element.h

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/* Copyright (c) 2008-2022 the MRtrix3 contributors.
 *
 * This Source Code Form is subject to the terms of the Mozilla Public
 * License, v. 2.0. If a copy of the MPL was not distributed with this
 * file, You can obtain one at http://mozilla.org/MPL/2.0/.
 *
 * Covered Software is provided under this License on an "as is"
 * basis, without warranty of any kind, either expressed, implied, or
 * statutory, including, without limitation, warranties that the
 * Covered Software is free of defects, merchantable, fit for a
 * particular purpose or non-infringing.
 * See the Mozilla Public License v. 2.0 for more details.
 *
 * For more details, see http://www.mrtrix.org/.
 */
 
#ifndef __file_dicom_element_h__
#define __file_dicom_element_h__
 
#include <unordered_map>
 
#include "memory.h"
#include "raw.h"
#include "types.h"
#include "file/mmap.h"
#include "file/dicom/definitions.h"
 
namespace MR {
  namespace File {
    namespace Dicom {
 
 
      class Sequence { NOMEMALIGN
        public:
          Sequence (uint16_t group, uint16_t element, uint8_t* end) : group (group), element (element), end (end) { }
          uint16_t group, element;
          uint8_t* end;
 
          bool is (uint16_t Group, uint16_t Element) const {
            if (group != Group)
              return false;
            return element == Element;
          }
      };
 
      class Date { NOMEMALIGN
        public:
          Date (const std::string& entry) :
            year(0), month(0), day(0) {
            if (entry.size() >= 8) {
              year = to<uint32_t> (entry.substr (0, 4));
              month = to<uint32_t> (entry.substr (4, 2));
              day = to<uint32_t> (entry.substr (6, 2));
            }
            if (year < 1000 || month > 12 || day > 31)
              throw Exception ("Error converting string \"" + entry + "\" to date");
          }
          uint32_t year, month, day;
          friend std::ostream& operator<< (std::ostream& stream, const Date& item);
      };
 
      class Time { NOMEMALIGN
        public:
          Time (const std::string& entry) : Time() {
            if (entry.size() < 6)
              throw Exception ("field \"" + entry + "\" is too short to be interpreted as a time");
            hour  = to<uint32_t> (entry.substr (0, 2));
            minute = to<uint32_t> (entry.substr (2, 2));
            second = to<uint32_t> (entry.substr (4, 2));
            fraction = entry.size() > 6 ? to<default_type> (entry.substr (6)) : 0.0;
          }
          Time (default_type i)
          {
            if (i < 0.0)
              throw Exception ("Error converting negative floating-point number to a time");
            hour = std::floor (i / 3600.0); i -= hour * 3600.0;
            if (hour >= 24)
              throw Exception ("Error converting floating-point number to a time: Beyond 24 hours");
            minute = std::floor (i / 60.0); i -= minute * 60;
            second = std::floor (i);
            fraction = i - second;
          }
          Time () : hour (0), minute (0), second (0), fraction (0.0) { }
          operator default_type() const { return (hour*3600.0 + minute*60 + second + fraction); }
          Time operator- (const Time& t) const { return Time (default_type (*this) - default_type (t)); }
          uint32_t hour, minute, second;
          default_type fraction;
          friend std::ostream& operator<< (std::ostream& stream, const Time& item);
      };
 
 
 
 
 
      class Element { NOMEMALIGN
        public:
          typedef enum _Type {
            INVALID,
            INT,
            UINT,
            FLOAT,
            DATE,
            TIME,
            DATETIME,
            STRING,
            SEQ,
            OTHER
          } Type;
 
          uint16_t group, element, VR;
          uint32_t size;
          uint8_t* data;
          vector<Sequence> parents;
          bool transfer_syntax_supported;
 
          void set (const std::string& filename, bool force_read = false, bool read_write = false);
          bool read ();
 
          bool is (uint16_t Group, uint16_t Element) const {
            if (group != Group)
              return false;
            return element == Element;
          }
 
          std::string tag_name () const {
            if (dict.empty()) init_dict();
            const char* s = dict[tag()];
            return (s ? s : "");
          }
 
          uint32_t tag () const {
            union __DICOM_group_element_pair__ { uint16_t s[2]; uint32_t i; } val = { {
#if MRTRIX_BYTE_ORDER_BIG_ENDIAN
              group, element
#else
              element, group
#endif
            } };
            return val.i;
          }
 
 
          size_t offset (uint8_t* address) const {
            return address - fmap->address();
          }
          bool is_big_endian () const {
            return is_BE;
          }
          bool is_new_sequence () const {
            return VR == VR_SQ || ( group == GROUP_DATA && element == ELEMENT_DATA && size == LENGTH_UNDEFINED );
          }
 
          bool ignore_when_parsing () const;
          bool is_in_series_ref_sequence () const;
 
          Type type () const;
          vector<int32_t> get_int () const;
          vector<uint32_t> get_uint () const;
          vector<default_type> get_float () const;
          Date get_date () const;
          Time get_time () const;
          std::pair<Date,Time> get_datetime () const;
          vector<std::string> get_string () const;
 
          int32_t     get_int (size_t idx, int32_t default_value = 0)                    const { auto v (get_int());    return check_get (idx, v.size()) ? v[idx] : default_value; }
          uint32_t    get_uint (size_t idx, uint32_t default_value = 0)                  const { auto v (get_uint());   return check_get (idx, v.size()) ? v[idx] : default_value; }
          double      get_float (size_t idx, double default_value = 0.0)                 const { auto v (get_float());  return check_get (idx, v.size()) ? v[idx] : default_value; }
          std::string get_string (size_t idx, std::string default_value = std::string()) const { auto v (get_string()); return check_get (idx, v.size()) ? v[idx] : default_value; }
 
          std::string   as_string () const;
 
          size_t level () const { return parents.size(); }
 
          friend std::ostream& operator<< (std::ostream& stream, const Element& item);
          static std::string print_header () {
             return "TYPE  GRP  ELEM VR     SIZE   OFFSET   NAME                                   CONTENTS\n"
                    "----- ---- ---- --  -------  -------   -------------------------------------  ---------------------------------------\n";
          }
 
 
          template <typename VectorType>
            FORCE_INLINE void check_size (const VectorType v, size_t min_size = 1) {
              if (v.size() < min_size)
                error_in_check_size (min_size, v.size());
            }
 
        protected:
 
          std::unique_ptr<File::MMap> fmap;
          void set_explicit_encoding();
          bool read_GR_EL();
 
          uint8_t* next;
          uint8_t* start;
          bool is_explicit, is_BE, is_transfer_syntax_BE;
 
          vector<uint8_t*>  end_seq;
 
 
          uint16_t get_VR_from_tag_name (const std::string& name) {
            union {
              char t[2];
              uint16_t i;
            } d = { { name[0], name[1] } };
            return ByteOrder::BE (d.i);
          }
 
          static std::unordered_map<uint32_t, const char*> dict;
          static void init_dict();
 
          bool check_get (size_t idx, size_t size) const { if (idx >= size) { error_in_get (idx); return false; } return true; }
          void error_in_get (size_t idx) const;
          void error_in_check_size (size_t min_size, size_t actual_size) const;
          void report_unknown_tag_with_implicit_syntax () const;
 
          static const char* type_as_str[];
      };
 
 
 
    }
  }
}
 
#endif