src2/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         //////////////////////////////////////////////////////////////
 147         // create a descriptor (name, attributes...) from a file)       //
 148         // @param : file path                                                                           //
 149         // return : -                                                                                           //
 150         //////////////////////////////////////////////////////////////
 151         void Descriptor::createDescriptorfromFile(const std::string &i_name)
 152         {
 153                 Clear();
 154
 155                 // read file and put in buffer
 156                 std::ifstream i_file(i_name.c_str());
 157                 std::stringstream buffer;
 158                 buffer << i_file.rdbuf();
 159                 std::string line;
 160                 bool bname;
 161                 int ilevel = -1;
 162
 163
 164                 while(std::getline(buffer, line))
 165                 {
 166                         if(line =="<level>")
 167                         {       //increment levels.
 168                                 ilevel++;
 169                                 bname = true;
 170                         }
 171                         else if(bname)
 172                         {
 173                                 // For each level, a name to describe it
 174                                 Add(LevelDescriptor(line));
 175                                 bname = false;
 176                         }
 177                         else
 178                         {
 179                                 // split line to find all tags
 180                                 std::vector<std::string> descriptors;
 181                                 std::string separator = " ";
 182                                 std::string::size_type last_pos = line.find_first_not_of(separator);
 183                                 //find first separator
 184                                 std::string::size_type pos = line.find_first_of(separator, last_pos);
 185                                 while(std::string::npos != pos || std::string::npos != last_pos)
 186                                 {
 187                                         descriptors.push_back(line.substr(last_pos, pos - last_pos));
 188                                         last_pos = line.find_first_not_of(separator, pos);
 189                                         pos = line.find_first_of(separator, last_pos);
 190                                 }
 191
 192                                 // By default, the last tag is at zero and not recorded but if take in count
 193                                 unsigned int flag = 0;
 194                                 if(descriptors.size() == 4)
 195                                 {
 196                                         std::stringstream val;
 197                                         val << std::dec << descriptors[3];
 198                                         val>> flag;
 199                                 }
 200
 201                                 // if Dicom tag, use "group" and "element" descriptor
 202                                 if(descriptors[0] == "D")
 203                                 {       std::stringstream val, val2;
 204                                         unsigned short group;
 205                                         unsigned short element;
 206                                         val <<   std::dec << descriptors[1] ;
 207                                         val >> std::hex >> group;
 208                                         val2 << std::dec <<  descriptors[2];
 209                                         val2 >> std::hex >> element;
 210                                         Add(AttributeDescriptor( group,element,flag), ilevel);
 211                                 }
 212
 213                                 else if(descriptors[0].find("#") != -1)
 214                                 {
 215                                                 // commented line continue to next line
 216                                 }
 217                                 else
 218                                 {       boost::algorithm::replace_all(descriptors[2],"_"," ");
 219                                         Add(AttributeDescriptor( descriptors[1].c_str(),descriptors[2].c_str(),flag), ilevel);
 220                                 }
 221                         }
 222                 }
 223         }
 224
 225
 226     //==================================================================
 227
 228     //==================================================================
 229     /// Adds a LevelDescriptor at the end of the list
 230     void Descriptor::Add(const LevelDescriptor& d)
 231     {
 232       mLevelDescriptorList.push_back(d);
 233     }
 234     //==================================================================
 235
 236     //==================================================================
 237     /// Adds an AttributeDescriptor to level l
 238     void Descriptor::Add(const AttributeDescriptor& d, int l)
 239     {
 240       mLevelDescriptorList[l].Add(d);
 241       // TO DO : update DicomTagToName and NameToDicomTag map
 242     }
 243     //==================================================================
 244
 245     //==================================================================
 246     /// Clears the Descriptor
 247     void Descriptor::Clear()
 248     {
 249       mLevelDescriptorList.clear();
 250     }
 251     //==================================================================
 252
 253     //==================================================================
 254     /// Builds the key to value map of all the attributes of the tree
 255     void Descriptor::BuildAttributeMap( std::map<std::string,std::string>& map ) const
 256     {
 257       map.clear();
 258       LevelDescriptorListType::const_iterator l;
 259       for (l = GetLevelDescriptorList().begin();
 260            l!= GetLevelDescriptorList().end();
 261            ++l)
 262         {
 263           LevelDescriptor::AttributeDescriptorListType::const_iterator a;
 264           for (a = l->GetAttributeDescriptorList().begin();
 265                a!= l->GetAttributeDescriptorList().end();
 266                ++a)
 267             {
 268               map[a->GetKey()]="";
 269             }
 270         }
 271     }
 272
 273   }
 274 }