C++ source code for calculating irradiation information and the daily light integrals from spectrometer derived datasets. These classes build upon and utilizes the previously posted classes. It is a rather specialized set of source code for those with access to a spectrometer or raw irradiance data. As such, part of the value presented here is within the methods utilized to generate the irradiation information.
For more information on spectrometer captured irradiance, see the following thread:
Also, see other source code using the tag: https://overgrow.com/tags/sourcecode
The classes presented here are able to read spectrometer data, dark values, and calibration data from data files that follow the Stellarnet SpectraWiz file formats (which are straightforward) and calculate various useful data such as PAR and DLI.
This is for the DIY types that have some software background. Questions/comment are great but I’d like to ask forum members to avoid the “what’s this good for” type questions within this thread to avoid clutter.
There are several classes and header files, as follows:
spectrum.cpp
//
// spectrum.cpp
// Version timestamp: 9-28-2019, 10:57 AM
//
// Attribution : Copyright (c) 2018 Northern_Loki (sha256::6F290BF833967127BE26C92C8F6B1C1A3949C55A7EABCEF3ECC785CD2D38D30D)
// License is granted under the Creative Commons Attribution-ShareAlike 4.0 International. https://creativecommons.org/licenses/by-sa/4.0/
//
# include "spectrum.h"
//Radiant flux W(J/s) The amount of radiant energy emitted, transmitted or received per unit time
//Radiant flux density (W / m^2) Radiant flux per unit area of a surface traversed by the radiation
//Irradiance(or emittance) (W / m^2) Radiant flux density incident on(or emitted by) a surface
//Spectral irradiance(or emittance) (W m^2 / µm) The radiant flux density incident on(or emitted by) a surface per unit wavelength interval
//Radiant intensity (W/sr) Radiant flux emanating from a surface per unit solid angle
//Radiance (W m^2/sr1) The radiant flux density emanating from a surface per unit solid angle
//Spectral radiance (W / m^2 / sr µm) The radiant flux density emanating from a surface per unit solid angle per unit wavelength interval
//Photon flux density (µmol / m^2 s) Number of micromoles of photons emitted, transmitted or received per unit area per unit time(usually within a specified wavelength such as the photosynthetically active region(400–700 nm))
//Emissivity – The ratio of the thermally generated radiance emitted by a body to the radiance that would be emitted by a black body(or perfect emitter) at the same temperature
/* Constructor. */
spectrum::spectrum()
{
}
/* Constructor. */
/* filename is the path of the CSV formatted spectrometer data. */
/* cal_filename is the path of the ICF formatted spectrometer calibration data. */
/* dark_filename is the path of the CSV formatted dark spectrometer data. */
spectrum::spectrum(std::string filename, std::string cal_filename, std::string dark_filename)
{
// float ICF_integration_time = 46.0;
// float Sample_integration_time = 12.0;
float ICF_integration_time = 44.0;
float Sample_integration_time = 44.0;
std::string RQE_filename("../Spectrums/RQE.csv"); /* Relative quantum efficiency */
std::string BLHF_filename("../Spectrums/BLHF.csv"); /* Blue light hazard function */
std::string AHF_filename("../Spectrums/AHF.csv"); /* Aphakic hazard function */
std::string RTHF_filename("../Spectrums/RTHF.csv"); /* Retinal thermal hazard function */
std::string sigmaR_filename("../Spectrums/sigmaR.csv"); /* Red phytochrome conversion */
std::string sigmaFR_filename("../Spectrums/sigmaFR.csv"); /* Far red phytochrome conversion */
csv(filename);
cal_icf(cal_filename);
dark_csv(dark_filename);
RQE(RQE_filename);
BLHF(BLHF_filename);
AHF(BLHF_filename);
RTHF(RTHF_filename);
sigmaR(sigmaR_filename);
sigmaFR(sigmaFR_filename);
spectrum_calculate(ICF_integration_time, Sample_integration_time);
}
spectrum::~spectrum()
{
}
void spectrum::spectrum_calculate(float ICF_integration_time, float Sample_integration_time)
{
/* Derives umols of irradiant photons from irradiant watts */
double NAhc = (1.0 / ((NA) * (SPEED_LIGHT) * (PLANKS_CONSTANT))) / 1000.0;
/* Derives radiance from irradiance using the maximum solid angle of 0.1 radians, for estimating maximum eye biological exposure */
/* See, http://www.olino.org/blog/us/articles/2011/09/13/blue-light-hazard-for-the-human-eye */
/* See, https://www.icnirp.org/cms/upload/publications/ICNIRPVisible_Infrared2013.pdf */
double L = (4 / (M_PI)) * (1 / 0.1);
this->sigmaR_energy.value = 0.0;
this->sigmaFR_energy.value = 0.0;
/* Calculate the actual reading by removing the dark offset. */
/* Dark offset is the spectrometer reading with no incident light energy on the sensor. */
spectral_data corrected_spectra = this->csv.ordered_spectra;
spectral_data dark_spectra = this->dark_csv.ordered_spectra;
corrected_spectra -= dark_spectra;
/* Correct the readings according to the calibration factors. */
float ICF_calibration_ratio = ICF_integration_time / Sample_integration_time;
spectral_data icf_spectra = this->cal_icf.ordered_spectra;
corrected_spectra *= ICF_calibration_ratio;
corrected_spectra *= icf_spectra;
/* Calculate the spectral irradiance. */
float previous_wavelength, previous_intensity;
for (std::pair<float, float> element : corrected_spectra)
{
static bool initial = true;
if (initial)
{
previous_wavelength = element.first;
previous_intensity = element.second;
initial = false;
continue;
}
float delta_wavelength = element.first - previous_wavelength;
float irradiant_energy = delta_wavelength * ((previous_intensity + element.second) / 2);
irradiance_energy.insert(std::pair<float, float>(previous_wavelength + (delta_wavelength / 2), irradiant_energy));
if ((element.first <= 700) && (element.first >= 400))
{
irradiance += delta_wavelength * ((previous_intensity + element.second) / 2);
}
previous_wavelength = element.first;
previous_intensity = element.second;
}
/* Calculate irradiation PAR in umols */
for (std::pair<float, float> element : irradiance_energy)
{
float local_PAR = element.first * element.second * (NAhc);
par_energy.insert(std::pair<float, float>(element.first, local_PAR));
float local_ypf = local_PAR * this->RQE.get_intensity(element.first);
ypf_energy.insert(std::pair<float, float>(element.first, local_ypf));
float local_blhf = L * element.second * this->BLHF.get_intensity(element.first);
float local_ahf = L * element.second * this->AHF.get_intensity(element.first);
float local_rthf = L * element.second * this->RTHF.get_intensity(element.first);
if ((element.first <= this->par_regions_bugbee.spectrum_max) && (element.first >= this->par_regions_bugbee.spectrum_min))
{
/* Standard PAR regions. */
int i = 0;
while (!this->par_regions.region[i].name.empty())
{
if ((element.first >= par_regions.region[i].starting_wavelength) && (element.first < par_regions.region[i].ending_wavelength))
{
this->par_regions.region[i].value += local_PAR;
break;
}
i++;
}
/* Standard YPF regions. */
i = 0;
while (!this->ypf_regions.region[i].name.empty())
{
if ((element.first >= ypf_regions.region[i].starting_wavelength) && (element.first < ypf_regions.region[i].ending_wavelength))
{
this->ypf_regions.region[i].value += local_ypf;
break;
}
i++;
}
/* Bugbee defined PAR regions. */
i = 0;
while (!this->par_regions_bugbee.region[i].name.empty())
{
if ((element.first >= par_regions_bugbee.region[i].starting_wavelength) && (element.first < par_regions_bugbee.region[i].ending_wavelength))
{
this->par_regions_bugbee.region[i].value += local_PAR;
break;
}
i++;
}
/* YPF over Bugbee defined PAR regions. */
i = 0;
while (!this->ypf_regions_bugbee.region[i].name.empty())
{
if ((element.first >= ypf_regions_bugbee.region[i].starting_wavelength) && (element.first < ypf_regions_bugbee.region[i].ending_wavelength))
{
this->ypf_regions_bugbee.region[i].value += local_ypf;
break;
}
i++;
}
if ((element.first <= this->par_regions.spectrum_max) && (element.first >= this->par_regions.spectrum_min))
{
this->par += local_PAR;
}
if ((element.first <= this->ypf_regions.spectrum_max) && (element.first >= this->ypf_regions.spectrum_min))
{
this->ypf += local_ypf;
}
if ((element.first <= this->sigmaFR_energy.spectrum_max) && (element.first >= this->sigmaFR_energy.spectrum_min))
{
this->sigmaR_energy.value += local_PAR * this->sigmaR.get_intensity(element.first);
this->sigmaFR_energy.value += local_PAR * this->sigmaFR.get_intensity(element.first);
}
if ((element.first <= this->blhf_regions.spectrum_max) && (element.first >= this->blhf_regions.spectrum_min))
{
this->blhf += local_blhf;
}
if ((element.first <= this->ahf_regions.spectrum_max) && (element.first >= this->ahf_regions.spectrum_min))
{
this->ahf += local_ahf;
}
if ((element.first <= this->rthf_regions.spectrum_max) && (element.first >= this->rthf_regions.spectrum_min))
{
this->rthf += local_rthf;
}
/* Total PAR from 287-850nm */
this->par_287_850 += local_PAR;
/* Total ypf from 287-850nm */
this->ypf_287_850 += local_ypf;
}
}
}
spectrum spectrum::set(std::string filename, std::string cal_filename, std::string dark_filename)
{
float ICF_integration_time = 46.0;
float Sample_integration_time = 12.0;
std::string RQE_filename("../Spectrums/RQE.csv");
std::string sigmaR_filename("../Spectrums/sigmaR.csv");
std::string sigmaFR_filename("../Spectrums/sigmaFR.csv");
csv(filename);
cal_icf(cal_filename);
dark_csv(dark_filename);
RQE(RQE_filename);
sigmaR(sigmaR_filename);
sigmaFR(sigmaFR_filename);
spectrum_calculate(ICF_integration_time, Sample_integration_time);
return (*this);
}
spectrum spectrum::operator()(std::string filename, std::string cal_filename, std::string dark_filename)
{
this->set(filename, cal_filename, dark_filename);
return (*this);
}
double spectrum::calculate_rayleigh_scattering(double wavelength)
{
}
/* Erythema action spectrum */
/* Komhyr, W.D. and L. Machta, "The relative response of erythema",
* in: The Perturbed Troposphere of 1990 and 2020 Vol. IV. CIAP, Dept. of Transportation,
* Washington. DC., 1973.
* # Parameterization by A.E.S. Green, T. Sawada, and E.P Shettle,
* The middle ultraviolet reaching the ground, Photochemistry and Photobiology, 19, 251-259, 1974.
* */
/* https://www.esrl.noaa.gov/gmd/grad/antuv/docs/version2/descVersion2Database3.html */
/* Integration range: 286 - 400 nm */
/* Output units : µW/cm2 */
double spectrum::calculate_komhyr_action_spectra(double wavelength)
{
double exp1 = exp((wavelength - 296.5) / 2.692);
double exp2 = exp((wavelength - 311.4) / 3.13);
double exp3 = (1.0 + exp1) * (1.0 + exp1);
double action = (0.04485 / (1 + exp2)) + ((4 * 0.9949*exp1) / exp3);
return (action);
}
/* Erythema action spectrum */
/* B.L. Diffey, "A comparison of dosimeters used for solar ultraviolet radiometry", Photochemistry and Photobiology, 46, 55-60, 1987. */
/* https://www.esrl.noaa.gov/gmd/grad/antuv/docs/version2/descVersion2Database3.html */
/* Integration range: 286 - 400 nm */
/* Output units : µW/cm2 */
double spectrum::calculate_diffey_action_spectra(double wavelength)
{
}
/* Erythema action spectrum */
/* A.F. McKinlay, A.F. and B.L. Diffey, "A reference action spectrum for ultraviolet induced erythema in human skin", CIE Research Note, 6(1), 17-22, 1987 */
/* https://www.esrl.noaa.gov/gmd/grad/antuv/docs/version2/descVersion2Database3.html */
/* Integration range: 286 - 400 nm */
/* Output units : UV Index, see http://uv.biospherical.com/Solar_Index_Guide.pdf */
double spectrum::calculate_mckinlay_action_spectra(double wavelength)
{
double action;
if (wavelength < 298.0)
{
action = 1.0;
}
else if (wavelength < 328.0)
{
action = pow(10, (0.094 * (298.0 - wavelength)));
}
else
{
action = pow(10, (0.015 * (139.0 - wavelength)));
}
return (action);
}
/* Action spectrum for growth responses of plants */
/* S. D. Flint and M. M. Caldwell
* "A biological spectral weighting function for ozone depletion research with higher plants", Physiologia Plantarum, 2003 */
/* https://www.esrl.noaa.gov/gmd/grad/antuv/docs/version2/descVersion2Database3.html */
/* Integration range: 286 - 390 nm. Wavelength in nm. */
/* Output units : µW/cm2 */
double spectrum::calculate_flint_action_spectra(double wavelength)
{
double exp1 = -1.0 * exp((0.1703411)*(wavelength - 307.867) / 1.15);
double exp2 = 4.688272 * exp(exp1);
double action = exp(exp2 + ((390.0 - wavelength) / 121.7557 - 4.183832));
return (action);
}
/* Generalized plant action spectrum */
/* M.M. Caldwell,
* "Solar UV irradiation and the growth and development of higher plants",Photophysiology,
* edited by A.C. Giese, Volume 6, Chapter 4, pp. 131 - 177, 1971 */
/* https://www.esrl.noaa.gov/gmd/grad/antuv/docs/version2/descVersion2Database3.html */
/* Integration range: 286 - 313 nm */
/* Output units : µW/cm2 */
double spectrum::calculate_caldwell_action_spectra(double wavelength)
{
double exp1 = exp((300.0 - wavelength) / 31.08);
double pow2 = 1.0 - ((wavelength / 313.3) * (wavelength / 313.3));
double action = 2.618*exp1*pow2;
return (action);
}The “RQE.csv”, “sigmaR.csv”, and “sigmaFR.csv” are generated files for calculating YPF and the red/far-red ratios. If you need these, PM your email address and request these files. Or, if you need example spectrum files, as well.
