Sorry if this has been asked before. It does seem very simple. I am wondering if there is a way to iterate over struct attributes.
E.g.
ctypedef struct Foo:
int a, b
cdef Foo foo = [1, 2]
#want something like this
for i in range(2):
print(foo[i])
As per #ShadowRanger's comment, the closest I can come up with how to do this is like so:
ctypedef struct Foo:
int a, b
cdef union Bar:
Foo *f
int *g
cdef Foo foo = [1, 2]
cdef Bar bar
bar.f = &foo
for i in range(2):
print(bar.g[i])
Wrapping the struct with a corresponding array. This would only work if the struct was a collection of all the same type, however.
Related
I have a some Cython code where if a variable equals a value from a list then values from another list are copied into a testing array.
double [:] signals
cdef int total_days=signals.shape[0]
cdef size_t epoch=0
cdef int total_animals
cdef int n
cdef double[:] animal_signals
for animal in range(total_animals):
individual_animal = uniq_instr[animal]
for element in range(total_days):
if list(animal_ids[n]) == individual_animal:
animal_signals.append(signals[n])
I am getting an error:
UnboundLocalError: local variable 'animal_signals' referenced before assignment
I have thought having the line
cdef double[:] animal_signals
would have meant the array was assigned.
Update
As suggested I have also tried declaring the array animal_signals (and removing the append):
cdef int total_days=signals.shape[0]
cdef size_t epoch=0
cdef int total_animals
cdef int n
cdef int count=0
for animal in range(total_animals):
count=0
individual_animal = uniq_instr[animal]
for element in range(total_days):
if list(animal_ids[element]) == individual_animal:
cdef double[:] animal_signals[count] = signals[n]
count=count+1
however when I compile the code I get the error:
Error compiling Cython file:
------------------------------------------------------------
...
for element in range(total_days):
if list(animal_ids[element]) == individual_animal:
cdef double[:] animal_signals[count] = signals[n]
^
------------------------------------------------------------
project/temps.pyx:288:21: cdef statement not allowed here
Where am I going wrong?
Indeed, your line cdef double[:] animal_signals
declares animal_signals as a variable, but you never assign anything to it before using it (in Python assignement is done with the = operator).
In Cython, using the slice ([:]) notation when defining a variable is usually done to get the memory view of an other object (see the reference documentation).
For example :
some_1d_numpy_array = np.zeros((10,10)).reshape(-1)
cdef double[:] animal_signals = some_1d_numpy_array
If you want to create a C array, you have to allocate the memory for it (here for a size of number entries containing double) :
cdef double *my_array = <double *> malloc(number * sizeof(double))
Also, regarding to your original code, note that in both case you won't be able to use the append method on this object because it will not be a Python list, you will have to access its member by their indexes.
I would like to know how can I create an array of structs in Cython that I can populate and make computations afterwards.
Example
Here I have the Cython code
%%cython
cimport numpy as cnp
cimport cython
from collections import namedtuple
Couple = namedtuple('Couple', ['female', 'male'], verbose=False)
cdef struct CyCouple:
int female
int male
cpdef int np_cy_count_women_earning_more2(list py_couples):
cdef:
int count = 0, r, N
CyCouple cy_couples[100_0000] # THIS IS HARDCODED
N = len(py_couples)
make_CyCouple_array(py_couples, cy_couples, N)
for n in range(N):
r = cy_couples[n].female > cy_couples[n].male
count += r
return count
I would like to have a general versions instead of the definition in # THIS IS HARDCODED.
What could I do?
I want to use a library that gives me a dynamic array. The dynamic array struct has a property void* _heap_ptr which gives the start of the array.
After having built the list, I want to access this pointer in cython (to make a copy of the array). But I cannot seem to get the pointer element from the struct.
Here is my pyx:
cimport src.clist as l
def main():
cdef l.ptr_list basic_list
cdef int i = 42
basic_list = l.create_list_size(sizeof(i), 100)
l.list_add_ptr(basic_list, &i)
cdef int* arr;
arr = basic_list._heap_ptr
for i in range(1):
print(arr[i])
This is the error message:
Error compiling Cython file:
------------------------------------------------------------
...
l.list_add_ptr(basic_list, &i)
cdef int* arr;
arr = basic_list._heap_ptr
^
------------------------------------------------------------
src/test.pyx:14:20: Cannot convert Python object to 'int *'
Error compiling Cython file:
------------------------------------------------------------
...
l.list_add_ptr(basic_list, &i)
cdef int* arr;
arr = basic_list._heap_ptr
^
------------------------------------------------------------
src/test.pyx:14:20: Storing unsafe C derivative of temporary Python reference
And my pxd:
cdef extern from "src/list.h":
ctypedef struct _list:
void* _heap_ptr
ctypedef struct ptr_list:
pass
ptr_list create_list_size(size_t size, int length)
list_destroy(ptr_list this_list)
void* list_at_ptr(ptr_list this_list, int index)
list_add_ptr(ptr_list this_list, void* value)
How can I fix my code? Why is this happening? From my investigations that error message pops up if you have forgotten to declare something as C (ie. use malloc not libc.stdlib.malloc, but I cannot see that anything similar is happening here.)
There are two issues in your code.
First: struct ptr_list has no members and thus no member _heap_ptr. It probably should have been
ctypedef struct ptr_list:
void* _heap_ptr
Cython's error message is not really helpful here, but as you said it pops up usually when a C-declaration is forgotten.
Second: you need to cast from void * to int * explicitly:
arr = <int*>basic_list._heap_ptr
I have a C function which take pointer to struct and i want to use it in python by C-Extensions by Cython way but when i want to pass pointer to struct from python give me an error: "Cannot convert Python object to 'Foo *'"
In the below example i make object to call the C function but what passed to C function is NULL pointer.
My Trial:
hello.h
#include <stdio.h>
typedef struct
{
int x;
} Foo;
int hello(Foo* what);
hello.c
#include "hello.h"
int hello(Foo* what)
{
printf("Hello Wrapper\n");
printf("what: %p\n", what);
what->x = 5;
return what->x;
}
phello.pxd
cdef extern from "hello.h":
ctypedef struct Foo:
int x
cdef int hello(Foo* what)
phello.pyx
cimport phello
cdef class Foo_c:
cdef phello.Foo* s
def hello_fn(self):
return phello.hello(self.s)
setup.py
from distutils.core import setup, Extension
from Cython.Distutils import build_ext
setup(
cmdclass = {'build_ext': build_ext},
ext_modules=[ Extension("hellomodule",
sources=["phello.pyx", "hello.c"],
) ]
test.py
import hellomodule
print "Hello test.py"
tobject = hellomodule.Foo_c()
print "Object:", tobject
tobject.hello_fn()
So i want create "Foo" struct in "test.py" and pass it to "hello_fn()" function to call the C function "hello()" after passing this struct, so i can read or write on this structure from both sides python & C.
Can Anyone help me in this, please?
Your code does not allocate memory for phello.Foo. Allocation can be done in __cinit__ with calloc (or malloc) and deallocation in __dealloc__ with free.
cimport phello
from libc.stdlib cimport calloc, free
cdef class Foo_c:
cdef phello.Foo* s
def __cinit__(self, int n):
self.s = <phello.Foo *>calloc(1, sizeof(phello.Foo))
def __dealloc__(self):
free(<void *>self.s)
def __init__(self, int n):
self.s.x = n
How to access a struct in Cython that has been in a list as a C struct, not as a dictionary. It appears that whenever I pass a C struct in a python list and retrieve it from the list it is wrapped as a dict. Even in my cython code. How can I directly access the c struct.
The example below creates an error. If it wouldn't my problem was solved.
optimization_functions.pyx
ctypedef struct sGrail:
int age
char* text
ctypedef sGrail Grail
def cythontest(char* a):
cdef sGrail grail
grail.age = 5
grail.text = a
return [grail]
def print_grail(grailarray):
print type(grailarray[0])
grail = grailarray[0]
print grail.age
grail.age = 99
print grailarray[0]
print "age here should be 99 not 5"
start.py
import optimization_functions
grailarray = optimization_functions.cythontest('test')
print grailarray
optimization_functions.print_grail(grailarray)