- absorption calculation

- sound velocity calculation using gswteos-10
- amplitude range correction functions
- apply correction functions for wci

meson.build

@@ -9,7 +9,7 @@ project(
   'cpp',
   license: 'MPL-2.0',
 
-  version: '0.8.1',
+  version: '0.8.2',
   default_options: ['warning_level=2', 'buildtype=release', 'cpp_std=c++20'],
   meson_version: '>=1.3.2' #first version with  clang-cl openmp support
 )

src/pymodule/amplitudecorrection/functions/module.hpp

@@ -0,0 +1,94 @@
+// SPDX-FileCopyrightText: 2022 - 2023 Peter Urban, Ghent University
+//
+// SPDX-License-Identifier: MPL-2.0
+
+#include <pybind11/iostream.h>
+#include <pybind11/pybind11.h>
+#include <xtensor-python/pytensor.hpp>
+
+#include <themachinethatgoesping/algorithms/amplitudecorrection/functions.hpp>
+
+namespace themachinethatgoesping {
+namespace algorithms {
+namespace pymodule {
+namespace py_amplitudecorrection {
+namespace py_functions {
+
+#define DOC_functions(ARG)                                                                         \
+    DOC(themachinethatgoesping, algorithms, amplitudecorrection, functions, ARG)
+
+void init_m_functions(pybind11::module& m)
+{
+    namespace py = pybind11;
+
+    pybind11::module submodule = m.def_submodule("functions");
+
+    submodule.doc() = "Submodule that holds functions used for amplitude corrections";
+
+    using namespace amplitudecorrection::functions;
+
+    // sound velocity
+    submodule.def("calc_sound_velocity",
+                  &calc_sound_velocity,
+                  DOC_functions(calc_sound_velocity),
+                  py::arg("depth_m"),
+                  py::arg("temperature_c"),
+                  py::arg("salinity_psu"),
+                  py::arg("latitude")  = 0.0,
+                  py::arg("longitude") = 0.0);
+
+    // absorption
+    submodule.def("calc_absorption_coefficient_db_m",
+                  &calc_absorption_coefficient_db_m,
+                  DOC_functions(calc_absorption_coefficient_db_m),
+                  py::arg("frequency_hz"),
+                  py::arg("depth_m"),
+                  py::arg("sound_velocity_m_s"),
+                  py::arg("temperature_c"),
+                  py::arg("salinity_psu"),
+                  py::arg("pH") = 8);
+
+    // range correction
+    submodule.def("get_sample_numbers_plus_half",
+                  &get_sample_numbers_plus_half<xt::pytensor, float, int64_t>,
+                  DOC_functions(get_sample_numbers_plus_half),
+                  py::arg("first_sample_nr"),
+                  py::arg("last_sample_nr"),
+                  py::arg("step") = 1);
+
+    submodule.def("approximate_range_factor",
+                  &approximate_range_factor<float>,
+                  DOC_functions(approximate_range_factor),
+                  py::arg("sample_interval_s"),
+                  py::arg("sound_velocity_m_s"));
+
+    submodule.def("approximate_ranges",
+                  &approximate_ranges<xt::pytensor, float, int64_t>,
+                  DOC_functions(approximate_ranges),
+                  py::arg("sample_interval_s"),
+                  py::arg("sound_velocity_m_s"),
+                  py::arg("first_sample_nr"),
+                  py::arg("last_sample_nr"),
+                  py::arg("step") = 1);
+
+    submodule.def("compute_cw_range_correction",
+                  &compute_cw_range_correction<xt::pytensor, float>,
+                  DOC_functions(compute_cw_range_correction),
+                  py::arg("ranges_m"),
+                  py::arg("absorption_db_m"),
+                  py::arg("tvg_factor"));
+
+    submodule.def("apply_wci_correction",
+                  &apply_wci_correction<xt::pytensor, float>,
+                  DOC_functions(apply_wci_correction),
+                  py::arg("wci"),
+                  py::arg("per_beam_offset"),
+                  py::arg("per_sample_offset"),
+                  py::arg("mp_cores") = 1);
+}
+
+} // namespace py_functions
+} // namespace py_amplitudecorrection
+} // namespace pymodule
+} // namespace algorithms
+} // namespace themachinethatgoesping

src/pymodule/amplitudecorrection/module.hpp

@@ -0,0 +1,27 @@
+// SPDX-FileCopyrightText: 2022 - 2023 Peter Urban, Ghent University
+//
+// SPDX-License-Identifier: MPL-2.0
+
+#include <pybind11/iostream.h>
+#include <pybind11/pybind11.h>
+
+#include "functions/module.hpp"
+
+namespace themachinethatgoesping {
+namespace algorithms {
+namespace pymodule {
+namespace py_amplitudecorrection {
+
+void init_m_amplitudecorrection(pybind11::module& m)
+{
+    pybind11::module submodule = m.def_submodule("amplitudecorrection");
+
+    submodule.doc() = "Submodule for amplitudecorrection (absorption, tvg, calibration factors, etc.)";
+
+    py_functions::init_m_functions(submodule);
+}
+
+} // namespace py_amplitudecorrection
+} // namespace pymodule
+} // namespace algorithms
+} // namespace themachinethatgoesping

src/pymodule/meson.build

@@ -33,6 +33,7 @@ py_algorithms = pymod.extension_module(
     dependencies : [
         tools_pybind_dep,
         algorithms_dep,
+        gswteos_10_dep,
         pybind11_dep,
         python3_dep],
     link_language : 'cpp',

src/pymodule/module.cpp

@@ -2,15 +2,16 @@
 //
 // SPDX-License-Identifier: MPL-2.0
 
+#define FORCE_IMPORT_ARRAY // this is needed for xtensor-python but must only be included once
+#include <xtensor-python/pyarray.hpp> // Numpy bindings
+
 #include <pybind11/iostream.h>
 #include <pybind11/pybind11.h>
 
+#include "amplitudecorrection/module.hpp"
 #include "geoprocessing/module.hpp"
 #include "signalprocessing/module.hpp"
 
-#define FORCE_IMPORT_ARRAY // this is needed for xtensor-python but must only be included once
-#include <xtensor-python/pyarray.hpp> // Numpy bindings
-
 namespace themachinethatgoesping {
 namespace algorithms {
 namespace pymodule {
@@ -26,6 +27,7 @@ PYBIND11_MODULE(MODULE_NAME, m)
                             "range/depth, raytrace ...";
     m.attr("__version__") = MODULE_VERSION;
 
+    py_amplitudecorrection::init_m_amplitudecorrection(m);
     py_geoprocessing::init_m_geoprocessing(m);
     py_signalprocessing::init_m_signalprocessing(m);
 }

src/themachinethatgoesping/algorithms/rangecorrection/.docstrings/functions.doc.hpp → src/themachinethatgoesping/algorithms/amplitudecorrection/.docstrings/functions.doc.hpp

@@ -1,4 +1,4 @@
-//sourcehash: fe33432f6337ae8971ac01f79910fbd6f7a7cf3746aa10ae1a41ce8176476dc9
+//sourcehash: 5c8188cb5f1b2d240c72954adc6430e13d22062d6b400c11476baed51945113c
 
 /*
   This file contains docstrings for use in the Python bindings.

src/themachinethatgoesping/algorithms/amplitudecorrection/functions.hpp

@@ -0,0 +1,13 @@
+// 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/functions.doc.hpp"
+
+#include "functions/absorption.hpp"
+#include "functions/rangecorrection.hpp"
+#include "functions/wcicorrection.hpp"

src/themachinethatgoesping/algorithms/rangecorrection/functions/.docstrings/absorption.doc.hpp → src/themachinethatgoesping/algorithms/amplitudecorrection/functions/.docstrings/absorption.doc.hpp

@@ -1,4 +1,4 @@
-//sourcehash: f832ca529d511eb1355e2ffa7576b496727810220ef0c08ce75b8943910b56b5
+//sourcehash: 50c3a9bed6dffaec83b931b6cf30653eaca9ebfdce0e73ee940aea068eac54b6
 
 /*
   This file contains docstrings for use in the Python bindings.
@@ -38,22 +38,22 @@
 #endif
 
 
-static const char *__doc_themachinethatgoesping_algorithms_rangecorrection_functions_calc_absorption_coefficient_db_m =
+static const char *__doc_themachinethatgoesping_algorithms_amplitudecorrection_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 ``frequency_hz``:
+    // Frequency_hz in Hz
 
-Parameter ``depth``:
-    // Depth in m
+Parameter ``depth_m``:
+    // Depth_m in m
 
-Parameter ``speedOfSound``:
+Parameter ``sound_velocity_m_s``:
     // Speed of sound in m/s
 
-Parameter ``temperature``:
-    // ITS-90 temperature in degrees Celsius
+Parameter ``temperature_c``:
+    // ITS-90 temperature_c in degrees Celsius
 
 Parameter ``salinity_psu``:
     // Salinity in PSU
@@ -64,8 +64,22 @@ Parameter ``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
+static const char *__doc_themachinethatgoesping_algorithms_amplitudecorrection_functions_calc_sound_velocity =
+R"doc(Compute the speed of sound in seawater using the TEOS-10 library
+
+Parameter ``depth_m``:
+    $Parameter ``temperature_c``:
+
+Parameter ``salinity_psu``:
+    $Parameter ``latitude``:
+
+Parameter ``longitude``:
+    $Returns:
+
+double)doc";
+
+static const char *__doc_themachinethatgoesping_algorithms_amplitudecorrection_functions_its90_to_its68 =
+R"doc(Convert temperature_c from ITS-68 to ITS-90
 
 Parameter ``T90``:
     $Returns:

src/themachinethatgoesping/algorithms/amplitudecorrection/functions/.docstrings/rangecorrection.doc.hpp

@@ -0,0 +1,53 @@
+//sourcehash: fd3765d68f5b2a0a54c3a4057bfde38c84b4a141f4eaacb1862ef398989d077a
+
+/*
+  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_amplitudecorrection_functions_approximate_range_factor = R"doc()doc";
+
+static const char *__doc_themachinethatgoesping_algorithms_amplitudecorrection_functions_approximate_ranges = R"doc()doc";
+
+static const char *__doc_themachinethatgoesping_algorithms_amplitudecorrection_functions_compute_cw_range_correction = R"doc()doc";
+
+static const char *__doc_themachinethatgoesping_algorithms_amplitudecorrection_functions_get_sample_numbers_plus_half = R"doc()doc";
+
+#if defined(__GNUG__)
+#pragma GCC diagnostic pop
+#endif
+
+

src/themachinethatgoesping/algorithms/amplitudecorrection/functions/.docstrings/wcicorrection.doc.hpp

@@ -0,0 +1,47 @@
+//sourcehash: 1ae8666ee5111ec85d545eb0598565f91fc501c9641654802e5948d424bae907
+
+/*
+  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_amplitudecorrection_functions_apply_wci_correction = R"doc()doc";
+
+#if defined(__GNUG__)
+#pragma GCC diagnostic pop
+#endif
+
+