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/*=========================================================================
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 "gdcmScanner2.h"
#include "gdcmReader.h"
#include "gdcmGlobal.h"
#include "gdcmDicts.h"
#include "gdcmDict.h"
#include "gdcmDictEntry.h"
#include "gdcmStringFilter.h"
#include "gdcmProgressEvent.h"
#include "gdcmFileNameEvent.h"
#include <algorithm> // std::find
namespace gdcm
{
Scanner2::~Scanner2() = default;
void Scanner2::ClearPublicTags()
{
PublicTags.clear();
}
void Scanner2::ClearPrivateTags()
{
PrivateTags.clear();
}
void Scanner2::ClearSkipTags()
{
SkipTags.clear();
}
bool Scanner2::AddSkipTag( Tag const & t )
{
SkipTags.insert( t );
return true;
}
bool Scanner2::AddPrivateTag( PrivateTag const & t )
{
if( !( t.IsPrivate() && t.GetOwner() && *t.GetOwner() ) ) return false;
// Do not check IsIllegal at this point
static const Global &g = GlobalInstance;
static const Dicts &dicts = g.GetDicts();
const DictEntry &entry = dicts.GetDictEntry( t );
// Is this tag an ASCII on ?
if( entry.GetVR() & VR::VRASCII )
{
PrivateTags.insert( t );
}
else if( entry.GetVR() == VR::INVALID )
{
gdcmWarningMacro( "Only tag with known VR are allowed. Tag " << t << " will be discarded" );
}
else
{
assert( entry.GetVR() & VR::VRBINARY );
//gdcmWarningMacro( "Only ASCII VR are supported for now. Tag " << t << " will be discarded" );
PrivateTags.insert( t );
}
return true;
}
bool Scanner2::AddPublicTag( Tag const & t )
{
if( !t.IsPublic() && !t.IsPrivateCreator() ) return false;
if( t.IsIllegal() ) return false;
static const Global &g = GlobalInstance;
static const Dicts &dicts = g.GetDicts();
const DictEntry &entry = dicts.GetDictEntry( t );
// Is this tag an ASCII on ?
if( entry.GetVR() & VR::VRASCII )
{
PublicTags.insert( t );
}
else if( entry.GetVR() == VR::INVALID )
{
gdcmWarningMacro( "Only tag with known VR are allowed. Tag " << t << " will be discarded" );
}
else
{
assert( entry.GetVR() & VR::VRBINARY );
//gdcmWarningMacro( "Only ASCII VR are supported for now. Tag " << t << " will be discarded" );
PublicTags.insert( t );
}
return true;
}
bool Scanner2::Scan( Directory::FilenamesType const & filenames )
{
this->InvokeEvent( StartEvent() );
// Is there at least one tag ?
if( !PublicTags.empty() || !PrivateTags.empty() )
{
// Prepare hash tables:
PublicMappings.clear();
PublicMappings[""]; // Create a fake table for dummy file
PrivateMappings.clear();
PrivateMappings[""]; // Create a fake table for dummy file
// Make our own copy:
Filenames = filenames;
// Find the tag with the highest value (get the one from the end of the std::set)
Tag last(0x0,0x0);
if( !PublicTags.empty() )
{
PublicTagsType::const_reverse_iterator it1 = PublicTags.rbegin();
const Tag & publiclast = *it1;
last = publiclast;
}
if( !PrivateTags.empty() )
{
PrivateTagsType::const_reverse_iterator pit1 = PrivateTags.rbegin();
Tag privatelast = *pit1;
// at this point we do not know the private creator, since it can go up
// to 0xff, simply read up to the next public group (simple logic).
privatelast.SetGroup( privatelast.GetGroup() + 1 );
privatelast.SetElement( 0x0 );
if( last < privatelast ) last = privatelast;
}
StringFilter sf;
Directory::FilenamesType::const_iterator it = Filenames.begin();
const double progresstick = 1. / (double)Filenames.size();
Progress = 0;
for(; it != Filenames.end(); ++it)
{
Reader reader;
const char *filename = it->c_str();
assert( filename );
reader.SetFileName( filename );
bool read = false;
try
{
// Start reading all tags, including the 'last' one:
read = reader.ReadUpToTag(last, SkipTags);
}
catch(std::exception & ex)
{
(void)ex;
gdcmWarningMacro( "Failed to read:" << filename << " with ex:" << ex.what() );
}
catch(...)
{
gdcmWarningMacro( "Failed to read:" << filename << " with unknown error" );
}
if( read )
{
// Keep the mapping:
sf.SetFile( reader.GetFile() );
Scanner2::ProcessPublicTag(sf, filename);
Scanner2::ProcessPrivateTag(sf, filename);
}
// Update progress
Progress += progresstick;
ProgressEvent pe;
pe.SetProgress( Progress );
this->InvokeEvent( pe );
// For outside application tell which file is being processed:
FileNameEvent fe( filename );
this->InvokeEvent( fe );
}
}
this->InvokeEvent( EndEvent() );
return true;
}
void Scanner2::Print( std::ostream & os ) const
{
os << "Values:\n";
for(ValuesType::const_iterator it = Values.begin() ; it != Values.end();
++it)
{
os << *it << "\n";
}
os << "Mapping:\n";
Directory::FilenamesType::const_iterator file = Filenames.begin();
for(; file != Filenames.end(); ++file)
{
const char *filename = file->c_str();
assert( filename && *filename );
bool b = IsKey(filename);
const char *comment = !b ? "could not be read" : "could be read";
os << "Filename: " << filename << " (" << comment << ")\n";
if( PublicMappings.find(filename) != PublicMappings.end() )
{
const PublicTagToValue &mapping = GetPublicMapping(filename);
PublicTagToValue::const_iterator it = mapping.begin();
for( ; it != mapping.end(); ++it)
{
const Tag & tag = it->first;
const char *value = it->second;
os << tag << " -> [" << value << "]\n";
}
}
if( PrivateMappings.find(filename) != PrivateMappings.end() )
{
const PrivateTagToValue &mapping = GetPrivateMapping(filename);
PrivateTagToValue::const_iterator it = mapping.begin();
for( ; it != mapping.end(); ++it)
{
const PrivateTag & tag = it->first;
const char *value = it->second;
os << tag << " -> [" << value << "]\n";
}
}
}
}
static bool IsVRUI(Tag const &tag)
{
static const Global &g = Global::GetInstance();
static const Dicts &dicts = g.GetDicts();
const DictEntry &dictentry = dicts.GetDictEntry(tag);
if( dictentry.GetVR() == VR::UI ) return true;
return false;
}
static bool IsVRUI(PrivateTag const &tag)
{
static const Global &g = Global::GetInstance();
static const Dicts &dicts = g.GetDicts();
const DictEntry &dictentry = dicts.GetDictEntry(tag);
if( dictentry.GetVR() == VR::UI ) return true;
return false;
}
void Scanner2::PrintTable( std::ostream & os, bool header ) const
{
if( header ) {
os << "\"Filename\"" << "\t";
{
PublicTagsType::const_iterator tag = PublicTags.begin();
for( ; tag != PublicTags.end(); ++tag )
{
const Tag &t = *tag;
os << '"' << t << '"';
os << "\t";
}
}
{
PrivateTagsType::const_iterator tag = PrivateTags.begin();
for( ; tag != PrivateTags.end(); ++tag )
{
const PrivateTag &t = *tag;
os << '"' << t << '"';
os << "\t";
}
}
os << "\n";
}
Directory::FilenamesType::const_iterator file = Filenames.begin();
for(; file != Filenames.end(); ++file)
{
const char *filename = file->c_str();
assert( filename && *filename );
os << '"' << filename << '"' << "\t";
{
PublicTagsType::const_iterator tag = PublicTags.begin();
const PublicTagToValue &mapping = GetPublicMapping(filename);
for( ; tag != PublicTags.end(); ++tag )
{
const Tag &t = *tag;
bool isui = IsVRUI(t);
const char *value = "";
if( mapping.find(t) != mapping.end() ) {
const char * v = mapping.find(t)->second;
if(v) value = v;
}
os << '"' << (isui ? String<>::Trim( value ) : value) << '"';
os << "\t";
}
}
{
PrivateTagsType::const_iterator tag = PrivateTags.begin();
const PrivateTagToValue &mapping = GetPrivateMapping(filename);
for( ; tag != PrivateTags.end(); ++tag )
{
const PrivateTag &t = *tag;
bool isui = IsVRUI(t);
const char *value = "";
if( mapping.find(t) != mapping.end() ) {
const char * v = mapping.find(t)->second;
if(v) value = v;
}
os << '"' << (isui ? String<>::Trim( value ) : value) << '"';
os << "\t";
}
}
os << "\n";
}
}
Scanner2::PublicTagToValue const & Scanner2::GetPublicMapping(const char *filename) const
{
assert( filename && *filename );
if( PublicMappings.find(filename) != PublicMappings.end() )
return PublicMappings.find(filename)->second;
return PublicMappings.find("")->second; // dummy file could not be found
}
Scanner2::PrivateTagToValue const & Scanner2::GetPrivateMapping(const char *filename) const
{
assert( filename && *filename );
if( PrivateMappings.find(filename) != PrivateMappings.end() )
return PrivateMappings.find(filename)->second;
return PrivateMappings.find("")->second; // dummy file could not be found
}
bool Scanner2::IsKey( const char * filename ) const
{
// Look for the file in Mappings tables:
assert( filename && *filename );
PublicMappingType::const_iterator it2 = PublicMappings.find(filename);
PrivateMappingType::const_iterator it3 = PrivateMappings.find(filename);
return it2 != PublicMappings.end() || it3 != PrivateMappings.end();
}
Directory::FilenamesType Scanner2::GetKeys() const
{
Directory::FilenamesType keys;
Directory::FilenamesType::const_iterator file = Filenames.begin();
for(; file != Filenames.end(); ++file)
{
const char *filename = file->c_str();
if( IsKey( filename ) )
{
keys.push_back( filename );
}
}
assert( keys.size() <= Filenames.size() );
return keys;
}
const char* Scanner2::GetPublicValue(const char *filename, Tag const &t) const
{
// \precondition
assert( PublicTags.find( t ) != PublicTags.end() );
PublicTagToValue const &ftv = GetPublicMapping(filename);
if( ftv.find(t) != ftv.end() )
{
return ftv.find(t)->second;
}
return nullptr;
}
const char* Scanner2::GetPrivateValue(const char *filename, PrivateTag const &t) const
{
// \precondition
assert( PrivateTags.find( t ) != PrivateTags.end() );
PrivateTagToValue const &ftv = GetPrivateMapping(filename);
if( ftv.find(t) != ftv.end() )
{
return ftv.find(t)->second;
}
return nullptr;
}
const char *Scanner2::GetFilenameFromPublicTagToValue(Tag const &t, const char *valueref) const
{
const char *filenameref = nullptr;
if( valueref )
{
Directory::FilenamesType::const_iterator file = Filenames.begin();
const std::string valueref_str = String<>::Trim( valueref );
for(; file != Filenames.end() && !filenameref; ++file)
{
const char *filename = file->c_str();
const char * value = GetPublicValue(filename, t);
if( value && valueref == value )
{
filenameref = filename;
}
}
}
return filenameref;
}
const char *Scanner2::GetFilenameFromPrivateTagToValue(PrivateTag const &pt, const char *valueref) const
{
const char *filenameref = nullptr;
if( valueref )
{
Directory::FilenamesType::const_iterator file = Filenames.begin();
const std::string valueref_str = String<>::Trim( valueref );
for(; file != Filenames.end() && !filenameref; ++file)
{
const char *filename = file->c_str();
const char * value = GetPrivateValue(filename, pt);
if( value && valueref_str == value )
{
filenameref = filename;
}
}
}
return filenameref;
}
/// Will loop over all files and return a vector of std::strings of filenames
/// where value match the reference value 'valueref'
Directory::FilenamesType Scanner2::GetAllFilenamesFromPublicTagToValue(Tag const &t, const char *valueref) const
{
Directory::FilenamesType theReturn;
if( valueref )
{
const std::string valueref_str = String<>::Trim( valueref );
Directory::FilenamesType::const_iterator file = Filenames.begin();
for(; file != Filenames.end(); ++file)
{
const char *filename = file->c_str();
const char * value = GetPublicValue(filename, t);
if( value && valueref_str == value )
{
theReturn.push_back( filename );
}
}
}
return theReturn;
}
Directory::FilenamesType Scanner2::GetAllFilenamesFromPrivateTagToValue(PrivateTag const &pt, const char *valueref) const
{
Directory::FilenamesType theReturn;
if( valueref )
{
const std::string valueref_str = String<>::Trim( valueref );
Directory::FilenamesType::const_iterator file = Filenames.begin();
for(; file != Filenames.end(); ++file)
{
const char *filename = file->c_str();
const char * value = GetPrivateValue(filename, pt);
if( value && valueref_str == value )
{
theReturn.push_back( filename );
}
}
}
return theReturn;
}
Scanner2::PublicTagToValue const & Scanner2::GetMappingFromPublicTagToValue(Tag const &t, const char *valueref) const
{
return GetPublicMapping( GetFilenameFromPublicTagToValue(t, valueref) );
}
Scanner2::PrivateTagToValue const & Scanner2::GetMappingFromPrivateTagToValue(PrivateTag const &pt, const char *valueref) const
{
return GetPrivateMapping( GetFilenameFromPrivateTagToValue(pt, valueref) );
}
Scanner2::ValuesType Scanner2::GetPublicValues(Tag const &t) const
{
ValuesType vt;
Directory::FilenamesType::const_iterator file = Filenames.begin();
for(; file != Filenames.end(); ++file)
{
const char *filename = file->c_str();
PublicTagToValue const &ttv = GetPublicMapping(filename);
if( ttv.find(t) != ttv.end() )
{
vt.insert( ttv.find(t)->second );
}
}
return vt;
}
Scanner2::ValuesType Scanner2::GetPrivateValues(PrivateTag const &pt) const
{
ValuesType vt;
Directory::FilenamesType::const_iterator file = Filenames.begin();
for(; file != Filenames.end(); ++file)
{
const char *filename = file->c_str();
PrivateTagToValue const &ttv = GetPrivateMapping(filename);
if( ttv.find(pt) != ttv.end() )
{
vt.insert( ttv.find(pt)->second );
}
}
return vt;
}
Directory::FilenamesType Scanner2::GetPublicOrderedValues(Tag const &t) const
{
Directory::FilenamesType theReturn;
Directory::FilenamesType::const_iterator file = Filenames.begin();
for(; file != Filenames.end(); ++file)
{
const char *filename = file->c_str();
PublicTagToValue const &ttv = GetPublicMapping(filename);
if( ttv.find(t) != ttv.end() )
{
std::string theVal = std::string(ttv.find(t)->second);
if (std::find(theReturn.begin(), theReturn.end(), theVal) == theReturn.end()){
theReturn.push_back( theVal );//only add new tags to the list
}
}
}
return theReturn;
}
Directory::FilenamesType Scanner2::GetPrivateOrderedValues(PrivateTag const &pt) const
{
Directory::FilenamesType theReturn;
Directory::FilenamesType::const_iterator file = Filenames.begin();
for(; file != Filenames.end(); ++file)
{
const char *filename = file->c_str();
PrivateTagToValue const &ttv = GetPrivateMapping(filename);
if( ttv.find(pt) != ttv.end() )
{
std::string theVal = std::string(ttv.find(pt)->second);
if (std::find(theReturn.begin(), theReturn.end(), theVal) == theReturn.end()){
theReturn.push_back( theVal );//only add new tags to the list
}
}
}
return theReturn;
}
void Scanner2::ProcessPublicTag(StringFilter &sf, const char *filename)
{
assert( filename );
PublicTagToValue &mapping = PublicMappings[filename];
const File& file = sf.GetFile();
const FileMetaInformation & header = file.GetHeader();
const DataSet & ds = file.GetDataSet();
PublicTagsType::const_iterator tag = PublicTags.begin();
for( ; tag != PublicTags.end(); ++tag )
{
if( tag->GetGroup() == 0x0002 )
{
if( header.FindDataElement( *tag ) )
{
DataElement const & de = header.GetDataElement( *tag );
std::string s = sf.ToString(de.GetTag());
// Store the potentially new value:
Values.insert( s );
assert( Values.find( s ) != Values.end() );
const char *value = Values.find( s )->c_str();
assert( value );
mapping.insert(
PublicTagToValue::value_type(*tag, value));
}
}
else
{
if( ds.FindDataElement( *tag ) )
{
DataElement const & de = ds.GetDataElement( *tag );
std::string s = sf.ToString(de.GetTag());
// Store the potentially new value:
Values.insert( s );
assert( Values.find( s ) != Values.end() );
const char *value = Values.find( s )->c_str();
assert( value );
mapping.insert(
PublicTagToValue::value_type(*tag, value));
}
}
} // end for
}
void Scanner2::ProcessPrivateTag(StringFilter &sf, const char *filename)
{
assert( filename );
PrivateTagToValue &mapping = PrivateMappings[filename];
const File& file = sf.GetFile();
const DataSet & ds = file.GetDataSet();
PrivateTagsType::const_iterator ptag = PrivateTags.begin();
for( ; ptag != PrivateTags.end(); ++ptag )
{
if( ds.FindDataElement( *ptag ) )
{
DataElement const & de = ds.GetDataElement( *ptag );
std::string s = sf.ToString(de.GetTag());
// Store the potentially new value:
Values.insert( s );
assert( Values.find( s ) != Values.end() );
const char *value = Values.find( s )->c_str();
assert( value );
mapping.insert(
PrivateTagToValue::value_type(*ptag, value));
}
} // end for
}
} // end namespace gdcm
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