Update cosmotool 2nd part

external/cosmotool/python/_cosmo_cic.pyx

@@ -0,0 +1,76 @@
+from libcpp cimport bool
+from libcpp cimport string as cppstring
+from libcpp cimport vector as cppvector
+import numpy as np
+cimport numpy as np
+from cpython cimport PyObject, Py_INCREF
+cimport cython
+
+np.import_array()
+
+cdef extern from "cic.hpp" namespace "CosmoTool":
+
+  ctypedef float CICType
+  ctypedef float Coordinates[3]
+  
+  cdef cppclass CICParticles:
+    float mass
+    Coordinates coords
+
+  cdef cppclass CICFilter:
+  
+    CICFilter(np.uint32_t resolution, double L) nogil
+    
+    void resetMesh() nogil
+    void putParticles(CICParticles* particles, np.uint32_t N) nogil
+    void getDensityField(CICType *& field, np.uint32_t& res) nogil
+
+
+@cython.boundscheck(False)
+@cython.cdivision(True)
+@cython.wraparound(False)
+def leanCic(float[:,:] particles, float L, int Resolution):
+  cdef cppvector.vector[CICParticles] *p
+  cdef CICFilter *cic
+  cdef np.uint64_t i
+  cdef CICType *field
+  cdef np.uint32_t dummyRes
+  cdef np.ndarray[np.float64_t, ndim=3] out_field
+  cdef np.ndarray[np.float64_t, ndim=1] out_field0
+  cdef np.float64_t[:] out_field_buf
+  cdef np.uint64_t j
+
+  cic = new CICFilter(Resolution, L)
+  print("Reset mesh")
+  cic.resetMesh()
+  
+  if particles.shape[1] != 3:
+    raise ValueError("Particles must be Nx3 array")
+  
+  print("Inserting particles")
+#  p = new cppvector.vector[CICParticles](particles.shape[0])
+#  for i in xrange(particles.shape[0]):
+#    *p[i].mass = 1
+#    *p[i].coords[0] = particles[i,0]
+#    *p[i].coords[1] = particles[i,1]
+#    *p[i].coords[2] = particles[i,2]
+
+#  cic.putParticles(&p[0], particles.shape[0])
+  del p
+    
+  print("Done")
+  field = <CICType*>0
+  dummyRes = 0
+  cic.getDensityField(field, dummyRes)
+
+  print("Got to allocate a numpy %dx%dx%d" % (dummyRes, dummyRes,dummyRes))
+  
+  out_field = np.empty((dummyRes, dummyRes, dummyRes), dtype=np.float64)
+  out_field0 = out_field.reshape(out_field.size)
+  out_field_buf = out_field
+  print("Copy")
+  for j in xrange(out_field_buf.size):
+    out_field_buf[j] = field[j]
+  
+  del cic
+  return out_field