Moved Elastix stuff to a separate file

[clitk.git] / common / clitkElastix.h

diff --git a/common/clitkElastix.h b/common/clitkElastix.h
new file mode 100644 (file)
index 0000000..ae5dc54
--- /dev/null
+++ b/common/clitkElastix.h
@@ -0,0 +1,156 @@
+/*=========================================================================
+  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
+===========================================================================**/
+
+#ifndef clitkElastix_h
+#define clitkElastix_h
+
+//--------------------------------------------------------------------
+namespace clitk {
+
+//-------------------------------------------------------------------
+bool
+GetElastixValueFromTag(std::ifstream & is,
+                       std::string tag,
+                       std::string & value)
+{
+  std::string line;
+  is.seekg (0, is.beg);
+  while(std::getline(is, line))   {
+    unsigned pos = line.find(tag);
+    if (pos<line.size()) {
+      value=line.substr(pos+tag.size(),line.size()-2);// remove last ')'
+      value.erase (std::remove (value.begin(), value.end(), '"'), value.end());
+      value.erase (std::remove (value.begin(), value.end(), ')'), value.end());
+      return true;
+    }
+  }
+  return false;
+}
+//-------------------------------------------------------------------
+
+
+//-------------------------------------------------------------------
+void
+GetValuesFromValue(const std::string & s,
+                   std::vector<std::string> & values)
+{
+  std::stringstream strstr(s);
+  std::istream_iterator<std::string> it(strstr);
+  std::istream_iterator<std::string> end;
+  std::vector<std::string> results(it, end);
+  values.clear();
+  values.resize(results.size());
+  for(uint i=0; i<results.size(); i++) values[i] = results[i];
+}
+//-------------------------------------------------------------------
+
+
+//-------------------------------------------------------------------
+template<unsigned int Dimension>
+typename itk::Matrix<double, Dimension+1, Dimension+1>
+createMatrixFromElastixFile(std::vector<std::string> & filename, bool verbose=true) {
+  if (Dimension != 3) {
+    FATAL("Only 3D yet" << std::endl);
+  }
+  typename itk::Matrix<double, Dimension+1, Dimension+1> matrix;
+
+  itk::CenteredEuler3DTransform<double>::Pointer mat = itk::CenteredEuler3DTransform<double>::New();
+  itk::CenteredEuler3DTransform<double>::Pointer previous;
+  for(uint j=0; j<filename.size(); j++) {
+
+    // Open file
+    if (verbose) std::cout << "Read elastix parameters in " << filename[j] << std::endl;
+    std::ifstream is;
+    clitk::openFileForReading(is, filename[j]);
+
+    // Check Transform
+    std::string s;
+    bool b = GetElastixValueFromTag(is, "Transform ", s);
+    if (!b) {
+      FATAL("Error must read 'Transform' in " << filename[j] << std::endl);
+    }
+    if (s != "EulerTransform") {
+      FATAL("Sorry only 'EulerTransform'" << std::endl);
+    }
+
+    // FIXME check
+    //    (InitialTransformParametersFilename[j] "NoInitialTransform")
+
+    // Get CenterOfRotationPoint
+    GetElastixValueFromTag(is, "CenterOfRotationPoint ", s); // space is needed
+    if (!b) {
+      FATAL("Error must read 'CenterOfRotationPoint' in " << filename[j] << std::endl);
+    }
+    std::vector<std::string> cor;
+    GetValuesFromValue(s, cor);
+
+    // Get Transformparameters
+    GetElastixValueFromTag(is, "TransformParameters ", s); // space is needed
+    if (!b) {
+      FATAL("Error must read 'TransformParameters' in " << filename[j] << std::endl);
+    }
+    std::vector<std::string> results;
+    GetValuesFromValue(s, results);
+
+    // construct a stream from the string
+    itk::CenteredEuler3DTransform<double>::ParametersType p;
+    p.SetSize(9);
+    for(uint i=0; i<3; i++)
+      p[i] = atof(results[i].c_str()); // Rotation
+    for(uint i=0; i<3; i++)
+      p[i+3] = atof(cor[i].c_str()); // Centre of rotation
+    for(uint i=0; i<3; i++)
+      p[i+6] = atof(results[i+3].c_str()); // Translation
+    mat->SetParameters(p);
+
+    if (verbose) {
+      std::cout << "Rotation      (deg) : " << rad2deg(p[0]) << " " << rad2deg(p[1]) << " " << rad2deg(p[2]) << std::endl;
+      std::cout << "Center of rot (phy) : " << p[3] << " " << p[4] << " " << p[5] << std::endl;
+      std::cout << "Translation   (phy) : " << p[6] << " " << p[7] << " " << p[8] << std::endl;
+    }
+
+    // Compose with previous if needed
+    if (j!=0) {
+      mat->Compose(previous);
+      if (verbose) {
+        std::cout << "Composed rotation      (deg) : " << rad2deg(mat->GetAngleX()) << " " << rad2deg(mat->GetAngleY()) << " " << rad2deg(mat->GetAngleZ()) << std::endl;
+        std::cout << "Composed center of rot (phy) : " << mat->GetCenter() << std::endl;
+        std::cout << "Compsoed translation   (phy) : " << mat->GetTranslation() << std::endl;
+      }
+    }
+    // previous = mat->Clone(); // ITK4
+    previous = itk::CenteredEuler3DTransform<double>::New();
+    previous->SetParameters(mat->GetParameters());
+  }
+
+  mat = previous;
+  for(uint i=0; i<3; i++)
+    for(uint j=0; j<3; j++)
+      matrix[i][j] = mat->GetMatrix()[i][j];
+  // Offset is -Rc + t + c
+  matrix[0][3] = mat->GetOffset()[0];
+  matrix[1][3] = mat->GetOffset()[1];
+  matrix[2][3] = mat->GetOffset()[2];
+  matrix[3][3] = 1;
+
+  return matrix;
+}
+}
+//-------------------------------------------------------------------
+
+#endif