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SWIG, C, Python - Ignoring NULL terminators when passing a char * to python

Put quickly:
I want to send a full char * from a C module (build with SWIG) to a python callback function.
I can already do most of this BUT: my char array is just binary data and therefore contains 0s which is being seen as a NULL terminator in the C->Python conversion. Python only receives the bytes up until the first 0 rather than the full array.
In the swig documentation it specifically says that treating char * as binary data is possible with a typemap but doesn't say how. I've been playing with cstring.i (%cstring_output_withsize etc) but I am relatively new to SWIG and am out of my depth.
How do I tell SWIG to ignore the NULL terminator and use a size value instead when passing to python?
=========================================================
If you need more detail:
For a little background, I'm writing a very simple network packet format/transfer protocol for a 802.15.4 RF network. There are multiple architectures, languages and transceivers on the network so I'm writing my library to have a unified settable callback function allowing a small wrapper to be written on each platform that passes a buffer of bytes to the transciever using that host language.
Below are the key parts of the code.
//defined in Packets.h
void (*send_callback_ptr)(char * payload, uint8_t payload_length, uint16_t destination, uint16_t sequence_no);
//a function to set the callback
void send_callback_set(void (*f)(char * payload_buffer, uint8_t payload_length, uint16_t destination, uint16_t sequence_no))
{
send_callback_ptr = f;
}
uint8_t send(uint16_t target, enum PACKET_TYPE type, void * packet_object) {
char * payload_buffer = malloc(128); //max buffer size is 128
uint8_t payload_length = 12;
pack(target, type, packet_object, payload_buffer);
uint16_t destination = target;
uint16_t sequence_no = GLOBAL.hash++;
send_callback_ptr(payload, payload_length, destination, sequence_no);
};
At the top is the callback and the callback-setting function. 'send' takes a target, a packet type and a packet object (void * so python can pass it a pointer to a PyObject). It then packs all the data into char * payload_buffer using 'pack()' (pack just uses a set of rules to pack a packet object into a byte array ready to send).
def py_callback(buffer, buffer_length, destination, seq_no):
print buffer_length
print "type:", type(buffer)
print "length:", len(buffer)
for i in range(len(buffer)):
print i, '{:02X}'.format(ord(buffer[i]))
MyModule.send_callback_set(py_callback)
The python then looks like this which recieves the payload, payload_length etc from the call to send_callback_ptr at the end of the C function send().
In one example, the python callback function only receives 3 bytes when it should get 13 because the 4th byte in the array is a 0.

Sending data using socket from Python(client) to C++(server) arrays

I have been attempting to send an array from Python to C++ using a socket however have kept running into issues.
Python side there are issues sending an array directly such as pickle not being compatible with C++, as such the only semi-reliable method I have found is sending it as a string:
import socket
import sys
import random
# Create a TCP/IP socket
sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
server_address = ('localhost', 5555)
print >>sys.stderr, 'connecting to %s port %s' % server_address
sock.connect(server_address)
# Message to be sent to C++
# message = [random.randint(1, 10),random.randint(1, 10),random.randint(1, 10)]
i = 0
while i < 5:
a_converted = (random.randint(1,255), random.randint(1,255), random.randint(1,255))
#a_converted = 'words'
print a_converted
# Sending message to C++
sock.sendall(str(a_converted))
i += 1
sock.close()
The issue with sending it as a string is that I actually require it as an double style array on the other side. The C++ code I have is currently the following:
#include "stdafx.h"
#include <iostream>
#include <winsock2.h>
#include <WS2tcpip.h> //for SOCKET communication
#include <sstream>
#include <stdlib.h>
//Linking Ws2_32.lib, Mswsock.lib, Advapi32.lib
#pragma comment (lib, "Ws2_32.lib")
#pragma comment (lib, "Mswsock.lib")
#pragma comment (lib, "AdvApi32.lib")
#pragma warning(disable:4996)//to disable warning message
using namespace std;
int main()
{
WSADATA WSAData;
SOCKET server, client;
SOCKADDR_IN serverAddr, clientAddr;
WSAStartup(MAKEWORD(2, 0), &WSAData);
server = socket(AF_INET, SOCK_STREAM, 0);
serverAddr.sin_addr.s_addr = INADDR_ANY;
serverAddr.sin_family = AF_INET;
serverAddr.sin_port = htons(5555);
::bind(server, (SOCKADDR *)&serverAddr, sizeof(serverAddr));
listen(server, 0);
cout << "Listening for incoming connections..." << endl;
string a_converted[1000];
int clientAddrSize = sizeof(clientAddr);
if ((client = accept(server, (SOCKADDR *)&clientAddr, &clientAddrSize)) != INVALID_SOCKET)
{
cout << "Client connected!" << endl;
// Loop
int i = 0;
while (i<5) {
recv(client, (char*)a_converted, sizeof(a_converted), 0);
char char_array[sizeof(a_converted)];
strcpy(char_array, (char*)a_converted);
memset(a_converted, 0, sizeof(a_converted));
cout << "Client says: " << char_array << endl;
cout << endl;
i = i++;
}
closesocket(client);
WSACleanup();
cout << "Client disconnected." << endl;
}
cout << "Press Enter to continue" << endl;
getchar();
}
The information is received and correct but I have been unable to correctly convert the data. I have tried to use atof and similar functions to convert on the C++ side but the presence of commas and brackets from the Python side seem to result in it erroring and giving zeros and I've had little luck trying to remove them from the string.
I can't help but think there must be a better way of doing this but I am really new to coding so would not be surprised if I am overlooking something.
I would appreciate either an explanation of how to send an array directly that C++ can read from Python or a way to convert the string it sends in C++.

The most straight-forward way to accomplish this is to employ python's struct module to encode your array into a binary format that will be convenient to receive in C++.
For example, to send an array of 32-bit integers, you might do something like this:
import struct
def encode_int_array(int_list):
buf = struct.pack("!I" + "I" * len(int_list), len(int_list), *int_list)
return buf
Explanation: The ! character specifies the byte-ordering to be used in the encoding (here, big-endian / "network" order), the I character is used here for the array length, then again once for each integer to be encoded. The actual array length and each integer is then packed.
So, if you called this function with the list [1, 2, 3], the format string given to pack will be "!IIII" and the the remaining arguments will be 3, 1, 2, 3 (the first '3' being the array length to encode). The end result is a bytes string containing the encoded 32-bit (4-byte) integers:
|ArrayLen|Integer0|Integer1|Integer2|....
Use the above along with sendall to transmit the resulting buffer:
sock.sendall(encode_int_array(
[random.randint(1,255), random.randint(1,255), random.randint(1,255)]))
On the C++ side, first read 4 bytes (to get the array length), convert the array length to native byte ordering, then read an additional 4 * array-length bytes to get all the integers; then convert each of those to native byte order. You should be careful never to assume that recv will receive all of the data you want. The SOCK_STREAM semantics do not guarantee that. So you need to ensure you receive exactly the number you expected.
The C++ side might look something like this:
#include <cstdint> // uint32_t et al definitions
// Function to receive exactly "len" bytes.
// Returns number of bytes received, or -1 on EOF or error
int recv_all(int sock, char *buf, unsigned int len)
{
unsigned int n = 0;
int status;
while (n < len) {
status = recv(sock, buf + n, len - n);
if (status == 0) {
// Unexpected End of File
return -1; // Or whatever
} else if (status < 0) {
// Error
return -1; // Need to look at errno to find out what happened
} else {
n += status;
}
}
return (int)n;
}
...
int status;
// Receive array length from client
uint32_t array_len;
status = recv_all(client, reinterpret_cast<char *>(&array_len), sizeof array_len);
if (status < 0) {
// handle error
}
array_len = ntohl(array_len); // Convert length to native byte order
// Receive array contents from client
uint32_t int_array[array_len];
status = recv_all(client, reinterpret_cast<char *>(&int_array[0]), sizeof int_array);
if (status < 0) {
// handle error
}
for (unsigned int n = 0; n < array_len; ++n)
int_array[n] = ntohl(int_array[n]); // Convert to native byte order
(If you only wanted to send single byte integers, substitute 'B' for 'I' in the pack calls above, and the C++ below will also need to be adjusted accordingly -- with uint8_t in place of uint32_t, say.)

This sounds like a serialization problem. As you want to connect two different languages, I suggest a standardized, well known format like JSON or XML. There are lots of libraries for converting JSON or XML into objects and vice versa.
Ultimate, dead-end solution is, to pack the data into a binary file and send this over the socket. Try external libraries for JSON or XML first
Edit:
JSON describes (in a very simple way), how objects can be saved as text (serialization). It is as simple as
{
"firstName": "John",
"lastName": "Smith",
"isAlive": true,
"age": 27,
"address": {
"streetAddress": "21 2nd Street",
"city": "New York",
"state": "NY",
"postalCode": "10021-3100"
},
"phoneNumbers": [
{
"type": "home",
"number": "212 555-1234"
},
{
"type": "office",
"number": "646 555-4567"
},
{
"type": "mobile",
"number": "123 456-7890"
}
],
"children": [],
"spouse": null
}
(taken from https://en.wikipedia.org/wiki/JSON)
You can imagine, it is a very straight forward process to read from the text to an object again (deserialization). There are libraries there which will do the job for you. This means for your project:
find a python JSON library which serializes your objects into JSON format
find a c++ JSON library which deserializes your data to an object
I have seen this in use, as every data type is treated as a string to send it, and on the deserialization side, you need to decice for each case which data type it really is (converting the string to double or int or float or bool etc..)

You need to convert String in python to Bytes while
sock.sendall
Refer Python: convert string to byte array
Based on your python syntax, it should be python 2.
Python 3 can easily find and insist to convert into Bytes while sendall.
In python 2, you can use bytearray like
sock.sendall (bytearray(str(a_converted)))
In python 3, you can call encode which defaults to UTF-8 while converting to bytes.
sock.sendall (str(a_converted).encode())

Arduino to Raspberry crc32 check

I'm trying to send messages through the serial USB interface of my Arduino (C++) to a Raspberry Pi (Python).
On the Arduino side I define a struct which I then copy into a char[]. The last part of the struct contains a checksum that I want to calculate using CRC32. I copy the struct into a temporary char array -4 bytes to strip the checksum field. The checksum is then calculated using the temporary array and the result is added to the struct. The struct is then copied into byteMsg which gets send over the serial connection.
On the raspberry end I do the reverse, I receive the bytestring and calculate the checksum over the message - 4 bytes. Then unpack the bytestring and compare the received and calculated checksum but this fails unfortunately.
For debugging I compared the crc32 check on both the python and arduino for the string "Hello World" and they generated the same checksum so doesn't seem to be a problem with the library. The raspberry is also able to decode the rest of the message just fine so the unpacking of the data into variables seem to be ok as well.
Any help would be much appreciated.
The Python Code:
def unpackMessage(self, message):
""" Processes a received byte string from the arduino """
# Unpack the received message into struct
(messageID, acknowledgeID, module, commandType,
data, recvChecksum) = struct.unpack('<LLBBLL', message)
# Calculate the checksum of the recv message minus the last 4
# bytes that contain the sent checksum
calcChecksum = crc32(message[:-4])
if recvChecksum == calcChecksum:
print "Checksum checks out"
The Aruino crc32 library taken from http://excamera.com/sphinx/article-crc.html
crc32.h
#include <avr/pgmspace.h>
static PROGMEM prog_uint32_t crc_table[16] = {
0x00000000, 0x1db71064, 0x3b6e20c8, 0x26d930ac,
0x76dc4190, 0x6b6b51f4, 0x4db26158, 0x5005713c,
0xedb88320, 0xf00f9344, 0xd6d6a3e8, 0xcb61b38c,
0x9b64c2b0, 0x86d3d2d4, 0xa00ae278, 0xbdbdf21c
};
unsigned long crc_update(unsigned long crc, byte data)
{
byte tbl_idx;
tbl_idx = crc ^ (data >> (0 * 4));
crc = pgm_read_dword_near(crc_table + (tbl_idx & 0x0f)) ^ (crc >> 4);
tbl_idx = crc ^ (data >> (1 * 4));
crc = pgm_read_dword_near(crc_table + (tbl_idx & 0x0f)) ^ (crc >> 4);
return crc;
}
unsigned long crc_string(char *s)
{
unsigned long crc = ~0L;
while (*s)
crc = crc_update(crc, *s++);
crc = ~crc;
return crc;
}
Main Arduino Sketch
struct message_t {
unsigned long messageID;
unsigned long acknowledgeID;
byte module;
byte commandType;
unsigned long data;
unsigned long checksum;
};
void sendMessage(message_t &msg)
{
// Set the messageID
msg.messageID = 10;
msg.checksum = 0;
// Copy the message minus the checksum into a char*
// Then perform the checksum on the message and copy
// the full msg into byteMsg
char byteMsgForCrc32[sizeof(msg)-4];
memcpy(byteMsgForCrc32, &msg, sizeof(msg)-4);
msg.checksum = crc_string(byteMsgForCrc32);
char byteMsg[sizeof(msg)];
memcpy(byteMsg, &msg, sizeof(msg));
Serial.write(byteMsg, sizeof(byteMsg));
void loop() {
message_t msg;
msg.module = 0x31;
msg.commandType = 0x64;
msg.acknowledgeID = 0;
msg.data = 10;
sendMessage(msg);
Kind Regards,
Thiezn

You are making the classic struct-to-network/serial/insert communication layer mistake. Structs have hidden padding in order to align the members onto suitable memory boundaries. This is not guaranteed to be the same across different computers, let alone different CPUs/microcontrollers.
Take this struct as an example:
struct Byte_Int
{
int x;
char y;
int z;
}
Now on a basic 32-bit x86 CPU you have a 4-byte memory boundary. Meaning that variables are aligned to either 4 bytes, 2 bytes or not at all according to the type of variable. The example would look like this in memory: int x on bytes 0,1,2,3, char y on byte 4, int z on bytes 8,9,10,11. Why not use the three bytes on the second line? Because then the memory controller would have to do two fetches to get a single number! A controller can only read one line at a time. So, structs (and all other kinds of data) have hidden padding in order to get variables aligned in memory. The example struct would have a sizeof() of 12, and not 9!
Now, how does that relate to your problem? You are memcpy()ing a struct directly into a buffer, including the padding. The computer on the other end doesn't know about this padding and misinterprets the data. What you need a serialization function that takes the members of your structs and pasts them into a buffer one at a time, that way you lose the padding and end up with something like this:
[0,1,2,3: int x][4: char y][5,6,7,8: int z]. All as one lengthy bytearray/string which can be safely sent using Serial(). Of course on the other end you would have to parse this string into intelligible data. Python's unpack() does this for you as long as you give the right format string.
Lastly, an int on an Arduino is 16 bits long. On a pc generally 4! So assemble your unpack format string with care.

The char array I was passing to the crc_string function contained '\0' characters. The crc_string was iterating through the array until it found a '\0' which shouldn't happen in this case since I was using the char array as a stream of bytes to be sent over a serial connection.
I've changed the crc_string function to take the array size as argument and iterate through the array using that value. This solved the issue.
Here's the new function
unsigned long crc_string(char *s, size_t arraySize)
{
unsigned long crc = ~0L;
for (int i=0; i < arraySize; i++) {
crc = crc_update(crc, s[i]);
}
crc = ~crc;
return crc;
}

RaspberryPi to Arduino -send and receive string

This is the code I am currently using to send and receive int values from a RaspberryPi to an Arduino using i2C. It works fine for values 0-255, but because of the 1 byte limit, anything larger fails.
To circumvent this, I'd like to send and receive string values instead, and then convert back to int if necessary.
What changes would I need to make in the following?
Here is my RPi Python code
import smbus
import time
# for RPI version 1, use "bus = smbus.SMBus(0)"
bus = smbus.SMBus(1)
# This is the address we setup in the Arduino Program
address = 0x04
def writeNumber(value):
bus.write_byte(address, value)
# bus.write_byte_data(address, 0, value)
return -1
def readNumber():
number = bus.read_byte(address)
# number = bus.read_byte_data(address, 1)
return number
while True:
try:
var = int(raw_input("Enter 1 - 9: "))
except ValueError:
print "Could you at least give me an actual number?"
continue
writeNumber(var)
print "RPI: Hi Arduino, I sent you ", var
# sleep one second
#time.sleep(1)
number = readNumber()
print "Arduino: Hey RPI, I received a digit ", number
print
And here is my Arduino code
#include <Wire.h>
#define SLAVE_ADDRESS 0x04
int number = 0;
int state = 0;
void setup() {
pinMode(13, OUTPUT);
Serial.begin(9600); // start serial for output
// initialize i2c as slave
Wire.begin(SLAVE_ADDRESS);
// define callbacks for i2c communication
Wire.onReceive(receiveData);
Wire.onRequest(sendData);
Serial.println("Ready!");
}
void loop() {
delay(100);
}
// callback for received data
void receiveData(int byteCount){
while(Wire.available()) {
number = Wire.read();
if (Wire.available() > 1) // at least 2 bytes
{
number = Wire.read() * 256 + Wire.read();
}
Serial.print("data received: ");
Serial.println(number);
//sendData();
if (number == 1){
if (state == 0){
digitalWrite(13, HIGH); // set the LED on
state = 1;
}
else{
digitalWrite(13, LOW); // set the LED off
state = 0;
}
}
}
}
// callback for sending data
void sendData(){
Wire.write(number);
}

This problem essentially has two parts: splitting an integer into its bytes and reassembling an integer from bytes. These parts must be replicated on both the Pi and Arduino. I'll address the Pi side first, in Python:
Splitting an integer:
def writeNumber(value):
# assuming we have an arbitrary size integer passed in value
for character in str(val): # convert into a string and iterate over it
bus.write_byte(address, ord(character)) # send each char's ASCII encoding
return -1
Reassembling an integer from bytes:
def readNumber():
# I'm not familiar with the SMbus library, so you'll have to figure out how to
# tell if any more bytes are available and when a transmission of integer bytes
# is complete. For now, I'll use the boolean variable "bytes_available" to mean
# "we are still transmitting a single value, one byte at a time"
byte_list = []
while bytes_available:
# build list of bytes in an integer - assuming bytes are sent in the same
# order they would be written. Ex: integer '123' is sent as '1', '2', '3'
byte_list.append(bus.read_byte(address))
# now recombine the list of bytes into a single string, then convert back into int
number = int("".join([chr(byte) for byte in byte_list]))
return number
Arduino Side, in C
Split an Integer:
void sendData(){
int i = 0;
String outString = String(number); /* convert integer to string */
int len = outString.length()+1 /* obtain length of string w/ terminator */
char ascii_num[len]; /* create character array */
outString.toCharArray(ascii_num, len); /* copy string to character array */
for (i=0; i<len); ++i){
Wire.write(ascii_num[i]);
}
}
Reassembling a received Integer:
Note: I'm having some trouble understanding what your other code in this routine is doing, so I'm going to reduce it to just assembling the integer.
void receiveData(int byteCount){
int inChar;
String inString = "";
/* As with the Python receive routine, it will be up to you to identify the
terminating condition for this loop - "bytes_available" means the same thing
as before */
while(bytes_available){
inChar = Wire.read();
inString += char(inChar);
}
number = inString.toInt();
}
I don't have the materials on hand to test this, so it's possible I've gotten the byte order flipped in one routine or another. If you find stuff coming in or out backwards, the easiest place to fix it is in the Python script by using the built-in function reversed() on the strings or lists.
References (I used some code from the Arduino Examples):
Arduino String objects
Arduino String Constructors
Python Built-ins chr() and ord()

Check the following Link:
[http://www.i2c-bus.org/][1]
When I was sending data back and forward using I2C I was converting the string characters to bytearrays and viceversa. So since you are always sending bytes. It will always work since you are sending numbers between 0-255.
Not sure this helps but at least may give you an idea.

You could convert the number to a string of digits like you said. But you could also send the raw bytes.
String of digits
Advantages
Number can have infinite digits. Note that when Arduino reads the number as a string, it is infinite, but you can't convert it all to integer if it overflows the 16-bit range (or 32-bit for Due).
Disadvantages
Variable size, thus requiring more effort in reading.
Waste of bytes, because each decimal digit would be a byte, plus the null-terminator totalizing (digits + 1) size.
Having to use decimal arithmetic (which really is only useful for human counting), note that a "number to string" operation also uses decimal arithmetic.
You can't send/receive negative numbers (unless you send the minus signal, wasting more time and bytes).
Raw bytes
Advantages
Number of bytes sent for each integer is always 4.
You can send/receive negative numbers.
The bitwise arithmetic in C++ for extracting each byte from the number is really fast.
Python already has the struct library which packs/unpacks each byte in a number to a string to send/receive, so you don't need to do the arithmetic like in C++.
Disadvantages
Number has a limited range (signed 32-bit integer in our case, which ranges from -2147483648 to 2147483647). But it doesn't matter because no Arduino can handle more than 32-bit anyways.
So I would use the raw bytes method, which I can provide some untested functions here:
import struct
# '<i' stands for litle-endian signed integer
def writeNumber(value):
strout = struct.pack('<i', value)
for i in range(4):
bus.write_byte(address, strout[i])
return -1
def readNumber():
strin = ""
for _ in range(4):
strin += bus.read_byte(address)
return struct.unpack('<i', strin)[0]
And the Arduino part:
void receiveData(int byteCount)
{
// Check if we have a 32-bit number (4 bytes) in queue
while(Wire.available() >= 4)
{
number = 0;
for(int i = 0; i < 32; i += 8)
{
// This is merging the bytes into a single integer
number |= ((int)Wire.read() << i);
}
Serial.print("data received: ");
Serial.println(number);
// ...
}
}
void sendData()
{
for(int i = 0; i < 32; i += 8)
{
// This is extracting each byte from the number
Wire.write((number >> i) & 0xFF);
}
}
I don't have any experience with I2C, but if its queue is a FIFO, then the code should work.

Sending integer values to Arduino from PySerial

I need to send integers greater than 255? Does anyone know how to do this?

Here's how (Thanks for the idea, Alex!):
Python:
def packIntegerAsULong(value):
"""Packs a python 4 byte unsigned integer to an arduino unsigned long"""
return struct.pack('I', value) #should check bounds
# To see what it looks like on python side
val = 15000
print binascii.hexlify(port.packIntegerAsULong(val))
# send and receive via pyserial
ser = serial.Serial(serialport, bps, timeout=1)
ser.write(packIntegerAsULong(val))
line = ser.readLine()
print line
Arduino:
unsigned long readULongFromBytes() {
union u_tag {
byte b[4];
unsigned long ulval;
} u;
u.b[0] = Serial.read();
u.b[1] = Serial.read();
u.b[2] = Serial.read();
u.b[3] = Serial.read();
return u.ulval;
}
unsigned long val = readULongFromBytes();
Serial.print(val, DEC); // send to python to check

Encode them into binary strings with Python's struct module. I don't know if arduino wants them little-endian or big-endian, but, if its docs aren't clear about this, a little experiment should easily settle the question;-).

Way easier :
crc_out = binascii.crc32(data_out) & 0xffffffff # create unsigned long
print "crc bytes written",arduino.write(struct.pack('<L', crc_out)) #L, I whatever u like to use just use 4 bytes value
unsigned long crc_python = 0;
for(uint8_t i=0;i<4;i++){
crc_python |= ((long) Serial.read() << (i*8));
}
No union needed and short !