[Gdcm-hackers] gdcm-git:Grassroots DICOM branch master updated. f40d2cc12477b80e68e0ce177c67eb10ff34aab5

[Mathieu M. <ma...@us...>]

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https://sourceforge.net/p/gdcm/gdcm/ci/f40d2cc12477b80e68e0ce177c67eb10ff34aab5/

commit f40d2cc12477b80e68e0ce177c67eb10ff34aab5
Author: Mathieu Malaterre <mat...@gm...>
Date:   Wed Dec 19 16:33:55 2012 +0100

    Provide an implementation of a file-based anonymizer
    
    The current gdcm::Anonymizer class suffer from the 'DOM' design selected in GDCM.
    This means that a DataSet needs to be completly held in memory before empty/remove/replac'ing any of its attribute.
    This does not work well in all cases, esp limited 32bits java VM. By providing a file based anonymizer
    user is now able to realize limited functionalities such as empty/remove/replac'ing attribute directly on file.

diff --git a/Examples/Csharp/CMakeLists.txt b/Examples/Csharp/CMakeLists.txt
index 3e1b627..83ae92a 100644
--- a/Examples/Csharp/CMakeLists.txt
+++ b/Examples/Csharp/CMakeLists.txt
@@ -22,6 +22,7 @@ set(CSHARP_EXAMPLES
   CompressLossyJPEG
   SendFileSCU
   MpegVideoInfo
+  FileAnonymize
   )
 
 if(BUILD_TESTING)
diff --git a/Examples/Csharp/FileAnonymize.cs b/Examples/Csharp/FileAnonymize.cs
new file mode 100644
index 0000000..526aed9
--- /dev/null
+++ b/Examples/Csharp/FileAnonymize.cs
@@ -0,0 +1,56 @@
+/*=========================================================================
+
+  Program: GDCM (Grassroots DICOM). A DICOM library
+
+  Copyright (c) 2006-2011 Mathieu Malaterre
+  All rights reserved.
+  See Copyright.txt or http://gdcm.sourceforge.net/Copyright.html for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notice for more information.
+
+=========================================================================*/
+
+/*
+ * Simple C# example
+ *
+ * Usage:
+ * $ mono bin/FileAnonymize.exe input.dcm output.dcm
+ */
+using System;
+using gdcm;
+
+public class FileAnonymize
+{
+  public static int Main(string[] args)
+    {
+    string filename = args[0];
+    string outfilename = args[1];
+
+    gdcm.FileAnonymizer fa = new gdcm.FileAnonymizer();
+    fa.SetInputFileName( filename );
+    fa.SetOutputFileName( outfilename );
+
+    // Empty Operations
+    // It will create elements, since those tags are non-registered public elements (2011):
+    fa.Empty( new Tag(0x0008,0x1313) );
+    fa.Empty( new Tag(0x0008,0x1317) );
+    // Remove Operations
+    // The following Tag are actually carefully chosen, since they refer to SQ:
+    fa.Remove( new Tag(0x0008,0x2112) );
+    fa.Remove( new Tag(0x0008,0x9215) );
+    // Replace Operations
+    // do not call replace operation on SQ attribute !
+    fa.Replace( new Tag(0x0018,0x5100), "MYVALUE " );
+    fa.Replace( new Tag(0x0008,0x1160), "MYOTHERVAL" );
+
+    if( !fa.Write() )
+      {
+      System.Console.WriteLine( "Could not write" );
+      return 1;
+      }
+
+    return 0;
+    }
+}
diff --git a/Examples/Cxx/CMakeLists.txt b/Examples/Cxx/CMakeLists.txt
index c9e28b8..4e38525 100644
--- a/Examples/Cxx/CMakeLists.txt
+++ b/Examples/Cxx/CMakeLists.txt
@@ -26,7 +26,6 @@ mark_as_advanced(QT_QMAKE_EXECUTABLE)
 endif()
 
 set(EXAMPLES_SRCS
-  RemoveInPlace
   DumpGEMSMovieGroup
   DumpExamCard
   ExtractIconFromFile
diff --git a/Examples/Cxx/RemoveInPlace.cxx b/Examples/Cxx/RemoveInPlace.cxx
deleted file mode 100644
index 73c096b..0000000
--- a/Examples/Cxx/RemoveInPlace.cxx
+++ /dev/null
@@ -1,127 +0,0 @@
-/*=========================================================================
-
-  Program: GDCM (Grassroots DICOM). A DICOM library
-
-  Copyright (c) 2006-2011 Mathieu Malaterre
-  All rights reserved.
-  See Copyright.txt or http://gdcm.sourceforge.net/Copyright.html for details.
-
-     This software is distributed WITHOUT ANY WARRANTY; without even
-     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-     PURPOSE.  See the above copyright notice for more information.
-
-=========================================================================*/
-#include "gdcmReader.h"
-#include "gdcmTag.h"
-#include "gdcmDataElement.h"
-
-#include <fstream>
-
-/*
- * A very simple example to anonymize in place.
- * Let's assume you cannot afford the memory consumption required
- * by gdcmanon --dumb, you could use this example to 'empty' some
- * tags.
- */
-int main(int argc, char *argv[])
-{
-  if( argc < 3 )
-    {
-    std::cerr << argv[0] << " input.dcm output.dcm" << std::endl;
-    return 1;
-    }
-  using namespace gdcm;
-
-  // Step 1. Get the offset
-  const char *filename = argv[1];
-  const char *outfilename = argv[2];
-
-  std::ifstream is( filename, std::ios::binary );
-
-  gdcm::Tag t1(0x0018,0x0022);
-  gdcm::Tag t2(0x0028,0x0002);
-  //gdcm::Tag t(0x0025,0x100a);
-  const gdcm::Tag &t = t2;
-  std::set<gdcm::Tag> removeme;
-  removeme.insert( t1 );
-
-  gdcm::Reader reader;
-  reader.SetStream( is );
-  if( !reader.ReadSelectedTags( removeme ) )
-    {
-    // not DICOM ?
-    return 1;
-    }
-  std::streampos pos0 = is.tellg();
-
-  const File & f = reader.GetFile();
-  const DataSet &ds = f.GetDataSet();
-
-#if 0
-  if( ds.FindDataElement( t1 ) )
-    {
-    const DataElement &de = ds.GetDataElement( t1 );
-    // skip value:
-    if( de.GetVL().IsUndefined() )
-      {
-      // TODO
-      assert( 0 );
-      }
-    else
-      {
-      is.seekg( de.GetVL(), std::ios::cur );
-      }
-    }
-#endif
-  removeme.clear();
-  removeme.insert( t2 );
-
-  std::streampos pos1 = is.tellg();
-
-  if( !reader.ReadSelectedTags( removeme ) )
-    {
-    // not DICOM ?
-    return 1;
-    }
-  std::streampos pos = is.tellg();
-  is.close();
-
-  // Step 2. Copy & skip proper portion
-  std::ofstream of( outfilename, std::ios::binary );
-  std::ifstream is2( filename, std::ios::binary );
-  if( ds.FindDataElement( t ) )
-    {
-    const DataElement &de = ds.GetDataElement( t );
-    int vrlen = de.GetVR().GetLength();
-
-    if( de.GetVL().IsUndefined() )
-      {
-      // TODO
-      assert( 0 );
-      }
-    else
-      {
-      std::streampos end = pos;
-      // seek back:
-      end -= de.GetVL();
-      end -= vrlen;
-
-      // FIXME: most efficient way to copy chunk of file in c++ ?
-      for( int i = 0; i < end; ++ i)
-        {
-        of.put( is2.get() );
-        }
-      for( int i = 0; i < vrlen; ++ i)
-        {
-        of.put( 0 );
-        }
-      is2.seekg( de.GetVL() + vrlen, std::ios::cur );
-      }
-    }
-
-  of << is2.rdbuf();
-  of.close();
-  is2.close();
-
-  return 0;
-}
diff --git a/Source/DataStructureAndEncodingDefinition/gdcmDataSet.txx b/Source/DataStructureAndEncodingDefinition/gdcmDataSet.txx
index f37b86d..d6fcf72 100644
--- a/Source/DataStructureAndEncodingDefinition/gdcmDataSet.txx
+++ b/Source/DataStructureAndEncodingDefinition/gdcmDataSet.txx
@@ -125,6 +125,16 @@ namespace gdcm
         const Tag& tag = dataElem.GetTag();
         if ( inputStream.fail() || maxTag < tag )
           {
+          if( inputStream.good() )
+            {
+            const int l = dataElem.GetVR().GetLength();
+            inputStream.seekg( - 4 - 2 * l, std::ios::cur );
+            }
+          else
+            {
+            inputStream.clear();
+            inputStream.seekg( 0, std::ios::end );
+            }
           // Failed to read the tag, or the read tag exceeds the maximum.
           // As we assume ascending tag ordering, we can exit the loop.
           break;
@@ -181,6 +191,16 @@ namespace gdcm
           const Tag tag = dataElem.GetTag();
           if ( inputStream.fail() || maxTag < tag )
             {
+            if( inputStream.good() )
+              {
+              const int l = dataElem.GetVR().GetLength();
+              inputStream.seekg( - 4 - 2 * l, std::ios::cur );
+              }
+            else
+              {
+              inputStream.clear();
+              inputStream.seekg( 0, std::ios::end );
+              }
             // Failed to read the tag, or the read tag exceeds the maximum.
             // As we assume ascending tag ordering, we can exit the loop.
             break;
diff --git a/Source/MediaStorageAndFileFormat/CMakeLists.txt b/Source/MediaStorageAndFileFormat/CMakeLists.txt
index de172b9..43eb0a6 100644
--- a/Source/MediaStorageAndFileFormat/CMakeLists.txt
+++ b/Source/MediaStorageAndFileFormat/CMakeLists.txt
@@ -2,6 +2,7 @@
 # MSFF
 set(MSFF_SRCS
   gdcmAnonymizer.cxx
+  gdcmFileAnonymizer.cxx
   gdcmIconImageFilter.cxx
   gdcmIconImageGenerator.cxx
   gdcmDICOMDIRGenerator.cxx
diff --git a/Source/MediaStorageAndFileFormat/gdcmFileAnonymizer.cxx b/Source/MediaStorageAndFileFormat/gdcmFileAnonymizer.cxx
new file mode 100644
index 0000000..d3be0cd
--- /dev/null
+++ b/Source/MediaStorageAndFileFormat/gdcmFileAnonymizer.cxx
@@ -0,0 +1,518 @@
+/*=========================================================================
+
+  Program: GDCM (Grassroots DICOM). A DICOM library
+
+  Copyright (c) 2006-2011 Mathieu Malaterre
+  All rights reserved.
+  See Copyright.txt or http://gdcm.sourceforge.net/Copyright.html for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notice for more information.
+
+=========================================================================*/
+#include "gdcmFileAnonymizer.h"
+
+#include "gdcmReader.h"
+
+#include <fstream>
+#include <set>
+#include <vector>
+#include <map>
+#include <algorithm> // sort
+
+namespace gdcm
+{
+
+enum Action
+{
+  EMPTY,
+  REMOVE,
+  REPLACE
+};
+
+struct PositionEmpty
+{
+  std::streampos BeginPos;
+  std::streampos EndPos;
+  Action action;
+  bool IsTagFound; // Required for EMPTY
+  DataElement DE;
+  bool operator() (const PositionEmpty & i, const PositionEmpty & j)
+    {
+    return (int)i.BeginPos < (int)j.BeginPos;
+    }
+};
+
+class FileAnonymizerInternals
+{
+public:
+  std::string InputFilename;
+  std::string OutputFilename;
+  std::set<Tag> EmptyTags;
+  std::set<Tag> RemoveTags;
+  std::map<Tag, std::string> ReplaceTags;
+  TransferSyntax TS;
+  std::vector<PositionEmpty> PositionEmptyArray;
+};
+
+FileAnonymizer::FileAnonymizer()
+{
+  Internals = new FileAnonymizerInternals;
+}
+
+FileAnonymizer::~FileAnonymizer()
+{
+  delete Internals;
+}
+
+void FileAnonymizer::Empty( Tag const &t )
+{
+  if( t.GetGroup() >= 0x0008 )
+    {
+    Internals->EmptyTags.insert( t );
+    }
+}
+
+void FileAnonymizer::Remove( Tag const &t )
+{
+  if( t.GetGroup() >= 0x0008 )
+    {
+    Internals->RemoveTags.insert( t );
+    }
+}
+
+void FileAnonymizer::Replace( Tag const &t, const char *value )
+{
+  if( t.GetGroup() >= 0x0008 )
+    {
+    Internals->ReplaceTags.insert(
+      std::make_pair<Tag,std::string>( t, value) );
+    }
+}
+
+void FileAnonymizer::Replace( Tag const &t, const char *value, VL const & vl )
+{
+  Internals->ReplaceTags.insert( std::make_pair<Tag,std::string>( t, std::string(value,vl) ) );
+}
+
+void FileAnonymizer::SetInputFileName(const char *filename_native)
+{
+  Internals->InputFilename = filename_native;
+}
+
+void FileAnonymizer::SetOutputFileName(const char *filename_native)
+{
+  Internals->OutputFilename = filename_native;
+}
+
+bool FileAnonymizer::ComputeReplaceTagPosition()
+{
+/*
+ Implementation details:
+ We should make sure that the user know what she is doing in case of SQ.
+ Let's assume a User call Replace( Tag(0x0008,0x2112), "FOOBAR" )
+ For quite a lot of DICOM implementation this Tag is required to be a SQ.
+ Therefore even if the Attribute is declared with VR:UN, some implementation
+ will try very hard to decode it as SQ...which obviously will fail
+ Instead do not support SQ at all here and document it should not be used for SQ
+ */
+  assert( !Internals->InputFilename.empty() );
+  const char *filename = Internals->InputFilename.c_str();
+  assert( filename );
+
+  std::map<Tag, std::string>::reverse_iterator rit = Internals->ReplaceTags.rbegin();
+  for ( ; rit != Internals->ReplaceTags.rend(); rit++ )
+    {
+    PositionEmpty pe;
+
+    std::set<Tag> removeme;
+    const Tag & t = rit->first;
+    const std::string & valuereplace = rit->second;
+    removeme.insert( t );
+
+    std::ifstream is( filename, std::ios::binary );
+    Reader reader;
+    reader.SetStream( is );
+    if( !reader.ReadSelectedTags( removeme ) )
+      {
+      return false;
+      }
+
+    pe.EndPos = pe.BeginPos = is.tellg();
+    pe.action = REPLACE;
+    pe.IsTagFound = false;
+    const File & f = reader.GetFile();
+    const DataSet &ds = f.GetDataSet();
+    const TransferSyntax &ts = f.GetHeader().GetDataSetTransferSyntax();
+    Internals->TS = ts;
+
+    pe.DE.SetTag( t );
+    if( ds.FindDataElement( t ) )
+      {
+      const DataElement &de = ds.GetDataElement( t );
+      pe.IsTagFound = true;
+      pe.DE.SetVL( de.GetVL() ); // Length is not used, unless to check undefined flag
+      pe.DE.SetVR( de.GetVR() );
+      assert( pe.DE.GetVL().IsUndefined() == de.GetVL().IsUndefined() );
+      assert( pe.DE.GetVR() == de.GetVR() );
+      assert( pe.DE.GetTag() == de.GetTag() );
+      if( de.GetVL().IsUndefined() )
+        {
+        // This is a SQ
+        gdcmErrorMacro( "Replacing a SQ is not supported. Use Remove() or Empty()" );
+        return false;
+        }
+      else
+        {
+        assert( !de.GetVL().IsUndefined() );
+        pe.BeginPos -= de.GetVL();
+        pe.BeginPos -= 2 * de.GetVR().GetLength(); // (VR+) VL
+        pe.BeginPos -= 4; // Tag
+        assert( pe.EndPos ==
+          (int)pe.BeginPos + (int)de.GetVL() + 2 * de.GetVR().GetLength() + 4 );
+        }
+      pe.DE.SetByteValue( valuereplace.c_str(), valuereplace.size() );
+      assert( pe.DE.GetVL() == valuereplace.size() );
+      }
+    else
+      {
+      // We need to insert an Empty Data Element !
+      //FIXME, for some public element we could do something nicer than VR:UN
+      pe.DE.SetVR( VR::UN );
+      pe.DE.SetByteValue( valuereplace.c_str(), valuereplace.size() );
+      assert( pe.DE.GetVL() == valuereplace.size() );
+      }
+
+    // We need to push_back outside of if() since Action:Empty
+    // on a missing tag, means insert it !
+    Internals->PositionEmptyArray.push_back( pe );
+
+    is.close();
+    }
+  return true;
+}
+
+bool FileAnonymizer::ComputeRemoveTagPosition()
+{
+  assert( !Internals->InputFilename.empty() );
+  const char *filename = Internals->InputFilename.c_str();
+  assert( filename );
+
+  std::set<Tag>::reverse_iterator rit = Internals->RemoveTags.rbegin();
+  for ( ; rit != Internals->RemoveTags.rend(); rit++ )
+    {
+    PositionEmpty pe;
+
+    std::set<Tag> removeme;
+    const Tag & t = *rit;
+    removeme.insert( t );
+
+    std::ifstream is( filename, std::ios::binary );
+    Reader reader;
+    reader.SetStream( is );
+    if( !reader.ReadSelectedTags( removeme ) )
+      {
+      return false;
+      }
+
+    pe.EndPos = pe.BeginPos = is.tellg();
+    pe.action = REMOVE;
+    pe.IsTagFound = false;
+    const File & f = reader.GetFile();
+    const DataSet &ds = f.GetDataSet();
+    const TransferSyntax &ts = f.GetHeader().GetDataSetTransferSyntax();
+    Internals->TS = ts;
+
+    pe.DE.SetTag( t );
+    if( ds.FindDataElement( t ) )
+      {
+      const DataElement &de = ds.GetDataElement( t );
+      pe.IsTagFound = true;
+      pe.DE.SetVL( de.GetVL() ); // Length is not used, unless to check undefined flag
+      pe.DE.SetVR( de.GetVR() );
+      assert( pe.DE.GetVL().IsUndefined() == de.GetVL().IsUndefined() );
+      assert( pe.DE.GetVR() == de.GetVR() );
+      assert( pe.DE.GetTag() == de.GetTag() );
+      if( de.GetVL().IsUndefined() )
+        {
+        // This is a SQ
+        VL vl;
+        if( ts.GetNegociatedType() == TransferSyntax::Implicit )
+          {
+          vl = de.GetLength<ImplicitDataElement>();
+          }
+        else
+          {
+          vl = de.GetLength<ExplicitDataElement>();
+          }
+        assert( pe.BeginPos > vl );
+        pe.BeginPos -= vl;
+        }
+      else
+        {
+        assert( !de.GetVL().IsUndefined() );
+        pe.BeginPos -= de.GetVL();
+        pe.BeginPos -= 2 * de.GetVR().GetLength(); // (VR+) VL
+        pe.BeginPos -= 4; // Tag
+        assert( pe.EndPos ==
+          (int)pe.BeginPos + (int)de.GetVL() + 2 * de.GetVR().GetLength() + 4 );
+        }
+      Internals->PositionEmptyArray.push_back( pe );
+      }
+    else
+      {
+      // Yay no need to do anything !
+      }
+
+    is.close();
+    }
+
+  return true;
+}
+
+bool FileAnonymizer::ComputeEmptyTagPosition()
+{
+  // FIXME we sometime empty, attributes that are already empty...
+  assert( !Internals->InputFilename.empty() );
+  const char *filename = Internals->InputFilename.c_str();
+  assert( filename );
+
+  std::set<Tag>::reverse_iterator rit = Internals->EmptyTags.rbegin();
+  for ( ; rit != Internals->EmptyTags.rend(); rit++ )
+    {
+    PositionEmpty pe;
+
+    std::set<Tag> removeme;
+    const Tag & t = *rit;
+    removeme.insert( t );
+
+    std::ifstream is( filename, std::ios::binary );
+    Reader reader;
+    reader.SetStream( is );
+    if( !reader.ReadSelectedTags( removeme ) )
+      {
+      return false;
+      }
+
+    pe.EndPos = pe.BeginPos = is.tellg();
+    pe.action = EMPTY;
+    pe.IsTagFound = false;
+    const File & f = reader.GetFile();
+    const DataSet &ds = f.GetDataSet();
+    const TransferSyntax &ts = f.GetHeader().GetDataSetTransferSyntax();
+    Internals->TS = ts;
+
+    pe.DE.SetTag( t );
+    if( ds.FindDataElement( t ) )
+      {
+      const DataElement &de = ds.GetDataElement( t );
+      pe.IsTagFound = true;
+      pe.DE.SetVL( de.GetVL() ); // Length is not used, unless to check undefined flag
+      pe.DE.SetVR( de.GetVR() );
+      assert( pe.DE.GetVL().IsUndefined() == de.GetVL().IsUndefined() );
+      assert( pe.DE.GetVR() == de.GetVR() );
+      assert( pe.DE.GetTag() == de.GetTag() );
+      if( de.GetVL().IsUndefined() )
+        {
+        // This is a SQ
+        VL vl;
+        if( ts.GetNegociatedType() == TransferSyntax::Implicit )
+          {
+          vl = de.GetLength<ImplicitDataElement>();
+          }
+        else
+          {
+          vl = de.GetLength<ExplicitDataElement>();
+          }
+        assert( pe.BeginPos > vl );
+        pe.BeginPos -= vl;
+        pe.BeginPos += 4; // Tag
+        if( ts.GetNegociatedType() == TransferSyntax::Implicit )
+          {
+          pe.BeginPos += 0;
+          }
+        else
+          {
+          pe.BeginPos += de.GetVR().GetLength();
+          }
+        }
+      else
+        {
+        assert( !de.GetVL().IsUndefined() );
+        pe.BeginPos -= de.GetVL();
+        if( ts.GetNegociatedType() == TransferSyntax::Implicit )
+          {
+          pe.BeginPos -= 4;
+          }
+        else
+          {
+          pe.BeginPos -= de.GetVR().GetLength();
+          assert( pe.EndPos ==
+            (int)pe.BeginPos + (int)de.GetVL() + de.GetVR().GetLength() );
+          }
+        }
+      }
+    else
+      {
+      // We need to insert an Empty Data Element !
+      //FIXME, for some public element we could do something nicer than VR:UN
+      pe.DE.SetVR( VR::UN );
+      pe.DE.SetVL( 0 );
+      }
+
+    // We need to push_back outside of if() since Action:Empty
+    // on a missing tag, means insert it !
+    Internals->PositionEmptyArray.push_back( pe );
+
+    is.close();
+    }
+
+  return true;
+}
+
+bool FileAnonymizer::Write()
+{
+  if( Internals->OutputFilename.empty() ) return false;
+  const char *outfilename = Internals->OutputFilename.c_str();
+  if( Internals->InputFilename.empty() ) return false;
+  const char *filename = Internals->InputFilename.c_str();
+
+  Internals->PositionEmptyArray.clear();
+
+  // Compute offsets
+  if( !ComputeRemoveTagPosition()
+    || !ComputeEmptyTagPosition()
+    || !ComputeReplaceTagPosition() )
+    {
+    return false;
+    }
+
+  // Make sure we will copy from lower offset to highest:
+  PositionEmpty pe_sort;
+  std::sort (Internals->PositionEmptyArray.begin(),
+    Internals->PositionEmptyArray.end(), pe_sort);
+
+  // Step 2. Copy & skip proper portion
+  std::ofstream of( outfilename, std::ios::binary );
+  std::ifstream is( filename, std::ios::binary );
+  std::vector<PositionEmpty>::const_iterator it =
+    Internals->PositionEmptyArray.begin();
+  std::streampos prev = 0;
+  const TransferSyntax &ts = Internals->TS;
+  for( ; it != Internals->PositionEmptyArray.end(); ++it )
+    {
+    const PositionEmpty & pe = *it;
+    Action action = pe.action;
+
+    if( pe.IsTagFound )
+      {
+      const DataElement & de = pe.DE;
+      int vrlen = de.GetVR().GetLength();
+      if( ts.GetNegociatedType() == TransferSyntax::Implicit )
+        {
+        vrlen = 4;
+        }
+
+      std::streampos end = pe.BeginPos;
+
+      // FIXME: most efficient way to copy chunk of file in c++ ?
+      for( int i = prev; i < end; ++i)
+        {
+        of.put( is.get() );
+        }
+      if( action == EMPTY )
+        {
+        // Create a 0 Value Length (VR+Tag was copied in previous loop)
+        for( int i = 0; i < vrlen; ++i)
+          {
+          of.put( 0 );
+          }
+        }
+      else if( action == REPLACE )
+        {
+        if( ts.GetSwapCode() == SwapCode::BigEndian )
+          {
+          if( ts.GetNegociatedType() == TransferSyntax::Implicit )
+            {
+            gdcmErrorMacro( "Cant write Virtual Big Endian" );
+            return 1;
+            }
+          else
+            {
+            pe.DE.Write<ExplicitDataElement,SwapperDoOp>( of );
+            }
+          }
+        else
+          {
+          if( ts.GetNegociatedType() == TransferSyntax::Implicit )
+            {
+            pe.DE.Write<ImplicitDataElement,SwapperNoOp>( of );
+            }
+          else
+            {
+            pe.DE.Write<ExplicitDataElement,SwapperNoOp>( of );
+            }
+          }
+        }
+      // Skip the Value
+      assert( is.good() );
+      is.seekg( pe.EndPos );
+      assert( is.good() );
+      prev = is.tellg();
+      assert( prev == pe.EndPos );
+      }
+    else
+      {
+      std::streampos end = pe.BeginPos;
+
+      // FIXME: most efficient way to copy chunk of file in c++ ?
+      for( int i = prev; i < end; ++i)
+        {
+        of.put( is.get() );
+        }
+      if( ts.GetSwapCode() == SwapCode::BigEndian )
+        {
+        if( ts.GetNegociatedType() == TransferSyntax::Implicit )
+          {
+          gdcmErrorMacro( "Cant write Virtual Big Endian" );
+          return 1;
+          }
+        else
+          {
+          pe.DE.Write<ExplicitDataElement,SwapperDoOp>( of );
+          }
+        }
+      else
+        {
+        if( ts.GetNegociatedType() == TransferSyntax::Implicit )
+          {
+          pe.DE.Write<ImplicitDataElement,SwapperNoOp>( of );
+          }
+        else
+          {
+          pe.DE.Write<ExplicitDataElement,SwapperNoOp>( of );
+          }
+        }
+      prev = is.tellg();
+      }
+    }
+
+  of << is.rdbuf();
+  of.close();
+  is.close();
+
+#if 0
+  Reader r;
+  r.SetFileName( outfilename );
+  if( !r.Read() )
+    {
+    gdcmErrorMacro( "Output file got corrupted, please report" );
+    return false;
+    }
+#endif
+
+  return true;
+}
+
+} // end namespace gdcm
diff --git a/Source/MediaStorageAndFileFormat/gdcmFileAnonymizer.h b/Source/MediaStorageAndFileFormat/gdcmFileAnonymizer.h
new file mode 100644
index 0000000..cd9db52
--- /dev/null
+++ b/Source/MediaStorageAndFileFormat/gdcmFileAnonymizer.h
@@ -0,0 +1,83 @@
+/*=========================================================================
+
+  Program: GDCM (Grassroots DICOM). A DICOM library
+
+  Copyright (c) 2006-2011 Mathieu Malaterre
+  All rights reserved.
+  See Copyright.txt or http://gdcm.sourceforge.net/Copyright.html for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notice for more information.
+
+=========================================================================*/
+#ifndef GDCMFILEANONYMIZER_H
+#define GDCMFILEANONYMIZER_H
+
+#include "gdcmSubject.h"
+#include "gdcmEvent.h"
+#include "gdcmTag.h"
+#include "gdcmVL.h"
+
+namespace gdcm
+{
+class FileAnonymizerInternals;
+
+/**
+ * \brief FileAnonymizer
+ *
+ * This Anonymizer is a file-based Anonymizer. It requires a valid DICOM
+ * file and will use the Value Length to skip over any information.
+ *
+ * It will not load the data into memory and should consume much less
+ * memory than gdcm::Anonymizer
+ *
+ * caveats:
+ * This class will NOT work with unordered attributes in a DICOM File.
+ *
+ * This class does neither recompute nor update the Group Length element.
+ *
+ * This class currently does not update the File Meta Information header
+ */
+class GDCM_EXPORT FileAnonymizer : public Subject
+{
+public:
+  FileAnonymizer();
+  ~FileAnonymizer();
+
+  /// Make Tag t empty
+  /// Warning: does not handle SQ element
+  void Empty( Tag const &t );
+
+  /// remove a tag (even a SQ can be removed)
+  void Remove( Tag const &t );
+
+  /// Replace tag with another value, if tag is not found it will be created:
+  /// WARNING: this function can only execute if tag is a VRASCII
+  /// WARNING: Do not ever try to write a value in a SQ Data Element !
+  void Replace( Tag const &t, const char *value );
+
+  /// when the value contains \0, it is a good idea to specify the length. This function
+  /// is required when dealing with VRBINARY tag
+  void Replace( Tag const &t, const char *value, VL const & vl );
+
+  /// Set input filename
+  void SetInputFileName(const char *filename_native);
+
+  /// Set output filename
+  void SetOutputFileName(const char *filename_native);
+
+  /// Write the output file
+  bool Write();
+
+private:
+  bool ComputeEmptyTagPosition();
+  bool ComputeRemoveTagPosition();
+  bool ComputeReplaceTagPosition();
+  FileAnonymizerInternals *Internals;
+
+};
+
+} // end namespace gdcm
+
+#endif //GDCMFILEANONYMIZER_H
diff --git a/Testing/Source/MediaStorageAndFileFormat/Cxx/CMakeLists.txt b/Testing/Source/MediaStorageAndFileFormat/Cxx/CMakeLists.txt
index a4b17d1..1dc159f 100644
--- a/Testing/Source/MediaStorageAndFileFormat/Cxx/CMakeLists.txt
+++ b/Testing/Source/MediaStorageAndFileFormat/Cxx/CMakeLists.txt
@@ -2,6 +2,9 @@
 # MSFF
 set(MSFF_TEST_SRCS
   TestAnonymizer
+  TestFileAnonymizer1
+  TestFileAnonymizer2
+  TestFileAnonymizer3
   TestIconImageFilter
   TestIconImageGenerator
   TestIconImageGenerator2
diff --git a/Testing/Source/MediaStorageAndFileFormat/Cxx/TestFileAnonymizer1.cxx b/Testing/Source/MediaStorageAndFileFormat/Cxx/TestFileAnonymizer1.cxx
new file mode 100644
index 0000000..ef676f4
--- /dev/null
+++ b/Testing/Source/MediaStorageAndFileFormat/Cxx/TestFileAnonymizer1.cxx
@@ -0,0 +1,117 @@
+/*=========================================================================
+
+  Program: GDCM (Grassroots DICOM). A DICOM library
+
+  Copyright (c) 2006-2011 Mathieu Malaterre
+  All rights reserved.
+  See Copyright.txt or http://gdcm.sourceforge.net/Copyright.html for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notice for more information.
+
+=========================================================================*/
+#include "gdcmFileAnonymizer.h"
+
+#include "gdcmTesting.h"
+#include "gdcmSystem.h"
+#include "gdcmReader.h"
+
+int TestFileAnonymize1(const char *filename, bool verbose = false)
+{
+  using namespace gdcm;
+  if( verbose )
+    std::cout << "Processing: " << filename << std::endl;
+
+  // Create directory first:
+  const char subdir[] = "TestFileAnonymize1";
+  std::string tmpdir = Testing::GetTempDirectory( subdir );
+  if( !System::FileIsDirectory( tmpdir.c_str() ) )
+    {
+    System::MakeDirectory( tmpdir.c_str() );
+    //return 1;
+    }
+  std::string outfilename = Testing::GetTempFilename( filename, subdir );
+
+  gdcm::Tag t1(0x0018,0x5100);
+  gdcm::Tag t2(0x0018,0x1312);
+  gdcm::Tag t3(0x0018,0x1313);
+  gdcm::Tag t4(0x0018,0x1317);
+  gdcm::Tag t5(0x0008,0x2112);
+  gdcm::Tag t6(0x0008,0x9215);
+  gdcm::Tag t7(0x0018,0x1020);
+  gdcm::Tag t8(0x0004,0x1130); // Test DICOMDIR !
+  gdcm::Tag t9(0x0008,0x0000); // Earliest possible Data Element
+  gdcm::Tag t0(0xffff,0xffff); // Latest Possible Element
+
+  std::vector<gdcm::Tag> tags;
+  tags.push_back( t0 );
+  tags.push_back( t1 );
+  tags.push_back( t2 );
+  tags.push_back( t3 );
+  tags.push_back( t4 );
+  tags.push_back( t5 );
+  tags.push_back( t6 );
+  tags.push_back( t7 );
+  tags.push_back( t8 );
+  tags.push_back( t9 );
+
+  gdcm::FileAnonymizer fa;
+  fa.SetInputFileName( filename );
+  fa.SetOutputFileName( outfilename.c_str() );
+  for( std::vector<gdcm::Tag>::const_iterator it = tags.begin();
+    it != tags.end(); ++it )
+    {
+    fa.Remove( *it );
+    }
+  if( !fa.Write() )
+    {
+    std::cerr << "Failed to write: " << outfilename << std::endl;
+    return 1;
+    }
+
+  // Read back and check:
+  gdcm::Reader r;
+  r.SetFileName( outfilename.c_str() );
+  if( !r.Read() )
+    {
+    return 1;
+    }
+  const File &f = r.GetFile();
+  const DataSet &ds = f.GetDataSet();
+  for( std::vector<gdcm::Tag>::const_iterator it = tags.begin();
+    it != tags.end(); ++it )
+    {
+    const gdcm::Tag & t = *it;
+    if( ds.FindDataElement( t ) )
+      {
+      return 1;
+      }
+    }
+
+  return 0;
+}
+
+int TestFileAnonymizer1(int argc, char *argv[])
+{
+  if( argc == 2 )
+    {
+    const char *filename = argv[1];
+    return TestFileAnonymize1(filename, true);
+    }
+
+  // else
+  gdcm::Trace::DebugOff();
+  gdcm::Trace::WarningOff();
+  gdcm::Trace::ErrorOff();
+  int r = 0, i = 0;
+  const char *filename;
+  const char * const *filenames = gdcm::Testing::GetFileNames();
+  while( (filename = filenames[i]) )
+    {
+    r += TestFileAnonymize1( filename );
+    ++i;
+    }
+
+  return r;
+}
diff --git a/Testing/Source/MediaStorageAndFileFormat/Cxx/TestFileAnonymizer2.cxx b/Testing/Source/MediaStorageAndFileFormat/Cxx/TestFileAnonymizer2.cxx
new file mode 100644
index 0000000..c8b5730
--- /dev/null
+++ b/Testing/Source/MediaStorageAndFileFormat/Cxx/TestFileAnonymizer2.cxx
@@ -0,0 +1,122 @@
+/*=========================================================================
+
+  Program: GDCM (Grassroots DICOM). A DICOM library
+
+  Copyright (c) 2006-2011 Mathieu Malaterre
+  All rights reserved.
+  See Copyright.txt or http://gdcm.sourceforge.net/Copyright.html for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notice for more information.
+
+=========================================================================*/
+#include "gdcmFileAnonymizer.h"
+
+#include "gdcmTesting.h"
+#include "gdcmSystem.h"
+#include "gdcmReader.h"
+
+static int TestFileAnonymize2(const char *filename, bool verbose = false)
+{
+  using namespace gdcm;
+  if( verbose )
+    std::cout << "Processing: " << filename << std::endl;
+
+  // Create directory first:
+  const char subdir[] = "TestFileAnonymize2";
+  std::string tmpdir = Testing::GetTempDirectory( subdir );
+  if( !System::FileIsDirectory( tmpdir.c_str() ) )
+    {
+    System::MakeDirectory( tmpdir.c_str() );
+    //return 1;
+    }
+  std::string outfilename = Testing::GetTempFilename( filename, subdir );
+
+  gdcm::Tag t1(0x0018,0x5100);
+  gdcm::Tag t2(0x0018,0x1312);
+  gdcm::Tag t3(0x0018,0x1313);
+  gdcm::Tag t4(0x0018,0x1317);
+  gdcm::Tag t5(0x0008,0x2112);
+  gdcm::Tag t6(0x0008,0x9215);
+  gdcm::Tag t7(0x0018,0x1020);
+  gdcm::Tag t8(0x0004,0x1130); // Test DICOMDIR !
+  gdcm::Tag t9(0x0008,0x0000); // Earliest possible Data Element
+  gdcm::Tag t0(0xffff,0xffff); // Latest Possible Element
+
+  std::vector<gdcm::Tag> tags;
+  tags.push_back( t0 );
+  tags.push_back( t1 );
+  tags.push_back( t2 );
+  tags.push_back( t3 );
+  tags.push_back( t4 );
+  tags.push_back( t5 );
+  tags.push_back( t6 );
+  tags.push_back( t7 );
+  tags.push_back( t8 );
+  tags.push_back( t9 );
+
+  gdcm::FileAnonymizer fa;
+  fa.SetInputFileName( filename );
+  fa.SetOutputFileName( outfilename.c_str() );
+  for( std::vector<gdcm::Tag>::const_iterator it = tags.begin();
+    it != tags.end(); ++it )
+    {
+    fa.Empty( *it );
+    }
+  if( !fa.Write() )
+    {
+    std::cerr << "Failed to write: " << outfilename << std::endl;
+    return 1;
+    }
+
+  // Read back and check:
+  gdcm::Reader r;
+  r.SetFileName( outfilename.c_str() );
+  if( !r.Read() )
+    {
+    return 1;
+    }
+  const File &f = r.GetFile();
+  const DataSet &ds = f.GetDataSet();
+  for( std::vector<gdcm::Tag>::const_iterator it = tags.begin();
+    it != tags.end(); ++it )
+    {
+    const gdcm::Tag & t = *it;
+    if( !ds.FindDataElement( t ) )
+      {
+      return 1;
+      }
+    const gdcm::DataElement & de = ds.GetDataElement( t );
+    if( de.GetVL() != 0 )
+      {
+      return 1;
+      }
+    }
+
+  return 0;
+}
+
+int TestFileAnonymizer2(int argc, char *argv[])
+{
+  if( argc == 2 )
+    {
+    const char *filename = argv[1];
+    return TestFileAnonymize2(filename, true);
+    }
+
+  // else
+  gdcm::Trace::DebugOff();
+  gdcm::Trace::WarningOff();
+  gdcm::Trace::ErrorOff();
+  int r = 0, i = 0;
+  const char *filename;
+  const char * const *filenames = gdcm::Testing::GetFileNames();
+  while( (filename = filenames[i]) )
+    {
+    r += TestFileAnonymize2( filename );
+    ++i;
+    }
+
+  return r;
+}
diff --git a/Testing/Source/MediaStorageAndFileFormat/Cxx/TestFileAnonymizer3.cxx b/Testing/Source/MediaStorageAndFileFormat/Cxx/TestFileAnonymizer3.cxx
new file mode 100644
index 0000000..8ae99a6
--- /dev/null
+++ b/Testing/Source/MediaStorageAndFileFormat/Cxx/TestFileAnonymizer3.cxx
@@ -0,0 +1,123 @@
+/*=========================================================================
+
+  Program: GDCM (Grassroots DICOM). A DICOM library
+
+  Copyright (c) 2006-2011 Mathieu Malaterre
+  All rights reserved.
+  See Copyright.txt or http://gdcm.sourceforge.net/Copyright.html for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notice for more information.
+
+=========================================================================*/
+#include "gdcmFileAnonymizer.h"
+
+#include "gdcmTesting.h"
+#include "gdcmSystem.h"
+#include "gdcmReader.h"
+
+#include <vector>
+
+static int TestFileAnonymize3(const char *filename, bool verbose = false)
+{
+  using namespace gdcm;
+  if( verbose )
+    std::cout << "Processing: " << filename << std::endl;
+
+  // Create directory first:
+  const char subdir[] = "TestFileAnonymize3";
+  std::string tmpdir = Testing::GetTempDirectory( subdir );
+  if( !System::FileIsDirectory( tmpdir.c_str() ) )
+    {
+    System::MakeDirectory( tmpdir.c_str() );
+    //return 1;
+    }
+  std::string outfilename = Testing::GetTempFilename( filename, subdir );
+
+  gdcm::Tag t1(0x0018,0x5100);
+  gdcm::Tag t2(0x0018,0x1312);
+  gdcm::Tag t3(0x0018,0x1313);
+  gdcm::Tag t4(0x0018,0x1317);
+  //gdcm::Tag t5(0x0008,0x2112); // SQ
+  //gdcm::Tag t6(0x0008,0x9215); // SQ
+  gdcm::Tag t7(0x0018,0x1020);
+  gdcm::Tag t8(0x0004,0x1130); // Test DICOMDIR !
+  gdcm::Tag t9(0x0008,0x0000); // Earliest possible Data Element
+  gdcm::Tag t0(0xffff,0xffff); // Latest Possible Element
+
+  std::vector<gdcm::Tag> tags;
+  tags.push_back( t0 );
+  tags.push_back( t1 );
+  tags.push_back( t2 );
+  tags.push_back( t3 );
+  tags.push_back( t4 );
+  tags.push_back( t7 );
+  tags.push_back( t8 );
+  tags.push_back( t9 );
+
+  gdcm::FileAnonymizer fa;
+  fa.SetInputFileName( filename );
+  fa.SetOutputFileName( outfilename.c_str() );
+  for( std::vector<gdcm::Tag>::const_iterator it = tags.begin();
+    it != tags.end(); ++it )
+    {
+    fa.Replace( *it, "TOTO" );
+    }
+  if( !fa.Write() )
+    {
+    std::cerr << "Failed to write: " << outfilename << std::endl;
+    return 1;
+    }
+
+  // Read back and check:
+  gdcm::Reader r;
+  r.SetFileName( outfilename.c_str() );
+  if( !r.Read() )
+    {
+    return 1;
+    }
+  const File &f = r.GetFile();
+  const DataSet &ds = f.GetDataSet();
+  for( std::vector<gdcm::Tag>::const_iterator it = tags.begin();
+    it != tags.end(); ++it )
+    {
+    const gdcm::Tag & t = *it;
+    if( !ds.FindDataElement( t ) )
+      {
+      return 1;
+      }
+    const gdcm::DataElement & de = ds.GetDataElement( t );
+    if( de.GetVL() != 4 )
+      {
+      return 1;
+      }
+    }
+
+
+  return 0;
+}
+
+int TestFileAnonymizer3(int argc, char *argv[])
+{
+  if( argc == 2 )
+    {
+    const char *filename = argv[1];
+    return TestFileAnonymize3(filename, true);
+    }
+
+  // else
+  gdcm::Trace::DebugOff();
+  gdcm::Trace::WarningOff();
+  gdcm::Trace::ErrorOff();
+  int r = 0, i = 0;
+  const char *filename;
+  const char * const *filenames = gdcm::Testing::GetFileNames();
+  while( (filename = filenames[i]) )
+    {
+    r += TestFileAnonymize3( filename );
+    ++i;
+    }
+
+  return r;
+}
diff --git a/Wrapping/Csharp/gdcm.i b/Wrapping/Csharp/gdcm.i
index e8d533c..29bcc2d 100644
--- a/Wrapping/Csharp/gdcm.i
+++ b/Wrapping/Csharp/gdcm.i
@@ -139,6 +139,7 @@ public class";
 #include "gdcmSubject.h"
 #include "gdcmCommand.h"
 #include "gdcmAnonymizer.h"
+#include "gdcmFileAnonymizer.h"
 #include "gdcmSystem.h"
 #include "gdcmTrace.h"
 #include "gdcmUIDs.h"
@@ -593,7 +594,7 @@ EXTEND_CLASS_PRINT(gdcm::Scanner)
 //%feature("unref") Anonymizer "coucou $this->Delete();"
 // http://www.swig.org/Doc1.3/SWIGPlus.html#SWIGPlus%5Fnn34
 %include "gdcmAnonymizer.h"
-
+%include "gdcmFileAnonymizer.h"
 
 //EXTEND_CLASS_PRINT(gdcm::Anonymizer)
 //%extend gdcm::Anonymizer

-----------------------------------------------------------------------

Summary of changes:
 Examples/Csharp/CMakeLists.txt                     |    1 +
 Examples/Csharp/FileAnonymize.cs                   |   56 +++
 Examples/Cxx/CMakeLists.txt                        |    1 -
 Examples/Cxx/RemoveInPlace.cxx                     |  127 -----
 .../gdcmDataSet.txx                                |   20 +
 Source/MediaStorageAndFileFormat/CMakeLists.txt    |    1 +
 .../gdcmFileAnonymizer.cxx                         |  518 ++++++++++++++++++++
 .../MediaStorageAndFileFormat/gdcmFileAnonymizer.h |   83 ++++
 .../MediaStorageAndFileFormat/Cxx/CMakeLists.txt   |    3 +
 .../Cxx/TestFileAnonymizer1.cxx                    |  117 +++++
 .../Cxx/TestFileAnonymizer2.cxx                    |  122 +++++
 .../Cxx/TestFileAnonymizer3.cxx                    |  123 +++++
 Wrapping/Csharp/gdcm.i                             |    3 +-
 13 files changed, 1046 insertions(+), 129 deletions(-)
 create mode 100644 Examples/Csharp/FileAnonymize.cs
 delete mode 100644 Examples/Cxx/RemoveInPlace.cxx
 create mode 100644 Source/MediaStorageAndFileFormat/gdcmFileAnonymizer.cxx
 create mode 100644 Source/MediaStorageAndFileFormat/gdcmFileAnonymizer.h
 create mode 100644 Testing/Source/MediaStorageAndFileFormat/Cxx/TestFileAnonymizer1.cxx
 create mode 100644 Testing/Source/MediaStorageAndFileFormat/Cxx/TestFileAnonymizer2.cxx
 create mode 100644 Testing/Source/MediaStorageAndFileFormat/Cxx/TestFileAnonymizer3.cxx


hooks/post-receive
-- 
Grassroots DICOM