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

Oliver Kranz o.kranz@gmx...
Thu Oct 25 09:23:34 CDT 2007


Timothy Hochberg wrote:
> 
> 
> On 10/25/07, *Oliver Kranz* <o.kranz@gmx.de <mailto:o.kranz@gmx.de>> wrote:
> 
>     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
> 
> 
> I believe that this is incorrect. Consider the following:
> 
>  >>> import numpy as np
>  >>> a  = np.arange(27).reshape(3,3,3)
>  >>> a.strides
> (36, 12, 4)
>  >>> a.transpose(2,1,0).strides
> (4, 12, 36)
>  >>> a.transpose(0,2,1).strides
> (36, 4, 12)
> 
>  I believe that the last transpose doesn't fit any of these four 
> categories and is simply discontiguous.

Yes, you are right. I did not consider this case.

>     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?
> 
> 
> 
> By Fortran and C-Order discontiguous, do you simply mean that the 
> strides are in increasing and decreasing order respectively? If so, you 
> could check for that without too much trouble.

Since I want to support all the different contiguous and non-contiguous 
arrays the best solution for me is always checking the strides if the 
array is not in C order contiguous.

Thanks,
Oliver


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