save Particle<T> object in HDF5

zhouyan · Feb 2, 2015 · 7875908 · 7875908
1 parent 3923074
commit 7875908
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Showing 5 changed files with 44 additions and 15 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -1,7 +1,11 @@
 # Changes since v1.0.0
 
-* Add support for [jemalloc][jemalloc] in `utility/aligned_memory.hpp`
+## New features
+
+* Support for [jemalloc][jemalloc] in `utility/aligned_memory.hpp`
 * `AlignedMemory` and `AlignedAllocator` default to [jemalloc][jemalloc] if it
-  is available.
+  is available
+* Store `Particle<T>` object in [HDF5][HDF5] format
 
+[HDF5]: http://www.hdfgroup.org/HDF5/
 [jemalloc]: http://www.canonware.com/jemalloc/
diff --git a/example/pf/include/pf_cl.hpp b/example/pf/include/pf_cl.hpp
@@ -180,15 +180,13 @@ inline void cv_do (vsmc::Sampler<cv> &sampler, vsmc::ResampleScheme res,
 
 #if VSMC_HAS_HDF5
     sampler.initialize(argv[1]);
-    vsmc::hdf5store<vsmc::RowMajor, cl_float>(
-            sampler.particle().value(),
+    vsmc::hdf5store<vsmc::RowMajor, cl_float>(sampler.particle(),
             argv[2] + rname + ".trace.h5", "Trace.0");
     for (std::size_t i = 0; i != DataNum - 1; ++i) {
         std::stringstream tss;
         tss << "Trace." << (i + 1);
         sampler.iterate();
-        vsmc::hdf5store<vsmc::RowMajor, cl_float>(
-                sampler.particle().value(),
+        vsmc::hdf5store<vsmc::RowMajor, cl_float>(sampler.particle(),
                 argv[2] + rname + ".trace.h5", tss.str(), true);
     }
 #else

diff --git a/example/pf/include/pf_mpi_do.hpp b/example/pf/include/pf_mpi_do.hpp
@@ -54,14 +54,14 @@ inline void cv_do (vsmc::ResampleScheme res, char **argv,
 
 #if VSMC_HAS_HDF5
     sampler.initialize(argv[1]);
-    vsmc::hdf5store(sampler.particle().value(),
-            argv[2] + rname + ".trace.h5", "Trace.0");
+    vsmc::hdf5store(sampler.particle(), argv[2] + rname + ".trace.h5",
+            "Trace.0");
     for (std::size_t i = 0; i != DataNum - 1; ++i) {
         std::stringstream tss;
         tss << "Trace." << (i + 1);
         sampler.iterate();
-        vsmc::hdf5store(sampler.particle().value(),
-                argv[2] + rname + ".trace.h5", tss.str(), true);
+        vsmc::hdf5store(sampler.particle(), argv[2] + rname + ".trace.h5",
+                tss.str(), true);
     }
 #else
     sampler.initialize(argv[1]);

diff --git a/example/pf/include/pf_smp_do.hpp b/example/pf/include/pf_smp_do.hpp
@@ -48,14 +48,14 @@ inline void cv_do (vsmc::ResampleScheme res, char **argv,
     sampler.monitor("pos").name(1) = "pos.y";
 #if VSMC_HAS_HDF5
     sampler.initialize(argv[1]);
-    vsmc::hdf5store(sampler.particle().value(),
-            argv[2] + name + ".trace.h5", "Trace.0");
+    vsmc::hdf5store(sampler.particle(), argv[2] + name + ".trace.h5",
+            "Trace.0");
     for (std::size_t i = 0; i != DataNum - 1; ++i) {
         std::stringstream ss;
         ss << "Trace." << (i + 1);
         sampler.iterate();
-        vsmc::hdf5store(sampler.particle().value(),
-                argv[2] + name + ".trace.h5", ss.str(), true);
+        vsmc::hdf5store(sampler.particle(), argv[2] + name + ".trace.h5",
+                ss.str(), true);
     }
 #else
     sampler.initialize(argv[1]);

diff --git a/include/vsmc/utility/hdf5io.hpp b/include/vsmc/utility/hdf5io.hpp
@@ -622,6 +622,33 @@ inline void hdf5store (const Sampler<T> &sampler,
             &resampled[0], "Resampled");
 }
 
+/// \brief Store a Particle in the HDF5 format
+/// \ingroup HDF5IO
+template <typename T>
+inline void hdf5store (const Particle<T> &particle,
+        const std::string &file_name, const std::string &data_name,
+        bool append = false)
+{
+    hdf5store_list_empty(file_name, data_name, append);
+    hdf5store(particle.value(), file_name, data_name + "/value", true);
+    hdf5store_matrix<ColMajor, double>(particle.size(), 1, file_name,
+            data_name + "/weight", particle.weight_set().weight_data(), true);
+}
+
+/// \brief Store a Particle with StateCL value type in the HDF5 format
+/// \ingroup HDF5IO
+template <MatrixOrder Order, typename T, typename U>
+inline void hdf5store (const Particle<U> &particle,
+        const std::string &file_name, const std::string &data_name,
+        bool append = false)
+{
+    hdf5store_list_empty(file_name, data_name, append);
+    hdf5store<Order, T>(particle.value(), file_name, data_name + "/value",
+            append);
+    hdf5store_matrix<ColMajor, double>(particle.size(), 1, file_name,
+            data_name + "/weight", particle.weight_set().weight_data(), true);
+}
+
 /// \brief Store a StateMatrix in the HDF5 format
 /// \ingroup HDF5IO
 template <MatrixOrder Order, std::size_t Dim, typename T>
@@ -689,7 +716,7 @@ inline void hdf5store (const StateTuple<ColMajor, T, Types...> &state,
 /// \brief Store a StateCL in the HDF5 format
 /// \ingroup HDF5IO
 template <MatrixOrder Order, typename T,
-         std::size_t StateSize, typename FPType, typename ID>
+    std::size_t StateSize, typename FPType, typename ID>
 inline void hdf5store (const StateCL<StateSize, FPType, ID> &state,
         const std::string &file_name, const std::string &data_name,
         bool append = false)