cosmotool/python/_cosmotool.pyx

from libcpp cimport bool
from libcpp cimport string as cppstring
import numpy as np
cimport numpy as np
from cpython cimport PyObject, Py_INCREF
cimport cython

np.import_array()

cdef extern from "loadSimu.hpp" namespace "CosmoTool":

  cdef cppclass SimuData:
    np.float_t BoxSize
    np.float_t time
    np.float_t Hubble

    np.float_t Omega_M
    np.float_t Omega_Lambda
    np.int64_t TotalNumPart
    np.int64_t NumPart
    np.int64_t *Id
    float *Pos[3]
    float *Vel[3]
    int *type
    float *Mass

    bool noAuto

  cdef const int NEED_GADGET_ID 
  cdef const int NEED_POSITION
  cdef const int NEED_VELOCITY
  cdef const int NEED_TYPE
  cdef const int NEED_MASS

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 NotImplementedError("getPositions is not implemented")
    
  def getVelocities(self):
    raise NotImplementedError("getVelocities is not implemented")
    
  def getIdentifiers(self):
    raise NotImplementedError("getIdentifiers is not implemented")

  def getTypes(self):
    raise NotImplementedError("getTypes is not implemented")

  def getOmega_M(self):
    raise NotImplementedError("getOmega_M is not implemented")
  
  def getOmega_Lambda(self):
    raise NotImplementedError("getOmega_Lambda is not implemented")

  def getTime(self):
    raise NotImplementedError("getTime is not implemented")

  def getHubble(self):
    raise NotImplementedError("getHubble is not implemented")

  def getBoxsize(self):
    raise NotImplementedError("getBoxsize is not implemented")

  def getMasses(self):
    raise NotImplementedError("getMasses is not implemented")

cdef class Simulation:

  cdef list positions
  cdef list velocities
  cdef object identifiers
  cdef object types
  cdef object masses

  cdef SimuData *data

  property BoxSize:
    def __get__(Simulation self):
        return self.data.BoxSize
        
  property time:
    def __get__(Simulation self):
        return self.data.time

  property Hubble:
    def __get__(Simulation self):
        return self.data.Hubble

  property Omega_M:
    def __get__(Simulation self):
        return self.data.Omega_M
        
  property Omega_Lambda:
    def __get__(Simulation self):
        return self.data.Omega_Lambda
        
  property positions:
    def __get__(Simulation self):
        return self.positions
        
  property velocities:
    def __get__(Simulation self):
        return self.velocities

  property identifiers:
    def __get__(Simulation self):
        return self.identifiers

  property types:
    def __get__(Simulation self):
        return self.types

  property masses:
    def __get__(Simulation self):
        return self.masses
        
  property numParticles:
    def __get__(Simulation self):
        return self.data.NumPart


  property totalNumParticles:
    def __get__(Simulation self):
        return self.data.TotalNumPart

  def __cinit__(Simulation self):
    self.data = <SimuData *>0
  
  def __dealloc__(Simulation self):
    if self.data != <SimuData *>0:
      print("Clearing simulation data")
      del self.data


class _PySimulationAdaptor(PySimulationBase):

  def __init__(self,sim):
    self.simu = sim

  def getBoxsize(self):
    return self.simu.BoxSize
    
  def getPositions(self):
    return self.simu.positions

  def getTypes(self):
    return self.simu.types
    
  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.simu.Hubble
    
  def getOmega_M(self):
    return self.simu.Omega_M
    
  def getOmega_Lambda(self):
    return self.simu.Omega_Lambda

  def getMasses(self):
    return self.simu.masses

cdef class ArrayWrapper:
    cdef void* data_ptr
    cdef int size
    cdef int type_array
    
    cdef set_data(self, int size, int type_array, void* data_ptr):
        """ Set the data of the array

This cannot be done in the constructor as it must recieve C-level
arguments.

Parameters:
-----------
size: int
Length of the array.
data_ptr: void*
Pointer to the data

    """
        self.data_ptr = data_ptr
        self.size = size
        self.type_array = type_array
     
    def __array__(self):
        """ Here we use the __array__ method, that is called when numpy
tries to get an array from the object."""
        cdef np.npy_intp shape[1]
        
        shape[0] = <np.npy_intp> self.size
        # Create a 1D array, of length 'size'
        ndarray = np.PyArray_SimpleNewFromData(1, shape, self.type_array, self.data_ptr)
        return ndarray
     
    def __dealloc__(self):
        """ Frees the array. This is called by Python when all the
references to the object are gone. """
        pass
 
cdef object wrap_array(void *p, np.uint64_t s, int typ):
    cdef np.ndarray ndarray
    cdef ArrayWrapper wrapper

    wrapper = ArrayWrapper()
    wrapper.set_data(s, typ, p)
    ndarray = np.array(wrapper, copy=False)
    ndarray.base = <PyObject*> wrapper
    Py_INCREF(wrapper)
    
    return ndarray


cdef object wrap_float_array(float *p, np.uint64_t s):
    return wrap_array(<void *>p, s, np.NPY_FLOAT32)

cdef object wrap_int64_array(np.int64_t* p, np.uint64_t s):
    return wrap_array(<void *>p, s, np.NPY_INT64)

cdef object wrap_int_array(int* p, np.uint64_t s):
    return wrap_array(<void *>p, s, np.NPY_INT)

cdef object wrap_simudata(SimuData *data, int flags):
  cdef Simulation simu

  simu = Simulation()
  simu.data = data
  if flags & NEED_POSITION:
     simu.positions = [wrap_float_array(data.Pos[i], data.NumPart) for i in xrange(3)]
  else:
     simu.positions = None

  if flags & NEED_VELOCITY:
     simu.velocities = [wrap_float_array(data.Vel[i], data.NumPart) for i in xrange(3)]
  else:
     simu.velocities = None

  if flags & NEED_GADGET_ID:
     simu.identifiers = wrap_int64_array(data.Id, data.NumPart)
  else:
     simu.identifiers = None

  if flags & NEED_TYPE:
     simu.types = wrap_int_array(data.type, data.NumPart)
  else:
     simu.types = None

  if flags & NEED_MASS:
     simu.masses = wrap_float_array(data.Mass, data.NumPart)
  else:
     simu.masses = None

  return simu

def loadGadget(str filename, int snapshot_id, bool loadPosition = True, bool loadVelocity = False, bool loadId = False, bool loadType = False, bool loadMass=False):
  """loadGadget(filename, cpu_id, loadPosition=True, loadVelocity=False, loadId=False, loadType=False)
It loads a gadget-1 snapshot and return a PySimulationBase object. If cpu_id is negative then the snapshot is considered not to be part of a set of snapshots written by different cpu. Otherwise the filename is modified to reflectt this cpu_id.
"""

  cdef int flags
  cdef SimuData *data
  cdef Simulation simu

  flags = 0
  if loadPosition:
     flags |= NEED_POSITION
  if loadVelocity:
     flags |= NEED_VELOCITY
  if loadId:
     flags |= NEED_GADGET_ID
  if loadType:
     flags |= NEED_TYPE
  if loadMass:
     flags |= NEED_MASS

  data = loadGadgetMulti(filename, snapshot_id, flags)
  if data == <SimuData*>0:
    return None

  return _PySimulationAdaptor(wrap_simudata(data, flags))

def writeGadget(str filename, object simulation):

  cdef SimuData simdata
  cdef np.ndarray[np.float32_t, ndim=1] pos, vel
  cdef np.ndarray[np.int64_t, ndim=1] ids
  cdef np.int64_t NumPart
  cdef int j
  
  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
  
  ids = simulation.getIdentifiers()
  simdata.Id = <np.int64_t *>ids.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)
  Loads the indicated snapshot based on the cpu id, snapshot id and basepath. It is important to specify the correct precision in doublePrecision.
"""
  cdef int flags
  cdef SimuData *data
  cdef Simulation simu

  flags = 0
  if loadPosition:
     flags |= NEED_POSITION
  if loadVelocity:
     flags |= NEED_VELOCITY

  data = loadRamsesSimu(basepath, snapshot_id, cpu_id, doublePrecision, flags)
  if data == <SimuData*>0:
    return None

  return _PySimulationAdaptor(wrap_simudata(data, flags))