| Geant4 Cross Reference |
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26 //
27 //
28 /// \file SDDData.hh
29 /// \brief Definition of the SDDData class
30
31 #ifndef SDDDATA_HH
32 #define SDDDATA_HH
33
34 #include <string>
35 #include <vector>
36 #include <sstream>
37 #include <map>
38 #include "Damage.hh"
39
40 class SDDData
41 {
42 public:
43
44 /** SDD header structure
45 *
46 * Define the content of SSD file header
47 */
48 struct SDDHeader
49 {
50 std::string sdd_version{""};
51
52 std::string software{""};
53
54 std::string author{""};
55
56 std::string sim_details{""};
57
58 std::string src_details{""};
59 int src_type{0};
60 std::vector<int> src_pdg;
61 std::vector<double> src_energy;
62 std::string energy_dist{""};
63 std::vector<double> part_fraction;
64 std::vector<double> dose;
65 double dose_rate{0};
66
67 std::string target{""};
68 std::vector<double> volumes;
69 std::vector<double> chromo_size;
70 double dna_density{0};
71
72 std::vector<double> cell_cycle;
73 std::vector<int> dna_struct;
74 int vitro_vivo{0};
75 std::string proliferation{""};
76 std::vector<double> microenv;
77
78 std::vector<double> damage_def;
79 double time{0};
80 std::vector<int> damage_prim_count;
81
82 std::vector<bool> entries;
83
84 std::string info{""};
85 };
86
87 /** SDD damage structure
88 *
89 * Define the content of a damage as stored in SDD file
90 */
91 struct SDDDamage
92 {
93 std::vector<int> classification;
94 std::vector<double> coordinates;
95 std::vector<int> chromo_ID;
96 std::vector<double> chromo_position;
97 std::vector<int> cause;
98 std::vector<int> types;
99
100 std::vector<int> break_spec;
101 std::vector<int> dna_seq;
102 std::vector<double> lesion_time;
103
104 std::vector<int> particles;
105 std::vector<double> energy;
106 std::vector<double> translation;
107 std::vector<double> direction;
108 std::vector<double> particle_time;
109 };
110
111 /** Constructor */
112 SDDData(std::string /*p_name*/);
113 /** Destructor */
114 ~SDDData() = default;
115
116 /** Read header
117 * Reads and returns the header of a SDD file
118 */
119 SDDHeader ReadHeader();
120
121 /** Chromosome sizes
122 * Returns the list of sizes of each chromosome in the cell geometry
123 */
124 std::map<int,unsigned long long int> GetChromosomeBpSizesMap(double &sum);
125
126 /** Dose
127 * Returns the absorbed dose
128 */
129 double GetDose();
130
131 /** Parse data
132 * Parse data of SDD files and stores the data
133 * as SDDDamage in data_
134 */
135 void ParseData();
136 /** Get SDD damage
137 * Returns all the SDD damage (i.e. data_)
138 */
139 std::vector<SDDDamage>& GetSDDDamage(){return data_;};
140
141 /** Get Damage
142 * Returns all the damage that have been converted into lighter object
143 * see Damage class
144 */
145 std::map<unsigned int,std::map<unsigned int,std::vector<Damage> > > GetAllDamage();
146
147 private:
148
149 std::string filename_;
150 SDDHeader header_;
151 std::vector<SDDDamage> data_;
152
153 void ParseLineData(std::string&);
154
155 void ReadString(std::ifstream&,std::string&);
156 void ReadInt(std::ifstream&,int&);
157 void ReadInts(std::ifstream&,std::vector<int>&);
158 void ReadDouble(std::ifstream&,double&);
159 void ReadDoubles(std::ifstream&,std::vector<double>&);
160 void ReadBools(std::ifstream&,std::vector<bool>&);
161
162 void ExtractInts(std::string&,int,std::vector<int>&);
163 void ExtractDoubles(std::string&,int,std::vector<double>&);
164
165 };
166
167 #endif // SDDDATA_HH
168