creaImageIO_lib
creaImageIOTreeDescriptor.cpp
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1 /*
2 # ---------------------------------------------------------------------
3 #
4 # Copyright (c) CREATIS (Centre de Recherche en Acquisition et Traitement de l'Image
5 # pour la Santé)
6 # Authors : Eduardo Davila, Frederic Cervenansky, Claire Mouton
7 # Previous Authors : Laurent Guigues, Jean-Pierre Roux
8 # CreaTools website : www.creatis.insa-lyon.fr/site/fr/creatools_accueil
9 #
10 # This software is governed by the CeCILL-B license under French law and
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14 # http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
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26 */
27 
28 
29 #include <creaImageIOTreeDescriptor.h>
30 #include <boost/algorithm/string/split.hpp>
31 #include <boost/algorithm/string/replace.hpp>
32 #include <creaImageIOSystem.h>
33 #include <boost/filesystem.hpp>
34 
35 
36 #include <fstream>
37 
38 
39 namespace creaImageIO
40 {
41 
42  namespace tree
43  {
44 
45  //==================================================================
47  const unsigned int AttributeDescriptor::PRIVATE = 1;
49  const unsigned int AttributeDescriptor::IDENTIFIER = 2;
51  const unsigned int AttributeDescriptor::EDITABLE = 3;
53  const unsigned int AttributeDescriptor::LABEL = 4;
54  //==================================================================
55 
56  //==================================================================
57  Descriptor::Descriptor()
58  {
59  CreateLevel0Descriptor();
60  }
61  //==================================================================
62 
63  //==================================================================
64  Descriptor::~Descriptor()
65  {
66  }
67  //==================================================================
68 
69  //==================================================================
70  void Descriptor::CreateLevel0Descriptor()
71  {
72  Add(LevelDescriptor("Root"));
73  }
74  //==================================================================
75 
76  //==================================================================
78  void Descriptor::CreateDefault()
79  {
80  // clears the existing one
81  Clear();
82 
83  // Creates the level 0 descriptor
84  CreateLevel0Descriptor();
85  // Creates the attribute "Name"
86  Add(AttributeDescriptor("Name","Name",
87  AttributeDescriptor::LABEL),0);
88 
89  // Patient level
90  Add(LevelDescriptor("Patient"));
91  Add(AttributeDescriptor("NumberOfChildren","#Series",0),1); // Number of Series
92  Add(AttributeDescriptor(0x0010,0x0010, // Patient name
93  AttributeDescriptor::LABEL),1);
94  Add(AttributeDescriptor(0x0010,0x0040),1); // Patient sex
95  Add(AttributeDescriptor(0x0010,0x0030),1); // Patient birthday
96  Add(AttributeDescriptor(0x0010,0x0020, // Patient ID
97  AttributeDescriptor::IDENTIFIER),1);
98 
99  // Study-series level
100  Add(LevelDescriptor("Series"));
101  Add(AttributeDescriptor("NumberOfChildren","#Images",0),2); // Number of images
102  Add(AttributeDescriptor(0x0008,0x0060, // Modality
103  AttributeDescriptor::LABEL),2);
104  Add(AttributeDescriptor(0x0008,0x1030),2); // Study Description
105  Add(AttributeDescriptor(0x0008,0x103E),2); // Description
106  Add(AttributeDescriptor(0x0008,0x0080),2); // Institution Name
107  Add(AttributeDescriptor(0x0008,0x0081),2); // Institution Adress
108  Add(AttributeDescriptor(0x0008,0x1010),2); // Station Name
109  Add(AttributeDescriptor(0x0008,0x1048),2); // Physician of Record
110  Add(AttributeDescriptor(0x0008,0x1050),2); // Performing Physician's Name
111  Add(AttributeDescriptor(0x0018,0x1030),2); // Protocol Name
112 
113  Add(AttributeDescriptor(0x0020,0x0010),2); // Study ID
114  Add(AttributeDescriptor(0x0008,0x0020),2); // Study Date
115  Add(AttributeDescriptor(0x0008,0x0030),2); // Study Time
116  Add(AttributeDescriptor(0x0008,0x0050),2); // Study Accession Number
117  Add(AttributeDescriptor(0x0008,0x0005),2); // Specific character set
118  Add(AttributeDescriptor(0x0008,0x0021),2); // Series Date
119  Add(AttributeDescriptor(0x0008,0x0031),2); // Series time
120 
121  Add(AttributeDescriptor(0x0020,0x000D // Study Instance UID
122  ),2);//AttributeDescriptor::IDENTIFIER),2);
123  Add(AttributeDescriptor(0x0020,0x000E, // Series Instance UID
124  AttributeDescriptor::IDENTIFIER),2);
125  // |
126  // AttributeDescriptor::LABEL),2);
127 
128 
129  // Image level
130  Add(LevelDescriptor("Image"));
131 
132  Add(AttributeDescriptor(0x0020,0x0013),3); // Image Number
133 
134  Add(AttributeDescriptor(0x0028,0x0010),3); // Rows
135  Add(AttributeDescriptor(0x0028,0x0011),3); // Columns
136  Add(AttributeDescriptor(0x0028,0x0012),3); // Planes
137  Add(AttributeDescriptor(0x0028,0x0002),3); // Sample per pixels
138  Add(AttributeDescriptor(0x0028,0x0008),3); // Number of Frames
139  Add(AttributeDescriptor(0x0028,0x0004),3); // Photometric Interpretation
140  Add(AttributeDescriptor(0x0028,0x0103),3); // Pixel Representation
141 
142  Add(AttributeDescriptor(0x0020,0x0032),3); // Image Position Patient
143  Add(AttributeDescriptor(0x0020,0x0037),3); // Image Orientation Patient
144  Add(AttributeDescriptor(0x0020,0x1041),3); // Slice Location
145  Add(AttributeDescriptor(0x0028,0x0006),3); // Planar Configuration
146 
147  Add(AttributeDescriptor(0x0028,0x0030),3); // Pixel Spacing
148  Add(AttributeDescriptor(0x0028,0x0100),3); // AlocatedBits
149  Add(AttributeDescriptor(0x0028,0x0101),3); // StoredBits
150 
151  Add(AttributeDescriptor(0x0008,0x0008),3); // Image Type
152  Add(AttributeDescriptor(0x0008,0x0023),3); // Content Date
153  Add(AttributeDescriptor(0x0008,0x0033),3); // Content Time
154 
155  Add(AttributeDescriptor(0x0020,0x4000),3); // Image Comments
156 
157  Add(AttributeDescriptor(0x0004,0x1500, // File Name
158  AttributeDescriptor::LABEL),3);
159  Add(AttributeDescriptor(0x0028,0x1052),3); // Rescale Intercept
160  Add(AttributeDescriptor(0x0028,0x1053),3); // Rescale Slope
161 
162  Add(AttributeDescriptor(0x0050,0x0004),3); // Calibration Image
163 
164  Add(AttributeDescriptor(0x0020,0x0052 // Frame Reference UID
165  ),3);
166  Add(AttributeDescriptor(0x0008,0x0016),3); // SOP Class UID
167  Add(AttributeDescriptor("FullFileName", // Full file name
168  "Full file name",
169  AttributeDescriptor::IDENTIFIER),3);
170 
171  }
172 
174  // create a descriptor (name, attributes...) from a file) //
175  // @param : file path //
176  // return : - //
178  void Descriptor::createDescriptorfromFile(const std::string &i_name)
179  {
180  Clear();
181 
182  // read file and put in buffer
183  std::ifstream i_file(i_name.c_str());
184  std::stringstream buffer;
185  buffer << i_file.rdbuf();
186  std::string line;
187  bool bname;
188  int ilevel = -1;
189 
190 
191  while(std::getline(buffer, line))
192  {
193  if(line =="<level>")
194  { //increment levels.
195  ilevel++;
196  bname = true;
197  }
198  else if(bname)
199  {
200  // For each level, a name to describe it
201  Add(LevelDescriptor(line));
202  bname = false;
203  }
204  else if(line.empty()) // to avoid end line
205  {
206  return;
207  }
208  else
209  {
210  // split line to find all tags
211  std::vector<std::string> descriptors;
212  std::string separator = " ";
213  std::string::size_type last_pos = line.find_first_not_of(separator);
214  //find first separator
215  std::string::size_type pos = line.find_first_of(separator, last_pos);
216  while(std::string::npos != pos || std::string::npos != last_pos)
217  {
218  descriptors.push_back(line.substr(last_pos, pos - last_pos));
219  last_pos = line.find_first_not_of(separator, pos);
220  pos = line.find_first_of(separator, last_pos);
221  }
222 
223  // By default, the last tag is at zero and not recorded but if take in count
224  unsigned int flag = 0;
225  if(descriptors.size() == 4)
226  {
227  std::stringstream val;
228  val << std::dec << descriptors[3];
229  val>> flag;
230  }
231 
232  // if Dicom tag, use "group" and "element" descriptor
233  if(descriptors[0] == "D")
234  { std::stringstream val, val2;
235  unsigned short group;
236  unsigned short element;
237  val << std::dec << descriptors[1] ;
238  val >> std::hex >> group;
239  val2 << std::dec << descriptors[2];
240  val2 >> std::hex >> element;
241  Add(AttributeDescriptor( group,element,flag), ilevel);
242  }
243 
244  else if(descriptors[0].find("#") != -1)
245  {
246  // commented line continue to next line
247  }
248  else
249  { boost::algorithm::replace_all(descriptors[2],"_"," ");
250  Add(AttributeDescriptor( descriptors[1].c_str(),descriptors[2].c_str(),flag), ilevel);
251  }
252  }
253  }
254  }
255 
256  //==================================================================
257 
258  //==================================================================
260  void Descriptor::Add(const LevelDescriptor& d)
261  {
262  mLevelDescriptorList.push_back(d);
263  }
264  //==================================================================
265 
266  //==================================================================
268  void Descriptor::Add(const AttributeDescriptor& d, int l)
269  {
270  mLevelDescriptorList[l].Add(d);
271  // TO DO : update DicomTagToName and NameToDicomTag map
272  }
273  //==================================================================
274 
275  //==================================================================
277  void Descriptor::Clear()
278  {
279  mLevelDescriptorList.clear();
280  }
281 
282  //==================================================================
283 
284  //==================================================================
286  void Descriptor::BuildAttributeMap( std::map<std::string,std::string>& map ) const
287  {
288  map.clear();
289  LevelDescriptorListType::const_iterator l;
290  for (l = GetLevelDescriptorList().begin();
291  l!= GetLevelDescriptorList().end();
292  ++l)
293  {
294  LevelDescriptor::AttributeDescriptorListType::const_iterator a;
295  for (a = l->GetAttributeDescriptorList().begin();
296  a!= l->GetAttributeDescriptorList().end();
297  ++a)
298  {
299  map[a->GetKey()]="";
300  }
301  }
302  }
303 
304 
305  //==================================================================
306  // test if an attribute is present in DescriptionList
307  // return level's name
308  const std::string Descriptor::isExist(const std::string i_attr)
309  {
310  std::string name = "";
311  LevelDescriptorListType::const_iterator l = GetLevelDescriptorList().begin();
312  for (; l!= GetLevelDescriptorList().end(); ++l)
313  {
314  LevelDescriptor::AttributeDescriptorListType::const_iterator a = l->GetAttributeDescriptorList().begin();
315  for(;a!= l->GetAttributeDescriptorList().end(); ++a)
316  {
317  if (a->GetKey() == i_attr)
318  {
319  name = l->GetName();
320  break;
321  }
322  }
323  }
324  return name.c_str();
325  }
326  }
327 }