1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415
|
/*=========================================================================
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 "gdcmScanner.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
{
Scanner::~Scanner()
{
}
void Scanner::ClearTags()
{
Tags.clear();
}
void Scanner::ClearSkipTags()
{
SkipTags.clear();
}
void Scanner::AddSkipTag( Tag const & t )
{
SkipTags.insert( t );
assert(0); // This is NOT implemented for now
}
// Warning: API is passing a public tag (no way to specify private tag)
void Scanner::AddPrivateTag( PrivateTag const & t )
{
static const Global &g = GlobalInstance;
static const Dicts &dicts = g.GetDicts();
const DictEntry &entry = dicts.GetDictEntry( t );
//std::cout << "Debug: " << entry << std::endl;
// 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 );
}
}
void Scanner::AddTag( Tag const & t )
{
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 )
{
Tags.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" );
Tags.insert( t );
}
}
bool Scanner::Scan( Directory::FilenamesType const & filenames )
{
this->InvokeEvent( StartEvent() );
// Is there at least one tag ?
if( !Tags.empty() || !PrivateTags.empty() )
{
//if( filenames.empty() ) return true;
// Prepare hash table:
Mappings.clear();
Mappings[""]; // 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;
if( !Tags.empty() )
{
TagsType::const_reverse_iterator it1 = Tags.rbegin();
const Tag & publiclast = *it1;
last = publiclast;
}
if( !PrivateTags.empty() )
{
PrivateTagsType::const_reverse_iterator pit1 = PrivateTags.rbegin();
Tag privatelast = *pit1;
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() );
Scanner::ProcessPublicTag(sf, filename);
//Scanner::ProcessPrivateTag(sf, filename);
}
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 Scanner::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";
//const FilenameToValue &mapping = Mappings[*tag];
if( Mappings.find(filename) != Mappings.end() )
{
const TagToValue &mapping = GetMapping(filename);
TagToValue::const_iterator it = mapping.begin();
for( ; it != mapping.end(); ++it)
{
const Tag & tag = it->first;
const char *value = it->second;
os << tag << " -> [" << value << "]\n";
}
}
}
}
Scanner::TagToValue const & Scanner::GetMapping(const char *filename) const
{
// assert( Mappings.find(filename) != Mappings.end() );
assert( filename && *filename );
if( Mappings.find(filename) != Mappings.end() )
return Mappings.find(filename)->second;
return Mappings.find("")->second; // dummy file could not be found
}
bool Scanner::IsKey( const char * filename ) const
{
/*
// std::find on contiguous array will operate in 0(n) which is way too slow, assume user is not too dumb...
Directory::FilenamesType::const_iterator it = std::find(Filenames.begin(), Filenames.end(), filename);
if( it == Filenames.end() )
{
gdcmErrorMacro( "The file: " << filename << " was not scanned" );
return false;
}
*/
// Look for the file in Mappings table:
assert( filename && *filename );
MappingType::const_iterator it2 = Mappings.find(filename);
return it2 != Mappings.end();
}
Directory::FilenamesType Scanner::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* Scanner::GetValue(const char *filename, Tag const &t) const
{
// \precondition
assert( Tags.find( t ) != Tags.end() );
TagToValue const &ftv = GetMapping(filename);
if( ftv.find(t) != ftv.end() )
{
return ftv.find(t)->second;
}
return NULL;
}
const char *Scanner::GetFilenameFromTagToValue(Tag const &t, const char *valueref) const
{
const char *filenameref = 0;
if( valueref )
{
Directory::FilenamesType::const_iterator file = Filenames.begin();
size_t len = strlen( valueref );
if( len && valueref[ len - 1 ] == ' ' )
{
--len;
}
for(; file != Filenames.end() && !filenameref; ++file)
{
const char *filename = file->c_str();
const char * value = GetValue(filename, t);
if( value && strncmp(value, valueref, len ) == 0 )
{
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
Scanner::GetAllFilenamesFromTagToValue(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 = GetValue(filename, t);
const std::string value_str = String<>::Trim( value );
if( value_str == valueref_str )
{
theReturn.push_back( filename );
}
}
}
return theReturn;
}
Scanner::TagToValue const & Scanner::GetMappingFromTagToValue(Tag const &t, const char *valueref) const
{
return GetMapping( GetFilenameFromTagToValue(t, valueref) );
}
Scanner::ValuesType Scanner::GetValues(Tag const &t) const
{
ValuesType vt;
Directory::FilenamesType::const_iterator file = Filenames.begin();
for(; file != Filenames.end(); ++file)
{
const char *filename = file->c_str();
TagToValue const &ttv = GetMapping(filename);
if( ttv.find(t) != ttv.end() )
{
vt.insert( ttv.find(t)->second );
}
}
return vt;
}
Directory::FilenamesType Scanner::GetOrderedValues(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();
TagToValue const &ttv = GetMapping(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;
}
void Scanner::ProcessPublicTag(StringFilter &sf, const char *filename)
{
assert( filename );
TagToValue &mapping = Mappings[filename];
const File& file = sf.GetFile();
const FileMetaInformation & header = file.GetHeader();
const DataSet & ds = file.GetDataSet();
TagsType::const_iterator tag = Tags.begin();
for( ; tag != Tags.end(); ++tag )
{
if( tag->GetGroup() == 0x2 )
{
if( header.FindDataElement( *tag ) )
{
//std::string s;
DataElement const & de = header.GetDataElement( *tag );
//const ByteValue *bv = de.GetByteValue();
////assert( VR::IsASCII( vr ) );
//if( bv ) // Hum, should I store an empty string or what ?
// {
// s = std::string( bv->GetPointer(), bv->GetLength() );
// s.resize( std::min( s.size(), strlen( s.c_str() ) ) );
// }
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(
TagToValue::value_type(*tag, value));
}
}
else
{
if( ds.FindDataElement( *tag ) )
{
//std::string s;
DataElement const & de = ds.GetDataElement( *tag );
//const ByteValue *bv = de.GetByteValue();
////assert( VR::IsASCII( vr ) );
//if( bv ) // Hum, should I store an empty string or what ?
// {
// s = std::string( bv->GetPointer(), bv->GetLength() );
// s.resize( std::min( s.size(), strlen( s.c_str() ) ) );
// }
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(
TagToValue::value_type(*tag, value));
}
}
} // end for
}
} // end namespace gdcm
|