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Shared memory between C and python

I want to share memory between a program in C and another in python.
The c program uses the following structure to define the data.
struct Memory_LaserFrontal {
char Data[372]; // original data
float Med[181]; // Measurements in [m]
charD; // 'I': Invalid -- 'V': Valid
charS; // 'L': Clean -- 'S': Dirty
char LaserStatus[2];
};
From python I have managed to read the variable in memory using sysv_ipc but they have no structure and is seen as a data array. How can I restructure them?
python code:
from time import sleep
import sysv_ipc
# Create shared memory object
memory = sysv_ipc.SharedMemory(1234)
# Read value from shared memory
memory_value = memory.read()
print (memory_value)
print (len(memory_value))
while True:
memory_value = memory.read()
print (float(memory_value[800]))
sleep(0.1)
I have captured and printed the data in python, I have modified the sensor reading and the read data is also modified, confirming that the read data corresponds to the data in the sensor's shared memory. But without the proper structure y cant use the data.

You need to unpack your binary data structure into Python types. The Python modules struct and array can do this for you.
import struct
import array
NB: Some C compilers, but not the comomn ones, may pad your member variables to align each of them with the expected width for your CPU ( almost always 4 bytes ). This means that it may add padding bytes. You may have to experiment with the struct format parameter 'x' between the appropriate parts of your struct if this is the case. Python's struct module does not expect aligned or padded types by default, you need to inform it. See my note at the very end for a guess on what the padding might look like. Again, per #Max's comment, this is unlikely.
NB: I think the members charD and charS are really char D; and char S;
Assuming you want the floats as a Python list or equivalent we have to do some more work with the Python array module . Same for the char[] Data.
# Get the initial char array - you can turn it into a string if you need to later.
my_chars = array.array("b") # f for float, b for byteetc.
my_chars.from_bytes(memory_value[:372]) # happens that 372 C chars is 372 bytes.
Data = my_chars.tolist() # Could be bytes list
# advance to the member after Data
end_of_Data = struct.calcsize("372c")
# get the length in bytes that 181 floats take up
end_of_Med = struct.calcsize("181f") + end_of_Data
# now we know where the floats are
floats_as_bytes = memory_value[ end_of_Data : end_of_Med ]
# unpack the remaining parts
( D, S, LaserStatus_1, LaserStatus_2 ) = struct.unpack( "cccc", memory_value[end_of_Med:] )
Now use the array module to unpack to make a Python list
my_floats = array.array("f") # f for float, c for char etc.
my_floats.from_bytes(floats_as_bytes)
Now Data might be a list of Python bytes type that you need to convert to your preferred string encoding. Usually .decode('utf-8') is good enough.
Data_S = "".join(Data).decode('utf-8') # get a usable string in Data_S
Padding
struct Memory_LaserFrontal {
char Data[372]; // 372 is a multiple of 4, probably no padding
float Med[181]; // floats are 4 bytes, probably no padding
charD; // single char, expect 3 padding bytes after
charS; // single char, expect 3 padding bytes after
char LaserStatus[2]; // double char expect 2 padding bytes after.
};
So the last Python line above might be - where the 'x' indicates a padding byte that can be ignored.
( D, S, LaserStatus_1, LaserStatus_2 ) = struct.unpack( "cxxxcxxxccxx", memory_value[end_of_Med:] )

I always like to leave the full source code of the problem solved so others can use it if they have a similar problem.
thanks a lot all!
from time import sleep
import sysv_ipc
import struct
import array
# Create shared memory object
while True:
memory = sysv_ipc.SharedMemory(1234)
# Read value from shared memory
memory_value = memory.read()
#print (memory_value)
#print (len(memory_value))
# Get the initial char array - you can turn it into a string if you need to later.
my_chars = array.array("b") # f for float, c for char etc.
#my_chars.from_bytes(memory_value[:372]) # happens that 372 chars is 372 bytes.
Data = my_chars.tolist() # Could be bytes list
# advance to the member after Data
end_of_Data = struct.calcsize("372c")
# get the length in bytes that 181 floats take up
end_of_Med = struct.calcsize("181f") + end_of_Data
# now we know where the floats are
floats_as_bytes = memory_value[ end_of_Data : end_of_Med ]
# unpack the remaining parts
( D, S, LaserStatus_1, LaserStatus_2 ) = struct.unpack( "cccc", memory_value[end_of_Med:] )
print(len(floats_as_bytes)/4)
a=[]
for i in range(0,len(floats_as_bytes),4):
a.append(struct.unpack('<f', floats_as_bytes[i:i+4]))
print (a[0])
sleep(0.1)

Get int value from each two bytes

I am trying to read bytes from an image, and get all the int (16 bit) values from that image.
After I parsed the image header, I got to the pixel values. The values that I get when the pair of bytes are like b"\xd4\x00" is incorrect. In this case it should be 54272, not 3392.
This are parts of the code:
I use a generator to get the bytes:
import itertools
def osddef_generator(in_file):
with open(in_file, mode='rb') as f:
dat = f.read()
for byte in dat:
yield byte
def take_slice(in_generator, size):
return ''.join(str(chr(i)) for i in itertools.islice(in_generator, size))
def take_single_pixel(in_generator):
pix = itertools.islice(in_generator, 2)
hex_list = [hex(i) for i in pix]
hex_str = "".join(hex_list)[2:].replace("0x", '')
intval = int(hex_str, 16)
print("hex_list: ", hex_list)
print("hex_str: ", hex_str)
print("intval: ", intval)
After I get the header correctly using the take_slice method, I get to the part with the pixel values, where I use the take_single_pixel method.
Here, I get the bad results.
This is what I get:
hex_list: ['0xd4', '0x0']
hex_str: d40
intval: 3392
But the actual sequence of bytes that should be interpreted is: \xd4\x00, which equals to 54272, so that my hex_list = ['0xd4', '0x00'] and hex_str = d400.
Something happens when I have a sequence of bytes when the second one is \x00.
Got any ideas? Thanks!

There are much better ways of converting bytes to integters:
int.from_bytes() takes bytes input, and a byte order argument:
>>> int.from_bytes(b"\xd4\x00", 'big')
54272
>>> int.from_bytes(b"\xd4\x00", 'little')
212
The struct.unpack() function lets you convert a whole series of bytes to integers following a pattern:
>>> import struct
>>> struct.unpack('!4H', b'\xd4\x00\xd4\x00\xd4\x00\xd4\x00')
(54272, 54272, 54272, 54272)
The array module lets you read binary data representing homogenous integer data into a memory structure efficiently:
>>> array.array('H', fileobject)
However, array can't be told what byte order to use. You'd have to determine the current architecture byte order and call arr.byteswap() to reverse order if the machine order doesn't match the file order.
When reading image data, it is almost always preferable to use the struct module to do the parsing. You generally then use file.read() calls with specific sizes; if the header consists of 10 bytes, use:
headerinfo = struct.unpack('<expected header pattern for 10 bytes>', f.read(10))
and go from there. For examples, look at the Pillow / PIL image plugins source code; here is how the Blizzard Mipmap image format header is read:
def _read_blp_header(self):
self._blp_compression, = struct.unpack("<i", self.fp.read(4))
self._blp_encoding, = struct.unpack("<b", self.fp.read(1))
self._blp_alpha_depth, = struct.unpack("<b", self.fp.read(1))
self._blp_alpha_encoding, = struct.unpack("<b", self.fp.read(1))
self._blp_mips, = struct.unpack("<b", self.fp.read(1))
self._size = struct.unpack("<II", self.fp.read(8))
if self.magic == b"BLP1":
# Only present for BLP1
self._blp_encoding, = struct.unpack("<i", self.fp.read(4))
self._blp_subtype, = struct.unpack("<i", self.fp.read(4))
self._blp_offsets = struct.unpack("<16I", self.fp.read(16 * 4))
self._blp_lengths = struct.unpack("<16I", self.fp.read(16 * 4))
Because struct.unpack() always returns tuples, you can assign individual elements in a tuple to name1, name2, ... names on the left-hand size, including single_name, = assignments to extract a single result.
The separate set of read calls above could also be compressed into fewer calls:
comp, enc, adepth, aenc, mips, *size = struct.unpack("<i4b2I", self.fp.read(16))
if self.magic == b"BLP1":
# Only present for BLP1
enc, subtype = struct.unpack("<2i", self.fp.read(8))
followed by specific attribute assignments.

Reading binary file into different hex "types" (8bit, 16bit, 32bit, ...)

I have a file which contains binary data. The content of this file is just one long line.
Example: 010101000011101010101
Originaly the content was an array of c++ objects with the following data types:
// Care pseudo code, just for visualisation
int64 var1;
int32 var2[50];
int08 var3;
I want to skip var1 and var3 and only extract the values of var2 into some readable decimal values. My idea was to read the file byte by byte and convert them into hex values. In the next step I though I could "combine" (append) 4 of those hex values to get one int32 value.
Example: 0x10 0xAA 0x00 0x50 -> 0x10AA0050
My code so far:
def append_hex(a, b):
return (a << 4) | b
with open("file.dat", "rb") as f:
counter = 0
tickdifcounter = 0
current_byte=" "
while True:
if (counter >= 8) and (counter < 208):
tickdifcounter+=1
if (tickdifcounter <= 4):
current_byte = append_hex(current_byte, f.read(1))
if (not current_byte):
break
val = ord(current_byte)
if (tickdifcounter > 4):
print hex(val)
tickdifcounter = 0
current_byte=""
counter+=1
if(counter == 209): #209 bytes = int64 + (int32*50) + int08
counter = 0
print
Now I have the problem that my append_hex is not working because the variables are strings so the bitshift is not working.
I am new to python so please give me hints when I can do something in a better way.

You can use struct module for reading binary files.
This can help you Reading a binary file into a struct in Python

A character can be converted to a int using the ord(x) method. In order to get the integer value of a multi-byte number, bitshift left. For example, from a earlier project:
def parseNumber(string, index):
return ord(string[index])<<24 + ord(string[index+1])<<16 + \
ord(string[index+2])<<8+ord(string[index+3])
Note this code assumes big-endian system, you will need to reverse the index for parsing little-endian code.
If you know exaclty what the size of the struct is going to be, (or can easily calculate it based on the size of the file) you are probably better of using the "struct" module.

How to byteswap 32bit integers inside a string in python?

I have a large string more than 256 bits and and I need to byte swap it by 32 bits. But the string is in a hexadecimal base. When I looked at numpy and array modules I couldnt find the right syntax as to how to do the coversion. Could someone please help me?
An example:(thought the data is much longer.I can use pack but then I would have to convert the little endian to decimal and then to big endian first which seems like a waste):
Input:12345678abcdeafa
Output:78563412faeacdab

Convert the string to bytes, unpack big-endian 32-bit and pack little-endian 32-bit (or vice versa) and convert back to a string:
#!python3
import binascii
import struct
Input = b'12345678abcdeafa'
Output = b'78563412faeacdab'
def convert(s):
s = binascii.unhexlify(s)
a,b = struct.unpack('>LL',s)
s = struct.pack('<LL',a,b)
return binascii.hexlify(s)
print(convert(Input),Output)
Output:
b'78563412faeacdab' b'78563412faeacdab'
Generalized for any string with length multiple of 4:
import binascii
import struct
Input = b'12345678abcdeafa'
Output = b'78563412faeacdab'
def convert(s):
if len(s) % 4 != 0:
raise ValueError('string length not multiple of 4')
s = binascii.unhexlify(s)
f = '{}L'.format(len(s)//4)
dw = struct.unpack('>'+f,s)
s = struct.pack('<'+f,*dw)
return binascii.hexlify(s)
print(convert(Input),Output)

If they really are strings, just do string operations on them?
>>> input = "12345678abcdeafa"
>>> input[7::-1]+input[:7:-1]
'87654321afaedcba'

My take:
slice the string in N digit chunks
reverse each chunk
concatenate everything
Example:
>>> source = '12345678abcdeafa87654321afaedcba'
>>> # small helper to slice the input in 8 digit chunks
>>> chunks = lambda iterable, sz: [iterable[i:i+sz]
for i in range(0, len(iterable), sz)]
>>> swap = lambda source, sz: ''.join([chunk[::-1]
for chunk in chunks(source, sz)])
Output asked in the original question:
>>> swap(source, 8)
'87654321afaedcba12345678abcdeafa'
It is easy to adapt in order to match the required output after icktoofay edit:
>>> swap(swap(source, 8), 2)
'78563412faeacdab21436587badcaeaf'
A proper implementation probably should check if len(source) % 8 == 0.

How to encode a long in Base64 in Python?

In Java, I can encode a BigInteger as:
java.math.BigInteger bi = new java.math.BigInteger("65537L");
String encoded = Base64.encodeBytes(bi.toByteArray(), Base64.ENCODE|Base64.DONT_GUNZIP);
// result: 65537L encodes as "AQAB" in Base64
byte[] decoded = Base64.decode(encoded, Base64.DECODE|Base64.DONT_GUNZIP);
java.math.BigInteger back = new java.math.BigInteger(decoded);
In C#:
System.Numerics.BigInteger bi = new System.Numerics.BigInteger("65537L");
string encoded = Convert.ToBase64(bi);
byte[] decoded = Convert.FromBase64String(encoded);
System.Numerics.BigInteger back = new System.Numerics.BigInteger(decoded);
How can I encode long integers in Python as Base64-encoded strings? What I've tried so far produces results different from implementations in other languages (so far I've tried in Java and C#), particularly it produces longer-length Base64-encoded strings.
import struct
encoded = struct.pack('I', (1<<16)+1).encode('base64')[:-1]
# produces a longer string, 'AQABAA==' instead of the expected 'AQAB'
When using this Python code to produce a Base64-encoded string, the resulting decoded integer in Java (for example) produces instead 16777472 in place of the expected 65537. Firstly, what am I missing?
Secondly, I have to figure out by hand what is the length format to use in struct.pack; and if I'm trying to encode a long number (greater than (1<<64)-1) the 'Q' format specification is too short to hold the representation. Does that mean that I have to do the representation by hand, or is there an undocumented format specifier for the struct.pack function? (I'm not compelled to use struct, but at first glance it seemed to do what I needed.)

Check out this page on converting integer to base64.
import base64
import struct
def encode(n):
data = struct.pack('<Q', n).rstrip('\x00')
if len(data)==0:
data = '\x00'
s = base64.urlsafe_b64encode(data).rstrip('=')
return s
def decode(s):
data = base64.urlsafe_b64decode(s + '==')
n = struct.unpack('<Q', data + '\x00'* (8-len(data)) )
return n[0]

The struct module:
… performs conversions between Python values and C structs represented as Python strings.
Because C doesn't have infinite-length integers, there's no functionality for packing them.
But it's very easy to write yourself. For example:
def pack_bigint(i):
b = bytearray()
while i:
b.append(i & 0xFF)
i >>= 8
return b
Or:
def pack_bigint(i):
bl = (i.bit_length() + 7) // 8
fmt = '<{}B'.format(bl)
# ...
And so on.
And of course you'll want an unpack function, like jbatista's from the comments:
def unpack_bigint(b):
b = bytearray(b) # in case you're passing in a bytes/str
return sum((1 << (bi*8)) * bb for (bi, bb) in enumerate(b))

This is a bit late, but I figured I'd throw my hat in the ring:
def inttob64(n):
"""
Given an integer returns the base64 encoded version of it (no trailing ==)
"""
parts = []
while n:
parts.insert(0,n & limit)
n >>= 32
data = struct.pack('>' + 'L'*len(parts),*parts)
s = base64.urlsafe_b64encode(data).rstrip('=')
return s
def b64toint(s):
"""
Given a string with a base64 encoded value, return the integer representation
of it
"""
data = base64.urlsafe_b64decode(s + '==')
n = 0
while data:
n <<= 32
(toor,) = struct.unpack('>L',data[:4])
n |= toor & 0xffffffff
data = data[4:]
return n
These functions turn an arbitrary-sized long number to/from a big-endian base64 representation.

Here is something that may help. Instead of using struct.pack() I am building a string of bytes to encode and then calling the BASE64 encode on that. I didn't write the decode, but clearly the decode can recover an identical string of bytes and a loop could recover the original value. I don't know if you need fixed-size integers (like always 128-bit) and I don't know if you need Big Endian so I left the decoder for you.
Also, encode64() and decode64() are from #msc's answer, but modified to work.
import base64
import struct
def encode64(n):
data = struct.pack('<Q', n).rstrip('\x00')
if len(data)==0:
data = '\x00'
s = base64.urlsafe_b64encode(data).rstrip('=')
return s
def decode64(s):
data = base64.urlsafe_b64decode(s + '==')
n = struct.unpack('<Q', data + '\x00'* (8-len(data)) )
return n[0]
def encode(n, big_endian=False):
lst = []
while True:
n, lsb = divmod(n, 0x100)
lst.append(chr(lsb))
if not n:
break
if big_endian:
# I have not tested Big Endian mode, and it may need to have
# some initial zero bytes prepended; like, if the integer is
# supposed to be a 128-bit integer, and you encode a 1, you
# would need this to have 15 leading zero bytes.
initial_zero_bytes = '\x00' * 2
data = initial_zero_bytes + ''.join(reversed(lst))
else:
data = ''.join(lst)
s = base64.urlsafe_b64encode(data).rstrip('=')
return s
print encode(1234567890098765432112345678900987654321)