Fixed a few errors in the PSPhdf5 version of the ParticleReader

Author: Martin D. Weinberg

exputil/ParticleReader.cc

@@ -705,7 +705,7 @@ namespace PR {
   }
 
 
-  PSPhdf5::PSPhdf5(const std::vector<std::string>& files, bool verbose) : ParticleReader()
+  PSPhdf5::PSPhdf5(const std::vector<std::string>& files, bool verbose) : PSP(verbose)
   {
     _files   = files;
     _verbose = verbose;

include/ParticleReader.H

@@ -234,90 +234,6 @@ namespace PR
 
   };
 
-  class PSPhdf5 : public ParticleReader
-  {
-  protected:
-
-    //@{
-    //! Parameters
-    double time;
-    std::vector<Particle> particles;
-    bool _verbose;
-    std::vector<std::string> _files;
-
-    std::vector<double> mass;
-    std::vector<int> Niattrib, Ndattrib;
-    std::vector<unsigned long> npart, nptot;
-    unsigned long totalCount;
-    bool real4, gadget4;
-    int ntypes, nfiles;
-    //@}
-    
-    //! Current file
-    std::vector<std::string>::iterator curfile;
-
-    //! Components
-    std::vector<std::string> comps;
-
-    //@{
-    //! Current component and index
-    std::string curcomp;
-    int curindx;
-    //@}
-
-    unsigned pcount;
-    template <typename Scalar> void read_and_load();
-    template <typename Scalar> void read_and_load_gadget4();
-    template <typename Scalar> void read_and_load_psp();
-
-    void getInfo();
-    void packParticle();
-    bool nextFile();
-
-  public:
-    
-    //! Constructor
-    PSPhdf5(const std::vector<std::string>& file, bool verbose=false);
-    
-    //! Select a particular particle type and reset the iterator
-    virtual void SelectType(const std::string& type) {
-      auto it = std::find(comps.begin(), comps.end(), type);
-      if (it != comps.end()) {
-	curcomp = type;
-	curindx = it - comps.begin();
-      }
-      else {
-	std::cerr << "PSPhdf5 error: could not find particle component <" << type << ">" << std::endl;
-	std::cerr << "Available particle components are:";
-	for (auto s : comps) std::cerr << " " << s;
-	std::cerr << std::endl;
-	throw std::runtime_error("PSPhdf5: non-existent component");
-      }
-
-      curfile = _files.begin();	// Set to first file and open
-      nextFile();
-    }
-    
-    //! Number of particles in the chosen type
-    virtual unsigned long CurrentNumber() { return totalCount; }
-    
-    //! Return list of particle types
-    virtual std::vector<std::string> GetTypes() { return comps; }
-    
-    //! Get current time
-    virtual double CurrentTime() { return time; }
-    
-    //! Reset to beginning of particles for this component
-    virtual const Particle* firstParticle();
-    
-    //! Get the next particle
-    virtual const Particle* nextParticle();
-    
-    //! Get file cound per snapshot
-    virtual int NumFiles() { return nfiles; }
-
-  };
-  
   class PSPstanza 
   {
   public:
@@ -646,6 +562,90 @@ namespace PR
     //@}
   };
 
+  class PSPhdf5 : public PSP
+  {
+  protected:
+
+    //@{
+    //! Parameters
+    double time;
+    std::vector<Particle> particles;
+    bool _verbose;
+    std::vector<std::string> _files;
+
+    std::vector<double> mass;
+    std::vector<int> Niattrib, Ndattrib;
+    std::vector<unsigned long> npart, nptot;
+    unsigned long totalCount;
+    bool real4, gadget4;
+    int ntypes, nfiles;
+    //@}
+    
+    //! Current file
+    std::vector<std::string>::iterator curfile;
+
+    //! Components
+    std::vector<std::string> comps;
+
+    //@{
+    //! Current component and index
+    std::string curcomp;
+    int curindx;
+    //@}
+
+    unsigned pcount;
+    template <typename Scalar> void read_and_load();
+    template <typename Scalar> void read_and_load_gadget4();
+    template <typename Scalar> void read_and_load_psp();
+
+    void getInfo();
+    void packParticle();
+    bool nextFile();
+
+  public:
+    
+    //! Constructor
+    PSPhdf5(const std::vector<std::string>& file, bool verbose=false);
+    
+    //! Select a particular particle type and reset the iterator
+    virtual void SelectType(const std::string& type) {
+      auto it = std::find(comps.begin(), comps.end(), type);
+      if (it != comps.end()) {
+	curcomp = type;
+	curindx = it - comps.begin();
+      }
+      else {
+	std::cerr << "PSPhdf5 error: could not find particle component <" << type << ">" << std::endl;
+	std::cerr << "Available particle components are:";
+	for (auto s : comps) std::cerr << " " << s;
+	std::cerr << std::endl;
+	throw std::runtime_error("PSPhdf5: non-existent component");
+      }
+
+      curfile = _files.begin();	// Set to first file and open
+      nextFile();
+    }
+    
+    //! Number of particles in the chosen type
+    virtual unsigned long CurrentNumber() { return nptot[curindx]; }
+    
+    //! Return list of particle types
+    virtual std::vector<std::string> GetTypes() { return comps; }
+    
+    //! Get current time
+    virtual double CurrentTime() { return time; }
+    
+    //! Reset to beginning of particles for this component
+    virtual const Particle* firstParticle();
+    
+    //! Get the next particle
+    virtual const Particle* nextParticle();
+    
+    //! Get file cound per snapshot
+    virtual int NumFiles() { return nfiles; }
+
+  };
+  
   typedef std::shared_ptr<ParticleReader> PRptr;
 }
 

pyEXP/ParticleReaderWrappers.cc

@@ -15,11 +15,12 @@ void ParticleReaderClasses(py::module &m) {
     "The available particle readers are:\n"
     "  1. PSPout         The monolithic EXP phase-space snapshot format\n"
     "  2. PSPspl         Like PSPout, but split into multiple file chunks\n"
-    "  3. GadgetNative   The original Gadget native format\n"
-    "  4  GadgetHDF5     The newer HDF5 Gadget format\n"
-    "  5. TipsyNative    The original Tipsy format\n"
-    "  6. TipsyXDR       The original XDR Tipsy format\n"
-    "  7. Bonsai         This is the Bonsai varient of Tipsy files\n\n"
+    "  3. PSPhdf5        The HDF5 version of the EXP phase-space format\n"
+    "  4. GadgetNative   The original Gadget native format\n"
+    "  5  GadgetHDF5     The newer HDF5 Gadget format\n"
+    "  6. TipsyNative    The original Tipsy format\n"
+    "  7. TipsyXDR       The original XDR Tipsy format\n"
+    "  8. Bonsai         This is the Bonsai varient of Tipsy files\n\n"
     "We have a helper function, getReaders, to get a list to help you\n"
     "remember.  Try: pyEXP.read.ParticleReader.getReaders()\n\n"
     "Each reader can manage snapshots split into many files by parallel,\n"
@@ -216,6 +217,38 @@ void ParticleReaderClasses(py::module &m) {
     }
   };
 
+  class PyPSPhdf5 : public PSPhdf5
+  {
+  public:
+
+    // Inherit the constructors
+    using PSPhdf5::PSPhdf5;
+
+    void SelectType(const std::string& type) override {
+      PYBIND11_OVERRIDE(void, PSPhdf5, SelectType, type);
+    }
+    
+    std::vector<std::string> GetTypes() override {
+      PYBIND11_OVERRIDE(std::vector<std::string>, PSPhdf5, GetTypes,);
+    }
+    
+    unsigned long CurrentNumber() override {
+      PYBIND11_OVERRIDE(unsigned long, PSPhdf5, CurrentNumber,);
+    }
+    
+    double CurrentTime() override {
+      PYBIND11_OVERRIDE(double, PSPhdf5, CurrentTime,);
+    }
+    
+    const Particle* firstParticle() override {
+      PYBIND11_OVERRIDE(const Particle*, PSPhdf5, firstParticle,);
+    }
+
+    const Particle* nextParticle() override {
+      PYBIND11_OVERRIDE(const Particle*, PSPhdf5, nextParticle,);
+    }
+  };
+
   class PyTipsy : public Tipsy
   {
   public:
@@ -401,8 +434,8 @@ void ParticleReaderClasses(py::module &m) {
   pr.def_static("getReaders", []()
   {
     const std::vector<std::string> formats = {
-      "PSPout", "PSPspl", "GadgetNative", "GadgetHDF5", "TipsyNative",
-      "TipsyXDR", "Bonsai"};
+      "PSPout", "PSPspl", "PSPhdf5", "GadgetNative", "GadgetHDF5",
+      "TipsyNative", "TipsyXDR", "Bonsai"};
 
     return formats;
     },
@@ -431,7 +464,7 @@ void ParticleReaderClasses(py::module &m) {
          Returns
          -------
          ParticleReader
-         )");
+         )", py::arg("files"), py::arg("verbose")=false);
 
   py::class_<GadgetNative, std::shared_ptr<GadgetNative>, PyGadgetNative, ParticleReader>(m, "GadgetNative")
     .def(py::init<const std::vector<std::string>&, bool>(),
@@ -448,7 +481,7 @@ void ParticleReaderClasses(py::module &m) {
          Returns
          -------
          ParticleReader
-         )");
+         )", py::arg("files"), py::arg("verbose")=false);
 
   py::class_<PSP, std::shared_ptr<PSP>, PyPSP, ParticleReader>(m, "PSP")
     .def(py::init<bool>(), "Base class for PSP reader")
@@ -464,19 +497,67 @@ void ParticleReaderClasses(py::module &m) {
 
   py::class_<PSPout, std::shared_ptr<PSPout>, PyPSPout, PSP>(m, "PSPout")
     .def(py::init<const std::vector<std::string>&, bool>(),
-	 "Reader for monolitic PSP format (single file written by root process)")
+	 R"(
+         Read PSP ascii monolithic format snapshot files
+
+         Parameters
+         ----------
+         files : list(str)
+             List of files with phase-space segments comprising a single snapshot
+         verbose : bool, default=False
+             Verbose, diagnostic output
+
+         Returns
+         -------
+         ParticleReader
+         )", py::arg("files"), py::arg("verbose")=false)
     .def("CurrentNumber",   &PSPout::CurrentNumber)
     .def("GetTypes",        &PSPout::GetTypes)
     .def("CurrentTime",     &PSPout::CurrentTime);
 
 
   py::class_<PSPspl, std::shared_ptr<PSPspl>, PyPSPspl, PSP>(m, "PSPspl")
     .def(py::init<const std::vector<std::string>&, bool>(),
-	 "Reader for split PSP files (multiple files written by each process)")
+	 R"(
+	 Reader for split PSP files (multiple files written by each process)
+
+         Parameters
+         ----------
+         files : list(str)
+             List of files with phase-space segments comprising a single snapshot
+         verbose : bool, default=False
+             Verbose, diagnostic output
+
+         Returns
+         -------
+         ParticleReader
+         )", py::arg("files"), py::arg("verbose")=false)
     .def("CurrentNumber",   &PSPspl::CurrentNumber)
     .def("GetTypes",        &PSPspl::GetTypes)
     .def("CurrentTime",     &PSPspl::CurrentTime);
 
+  py::class_<PSPhdf5, std::shared_ptr<PSPhdf5>, PyPSPhdf5, PSP>(m, "PSPhdf5")
+    .def(py::init<const std::vector<std::string>&, bool>(),
+	 R"(
+	 Reader for HDF5 PSP files (both single and multiple files)
+
+         Parameters
+         ----------
+         files : list(str)
+             List of files with phase-space segments comprising a single snapshot
+         verbose : bool, default=False
+             Verbose, diagnostic output
+
+         Returns
+         -------
+         ParticleReader
+         )", py::arg("files"), py::arg("verbose")=false)
+    .def("SelectType",      &PSPhdf5::SelectType)
+    .def("NumFiles",        &PSPhdf5::NumFiles)
+    .def("CurrentNumber",   &PSPhdf5::CurrentNumber)
+    .def("GetTypes",        &PSPhdf5::GetTypes)
+    .def("CurrentTime",     &PSPhdf5::CurrentTime);
+	 
   py::class_<Tipsy, std::shared_ptr<Tipsy>, PyTipsy, ParticleReader> tipsy(m, "Tipsy");
 
   py::enum_<Tipsy::TipsyType>(tipsy, "TipsyType")
@@ -485,12 +566,28 @@ void ParticleReaderClasses(py::module &m) {
     .value("bonsai", Tipsy::TipsyType::bonsai)
     .export_values();
 
-  tipsy.def(py::init<const std::string&, Tipsy::TipsyType, bool>())
+  tipsy.def(py::init<const std::string&, Tipsy::TipsyType, bool>(),
+	    R"(
+            Read Tipsy format snapshots
+
+            Parameters
+            ----------
+            file : str
+                   The Tipsy snapshot file
+            type : TipsyType
+                   The Tipsy file type (native, xdr, bonsai)
+            verbose : bool, default=False
+                   Verbose, diagnostic output
+
+            Returns
+            -------
+            ParticleReader
+
+            )", py::arg("file"), py::arg("type"), py::arg("verbose")=false)
     .def(py::init<const std::vector<std::string>&, Tipsy::TipsyType, bool>())
     .def("SelectType",      &Tipsy::SelectType)
     .def("CurrentNumber",   &Tipsy::CurrentNumber)
     .def("GetTypes",        &Tipsy::GetTypes)
     .def("CurrentTime",     &Tipsy::CurrentTime);
 
 }
-