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towards absorption etc.
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@peter-urban
peter-urban committed Sep 23, 2024
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45 changes: 45 additions & 0 deletions src/themachinethatgoesping/algorithms/rangecorrection/.docstrings/functions.doc.hpp
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//sourcehash: fe33432f6337ae8971ac01f79910fbd6f7a7cf3746aa10ae1a41ce8176476dc9

/*
This file contains docstrings for use in the Python bindings.
Do not edit! They were automatically extracted by pybind11_mkdoc.
This is a modified version which allows for more than 8 arguments and includes def-guard
*/

#pragma once

#ifndef __DOCSTRINGS_HPP__

#define __EXPAND(x) x
#define __COUNT(_1, _2, _3, _4, _5, _6, _7, _8, _9, _10, COUNT, ...) COUNT
#define __VA_SIZE(...) __EXPAND(__COUNT(__VA_ARGS__, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1))
#define __CAT1(a, b) a##b
#define __CAT2(a, b) __CAT1(a, b)
#define __DOC1(n1) __doc_##n1
#define __DOC2(n1, n2) __doc_##n1##_##n2
#define __DOC3(n1, n2, n3) __doc_##n1##_##n2##_##n3
#define __DOC4(n1, n2, n3, n4) __doc_##n1##_##n2##_##n3##_##n4
#define __DOC5(n1, n2, n3, n4, n5) __doc_##n1##_##n2##_##n3##_##n4##_##n5
#define __DOC6(n1, n2, n3, n4, n5, n6) __doc_##n1##_##n2##_##n3##_##n4##_##n5##_##n6
#define __DOC7(n1, n2, n3, n4, n5, n6, n7) __doc_##n1##_##n2##_##n3##_##n4##_##n5##_##n6##_##n7
#define __DOC8(n1, n2, n3, n4, n5, n6, n7, n8) \
__doc_##n1##_##n2##_##n3##_##n4##_##n5##_##n6##_##n7##_##n8
#define __DOC9(n1, n2, n3, n4, n5, n6, n7, n8, n9) \
__doc_##n1##_##n2##_##n3##_##n4##_##n5##_##n6##_##n7##_##n8##_##n9
#define __DOC10(n1, n2, n3, n4, n5, n6, n7, n8, n9, n10) \
__doc_##n1##_##n2##_##n3##_##n4##_##n5##_##n6##_##n7##_##n8##_##n9##_##n10
#define DOC(...) __EXPAND(__EXPAND(__CAT2(__DOC, __VA_SIZE(__VA_ARGS__)))(__VA_ARGS__))

#endif // NEW_DOC_HEADER_HPP
#if defined(__GNUG__)
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wunused-variable"
#endif


#if defined(__GNUG__)
#pragma GCC diagnostic pop
#endif


10 changes: 10 additions & 0 deletions src/themachinethatgoesping/algorithms/rangecorrection/functions.hpp
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// Kiel SPDX-FileCopyrightText: 2024 Peter Urban, Ghent University
//
// SPDX-License-Identifier: MPL-2.0

#pragma once

/* generated doc strings */
#include ".docstrings/functions.doc.hpp"

#include " absorption.hpp"
79 changes: 79 additions & 0 deletions ...hemachinethatgoesping/algorithms/rangecorrection/functions/.docstrings/absorption.doc.hpp
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//sourcehash: f832ca529d511eb1355e2ffa7576b496727810220ef0c08ce75b8943910b56b5

/*
This file contains docstrings for use in the Python bindings.
Do not edit! They were automatically extracted by pybind11_mkdoc.
This is a modified version which allows for more than 8 arguments and includes def-guard
*/

#pragma once

#ifndef __DOCSTRINGS_HPP__

#define __EXPAND(x) x
#define __COUNT(_1, _2, _3, _4, _5, _6, _7, _8, _9, _10, COUNT, ...) COUNT
#define __VA_SIZE(...) __EXPAND(__COUNT(__VA_ARGS__, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1))
#define __CAT1(a, b) a##b
#define __CAT2(a, b) __CAT1(a, b)
#define __DOC1(n1) __doc_##n1
#define __DOC2(n1, n2) __doc_##n1##_##n2
#define __DOC3(n1, n2, n3) __doc_##n1##_##n2##_##n3
#define __DOC4(n1, n2, n3, n4) __doc_##n1##_##n2##_##n3##_##n4
#define __DOC5(n1, n2, n3, n4, n5) __doc_##n1##_##n2##_##n3##_##n4##_##n5
#define __DOC6(n1, n2, n3, n4, n5, n6) __doc_##n1##_##n2##_##n3##_##n4##_##n5##_##n6
#define __DOC7(n1, n2, n3, n4, n5, n6, n7) __doc_##n1##_##n2##_##n3##_##n4##_##n5##_##n6##_##n7
#define __DOC8(n1, n2, n3, n4, n5, n6, n7, n8) \
__doc_##n1##_##n2##_##n3##_##n4##_##n5##_##n6##_##n7##_##n8
#define __DOC9(n1, n2, n3, n4, n5, n6, n7, n8, n9) \
__doc_##n1##_##n2##_##n3##_##n4##_##n5##_##n6##_##n7##_##n8##_##n9
#define __DOC10(n1, n2, n3, n4, n5, n6, n7, n8, n9, n10) \
__doc_##n1##_##n2##_##n3##_##n4##_##n5##_##n6##_##n7##_##n8##_##n9##_##n10
#define DOC(...) __EXPAND(__EXPAND(__CAT2(__DOC, __VA_SIZE(__VA_ARGS__)))(__VA_ARGS__))

#endif // NEW_DOC_HEADER_HPP
#if defined(__GNUG__)
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wunused-variable"
#endif


static const char *__doc_themachinethatgoesping_algorithms_rangecorrection_functions_calc_absorption_coefficient_db_m =
R"doc(Compute the logarithmic absorption coefficient in dB/m based on
Francois and Garrison (1982) [taken from Fisheries Acoustics Theory
and Practice, 2nd Edition, Simmonds and MacLennan, 2005]
Parameter ``frequency``:
// Frequency in Hz
Parameter ``depth``:
// Depth in m
Parameter ``speedOfSound``:
// Speed of sound in m/s
Parameter ``temperature``:
// ITS-90 temperature in degrees Celsius
Parameter ``salinity_psu``:
// Salinity in PSU
Parameter ``pH``:
// pH
Returns:
double)doc";

static const char *__doc_themachinethatgoesping_algorithms_rangecorrection_functions_its90_to_its68 =
R"doc(Convert temperature from ITS-68 to ITS-90
Parameter ``T90``:
$Returns:
double)doc";

#if defined(__GNUG__)
#pragma GCC diagnostic pop
#endif


98 changes: 98 additions & 0 deletions src/themachinethatgoesping/algorithms/rangecorrection/functions/absorption.hpp
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// SPDX-FileCopyrightText: 2024 Peter Urban, Ghent University
// SPDX-FileCopyrightText: 2022 GEOMAR Helmholtz Centre for Ocean Research Kiel
//
// SPDX-License-Identifier: MPL-2.0

#pragma once

/* generated doc strings */
#include ".docstrings/absorption.doc.hpp"

#include <gswteos-10.h>
#include <themachinethatgoesping/tools/helper.hpp>

namespace themachinethatgoesping {
namespace algorithms {
namespace rangecorrection {
namespace functions {

// --- helper functions ---
/**
* @brief Convert temperature from ITS-68 to ITS-90
*
* @param T90
* @return double
*/
inline double its90_to_its68(double T90)
{
// return (T90*T90)/gsw_t90_from_t68(T90);
return T90 * 1.00024;
}

/**
* @brief Compute the logarithmic absorption coefficient in dB/m based on Francois and Garrison
* (1982) [taken from Fisheries Acoustics Theory and Practice, 2nd Edition, Simmonds and MacLennan,
* 2005]
*
* @param frequency // Frequency in Hz
* @param depth // Depth in m
* @param speedOfSound // Speed of sound in m/s
* @param temperature // ITS-90 temperature in degrees Celsius
* @param salinity_psu // Salinity in PSU
* @param pH // pH
* @return double
*/
double calc_absorption_coefficient_db_m(double frequency,
double depth,
double speedOfSound,
double temperature,
double salinity_psu,
double pH = 8)
{
// Convert frequency to kHz
frequency = frequency / 1000.0;

// Convert temperature from ITS-90 to ITS-68
temperature = its90_to_its68(temperature);

//
double temperature2 = temperature * temperature;
double temperature3 = temperature2 * temperature;
double depth2 = depth * depth;
double frequency2 = frequency2 * frequency2;

double A1 = 8.86 * std::pow(10., 0.78 * pH - 5.0) / speedOfSound;
double A2 = 21.44 * salinity_psu * (1 + 0.025 * temperature) / speedOfSound;
// Only for temperature
double A3;
if (temperature <= 20)
A3 = 0.0004937 - 0.0000259 * temperature + 0.000000911 * temperature2 -
0.000000015 * temperature3;
else
A3 = 0.0003964 - 0.00001146 * temperature + 0.000000145 * temperature2 -
0.00000000065 * temperature3;

double f1 =
2.8 * std::sqrt(salinity_psu / 35.) * std::pow(10., 4. - (1245. / (temperature + 273.)));

double f2 = 8.17 * std::pow(10., 8 - (1990. / (temperature + 273.)));
f2 /= (1. + 0.0018 * (salinity_psu - 35.));

double P2 = 1 - 0.000137 * depth + 0.0000000062 * depth2;
double P3 = 1 - 0.0000383 * depth + 0.00000000049 * depth2;

double absorption = 0;

absorption += A1 * f1 / (f1 * f1 + frequency2);
absorption += A2 * P2 * f2 / (f2 * f2 + frequency2);
absorption += A3 * P3;
absorption *= frequency2;

// Convert dB/km to dB/m
return absorption / 1000.0;
}

}
}
}
}

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