////////////////////////////////////////////////////////////////////////////// // // Phasor.h, (c) 2006-2017, Ryan A. Colyer // // For detail on the theory and mathematics behind the formulas used here, // you can consult the following two references. These would also be // appropriate references to cite if reusing this library in an academic // publication, as this was initially developed in concert with those two // publications. // // A Novel Fluorescence Lifetime Imaging System that Optimizes Photon // Efficiency - Ryan A. Colyer, Claudia Lee, Enrico Gratton // Microsc Res Tech 71(3):201-13, 2008 // // Phasor imaging with a widefield photon-counting detector - // Ryan A. Colyer, Oswald H. W. Siegmund, Anton S. Tremsin, John V. Vallerga, // Shimon Weiss, Xavier Michalet // Journal of Biomedical Optics 17(1), 016008, 2012 // ////////////////////////////////////////////////////////////////////////////// // // Boost Software License - Version 1.0 - August 17th, 2003 // // Permission is hereby granted, free of charge, to any person or organization // obtaining a copy of the software and accompanying documentation covered by // this license (the "Software") to use, reproduce, display, distribute, // execute, and transmit the Software, and to prepare derivative works of the // Software, and to permit third-parties to whom the Software is furnished to // do so, all subject to the following: // // The copyright notices in the Software and this entire statement, including // the above license grant, this restriction and the following disclaimer, // must be included in all copies of the Software, in whole or in part, and // all derivative works of the Software, unless such copies or derivative // works are solely in the form of machine-executable object code generated by // a source language processor. // // THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR // IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, // FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT // SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE // FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE, // ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER // DEALINGS IN THE SOFTWARE. // ////////////////////////////////////////////////////////////////////////////// #ifndef PHASOR_H #define PHASOR_H #include "macros.h" #include "RC/RC.h" #include using namespace std; namespace PhasorApp { class Phasor { public: // Construct a phasor with 0 counts. Phasor(); // Clear the phasor of counts. void Clear(); // Get the modulation value of the phasor. float GetM() const; // Get the phase (angle) of the phasor. float GetPhi() const; // Set the phasor from normalized g and s values. void SetGS(float g, float s); // Set the phasor from modulation and phase values. void SetMPhi(float m, float phi); // Set the phasor from a lifetime and frequency. void SetTau(float tau, float freq); // Get the phase lifetime of this phasor for a given frequency. float GetTauP(float freq) const; // Get the modulation lifetime of this phasor for a given frequency. float GetTauM(float freq) const; // Perform a reference calculation for a modulation factor and phase shift. void Reference(float m_fact, float phi_shift); // Perform a reference calculation including a background adjustment. void ReferenceBG(float m_fact, float phi_shift, float background); // Return the modulation factor to convert this sample to the target value. float IsReferenceMod(Phasor target) const; // Return the phase shift to convert this sample to the target value. float IsReferencePhi(Phasor target) const; // Return the modulation factor including a background adjustment. float IsReferenceModBG(Phasor target, float background) const; // Reference only the phase value. void PhaseReference(float phi_shift); // Add a photon count to this phasor at the given phase. inline void AddCount(float phase) { counts++; bigG += cos(phase); bigS += sin(phase); bigG2 += cos(2*phase); bigS2 += sin(2*phase); } // Return the modulation value of the second harmonic. float GetM2() const; // Return the phase value of the second harmonic. float GetPhi2() const; // Return the theoretical standard deviation in phi. // Only valid for an unreferenced phasor. float SigmaPhi() const; // Return the theoretical standard deviation in modulation. // Only valud for an unreferenced phasor. // The input m_fact = 1/m_IR from the paper. float SigmaM(float m_fact) const; // Return the theoretical standard deviation in the phase lifetime. // The input phi_shift = -phi_IR from the paper. float SigmaTauP(float freq_times_harmonic, float phi_shift) const; // Return the theoretical standard deviation in the modulation lifetime. // The input m_fact = 1/m_IR from the paper. float SigmaTauM(float freq_times_harmonic, float m_fact) const; // Add a phasor to this one. inline Phasor& operator+=(const Phasor &ph) { counts += ph.counts; bigG += ph.bigG; bigS += ph.bigS; bigG2 += ph.bigG2; bigS2 += ph.bigS2; return *this; } // Subtract a phasor from this one. inline Phasor& operator-=(const Phasor &ph) { counts -= ph.counts; bigG -= ph.bigG; bigS -= ph.bigS; bigG2 -= ph.bigG2; bigS2 -= ph.bigS2; return *this; } // Scale this phasor by a constant factor. inline Phasor& operator*=(const float fact) { counts *= fact; bigG *= fact; bigS *= fact; bigG2 *= fact; bigS2 *= fact; return *this; } // Scale this phasor down by a constant factor. inline Phasor& operator/=(const float fact) { counts /= fact; bigG /= fact; bigS /= fact; bigG2 /= fact; bigS2 /= fact; return *this; } // Add two phasors. inline const Phasor operator+(const Phasor &ph) const { Phasor result = *this; result += ph; return result; } // Subtract two phasors. inline const Phasor operator-(const Phasor &ph) const { Phasor result = *this; result -= ph; return result; } // Scale a phasor by a constant factor. inline const Phasor operator*(const float fact) const { Phasor result = *this; result *= fact; return result; } // Scale a phasor down by a constant factor. inline const Phasor operator/(const float fact) const { Phasor result = *this; result /= fact; return result; } // Return a string representation of the phasor's two harmonics. inline RC::RStr ToString() const { return RC::RStr(counts) + " (" + g() + ", " + s() + ")" + " (" + g2() + ", " + s2() + ")"; } // Return the normalized g value. inline float g() const { return (bigG / counts); } // Return the normalized s value. inline float s() const { return (bigS / counts); } // Return the normalized second harmonic g value. inline float g2() const { return (bigG2 / counts); } // Return the normalized second harmonic s value. inline float s2() const { return (bigS2 / counts); } float counts; // The number of photons the phasor represents. float bigG; // The unnormalized big-G value. float bigS; // The unnormalized big-S value. float bigG2; // The unnormalized big-G value for the second harmonic. float bigS2; // The unnormalized big-S value for the second harmonic. }; // Outputs a phasor's value as text "(g, s) (g2, s2)" inline ostream& operator<< (ostream &out, const Phasor &ph) { out << ph.ToString(); return out; } // Scale a phasor by multiplication with a constant value on the left. inline const Phasor operator* (const float& left, const Phasor& right) { return right * left; } } #endif // PHASOR_H