#include <iostream>
#include <fstream>
+#include <vtkSmartPointer.h>
+#include <vtkPoints.h>
+#include <vtkPolyData.h>
+#include "vtkPolyDataReader.h"
+#include "vtkPolyDataWriter.h"
+#include <vtkTransform.h>
+#include <vtkTransformFilter.h>
+
typedef itk::Matrix<double, 4, 4> MatrixType;
typedef itk::Point<double, 4> PointType;
typedef std::vector<PointType> PointArrayType;
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);
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) {
read_points_txt(args_info.input_arg, inputPoints, data);
}
+ else if (strcmp(args_info.type_arg, "vtk") == 0) {
+ vtkSmartPointer<vtkPolyDataReader> reader = vtkSmartPointer<vtkPolyDataReader>::New();
+ reader->SetFileName(args_info.input_arg);
+ reader->Update();
+ vtkSmartPointer<vtkPolyDataWriter> writer = vtkSmartPointer<vtkPolyDataWriter>::New();
+ writer->SetFileName( args_info.output_arg );
+
+ if (args_info.matrix_given) {
+ vtkSmartPointer<vtkTransformFilter> transformFilter = vtkSmartPointer<vtkTransformFilter>::New();
+ vtkSmartPointer<vtkTransform> transform = vtkSmartPointer<vtkTransform>::New();
+ vtkMatrix4x4* matrix = clitk::ReadVTKMatrix3D(args_info.matrix_arg);
+ vtkSmartPointer<vtkMatrix4x4> matrixT = vtkSmartPointer<vtkMatrix4x4>::New();
+ vtkMatrix4x4::Invert(matrix, matrixT); //not sure why, but this seems necessary for using the same .mat as when loading file with vv (probably due to the inversion trick performed in the vv reader...)
+ transform->SetMatrix(matrixT);
+ transformFilter->SetInputConnection(reader->GetOutputPort());
+ transformFilter->SetTransform(transform);
+ writer->SetInputConnection(transformFilter->GetOutputPort());
+
+ }
+ else { //just write the output
+ writer->SetInputConnection( reader->GetOutputPort() );
+ }
+
+ writer->Write();
+ return 0;
+ }
else {
read_points_pts(args_info.input_arg, inputPoints);
}
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;
{
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);
}
{
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);
}
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++) {