[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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