creaImageIOTreeDescriptor.cpp

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#include <creaImageIOTreeDescriptor.h>
#include <boost/algorithm/string/split.hpp>
#include <boost/algorithm/string/replace.hpp>
#include <creaImageIOSystem.h>
#include <boost/filesystem.hpp>


#include <fstream>


namespace creaImageIO
{

  namespace tree
  {

    //==================================================================
    const unsigned int AttributeDescriptor::PRIVATE = 1;
    const unsigned int AttributeDescriptor::IDENTIFIER = 2;
    const unsigned int AttributeDescriptor::EDITABLE = 3;
    const unsigned int AttributeDescriptor::LABEL = 4;
    //==================================================================

    //==================================================================
    Descriptor::Descriptor()
    {
      CreateLevel0Descriptor();
    }
    //==================================================================

   //==================================================================
    Descriptor::~Descriptor()
    {
    }
    //==================================================================

    //==================================================================
    void Descriptor::CreateLevel0Descriptor()
    {
      Add(LevelDescriptor("Root"));
    }
    //==================================================================
    
    //==================================================================
    void Descriptor::CreateDefault()
    {
      // clears the existing one
      Clear();
      
      // Creates the level 0 descriptor 
      CreateLevel0Descriptor();
      // Creates the attribute "Name"
      Add(AttributeDescriptor("Name","Name",
                              AttributeDescriptor::LABEL),0);
      
      // Patient level
      Add(LevelDescriptor("Patient"));
      Add(AttributeDescriptor("NumberOfChildren","#Series",0),1);   // Number of Series
      Add(AttributeDescriptor(0x0010,0x0010,   // Patient name
                              AttributeDescriptor::LABEL),1);
      Add(AttributeDescriptor(0x0010,0x0040),1); // Patient sex
      Add(AttributeDescriptor(0x0010,0x0030),1); // Patient birthday
      Add(AttributeDescriptor(0x0010,0x0020,   // Patient ID
                              AttributeDescriptor::IDENTIFIER),1);

      // Study-series level
      Add(LevelDescriptor("Series"));
      Add(AttributeDescriptor("NumberOfChildren","#Images",0),2);   // Number of images
      Add(AttributeDescriptor(0x0008,0x0060,    // Modality
                              AttributeDescriptor::LABEL),2);
      Add(AttributeDescriptor(0x0008,0x1030),2); // Study Description
      Add(AttributeDescriptor(0x0008,0x103E),2); // Description
      Add(AttributeDescriptor(0x0008,0x0080),2); // Institution Name
      Add(AttributeDescriptor(0x0008,0x0081),2); // Institution Adress
      Add(AttributeDescriptor(0x0008,0x1010),2); // Station Name
      Add(AttributeDescriptor(0x0008,0x1048),2); // Physician of Record
      Add(AttributeDescriptor(0x0008,0x1050),2); // Performing Physician's Name
      Add(AttributeDescriptor(0x0018,0x1030),2); // Protocol Name

      Add(AttributeDescriptor(0x0020,0x0010),2); // Study ID
      Add(AttributeDescriptor(0x0008,0x0020),2); // Study Date
      Add(AttributeDescriptor(0x0008,0x0030),2); // Study Time
      Add(AttributeDescriptor(0x0008,0x0050),2); // Study Accession Number
      Add(AttributeDescriptor(0x0008,0x0005),2); // Specific character set
      Add(AttributeDescriptor(0x0008,0x0021),2); // Series Date
      Add(AttributeDescriptor(0x0008,0x0031),2); // Series time

      Add(AttributeDescriptor(0x0020,0x000D   // Study Instance UID  
                                                    ),2);//AttributeDescriptor::IDENTIFIER),2);
      Add(AttributeDescriptor(0x0020,0x000E,   // Series Instance UID  
                                AttributeDescriptor::IDENTIFIER),2);
      // |
      //                        AttributeDescriptor::LABEL),2);
     

      // Image level
      Add(LevelDescriptor("Image"));

      Add(AttributeDescriptor(0x0020,0x0013),3); // Image Number

      Add(AttributeDescriptor(0x0028,0x0010),3); // Rows
      Add(AttributeDescriptor(0x0028,0x0011),3); // Columns
      Add(AttributeDescriptor(0x0028,0x0012),3); // Planes
      Add(AttributeDescriptor(0x0028,0x0002),3); // Sample per pixels
      Add(AttributeDescriptor(0x0028,0x0008),3); // Number of Frames 
      Add(AttributeDescriptor(0x0028,0x0004),3); // Photometric Interpretation
      Add(AttributeDescriptor(0x0028,0x0103),3); // Pixel Representation

      Add(AttributeDescriptor(0x0020,0x0032),3); // Image Position Patient
      Add(AttributeDescriptor(0x0020,0x0037),3); // Image Orientation Patient
      Add(AttributeDescriptor(0x0020,0x1041),3); // Slice Location
      Add(AttributeDescriptor(0x0028,0x0006),3); // Planar Configuration

      Add(AttributeDescriptor(0x0028,0x0030),3); // Pixel Spacing
      Add(AttributeDescriptor(0x0028,0x0100),3); // AlocatedBits
      Add(AttributeDescriptor(0x0028,0x0101),3); // StoredBits

      Add(AttributeDescriptor(0x0008,0x0008),3); // Image Type
      Add(AttributeDescriptor(0x0008,0x0023),3); // Content Date
      Add(AttributeDescriptor(0x0008,0x0033),3); // Content Time

      Add(AttributeDescriptor(0x0020,0x4000),3); // Image Comments

      Add(AttributeDescriptor(0x0004,0x1500,   // File Name
                                AttributeDescriptor::LABEL),3);
      Add(AttributeDescriptor(0x0028,0x1052),3); // Rescale Intercept
      Add(AttributeDescriptor(0x0028,0x1053),3); // Rescale Slope

      Add(AttributeDescriptor(0x0050,0x0004),3); // Calibration Image

      Add(AttributeDescriptor(0x0020,0x0052   // Frame Reference UID
                                           ),3);
      Add(AttributeDescriptor(0x0008,0x0016),3); // SOP Class UID
      Add(AttributeDescriptor("FullFileName",  // Full file name
                                "Full file name",
                                AttributeDescriptor::IDENTIFIER),3); 

    }

        // create a descriptor (name, attributes...) from a file)       //
        // @param : file path                                           //
        // return : -                                                   //
        void Descriptor::createDescriptorfromFile(const std::string &i_name)
        {
                Clear();
                
                // read file and put in buffer
                std::ifstream i_file(i_name.c_str());
                std::stringstream buffer;
                buffer << i_file.rdbuf();
                std::string line;
                bool bname;
                int ilevel = -1;

                
                while(std::getline(buffer, line))
                {
                        if(line =="<level>")
                        {       //increment levels.
                                ilevel++;
                                bname = true;
                        }
                        else if(bname)
                        {
                                // For each level, a name to describe it
                                Add(LevelDescriptor(line));
                                bname = false;
                        }
                        else if(line.empty()) // to avoid end line
                        {
                                return;
                        }
                        else
                        { 
                                // split line to find all tags
                                std::vector<std::string> descriptors;
                                std::string separator = " ";
                                std::string::size_type last_pos = line.find_first_not_of(separator);
                                //find first separator
                                std::string::size_type pos = line.find_first_of(separator, last_pos);
                                while(std::string::npos != pos || std::string::npos != last_pos)
                                {
                                        descriptors.push_back(line.substr(last_pos, pos - last_pos));
                                        last_pos = line.find_first_not_of(separator, pos);
                                        pos = line.find_first_of(separator, last_pos);
                                }
                                
                                // By default, the last tag is at zero and not recorded but if take in count
                                unsigned int flag = 0;
                                if(descriptors.size() == 4)
                                {
                                        std::stringstream val;
                                        val << std::dec << descriptors[3];
                                        val>> flag;
                                }

                                // if Dicom tag, use "group" and "element" descriptor
                                if(descriptors[0] == "D")
                                {       std::stringstream val, val2;
                                        unsigned short group;
                                        unsigned short element;
                                        val <<   std::dec << descriptors[1] ;
                                        val >> std::hex >> group;
                                        val2 << std::dec <<  descriptors[2];
                                        val2 >> std::hex >> element;
                                        Add(AttributeDescriptor( group,element,flag), ilevel);
                                }

                                else if(descriptors[0].find("#") != -1)
                                {
                                        // commented line continue to next line
                                }
                                else
                                {       boost::algorithm::replace_all(descriptors[2],"_"," ");
                                        Add(AttributeDescriptor( descriptors[1].c_str(),descriptors[2].c_str(),flag), ilevel);
                                }
                        }
                }
        }

    //==================================================================

    //==================================================================
    void Descriptor::Add(const LevelDescriptor& d)
    {
      mLevelDescriptorList.push_back(d);
    }
    //==================================================================
    
    //==================================================================  
    void Descriptor::Add(const AttributeDescriptor& d, int l)
    {
      mLevelDescriptorList[l].Add(d);
      // TO DO : update DicomTagToName and NameToDicomTag map
    }
    //==================================================================

    //==================================================================
    void Descriptor::Clear()
    {
      mLevelDescriptorList.clear();
    }

    //==================================================================

    //==================================================================
    void Descriptor::BuildAttributeMap( std::map<std::string,std::string>& map ) const
    {
      map.clear();
      LevelDescriptorListType::const_iterator l;
      for (l = GetLevelDescriptorList().begin();
           l!= GetLevelDescriptorList().end();
           ++l)
        {
          LevelDescriptor::AttributeDescriptorListType::const_iterator a;
          for (a = l->GetAttributeDescriptorList().begin();
               a!= l->GetAttributeDescriptorList().end();
               ++a)
            {
              map[a->GetKey()]="";
            }
        }
    }

        
    //==================================================================
        // test if an attribute is present in DescriptionList
        // return level's name
        const std::string Descriptor::isExist(const std::string i_attr)
        {
                std::string name = "";
                LevelDescriptorListType::const_iterator l = GetLevelDescriptorList().begin();
                for (;     l!= GetLevelDescriptorList().end(); ++l)
                {
                        LevelDescriptor::AttributeDescriptorListType::const_iterator a = l->GetAttributeDescriptorList().begin();
                for(;a!= l->GetAttributeDescriptorList().end(); ++a)
                        {
                                if (a->GetKey() == i_attr)
                                {
                                        name = l->GetName();
                                        break;
                                }
                        }
                }
                return name.c_str();
        }
  }
}