[Numpy-discussion] C-API for non-contiguous arrays

Oliver Kranz o.kranz@gmx...
Thu Oct 25 05:35:33 CDT 2007


Hi,

I am working on a Python extension module using of the NumPy C-API. The 
extension module is an interface to an image processing and analysis 
library written in C++. The C++ functions are exported with 
boos::python. Currently I am implementing the support of 
three-dimensional data sets which can consume a huge amount of memory. 
The 3D data is stored in a numpy.ndarray. This array is passed to C++ 
functions which do the calculations.

In general, multi-dimensional arrays can be organized in memory in four 
different ways:
1. C order contiguous
2. Fortran order contiguous
3. C order non-contiguous
4. Fortran order non-contiguous

Am I right that the NumPy C-API can only distinguish between three ways 
the array is organized in memory? These are:
1. C order contiguous e.g. with PyArray_ISCONTIGUOUS(arr)
2. Fortran order contiguous e.g. with PyArray_ISFORTRAN(arr)
3. non-contiguous e.g. with !PyArray_ISCONTIGUOUS(arr) &&
!PyArray_ISFORTRAN(arr)

So there is no way to find out if a non-contiguous array has C order or 
Fortran order. The same holds for Python code e.g. by use of the flags.

a.flags.contiguous
a.flags.fortran

This is very important for me because I just want to avoid to copy every 
non-contiguous array into a contiguous array. This would be very 
inefficient. But I can't find an other solution than copying the array.

Also the iterator provided by the C-API only loops over the array in C 
order. Even if the array is in Fortran non-contiguous order.

Or are there just no Fortran order non-contiguous arrays? I think I can 
construct one.

a = numpy.ndarray((3,4,5), order="F")
b = a[:,1:2,:]

Now, I think b's elements are organized in memory in Fortran 
non-contiguous order. But the flags only tell me that it is 
non-contiguous and not if it is in Fortran order or in C order. And if b 
would be passed to a C++ function it would not be possible to find out 
with the C-API if it is in Fortran order or in C order, too.

Any ideas? Or do I always have to create contiguous arrays?

Cheers,
Oliver



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