Romulo:

- Tool now supports files in pts (Jef) and txt (VV) formats (-t/--type option)

diff --git a/tools/clitkTransformLandmarks.cxx b/tools/clitkTransformLandmarks.cxx
index 4d424081d7e0d92b69ccf6e88be4a992c4864f47..4db65a54b92fefdf6454651aaf45c51c9b913e0d 100644 (file)
--- a/tools/clitkTransformLandmarks.cxx
+++ b/tools/clitkTransformLandmarks.cxx
@@ -9,10 +9,18 @@
 typedef itk::Matrix<double, 4, 4> MatrixType;
 typedef itk::Point<double, 4> PointType;
 typedef std::vector<PointType> PointArrayType;
+typedef itk::FixedArray<std::string, 2> TxtDataType;
+typedef std::vector<TxtDataType> TxtDataArrayType;
+
+
+void read_points_txt(const std::string& fileName, PointArrayType& points, TxtDataArrayType& data);
+void write_points_txt(const std::string& fileName, const PointArrayType& points, const TxtDataArrayType& data);
+
+void read_points_pts(const std::string& fileName, PointArrayType& points);
+void write_points_pts(const std::string& fileName, const PointArrayType& points);
 
-void read_points(const std::string& fileName, PointArrayType& points);
 void transform_points(const PointArrayType& input, const MatrixType& matrix, PointArrayType& output);
-void write_points(const std::string& fileName, const PointArrayType& points);
+
 
 bool verbose = false;
 
@@ -21,19 +29,31 @@ int main(int argc, char** argv)
   GGO(clitkTransformLandmarks, args_info);
   verbose = args_info.verbose_flag;
 
-  PointArrayType inputPoints;
-  read_points(args_info.input_arg, inputPoints);
-  
   MatrixType matrix = clitk::ReadMatrix3D(args_info.matrix_arg);
 
+  TxtDataArrayType data;
+  PointArrayType inputPoints;
+  if (strcmp(args_info.type_arg, "txt") == 0) {
+    read_points_txt(args_info.input_arg, inputPoints, data);
+  }
+  else {
+    read_points_pts(args_info.input_arg, inputPoints);
+  }
+  
   PointArrayType outputPoints;
   transform_points(inputPoints, matrix, outputPoints);
+
+  if (strcmp(args_info.type_arg, "txt") == 0) {
+    write_points_txt(args_info.output_arg, outputPoints, data);
+  }
+  else {
+    write_points_pts(args_info.output_arg, outputPoints);
+  }
   
-  write_points(args_info.output_arg, outputPoints);
   return 0;
 }
 
-void read_points(const std::string& fileName, PointArrayType& points)
+void read_points_txt(const std::string& fileName, PointArrayType& points, TxtDataArrayType& data)
 {
   std::ifstream landmarksFile(fileName.c_str());
   if (landmarksFile.fail()) {
@@ -48,38 +68,81 @@ void read_points(const std::string& fileName, PointArrayType& points)
     exit(-3);
   }
   
-  int id = 0;
-  PointType point;
-  point.Fill(1);
+  PointType p;
+  p.Fill(1);
+  
+  TxtDataType d;
   
-  std::istringstream linestr; 
   while (!landmarksFile.eof()) {
-    std::getline(landmarksFile, line);
-    if (verbose) std::cout << "line " << line << std::endl;
+    // read id, x, y, z, d1, d2
+    landmarksFile >> d[0] >> p[0] >> p[1] >> p[2] >> d[1];// >> d[2];
+    if (landmarksFile.fail())
+      break;
     
-    if (!line.empty()) {
-      linestr.str(line);
-      linestr >> id >> point[0] >> point[1] >> point[2];
-      
-      if (verbose) std::cout << "point " << point << std::endl;
-      
-      points.push_back(point);
+    if (verbose){
+      std::cout << "point " << p << std::endl;
+      std::cout << "data " << " " << d[0] << " " << d[1] << std::endl;
     }
+    
+    points.push_back(p);
+    data.push_back(d);
   }
 }
 
-void transform_points(const PointArrayType& input, const MatrixType& matrix, PointArrayType& output)
+void write_points_txt(const std::string& fileName, const PointArrayType& points, const TxtDataArrayType& data) 
 {
-  for (size_t i = 0; i < input.size(); i++) {
-    output.push_back(matrix * input[i]);
+  std::ofstream landmarksFile(fileName.c_str());
+  
+  landmarksFile << "LANDMARKS1" << std::endl;
+  for (size_t i = 0; i < points.size(); i++)
+    landmarksFile << data[i][0] << " " << points[i][0] << " " << points[i][1] << " " << points[i][2] << " " << data[i][1] << " " << std::endl;
+}
+
+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;
+    exit(-2);
+  }
+  
+  std::string line;
+  std::getline(landmarksFile, line);
+  if (line.find("#X") != 0) {
+    std::cout << "ERROR: invalid landmarks file '" << fileName << "'" << std::endl;
+    exit(-3);
+  }
+  
+  PointType p;
+  p.Fill(1);
+  
+  while (!landmarksFile.eof()) {
+    // read id, x, y, z, d1, d2
+    landmarksFile >> p[0] >> p[1] >> p[2];
+    if (landmarksFile.fail())
+      break;
+    
+    if (verbose){
+      std::cout << "point " << p << std::endl;
+    }
+    
+    points.push_back(p);
   }
 }
 
-void write_points(const std::string& fileName, const PointArrayType& points) 
+void write_points_pts(const std::string& fileName, const PointArrayType& points)
 {
   std::ofstream landmarksFile(fileName.c_str());
   
-  landmarksFile << "LANDMARKS1" << std::endl;
+  landmarksFile << "#X\tY\tZ" << std::endl;
   for (size_t i = 0; i < points.size(); i++)
-    landmarksFile << i << " " << points[i][0] << " " << points[i][1] << " " << points[i][2] << " " << "0" << " " << std::endl;
-}
\ No newline at end of file
+    landmarksFile << points[i][0] << "\t" << points[i][1] << "\t" << points[i][2] << "\t" << std::endl;
+}
+
+void transform_points(const PointArrayType& input, const MatrixType& matrix, PointArrayType& output)
+{
+  for (size_t i = 0; i < input.size(); i++) {
+    output.push_back(matrix * input[i]);
+  }
+}
+

diff --git a/tools/clitkTransformLandmarks.ggo b/tools/clitkTransformLandmarks.ggo
index c9eac335030afd809cdd77a8a42bedae5e6134e5..71186ef19eec14c84b3a8f35af5e5a55a1d4f6f4 100644 (file)
--- a/tools/clitkTransformLandmarks.ggo
+++ b/tools/clitkTransformLandmarks.ggo
@@ -8,6 +8,7 @@ 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 "output"   o "Output landmarks filename"      string    yes
+option "output"                o       "Output landmarks filename"                     string          yes
+option "type"          t       "Landmarks type ('pts' for Jef; 'txt' for VV)"          string          no              default="txt"