File: gdcmXMLPrinter.cxx

package info (click to toggle)
gdcm 2.4.4-3%2Bdeb8u1
  • links: PTS, VCS
  • area: main
  • in suites: jessie
  • size: 32,912 kB
  • ctags: 52,166
  • sloc: cpp: 188,527; ansic: 124,526; xml: 41,799; sh: 7,162; python: 3,667; cs: 2,128; java: 1,344; lex: 1,290; tcl: 677; php: 128; makefile: 116
file content (583 lines) | stat: -rw-r--r-- 15,289 bytes parent folder | download | duplicates (2)
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
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
/*=========================================================================

  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 "gdcmXMLPrinter.h"
#include "gdcmSequenceOfItems.h"
#include "gdcmSequenceOfFragments.h"
#include "gdcmDict.h"
#include "gdcmDicts.h"
#include "gdcmGroupDict.h"
#include "gdcmVR.h"
#include "gdcmVM.h"
#include "gdcmElement.h"
#include "gdcmGlobal.h"
#include "gdcmAttribute.h"
#include "gdcmDataSetHelper.h"
#include "gdcmUUIDGenerator.h"

#include "gdcmDataSet.h"

#include <typeinfo>


namespace gdcm
{
//-----------------------------------------------------------------------------
XMLPrinter::XMLPrinter():PrintStyle(XMLPrinter::OnlyUUID),F(0)
{
}

//-----------------------------------------------------------------------------
XMLPrinter::~XMLPrinter()
{
}

// Carried forward from Printer Class
// SIEMENS_GBS_III-16-ACR_NEMA_1.acr is a tough kid: 0009,1131 is supposed to be VR::UL, but
// there are only two bytes...

VR XMLPrinter::PrintDataElement(std::ostream &os, const Dicts &dicts, const DataSet & ds,
  const DataElement &de, const TransferSyntax & ts)
{

  const ByteValue *bv = de.GetByteValue();
  const SequenceOfItems *sqi = 0;
  const Value &value = de.GetValue();
  const SequenceOfFragments *sqf = de.GetSequenceOfFragments();

  std::string strowner;
  const char *owner = 0;
  const Tag& t = de.GetTag();
  UUIDGenerator UIDgen;

  if( t.IsPrivate() && !t.IsPrivateCreator() )
    {
    strowner = ds.GetPrivateCreator(t);
    owner = strowner.c_str();
    }
  const DictEntry &entry = dicts.GetDictEntry(t,owner);
  const VR &vr = entry.GetVR();
  const VM &vm = entry.GetVM();
  (void)vm;
  const char *name = entry.GetKeyword();
  bool retired = entry.GetRetired();

  const VR &vr_read = de.GetVR();
  const VL &vl_read = de.GetVL();

  //Printing Tag

  
  os << " tag = \"" << std::uppercase << std::hex << std::setw(4) << std::setfill('0') <<
      t.GetGroup() <<  std::setw(4) << t.GetElement() << std::nouppercase <<"\"" << std::dec;

  //Printing Private Creator
  if( owner && *owner )
    {
    os << " privateCreator = \"" << owner << "\" ";
    }

  VR refvr;

  // Prefer the vr from the file:

  if( vr_read == VR::INVALID )
    {
    refvr = vr;
    }
  else if ( vr_read == VR::UN && vr != VR::INVALID ) // File is explicit, but still prefer vr from dict when UN
    {
    refvr = vr;
    }
  else // The file is Explicit !
    {
    refvr = vr_read;
    }

  if( refvr.IsDual() ) // This means vr was read from a dict entry:
    {
    refvr = DataSetHelper::ComputeVR(*F,ds, t);
    }

  //as DataSetHelper would have been called
  assert( refvr != VR::US_SS );
  assert( refvr != VR::OB_OW );

  if( dynamic_cast<const SequenceOfItems*>( &value ) )
    {
    sqi = de.GetValueAsSQ();
    refvr = VR::SQ;
    assert( refvr == VR::SQ );
    }
#if 0
  else if( vr == VR::SQ && vr_read != VR::SQ )
    {
    sqi = de.GetValueAsSQ();
    refvr = VR::SQ;
    assert( refvr == VR::SQ );
    }
#endif

  if( (vr_read == VR::INVALID || vr_read == VR::UN ) && vl_read.IsUndefined() )
    {
    assert( refvr == VR::SQ );
    }

//  if( vr_read == VR::SQ || vr_read == VR::UN )
//    {
//    sqi = de.GetValueAsSQ();
//    }
  if( vr != VR::INVALID && (!vr.Compatible( vr_read ) || vr_read == VR::INVALID || vr_read == VR::UN ) )
    {
    assert( vr != VR::INVALID );

    /*
    No need as we will save only the VR to which it is stored by GDCM in the XML file
    
    if( vr == VR::US_SS || vr == VR::OB_OW )
      {
      os << "(" << vr << " => " << refvr << ") ";
      }
    else
      {
      os << "(" << vr << ") ";
      }
     */ 
    
    }
  else if( sqi /*de.GetSequenceOfItems()*/ && refvr == VR::INVALID )
    {
    // when vr == VR::INVALID and vr_read is also VR::INVALID, we have a seldom case where we can guess
    // the vr
    // eg. CD1/647662/647663/6471066 has a SQ at (2001,9000)

    assert( refvr == VR::INVALID );
    refvr = VR::SQ;
    }

  if(refvr == VR::INVALID)
    refvr = VR::UN;

  // Printing the VR -- Value Representation
  os << " vr = \"" << refvr << "\" ";

  // Add the keyword attribute :

  if( t.IsPublic())
    {
    if( name && *name )
      {
      os <<"keyword = \"";

      /*  No owner */
      if( t.IsPrivate() && (owner == 0 || *owner == 0 ) && !t.IsPrivateCreator() )
        {
        //os << name;
        //os = PrintXML_char(os,name);
        }
      /* retired element */
      else if( retired )
        {
        assert( t.IsPublic() || t.GetElement() == 0x0 ); // Is there such thing as private and retired element ?
        //os << name;
        //os = PrintXML_char(os,name);
        }
      /* Public element */
      else
        {
        //os << name;
        //os = PrintXML_char(os,name);
        }

      char c;
      for (; (*name)!='\0'; name++)
        {
        c = *name;
        if(c == '&')
          os << "&amp;";
        else if(c == '<')
          os << "&lt;";
        else if(c == '>')
          os << "&gt;";
        else if(c == '\'')
          os << "&apos;";
        else if(c == '\"')
          os << "&quot;";
        else
          os << c;
        }
      os << "\"";
      }
    else
      {
      if( t.IsPublic() )
        {
        gdcmWarningMacro( "An unknown public element.");
        }
      //    os << ""; // Special keyword
      }
    }
  os << ">\n";

#define StringFilterCase(type) \
  case VR::type: \
    { \
      Element<VR::type,VM::VM1_n> el; \
      if( !de.IsEmpty() ) { \
      el.Set( de.GetValue() ); \
      if( el.GetLength() ) { \
      os << "<Value number = \"1\" >" ;os << "" << el.GetValue();os << "</Value>\n"; \
      const uint32_t l = (uint32_t)el.GetLength(); \
      for(uint32_t i = 1; i < l; ++i) \
      { \
      os << "<Value number = \"" << (i+1) << "\" >" ;\
      os << el.GetValue(i);os << "</Value>\n";} \
      } \
      else { if( de.IsEmpty() ) \
                 {} } } \
      else { assert( de.IsEmpty()); } \
    } break


  // Print Value now:

  //Handle PN first, acc. to Standard
  if(refvr == VR::PN)
    {
    if( bv )
      {
      bv->PrintPNXML(os);    //new function to print each value in new child tag
      }
    else
      {
      assert( de.IsEmpty() );
      }
    }
  else if( refvr & VR::VRASCII )
    {
    //assert( !sqi && !sqf);
    assert(!sqi);
    if( bv )
      {
      bv->PrintASCIIXML(os);    //new function to print each value in new child tag
      }
    else
      {
      assert( de.IsEmpty() );
      }
    }
  else
    {
    assert( refvr & VR::VRBINARY || (vr == VR::INVALID && refvr == VR::INVALID) );
    std::string s;
    switch(refvr)
      {
      StringFilterCase(AT);
      StringFilterCase(FL);
      StringFilterCase(FD);
      StringFilterCase(OF);
      StringFilterCase(SL);
      StringFilterCase(SS);
      StringFilterCase(UL);
      StringFilterCase(US);
    case VR::OB:
    case VR::OW:
    case VR::OB_OW:
    case VR::UN:
    case VR::US_SS_OW: 
        {
        if ( bv )
          {
          if(PrintStyle)
            {
            bv->PrintHexXML(os);
            }
          else
            {
            if(bv->GetLength())
              {
              const char *suid = UIDgen.Generate();
              os << "<BulkData uuid = \""<<
                suid << "\" />\n";
              HandleBulkData( suid, ts, bv->GetPointer(), bv->GetLength() );
              }
            }
          }
        else if ( sqf )
          {
          assert( t == Tag(0x7fe0,0x0010) );
          }
        else if ( sqi )
          {
          gdcmErrorMacro( "Should not happen: VR=UN but contains a SQ" );
          }
        else
          {
          assert( !sqi && !sqf );
          assert( de.IsEmpty() );
          }
        }
      break;
    case VR::US_SS:
      assert( refvr != VR::US_SS );
      break;
    case VR::SQ://The below info need not be printed into the XML infoset acc. to the standard
      if( !sqi && !de.IsEmpty() && de.GetValue().GetLength() )
        {
        }
      else
        {
        if( vl_read.IsUndefined() )
          {
          //os << "(Sequence with undefined length)";
          }
        else
          {
          //os << "(Sequence with defined length)";
          }
        }
      break;
    case VR::INVALID:
      if( bv )
        {
        if(PrintStyle)
          bv->PrintHexXML(os);
        else
          {
          if(bv->GetLength())
            {
            const char *suid = UIDgen.Generate();
            os << "<BulkData uuid = \""<<
              suid << "\" />\n";
            HandleBulkData( suid, ts, bv->GetPointer(), bv->GetLength() );
            }
          }
        }
      else
        {
        assert( !sqi && !sqf );
        assert( de.IsEmpty() );
        }
      break;
    default:
      assert(0 && "No Match! Impossible!!");
      break;
      }
    }

  //os << "\n";
  return refvr;
}

void XMLPrinter::PrintSQ(const SequenceOfItems *sqi, const TransferSyntax & ts, std::ostream & os)
{
  if( !sqi ) return;
  
  int noItems = 1;

  SequenceOfItems::ItemVector::const_iterator it = sqi->Items.begin();
  for(; it != sqi->Items.end(); ++it)
    {
    const Item &item = *it;
    const DataSet &ds = item.GetNestedDataSet();
    //const DataElement &deitem = item;
    /*
    os << "<DicomAttribute  tag = \"";
    os << std::hex << std::setw(4) << std::setfill('0') <<
      deitem.GetTag().GetGroup() <<  std::setw(4) << ((uint16_t)(deitem.GetTag().GetElement() << 8) >> 8) << "\" ";
    os << " VR = \"UN\"  keyword = ";     

    if( deitem.GetVL().IsUndefined() )
      {
      os << "\"ItemWithUndefinedLength\"";
      }
    else
      {
      os << "\"ItemWithDefinedLength\"";
      }
    os << ">\n";
    */
    os << "<Item number = \"" << noItems++ << "\">\n";
    PrintDataSet(ds, ts, os);
    /*
    if( deitem.GetVL().IsUndefined() )
      {
            os << "<DicomAttribute    tag = \"fffee00d\"  VR = \"UN\" keyword = \"ItemDelimitationItem\"/>\n";
      }
    os << "</DicomAttribute>\n\n";  
    */
    os << "</Item>\n";
    }
  /*
  if( sqi->GetLength().IsUndefined() )
    {
        os << "<DicomAttribute    tag = \"fffee0dd\"  VR = \"UN\" keyword = \"SequenceDelimitationItem\"/>\n";
    }
  */  
}

void XMLPrinter::PrintDataSet(const DataSet &ds, const TransferSyntax & ts, std::ostream &os)
{
  const Global& g = GlobalInstance;
  const Dicts &dicts = g.GetDicts();
  const Dict &d = dicts.GetPublicDict(); (void)d;

  DataSet::ConstIterator it = ds.Begin();
  UUIDGenerator UIDgen;
  
  for( ; it != ds.End(); ++it )
    {
    const DataElement &de = *it;
    
    const SequenceOfFragments *sqf = de.GetSequenceOfFragments();
    
    os << "<DicomAttribute  " ;
    VR refvr = PrintDataElement(os, dicts, ds, de, ts);

    if( refvr == VR::SQ /*|| sqi*/ )
      {
      SmartPointer<SequenceOfItems> sqi2 = de.GetValueAsSQ();
      PrintSQ(sqi2, ts, os);
      }
    else if ( sqf )
      {
      /*I have appended all fragments into one by calling the GetBuffer method in 
      gdcmSequenceOfFragments which does not write the Table to the buffer.
      It is slightly buggy as the size returnes includes that of the table.
      Should I get the Table size and subtract it?
      Or should I append the table as well in the BulkData??
      */
      unsigned long size = sqf->ComputeByteLength();
      char *bulkData = new char [size];
      if(sqf->GetBuffer(bulkData, size))
      	{
      	if(size)
      		{
      		const char *suid = UIDgen.Generate();
        	os << "<BulkData uuid = \""<<
        				 suid << "\" />\n";
        	HandleBulkData( suid, ts, bulkData, size);
      		}
      	}
      /*      
      const BasicOffsetTable & table = sqf->GetTable();
      const ByteValue *bv = table.GetByteValue();
      
      if(bv->GetLength())
      	{
        const char *suid = UIDgen.Generate();
        os << "<BulkData uuid = \""<<
        			 suid << "\" />\n";
        HandleBulkData( suid, ts, bv->GetPointer(), bv->GetLength() );
        }
      
      unsigned int numfrag = sqf->GetNumberOfFragments();
      for(unsigned int i = 0; i < numfrag; i++)
        {        
        const Fragment& frag = sqf->GetFragment(i);
        const ByteValue *bv = frag.GetByteValue();
        if(bv->GetLength())
      		{
        	const char *suid = UIDgen.Generate();
        	os << "<BulkData uuid = \""<<
        				 suid << "\" />\n";
        	HandleBulkData( suid, ts, bv->GetPointer(), bv->GetLength() );
        	}        
        }
      */
      }
    else
      {
      // This is a byte value, so it should have been already treated.
      }
    os << "</DicomAttribute>\n";
    }
}



/*------------------------------------------------------------------------------------------------------------------------------------------------*/

void XMLPrinter::Print(std::ostream& os)
{
  /* XML Meta Info */
  const Tag CharacterEncoding(0x0008,0x0005);

  const DataSet &ds = F->GetDataSet();
  const FileMetaInformation &header = F->GetHeader();
  const TransferSyntax &ts = header.GetDataSetTransferSyntax();

  os << "<?xml version=\"1.0\" encoding=\"";
  if(ds.FindDataElement(CharacterEncoding))
    {
    const DataElement &de = ds.GetDataElement(CharacterEncoding);
    if( !de.IsEmpty() )
      {
      Attribute<0x8,0x5> at;
      at.SetFromDataElement( de );
      const char* EncodingFromFile = at.GetValue(0);
      if (!strcmp(EncodingFromFile,"ISO_IR 6"))
        os << "UTF-8";
      else if (!strcmp(EncodingFromFile,"ISO_IR 192"))
        os << "UTF-8";
      else if (!strcmp(EncodingFromFile,"ISO_IR 100"))
        os << "ISO-8859-1";
      else if (!strcmp(EncodingFromFile,"ISO_IR 101"))
        os << "ISO-8859-2";
      else if (!strcmp(EncodingFromFile,"ISO_IR 109"))
        os << "ISO-8859-3";
      else if (!strcmp(EncodingFromFile,"ISO_IR 110"))
        os << "ISO-8859-4";
      else if (!strcmp(EncodingFromFile,"ISO_IR 148"))
        os << "ISO-8859-9";
      else if (!strcmp(EncodingFromFile,"ISO_IR 144"))
        os << "ISO-8859-5";
      else if (!strcmp(EncodingFromFile,"ISO_IR 127"))
        os << "ISO-8859-6";
      else if (!strcmp(EncodingFromFile,"ISO_IR 126"))
        os << "ISO-8859-7";
      else if (!strcmp(EncodingFromFile,"ISO_IR 138"))
        os << "ISO-8859-8";
      else
        os << "UTF-8";
      os << "\"?>\n";
      }
    else
      {
      os << "UTF-8\"?>\n\n";
      }
    }
  else
    {
    os << "UTF-8\"?>\n\n";
    }
  os << "<NativeDicomModel xmlns=\"http://dicom.nema.org/PS3.19/models/NativeDICOM\">\n";

  PrintDataSet(ds, ts, os);

  os << "</NativeDicomModel>";
}

// Drop BulkData by default.
// Application programmer can override this mechanism.
void XMLPrinter::HandleBulkData(const char *uuid, const TransferSyntax & ts,
  const char *bulkdata, size_t bulklen)
{
  (void)ts;
  (void)uuid;
  (void)bulkdata;
  (void)bulklen;
}

}//end namespace gdcm