Add simple Python bindings and an example

Author: franzpoeschel

CMakeLists.txt

@@ -602,6 +602,7 @@ if(openPMD_HAVE_PYTHON)
         src/binding/python/BaseRecordComponent.cpp
         src/binding/python/ChunkInfo.cpp
         src/binding/python/Container.cpp
+        src/binding/python/CustomHierarchy.cpp
         src/binding/python/Dataset.cpp
         src/binding/python/Datatype.cpp
         src/binding/python/Error.cpp
@@ -773,6 +774,7 @@ set(openPMD_PYTHON_EXAMPLE_NAMES
     11_particle_dataframe
     12_span_write
     13_write_dynamic_configuration
+    14_custom_hierarchy
 )
 
 if(openPMD_USE_INVASIVE_TESTS)

examples/14_custom_hierarchy.py

@@ -0,0 +1,48 @@
+import numpy as np
+import openpmd_api as io
+
+
+def main():
+    if "bp" in io.file_extensions:
+        filename = "../samples/custom_hierarchy.bp"
+    else:
+        filename = "../samples/custom_hierarchy.json"
+    s = io.Series(filename, io.Access.create)
+    it = s.write_iterations()[100]
+
+    # write openPMD part
+    temp = it.meshes["temperature"]
+    temp.axis_labels = ["x", "y"]
+    temp.unit_dimension = {io.Unit_Dimension.T: 1}
+    temp.position = [0.5, 0.5]
+    temp.grid_spacing = [1, 1]
+    temp.grid_global_offset = [0, 0]
+    temp.reset_dataset(io.Dataset(np.dtype("double"), [5, 5]))
+    temp[()] = np.zeros((5, 5))
+
+    # write NeXus part
+    nxentry = it["Scan"]
+    nxentry.set_attribute("NX_class", "NXentry")
+    nxentry.set_attribute("default", "data")
+
+    data = nxentry["data"]
+    data.set_attribute("NX_class", "NXdata")
+    data.set_attribute("signal", "counts")
+    data.set_attribute("axes", ["two_theta"])
+    data.set_attribute("two_theta_indices", [0])
+
+    counts = data.as_container_of_datasets()["counts"]
+    counts.set_attribute("units", "counts")
+    counts.set_attribute("long_name", "photodiode counts")
+    counts.reset_dataset(io.Dataset(np.dtype("int"), [15]))
+    counts[()] = np.zeros(15, dtype=np.dtype("int"))
+
+    two_theta = data.as_container_of_datasets()["two_theta"]
+    two_theta.set_attribute("units", "degrees")
+    two_theta.set_attribute("long_name", "two_theta (degrees)")
+    two_theta.reset_dataset(io.Dataset(np.dtype("double"), [15]))
+    two_theta[()] = np.zeros(15)
+
+
+if __name__ == "__main__":
+    main()

src/binding/python/Container.cpp

@@ -26,6 +26,7 @@
 
 #include <pybind11/pybind11.h>
 
+#include "openPMD/CustomHierarchy.hpp"
 #include "openPMD/Iteration.hpp"
 #include "openPMD/Mesh.hpp"
 #include "openPMD/ParticlePatches.hpp"
@@ -52,6 +53,7 @@ using PyPatchRecordContainer = Container<PatchRecord>;
 using PyRecordComponentContainer = Container<RecordComponent>;
 using PyMeshRecordComponentContainer = Container<MeshRecordComponent>;
 using PyPatchRecordComponentContainer = Container<PatchRecordComponent>;
+using PyCustomHierarchyContainer = Container<CustomHierarchy>;
 PYBIND11_MAKE_OPAQUE(PyIterationContainer)
 PYBIND11_MAKE_OPAQUE(PyMeshContainer)
 PYBIND11_MAKE_OPAQUE(PyPartContainer)
@@ -61,6 +63,7 @@ PYBIND11_MAKE_OPAQUE(PyPatchRecordContainer)
 PYBIND11_MAKE_OPAQUE(PyRecordComponentContainer)
 PYBIND11_MAKE_OPAQUE(PyMeshRecordComponentContainer)
 PYBIND11_MAKE_OPAQUE(PyPatchRecordComponentContainer)
+PYBIND11_MAKE_OPAQUE(PyCustomHierarchyContainer)
 
 void init_Container(py::module &m)
 {
@@ -85,4 +88,7 @@ void init_Container(py::module &m)
     ::detail::create_and_bind_container<
         PyPatchRecordComponentContainer,
         Attributable>(m, "Patch_Record_Component_Container");
+    ::detail::
+        create_and_bind_container<PyCustomHierarchyContainer, Attributable>(
+            m, "Custom_Hierarchy_Container");
 }

src/binding/python/CustomHierarchy.cpp

@@ -0,0 +1,36 @@
+
+
+#include "openPMD/CustomHierarchy.hpp"
+#include "openPMD/ParticleSpecies.hpp"
+#include "openPMD/RecordComponent.hpp"
+#include "openPMD/backend/Attributable.hpp"
+#include <pybind11/pybind11.h>
+
+namespace py = pybind11;
+using namespace openPMD;
+
+void init_CustomHierarchy(py::module &m)
+{
+    py::class_<CustomHierarchy, Container<CustomHierarchy>, Attributable>(
+        m, "CustomHierarchy")
+        .def(
+            "as_container_of_datasets",
+            &CustomHierarchy::asContainerOf<RecordComponent>)
+        .def("as_container_of_meshes", &CustomHierarchy::asContainerOf<Mesh>)
+        .def(
+            "as_container_of_particles",
+            &CustomHierarchy::asContainerOf<ParticleSpecies>)
+
+        .def_readwrite(
+            "meshes",
+            &CustomHierarchy::meshes,
+            py::return_value_policy::copy,
+            // garbage collection: return value must be freed before Iteration
+            py::keep_alive<1, 0>())
+        .def_readwrite(
+            "particles",
+            &CustomHierarchy::particles,
+            py::return_value_policy::copy,
+            // garbage collection: return value must be freed before Iteration
+            py::keep_alive<1, 0>());
+}

src/binding/python/Iteration.cpp

@@ -21,6 +21,7 @@
 #include <pybind11/pybind11.h>
 #include <pybind11/stl.h>
 
+#include "openPMD/CustomHierarchy.hpp"
 #include "openPMD/Iteration.hpp"
 
 #include <ios>
@@ -32,7 +33,11 @@ using namespace openPMD;
 
 void init_Iteration(py::module &m)
 {
-    py::class_<Iteration, Attributable>(m, "Iteration")
+    py::class_<
+        Iteration,
+        CustomHierarchy,
+        Container<CustomHierarchy>,
+        Attributable>(m, "Iteration")
         .def(py::init<Iteration const &>())
 
         .def(
@@ -83,18 +88,5 @@ void init_Iteration(py::module &m)
         // TODO remove in future versions (deprecated)
         .def("set_time", &Iteration::setTime<double>)
         .def("set_dt", &Iteration::setDt<double>)
-        .def("set_time_unit_SI", &Iteration::setTimeUnitSI)
-
-        .def_readwrite(
-            "meshes",
-            &Iteration::meshes,
-            py::return_value_policy::copy,
-            // garbage collection: return value must be freed before Iteration
-            py::keep_alive<1, 0>())
-        .def_readwrite(
-            "particles",
-            &Iteration::particles,
-            py::return_value_policy::copy,
-            // garbage collection: return value must be freed before Iteration
-            py::keep_alive<1, 0>());
+        .def("set_time_unit_SI", &Iteration::setTimeUnitSI);
 }

src/binding/python/openPMD.cpp

@@ -41,6 +41,7 @@ void init_Dataset(py::module &);
 void init_Datatype(py::module &);
 void init_Error(py::module &);
 void init_Helper(py::module &);
+void init_CustomHierarchy(py::module &);
 void init_Iteration(py::module &);
 void init_IterationEncoding(py::module &);
 void init_Mesh(py::module &);
@@ -94,6 +95,7 @@ PYBIND11_MODULE(openpmd_api_cxx, m)
     init_Dataset(m);
     init_Datatype(m);
     init_Helper(m);
+    init_CustomHierarchy(m);
     init_Iteration(m);
     init_IterationEncoding(m);
     init_BaseRecordComponent(m);