Same trick for Dataset() constructor

Author: franzpoeschel

CMakeLists.txt

@@ -550,6 +550,7 @@ endif()
 if(openPMD_HAVE_PYTHON)
     add_library(openPMD.py MODULE
         src/binding/python/openPMD.cpp
+        src/binding/python/auxiliary.cpp
         src/binding/python/Access.cpp
         src/binding/python/Attributable.cpp
         src/binding/python/BaseRecordComponent.cpp

examples/13_write_dynamic_configuration.py

@@ -1,6 +1,4 @@
 #!/usr/bin/env python
-import json
-
 import numpy as np
 import openpmd_api as io
 
@@ -20,7 +18,8 @@
 # be passed by adding an at-sign `@` in front of the path
 # The format will then be recognized by filename extension, i.e. .json or .toml
 # In Python, normal Python dictionaries can also be used which will then be
-# converted via `json.dumps()` in the Series constructor.
+# converted via `json.dumps()` in the Series constructor
+# (see below for an example in terms of the Dataset constructor)
 
 backend = "adios2"
 iteration_encoding = "group_based"
@@ -107,9 +106,6 @@ def main():
                 'dataset': {
                     'operators': []
                 }
-            },
-            'adios1': {
-                'dataset': {}
             }
         }
         config['adios2']['dataset'] = {
@@ -120,9 +116,6 @@ def main():
                 }
             }]
         }
-        config['adios1']['dataset'] = {
-            'transform': 'blosc:compressor=zlib,shuffle=bit,lvl=1;nometa'
-        }
 
         temperature = iteration.meshes["temperature"]
         temperature.unit_dimension = {io.Unit_Dimension.theta: 1.0}
@@ -131,8 +124,7 @@ def main():
         # temperature has no x,y,z components, so skip the last layer:
         temperature_dataset = temperature
         # let's say we are in a 3x3 mesh
-        dataset = io.Dataset(np.dtype("double"), [3, 3])
-        dataset.options = json.dumps(config)
+        dataset = io.Dataset(np.dtype("double"), [3, 3], config)
         temperature_dataset.reset_dataset(dataset)
         # temperature is constant
         local_data = np.arange(i * 9, (i + 1) * 9, dtype=np.dtype("double"))

examples/7_extended_write_serial.py

@@ -6,8 +6,6 @@
 Authors: Axel Huebl, Fabian Koller
 License: LGPLv3+
 """
-import json
-
 import numpy as np
 from openpmd_api import (Access, Dataset, Mesh_Record_Component, Series,
                          Unit_Dimension)
@@ -104,7 +102,6 @@
     # before storing record data, you must specify the dataset once per
     # component this describes the datatype and shape of data as it should be
     # written to disk
-    d = Dataset(partial_mesh.dtype, extent=[2, 5])
     dataset_config = {
         "adios2": {
             "dataset": {
@@ -117,7 +114,7 @@
             }
         }
     }
-    d.options = json.dumps(dataset_config)
+    d = Dataset(partial_mesh.dtype, extent=[2, 5], options=dataset_config)
     mesh["x"].reset_dataset(d)
 
     electrons = cur_it.particles["electrons"]

include/openPMD/binding/python/auxiliary.hpp

@@ -0,0 +1,29 @@
+/* Copyright 2025 Franz Poeschel
+ *
+ * This file is part of openPMD-api.
+ *
+ * openPMD-api is free software: you can redistribute it and/or modify
+ * it under the terms of of either the GNU General Public License or
+ * the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * openPMD-api is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License and the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * and the GNU Lesser General Public License along with openPMD-api.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#pragma once
+
+#include "openPMD/binding/python/Common.hpp"
+
+namespace auxiliary
+{
+auto json_dumps(py::object const &obj) -> std::string;
+}

src/binding/python/Dataset.cpp

@@ -22,34 +22,43 @@
 
 #include "openPMD/binding/python/Common.hpp"
 #include "openPMD/binding/python/Numpy.hpp"
+#include "openPMD/binding/python/auxiliary.hpp"
 
 #include <string>
 
 void init_Dataset(py::module &m)
 {
     auto pyDataset =
         py::class_<Dataset>(m, "Dataset")
+            .def(py::init<Extent>(), py::arg("extent"))
             .def(
-                py::init<Datatype, Extent>(),
+                py::init<Datatype, Extent, std::string>(),
                 py::arg("dtype"),
-                py::arg("extent"))
-            .def(py::init<Extent>(), py::arg("extent"))
+                py::arg("extent"),
+                py::arg("options") = "{}")
             .def(
-                py::init([](py::dtype dt, Extent const &e) {
+                py::init([](py::dtype dt, Extent e, std::string options) {
                     auto const d = dtype_from_numpy(std::move(dt));
-                    return new Dataset{d, e};
+                    return new Dataset{d, std::move(e), std::move(options)};
                 }),
                 py::arg("dtype"),
-                py::arg("extent"))
+                py::arg("extent"),
+                py::arg("options") = "{}")
             .def(
-                py::init<Datatype, Extent, std::string>(),
+                py::init([](Datatype dt, Extent e, py::object const &options) {
+                    auto resolved_options = ::auxiliary::json_dumps(options);
+                    return new Dataset{
+                        dt, std::move(e), std::move(resolved_options)};
+                }),
                 py::arg("dtype"),
                 py::arg("extent"),
                 py::arg("options"))
             .def(
-                py::init([](py::dtype dt, Extent e, std::string options) {
+                py::init([](py::dtype dt, Extent e, py::object const &options) {
                     auto const d = dtype_from_numpy(std::move(dt));
-                    return new Dataset{d, std::move(e), std::move(options)};
+                    auto resolved_options = ::auxiliary::json_dumps(options);
+                    return new Dataset{
+                        d, std::move(e), std::move(resolved_options)};
                 }),
                 py::arg("dtype"),
                 py::arg("extent"),

src/binding/python/Series.cpp

@@ -37,6 +37,7 @@
 //  re-implemented signatures:
 //  include <mpi4py/mpi4py.h>
 #include "openPMD/binding/python/Mpi.hpp"
+#include "openPMD/binding/python/auxiliary.hpp"
 #include <mpi.h>
 #endif
 
@@ -81,10 +82,7 @@ struct DefineSeriesConstructorPerPathType
 
     static auto json_cfg_as_string(py::object const &obj) -> std::string
     {
-        py::module_ json = py::module_::import("json");
-        auto dumps = json.attr("dumps");
-        auto dumped = dumps(obj);
-        return py::cast<std::string>(dumped);
+        return ::auxiliary::json_dumps(obj);
     }
 
     template <typename TupleType>

src/binding/python/auxiliary.cpp

@@ -0,0 +1,33 @@
+/* Copyright 2025 Franz Poeschel
+ *
+ * This file is part of openPMD-api.
+ *
+ * openPMD-api is free software: you can redistribute it and/or modify
+ * it under the terms of of either the GNU General Public License or
+ * the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * openPMD-api is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License and the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * and the GNU Lesser General Public License along with openPMD-api.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include "openPMD/binding/python/auxiliary.hpp"
+
+namespace auxiliary
+{
+auto json_dumps(py::object const &obj) -> std::string
+{
+    py::module_ json = py::module_::import("json");
+    auto dumps = json.attr("dumps");
+    auto dumped = dumps(obj);
+    return py::cast<std::string>(dumped);
+}
+} // namespace auxiliary

test/python/unittest/API/APITest.py

@@ -2129,8 +2129,7 @@ def testJsonConfigADIOS2(self):
         E_x.store_chunk(data, [0], [1000])
 
         E_y = series.iterations[0].meshes["E"]["y"]
-        import json
-        E_y.reset_dataset(DS(np.dtype("double"), [1000], json.dumps(local_config)))
+        E_y.reset_dataset(DS(np.dtype("double"), [1000], local_config))
         E_y.store_chunk(data, [0], [1000])
 
         self.assertTrue(series)