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eleonareleonar
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Added CAMIO and began transitioning code from specFile_cnf.cpp to CAMIO.cpp
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4 files changed

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-274
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4 files changed

+2586
-274
lines changed

‎CMakeLists.txt

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@@ -253,7 +253,7 @@ else( SpecUtils_SHARED_LIB )
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set( SpecUtils_LIB_TYPE STATIC )
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endif( SpecUtils_SHARED_LIB )
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add_library( SpecUtils ${SpecUtils_LIB_TYPE} ${sources} ${headers} ${OTHER_SUPPORT_FILES} )
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add_library( SpecUtils ${SpecUtils_LIB_TYPE} ${sources} ${headers} ${OTHER_SUPPORT_FILES} "SpecUtils/CAMIO.h" "src/CAMIO.cpp")
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set_target_properties( SpecUtils PROPERTIES PREFIX "lib" OUTPUT_NAME "SpecUtils" )
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set( SpecUtils_USE_FAST_FLOAT OFF ) # Uses https://github.com/fastfloat/fast_float . If fast_float.h isnt found, will be fetched

‎SpecUtils/CAMIO.h

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#pragma once
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#include <vector>
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#include <string>
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#include <cstdint>
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#include <map>
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#include <memory>
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#include <chrono>
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namespace CAMInputOutput {
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// Structs
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struct EfficiencyPoint {
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int Index;
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double Energy;
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double Efficiency;
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double EfficiencyUncertainty;
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};
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struct Peak {
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double Energy;
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double Centroid;
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double CentroidUncertainty;
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double FullWidthAtHalfMaximum;
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double LowTail;
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double Area;
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double AreaUncertainty;
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double Continuum;
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double CriticalLevel;
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double CountRate;
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double CountRateUncertainty;
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Peak() = default;
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Peak(double energy, double centrd, double centrdUnc, double fwhm, double lowTail,
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double area, double areaUnc, double continuum, double critialLevel,
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double cntRate, double cntRateUnc);
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};
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struct Nuclide {
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std::string Name;
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double HalfLife = 0.;
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double HalfLifeUncertainty = 0.;
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std::string HalfLifeUnit;
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int Index = -1;
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int AtomicNumber = 0;
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std::string ElementSymbol;
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std::string Metastable;
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Nuclide() = default;
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Nuclide(const std::string& name, double halfLife, double halfLifeUnc,
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const std::string& halfLifeUnit, int nucNo);
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inline bool operator==(const Nuclide & other) const
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{
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return Name == other.Name;
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}
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};
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struct Line {
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double Energy;
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double EnergyUncertainty;
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double Abundance;
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double AbundanceUncertainty;
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bool IsKeyLine;
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int NuclideIndex;
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bool NoWeightMean;
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Line() = default;
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Line(double energy, double energyUnc, double abundance, double abundanceUnc,
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int nucNo, bool key = false, bool noWgtMean = false);
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};
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// Main CAMIO class
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class CAMIO {
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public:
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enum class CAMBlock : uint32_t {
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ACQP = 0x00012000,
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SAMP = 0x00012001,
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GEOM = 0x00012002,
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PROC = 0x00012003,
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DISP = 0x00012004,
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SPEC = 0x00012005, //also known as DATA
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PEAK = 0x00012006,
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NUCL = 0x00012007,
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NLINES = 0x00012008
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};
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enum class RecordSize : uint16_t {
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ACQP = 0x051C,
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NUCL = 0x023B,
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NLINES = 0x0085
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};
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enum class BlockSize : uint16_t {
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ACQP = 0xA00U,
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PROC = 0x800,
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NUCL = 0x4800U,
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NLINES = 0x4200U
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};
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enum class PeakParameterLocation : uint8_t {
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Energy = 0x0,
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Centroid = 0x40,
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CentroidUncertainty = 0x40,
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FullWidthAtHalfMaximum = 0x10,
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LowTail = 0x50,
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Area = 0x34,
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AreaUncertainty = 0x84,
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Continuum = 0x0C,
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CriticalLevel = 0x0D1,
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CountRate = 0x18,
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CountRateUncertainty = 0x1C
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};
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enum class EfficiencyPointParameterLocation : uint8_t {
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Energy = 0x01,
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Efficiency = 0x05,
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EfficiencyUncertainty = 0x09
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};
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enum NuclideParameterLocation : uint8_t
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{
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Name = 0x03,
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HalfLife = 0x1B,
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HalfLifeUncertainty = 0x89,
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HalfLifeUnit = 0x61,
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MeanActivity = 0x57,
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MeanActivityUnceratinty = 0x69,
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NuclideMDA = 0x27
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};
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enum LineParameterLocation : uint8_t
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{
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Energy = 0x01,
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EnergyUncertainty = 0x21,
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Abundance = 0x05,
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AbundanceUncertainty = 0x39,
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IsKeyLine = 0x1D,
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NuclideIndex = 0x1B,
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NoWeightMean = 0x1F,
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LineActivity = 0x0B,
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LineActivityUnceratinty = 0x13,
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LineEfficiency = 0x31,
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LineEfficiencyUncertainty = 0x35,
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LineMDA = 0x25,
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};
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private:
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std::multimap<CAMBlock, uint32_t> blockAddresses;
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std::vector<uint8_t> readData;
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std::vector<std::vector<uint8_t>> lines;
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std::vector<std::vector<uint8_t>> nucs;
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std::vector<Nuclide> writeNuclides;
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std::vector<Line> fileLines;
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std::vector<Nuclide> fileNuclides;
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std::vector<EfficiencyPoint> efficiencyPoints;
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std::vector<Peak> peaks;
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static constexpr uint16_t header_size = 0x800;
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static constexpr uint16_t block_header_size = 0x30;
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static constexpr uint8_t nuclide_line_size = 0x03;
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float key_line_intf_limit = 2.0; //keV
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public:
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CAMIO();
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void ReadFile(const std::string& fileName);
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std::vector<Line> GetLines();
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std::vector<Nuclide> GetNuclides();
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std::vector<Peak> GetPeaks();
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std::vector<EfficiencyPoint> GetEfficiencyPoints();
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SpecUtils::time_point_t GetSampleTime();
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SpecUtils::time_point_t GetAquisitionTime();
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float GetLiveTime();
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float GetRealTime();
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std::vector<float> GetShapeCalibration();
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std::vector<float> GetEnergyCalibration();
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std::vector<uint32_t> GetSpectrum();
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void CreateFile(const std::string& filePath);
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void CreateFile(std::shared_ptr<SpecUtils::Measurement> summed);
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void AddNuclide(const std::string& name, const float halfLife,
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const float halfLifeUnc, const std::string& halfLifeUnit, const int nucNo = -1);
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void AddNuclide(const Nuclide& nuc);
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void AddLine(const float energy, const float enUnc, const float yield,
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const float yieldUnc, const int nucNo, const bool key = false);
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void AddLine(const Line& line);
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void AddLineAndNuclide(const float energy, const float yield, const std::string& name,
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const float halfLife, const std::string& halfLifeUnit, const bool noWeightMean = false,
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const float enUnc = -1, const float yieldUnc = -1, const float halfLifeUnc = -1 );
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inline void SetKeyLineInerferenceLimit(const float limit) { key_line_intf_limit = limit; };
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float GetKeyLineInerferenceLimit() const { return key_line_intf_limit; }
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protected:
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std::multimap<CAMBlock, uint32_t> ReadHeader();
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void ReadBlock(CAMBlock block);
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std::vector<uint8_t> GenerateBlock(CAMBlock block, size_t loc,
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const std::vector<std::vector<uint8_t>>& records = std::vector<std::vector<uint8_t>>(),
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uint16_t blockNo = 0, bool hasCommon = true);
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std::vector<uint8_t> GenerateBlockHeader(CAMBlock block, size_t loc, uint16_t numRec = 1,
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uint16_t numLines = 1, uint16_t blockNum = 0, bool hasCommon = false);
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uint16_t GetNumLines(const std::vector<uint8_t>& nuclRecord);
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std::vector<uint8_t> GenerateNuclide(const std::string& name, float halfLife,
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float halfLifeUnc, const std::string& halfLifeUnit,
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const std::vector<uint16_t>& lineNums);
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std::vector<uint8_t> AddLinesToNuclide(const std::vector<uint8_t>& nuc,
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const std::vector<uint8_t>& lineNums);
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std::vector<uint8_t> GenerateLine(float energy, float enUnc, float yield,
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float yieldUnc, bool key, uint8_t nucNo, bool noWgtMn);
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void AssignKeyLines();
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protected:
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// Add block reading function declarations
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void ReadGeometryBlock(size_t pos, uint16_t records);
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void ReadLinesBlock(size_t pos, uint16_t records);
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void ReadNuclidesBlock(size_t pos, uint16_t records);
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void ReadPeaksBlock(size_t pos, uint16_t records);
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// Add GenerateFile declaration
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std::vector<uint8_t> GenerateFile(const std::vector<std::vector<uint8_t>>& blocks);
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float ComputeUncertainty(float value);
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};
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// Helper class for comparing lines
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class LineComparer {
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public:
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bool operator()(const std::vector<uint8_t>& x, const std::vector<uint8_t>& y) const;
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};
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class NuclideComparer {
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public:
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bool operator()(const std::vector<uint8_t>& x, const std::vector<uint8_t>& y) const;
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};
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} // namespace CAMInputOutput

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