Add clitkChangeDicomTag tool

[clitk.git] / common / clitkChangeDicomTagGenericFilter.txx

diff --git a/common/clitkChangeDicomTagGenericFilter.txx b/common/clitkChangeDicomTagGenericFilter.txx
new file mode 100644 (file)
index 0000000..0bb9882
--- /dev/null
+++ b/common/clitkChangeDicomTagGenericFilter.txx
@@ -0,0 +1,122 @@
+/*=========================================================================
+  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 clitkChangeDicomTagGenericFilter_txx
+#define clitkChangeDicomTagGenericFilter_txx
+
+/* =================================================
+ * @file   clitkChangeDicomTagGenericFilter.txx
+ * @author
+ * @date
+ *
+ * @brief
+ *
+ ===================================================*/
+
+// clitk
+#include "clitkResampleImageWithOptionsFilter.h"
+#if GDCM_MAJOR_VERSION >= 2
+#include "gdcmUIDGenerator.h"
+#include <gdcmImageHelper.h>
+#include <gdcmAttribute.h>
+#include <gdcmReader.h>
+#include <gdcmWriter.h>
+#include <gdcmDataElement.h>
+#include <gdcmTag.h>
+#else
+#include "gdcmFile.h"
+#include "gdcmUtil.h"
+#endif
+
+
+namespace clitk
+{
+
+
+//-----------------------------------------------------------
+// Constructor
+//-----------------------------------------------------------
+template<class args_info_type>
+ChangeDicomTagGenericFilter<args_info_type>::ChangeDicomTagGenericFilter()
+{
+  m_Verbose=false;
+}
+
+
+//-----------------------------------------------------------
+// Update
+//-----------------------------------------------------------
+template<class args_info_type>
+void ChangeDicomTagGenericFilter<args_info_type>::Update()
+{
+  UpdateWithDimAndPixelType();
+}
+
+//-------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype read from
+// the dicom files. The MHD files may be resampled to match the
+// dicom spacing (and number of slices). Rounding errors in resampling
+// are handled by removing files when generating the output dicom
+// series.
+//-------------------------------------------------------------------
+template<class args_info_type>
+void
+ChangeDicomTagGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
+{
+  //Read the dicom file
+  gdcm::Reader reader;
+  reader.SetFileName( m_ArgsInfo.input_arg );
+  reader.Read();
+  gdcm::File &fileOutput = reader.GetFile();
+  gdcm::DataSet &dsOutput = fileOutput.GetDataSet();
+  const unsigned int ptr_len = 42;
+  char *ptr = new char[ptr_len];
+  memset(ptr,0,ptr_len);
+
+  unsigned int numberOfKeysGiven=m_ArgsInfo.key_given;
+  // For all input tag
+  for (unsigned int i = 0; i < numberOfKeysGiven; i++) {
+    // Split the tag element separated with '|' in 2 parts
+    char* copy = (char*)m_ArgsInfo.key_arg[i];
+    std::vector<char*> v;
+    char* chars_array = strtok(copy, "|");
+    while(chars_array) {
+      v.push_back(chars_array);
+      chars_array = strtok(NULL, "|");
+    }
+    std::stringstream str0(v[0]), str1(v[1]);
+    int first, second;
+    str0 >> first;
+    str1 >> second;
+
+    //Change the tag element by the corresponding value
+    gdcm::DataElement tagDE( gdcm::Tag(first, second) );
+    std::string value( m_ArgsInfo.tag_arg[i] );
+    tagDE.SetByteValue(value.c_str(), (uint32_t)strlen(value.c_str()));
+    dsOutput.Insert(tagDE);
+  }
+
+  //Write the output dicom file
+  gdcm::Writer w;
+  w.SetFile( fileOutput );
+  w.SetFileName( m_ArgsInfo.output_arg );
+  w.Write();
+}
+
+}//end clitk
+
+#endif //#define clitkChangeDicomTagGenericFilter_txx