Pass python 3 open file object to C function as FILE * - python-3.x

I want to pass my file to C function.
I have problem with this. I saw "Segmentation fault"
My C code:
// cc -fPIC -shared -o w.so w.c
#include <stdio.h>
void my_writer(FILE *fp, int num) {
fprintf(fp, "%d\n", num);
}
My python code:
#!/usr/bin/python3
#
from ctypes import *
so_file = "./w.so"
my_c_writer = CDLL(so_file)
my_num = 2022
try:
convert_file = pythonapi.PyObject_AsFileDescriptor
convert_file.argtypes = [py_object]
convert_file.restype = c_int
# fp = open('path').fp there is no .fp attribute!
fp = open('num.txt', 'w')
c_file = convert_file(fp)
my_c_writer.my_writer(c_file, c_int(my_num))
fp.close()
except Exception as e:
print(e)
I searched a lot but I found nothing.
The C code file is unchangeable.
I would very appreciate if you help me.

As Mark mentioned, c_file in your Python module is a file descriptor and not FILE*. I was able to get the code to work after I wrote a wrapper function in C.
void my_writer_wrapper(int fildes, int num) {
FILE *fp = fdopen(fildes, "w");
my_writer(fp, num);
fflush(fp);
}
Instead of using my_writer directly, you can use the wrapper:
...
fp = open('num.txt', 'w')
c_file = convert_file(fp)
my_c_writer.my_writer_wrapper(c_file, c_int(my_num))
fp.close()
...

Related

Assign memory blob to py-torch output tensor (C++ API)

I am training a linear model using py-torch and I am saving it to a file with the "save" function call. I have another code that loads the model in C++ and performs inference.
I would like to instruct the Torch CPP Library to use a specific memory blob at the final output tensor. Is this even possible? If yes, how? Below you can see a small example of what I am trying to achieve.
#include <iostream>
#include <memory>
#include <torch/script.h>
int main(int argc, const char* argv[]) {
if (argc != 3) {
std::cerr << "usage: example-app <path-to-exported-script-module>\n";
return -1;
}
long numElements = (1024*1024)/sizeof(float) * atoi(argv[2]);
float *a = new float[numElements];
float *b = new float[numElements];
float *c = new float[numElements*4];
for (int i = 0; i < numElements; i++){
a[i] = i;
b[i] = -i;
}
//auto options = torch::TensorOptions().dtype(torch::kFloat64);
at::Tensor a_t = torch::from_blob((float*) a, {numElements,1});
at::Tensor b_t = torch::from_blob((float*) b, {numElements,1});
at::Tensor out = torch::from_blob((float*) c, {numElements,4});
at::Tensor c_t = at::cat({a_t,b_t}, 1);
at::Tensor d_t = at::reshape(c_t, {numElements,2});
torch::jit::script::Module module;
try {
module = torch::jit::load(argv[1]);
}
catch (const c10::Error& e) {
return -1;
}
out = module.forward({d_t}).toTensor();
std::cout<< out.sizes() << "\n";
delete [] a;
delete [] b;
delete [] c;
return 0;
}
So, I am allocating memory into "c" and then I am casting creating a tensor out of this memory. I store this memory into a tensor named "out". I load the model when I call the forward method. I observe that the resulted data are copied/moved into the "out" tensor. However, I would like to instruct Torch to directly store into "out" memory. Is this possible?
Somewhere in libtorch source code (I don' remember where, I'll try to find the file), there is an operator which is something like below (notice the last &&)
torch::tensor& operator=(torch::Tensor rhs) &&;
and which does what you need if I remember correctly. Basically torch assumes that if you allocate a tensor rhs to an rvalue reference tensor, then you actually mean to copy rhs into the underlying storage.
So in your case, that would be
std::move(out) = module.forward({d_t}).toTensor();
or
torch::from_blob((float*) c, {numElements,4}) = module.forward({d_t}).toTensor();

Scons checking for compiler option

I want to check in Scons that my compiler support some option (for example
-fcilkplus). The only way I manage to do it is the following sequence of
operations:
env.Prepend(CXXFLAGS = ['-fcilkplus'], LIBS = ['cilkrts'])
Then I launch my custom checker:
def CheckCilkPlusCompiler(context):
test = """
#include <cilk/cilk.h>
#include <assert.h>
int fib(int n) {
if (n < 2) return n;
int a = cilk_spawn fib(n-1);
int b = fib(n-2);
cilk_sync;
return a + b;
}
int main() {
int result = fib(30);
assert(result == 832040);
return 0;
}
"""
context.Message('Checking Cilk++ compiler ... ')
result = context.TryRun(test, '.cpp')
context.Result(result[0])
return result[0]
Now if it fails, I have to remove the two options extra flags -fcilkplus
cilkrts from the environment variables. Is there a better way to do that ?
The problem is that I can't manage to access to the env from the context and
therefore I can't make a clone of it.
You can use check the availability of a library with SCons as follows:
env = Environment()
conf = Configure(env)
if not conf.CheckLib('cilkrts'):
print 'Did not find libcilkrts.a, exiting!'
Exit(1)
else:
env.Prepend(CXXFLAGS = ['-fcilkplus'], LIBS = ['cilkrts'])
env = conf.Finish()
You could also check the availability of a header as follows:
env = Environment()
conf = Configure(env)
if conf.CheckCHeader('cilk/cilk.h'):
env.Prepend(CXXFLAGS = ['-fcilkplus'], LIBS = ['cilkrts'])
env = conf.Finish()
Update:
I just realized, you can access the environment on the Configure object as follows:
conf.env.Append(...)

Does D have anything like Java's Scanner?

Is there a stream-parser in D like Java's scanner? Where you can just go nextInt() to fetch an int and nextLong() for a long, etc.
std.conv.parse is similar:
http://dlang.org/phobos/std_conv.html#parse
The example is a string, though it is also possible to use it with other character sources.
import std.conv;
import std.stdio;
void main() {
// a char source from the user
auto source = LockingTextReader(stdin);
int a = parse!int(source); // use it with parse
writeln("you wrote ", a);
// munch only works on actual strings so we have to advance
// this manually
for(; !source.empty; source.popFront()) {
auto ch = source.front;
if(ch != ' ' && ch != '\n')
break;
}
int b = parse!int(source);
writeln("then you wrote ", b);
}
$ ./test56
12 23
you wrote 12
then you wrote 23

Weird define in C++ preprocessor

I've come across this
#define DsHook(a,b,c) if (!c##_) { INT_PTR* p=b+*(INT_PTR**)a; VirtualProtect(&c##_,4,PAGE_EXECUTE_READWRITE,&no); *(INT_PTR*)&c##_=*p; VirtualProtect(p,4,PAGE_EXECUTE_READWRITE,&no); *p=(INT_PTR)c; }
and everything is clear except the "c##_" word, what does that mean?
It means to "glue" together, so c and _ get "glued together" to form c_. This glueing happens after argument replacement in the macro. See my example:
#define glue(a,b) a##_##b
const char *hello_world = "Hello, World!";
int main(int arg, char *argv[]) {
printf("%s\n", glue(hello,world)); // prints Hello, World!
return 0;
}
It is called a token-pasting operator. Example:
// preprocessor_token_pasting.cpp
#include <stdio.h>
#define paster( n ) printf( "token" #n " = %d", token##n )
int token9 = 9;
int main()
{
paster(9);
}
Output
token9 = 9
That's concatenation that appends an underscore to the name passed as c. So when you use
DsHook(a,b,Something)
that part turns into
if (!Something_)
After the preprocessor, your macro will be expanded as:
if (!c_) { INT_PTR* p=b+*(INT_PTR**)a; VirtualProtect(&c_,4,PAGE_EXECUTE_READWRITE,&no); *(INT_PTR*)&c_=*p; VirtualProtect(p,4,PAGE_EXECUTE_READWRITE,&no); *p=(INT_PTR)c; }
The ## directive concatenates the value of c which you pass as a macro parameter to _
Simple one:
#define Check(a) if(c##x == 0) { }
At call site:
int varx; // Note the x
Check(var);
Would expand as:
if(varx == 0) { }
It is called Token Concatenation and it is used to concatenate tokens during the preprocessing
For example the following code will print out the values of the values of c, c_, c_spam:
#include<stdio.h>
#define DsHook(a,b,c) if (!c##_) \
{printf("c=%d c_ = %d and c_spam = %d\n",\
c, c##_,c##_spam);}
int main(){
int a,b,c=3;
int c_ = 0, c_spam = 4;
DsHook(a,b,c);
return 0;
}
Output:
c=3 c_ = 0 and c_spam = 4

Find Unique Characters in a File

I have a file with 450,000+ rows of entries. Each entry is about 7 characters in length. What I want to know is the unique characters of this file.
For instance, if my file were the following;
Entry
-----
Yabba
Dabba
Doo
Then the result would be
Unique characters: {abdoy}
Notice I don't care about case and don't need to order the results. Something tells me this is very easy for the Linux folks to solve.
Update
I'm looking for a very fast solution. I really don't want to have to create code to loop over each entry, loop through each character...and so on. I'm looking for a nice script solution.
Update 2
By Fast, I mean fast to implement...not necessarily fast to run.
BASH shell script version (no sed/awk):
while read -n 1 char; do echo "$char"; done < entry.txt | tr [A-Z] [a-z] | sort -u
UPDATE: Just for the heck of it, since I was bored and still thinking about this problem, here's a C++ version using set. If run time is important this would be my recommended option, since the C++ version takes slightly more than half a second to process a file with 450,000+ entries.
#include <iostream>
#include <set>
int main() {
std::set<char> seen_chars;
std::set<char>::const_iterator iter;
char ch;
/* ignore whitespace and case */
while ( std::cin.get(ch) ) {
if (! isspace(ch) ) {
seen_chars.insert(tolower(ch));
}
}
for( iter = seen_chars.begin(); iter != seen_chars.end(); ++iter ) {
std::cout << *iter << std::endl;
}
return 0;
}
Note that I'm ignoring whitespace and it's case insensitive as requested.
For a 450,000+ entry file (chars.txt), here's a sample run time:
[user#host]$ g++ -o unique_chars unique_chars.cpp
[user#host]$ time ./unique_chars < chars.txt
a
b
d
o
y
real 0m0.638s
user 0m0.612s
sys 0m0.017s
As requested, a pure shell-script "solution":
sed -e "s/./\0\n/g" inputfile | sort -u
It's not nice, it's not fast and the output is not exactly as specified, but it should work ... mostly.
For even more ridiculousness, I present the version that dumps the output on one line:
sed -e "s/./\0\n/g" inputfile | sort -u | while read c; do echo -n "$c" ; done
Use a set data structure. Most programming languages / standard libraries come with one flavour or another. If they don't, use a hash table (or generally, dictionary) implementation and just omit the value field. Use your characters as keys. These data structures generally filter out duplicate entries (hence the name set, from its mathematical usage: sets don't have a particular order and only unique values).
Quick and dirty C program that's blazingly fast:
#include <stdio.h>
int main(void)
{
int chars[256] = {0}, c;
while((c = getchar()) != EOF)
chars[c] = 1;
for(c = 32; c < 127; c++) // printable chars only
{
if(chars[c])
putchar(c);
}
putchar('\n');
return 0;
}
Compile it, then do
cat file | ./a.out
To get a list of the unique printable characters in file.
Python w/sets (quick and dirty)
s = open("data.txt", "r").read()
print "Unique Characters: {%s}" % ''.join(set(s))
Python w/sets (with nicer output)
import re
text = open("data.txt", "r").read().lower()
unique = re.sub('\W, '', ''.join(set(text))) # Ignore non-alphanumeric
print "Unique Characters: {%s}" % unique
Here's a PowerShell example:
gc file.txt | select -Skip 2 | % { $_.ToCharArray() } | sort -CaseSensitive -Unique
which produces:
D
Y
a
b
o
I like that it's easy to read.
EDIT: Here's a faster version:
$letters = #{} ; gc file.txt | select -Skip 2 | % { $_.ToCharArray() } | % { $letters[$_] = $true } ; $letters.Keys
A very fast solution would be to make a small C program that reads its standard input, does the aggregation and spits out the result.
Why the arbitrary limitation that you need a "script" that does it?
What exactly is a script anyway?
Would Python do?
If so, then this is one solution:
import sys;
s = set([]);
while True:
line = sys.stdin.readline();
if not line:
break;
line = line.rstrip();
for c in line.lower():
s.add(c);
print("".join(sorted(s)));
Algorithm:
Slurp the file into memory.
Create an array of unsigned ints, initialized to zero.
Iterate though the in memory file, using each byte as a subscript into the array.
increment that array element.
Discard the in memory file
Iterate the array of unsigned int
if the count is not zero,
display the character, and its corresponding count.
cat yourfile |
perl -e 'while(<>){chomp;$k{$_}++ for split(//, lc $_)}print keys %k,"\n";'
Alternative solution using bash:
sed "s/./\l\0\n/g" inputfile | sort -u | grep -vc ^$
EDIT Sorry, I actually misread the question. The above code counts the unique characters. Just omitting the c switch at the end obviously does the trick but then, this solution has no real advantage to saua's (especially since he now uses the same sed pattern instead of explicit captures).
While not an script this java program will do the work. It's easy to understand an fast ( to run )
import java.util.*;
import java.io.*;
public class Unique {
public static void main( String [] args ) throws IOException {
int c = 0;
Set s = new TreeSet();
while( ( c = System.in.read() ) > 0 ) {
s.add( Character.toLowerCase((char)c));
}
System.out.println( "Unique characters:" + s );
}
}
You'll invoke it like this:
type yourFile | java Unique
or
cat yourFile | java Unique
For instance, the unique characters in the HTML of this question are:
Unique characters:[ , , , , !, ", #, $, %, &, ', (, ), +, ,, -, ., /, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, :, ;, <, =, >, ?, #, [, \, ], ^, _, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y, z, {, |, }]
Print unique characters (ASCII and Unicode UTF-8)
import codecs
file = codecs.open('my_file_name', encoding='utf-8')
# Runtime: O(1)
letters = set()
# Runtime: O(n^2)
for line in file:
for character in line:
letters.add(character)
# Runtime: O(n)
letter_str = ''.join(letters)
print(letter_str)
Save as unique.py, and run as python unique.py.
in c++ i would first loop through the letters in the alphabet then run a strchr() on each with the file as a string. this will tell you if that letter exists, then just add it to the list.
Try this file with JSDB Javascript (includes the javascript engine in the Firefox browser):
var seenAlreadyMap={};
var seenAlreadyArray=[];
while (!system.stdin.eof)
{
var L = system.stdin.readLine();
for (var i = L.length; i-- > 0; )
{
var c = L[i].toLowerCase();
if (!(c in seenAlreadyMap))
{
seenAlreadyMap[c] = true;
seenAlreadyArray.push(c);
}
}
}
system.stdout.writeln(seenAlreadyArray.sort().join(''));
Python using a dictionary. I don't know why people are so tied to sets or lists to hold stuff. Granted a set is probably more efficient than a dictionary. However both are supposed to take constant time to access items. And both run circles around a list where for each character you search the list to see if the character is already in the list or not. Also Lists and Dictionaries are built in Python datatatypes that everyone should be using all the time. So even if set doesn't come to mind, dictionary should.
file = open('location.txt', 'r')
letters = {}
for line in file:
if line == "":
break
for character in line.strip():
if character not in letters:
letters[character] = True
file.close()
print "Unique Characters: {" + "".join(letters.keys()) + "}"
A C solution. Admittedly it is not the fastest to code solution in the world. But since it is already coded and can be cut and pasted, I think it counts as "fast to implement" for the poster :) I didn't actually see any C solutions so I wanted to post one for the pure sadistic pleasure :)
#include<stdio.h>
#define CHARSINSET 256
#define FILENAME "location.txt"
char buf[CHARSINSET + 1];
char *getUniqueCharacters(int *charactersInFile) {
int x;
char *bufptr = buf;
for (x = 0; x< CHARSINSET;x++) {
if (charactersInFile[x] > 0)
*bufptr++ = (char)x;
}
bufptr = '\0';
return buf;
}
int main() {
FILE *fp;
char c;
int *charactersInFile = calloc(sizeof(int), CHARSINSET);
if (NULL == (fp = fopen(FILENAME, "rt"))) {
printf ("File not found.\n");
return 1;
}
while(1) {
c = getc(fp);
if (c == EOF) {
break;
}
if (c != '\n' && c != '\r')
charactersInFile[c]++;
}
fclose(fp);
printf("Unique characters: {%s}\n", getUniqueCharacters(charactersInFile));
return 0;
}
Quick and dirty solution using grep (assuming the file name is "file"):
for char in a b c d e f g h i j k l m n o p q r s t u v w x y z; do
if [ ! -z "`grep -li $char file`" ]; then
echo -n $char;
fi;
done;
echo
I could have made it a one-liner but just want to make it easier to read.
(EDIT: forgot the -i switch to grep)
Well my friend, I think this is what you had in mind....At least this is the python version!!!
f = open("location.txt", "r") # open file
ll = sorted(list(f.read().lower())) #Read file into memory, split into individual characters, sort list
ll = [val for idx, val in enumerate(ll) if (idx == 0 or val != ll[idx-1])] # eliminate duplicates
f.close()
print "Unique Characters: {%s}" % "".join(ll) #print list of characters, carriage return will throw in a return
It does not iterate through each character, it is relatively short as well. You wouldn't want to open a 500 MB file with it (depending upon your RAM) but for shorter files it is fun :)
I also have to add my final attack!!!! Admittedly I eliminated two lines by using standard input instead of a file, I also reduced the active code from 3 lines to 2. Basically if I replaced ll in the print line with the expression from the line above it, I could have had 1 line of active code and one line of imports.....Anyway now we are having fun :)
import itertools, sys
# read standard input into memory, split into characters, eliminate duplicates
ll = map(lambda x:x[0], itertools.groupby(sorted(list(sys.stdin.read().lower()))))
print "Unique Characters: {%s}" % "".join(ll) #print list of characters, carriage return will throw in a return
This answer above mentioned using a dictionary.
If so, the code presented there can be streamlined a bit, since the Python documentation states:
It is best to think of a dictionary as
an unordered set of key: value pairs,
with the requirement that the keys are
unique (within one dictionary).... If
you store using a key that is already
in use, the old value associated with
that key is forgotten.
Therefore, this line of the code can be removed, since the dictionary keys will always be unique anyway:
if character not in letters:
And that should make it a little faster.
Where C:/data.txt contains 454,863 rows of seven random alphabetic characters, the following code
using System;
using System.IO;
using System.Collections;
using System.Diagnostics;
namespace ConsoleApplication {
class Program {
static void Main(string[] args) {
FileInfo fileInfo = new FileInfo(#"C:/data.txt");
Console.WriteLine(fileInfo.Length);
Stopwatch sw = new Stopwatch();
sw.Start();
Hashtable table = new Hashtable();
StreamReader sr = new StreamReader(#"C:/data.txt");
while (!sr.EndOfStream) {
char c = Char.ToLower((char)sr.Read());
if (!table.Contains(c)) {
table.Add(c, null);
}
}
sr.Close();
foreach (char c in table.Keys) {
Console.Write(c);
}
Console.WriteLine();
sw.Stop();
Console.WriteLine(sw.ElapsedMilliseconds);
}
}
}
produces output
4093767
mytojevqlgbxsnidhzupkfawr
c
889
Press any key to continue . . .
The first line of output tells you the number of bytes in C:/data.txt (454,863 * (7 + 2) = 4,093,767 bytes). The next two lines of output are the unique characters in C:/data.txt (including a newline). The last line of output tells you the number of milliseconds the code took to execute on a 2.80 GHz Pentium 4.
s=open("text.txt","r").read()
l= len(s)
unique ={}
for i in range(l):
if unique.has_key(s[i]):
unique[s[i]]=unique[s[i]]+1
else:
unique[s[i]]=1
print unique
Python without using a set.
file = open('location', 'r')
letters = []
for line in file:
for character in line:
if character not in letters:
letters.append(character)
print(letters)
Old question, I know, but here's a fast solution, meaning it runs fast, and it's probably also pretty fast to code if you know how to copy/paste ;)
BACKGROUND
I had a huge csv file (12 GB, 1.34 million lines, 12.72 billion characters) that I was loading into postgres that was failing because it had some "bad" characters in it, so naturally I was trying to find a character not in that file that I could use as a quote character.
1. First try: Jay's C++ solution
I started with #jay's C++ answer:
(Note: all of these code examples were compiled with g++ -O2 uniqchars.cpp -o uniqchars)
#include <iostream>
#include <set>
int main() {
std::set<char> seen_chars;
std::set<char>::const_iterator iter;
char ch;
/* ignore whitespace and case */
while ( std::cin.get(ch) ) {
if (! isspace(ch) ) {
seen_chars.insert(tolower(ch));
}
}
for( iter = seen_chars.begin(); iter != seen_chars.end(); ++iter ) {
std::cout << *iter << std::endl;
}
return 0;
}
Timing for this one:
real 10m55.026s
user 10m51.691s
sys 0m3.329s
2. Read entire file at once
I figured it'd be more efficient to read in the entire file into memory at once, rather than all those calls to cin.get(). This reduced the run time by more than half.
(I also added a filename as a command line argument, and made it print out the characters separated by spaces instead of newlines).
#include <set>
#include <string>
#include <iostream>
#include <fstream>
#include <iterator>
int main(int argc, char **argv) {
std::set<char> seen_chars;
std::set<char>::const_iterator iter;
std::ifstream ifs(argv[1]);
ifs.seekg(0, std::ios::end);
size_t size = ifs.tellg();
fprintf(stderr, "Size of file: %lu\n", size);
std::string str(size, ' ');
ifs.seekg(0);
ifs.read(&str[0], size);
/* ignore whitespace and case */
for (char& ch : str) {
if (!isspace(ch)) {
seen_chars.insert(tolower(ch));
}
}
for(iter = seen_chars.begin(); iter != seen_chars.end(); ++iter) {
std::cout << *iter << " ";
}
std::cout << std::endl;
return 0;
}
Timing for this one:
real 4m41.910s
user 3m32.014s
sys 0m17.858s
3. Remove isspace() check and tolower()
Besides the set insert, isspace() and tolower() are the only things happening in the for loop, so I figured I'd remove them. It shaved off another 1.5 minutes.
#include <set>
#include <string>
#include <iostream>
#include <fstream>
#include <iterator>
int main(int argc, char **argv) {
std::set<char> seen_chars;
std::set<char>::const_iterator iter;
std::ifstream ifs(argv[1]);
ifs.seekg(0, std::ios::end);
size_t size = ifs.tellg();
fprintf(stderr, "Size of file: %lu\n", size);
std::string str(size, ' ');
ifs.seekg(0);
ifs.read(&str[0], size);
for (char& ch : str) {
// removed isspace() and tolower()
seen_chars.insert(ch);
}
for(iter = seen_chars.begin(); iter != seen_chars.end(); ++iter) {
std::cout << *iter << " ";
}
std::cout << std::endl;
return 0;
}
Timing for final version:
real 3m12.397s
user 2m58.771s
sys 0m13.624s
The simple solution from #Triptych helped me already (my input was a file of 124 MB in size, so this approach to read the entire contents into memory still worked).
However, I had a problem with encoding, python didn't interpret the UTF8 encoded input correctly. So here's a slightly modified version which works for UTF8 encoded files (and also sorts the collected characters in the output):
import io
with io.open("my-file.csv",'r',encoding='utf8') as f:
text = f.read()
print "Unique Characters: {%s}" % ''.join(sorted(set(text)))

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