Add ability to get species names in gas_data (spec_name) and aero_data (spec_name and source_name) (#327)

Co-authored-by: Sylwester Arabas <[email protected]>

Author: jcurtis2

CMakeLists.txt

@@ -438,7 +438,7 @@ string(CONCAT
   "print(''.join([f'#define {line.split()[3]} {line.split()[5]}\\n' for line in sys.stdin if 'parameter ::' in line]))"
 )
 include(CheckFunctionExists)
-foreach(file aero_data;output)
+foreach(file aero_data;gas_data;output)
   execute_process(
     COMMAND ${PYTHON_EXECUTABLE} "-c" "${cmd}"
     INPUT_FILE ${CMAKE_SOURCE_DIR}/gitmodules/partmc/src/${file}.F90

src/aero_data.F90

@@ -196,4 +196,48 @@ subroutine f_aero_data_n_source(ptr_c, n_source) bind(C)
 
   end subroutine
 
+  subroutine f_aero_data_source_name_by_index(ptr_c, i_source, &
+      name_data &
+      ) bind(C)
+    type(aero_data_t), pointer :: ptr_f => null()
+    type(c_ptr), intent(in) :: ptr_c
+    character(kind=c_char), dimension(AERO_SOURCE_NAME_LEN) :: name_data
+    integer(c_int) :: name_size
+    integer(c_int), intent(in) :: i_source
+    integer :: i
+    character(len=1000) :: name
+
+    call c_f_pointer(ptr_c, ptr_f)
+
+    name = ptr_f%source_name(i_source+1)
+    name_size = len(trim(ptr_f%source_name(i_source+1)))
+    do i = 1,name_size
+       name_data(i) = name(i:i)
+    end do
+    name_data(i) = CHAR(0)
+
+  end subroutine
+
+  subroutine f_aero_data_spec_name_by_index(ptr_c, i_spec, &
+      name_data &
+      ) bind(C)
+    type(aero_data_t), pointer :: ptr_f => null()
+    type(c_ptr), intent(in) :: ptr_c
+    character(kind=c_char), dimension(AERO_NAME_LEN) :: name_data
+    integer(c_int) :: name_size
+    integer(c_int), intent(in) :: i_spec
+    integer :: i
+    character(len=AERO_NAME_LEN) :: name
+
+    call c_f_pointer(ptr_c, ptr_f)
+
+    name = ptr_f%name(i_spec+1)
+    name_size = len(trim(ptr_f%name(i_spec+1)))
+    do i = 1,name_size
+       name_data(i) = name(i:i)
+    end do
+    name_data(i) = CHAR(0)
+
+  end subroutine
+
 end module

src/aero_data.hpp

@@ -8,6 +8,7 @@
 
 #include "pmc_resource.hpp"
 #include "gimmicks.hpp"
+#include "pybind11/stl.h"
 #include "aero_data_parameters.hpp"
 
 extern "C" void f_aero_data_ctor(void *ptr) noexcept;
@@ -27,6 +28,10 @@ extern "C" void f_aero_data_vol2rad(const void *ptr, const double*, double*) noe
 extern "C" void f_aero_data_diam2vol(const void *ptr, const double*, double*) noexcept;
 extern "C" void f_aero_data_vol2diam(const void *ptr, const double*, double*) noexcept;
 extern "C" void f_aero_data_get_species_density(const void *ptr, const int *idx, double *val) noexcept;
+extern "C" void f_aero_data_source_name_by_index(const void *ptr, const int *i_source,
+    char *name_data) noexcept;
+extern "C" void f_aero_data_spec_name_by_index(const void *ptr, const int *i_spec,
+    char *name_data) noexcept;
 
 struct AeroData {
     PMCResource ptr;
@@ -206,5 +211,46 @@ struct AeroData {
         return len;
     }
 
+    static auto sources(const AeroData &self) {
+
+        int len;
+        f_aero_data_n_source(
+            self.ptr.f_arg(),
+            &len
+        );
+
+        char name[AERO_SOURCE_NAME_LEN];
+        auto names = pybind11::tuple(len);
+        for (int idx = 0; idx < len; idx++) {
+             f_aero_data_source_name_by_index(
+                 self.ptr.f_arg(),
+                 &idx,
+                 name
+            );
+            names[idx] = std::string(name);
+        }
+        return names;
+    }
+
+    static auto names(const AeroData &self) {
+
+        int len;
+        f_aero_data_len(
+            self.ptr.f_arg(),
+            &len
+        );
+
+        char name[AERO_NAME_LEN];
+        auto names = pybind11::tuple(len);
+        for (int idx = 0; idx < len; idx++) {
+             f_aero_data_spec_name_by_index(
+                 self.ptr.f_arg(),
+                 &idx,
+                 name
+            );
+            names[idx] = std::string(name);
+        }
+        return names;
+    }
 };
 

src/gas_data.F90

@@ -65,4 +65,26 @@ subroutine f_gas_data_spec_by_name(ptr_c, value, name_data, name_size) &
 
     end subroutine
 
+  subroutine f_gas_data_spec_name_by_index(ptr_c, i_spec, &
+      name_data &
+      ) bind(C)
+    type(gas_data_t), pointer :: ptr_f => null()
+    type(c_ptr), intent(in) :: ptr_c
+    character(kind=c_char), dimension(GAS_NAME_LEN) :: name_data
+    integer(c_int) :: name_size
+    integer(c_int), intent(in) :: i_spec
+    integer :: i
+    character(len=GAS_NAME_LEN) :: name
+
+    call c_f_pointer(ptr_c, ptr_f)
+
+    name = ptr_f%name(i_spec+1)
+    name_size = len(trim(ptr_f%name(i_spec+1)))
+    do i = 1,name_size
+       name_data(i) = name(i:i)
+    end do
+    name_data(i) = CHAR(0)
+
+  end subroutine
+
 end module

src/gas_data.hpp

@@ -8,6 +8,7 @@
 
 #include "gimmicks.hpp" // TODO #119: rename to something like json_resource.hpp?
 #include "pmc_resource.hpp"
+#include "gas_data_parameters.hpp"
 #include "pybind11/stl.h"
 #include "pybind11_json/pybind11_json.hpp"
 
@@ -18,6 +19,8 @@ extern "C" void f_gas_data_from_json(const void *ptr) noexcept;
 extern "C" void f_gas_data_to_json(const void *ptr) noexcept;
 extern "C" void f_gas_data_spec_by_name(const void *ptr, int *value, const char *name_data,
     const int *name_size) noexcept;
+extern "C" void f_gas_data_spec_name_by_index(const void *ptr, const int *i_spec,
+    char *name_data) noexcept;
 
 struct GasData {
     PMCResource ptr;
@@ -64,5 +67,26 @@ struct GasData {
             throw std::runtime_error("Element not found.");
         return value - 1;
     }
+
+    static auto names(const GasData &self) {
+
+        int len;
+        f_gas_data_len(
+            self.ptr.f_arg(),
+            &len
+        );
+
+        char name[GAS_NAME_LEN];
+        auto names = pybind11::tuple(len);
+        for (int idx = 0; idx < len; idx++) {
+             f_gas_data_spec_name_by_index(
+                 self.ptr.f_arg(),
+                 &idx,
+                 name
+            );
+            names[idx] = std::string(name);
+        }
+        return names;
+    }
 };
 

src/pypartmc.cpp

@@ -88,6 +88,7 @@ PYBIND11_MODULE(_PyPartMC, m) {
         .def("__len__", AeroData::__len__, "Number of aerosol species")
         .def_property_readonly("n_source", AeroData::n_source,
              "Number of aerosol sources")
+        .def_property_readonly("sources", AeroData::sources, "return list of source names")
         .def_property("frac_dim", &AeroData::get_frac_dim, &AeroData::set_frac_dim,
              "Volume fractal dimension (1)")
         .def_property("vol_fill_factor", &AeroData::get_vol_fill_factor,
@@ -105,6 +106,8 @@ PYBIND11_MODULE(_PyPartMC, m) {
             "Convert geometric diameter (m) to mass-equivalent volume (m^3).")
         .def("vol2diam", AeroData::vol2diam,
             "Convert mass-equivalent volume (m^3) to geometric diameter (m).")
+        .def_property_readonly("species", AeroData::names,
+            "returns list of aerosol species names")
     ;
 
     py::class_<AeroParticle>(m, "AeroParticle",
@@ -262,6 +265,7 @@ PYBIND11_MODULE(_PyPartMC, m) {
             "returns a string with JSON representation of the object")
         .def("spec_by_name", GasData::spec_by_name,
             "returns the number of the species in gas with the given name")
+        .def_property_readonly("species", GasData::names, "returns list of gas species names")
     ;
 
     py::class_<EnvState>(m,

tests/test_aero_data.py

@@ -10,6 +10,8 @@
 import PyPartMC as ppmc
 from PyPartMC import si
 
+# pylint: disable=R0904
+
 AERO_DATA_CTOR_ARG_MINIMAL = (
     {"H2O": [1000 * si.kg / si.m**3, 1, 18e-3 * si.kg / si.mol, 0]},
 )
@@ -354,6 +356,21 @@ def test_aero_data_density():
             # assert
             assert density == val[0]
 
+    @staticmethod
+    @pytest.mark.parametrize(
+        "ctor_arg", (AERO_DATA_CTOR_ARG_MINIMAL, AERO_DATA_CTOR_ARG_FULL)
+    )
+    def test_names(ctor_arg):
+        # arrange
+        sut = ppmc.AeroData(ctor_arg)
+        names = sut.species
+
+        # assert
+        for i, item in enumerate(ctor_arg):
+            key = tuple(item.keys())[0]
+            # pylint: disable=unsubscriptable-object
+            assert names[i] == key
+
     @staticmethod
     def test_ctor_error_on_nonunique_keys():
         # act
@@ -374,3 +391,18 @@ def test_n_source_uninitialized():
 
         # assert
         assert str(exc_info.value) == "No sources defined."
+
+    @staticmethod
+    def test_names_immutable():
+        # arrange
+        sut = ppmc.AeroData(
+            AERO_DATA_CTOR_ARG_MINIMAL,
+        )
+        names = sut.species
+
+        # act
+        with pytest.raises(TypeError) as exc_info:
+            names[0] = "Z"  # pylint: disable=unsupported-assignment-operation
+
+        # assert
+        assert "not support item assignment" in str(exc_info.value)

tests/test_aero_dist.py

@@ -13,7 +13,7 @@
 import PyPartMC as ppmc
 from PyPartMC import si
 
-from .test_aero_data import AERO_DATA_CTOR_ARG_MINIMAL
+from .test_aero_data import AERO_DATA_CTOR_ARG_FULL, AERO_DATA_CTOR_ARG_MINIMAL
 from .test_aero_mode import (
     AERO_MODE_CTOR_LOG_NORMAL,
     AERO_MODE_CTOR_LOG_NORMAL_COAGULATION,
@@ -172,6 +172,20 @@ def test_get_mode_is_a_copy(sut_minimal):
         # assert
         assert sut_minimal.mode(mode_idx).type != new_type
 
+    @staticmethod
+    def test_get_source_names():
+        # arrange
+        aero_data = ppmc.AeroData(AERO_DATA_CTOR_ARG_FULL)
+        _ = ppmc.AeroDist(aero_data, AERO_DIST_CTOR_ARG_AVERAGE)
+
+        # act
+        sources = aero_data.sources
+
+        # assert
+        keys = tuple(AERO_DIST_CTOR_ARG_AVERAGE[0].keys())
+        for i, key in enumerate(keys):
+            assert sources[i] == key  # pylint: disable=unsubscriptable-object
+
     @staticmethod
     def test_ctor_multimode_error_on_repeated_mode_names():
         # arrange

tests/test_gas_data.py

@@ -62,3 +62,32 @@ def test_spec_by_name(ctor_arg):
 
         # assert
         assert indices == list(range(len(ctor_arg)))
+
+    @staticmethod
+    @pytest.mark.parametrize(
+        "ctor_arg", (GAS_DATA_CTOR_ARG_MINIMAL, ("SO2", "NO2"), ("A", "B", "C"))
+    )
+    def test_species(ctor_arg):
+        # arrange
+        sut = ppmc.GasData(ctor_arg)
+
+        # act
+        names = sut.species
+
+        # assert
+        for i in range(len(sut)):
+            # pylint: disable=unsubscriptable-object
+            assert names[i] == ctor_arg[i]
+
+    @staticmethod
+    def test_species_immutable():
+        # arrange
+        sut = ppmc.GasData(GAS_DATA_CTOR_ARG_MINIMAL)
+        names = sut.species
+
+        # assert
+        with pytest.raises(TypeError) as exc_info:
+            names[0] = "Z"  # pylint: disable=unsupported-assignment-operation
+
+        # assert
+        assert "not support item assignment" in str(exc_info.value)