gdcm_conv 0.2.0

/*=========================================================================

  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.

=========================================================================*/
#ifndef GDCMDATASET_H
#define GDCMDATASET_H

#include "gdcmDataElement.h"
#include "gdcmTag.h"
#include "gdcmVR.h"
#include "gdcmElement.h"
#include "gdcmMediaStorage.h"

#include <set>
#include <iterator>

namespace gdcm_ns
{
class GDCM_EXPORT DataElementException : public std::exception {};

class PrivateTag;
/**
 * \brief Class to represent a Data Set (which contains Data Elements)
 * \details A Data Set represents an instance of a real world Information Object
 * \note
 * DATA SET:
 * Exchanged information consisting of a structured set of Attribute values
 * directly or indirectly related to Information Objects. The value of each
 * Attribute in a Data Set is expressed as a Data Element.
 * A collection of Data Elements ordered by increasing Data Element Tag
 * number that is an encoding of the values of Attributes of a real world
 * object.
 * \note
 * Implementation note. If one do:
 * DataSet ds;
 * ds.SetLength(0);
 * ds.Read(is);
 * setting length to 0 actually means try to read is as if it was a root
 * DataSet. Other value are undefined (nested dataset with undefined length)
 * or defined length (different from 0) means nested dataset with defined
 * length.
 *
 * \warning
 * a DataSet does not have a Transfer Syntax type, only a File does.
 */
class GDCM_EXPORT DataSet
{
  friend class CSAHeader;
public:
  typedef std::set<DataElement> DataElementSet;
  typedef DataElementSet::const_iterator ConstIterator;
  typedef DataElementSet::iterator Iterator;
  typedef DataElementSet::size_type SizeType;
  //typedef typename DataElementSet::iterator iterator;
  ConstIterator Begin() const { return DES.begin(); }
  Iterator Begin() { return DES.begin(); }
  ConstIterator End() const { return DES.end(); }
  Iterator End() { return DES.end(); }
  const DataElementSet &GetDES() const { return DES; }
  DataElementSet &GetDES() { return DES; }
  void Clear() {
    DES.clear();
    gdcm_assert( DES.empty() );
  }

  SizeType Size() const {
    return DES.size();
  }

  void Print(std::ostream &os, std::string const &indent = "") const {
    // CT_Phillips_JPEG2K_Decompr_Problem.dcm has a SQ of length == 0
    //int s = DES.size();
    //gdcm_assert( s );
    //std::copy(DES.begin(), DES.end(),
    //  std::ostream_iterator<DataElement>(os, "\n"));
    ConstIterator it = DES.begin();
    for( ; it != DES.end(); ++it)
      {
      os << indent << *it << "\n";
      }
  }

  template <typename TDE>
  unsigned int ComputeGroupLength(Tag const &tag) const
    {
    gdcm_assert( tag.GetElement() == 0x0 );
    const DataElement r(tag);
    ConstIterator it = DES.find(r);
    unsigned int res = 0;
    for( ++it; it != DES.end()
      && it->GetTag().GetGroup() == tag.GetGroup(); ++it)
      {
      gdcm_assert( it->GetTag().GetElement() != 0x0 );
      gdcm_assert( it->GetTag().GetGroup() == tag.GetGroup() );
      res += it->GetLength<TDE>();
      }
    return res;
    }

  template <typename TDE>
  VL GetLength() const {
    if( DES.empty() ) return 0;
    gdcm_assert( !DES.empty() );
    VL ll = 0;
    gdcm_assert( ll == 0 );
    ConstIterator it = DES.begin();
    for( ; it != DES.end(); ++it)
      {
      gdcm_assert( !(it->GetLength<TDE>().IsUndefined()) );
      if ( it->GetTag() != Tag(0xfffe,0xe00d) )
        {
        ll += it->GetLength<TDE>();
        }
      }
    return ll;
  }
  /// Insert a DataElement in the DataSet.
  /// \warning: Tag need to be >= 0x8 to be considered valid data element
  void Insert(const DataElement& de) {
    // FIXME: there is a special case where a dataset can have value < 0x8, see:
    // $ gdcmdump --csa gdcmData/SIEMENS-JPEG-CorruptFrag.dcm
    if( de.GetTag().GetGroup() >= 0x0008 || de.GetTag().GetGroup() == 0x4 )
      {
      // prevent user error:
      if( de.GetTag() == Tag(0xfffe,0xe00d)
      || de.GetTag() == Tag(0xfffe,0xe0dd)
      || de.GetTag() == Tag(0xfffe,0xe000) )
        {
        }
      else
        {
        InsertDataElement( de );
        }
      }
    else
      {
      gdcmErrorMacro( "Cannot add element with group < 0x0008 and != 0x4 in the dataset: " << de.GetTag() );
      }
  }
  /// Replace a dataelement with another one
  void Replace(const DataElement& de) {
    ConstIterator it = DES.find(de);
	if( it != DES.end() )
	{
	  // detect loop:
	  gdcmAssertAlwaysMacro( &*it != &de );
	  DES.erase(it);
	}
    DES.insert(de);
  }
  /// Only replace a DICOM attribute when it is missing or empty
  void ReplaceEmpty(const DataElement& de) {
    ConstIterator it = DES.find(de);
    if( it != DES.end() && it->IsEmpty() )
    {
      // detect loop:
	  gdcmAssertAlwaysMacro( &*it != &de );
	  DES.erase(it);
    }
	DES.insert(de);
  }
  /// Completely remove a dataelement from the dataset
  SizeType Remove(const Tag& tag) {
    DataElementSet::size_type count = DES.erase(tag);
    gdcm_assert( count == 0 || count == 1 );
    return count;
  }

  /// Return the DataElement with Tag 't'
  /// \warning:
  /// This only search at the 'root level' of the DataSet
  //DataElement& GetDataElement(const Tag &t) {
  //  DataElement r(t);
  //  Iterator it = DES.find(r);
  //  if( it != DES.end() )
  //    return *it;
  //  return GetDEEnd();
  //  }
  const DataElement& GetDataElement(const Tag &t) const {
    const DataElement r(t);
    ConstIterator it = DES.find(r);
    if( it != DES.end() )
      return *it;
    return GetDEEnd();
    }
  const DataElement& operator[] (const Tag &t) const { return GetDataElement(t); }
  const DataElement& operator() (uint16_t group, uint16_t element) const { return GetDataElement( Tag(group,element) ); }

  /// Return the private creator of the private tag 't':
  /// or an empty string when not found
  std::string GetPrivateCreator(const Tag &t) const;

  /// Return the private tag of the private tag 't', private creator will be set to empty if not found
  PrivateTag GetPrivateTag(const Tag &t) const;

  /// Look up if private tag 't' is present in the dataset:
  bool FindDataElement(const PrivateTag &t) const;
  /// Return the dataelement
  const DataElement& GetDataElement(const PrivateTag &t) const;

  // DUMB: this only search within the level of the current DataSet
  bool FindDataElement(const Tag &t) const {
    const auto it = GetDataElement(t);
    // Return if tag is found
    return it != GetDEEnd();
    }

  // WARNING:
  // This only search at the same level as the DataSet is !
  const DataElement& FindNextDataElement(const Tag &t) const {
    const DataElement r(t);
    ConstIterator it = DES.lower_bound(r);
    if( it != DES.end() )
      return *it;
    return GetDEEnd();
    }

  /// Returns if the dataset is empty
  bool IsEmpty() const { return DES.empty(); }

  DataSet& operator=(DataSet const &)
  = default;

  template <typename TDE, typename TSwap>
  std::istream &ReadNested(std::istream &is);

  template <typename TDE, typename TSwap>
  std::istream &Read(std::istream &is);

  template <typename TDE, typename TSwap>
  std::istream &ReadUpToTag(std::istream &is, const Tag &t, std::set<Tag> const & skiptags);

  template <typename TDE, typename TSwap>
  std::istream &ReadUpToTagWithLength(std::istream &is, const Tag &t, std::set<Tag> const & skiptags, VL & length);

  template <typename TDE, typename TSwap>
  std::istream &ReadSelectedTags(std::istream &is, const std::set<Tag> & tags, bool readvalues = true);
  template <typename TDE, typename TSwap>
  std::istream &ReadSelectedTagsWithLength(std::istream &is, const std::set<Tag> & tags, VL & length, bool readvalues = true);

  template <typename TDE, typename TSwap>
  std::istream &ReadSelectedPrivateTags(std::istream &is, const std::set<PrivateTag> & tags, bool readvalues = true);
  template <typename TDE, typename TSwap>
  std::istream &ReadSelectedPrivateTagsWithLength(std::istream &is, const std::set<PrivateTag> & tags, VL & length, bool readvalues = true);

  template <typename TDE, typename TSwap>
  std::ostream const &Write(std::ostream &os) const;

  template <typename TDE, typename TSwap>
  std::istream &ReadWithLength(std::istream &is, VL &length);

  MediaStorage GetMediaStorage() const;

protected:
  /* GetDEEnd is a Win32 only issue, one cannot use a dllexported
   * static member data in an inline function, otherwise symbol
   * will get reported as missing in any dll using the inlined function
   */
  const DataElement& GetDEEnd() const;

  // This function is not safe, it does not check for the value of the tag
  // so depending whether we are getting called from a dataset or file meta header
  // the condition is different
  void InsertDataElement(const DataElement& de) {
    //if( de.GetTag() == Tag(0xfffe,0xe00d) ) return;
    //if( de.GetTag() == Tag(0xfffe,0xe0dd) ) return;
#ifndef NDEBUG
    std::pair<Iterator,bool> pr = DES.insert(de);
    if( pr.second == false )
      {
      gdcmWarningMacro( "DataElement: " << de << " was already found, skipping duplicate entry.\n"
        "Original entry kept is: " << *pr.first );
      }
#else
    DES.insert(de);
#endif
    gdcm_assert( de.IsEmpty() || de.GetVL() == de.GetValue().GetLength() );
    }

protected:
  // Internal function, that will compute the actual Tag (if found) of
  // a requested Private Tag (XXXX,YY,"PRIVATE")
  Tag ComputeDataElement(const PrivateTag & t) const;

private:
  DataElementSet DES;
  static DataElement DEEnd;
  friend std::ostream& operator<<(std::ostream &_os, const DataSet &);
};
//-----------------------------------------------------------------------------
inline std::ostream& operator<<(std::ostream &os, const DataSet &val)
{
  val.Print(os);
  return os;
}

#if defined(SWIGPYTHON) || defined(SWIGCSHARP) || defined(SWIGJAVA) || defined(SWIGPHP)
/*
 * HACK: I need this temp class to be able to manipulate a std::set from python,
 * swig does not support wrapping of simple class like std::set...
 */
class SWIGDataSet
{
public:
  SWIGDataSet(DataSet &des):Internal(des),it(des.Begin()) {}
  const DataElement& GetCurrent() const { return *it; }
  void Start() { it = Internal.Begin(); }
  bool IsAtEnd() const { return it == Internal.End(); }
  void Next() { ++it; }
private:
  DataSet & Internal;
  DataSet::ConstIterator it;
};
#endif /* SWIG */

/**
 * \example SimplePrint.cs
 * This is a C# example on how to use gdcm::SWIGDataSet
 */

} // end namespace gdcm_ns

#include "gdcmDataSet.txx"

#endif //GDCMDATASET_H