File: gdcmPDBHeader.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 (303 lines) | stat: -rw-r--r-- 7,593 bytes parent folder | download | duplicates (3)
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
/*=========================================================================

  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 "gdcmPDBHeader.h"
#include "gdcmPrivateTag.h"
#include "gdcmDataElement.h"
#include "gdcmDataSet.h"
#include "gdcmExplicitDataElement.h"
#include "gdcmSwapper.h"
#include "gdcmDeflateStream.h"

namespace gdcm
{

/*
 * In some GE MEDICAL SYSTEMS image one can find a Data Element: 0025,xx1b,GEMS_SERS_01
 * which is documented as Protocol Data Block (compressed).
 * in fact this is a simple text format compressed using the gzip algorithm
 *
 * Typically one could do:
 *
 *   $ gdcmraw -i input.dcm -o output.raw -t 0025,101b
 *
 * Skip the binary length (little endian encoding):
 *
 *   $ dd bs=4 skip=1 if=output.raw of=foo
 *
 * Check file type:
 *
 *   $ file foo
 *   foo: gzip compressed data, was "Ex421Ser8Scan1", from Unix
 *
 * Gunzip !
 *   $ gzip -dc < foo > bar
 *   $ cat bar
 *
 * THANKS to: John Reiser (BitWagon.com) for hints
 *
 * For sample see:
 * GE_MR_0025xx1bProtocolDataBlock.dcm
 * ( <=> http://server.oersted.dtu.dk/personal/jw/jwpublic/courses/31540/mri/second_set/dicom/t2/b17.dcm)
 */

/* Typical output:
 *
 * ENTRY "Head First"
 * POSITION "Supine"
 * ANREF "NA"
 * COIL "HEAD"
 * PLANE "OBLIQUE"
 * SEDESCFLAG "1"
 * SEDESC "AX FSE T2"
 * IMODE "2D"
 * PSEQ "FSE-XL"
 * IOPT "FC, EDR, TRF, Fast"
 * PLUG "22"
 * FILTCHOICE "None"
 * BWRT "-1"
 * TRICKSIMG "1"
 * TAG_SPACE "7"
 * TAG_TYPE "None"
 * USERCV0 "0.00"
 * USERCV6 "0.00"
 * USERCV7 "0.00"
 * USERCV21 "0.00"
 * USERCV_MASK "2097344"
 * TE "102.0"
 * NECHO "1"
 * TR "5720.0"
 * NUMACQS "1"
 * ETL "17"
 * BPMMODE "0"
 * AUTOTRGTYPE "0"
 * PSDTRIG "0"
 * SLICEORDER "1"
 * VIEWORDER "1"
 * TRREST "0"
 * TRACTIVE "0"
 * SLICEASSET "1.00"
 * PHASEASSET "1.00"
 * SEPSERIES "0"
 * AUTOTRIGWIN "0"
 * FOV "24.0"
 * SLTHICK "2.0"
 * SPC "2.0"
 * GRXOPT "0"
 * SLOC1 "L11.8"
 * SLOC2 "P29.9"
 * SLOC3 "I50.0"
 * ELOC1 "L11.6"
 * ELOC2 "P29.4"
 * ELOC3 "S53.9"
 * NOSLC "27"
 * SL3PLANE "0"
 * SL3PLANE1 "0"
 * SL3PLANE2 "0"
 * SL3PLANE3 "0"
 * SPCPERPLANE1 "0.0"
 * SPCPERPLANE2 "0.0"
 * SPCPERPLANE3 "0.0"
 * MATRIXX "448"
 * MATRIXY "224"
 * SWAPPF "A/P"
 * NEX "4.00"
 * CONTRAST "No"
 * CONTAM "Yes   "
 * TBLDELTA "0.00"
 * PHASEFOV "0.75"
 * RBW "31.25"
 * AUTOSHIM "Auto"
 * PHASECORR "Yes"
 * FLDIR "Freq"
 * NUMACCELFACTOR "1.00"
 * PAUSEDELMASKACQ "1"
 * NOTES ".pn/_3"
 * GRIP_NUMSLGROUPS "1"
 * GRIP_SLGROUP1 "-11.703952 -29.677423 1.949659 0.002380 0.004775 0.999985 0.999997 0.000175 -0.002380 0.000186 -0.999988 0.004775 27 0.000000 1 0 0"
 * GRIP_SATGROUP1 "0"
 * GRIP_SATGROUP2 "0"
 * GRIP_SATGROUP3 "0"
 * GRIP_SATGROUP4 "0"
 * GRIP_SATGROUP5 "0"
 * GRIP_SATGROUP6 "0"
 * GRIP_TRACKER "0"
 * GRIP_SPECTRO "0"
 * GRIP_NUMPSCVOL "0"
 * GRIP_PSCVOL1 "0"
 * GRIP_PSCVOL2 "0"
 * GRIP_PSCVOLFOV "0.000000"
 * GRIP_PSCVOLTHICK "0.000000"
 * AUTOSUBOPTIONS "0"
 * AUTOSCIC "0"
 * AUTOVOICE "0"
 * PRESETDELAY "0.0"
 * MASKPHASE "0"
 * MASKPAUSE "0"
 * TOTALNOSTATION "0"
 * STATION "0"
 */

PDBElement PDBHeader::PDBEEnd = PDBElement( );

  const PDBElement& PDBHeader::GetPDBEEnd() const
  {
    return PDBEEnd;
  }

int PDBHeader::readprotocoldatablock(const char *input, size_t inputlen, bool verbose)
{
  (void)verbose;
  // First 4 bytes are the length (again)
  uint32_t len = *(uint32_t*)input;
  SwapperNoOp::SwapArray(&len,1);
  //if( verbose )
  //  std::cout << len << "," << inputlen << std::endl;
  if( len + 4 + 1 == inputlen )
    {
    //if( verbose )
    //  std::cout << "gzip stream was padded with an extra 0 \n";
    }
  else if( len + 4 == inputlen )
    {
    //if( verbose )
    //  std::cout << "gzip stream was not padded with an extra 0 \n";
    }
  else
    {
    //std::cerr << "Found the Protocol Data Block but could not read length..." << std::endl;
    return 1;
    }
  // Alright we need to check if the binary blob was padded, if padded we need to
  // discard the trailing \0 to please gzip:
  std::string str( input + 4, input + len );
  std::istringstream is( str );

  zlib_stream::zip_istream gzis( is );

//  if (gzis.is_gzip())
//    {
//    std::cout<<"crc check: "<<( gzis.check_crc() ? "ok" : "failed");
//    std::cout << std::endl;
//    }

  std::string out;
  //while( gzis >> out )
  while( std::getline(gzis , out ) )
    {
    PDBElement pdbel;
    //std::cout << out << std::endl;
    std::istringstream is2( out );
    std::string name, value;
    is2 >> name;
    std::getline(is2, value);
    pdbel.SetName( name.c_str() );
    // remove the first space character and the first & last " character
    std::string value2( value.begin()+2, value.end()-1);
    pdbel.SetValue( value2.c_str() );
    InternalPDBDataSet.push_back( pdbel );
    }
  //std::cout << out.size();

  return 0;
}

/*
int DumpProtocolDataBlock(const std::string & filename, bool verbose)
{
  gdcm::Reader reader;
  reader.SetFileName( filename.c_str() );
  if( !reader.Read() )
    {
    std::cerr << "Failed to read: " << filename << std::endl;
    return 1;
    }
  const gdcm::DataSet& ds = reader.GetFile().GetDataSet();

  const gdcm::PrivateTag tprotocoldatablock(0x0025,0x1b,"GEMS_SERS_01");
  if( !ds.FindDataElement( tprotocoldatablock) )
    {
    std::cerr << "Could not find tag: " << tprotocoldatablock << std::endl;
    return 1;
    }
  const gdcm::DataElement& protocoldatablock= ds.GetDataElement( tprotocoldatablock);
  if ( protocoldatablock.IsEmpty() ) return 1;
  const gdcm::ByteValue * bv = protocoldatablock.GetByteValue();

  std::cout << "Dumping: " << tprotocoldatablock << std::endl;
  int ret = readprotocoldatablock( bv->GetPointer(), bv->GetLength(), verbose );

  return ret;
}
*/

bool PDBHeader::LoadFromDataElement(DataElement const &protocoldatablock)
{
  InternalPDBDataSet.clear();
  if ( protocoldatablock.IsEmpty() ) return false;
  const gdcm::ByteValue * bv = protocoldatablock.GetByteValue();

  //std::cout << "Dumping: " << tprotocoldatablock << std::endl;
  int ret = readprotocoldatablock( bv->GetPointer(), bv->GetLength(), false);

  if(ret) return false;
  return true;
}

void PDBHeader::Print(std::ostream &os) const
{
  std::vector<PDBElement>::const_iterator it = InternalPDBDataSet.begin();

  for(; it != InternalPDBDataSet.end(); ++it)
    {
    os << *it << std::endl;
    }
}

const PDBElement &PDBHeader::GetPDBElementByName(const char *name)
{
  std::vector<PDBElement>::const_iterator it = InternalPDBDataSet.begin();
  for(; it != InternalPDBDataSet.end(); ++it)
    {
    const char *itname = it->GetName();
    if( strcmp(name, itname) == 0 )
      {
      return *it;
      }
    }
    return GetPDBEEnd();
}

bool PDBHeader::FindPDBElementByName(const char *name)
{
  std::vector<PDBElement>::const_iterator it = InternalPDBDataSet.begin();
  for(; it != InternalPDBDataSet.end(); ++it)
    {
    const char *itname = it->GetName();
    if( strcmp(name, itname) == 0 )
      {
      return true;
      }
    }
  return false;
}

static const char pdbheader[] = "GEMS_SERS_01";
static const gdcm::PrivateTag t1(0x0025,0x001b,pdbheader);

const PrivateTag & PDBHeader::GetPDBInfoTag()
{
  return t1;
}

} // end namespace gdcm