cpxSR2bnPUihaNxIFFA8Sc+8gUnWuJxJi8ywSW5ju0npWrFJHW2MSZAeMklcZ71IjrBySF2ci0gdecRI0vD/SM4ZF0m1ZSJJBY8bSZJl/0intaxIlQJBSPdY3EdBLM9Hp4wLSOK8Nki8L1pIoglxSAvNbkjHg0VIDlv7R6B2Y0elCqVGFWuVRgagAkdxHTdHELxRR9i2VkdyEUlHU84kRzTS2kalKFxG
This is a string from an XML file from my mass spectrometer. I am trying to write a program to load two such files, subtract one set of values from another, and write the results to a new file. According to the specification file for the .mzML format, the encoding of the numerical data is alleged to be base64. I can't convert this data string to anything legible using any of the many online base64 converter or using NotepaD++ and the MIME toolkit's base64 converter.
The string, in the context of the results file, looks like this:
<binaryDataArray encodedLength="224">
<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitAccession="MS:1000131" unitName="number of counts" unitCvRef="MS"/>
<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" />
<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
<binary>cpxSR2bnPUihaNxIFFA8Sc+8gUnWuJxJi8ywSW5ju0npWrFJHW2MSZAeMklcZ71IjrBySF2ci0gdecRI0vD/SM4ZF0m1ZSJJBY8bSZJl/0intaxIlQJBSPdY3EdBLM9Hp4wLSOK8Nki8L1pIoglxSAvNbkjHg0VIDlv7R6B2Y0elCqVGFWuVRgagAkdxHTdHELxRR9i2VkdyEUlHU84kRzTS2kalKFxG</binary>
I can't proceed until I can work out what format this encoding is meant to be!
Thanks in advance for any replies.
You can use this trivial program to convert it to plaintext:
#include <stdio.h>
int main(void)
{
float f;
while (fread(&f, 1, 4, stdin) == 4)
printf("%f\n", f);
}
I compiled this to "floatdecode" and used this command:
echo "cpxSR2bnPUihaNxIFFA8Sc+8gUnWuJxJi8ywSW5ju0npWrFJHW2MSZAeMklcZ71IjrBySF2ci0gdecRI0vD/SM4ZF0m1ZSJJBY8bSZJl/0intaxIlQJBSPdY3EdBLM9Hp4wLSOK8Nki8L1pIoglxSAvNbkjHg0VIDlv7R6B2Y0elCqVGFWuVRgagAkdxHTdHELxRR9i2VkdyEUlHU84kRzTS2kalKFxG" | base64 -d | ./floatdecode
Output is:
53916.445312
194461.593750
451397.031250
771329.250000
1062809.875000
1283866.750000
1448337.375000
1535085.750000
1452893.125000
1150371.625000
729577.000000
387898.875000
248514.218750
285922.906250
402376.906250
524166.562500
618908.875000
665179.312500
637168.312500
523052.562500
353709.218750
197642.328125
112817.929688
106072.507812
142898.609375
187123.531250
223422.937500
246822.531250
244532.171875
202255.109375
128694.109375
58230.625000
21125.322266
19125.541016
33440.023438
46877.441406
53692.062500
54966.843750
51473.445312
42190.324219
28009.101562
14090.161133
Yet another Java Base64 decode with options to uncompress should you need it.
Vendor spec indicated "32-bit float" = IEEE-754 and specified little-endian.
Schmidt's converter shows the bit pattern for IEEE-754.
One more Notepad++ step to look at the hex codes:
Notepad++ TextFX plugin (after the Base64 decode you already did)
select the text
TextFX > TextFX Convert > Convert text to Hex-32
lets you look at the hex codes:
"000000000 72 9C 52 47 66 E7 3D 48- ... 6E 63 BB 49 |rœRGfç=H¡hÜHP
Little-endian: 47529C72 converts (via Schmidt) as shown above by David.
You can access such data from mzML files in Python through pymzML, a python interface to mzML files.
http://pymzml.github.com/
Related
I run this code
cmd := exec.Command(sArg[0], sArg[1:]...)
d, err := cmd.Output()
if len(arg) == 0 {
return err
}
file.WriteString(string(d))
After running it, the string is printed well in the debugging console, but the character is broken in the file.
Original Output
HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\services\SharedAccess\Parameters\FirewallPolicy\StandardProfile
DisableNotifications REG_DWORD 0x0
EnableFirewall REG_DWORD 0x1
HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\services\SharedAccess\Parameters\FirewallPolicy\StandardProfile\Logging
Broken Output in File
How can characters be correctly written to a file?
If I take 0d, 0a, 48, 4b, 45, 59, 4b, 4c, 4f, 43, 41, 4c, 5f, 4d, 61 43, 48 and assume it's encoded using UTF-16-LE this will be displayed as 䭈奅䱋䍏䱁䵟䍡 which looks about the same as the first section of your screenshot. As such it appears to me that your program is saving the data correctly but the application you are using to view the file is incorrectly interpreting it as UTF-16-LE encoded.
It is possible that this is due to whatever you wrote to the file previously (you mention that this data is being appended to data written earlier). If the first two bytes are FF, FE this can be taken as a signal that the file is UTF-16-LE encoded but not all editors will recognise this).
If you open the file in a hex editor I expect that you will see the data as expected (i.e. 0d, 0a, 48,...).
I'm reading binary file http://snap.stanford.edu/data/amazon/productGraph/image_features/image_features.b
using pyspark.
import array
from io import StringIO
img_embedding_file = sc.binaryRecords("s3://bucket/image_features.b", 4106)
def mapper(features):
a = array.array('f')
a.frombytes(features)
return a.tolist()
def byte_mapper(bytes):
return str(bytes)
decoded_embeddings = img_embedding_file.map(lambda x: [byte_mapper(x[:10]), mapper(x[10:])])
When just product_id is selected from the rdd using
decoded_embeddings = img_embedding_file.map(lambda x: [byte_mapper(x[:10]), mapper(x[10:])])
The output for product_id is
["b'1582480311'", "b'\\x00\\x00\\x00\\x00\\x88c-?\\xeb\\xe2'", "b'7#\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00'", "b'\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00'", "b'\\xec/\\x0b?\\x00\\x00\\x00\\x00K\\xea'", "b'\\x00\\x00c\\x7f\\xd9?\\x00\\x00\\x00\\x00'", "b'L\\xa6\\n>\\x00\\x00\\x00\\x00\\xfe\\xd4'", "b'\\x00\\x00\\x00\\x00\\x00\\x00\\xe5\\xd0\\xa2='", "b'\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00'", "b'\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00'"]
The file is hosted on s3.
The file in each row has first 10 bytes for product_id next 4096 bytes as image_features
I'm able to extract all the 4096 image features but facing issue when reading the first 10 bytes and converting it into proper readable format.
EDIT:
Finally, the problem comes from the recordLength. It's not 4096 + 10 but 4096*4 + 10. Chaging to :
img_embedding_file = sc.binaryRecords("s3://bucket/image_features.b", 16394)
Should work.
Actually you can find this in the provided code from the web site you downloaded the binary file:
for i in range(4096):
feature.append(struct.unpack('f', f.read(4))) # <-- so 4096 * 4
Old answer:
I think the issue comes from your byte_mapper function.
That's not the correct way to convert bytes to string. You should be using decode:
bytes = b'1582480311'
print(str(bytes))
# output: "b'1582480311'"
print(bytes.decode("utf-8"))
# output: '1582480311'
If you're getting the error:
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x88 in position 4: invalid start byte
That means product_id string contains non-utf8 characters. If you don't know the input encoding, it's difficult to convert into strings.
However, you may want to ignore those characters by adding option ignore to decode function:
bytes.decode("utf-8", "ignore")
I'm building my custom wrapper around wmic using node.js and I have problems parsing it's output. Not a problem, but I just don't know why this happens.
I thought line endings are either \r or \r\n and decided to look on it
Here's a demo piece of code:
exec('wmic process', {maxBuffer :1000*1024}, function (err, stdout, stderr){
let location =stdout.indexOf('\n')-6;
let region =stdout.substr(location, 10);
console.log(region);
let buf = new Buffer(stdout);
let buf2 = new Buffer(30);
buf.copy(buf2, 0, location, location+30);
console.log(buf2);
});
I looked at region and saw this:
For some reason there are two \rs instead of one!
Output of console.log(buf2) also shows this:
<Buffer 6f 75 6e 74 20 20 0d 0d 0a 53 79 73 ...
^^ ^^ ^^
I was ready to split lines by \r\r\n when I decided to pipe its output to text file and look through a hex editor:
wmic process > wmic.txt
What? Where are two \rs?
I have two questions:
Where does Node get second \r from? I tried to find some info, but Google is kind of heavy on queries such as \r\r\n, this is the closest I could get, I'm not sure if it's related
Why hex editor shows 16bit encoding and Node doesn't? I suppose I should've specified encoding in exec() options but I don't know which one. chcp shows 437th codepage, but I kind of want it to work in other codepages as well.
When i write '你' in agend and save it as test-unicode.txt in unicode mode,open it with xxd g:\\test-unicode.txt ,i got :
0000000: fffe 604f ..`O
1.fffe stand for little endian
2.the unicode of 你 is \x4f\x60
I want to write the 你 as 604f or 4f60 in the file.
output=open("g://test-unicode.txt","wb")
str1="你"
output.write(str1)
output.close()
error:
TypeError: 'str' does not support the buffer interface
When i change it into the following ,there is no errror.
output=open("g://test-unicode.txt","wb")
str1="你"
output.write(str1.encode())
output.close()
when open it with xxd g:\\test-unicode.txt ,i got :
0000000: e4bd a0 ...
How can i write 604f or 4f60 into my file the same way as microsoft aengda do(save as unicode format)?
"Unicode" as an encoding is actually UTF-16LE.
with open("g:/test-unicode.txt", "w", encoding="utf-16le") as output:
output.write(str1)
I'm trying to use the md5 digest of an attachment I put on the CouchDB, but I can't understand what format it uses.
{
"_id":"ef467479af422db0c388fa00b3000d40",
"_rev":"3-6d1015e7d25103180817136eefa9f942",
"_attachments":{
"foo":{
"content_type":"application/octet-stream",
"revpos":2,
"digest":"md5-yDbs1scfYdqqLpxyFb1gFw==",
"length":1952913,"stub":true }
}
}
That md5 is not hexadecimal but still it is ASCII, how do I use it?
The part of the digest after the md5- prefix looks like it's in Base-64 format.
If parsing in Javascript, the atob function can turn it back into binary data.
Assuming the above is correct then the hexadecimal equivalent is:
c8 36 ec d6 c7 1f 61 da aa 2e 9c 72 15 bd 60 17
For anyone looking to work with the digest format used by couchdb using nodejs you can turn the base64 encoded digest into a "normal" hex string by removing the "md5-" prefix and then do:
new Buffer('yDbs1scfYdqqLpxyFb1gFw==', 'base64').toString('hex')
To go the other way and create the digest string from a hex value:
new Buffer('c836ecd6c71f61daaa2e9c7215bd6017', 'hex').toString('base64')