Copying content of C buffer to numpy array
I have a function in C like this:
source file
// foo.cpp
int foo(int input1, double *output1, int size1, int* output2, int size2)
{
// does stuff and allocate space for output1 and output2
return 0;
}
header file
// foo.h
int foo(int input1, double *output1, int size1, int* output2, int size2);
In Cython I need to convert output1 and output2 to a numpy array, so in my foo.pyx I do the following steps:
cdef extern from "foo.h":
cdef int foo(int input1, double* output1, int size1, double* output2, int size2)
cdef double* ptnOutput1
cdef int* ptnOutput2
foo(1, ptnOutput1, 10, ptnOutput2, 10)
but now I'm not able to get the output in form of two np.array. How should I align the pointers ptnOutput1 and ptnOutput2 to two numpy arrays?
I've tried np.frombuffer as well as np.PyArray_SimpleNewFromData but with no luck. I always get segmentation fault.
Any idea how to do it correctly?
python c++ c data-binding cython
asked Nov 4 '16 at 16:08
linello
3,47774982
add a comment |
I have a function in C like this:
source file
// foo.cpp
int foo(int input1, double *output1, int size1, int* output2, int size2)
{
// does stuff and allocate space for output1 and output2
return 0;
}
header file
// foo.h
int foo(int input1, double *output1, int size1, int* output2, int size2);
In Cython I need to convert output1 and output2 to a numpy array, so in my foo.pyx I do the following steps:
cdef extern from "foo.h":
cdef int foo(int input1, double* output1, int size1, double* output2, int size2)
cdef double* ptnOutput1
cdef int* ptnOutput2
foo(1, ptnOutput1, 10, ptnOutput2, 10)
but now I'm not able to get the output in form of two np.array. How should I align the pointers ptnOutput1 and ptnOutput2 to two numpy arrays?
I've tried np.frombuffer as well as np.PyArray_SimpleNewFromData but with no luck. I always get segmentation fault.
Any idea how to do it correctly?
python c++ c data-binding cython
asked Nov 4 '16 at 16:08
linello
3,47774982
2
Ignoring the Cython aspect of it for the moment, how would you call this in C? I'd have thoughtptnOutput1andptnOutput2need to already be allocated when you callfoo(which then fills in their contents)?
– DavidW
Nov 4 '16 at 16:32
cython.readthedocs.io/en/latest/src/userguide/memoryviews.html is a good description of how to work with arrays, cython native memoryviews and C arrays.
– hpaulj
Nov 4 '16 at 17:06
add a comment |
I have a function in C like this:
source file
// foo.cpp
int foo(int input1, double *output1, int size1, int* output2, int size2)
{
// does stuff and allocate space for output1 and output2
return 0;
}
header file
// foo.h
int foo(int input1, double *output1, int size1, int* output2, int size2);
In Cython I need to convert output1 and output2 to a numpy array, so in my foo.pyx I do the following steps:
cdef extern from "foo.h":
cdef int foo(int input1, double* output1, int size1, double* output2, int size2)
cdef double* ptnOutput1
cdef int* ptnOutput2
foo(1, ptnOutput1, 10, ptnOutput2, 10)
but now I'm not able to get the output in form of two np.array. How should I align the pointers ptnOutput1 and ptnOutput2 to two numpy arrays?
I've tried np.frombuffer as well as np.PyArray_SimpleNewFromData but with no luck. I always get segmentation fault.
Any idea how to do it correctly?
python c++ c data-binding cython
asked Nov 4 '16 at 16:08
linello
3,47774982
I have a function in C like this:
source file
// foo.cpp
int foo(int input1, double *output1, int size1, int* output2, int size2)
{
// does stuff and allocate space for output1 and output2
return 0;
}
header file
// foo.h
int foo(int input1, double *output1, int size1, int* output2, int size2);
In Cython I need to convert output1 and output2 to a numpy array, so in my foo.pyx I do the following steps:
cdef extern from "foo.h":
cdef int foo(int input1, double* output1, int size1, double* output2, int size2)
cdef double* ptnOutput1
cdef int* ptnOutput2
foo(1, ptnOutput1, 10, ptnOutput2, 10)
but now I'm not able to get the output in form of two np.array. How should I align the pointers ptnOutput1 and ptnOutput2 to two numpy arrays?
I've tried np.frombuffer as well as np.PyArray_SimpleNewFromData but with no luck. I always get segmentation fault.
Any idea how to do it correctly?
python c++ c data-binding cython
python c++ c data-binding cython
asked Nov 4 '16 at 16:08
linello
3,47774982
asked Nov 4 '16 at 16:08
linello
3,47774982
asked Nov 4 '16 at 16:08
linello
3,47774982
asked Nov 4 '16 at 16:08
linello
3,47774982
asked Nov 4 '16 at 16:08
linello
3,47774982
3,47774982
2
Ignoring the Cython aspect of it for the moment, how would you call this in C? I'd have thoughtptnOutput1andptnOutput2need to already be allocated when you callfoo(which then fills in their contents)?
– DavidW
Nov 4 '16 at 16:32
cython.readthedocs.io/en/latest/src/userguide/memoryviews.html is a good description of how to work with arrays, cython native memoryviews and C arrays.
– hpaulj
Nov 4 '16 at 17:06
add a comment |
2
Ignoring the Cython aspect of it for the moment, how would you call this in C? I'd have thoughtptnOutput1andptnOutput2need to already be allocated when you callfoo(which then fills in their contents)?
– DavidW
Nov 4 '16 at 16:32
cython.readthedocs.io/en/latest/src/userguide/memoryviews.html is a good description of how to work with arrays, cython native memoryviews and C arrays.
– hpaulj
Nov 4 '16 at 17:06
2
2
Ignoring the Cython aspect of it for the moment, how would you call this in C? I'd have thought
ptnOutput1 and ptnOutput2 need to already be allocated when you call foo (which then fills in their contents)?– DavidW
Nov 4 '16 at 16:32
Ignoring the Cython aspect of it for the moment, how would you call this in C? I'd have thought
ptnOutput1 and ptnOutput2 need to already be allocated when you call foo (which then fills in their contents)?– DavidW
Nov 4 '16 at 16:32
cython.readthedocs.io/en/latest/src/userguide/memoryviews.html is a good description of how to work with arrays, cython native memoryviews and C arrays.
– hpaulj
Nov 4 '16 at 17:06
cython.readthedocs.io/en/latest/src/userguide/memoryviews.html is a good description of how to work with arrays, cython native memoryviews and C arrays.
– hpaulj
Nov 4 '16 at 17:06
add a comment |
1 Answer
1
active
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votes
The numpy documentation mentions that
In order to make use of the C-API from another extension module, the
import_arrayfunction must be called
It seems you got the segmentation fault error because you didn't include import_array in your code.
The internal machinery of import_array is more complex than what you may expect because it's actually a very lengthy macro, not a plain function. Refer to this for more information
answered Sep 4 at 5:17
bombs
90110
add a comment |
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1 Answer
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1 Answer
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active
oldest
votes
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oldest
votes
active
oldest
votes
The numpy documentation mentions that
In order to make use of the C-API from another extension module, the
import_arrayfunction must be called
It seems you got the segmentation fault error because you didn't include import_array in your code.
The internal machinery of import_array is more complex than what you may expect because it's actually a very lengthy macro, not a plain function. Refer to this for more information
answered Sep 4 at 5:17
bombs
90110
add a comment |
The numpy documentation mentions that
In order to make use of the C-API from another extension module, the
import_arrayfunction must be called
It seems you got the segmentation fault error because you didn't include import_array in your code.
The internal machinery of import_array is more complex than what you may expect because it's actually a very lengthy macro, not a plain function. Refer to this for more information
answered Sep 4 at 5:17
bombs
90110
add a comment |
The numpy documentation mentions that
In order to make use of the C-API from another extension module, the
import_arrayfunction must be called
It seems you got the segmentation fault error because you didn't include import_array in your code.
The internal machinery of import_array is more complex than what you may expect because it's actually a very lengthy macro, not a plain function. Refer to this for more information
answered Sep 4 at 5:17
bombs
90110
The numpy documentation mentions that
In order to make use of the C-API from another extension module, the
import_arrayfunction must be called
It seems you got the segmentation fault error because you didn't include import_array in your code.
The internal machinery of import_array is more complex than what you may expect because it's actually a very lengthy macro, not a plain function. Refer to this for more information
answered Sep 4 at 5:17
bombs
90110
edited Nov 21 at 2:03
answered Sep 4 at 5:17
bombs
90110
answered Sep 4 at 5:17
bombs
90110
answered Sep 4 at 5:17
bombs
90110
90110
add a comment |
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2
Ignoring the Cython aspect of it for the moment, how would you call this in C? I'd have thought
ptnOutput1andptnOutput2need to already be allocated when you callfoo(which then fills in their contents)?– DavidW
Nov 4 '16 at 16:32
cython.readthedocs.io/en/latest/src/userguide/memoryviews.html is a good description of how to work with arrays, cython native memoryviews and C arrays.
– hpaulj
Nov 4 '16 at 17:06