Reading binary files in Cython
I am attempting to read a binary file in Cython. Previously this was working in Python, but I am looking to speed up the process. This code below was written as a familiarisation and logic check before writing the complete module. Once this section is complete the code will be expanded to read in multiple 400 Mb files and process.
A function was created that opens the file, reads in a number of data point and returns them to an array.
from libc.stdlib cimport malloc, free
from libc.stdio cimport fopen, fclose, FILE, fscanf, fread
def readin_binary(filename, int number_of_points):
"""
Test reading in a file and returning data
"""
header_bytes = <unsigned char*>malloc(number_of_points)
filename_byte_string = filename.encode("UTF-8")
cdef FILE *in_binary_file
in_binary_file = fopen(filename_byte_string, 'rb')
if in_binary_file is NULL:
print("file not found")
else:
print("Read file {}".format(filename))
fread(&header_bytes, 1, number_of_points, in_binary_file)
fclose(in_binary_file)
return header_bytes
print(hDVS.readin_binary(filename, 10))
The code compiles.
When the code is run the following error occurs:
Python has stopped working error
I've been playing with this for a few days now. I think there is a simple error but I can not see it. Any ideas?
cython binaryfiles
asked Nov 22 '18 at 16:18
Christopher BridgeChristopher Bridge
42
|
show 4 more comments
I am attempting to read a binary file in Cython. Previously this was working in Python, but I am looking to speed up the process. This code below was written as a familiarisation and logic check before writing the complete module. Once this section is complete the code will be expanded to read in multiple 400 Mb files and process.
A function was created that opens the file, reads in a number of data point and returns them to an array.
from libc.stdlib cimport malloc, free
from libc.stdio cimport fopen, fclose, FILE, fscanf, fread
def readin_binary(filename, int number_of_points):
"""
Test reading in a file and returning data
"""
header_bytes = <unsigned char*>malloc(number_of_points)
filename_byte_string = filename.encode("UTF-8")
cdef FILE *in_binary_file
in_binary_file = fopen(filename_byte_string, 'rb')
if in_binary_file is NULL:
print("file not found")
else:
print("Read file {}".format(filename))
fread(&header_bytes, 1, number_of_points, in_binary_file)
fclose(in_binary_file)
return header_bytes
print(hDVS.readin_binary(filename, 10))
The code compiles.
When the code is run the following error occurs:
Python has stopped working error
I've been playing with this for a few days now. I think there is a simple error but I can not see it. Any ideas?
cython binaryfiles
asked Nov 22 '18 at 16:18
Christopher BridgeChristopher Bridge
42
1
That is a crash.
– Robert Harvey♦
Nov 22 '18 at 16:19
1
Have you determined yet if you're not already reading data as fast as the hard drive can provide it?
– Robert Harvey♦
Nov 22 '18 at 16:20
Did you inspect the generated C Code? Does it happen for any file? If yes could you provide a minimal file and Python code needed to reproduce the shown error?
– MSeifert
Nov 22 '18 at 16:22
Hi @MSeifert I have checked a few files and the result is the same. I had a look at the *.c file. I do not know where to start with this file - very complex. The attached zip file contains the test python module. In the test directory is test.py which calls the Cython function readin_binary().
– Christopher Bridge
Nov 22 '18 at 16:46
2
Assuming it is fread from c ( how to know without cimports?), it should be fread(header_bytes,....), without &.
– ead
Nov 22 '18 at 16:59
|
show 4 more comments
I am attempting to read a binary file in Cython. Previously this was working in Python, but I am looking to speed up the process. This code below was written as a familiarisation and logic check before writing the complete module. Once this section is complete the code will be expanded to read in multiple 400 Mb files and process.
A function was created that opens the file, reads in a number of data point and returns them to an array.
from libc.stdlib cimport malloc, free
from libc.stdio cimport fopen, fclose, FILE, fscanf, fread
def readin_binary(filename, int number_of_points):
"""
Test reading in a file and returning data
"""
header_bytes = <unsigned char*>malloc(number_of_points)
filename_byte_string = filename.encode("UTF-8")
cdef FILE *in_binary_file
in_binary_file = fopen(filename_byte_string, 'rb')
if in_binary_file is NULL:
print("file not found")
else:
print("Read file {}".format(filename))
fread(&header_bytes, 1, number_of_points, in_binary_file)
fclose(in_binary_file)
return header_bytes
print(hDVS.readin_binary(filename, 10))
The code compiles.
When the code is run the following error occurs:
Python has stopped working error
I've been playing with this for a few days now. I think there is a simple error but I can not see it. Any ideas?
cython binaryfiles
asked Nov 22 '18 at 16:18
Christopher BridgeChristopher Bridge
42
I am attempting to read a binary file in Cython. Previously this was working in Python, but I am looking to speed up the process. This code below was written as a familiarisation and logic check before writing the complete module. Once this section is complete the code will be expanded to read in multiple 400 Mb files and process.
A function was created that opens the file, reads in a number of data point and returns them to an array.
from libc.stdlib cimport malloc, free
from libc.stdio cimport fopen, fclose, FILE, fscanf, fread
def readin_binary(filename, int number_of_points):
"""
Test reading in a file and returning data
"""
header_bytes = <unsigned char*>malloc(number_of_points)
filename_byte_string = filename.encode("UTF-8")
cdef FILE *in_binary_file
in_binary_file = fopen(filename_byte_string, 'rb')
if in_binary_file is NULL:
print("file not found")
else:
print("Read file {}".format(filename))
fread(&header_bytes, 1, number_of_points, in_binary_file)
fclose(in_binary_file)
return header_bytes
print(hDVS.readin_binary(filename, 10))
The code compiles.
When the code is run the following error occurs:
Python has stopped working error
I've been playing with this for a few days now. I think there is a simple error but I can not see it. Any ideas?
cython binaryfiles
cython binaryfiles
asked Nov 22 '18 at 16:18
Christopher BridgeChristopher Bridge
42
asked Nov 22 '18 at 16:18
Christopher BridgeChristopher Bridge
42
edited Nov 22 '18 at 21:08
Christopher Bridge
asked Nov 22 '18 at 16:18
Christopher BridgeChristopher Bridge
42
asked Nov 22 '18 at 16:18
Christopher BridgeChristopher Bridge
42
asked Nov 22 '18 at 16:18
Christopher BridgeChristopher Bridge
42
42
1
That is a crash.
– Robert Harvey♦
Nov 22 '18 at 16:19
1
Have you determined yet if you're not already reading data as fast as the hard drive can provide it?
– Robert Harvey♦
Nov 22 '18 at 16:20
Did you inspect the generated C Code? Does it happen for any file? If yes could you provide a minimal file and Python code needed to reproduce the shown error?
– MSeifert
Nov 22 '18 at 16:22
Hi @MSeifert I have checked a few files and the result is the same. I had a look at the *.c file. I do not know where to start with this file - very complex. The attached zip file contains the test python module. In the test directory is test.py which calls the Cython function readin_binary().
– Christopher Bridge
Nov 22 '18 at 16:46
2
Assuming it is fread from c ( how to know without cimports?), it should be fread(header_bytes,....), without &.
– ead
Nov 22 '18 at 16:59
|
show 4 more comments
1
That is a crash.
– Robert Harvey♦
Nov 22 '18 at 16:19
1
Have you determined yet if you're not already reading data as fast as the hard drive can provide it?
– Robert Harvey♦
Nov 22 '18 at 16:20
Did you inspect the generated C Code? Does it happen for any file? If yes could you provide a minimal file and Python code needed to reproduce the shown error?
– MSeifert
Nov 22 '18 at 16:22
Hi @MSeifert I have checked a few files and the result is the same. I had a look at the *.c file. I do not know where to start with this file - very complex. The attached zip file contains the test python module. In the test directory is test.py which calls the Cython function readin_binary().
– Christopher Bridge
Nov 22 '18 at 16:46
2
Assuming it is fread from c ( how to know without cimports?), it should be fread(header_bytes,....), without &.
– ead
Nov 22 '18 at 16:59
1
1
That is a crash.
– Robert Harvey♦
Nov 22 '18 at 16:19
That is a crash.
– Robert Harvey♦
Nov 22 '18 at 16:19
1
1
Have you determined yet if you're not already reading data as fast as the hard drive can provide it?
– Robert Harvey♦
Nov 22 '18 at 16:20
Have you determined yet if you're not already reading data as fast as the hard drive can provide it?
– Robert Harvey♦
Nov 22 '18 at 16:20
Did you inspect the generated C Code? Does it happen for any file? If yes could you provide a minimal file and Python code needed to reproduce the shown error?
– MSeifert
Nov 22 '18 at 16:22
Did you inspect the generated C Code? Does it happen for any file? If yes could you provide a minimal file and Python code needed to reproduce the shown error?
– MSeifert
Nov 22 '18 at 16:22
Hi @MSeifert I have checked a few files and the result is the same. I had a look at the *.c file. I do not know where to start with this file - very complex. The attached zip file contains the test python module. In the test directory is test.py which calls the Cython function readin_binary().
– Christopher Bridge
Nov 22 '18 at 16:46
Hi @MSeifert I have checked a few files and the result is the same. I had a look at the *.c file. I do not know where to start with this file - very complex. The attached zip file contains the test python module. In the test directory is test.py which calls the Cython function readin_binary().
– Christopher Bridge
Nov 22 '18 at 16:46
2
2
Assuming it is fread from c ( how to know without cimports?), it should be fread(header_bytes,....), without &.
– ead
Nov 22 '18 at 16:59
Assuming it is fread from c ( how to know without cimports?), it should be fread(header_bytes,....), without &.
– ead
Nov 22 '18 at 16:59
|
show 4 more comments
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1
That is a crash.
– Robert Harvey♦
Nov 22 '18 at 16:19
1
Have you determined yet if you're not already reading data as fast as the hard drive can provide it?
– Robert Harvey♦
Nov 22 '18 at 16:20
Did you inspect the generated C Code? Does it happen for any file? If yes could you provide a minimal file and Python code needed to reproduce the shown error?
– MSeifert
Nov 22 '18 at 16:22
Hi @MSeifert I have checked a few files and the result is the same. I had a look at the *.c file. I do not know where to start with this file - very complex. The attached zip file contains the test python module. In the test directory is test.py which calls the Cython function readin_binary().
– Christopher Bridge
Nov 22 '18 at 16:46
2
Assuming it is fread from c ( how to know without cimports?), it should be fread(header_bytes,....), without &.
– ead
Nov 22 '18 at 16:59