Implementation of strict scanner

This new class will work around a low level implementation issue with the legacy gdcm.Scanner class.
It is now possible to compile gdcm using the relaxed DICOM parser while at the same time acccess the very strict DICOM parser.
This commit uses a complex build system which will hide a gdcmstrict namespace away from the user but allow developer to use it.

Examples/Csharp/ScanDirectory.cs

@@ -14,32 +14,59 @@ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
 
 /*
  * Usage:
- * $ export LD_LIBRARY_PATH=$HOME/Projects/gdcm/debug-gcc/bin
- * $ mono bin/ScanDirectory.exe /path/to/gdcmData/
+ * $ bin/ScanDirectory.exe /path/to/gdcmData/
  */
 using System;
 using gdcm;
 
+// We will print each filename being processed
+public class MyWatcher : SimpleSubjectWatcher
+{
+  public MyWatcher(Subject s):base(s,"Override String"){}
+  protected override void ShowFileName(Subject caller, Event evt){
+    FileNameEvent fne = FileNameEvent.Cast(evt);
+    if( fne != null )
+      {
+      string fn = fne.GetFileName();
+      System.Console.WriteLine( "This is my Scanner. Processing FileName: " + fn );
+      }
+    else
+      {
+      System.Console.WriteLine( "This is my Anonymization. Unhandled Event type: " + evt.GetEventName() );
+      }
+  }
+}
+
 public class ScanDirectory
 {
   public static int Main(string[] args)
     {
     string directory = args[0];
-    Tag t = new Tag(0x8,0x8);
+    Tag t = new Tag(0x8,0x80);
 
     Directory d = new Directory();
     uint nfiles = d.Load( directory );
     if(nfiles == 0) return 1;
     //System.Console.WriteLine( "Files:\n" + d.toString() );
 
-    //Scanner s = new Scanner();
-    SmartPtrScan sscan = Scanner.New();
-    Scanner s = sscan.__ref__();
-    SimpleSubjectWatcher watcher = new SimpleSubjectWatcher(s, "MySimple");
+    // Use a StrictScanner, need to use a reference to pass the C++ pointer to
+    // MyWatcher implementation
+    SmartPtrStrictScan sscan = StrictScanner.New();
+    StrictScanner s = sscan.__ref__();
+    MyWatcher watcher = new MyWatcher(s);
+
     s.AddTag( t );
     bool b = s.Scan( d.GetFilenames() );
     if(!b) return 1;
 
+    for(int i = 0; i < (int)nfiles; ++i)
+      {
+      if( !s.IsKey( d.GetFilenames()[i] ) )
+        {
+        System.Console.WriteLine( "File is not DICOM or could not be read: " + d.GetFilenames()[i] );
+        }
+      }
+
     System.Console.WriteLine( "Scan:\n" + s.toString() );
 
     System.Console.WriteLine( "success" );

Examples/Cxx/SimpleScanner.cxx

@@ -26,7 +26,7 @@
  * ./SimpleScanner gdcmData/012345.002.050.dcm
  */
 
-#include "gdcmScanner.h"
+#include "gdcmStrictScanner.h"
 #include "gdcmSimpleSubjectWatcher.h"
 #include "gdcmFileNameEvent.h"
 
@@ -53,19 +53,21 @@ int main(int argc, char *argv[])
   const char filename_invalid[] = "this is a file that may not exist on this disk.dcm";
 
 
-  gdcm::SmartPointer<gdcm::Scanner> sp = new gdcm::Scanner;
-  gdcm::Scanner &s = *sp;
+  gdcm::SmartPointer<gdcm::StrictScanner> sp = new gdcm::StrictScanner;
+  gdcm::StrictScanner &s = *sp;
   //gdcm::SimpleSubjectWatcher w(&s, "TestFileName" );
   MyFileWatcher w(&s, "TestFileName" );
 
   const gdcm::Tag tag_array[] = {
     gdcm::Tag(0x8,0x50),
     gdcm::Tag(0x8,0x51),
     gdcm::Tag(0x8,0x60),
+    gdcm::Tag(0x8,0x80),
   };
   s.AddTag( tag_array[0] );
   s.AddTag( tag_array[1] );
   s.AddTag( tag_array[2] );
+  s.AddTag( tag_array[3] );
 
   gdcm::Directory::FilenamesType filenames;
   filenames.push_back( filename );
@@ -79,22 +81,25 @@ int main(int argc, char *argv[])
   //s.Print( std::cout );
 
 
-  if( s.IsKey( filename ) )
+  gdcm::Directory::FilenamesType::const_iterator it = filenames.begin();
+  for( ; it != filenames.end(); ++it )
     {
-    std::cout << "INFO:" << filename << " is a proper Key for the Scanner (this is a DICOM file)" << std::endl;
-    }
-
-  if( !s.IsKey( filename_invalid ) )
-    {
-    std::cout << "INFO:" << filename_invalid << " is not a proper Key for the Scanner (this is either not a DICOM file or file does not exist)" << std::endl;
+    if( s.IsKey( it->c_str() ) )
+      {
+      std::cout << "INFO:" << it->c_str() << " is a proper Key for the Scanner (this is a DICOM file)" << std::endl;
+      }
+    else
+      {
+      std::cout << "INFO:" << it->c_str() << " is not a proper Key for the Scanner (this is either not a DICOM file or file does not exist)" << std::endl;
+      }
     }
 
-  gdcm::Scanner::TagToValue const &ttv = s.GetMapping(filename);
+  gdcm::StrictScanner::TagToValue const &ttv = s.GetMapping(filename);
 
   const gdcm::Tag *ptag = tag_array;
   for( ; ptag != tag_array + 3; ++ptag )
     {
-    gdcm::Scanner::TagToValue::const_iterator it = ttv.find( *ptag );
+    gdcm::StrictScanner::TagToValue::const_iterator it = ttv.find( *ptag );
     if( it != ttv.end() )
       {
       std::cout << *ptag << " was properly found in this file" << std::endl;

PACKAGER

@@ -48,3 +48,9 @@ Examples:
 GDCM comes with some examples for user, but setting the following:
 GDCM_BUILD_EXAMPLES:BOOL=ON
 will not do anything since there is no install rule for examples...
+
+The library attempts to provide a clean API, therefore it is highly suggested that you compile GDCM using:
+
+$ CFLAGS=-fvisibility=hidden CXXFLAGS=-fvisibility=hidden cmake /path/to/gdcm/sources
+
+This make sure that on UNIX, the API is actually identical at what is found on Windows.

Source/Common/gdcmConfigure.h.in

@@ -130,10 +130,15 @@
 
 #cmakedefine GDCM_FORCE_BIGENDIAN_EMULATION
 
+#ifndef GDCM_OVERRIDE_BROKEN_IMPLEMENTATION
 /* To Remove code that support broken DICOM implementation and therefore
  * add some over head. Turn Off at your own risk
  */
 #cmakedefine GDCM_SUPPORT_BROKEN_IMPLEMENTATION
+#endif
+#ifndef gdcm_ns
+#define gdcm_ns gdcm
+#endif
 
 #define GDCM_PVRG_JPEG_EXECUTABLE "@PVRGJPEG_EXECUTABLE@"
 #define GDCM_KAKADU_EXPAND_EXECUTABLE "@KDU_EXPAND_EXECUTABLE@"

Source/Common/gdcmWin32.h

@@ -35,6 +35,11 @@
   #endif
 #endif
 
+#if defined(GDCM_OVERRIDE_BROKEN_IMPLEMENTATION) && !defined(GDCM_FORCE_EXPORT)
+#undef GDCM_EXPORT
+#define GDCM_EXPORT
+#endif
+
 // In VTK 4.2 vtkWrapPython does not like anything other than VTK_*EXPORT
 // [ 86%] Generating vtkGDCMImageReaderPython.cxx
 // syntax error

Source/DataStructureAndEncodingDefinition/CMakeLists.txt

@@ -1,36 +1,63 @@
 # Define the srcs for Data Structure and Encoding Definitions
 # DSED
-set(DSED_SRCS
-  gdcmTag.cxx
-  gdcmTagToVR.cxx
-  gdcmPrivateTag.cxx
-  gdcmCodeString.cxx
+
+# dual compilation (namespace gdcm_ns), all the following either directly
+# reference code using GDCM_SUPPORT_BROKEN_IMPLEMENTATION or indirectly
+set(DSED2_SRCS
   gdcmByteValue.cxx
-  gdcmValue.cxx
-  gdcmFileSet.cxx
+  gdcmDataElement.cxx
   gdcmDataSet.cxx
-  gdcmByteSwapFilter.cxx
-  gdcmUNExplicitImplicitDataElement.cxx
   gdcmExplicitDataElement.cxx
-  gdcmFileMetaInformation.cxx
+  gdcmFile.cxx # FileMeta is class member
+  gdcmFileMetaInformation.cxx # subclass of DataSet
   gdcmFragment.cxx
   gdcmImplicitDataElement.cxx
   gdcmItem.cxx
+  gdcmMediaStorage.cxx # SetFromModality takes a DataSet
+  gdcmPrivateTag.cxx
   gdcmReader.cxx
+  gdcmSequenceOfFragments.cxx
+  gdcmSequenceOfItems.cxx
+  gdcmValue.cxx # friend decl
+  )
+# need to prepare duplicate files to help cmake handle setting compile
+# definitions (cmake cannot handle duplicate source file in same target).
+# this trick allows us to avoid a static compilation which may not be portable
+foreach(src ${DSED2_SRCS})
+  configure_file(
+    ${CMAKE_CURRENT_SOURCE_DIR}/${src}
+    ${CMAKE_CURRENT_SOURCE_DIR}/strict_${src}
+    COPYONLY
+    )
+  list(APPEND DSED3_SRCS
+    ${CMAKE_CURRENT_SOURCE_DIR}/strict_${src}
+    )
+  set_property(
+    SOURCE ${CMAKE_CURRENT_SOURCE_DIR}/strict_${src}
+    PROPERTY COMPILE_DEFINITIONS "GDCM_OVERRIDE_BROKEN_IMPLEMENTATION" "gdcm_ns=gdcmstrict"
+    )
+endforeach()
+
+# the following source code do not need a duplicate compilation to handle
+# GDCM_SUPPORT_BROKEN_IMPLEMENTATION
+set(DSED_SRCS
+  ${DSED2_SRCS}
+  gdcmReader.strict.cxx # hook to call gdcmstrict API
+  gdcmTag.cxx
+  gdcmTagToVR.cxx
+  gdcmCodeString.cxx
+  gdcmFileSet.cxx
+  gdcmByteSwapFilter.cxx
+  gdcmUNExplicitImplicitDataElement.cxx
   gdcmWriter.cxx
   #gdcmParser.cxx
   gdcmCSAHeader.cxx
   gdcmPDBHeader.cxx
-  gdcmSequenceOfFragments.cxx
-  gdcmSequenceOfItems.cxx
   gdcmTransferSyntax.cxx
-  gdcmMediaStorage.cxx
   gdcmVM.cxx
   gdcmVR.cxx
-  gdcmFile.cxx
   gdcmPreamble.cxx
   gdcmParseException.cxx
-  gdcmDataElement.cxx
   gdcmUNExplicitDataElement.cxx
   gdcmCP246ExplicitDataElement.cxx
   gdcmExplicitImplicitDataElement.cxx
@@ -56,8 +83,7 @@ if(NOT GDCM_USE_SYSTEM_ZLIB)
     )
 endif()
 
-
-add_library(gdcmDSED ${DSED_SRCS})
+add_library(gdcmDSED ${DSED_SRCS} ${DSED3_SRCS})
 target_link_libraries(gdcmDSED gdcmCommon)
 # zlib stuff are actually included (template) so we need to link them here.
 target_link_libraries(gdcmDSED ${GDCM_ZLIB_LIBRARIES})

Source/DataStructureAndEncodingDefinition/gdcmAttribute.h

@@ -27,7 +27,7 @@
 #include <vector>
 #include <sstream>
 
-namespace gdcm
+namespace gdcm_ns
 {
 
 struct void_;
@@ -1045,6 +1045,6 @@ class Attribute<Group,Element, VR::SQ, VM::VM1, SQA>
  * This is a C++ example on how to use gdcm::Attribute
  */
 
-} // namespace gdcm
+} // namespace gdcm_ns
 
 #endif //GDCMATTRIBUTE_H

Source/DataStructureAndEncodingDefinition/gdcmBasicOffsetTable.h

@@ -17,7 +17,7 @@
 
 #include "gdcmFragment.h"
 
-namespace gdcm
+namespace gdcm_ns
 {
 /**
  * \brief Class to represent a BasicOffsetTable
@@ -121,6 +121,6 @@ inline std::ostream &operator<<(std::ostream &os, const BasicOffsetTable &val)
 }
 
 
-} // end namespace gdcm
+} // end namespace gdcm_ns
 
 #endif //GDCMBASICOFFSETTABLE_H

Source/DataStructureAndEncodingDefinition/gdcmByteValue.cxx

@@ -16,9 +16,42 @@
 #include <algorithm> // req C++11
 #include <cstring> // memcpy
 
-namespace gdcm
+namespace gdcm_ns
 {
 
+  void ByteValue::SetLength(VL vl) {
+    VL l(vl);
+#ifdef GDCM_SUPPORT_BROKEN_IMPLEMENTATION
+    // CompressedLossy.dcm
+    if( l.IsUndefined() ) throw Exception( "Impossible" );
+    if ( l.IsOdd() ) {
+      gdcmDebugMacro(
+        "BUGGY HEADER: Your dicom contain odd length value field." );
+      ++l;
+      }
+#else
+    assert( !l.IsUndefined() && !l.IsOdd() );
+#endif
+    // I cannot use reserve for now. I need to implement:
+    // STL - vector<> and istream
+    // http://groups.google.com/group/comp.lang.c++/msg/37ec052ed8283e74
+//#define SHORT_READ_HACK
+    try
+      {
+#ifdef SHORT_READ_HACK
+    if( l <= 0xff )
+#endif
+      Internal.resize(l);
+      //Internal.reserve(l);
+      }
+    catch(...)
+      {
+      //throw Exception("Impossible to allocate: " << l << " bytes." );
+      throw Exception("Impossible to allocate" );
+      }
+    // Keep the exact length
+    Length = vl;
+  }
   void ByteValue::PrintASCII(std::ostream &os, VL maxlength ) const {
     VL length = std::min(maxlength, Length);
     // Special case for VR::UI, do not print the trailing \0
@@ -295,4 +328,4 @@ namespace gdcm
     assert( Internal.size() % 2 == 0 && Internal.size() == Length );
     }
 
-}
+} // end namespace gdcm_ns