Mixing
Serialize array data from C code, deserialize in Python
I need to store dense array data (3D arrays) from C code and then to read them into NumPy arrays (in another application). The data is around 100 kbytes of float values, C array as a pointer to the data. I am looking for a solution that does not require any external dependencies and can be implemented with the least effort.
What would be a good solution for that?
Thanks.
python c numpy serialization
edited Nov 19 '18 at 14:12
user694733
10.8k12750
asked Nov 19 '18 at 12:54
Dmytro Prylipko
741516
|
show 2 more comments
I need to store dense array data (3D arrays) from C code and then to read them into NumPy arrays (in another application). The data is around 100 kbytes of float values, C array as a pointer to the data. I am looking for a solution that does not require any external dependencies and can be implemented with the least effort.
What would be a good solution for that?
Thanks.
python c numpy serialization
edited Nov 19 '18 at 14:12
user694733
10.8k12750
asked Nov 19 '18 at 12:54
Dmytro Prylipko
741516
What you want in result? May be JSON would be best solution for you.
– Alexander Tolkachev
Nov 19 '18 at 12:57
I would prefer binary format, since data amounts are very large. Also, no external dependencies in C.
– Dmytro Prylipko
Nov 19 '18 at 12:59
2
The question is too broad because the properties of the input data (type of data, amount of data and is it constant/dynamic, etc.) are not specified. Question is also missing a metric by which solution can be considered "good solution".
– user694733
Nov 19 '18 at 13:10
The data is around 100 kbytes of float values, C array as a pointer to the data. I am looking for a solution that does not require any external dependencies and can be implemented with the least effort. So, simple and elegant.
– Dmytro Prylipko
Nov 19 '18 at 13:52
1
If by 3D array you mean[someNumber][someNumber](i.e. a continuous block of data) instead of**(i.e. pointer to pointer to array), you can simplyfwriteto a file thennp.fromfile(with the correct dtype) +np.reshape
– ZisIsNotZis
Nov 21 '18 at 4:53
|
show 2 more comments
I need to store dense array data (3D arrays) from C code and then to read them into NumPy arrays (in another application). The data is around 100 kbytes of float values, C array as a pointer to the data. I am looking for a solution that does not require any external dependencies and can be implemented with the least effort.
What would be a good solution for that?
Thanks.
python c numpy serialization
edited Nov 19 '18 at 14:12
user694733
10.8k12750
asked Nov 19 '18 at 12:54
Dmytro Prylipko
741516
I need to store dense array data (3D arrays) from C code and then to read them into NumPy arrays (in another application). The data is around 100 kbytes of float values, C array as a pointer to the data. I am looking for a solution that does not require any external dependencies and can be implemented with the least effort.
What would be a good solution for that?
Thanks.
python c numpy serialization
python c numpy serialization
edited Nov 19 '18 at 14:12
user694733
10.8k12750
asked Nov 19 '18 at 12:54
Dmytro Prylipko
741516
edited Nov 19 '18 at 14:12
user694733
10.8k12750
asked Nov 19 '18 at 12:54
Dmytro Prylipko
741516
edited Nov 19 '18 at 14:12
user694733
10.8k12750
edited Nov 19 '18 at 14:12
user694733
10.8k12750
edited Nov 19 '18 at 14:12
user694733
10.8k12750
10.8k12750
asked Nov 19 '18 at 12:54
Dmytro Prylipko
741516
asked Nov 19 '18 at 12:54
Dmytro Prylipko
741516
asked Nov 19 '18 at 12:54
Dmytro Prylipko
741516
741516
What you want in result? May be JSON would be best solution for you.
– Alexander Tolkachev
Nov 19 '18 at 12:57
I would prefer binary format, since data amounts are very large. Also, no external dependencies in C.
– Dmytro Prylipko
Nov 19 '18 at 12:59
2
The question is too broad because the properties of the input data (type of data, amount of data and is it constant/dynamic, etc.) are not specified. Question is also missing a metric by which solution can be considered "good solution".
– user694733
Nov 19 '18 at 13:10
The data is around 100 kbytes of float values, C array as a pointer to the data. I am looking for a solution that does not require any external dependencies and can be implemented with the least effort. So, simple and elegant.
– Dmytro Prylipko
Nov 19 '18 at 13:52
1
If by 3D array you mean[someNumber][someNumber](i.e. a continuous block of data) instead of**(i.e. pointer to pointer to array), you can simplyfwriteto a file thennp.fromfile(with the correct dtype) +np.reshape
– ZisIsNotZis
Nov 21 '18 at 4:53
|
show 2 more comments
What you want in result? May be JSON would be best solution for you.
– Alexander Tolkachev
Nov 19 '18 at 12:57
I would prefer binary format, since data amounts are very large. Also, no external dependencies in C.
– Dmytro Prylipko
Nov 19 '18 at 12:59
2
The question is too broad because the properties of the input data (type of data, amount of data and is it constant/dynamic, etc.) are not specified. Question is also missing a metric by which solution can be considered "good solution".
– user694733
Nov 19 '18 at 13:10
The data is around 100 kbytes of float values, C array as a pointer to the data. I am looking for a solution that does not require any external dependencies and can be implemented with the least effort. So, simple and elegant.
– Dmytro Prylipko
Nov 19 '18 at 13:52
1
If by 3D array you mean[someNumber][someNumber](i.e. a continuous block of data) instead of**(i.e. pointer to pointer to array), you can simplyfwriteto a file thennp.fromfile(with the correct dtype) +np.reshape
– ZisIsNotZis
Nov 21 '18 at 4:53
What you want in result? May be JSON would be best solution for you.
– Alexander Tolkachev
Nov 19 '18 at 12:57
What you want in result? May be JSON would be best solution for you.
– Alexander Tolkachev
Nov 19 '18 at 12:57
I would prefer binary format, since data amounts are very large. Also, no external dependencies in C.
– Dmytro Prylipko
Nov 19 '18 at 12:59
I would prefer binary format, since data amounts are very large. Also, no external dependencies in C.
– Dmytro Prylipko
Nov 19 '18 at 12:59
2
2
The question is too broad because the properties of the input data (type of data, amount of data and is it constant/dynamic, etc.) are not specified. Question is also missing a metric by which solution can be considered "good solution".
– user694733
Nov 19 '18 at 13:10
The question is too broad because the properties of the input data (type of data, amount of data and is it constant/dynamic, etc.) are not specified. Question is also missing a metric by which solution can be considered "good solution".
– user694733
Nov 19 '18 at 13:10
The data is around 100 kbytes of float values, C array as a pointer to the data. I am looking for a solution that does not require any external dependencies and can be implemented with the least effort. So, simple and elegant.
– Dmytro Prylipko
Nov 19 '18 at 13:52
The data is around 100 kbytes of float values, C array as a pointer to the data. I am looking for a solution that does not require any external dependencies and can be implemented with the least effort. So, simple and elegant.
– Dmytro Prylipko
Nov 19 '18 at 13:52
1
1
If by 3D array you mean
[someNumber][someNumber] (i.e. a continuous block of data) instead of ** (i.e. pointer to pointer to array), you can simply fwrite to a file then np.fromfile (with the correct dtype) + np.reshape– ZisIsNotZis
Nov 21 '18 at 4:53
If by 3D array you mean
[someNumber][someNumber] (i.e. a continuous block of data) instead of ** (i.e. pointer to pointer to array), you can simply fwrite to a file then np.fromfile (with the correct dtype) + np.reshape– ZisIsNotZis
Nov 21 '18 at 4:53
|
show 2 more comments
1 Answer
1
active
oldest
votes
I've done some serialization for arm devices and network and I'would be happy to share my experience since you prefer binary serialization.
I am using unions to serialize.Lets assume that you have a struct that holds some element, data and pointers and this holds data for a family member :
struct fam_member
{
char name [ MAX_NAME_LEN + 1 ];
int height;
age_bracket_t age_bracket;
fam_member_t* mother;
fam_member_t* father;
}fam_member_t;
Age bracket is an enum:
typedef enum age_bracket
{
under_18 = 0 , from_18_to_25 = 1 , from_26_to_40 = 2 , over_40 = 3
}age_bracket_t;
The main problem and the most common mistake is struct padding and not taking this to serious.Here is a good start if someone is not familiar with the issue.
My simple solution is stream data down byte to byte (or bit to bit), do what you need to do with the serialized data (i.e. send them over a socket) and deserialize in the end.
I define a Union like this:
typedef union serialized_struct
{
fam_member_t family_member;
unsigned char data[ (MAX_NAME_LEN + 1 ) + (sizeof(int)*3) ];
}serialized_struct_t;
(A few think about union here)
The purpose of union is to save memory by using the same memory region for storing different objects at different times.In this example this will help us and actually serialize the family object struct for free.
Here is a function that serializes an array of family members (if you can do an area, single will be a piece of cake.That's why I choose an array here).
int serialize_array(fam_member_t* people , char* message , int elements)
{
if((people == NULL ) || (message == NULL) || (elements < 1))
{
return -1;
}
int size = sizeof(fam_member_t);
int i;
for(i=0 ; i < elements ; i++)
{
serialized_struct_t x;
memcpy((x.family_member.name) , people[i].name , MAX_NAME_LEN);
x.family_member.age_bracket = people[i].age_bracket;
x.family_member.height = people[i].age_bracket
x.family_member.mother = people[i].mother;
x.family_member.father = people[i].father;
memcpy ( (message + (size * i)) , x.data , size );
}
return 0;
}
Here we initiate every data of every member inside the struct which lies in the union.Message holds serialized data.This is the deserialized function which will do the reverse
int desirialize_array(fam_member_t* people , char* message , int elements)
{
if((people == NULL ) || (message == NULL) || (elements < 1))
{
return -1;
}
int size = sizeof(fam_member_t);
serialized_struct_t y;
int i;
for (i =0 ; i < elements ; i ++ )
{
memcpy ( y.data , (message + (size * i)) , size );
memcpy ( people[i].name , y.family_member.name , MAX_NAME_LEN);
people[i].age_bracket = y.family_member.age_bracket;
people[i].height = y.family_member.height;
people[i].mother = y.family_member.mother;
people[i].father = y.family_member.father;
}
return 0;
}
This is serialize and deserialize in c example.For your case where you need to deserialize this in python I think it will be easy if you figured out which will be the mean of serialization.JSON that @Alexander Tolkachev said for example could be a solution.
I hope this simplified example helps you.
answered Nov 19 '18 at 16:34
Tsakiroglou Fotis
502315
add a comment |
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1 Answer
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oldest
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oldest
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I've done some serialization for arm devices and network and I'would be happy to share my experience since you prefer binary serialization.
I am using unions to serialize.Lets assume that you have a struct that holds some element, data and pointers and this holds data for a family member :
struct fam_member
{
char name [ MAX_NAME_LEN + 1 ];
int height;
age_bracket_t age_bracket;
fam_member_t* mother;
fam_member_t* father;
}fam_member_t;
Age bracket is an enum:
typedef enum age_bracket
{
under_18 = 0 , from_18_to_25 = 1 , from_26_to_40 = 2 , over_40 = 3
}age_bracket_t;
The main problem and the most common mistake is struct padding and not taking this to serious.Here is a good start if someone is not familiar with the issue.
My simple solution is stream data down byte to byte (or bit to bit), do what you need to do with the serialized data (i.e. send them over a socket) and deserialize in the end.
I define a Union like this:
typedef union serialized_struct
{
fam_member_t family_member;
unsigned char data[ (MAX_NAME_LEN + 1 ) + (sizeof(int)*3) ];
}serialized_struct_t;
(A few think about union here)
The purpose of union is to save memory by using the same memory region for storing different objects at different times.In this example this will help us and actually serialize the family object struct for free.
Here is a function that serializes an array of family members (if you can do an area, single will be a piece of cake.That's why I choose an array here).
int serialize_array(fam_member_t* people , char* message , int elements)
{
if((people == NULL ) || (message == NULL) || (elements < 1))
{
return -1;
}
int size = sizeof(fam_member_t);
int i;
for(i=0 ; i < elements ; i++)
{
serialized_struct_t x;
memcpy((x.family_member.name) , people[i].name , MAX_NAME_LEN);
x.family_member.age_bracket = people[i].age_bracket;
x.family_member.height = people[i].age_bracket
x.family_member.mother = people[i].mother;
x.family_member.father = people[i].father;
memcpy ( (message + (size * i)) , x.data , size );
}
return 0;
}
Here we initiate every data of every member inside the struct which lies in the union.Message holds serialized data.This is the deserialized function which will do the reverse
int desirialize_array(fam_member_t* people , char* message , int elements)
{
if((people == NULL ) || (message == NULL) || (elements < 1))
{
return -1;
}
int size = sizeof(fam_member_t);
serialized_struct_t y;
int i;
for (i =0 ; i < elements ; i ++ )
{
memcpy ( y.data , (message + (size * i)) , size );
memcpy ( people[i].name , y.family_member.name , MAX_NAME_LEN);
people[i].age_bracket = y.family_member.age_bracket;
people[i].height = y.family_member.height;
people[i].mother = y.family_member.mother;
people[i].father = y.family_member.father;
}
return 0;
}
This is serialize and deserialize in c example.For your case where you need to deserialize this in python I think it will be easy if you figured out which will be the mean of serialization.JSON that @Alexander Tolkachev said for example could be a solution.
I hope this simplified example helps you.
answered Nov 19 '18 at 16:34
Tsakiroglou Fotis
502315
add a comment |
I've done some serialization for arm devices and network and I'would be happy to share my experience since you prefer binary serialization.
I am using unions to serialize.Lets assume that you have a struct that holds some element, data and pointers and this holds data for a family member :
struct fam_member
{
char name [ MAX_NAME_LEN + 1 ];
int height;
age_bracket_t age_bracket;
fam_member_t* mother;
fam_member_t* father;
}fam_member_t;
Age bracket is an enum:
typedef enum age_bracket
{
under_18 = 0 , from_18_to_25 = 1 , from_26_to_40 = 2 , over_40 = 3
}age_bracket_t;
The main problem and the most common mistake is struct padding and not taking this to serious.Here is a good start if someone is not familiar with the issue.
My simple solution is stream data down byte to byte (or bit to bit), do what you need to do with the serialized data (i.e. send them over a socket) and deserialize in the end.
I define a Union like this:
typedef union serialized_struct
{
fam_member_t family_member;
unsigned char data[ (MAX_NAME_LEN + 1 ) + (sizeof(int)*3) ];
}serialized_struct_t;
(A few think about union here)
The purpose of union is to save memory by using the same memory region for storing different objects at different times.In this example this will help us and actually serialize the family object struct for free.
Here is a function that serializes an array of family members (if you can do an area, single will be a piece of cake.That's why I choose an array here).
int serialize_array(fam_member_t* people , char* message , int elements)
{
if((people == NULL ) || (message == NULL) || (elements < 1))
{
return -1;
}
int size = sizeof(fam_member_t);
int i;
for(i=0 ; i < elements ; i++)
{
serialized_struct_t x;
memcpy((x.family_member.name) , people[i].name , MAX_NAME_LEN);
x.family_member.age_bracket = people[i].age_bracket;
x.family_member.height = people[i].age_bracket
x.family_member.mother = people[i].mother;
x.family_member.father = people[i].father;
memcpy ( (message + (size * i)) , x.data , size );
}
return 0;
}
Here we initiate every data of every member inside the struct which lies in the union.Message holds serialized data.This is the deserialized function which will do the reverse
int desirialize_array(fam_member_t* people , char* message , int elements)
{
if((people == NULL ) || (message == NULL) || (elements < 1))
{
return -1;
}
int size = sizeof(fam_member_t);
serialized_struct_t y;
int i;
for (i =0 ; i < elements ; i ++ )
{
memcpy ( y.data , (message + (size * i)) , size );
memcpy ( people[i].name , y.family_member.name , MAX_NAME_LEN);
people[i].age_bracket = y.family_member.age_bracket;
people[i].height = y.family_member.height;
people[i].mother = y.family_member.mother;
people[i].father = y.family_member.father;
}
return 0;
}
This is serialize and deserialize in c example.For your case where you need to deserialize this in python I think it will be easy if you figured out which will be the mean of serialization.JSON that @Alexander Tolkachev said for example could be a solution.
I hope this simplified example helps you.
answered Nov 19 '18 at 16:34
Tsakiroglou Fotis
502315
add a comment |
I've done some serialization for arm devices and network and I'would be happy to share my experience since you prefer binary serialization.
I am using unions to serialize.Lets assume that you have a struct that holds some element, data and pointers and this holds data for a family member :
struct fam_member
{
char name [ MAX_NAME_LEN + 1 ];
int height;
age_bracket_t age_bracket;
fam_member_t* mother;
fam_member_t* father;
}fam_member_t;
Age bracket is an enum:
typedef enum age_bracket
{
under_18 = 0 , from_18_to_25 = 1 , from_26_to_40 = 2 , over_40 = 3
}age_bracket_t;
The main problem and the most common mistake is struct padding and not taking this to serious.Here is a good start if someone is not familiar with the issue.
My simple solution is stream data down byte to byte (or bit to bit), do what you need to do with the serialized data (i.e. send them over a socket) and deserialize in the end.
I define a Union like this:
typedef union serialized_struct
{
fam_member_t family_member;
unsigned char data[ (MAX_NAME_LEN + 1 ) + (sizeof(int)*3) ];
}serialized_struct_t;
(A few think about union here)
The purpose of union is to save memory by using the same memory region for storing different objects at different times.In this example this will help us and actually serialize the family object struct for free.
Here is a function that serializes an array of family members (if you can do an area, single will be a piece of cake.That's why I choose an array here).
int serialize_array(fam_member_t* people , char* message , int elements)
{
if((people == NULL ) || (message == NULL) || (elements < 1))
{
return -1;
}
int size = sizeof(fam_member_t);
int i;
for(i=0 ; i < elements ; i++)
{
serialized_struct_t x;
memcpy((x.family_member.name) , people[i].name , MAX_NAME_LEN);
x.family_member.age_bracket = people[i].age_bracket;
x.family_member.height = people[i].age_bracket
x.family_member.mother = people[i].mother;
x.family_member.father = people[i].father;
memcpy ( (message + (size * i)) , x.data , size );
}
return 0;
}
Here we initiate every data of every member inside the struct which lies in the union.Message holds serialized data.This is the deserialized function which will do the reverse
int desirialize_array(fam_member_t* people , char* message , int elements)
{
if((people == NULL ) || (message == NULL) || (elements < 1))
{
return -1;
}
int size = sizeof(fam_member_t);
serialized_struct_t y;
int i;
for (i =0 ; i < elements ; i ++ )
{
memcpy ( y.data , (message + (size * i)) , size );
memcpy ( people[i].name , y.family_member.name , MAX_NAME_LEN);
people[i].age_bracket = y.family_member.age_bracket;
people[i].height = y.family_member.height;
people[i].mother = y.family_member.mother;
people[i].father = y.family_member.father;
}
return 0;
}
This is serialize and deserialize in c example.For your case where you need to deserialize this in python I think it will be easy if you figured out which will be the mean of serialization.JSON that @Alexander Tolkachev said for example could be a solution.
I hope this simplified example helps you.
answered Nov 19 '18 at 16:34
Tsakiroglou Fotis
502315
I've done some serialization for arm devices and network and I'would be happy to share my experience since you prefer binary serialization.
I am using unions to serialize.Lets assume that you have a struct that holds some element, data and pointers and this holds data for a family member :
struct fam_member
{
char name [ MAX_NAME_LEN + 1 ];
int height;
age_bracket_t age_bracket;
fam_member_t* mother;
fam_member_t* father;
}fam_member_t;
Age bracket is an enum:
typedef enum age_bracket
{
under_18 = 0 , from_18_to_25 = 1 , from_26_to_40 = 2 , over_40 = 3
}age_bracket_t;
The main problem and the most common mistake is struct padding and not taking this to serious.Here is a good start if someone is not familiar with the issue.
My simple solution is stream data down byte to byte (or bit to bit), do what you need to do with the serialized data (i.e. send them over a socket) and deserialize in the end.
I define a Union like this:
typedef union serialized_struct
{
fam_member_t family_member;
unsigned char data[ (MAX_NAME_LEN + 1 ) + (sizeof(int)*3) ];
}serialized_struct_t;
(A few think about union here)
The purpose of union is to save memory by using the same memory region for storing different objects at different times.In this example this will help us and actually serialize the family object struct for free.
Here is a function that serializes an array of family members (if you can do an area, single will be a piece of cake.That's why I choose an array here).
int serialize_array(fam_member_t* people , char* message , int elements)
{
if((people == NULL ) || (message == NULL) || (elements < 1))
{
return -1;
}
int size = sizeof(fam_member_t);
int i;
for(i=0 ; i < elements ; i++)
{
serialized_struct_t x;
memcpy((x.family_member.name) , people[i].name , MAX_NAME_LEN);
x.family_member.age_bracket = people[i].age_bracket;
x.family_member.height = people[i].age_bracket
x.family_member.mother = people[i].mother;
x.family_member.father = people[i].father;
memcpy ( (message + (size * i)) , x.data , size );
}
return 0;
}
Here we initiate every data of every member inside the struct which lies in the union.Message holds serialized data.This is the deserialized function which will do the reverse
int desirialize_array(fam_member_t* people , char* message , int elements)
{
if((people == NULL ) || (message == NULL) || (elements < 1))
{
return -1;
}
int size = sizeof(fam_member_t);
serialized_struct_t y;
int i;
for (i =0 ; i < elements ; i ++ )
{
memcpy ( y.data , (message + (size * i)) , size );
memcpy ( people[i].name , y.family_member.name , MAX_NAME_LEN);
people[i].age_bracket = y.family_member.age_bracket;
people[i].height = y.family_member.height;
people[i].mother = y.family_member.mother;
people[i].father = y.family_member.father;
}
return 0;
}
This is serialize and deserialize in c example.For your case where you need to deserialize this in python I think it will be easy if you figured out which will be the mean of serialization.JSON that @Alexander Tolkachev said for example could be a solution.
I hope this simplified example helps you.
answered Nov 19 '18 at 16:34
Tsakiroglou Fotis
502315
answered Nov 19 '18 at 16:34
Tsakiroglou Fotis
502315
answered Nov 19 '18 at 16:34
Tsakiroglou Fotis
502315
answered Nov 19 '18 at 16:34
Tsakiroglou Fotis
502315
502315
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What you want in result? May be JSON would be best solution for you.
– Alexander Tolkachev
Nov 19 '18 at 12:57
I would prefer binary format, since data amounts are very large. Also, no external dependencies in C.
– Dmytro Prylipko
Nov 19 '18 at 12:59
2
The question is too broad because the properties of the input data (type of data, amount of data and is it constant/dynamic, etc.) are not specified. Question is also missing a metric by which solution can be considered "good solution".
– user694733
Nov 19 '18 at 13:10
The data is around 100 kbytes of float values, C array as a pointer to the data. I am looking for a solution that does not require any external dependencies and can be implemented with the least effort. So, simple and elegant.
– Dmytro Prylipko
Nov 19 '18 at 13:52
1
If by 3D array you mean
[someNumber][someNumber](i.e. a continuous block of data) instead of**(i.e. pointer to pointer to array), you can simplyfwriteto a file thennp.fromfile(with the correct dtype) +np.reshape– ZisIsNotZis
Nov 21 '18 at 4:53