Cython structure, line from python to cython
I would like to convert a python object to a cython structure by doing as I did but does not assign simres [1] values to resulta [x] .cpt1
cdef struct resultaStructure:
double score
char **cpt1
simRes = [1.0,
['http://bioontology.org/projects/ontologies/fma/fmaOwlDlComponent_2_0#Abdomen',
'Abdomen']]
cdef x = 0
cdef resultaStructure *resulta = <resultaStructure *> malloc(sizeof(resultaStructure)*labelsSourceTaille)
resulta[x].score = simRes[0]
print("score : ",resulta[0].score)
resulta[x].cpt1 = <char**> malloc (sizeof (char**)*2)
print('2')
resulta[x].cpt1[0] = <char*> malloc (sizeof (char)*simRes[1][0].__len__()+1)
print('3')
resulta[x].cpt1[1] = <char*> malloc (sizeof (char)*simRes[1][1].__len__()+1)
print('4')
resulta[x].cpt1[0] = <char*> simRes[1][0]
print('5')
resulta[x].cpt1[1] = <char*> simRes[1][1]
print('6')
print("cpt1 0 : ",resulta[0].cpt1[0])
print("cpt1 1 : ",resulta[0].cpt1[1])
here is the result
('score:', 1.0)
2
3
4
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The code in the question and in the OP's answer has serious issues that are likely to cause the program to crash in the long run.
1)
resulta[x].cpt1 = <char**> malloc (sizeof (char**)*2)
cpt1
is a pointer to (array of) char pointers. So it should be assigned as
resulta[x].cpt1 = <char*> malloc (sizeof (char*)*2)
(Better yet, if the length is always 2
, then assign char *cpt1[2]
in the struct definition and you don't need malloc
it.)
This is unlikely to cause a real problem as all pointers are the same size but still not the same.
2) (Real part of problem a)
resulta[x].cpt1[0] = <char*> malloc (sizeof (char)*simRes[1][0].__len__()+1)
# ...
resulta[x].cpt1[0] = <char*>some_python_string
This is where you allocate some memory, promptly forget about the allocated memory if you want to make a pointer in another memory area belonging to a Python string. What you are not doing is copying the data from the Python string to the allocated memory.
3) (Real part of problem b)
str1 = simRes[1][0].encode('UTF-8')
resulta[x].cpt1[0] = <char*> str1
The memory it points cpt1[0]
to belongs to str1
. If str1
freed before you finish using your structure, then the structure is pointing to invalid memory and your program will crash or read some random data that was allocated later, or some other bad thing.
If you can guarantee that it str1
will outlive your structure (for example, your structure is being used as an argument to a single C function call), then that's ok, but in general it probably isn't.
The solution is to copy the content or str1
to a new allocated memory:
resulta[x].cpt1[0] = <char*> malloc (sizeof (char)*len(simRes[1][0])+1)
strcpy(resulta[x].cpt1[0],str1)
(Also, you remember free
all the malloc
ed memory you have , right?)
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