5a55a1d4f6f4..c731c23086539cfdecd138621afd6b8a6c0606a9 100644 (file)
--- a/tools/clitkTransformLandmarks.ggo
+++ b/tools/clitkTransformLandmarks.ggo
@@ -7,7 +7,8 @@ option "config"     - "Config file"       string    no
 option "verbose"    v     "Verbose"       flag    off
 
 option "input"    i "Input landmarks filename"      string    yes
-option "matrix"   m "Input 4x4 matrix filename ('.mat' file)"      string    yes
+option "matrix"   m "Input 4x4 matrix filename ('.mat' file)"      string    no
+option "spacing"   s "If given, applies the given spacing (x,y,z) to the input points."      double    no multiple  default="1"
 option "output"                o       "Output landmarks filename"                     string          yes
 option "type"          t       "Landmarks type ('pts' for Jef; 'txt' for VV)"          string          no              default="txt"