Finished early binding

FindNumPy.cmake

@@ -0,0 +1,102 @@
+# - Find the NumPy libraries
+# This module finds if NumPy is installed, and sets the following variables
+# indicating where it is.
+#
+# TODO: Update to provide the libraries and paths for linking npymath lib.
+#
+#  NUMPY_FOUND               - was NumPy found
+#  NUMPY_VERSION             - the version of NumPy found as a string
+#  NUMPY_VERSION_MAJOR       - the major version number of NumPy
+#  NUMPY_VERSION_MINOR       - the minor version number of NumPy
+#  NUMPY_VERSION_PATCH       - the patch version number of NumPy
+#  NUMPY_VERSION_DECIMAL     - e.g. version 1.6.1 is 10601
+#  NUMPY_INCLUDE_DIRS        - path to the NumPy include files
+
+#============================================================================
+# Copyright 2012 Continuum Analytics, Inc.
+#
+# MIT License
+#
+# Permission is hereby granted, free of charge, to any person obtaining
+# a copy of this software and associated documentation files
+# (the "Software"), to deal in the Software without restriction, including
+# without limitation the rights to use, copy, modify, merge, publish,
+# distribute, sublicense, and/or sell copies of the Software, and to permit
+# persons to whom the Software is furnished to do so, subject to
+# the following conditions:
+#
+# The above copyright notice and this permission notice shall be included
+# in all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+# OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR
+# OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
+# ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+# OTHER DEALINGS IN THE SOFTWARE.
+#
+#============================================================================
+
+# Finding NumPy involves calling the Python interpreter
+if(NumPy_FIND_REQUIRED)
+    find_package(PythonInterp REQUIRED)
+else()
+    find_package(PythonInterp)
+endif()
+
+if(NOT PYTHONINTERP_FOUND)
+    set(NUMPY_FOUND FALSE)
+    return()
+endif()
+
+execute_process(COMMAND "${PYTHON_EXECUTABLE}" "-c"
+    "import numpy as n; print(n.__version__); print(n.get_include());"
+    RESULT_VARIABLE _NUMPY_SEARCH_SUCCESS
+    OUTPUT_VARIABLE _NUMPY_VALUES_OUTPUT
+    ERROR_VARIABLE _NUMPY_ERROR_VALUE
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+
+if(NOT _NUMPY_SEARCH_SUCCESS MATCHES 0)
+    if(NumPy_FIND_REQUIRED)
+        message(FATAL_ERROR
+            "NumPy import failure:\n${_NUMPY_ERROR_VALUE}")
+    endif()
+    set(NUMPY_FOUND FALSE)
+    return()
+endif()
+
+# Convert the process output into a list
+string(REGEX REPLACE ";" "\\\\;" _NUMPY_VALUES ${_NUMPY_VALUES_OUTPUT})
+string(REGEX REPLACE "\n" ";" _NUMPY_VALUES ${_NUMPY_VALUES})
+# Just in case there is unexpected output from the Python command.
+list(GET _NUMPY_VALUES -2 NUMPY_VERSION)
+list(GET _NUMPY_VALUES -1 NUMPY_INCLUDE_DIRS)
+
+string(REGEX MATCH "^[0-9]+\\.[0-9]+\\.[0-9]+" _VER_CHECK "${NUMPY_VERSION}")
+if("${_VER_CHECK}" STREQUAL "")
+    # The output from Python was unexpected. Raise an error always
+    # here, because we found NumPy, but it appears to be corrupted somehow.
+    message(FATAL_ERROR
+        "Requested version and include path from NumPy, got instead:\n${_NUMPY_VALUES_OUTPUT}\n")
+    return()
+endif()
+
+# Make sure all directory separators are '/'
+string(REGEX REPLACE "\\\\" "/" NUMPY_INCLUDE_DIRS ${NUMPY_INCLUDE_DIRS})
+
+# Get the major and minor version numbers
+string(REGEX REPLACE "\\." ";" _NUMPY_VERSION_LIST ${NUMPY_VERSION})
+list(GET _NUMPY_VERSION_LIST 0 NUMPY_VERSION_MAJOR)
+list(GET _NUMPY_VERSION_LIST 1 NUMPY_VERSION_MINOR)
+list(GET _NUMPY_VERSION_LIST 2 NUMPY_VERSION_PATCH)
+string(REGEX MATCH "[0-9]*" NUMPY_VERSION_PATCH ${NUMPY_VERSION_PATCH})
+math(EXPR NUMPY_VERSION_DECIMAL
+    "(${NUMPY_VERSION_MAJOR} * 10000) + (${NUMPY_VERSION_MINOR} * 100) + ${NUMPY_VERSION_PATCH}")
+
+find_package_message(NUMPY
+    "Found NumPy: version \"${NUMPY_VERSION}\" ${NUMPY_INCLUDE_DIRS}"
+    "${NUMPY_INCLUDE_DIRS}${NUMPY_VERSION}")
+
+set(NUMPY_FOUND TRUE)
+

python/CMakeLists.txt

@@ -42,7 +42,7 @@ if (WIN32 AND NOT CYGWIN)
 endif (WIN32 AND NOT CYGWIN)
 
 INSTALL(TARGETS _cosmotool
-  LIBRARY DESTINATION ${PYTHON_SITE_PACKAGES}/flints
+  LIBRARY DESTINATION ${PYTHON_SITE_PACKAGES}/cosmotool
 )
 
 INSTALL(DIRECTORY cosmotool DESTINATION ${PYTHON_SITE_PACKAGES} 

python/_cosmotool.pyx

@@ -1,6 +1,9 @@
 from libcpp cimport bool
 import numpy as np
 cimport numpy as np
+from cpython cimport PyObject, Py_INCREF
+
+np.import_array()
 
 
 cdef extern from "loadSimu.hpp" namespace "CosmoTool":
@@ -12,11 +15,11 @@ cdef extern from "loadSimu.hpp" namespace "CosmoTool":
 
     np.float_t Omega_M
     np.float_t Omega_Lambda
-    np.int64_t TotalNumParticles
+    np.int64_t TotalNumPart
-    np.int64_t NumParticles
+    np.int64_t NumPart
     np.int64_t *Id
-    np.float_t *Pos[3]
+    float *Pos[3]
-    np.float_t *Vel[3]
+    float *Vel[3]
     int *type
 
   cdef const int NEED_GADGET_ID 
@@ -29,23 +32,94 @@ cdef extern from "loadGadget.hpp" namespace "CosmoTool":
   SimuData *loadGadgetMulti(const char *fname, int id, int flags) except +
 
 
-
 cdef class Simulation:
 
-  cdef float BoxSize
+  cdef list positions
-  cdef float Hubble
+  cdef list velocities
-  cdef list Position
-  cdef list Velocities
 
   cdef SimuData *data
 
+  property BoxSize:
+    def __get__(Simulation self):
+        return self.data.BoxSize
+        
+  property Hubble:
+    def __get__(Simulation self):
+        return self.data.Hubble
+
+  property Omega_M:
+    def __get__(Simulation self):
+        return self.data.Omega_M
+        
+  property positions:
+    def __get__(Simulation self):
+        return self.positions
+        
+  property velocities:
+    def __get__(Simulation self):
+        return self.velocities
+        
+  property numParticles:
+    def __get__(Simulation self):
+        return self.data.NumPart
+
   def __cinit__(Simulation self):
     self.data = <SimuData *>0
   
   def __dealloc__(Simulation self):
     if self.data != <SimuData *>0:
+      print("Clearing simulation data")
       del self.data
 
+
+cdef class ArrayWrapper:
+    cdef void* data_ptr
+    cdef int size
+    
+    cdef set_data(self, int size, 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
+     
+    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, np.NPY_FLOAT, 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_float_array(float *p, np.uint64_t s):
+    cdef np.ndarray ndarray
+    cdef ArrayWrapper wrapper
+
+    wrapper = ArrayWrapper()
+    wrapper.set_data(s, <void *>p)
+    ndarray = np.array(wrapper, copy=False)
+    ndarray.base = <PyObject*> wrapper
+    Py_INCREF(wrapper)
+    
+    return ndarray
+
 def loadGadget(str filename, int snapshot_id, bool loadPosition = True, bool loadVelocity = True):
 
   cdef int flags
@@ -62,4 +136,9 @@ def loadGadget(str filename, int snapshot_id, bool loadPosition = True, bool loa
 
   simu = Simulation()
   simu.data = data
+  if loadPosition:
+     simu.positions = [wrap_float_array(data.Pos[i], data.NumPart) for i in xrange(3)]
+  if loadVelocity:
+     simu.velocities = [wrap_float_array(data.Vel[i], data.NumPart) for i in xrange(3)]
+     
   return simu

python/cosmotool/__init__.py

@@ -0,0 +1 @@
+from _cosmotool import *