[Pyrex] Numarray demo

[Michael Hoffman]

I wanted to use Pyrex with Numarray, which is the supported
implementation of Numeric, which is no longer supported. Changing the
demo that comes with Pyrex to use Numarray instead of Numeric was
instructive. I thought the results of this might be useful to anyone
else trying to do the same thing. Here are diffs:

--- numeric_demo.pyx	2003-07-09 11:37:15.000000000 +0100
+++ numarray_demo.pyx	2004-08-25 15:30:12.000000000 +0100
@@ -1,33 +1,92 @@
 #
 #  This example demonstrates how to access the internals
-#  of a Numeric array object.
+#  of a Numarray object.
 #

-cdef extern from "Numeric/arrayobject.h":
+cdef extern from "numarray/libnumarray.h":
+  ctypedef int maybelong

-  struct PyArray_Descr:
-    int type_num, elsize
-    char type
+  cdef struct PyArray_Descr:
+    int type_num # PyArray_TYPES
+    int elsize   # bytes for 1 element
+    char type    # One of "cb1silfdFD "  Object array not supported
+    # function pointers omitted

-  ctypedef class Numeric.ArrayType [object PyArrayObject]:
+  ctypedef class numarray._numarray._numarray [object PyArrayObject]:
     cdef char *data
     cdef int nd
-    cdef int *dimensions, *strides
+    cdef maybelong *dimensions
+    cdef maybelong *strides
     cdef object base
     cdef PyArray_Descr *descr
     cdef int flags
+
+    # numarray extras
+    cdef maybelong *_dimensions
+    cdef maybelong *_strides

-def print_2d_array(ArrayType a):
-  print "Type:", chr(a.descr.type)
-  if chr(a.descr.type) <> "f":
+    cdef object _data         # object must meet buffer API
+    cdef object _shadows      # ill-behaved original array.
+    cdef int    nstrides      # elements in strides array
+    cdef long   byteoffset    # offset into buffer where array data begins
+    cdef long   bytestride    # basic seperation of elements in bytes
+    cdef long   itemsize      # length of 1 element in bytes
+
+    cdef char   byteorder     # NUM_BIG_ENDIAN, NUM_LITTLE_ENDIAN
+
+    cdef char   _aligned      # test override flag
+    cdef char   _contiguous   # test override flag
+
+  ctypedef enum:
+    NUM_UNCONVERTED # 0
+    NUM_CONTIGUOUS  # 1
+    NUM_NOTSWAPPED  # 2
+    NUM_ALIGNED     # 4
+    NUM_WRITABLE    # 8
+    NUM_COPY        # 16
+    NUM_C_ARRAY     #  = (NUM_CONTIGUOUS | NUM_ALIGNED | NUM_NOTSWAPPED)
+
+  ctypedef enum NumarrayType:
+    tAny
+    tBool
+    tInt8
+    tUInt8
+    tInt16
+    tUInt16
+    tInt32
+    tUInt32
+    tInt64
+    tUInt64
+    tFloat32
+    tFloat64
+    tComplex32
+    tComplex64
+    tObject                   # placeholder... does nothing
+    tDefault = tFloat64
+    tLong = tInt32,
+    tMaxType
+
+  void import_libnumarray()
+  _numarray NA_InputArray (object, NumarrayType, int)
+  void *NA_OFFSETDATA(_numarray)
+
+import_libnumarray()
+
+def print_2d_array(_numarray _a):
+  print "Type:", chr(_a.descr.type)
+  if chr(_a.descr.type) <> "f":
     raise TypeError("Float array required")
-  if a.nd <> 2:
+  if _a.nd <> 2:
     raise ValueError("2 dimensional array required")
+
+  cdef _numarray a
+  a = NA_InputArray(_a, tFloat32, NUM_C_ARRAY)
+
   cdef int nrows, ncols
   cdef float *elems, x
   nrows = a.dimensions[0]
   ncols = a.dimensions[1]
-  elems = <float *>a.data
+  elems = <float *>NA_OFFSETDATA(a)
   hyphen = "-"
   divider = ("+" + 10 * hyphen) * ncols + "+"
   print divider

--- run_numeric_demo.py	2003-07-09 11:37:15.000000000 +0100
+++ run_numarray_demo.py	2004-08-25 12:06:47.000000000 +0100
@@ -1,5 +1,5 @@
-import Numeric
-import numeric_demo
+import numarray
+import numarray_demo

-a = Numeric.array([[1.0, 3.5, 8.4], [2.3, 6.6, 4.1]], "f")
-numeric_demo.print_2d_array(a)
+a = numarray.array([[1.0, 3.5, 8.4], [2.3, 6.6, 4.1]], "f")
+numarray_demo.print_2d_array(a)
-- 
Michael Hoffman <hoffman at ebi.ac.uk>
European Bioinformatics Institute

P.S. Thanks for Pyrex! I just coded a Python implementation of a
bioinformatics algorithm with the inner loop in Pyrex and it runs as
fast as the pure C implementation we use in my group.