3

Suppose I have

a = np.zeros(2, dtype=[('a', np.int),  ('b', np.float, 2)])
a[0] = (2,[3,4])
a[1] = (6,[7,8])

then I define the same Cython structure

import numpy as np
cimport numpy as np

cdef packed struct mystruct:
  np.int_t a
  np.float_t b[2]

def test_mystruct(mystruct[:] x):
  cdef:
    int k
    mystruct y

  for k in range(2):
    y = x[k]
    print y.a
    print y.b[0]
    print y.b[1]

after this, I run

test_mystruct(a)

and I got error:

ValueError                                Traceback (most recent call last)
<ipython-input-231-df126299aef1> in <module>()
----> 1 test_mystruct(a)
_cython_magic_5119cecbaf7ff37e311b745d2b39dc32.pyx in _cython_magic_5119cecbaf7ff37e311b745d2b39dc32.test_mystruct (/auto/users/pwang/.cache/ipython/cython/_cython_magic_5119cecbaf7ff37e311b745d2b39dc32.c:1364)()
ValueError: Expected 1 dimension(s), got 1

My question is how to fix it? Thank you.

Improve this question
6
  • How is that a duplicate? Commented May 4, 2015 at 18:40
  • Sorry, I edited the question, could you please remove duplicate flag @CristiánAntuña . Thank you. Commented May 4, 2015 at 18:42
  • @hpaulj: it was a different question at first. Pengyu: comment removed. Commented May 4, 2015 at 18:46
  • stackoverflow.com/questions/9423207/… successfully passes a structured array to C packed structure. And this finds a way around the same error: stackoverflow.com/questions/17239091/… Commented May 4, 2015 at 20:26
  • @hpaulj, the problem is that if there is an array definition inside C structure, it will cause an error. I don't see how to get around this error in two posts. Commented May 4, 2015 at 21:24

2 Answers 2

Reset to default
4

This pyx compiles and imports ok:

import numpy as np
cimport numpy as np

cdef packed struct mystruct:
  int a[2]    # change from plain int
  float b[2]
  int c

def test_mystruct(mystruct[:] x):
  cdef:
    int k
    mystruct y

  for k in range(2):
    y = x[k]
    print y.a
    print y.b[0]
    print y.b[1]

dt='2i,2f,i'
b=np.zeros((3,),dtype=dt)
test_mystruct(b)

I started with the test example mentioned in my comment, and played with your case. I think the key change was to define the first element of the packed structure to be int a[2]. So if any element is an array, the first must an array to properly set up the structure.

Clearly an error that the test file isn't catching.

Defining the element as int a[1] doesn't work, possibly because the dtype removes such a dimension:

In [47]: np.dtype([('a', np.int, 1),  ('b', np.float, 2)])
Out[47]: dtype([('a', '<i4'), ('b', '<f8', (2,))])

Defining the dtype to get around this shouldn't be hard until the issue is raised and patched.

The struct could have a[1], but the array dtype would have to specify the size with a tuple: ('a','i',(1,)). ('a','i',1) would make the size ().

If one of the struct arrays is 2d, it looks like all of them have to be:

cdef packed struct mystruct:
  int a[1][1]
  float b[2][1]
  int c[2][2]

https://github.com/cython/cython/blob/c4c2e3d8bd760386b26dbd6cffbd4e30ba0a7d13/tests/memoryview/numpy_memoryview.pyx

Stepping back a bit, I wonder what's the point to processing a complex structured array in cython. For some operations wouldn't it work just as well to pass the fields as separate variables. For example myfunc(a['a'],a['b']) instead of myfunc(a).

Improve this answer
Sign up to request clarification or add additional context in comments.

Comments

1

There is a general method to get the dtype for a c struct, but it involves a temporary variable:

cdef mystruct _tmp
dt = np.asarray(<mystruct[:1]>(&_tmp)).dtype

This requires at least numpy 1.5. See discussion here: https://github.com/scikit-learn/scikit-learn/pull/2298

Improve this answer

Comments

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Start asking to get answers

Find the answer to your question by asking.

Ask question

Explore related questions

See similar questions with these tags.