src/creaImageIOTreeDescriptor.cpp

   1 #include <creaImageIOTreeDescriptor.h>
   2 #include <boost/algorithm/string/split.hpp>
   3 #include <boost/algorithm/string/replace.hpp>
   4 #include <creaImageIOSystem.h>
   5 #include <boost/filesystem.hpp>
   6
   7
   8 #include <fstream>
   9
  10
  11 namespace creaImageIO
  12 {
  13
  14   namespace tree
  15   {
  16
  17     //==================================================================
  18     /// The attribute is hidden (not visible to user)
  19     const unsigned int AttributeDescriptor::PRIVATE = 1;
  20     /// The attribute enters in unique identifier constitution
  21     const unsigned int AttributeDescriptor::IDENTIFIER = 2;
  22     /// The attribute can be edited
  23     const unsigned int AttributeDescriptor::EDITABLE = 3;
  24     /// the attribute describes the node
  25     const unsigned int AttributeDescriptor::LABEL = 4;
  26     //==================================================================
  27
  28     //==================================================================
  29     Descriptor::Descriptor()
  30     {
  31       CreateLevel0Descriptor();
  32     }
  33     //==================================================================
  34
  35    //==================================================================
  36     Descriptor::~Descriptor()
  37     {
  38     }
  39     //==================================================================
  40
  41     //==================================================================
  42     void Descriptor::CreateLevel0Descriptor()
  43     {
  44       Add(LevelDescriptor("Root"));
  45     }
  46     //==================================================================
  47
  48     //==================================================================
  49     /// Creates the default descriptor
  50     void Descriptor::CreateDefault()
  51     {
  52       // clears the existing one
  53       Clear();
  54
  55       // Creates the level 0 descriptor
  56       CreateLevel0Descriptor();
  57       // Creates the attribute "Name"
  58       Add(AttributeDescriptor("Name","Name",
  59                               AttributeDescriptor::LABEL),0);
  60
  61       // Patient level
  62       Add(LevelDescriptor("Patient"));
  63       Add(AttributeDescriptor("NumberOfChildren","#Series",0),1);   // Number of Series
  64       Add(AttributeDescriptor(0x0010,0x0010,   // Patient name
  65                               AttributeDescriptor::LABEL),1);
  66       Add(AttributeDescriptor(0x0010,0x0040),1); // Patient sex
  67       Add(AttributeDescriptor(0x0010,0x0030),1); // Patient birthday
  68       Add(AttributeDescriptor(0x0010,0x0020,   // Patient ID
  69                               AttributeDescriptor::IDENTIFIER),1);
  70
  71       // Study-series level
  72       Add(LevelDescriptor("Series"));
  73       Add(AttributeDescriptor("NumberOfChildren","#Images",0),2);   // Number of images
  74       Add(AttributeDescriptor(0x0008,0x0060,    // Modality
  75                               AttributeDescriptor::LABEL),2);
  76       Add(AttributeDescriptor(0x0008,0x1030),2); // Study Description
  77       Add(AttributeDescriptor(0x0008,0x103E),2); // Description
  78       Add(AttributeDescriptor(0x0008,0x0080),2); // Institution Name
  79       Add(AttributeDescriptor(0x0008,0x0081),2); // Institution Adress
  80       Add(AttributeDescriptor(0x0008,0x1010),2); // Station Name
  81       Add(AttributeDescriptor(0x0008,0x1048),2); // Physician of Record
  82       Add(AttributeDescriptor(0x0008,0x1050),2); // Performing Physician's Name
  83       Add(AttributeDescriptor(0x0018,0x1030),2); // Protocol Name
  84
  85       Add(AttributeDescriptor(0x0020,0x0010),2); // Study ID
  86       Add(AttributeDescriptor(0x0008,0x0020),2); // Study Date
  87       Add(AttributeDescriptor(0x0008,0x0030),2); // Study Time
  88       Add(AttributeDescriptor(0x0008,0x0050),2); // Study Accession Number
  89       Add(AttributeDescriptor(0x0008,0x0005),2); // Specific character set
  90       Add(AttributeDescriptor(0x0008,0x0021),2); // Series Date
  91       Add(AttributeDescriptor(0x0008,0x0031),2); // Series time
  92
  93       Add(AttributeDescriptor(0x0020,0x000D   // Study Instance UID
  94                                                     ),2);//AttributeDescriptor::IDENTIFIER),2);
  95       Add(AttributeDescriptor(0x0020,0x000E,   // Series Instance UID
  96                                 AttributeDescriptor::IDENTIFIER),2);
  97       // |
  98       //                        AttributeDescriptor::LABEL),2);
  99
 100
 101       // Image level
 102       Add(LevelDescriptor("Image"));
 103
 104       Add(AttributeDescriptor(0x0020,0x0013),3); // Image Number
 105
 106       Add(AttributeDescriptor(0x0028,0x0010),3); // Rows
 107       Add(AttributeDescriptor(0x0028,0x0011),3); // Columns
 108       Add(AttributeDescriptor(0x0028,0x0012),3); // Planes
 109       Add(AttributeDescriptor(0x0028,0x0002),3); // Sample per pixels
 110       Add(AttributeDescriptor(0x0028,0x0008),3); // Number of Frames
 111       Add(AttributeDescriptor(0x0028,0x0004),3); // Photometric Interpretation
 112       Add(AttributeDescriptor(0x0028,0x0103),3); // Pixel Representation
 113
 114       Add(AttributeDescriptor(0x0020,0x0032),3); // Image Position Patient
 115       Add(AttributeDescriptor(0x0020,0x0037),3); // Image Orientation Patient
 116       Add(AttributeDescriptor(0x0020,0x1041),3); // Slice Location
 117       Add(AttributeDescriptor(0x0028,0x0006),3); // Planar Configuration
 118
 119       Add(AttributeDescriptor(0x0028,0x0030),3); // Pixel Spacing
 120       Add(AttributeDescriptor(0x0028,0x0100),3); // AlocatedBits
 121       Add(AttributeDescriptor(0x0028,0x0101),3); // StoredBits
 122
 123       Add(AttributeDescriptor(0x0008,0x0008),3); // Image Type
 124       Add(AttributeDescriptor(0x0008,0x0023),3); // Content Date
 125       Add(AttributeDescriptor(0x0008,0x0033),3); // Content Time
 126
 127       Add(AttributeDescriptor(0x0020,0x4000),3); // Image Comments
 128
 129       Add(AttributeDescriptor(0x0004,0x1500,   // File Name
 130                                 AttributeDescriptor::LABEL),3);
 131       Add(AttributeDescriptor(0x0028,0x1052),3); // Rescale Intercept
 132       Add(AttributeDescriptor(0x0028,0x1053),3); // Rescale Slope
 133
 134       Add(AttributeDescriptor(0x0050,0x0004),3); // Calibration Image
 135
 136       Add(AttributeDescriptor(0x0020,0x0052   // Frame Reference UID
 137                                            ),3);
 138       Add(AttributeDescriptor(0x0008,0x0016),3); // SOP Class UID
 139       Add(AttributeDescriptor("FullFileName",  // Full file name
 140                                 "Full file name",
 141                                 AttributeDescriptor::IDENTIFIER),3);
 142
 143     }
 144
 145         //////////////////////////////////////////////////////////////
 146         // create a descriptor (name, attributes...) from a file)       //
 147         // @param : file path                                           //
 148         // return : -                                                   //
 149         //////////////////////////////////////////////////////////////
 150         void Descriptor::createDescriptorfromFile(const std::string &i_name)
 151         {
 152                 Clear();
 153
 154                 // read file and put in buffer
 155                 std::ifstream i_file(i_name.c_str());
 156                 std::stringstream buffer;
 157                 buffer << i_file.rdbuf();
 158                 std::string line;
 159                 bool bname;
 160                 int ilevel = -1;
 161
 162
 163                 while(std::getline(buffer, line))
 164                 {
 165                         if(line =="<level>")
 166                         {       //increment levels.
 167                                 ilevel++;
 168                                 bname = true;
 169                         }
 170                         else if(bname)
 171                         {
 172                                 // For each level, a name to describe it
 173                                 Add(LevelDescriptor(line));
 174                                 bname = false;
 175                         }
 176                         else if(line.empty()) // to avoid end line
 177                         {
 178                                 return;
 179                         }
 180                         else
 181                         {
 182                                 // split line to find all tags
 183                                 std::vector<std::string> descriptors;
 184                                 std::string separator = " ";
 185                                 std::string::size_type last_pos = line.find_first_not_of(separator);
 186                                 //find first separator
 187                                 std::string::size_type pos = line.find_first_of(separator, last_pos);
 188                                 while(std::string::npos != pos || std::string::npos != last_pos)
 189                                 {
 190                                         descriptors.push_back(line.substr(last_pos, pos - last_pos));
 191                                         last_pos = line.find_first_not_of(separator, pos);
 192                                         pos = line.find_first_of(separator, last_pos);
 193                                 }
 194
 195                                 // By default, the last tag is at zero and not recorded but if take in count
 196                                 unsigned int flag = 0;
 197                                 if(descriptors.size() == 4)
 198                                 {
 199                                         std::stringstream val;
 200                                         val << std::dec << descriptors[3];
 201                                         val>> flag;
 202                                 }
 203
 204                                 // if Dicom tag, use "group" and "element" descriptor
 205                                 if(descriptors[0] == "D")
 206                                 {       std::stringstream val, val2;
 207                                         unsigned short group;
 208                                         unsigned short element;
 209                                         val <<   std::dec << descriptors[1] ;
 210                                         val >> std::hex >> group;
 211                                         val2 << std::dec <<  descriptors[2];
 212                                         val2 >> std::hex >> element;
 213                                         Add(AttributeDescriptor( group,element,flag), ilevel);
 214                                 }
 215
 216                                 else if(descriptors[0].find("#") != -1)
 217                                 {
 218                                         // commented line continue to next line
 219                                 }
 220                                 else
 221                                 {       boost::algorithm::replace_all(descriptors[2],"_"," ");
 222                                         Add(AttributeDescriptor( descriptors[1].c_str(),descriptors[2].c_str(),flag), ilevel);
 223                                 }
 224                         }
 225                 }
 226         }
 227
 228     //==================================================================
 229
 230     //==================================================================
 231     /// Adds a LevelDescriptor at the end of the list
 232     void Descriptor::Add(const LevelDescriptor& d)
 233     {
 234       mLevelDescriptorList.push_back(d);
 235     }
 236     //==================================================================
 237
 238     //==================================================================
 239     /// Adds an AttributeDescriptor to level l
 240     void Descriptor::Add(const AttributeDescriptor& d, int l)
 241     {
 242       mLevelDescriptorList[l].Add(d);
 243       // TO DO : update DicomTagToName and NameToDicomTag map
 244     }
 245     //==================================================================
 246
 247     //==================================================================
 248     /// Clears the Descriptor
 249     void Descriptor::Clear()
 250     {
 251       mLevelDescriptorList.clear();
 252     }
 253
 254     //==================================================================
 255
 256     //==================================================================
 257     /// Builds the key to value map of all the attributes of the tree
 258     void Descriptor::BuildAttributeMap( std::map<std::string,std::string>& map ) const
 259     {
 260       map.clear();
 261       LevelDescriptorListType::const_iterator l;
 262       for (l = GetLevelDescriptorList().begin();
 263            l!= GetLevelDescriptorList().end();
 264            ++l)
 265         {
 266           LevelDescriptor::AttributeDescriptorListType::const_iterator a;
 267           for (a = l->GetAttributeDescriptorList().begin();
 268                a!= l->GetAttributeDescriptorList().end();
 269                ++a)
 270             {
 271               map[a->GetKey()]="";
 272             }
 273         }
 274     }
 275
 276
 277     //==================================================================
 278         // test if an attribute is present in DescriptionList
 279         // return level's name
 280         const std::string Descriptor::isExist(const std::string i_attr)
 281         {
 282                 std::string name = "";
 283                 LevelDescriptorListType::const_iterator l = GetLevelDescriptorList().begin();
 284                 for (;     l!= GetLevelDescriptorList().end(); ++l)
 285                 {
 286                         LevelDescriptor::AttributeDescriptorListType::const_iterator a = l->GetAttributeDescriptorList().begin();
 287                 for(;a!= l->GetAttributeDescriptorList().end(); ++a)
 288                         {
 289                                 if (a->GetKey() == i_attr)
 290                                 {
 291                                         name = l->GetName();
 292                                         break;
 293                                 }
 294                         }
 295                 }
 296                 return name.c_str();
 297         }
 298   }
 299 }