Hardened SimuData. Support writeGadget

python/_cosmotool.pyx

@@ -1,4 +1,5 @@
 from libcpp cimport bool
+from libcpp cimport string as cppstring
 import numpy as np
 cimport numpy as np
 from cpython cimport PyObject, Py_INCREF
@@ -22,6 +23,8 @@ cdef extern from "loadSimu.hpp" namespace "CosmoTool":
     float *Vel[3]
     int *type
 
+    bool noAuto
+
   cdef const int NEED_GADGET_ID 
   cdef const int NEED_POSITION
   cdef const int NEED_VELOCITY
@@ -30,10 +33,35 @@ cdef extern from "loadSimu.hpp" namespace "CosmoTool":
 cdef extern from "loadGadget.hpp" namespace "CosmoTool":
 
   SimuData *loadGadgetMulti(const char *fname, int id, int flags) except +
+  void cxx_writeGadget "CosmoTool::writeGadget" (const char * s, SimuData *data) except +
+
 
 cdef extern from "loadRamses.hpp" namespace "CosmoTool":
   SimuData *loadRamsesSimu(const char *basename, int id, int cpuid, bool dp, int flags) except +
 
+
+class PySimulationBase(object):
+  def getPositions(self):
+    raise NotImplemented("getPositions is not implemented")
+    
+  def getVelocities(self):
+    raise NotImplemented("getVelocities is not implemented")
+    
+  def getIdentifiers(self):
+    raise NotImplemented("getIdentifiers is not implemented")
+
+  def getOmega_M(self):
+    raise NotImplemented("getOmega_M is not implemented")
+  
+  def getOmega_Lambda(self):
+    raise NotImplemented("getOmega_Lambda is not implemented")
+
+  def getTime(self):
+    raise NotImplemented("getTime is not implemented")
+
+  def getHubble(self):
+    raise NotImplemented("getHubble is not implemented")
+
 cdef class Simulation:
 
   cdef list positions
@@ -79,6 +107,27 @@ cdef class Simulation:
       del self.data
 
 
+class _PySimulationAdaptor(PySimulationBase):
+
+  def __init__(self,sim):
+  
+    self.simu = sim
+    
+  def getPositions(self):
+    return self.simu.positions
+    
+  def getVelocities(self):
+    return self.simu.velocities
+    
+  def getIdentifiers(self):
+    return self.simu.identifiers
+
+  def getTime(self):
+    return self.simu.time
+    
+  def getHubble(self):
+    return self.simul.Hubble
+
 cdef class ArrayWrapper:
     cdef void* data_ptr
     cdef int size
@@ -167,7 +216,39 @@ def loadGadget(str filename, int snapshot_id, bool loadPosition = True, bool loa
   if data == <SimuData*>0:
     return None
 
-  return wrap_simudata(data, flags)
+  return _PySimulationAdaptor(wrap_simudata(data, flags))
+
+def writeGadget(str filename, object simulation):
+
+  cdef SimuData simdata
+  cdef np.ndarray[np.float_t, ndim=1] pos, vel
+  cdef np.int64_t NumPart
+  
+  if not isinstance(simulation,PySimulationBase):
+    raise TypeError("Second argument must be of type SimulationBase")
+  
+  NumPart = simulation.positions[0].size
+  simdata.noAuto = True
+  
+  for j in xrange(3):
+    pos = simulation.getPositions()[j]
+    vel = simulation.getVelocities()[j]
+    
+    if pos.size != NumPart or vel.size != NumPart:
+      raise ValueError("Invalid number of particles")
+    
+    simdata.Pos[j] = <float *>pos.data
+    simdata.Vel[j] = <float *>vel.data
+
+  simdata.BoxSize = simulation.getBoxSize()
+  simdata.time = simulation.getTime()
+  simdata.Hubble = simulation.getHubble()
+  simdata.Omega_M = simulation.getOmega_M()
+  simdata.Omega_Lambda = simulation.getOmega_Lambda()
+  simdata.TotalNumPart = NumPart
+  simdata.NumPart = NumPart
+
+  cxx_writeGadget(filename, &simdata)
 
 def loadRamses(str basepath, int snapshot_id, int cpu_id, bool doublePrecision = False, bool loadPosition = True, bool loadVelocity = False):
   """ loadRamses(basepath, snapshot_id, cpu_id, doublePrecision=False, loadPosition=True, loadVelocity=False)
@@ -187,4 +268,4 @@ def loadRamses(str basepath, int snapshot_id, int cpu_id, bool doublePrecision =
   if data == <SimuData*>0:
     return None
 
-  return wrap_simudata(data, flags)
+  return _PySimulationAdaptor(wrap_simudata(data, flags))

src/loadSimu.hpp

@@ -64,6 +64,8 @@ namespace CosmoTool
     typedef void (*FreeFunction)(void *);
     typedef std::map<std::string, std::pair<void *, FreeFunction> > AttributeMap;
 
+    bool noAuto;
+
     float BoxSize;
     float time;
     float Hubble;
@@ -81,21 +83,22 @@ namespace CosmoTool
     AttributeMap attributes;
     
   public:
-    SimuData() : Id(0),NumPart(0),type(0)  { Pos[0]=Pos[1]=Pos[2]=0; Vel[0]=Vel[1]=Vel[2]=0; }
+    SimuData() : Id(0),NumPart(0),type(0),noAuto(false)  { Pos[0]=Pos[1]=Pos[2]=0; Vel[0]=Vel[1]=Vel[2]=0; }
     ~SimuData() 
     {
-      for (int j = 0; j < 3; j++)
-	{
-	  if (Pos[j])
-	    delete[] Pos[j];
-	  if (Vel[j])
-	    delete[] Vel[j];
-	}
-      if (type)
-	delete[] type;
-      if (Id)
-	delete[] Id;
-
+      if (!noAuto)  {
+        for (int j = 0; j < 3; j++)
+	  {
+	    if (Pos[j])
+	      delete[] Pos[j];
+	    if (Vel[j])
+	      delete[] Vel[j];
+          }
+        if (type)
+	  delete[] type;
+        if (Id)
+	  delete[] Id;
+      }
       for (AttributeMap::iterator i = attributes.begin();
 	   i != attributes.end();
 	   ++i)