+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================*/
#include "clitkTransformLandmarks_ggo.h"
#include "clitkTransformUtilities.h"
#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;
+typedef itk::FixedArray<std::string, 2> TxtDataType;
+typedef std::vector<TxtDataType> TxtDataArrayType;
-void read_points(const std::string& fileName, PointArrayType& points);
+
+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 apply_spacing(const PointArrayType& input, const double* spacing, PointArrayType& output);
void transform_points(const PointArrayType& input, const MatrixType& matrix, PointArrayType& output);
-void write_points(const PointArrayType& points);
+
bool verbose = false;
int main(int argc, char** argv)
{
GGO(clitkTransformLandmarks, args_info);
+ verbose = args_info.verbose_flag;
+ TxtDataArrayType data;
PointArrayType inputPoints;
- read_points(args_info.input_arg, inputPoints);
-
- MatrixType matrix = clitk::ReadMatrix3D(args_info.matrix_arg);
+ 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, *workingOutputPoints, data);
+ }
+ else {
+ write_points_pts(args_info.output_arg, *workingOutputPoints);
+ }
- write_points(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()) {
- 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);
}
- 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 write_points_txt(const std::string& fileName, const PointArrayType& points, const TxtDataArrayType& data)
+{
+ 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::cerr << "ERROR: could not open '" << fileName << "'" << std::endl;
+ exit(-2);
+ }
+
+ std::string line;
+ std::getline(landmarksFile, line);
+ if (line.find("#X") != 0) {
+ std::cerr << "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_pts(const std::string& fileName, const PointArrayType& points)
+{
+ std::ofstream landmarksFile(fileName.c_str());
+
+ landmarksFile << "#X\tY\tZ" << std::endl;
+ for (size_t i = 0; i < points.size(); i++)
+ 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 write_points(const PointArrayType& points)
-{
- std::cout << "LANDMARKS1" << std::endl;
- for (size_t i = 0; i < points.size(); i++)
- std::cout << i << " " << points[i][0] << " " << points[i][1] << " " << points[i][2] << " " << "0" << " " << std::endl;
-}
\ No newline at end of file
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff