X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=tools%2FclitkDicomWave2Text.cxx;h=694a98b83f744c14b72006ecf2e8e6c50a0fa59d;hb=3c2462eafabcf428b4d2775c414a7b5f62511d3f;hp=7fc7c6bb48db5730f4fce4964326161baa336f02;hpb=b52dd3c5ebaddf789b044a6baca5aec8c724988f;p=clitk.git

diff --git a/tools/clitkDicomWave2Text.cxx b/tools/clitkDicomWave2Text.cxx
index 7fc7c6b..694a98b 100644
--- a/tools/clitkDicomWave2Text.cxx
+++ b/tools/clitkDicomWave2Text.cxx
@@ -1,113 +1,136 @@
+/*=========================================================================
+  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 "clitkDicomWave2Text.h"
 #include "clitkDicomWave2Text_ggo.h"
 
 #include "clitkCommon.h"
-//gdcm include
-#include "gdcmFile.h"
 
+#include "gdcmFile.h"
 #if GDCM_MAJOR_VERSION < 2
-  #include "gdcmUtil.h"
   #include "gdcmBinEntry.h"
-  #include "gdcmValEntry.h"
-  #include "gdcmSeqEntry.h"
-  #include "gdcmSQItem.h"
+#else
+  #include "gdcmReader.h"
+  #include "gdcmPrivateTag.h"
 #endif
 
-#include "gdcmSerieHelper.h"
-
 #include <iostream>
 #include <fstream>
 
-//==========================================================================================================================
-
-int main(int argc, char * argv[]) {
-
-//-----------------------------------------------------------------------------
-// init command line
-GGO(clitkDicomWave2Text, args_info);
-//-----------------------------------------------------------------------------
 
-#if GDCM_MAJOR_VERSION < 2
-//-----------------------------------------------------------------------
-// opening dicom input file
-gdcm::File * mDCMFile = new gdcm::File();
-mDCMFile->SetFileName(args_info.InputFile_arg);
-mDCMFile->AddForceLoadElement(0x01e1,0x1018); //Load wave data no matter its size
-
-if (!mDCMFile->OpenFile ()) {
-	std::cerr << "Sorry, the file does not exist or does not appear to be a DICOM file. Abort." << std::endl;
-    exit(0);
-}
-mDCMFile->Load();
-std::cout << "File:   "<< args_info.InputFile_arg << "   loaded !"<< std::endl;
-
-
-//-----------------------------------------------------------------------
-// read data
-gdcm::DocEntrySet* item = mDCMFile;
-#define T short
-
-gdcm::BinEntry* entry = item->GetBinEntry(0x01e1,0x1018);
-DD(entry);
-T* buffer = reinterpret_cast<T*>(entry->GetBinArea());
-int length=item->GetEntryLength(0x01e1,0x1018)/sizeof(T);
-std::ofstream text_file(args_info.OutputFile_arg, std::ios::out | std::ios::trunc);
-if(text_file)
+bool wave2stream( std::ostream &text_file, const short *buffer, int length )
 {
-    std::string stat="";
-    text_file << "COMPLETE_WAVE" << '\t' << "MASK"       << '\t' << "AQUISITION_PROFIL" << '\t' << "END-INHALE" << '\t' << "END-EXHALE" << '\t' << "AQUISITION_WAVE" << '\t' << "WAVE_STATISTICS" << '\t' << "MASK"        << std::endl;
-    for (int i=0;i<length-76;i+=2)
+  std::string stat="";
+  text_file << "COMPLETE_WAVE" << '\t' << "MASK"       << '\t' << "AQUISITION_PROFIL" << '\t' << "END-INHALE" << '\t' << "END-EXHALE" << '\t' << "AQUISITION_WAVE" << '\t' << "WAVE_STATISTICS" << '\t' << "MASK"        << std::endl;
+  for (int i=0;i<length-76;i+=2)
     {
-	    if ( i < 74 )
-	    {
-		    switch(i)
-		    {
-		      case 68 :
-			stat="Total points";
-			break;
-		      case 70 :
-			stat="Sampling rate (Hz)";
-			break;
-		      default :
-			stat="";
-			break;
-		    }
-		      
-		    if (buffer[i+75] == 0)
-			text_file << buffer[i+74]    << '\t' << buffer[i+75] << '\t' << 0                   << '\t' << "  "         << '\t' << "  "         << '\t' << "  "              << '\t' << buffer[i]         << '\t' << buffer[i+1] << '\t' << stat << std::endl;
-		    if (buffer[i+75] == 16384)
-			text_file << buffer[i+74]    << '\t' << buffer[i+75] << '\t' << 0                   << '\t' << buffer[i+74] << '\t' << "  "         << '\t' << "  "              << '\t' << buffer[i]         << '\t' << buffer[i+1] << '\t' << stat << std::endl;
-		    if (buffer[i+75] == 256)
-			text_file << buffer[i+74]    << '\t' << buffer[i+75] << '\t' << 0                   << '\t' << "  "         << '\t' << buffer[i+74] << '\t' << "  "              << '\t' << buffer[i]         << '\t' << buffer[i+1] << '\t' << stat << std::endl;
-		    if (buffer[i+75] == -32768)
-			text_file << buffer[i+74]    << '\t' << buffer[i+75] << '\t' << 1                   << '\t' << "  "         << '\t' << "  "         << '\t' << buffer[i+74]      << '\t' << buffer[i]         << '\t' << buffer[i+1] << '\t' << stat << std::endl;
-		    if (buffer[i+75] == -16384)
-			text_file << buffer[i+74]    << '\t' << buffer[i+75] << '\t' << 1                   << '\t' << buffer[i+74] << '\t' << "  "         << '\t' << buffer[i+74]      << '\t' << buffer[i]         << '\t' << buffer[i+1] << '\t' << stat << std::endl;
-		    if (buffer[i+75] == -32512)
-			text_file << buffer[i+74]    << '\t' << buffer[i+75] << '\t' << 1                   << '\t' << "  "         << '\t' << buffer[i+74] << '\t' << buffer[i+74]      << '\t' << buffer[i]         << '\t' << buffer[i+1] << '\t' << stat << std::endl;
-	    }
-	    else
-	    {
-		    if (buffer[i+75] == 0)
-			text_file << buffer[i+74]    << '\t' << buffer[i+75] << '\t' << 0                   << '\t' << "  "         << '\t' << "  "         << '\t' << "  "              << '\t' << "  "              << '\t' << "  "        << std::endl;
-		    if (buffer[i+75] == 16384)
-			text_file << buffer[i+74]    << '\t' << buffer[i+75] << '\t' << 0                   << '\t' << buffer[i+74] << '\t' << "  "         << '\t' << "  "              << '\t' << "  "              << '\t' << "  "        << std::endl;
-		    if (buffer[i+75] == 256)
-			text_file << buffer[i+74]    << '\t' << buffer[i+75] << '\t' << 0                   << '\t' << "  "         << '\t' << buffer[i+74] << '\t' << "  "              << '\t' << "  "              << '\t' << "  "        << std::endl;
-		    if (buffer[i+75] == -32768)
-			text_file << buffer[i+74]    << '\t' << buffer[i+75] << '\t' << 1                   << '\t' << "  "         << '\t' << "  "         << '\t' << buffer[i+74]      << '\t' << "  "              << '\t' << "  "        << std::endl;
-		    if (buffer[i+75] == -16384)
-			text_file << buffer[i+74]    << '\t' << buffer[i+75] << '\t' << 1                   << '\t' << buffer[i+74] << '\t' << "  "         << '\t' << buffer[i+74]      << '\t' << "  "              << '\t' << "  "        << std::endl;
-		    if (buffer[i+75] == -32512)
-			text_file << buffer[i+74]    << '\t' << buffer[i+75] << '\t' << 1                   << '\t' << "  "         << '\t' << buffer[i+74] << '\t' << buffer[i+74]      << '\t' << "  "              << '\t' << "  "        << std::endl;
-	    }
+    if ( i < 74 )
+      {
+      switch(i)
+	{
+	case 68 :
+	  stat="Total points";
+	  break;
+	case 70 :
+	  stat="Sampling rate (Hz)";
+	  break;
+	default :
+	  stat="";
+	  break;
+	}      
+	if (buffer[i+75] == 0)
+	  text_file << buffer[i+74]    << '\t' << buffer[i+75] << '\t' << 0                   << '\t' << "  "         << '\t' << "  "         << '\t' << "  "              << '\t' << buffer[i]         << '\t' << buffer[i+1] << '\t' << stat << std::endl;
+	if (buffer[i+75] == 16384)
+	  text_file << buffer[i+74]    << '\t' << buffer[i+75] << '\t' << 0                   << '\t' << buffer[i+74] << '\t' << "  "         << '\t' << "  "              << '\t' << buffer[i]         << '\t' << buffer[i+1] << '\t' << stat << std::endl;
+	if (buffer[i+75] == 256)
+	  text_file << buffer[i+74]    << '\t' << buffer[i+75] << '\t' << 0                   << '\t' << "  "         << '\t' << buffer[i+74] << '\t' << "  "              << '\t' << buffer[i]         << '\t' << buffer[i+1] << '\t' << stat << std::endl;
+	if (buffer[i+75] == -32768)
+	  text_file << buffer[i+74]    << '\t' << buffer[i+75] << '\t' << 1                   << '\t' << "  "         << '\t' << "  "         << '\t' << buffer[i+74]      << '\t' << buffer[i]         << '\t' << buffer[i+1] << '\t' << stat << std::endl;
+	if (buffer[i+75] == -16384)
+	  text_file << buffer[i+74]    << '\t' << buffer[i+75] << '\t' << 1                   << '\t' << buffer[i+74] << '\t' << "  "         << '\t' << buffer[i+74]      << '\t' << buffer[i]         << '\t' << buffer[i+1] << '\t' << stat << std::endl;
+	if (buffer[i+75] == -32512)
+	  text_file << buffer[i+74]    << '\t' << buffer[i+75] << '\t' << 1                   << '\t' << "  "         << '\t' << buffer[i+74] << '\t' << buffer[i+74]      << '\t' << buffer[i]         << '\t' << buffer[i+1] << '\t' << stat << std::endl;
+      }
+      else
+      {
+	if (buffer[i+75] == 0)
+	  text_file << buffer[i+74]    << '\t' << buffer[i+75] << '\t' << 0                   << '\t' << "  "         << '\t' << "  "         << '\t' << "  "              << '\t' << "  "              << '\t' << "  "        << std::endl;
+	if (buffer[i+75] == 16384)
+	  text_file << buffer[i+74]    << '\t' << buffer[i+75] << '\t' << 0                   << '\t' << buffer[i+74] << '\t' << "  "         << '\t' << "  "              << '\t' << "  "              << '\t' << "  "        << std::endl;
+	if (buffer[i+75] == 256)
+	  text_file << buffer[i+74]    << '\t' << buffer[i+75] << '\t' << 0                   << '\t' << "  "         << '\t' << buffer[i+74] << '\t' << "  "              << '\t' << "  "              << '\t' << "  "        << std::endl;
+	if (buffer[i+75] == -32768)
+	  text_file << buffer[i+74]    << '\t' << buffer[i+75] << '\t' << 1                   << '\t' << "  "         << '\t' << "  "         << '\t' << buffer[i+74]      << '\t' << "  "              << '\t' << "  "        << std::endl;
+	if (buffer[i+75] == -16384)
+	  text_file << buffer[i+74]    << '\t' << buffer[i+75] << '\t' << 1                   << '\t' << buffer[i+74] << '\t' << "  "         << '\t' << buffer[i+74]      << '\t' << "  "              << '\t' << "  "        << std::endl;
+	if (buffer[i+75] == -32512)
+	  text_file << buffer[i+74]    << '\t' << buffer[i+75] << '\t' << 1                   << '\t' << "  "         << '\t' << buffer[i+74] << '\t' << buffer[i+74]      << '\t' << "  "              << '\t' << "  "        << std::endl;
+      }
     }
-    text_file.close();
+  return true;
 }
-else
-    std::cerr << "Error openning "<< args_info.OutputFile_arg << std::endl;
-#else
-    std::cerr << argv[0] << " is not compatible with GDCM 2.x you should use GDCM 1.x" << std::endl;
-    return 1;
-#endif
+
+
+int main(int argc, char * argv[])
+{
+  GGO(clitkDicomWave2Text, args_info);
+  
+  std::ofstream os(args_info.OutputFile_arg, std::ios::out | std::ios::trunc);
+  
+  #if GDCM_MAJOR_VERSION < 2
+  
+    gdcm::File * mDCMFile = new gdcm::File();
+    mDCMFile->SetFileName(args_info.InputFile_arg);
+    mDCMFile->AddForceLoadElement(0x01e1,0x1018); //Load wave data no matter its size
+    if ( !mDCMFile->OpenFile() )
+      {
+      std::cerr << "Failed to read: " << args_info.InputFile_arg << std::endl;
+      return 1;
+      }
+    mDCMFile->Load();
+    gdcm::DocEntrySet* item = mDCMFile;
+    #define T short
+    gdcm::BinEntry * entry = item->GetBinEntry(0x01e1,0x1018);
+    T* buffer = reinterpret_cast<T*>(entry->GetBinArea());
+    int length=item->GetEntryLength(0x01e1,0x1018)/sizeof(T);
+    
+  #else
+  
+    gdcm::Reader reader;
+    reader.SetFileName(args_info.InputFile_arg);
+    if( !reader.Read() )
+      {
+      std::cerr << "Failed to read: " << args_info.InputFile_arg << std::endl;
+      return 1;
+      }
+    const gdcm::DataSet& ds = reader.GetFile().GetDataSet();
+    const gdcm::PrivateTag twave(0x01e1,0x18,"ELSCINT1");
+    if( !ds.FindDataElement( twave ) ) return 1;
+    const gdcm::DataElement& wave = ds.GetDataElement( twave );
+    if ( wave.IsEmpty() ) return 1;
+    const gdcm::ByteValue * bv = wave.GetByteValue();
+    short * buffer = (short*)bv->GetPointer();
+    int length = bv->GetLength() / sizeof( short );
+    
+  #endif
+  
+  // Dump that to a CSV file:
+  wave2stream( os, buffer, length );
+  os.close();
+  return 0;
 }