How to read a text file containing NUL characters? - r

I have a file that contains NUL characters.
This file is generated by another program I have no control over, but I have to read it in order to get some crucial information.
Unfortunately, readChar() truncates the output with this warning:
In readChar("output.txt", 1e+05) :
truncating string with embedded nuls
Is there a way around this problem?

By convention, a text file cannot contain non-printable characters (including NUL). If a file contains such characters, it isn’t a text file — it’s a binary file.
R strictly1 adheres to this convention, and completely disallows NUL characters. You really need to read and treat the data as binary data. This means using readBin and the raw data type:
n = file.size(filename)
buffer = readBin(filename, 'raw', n = n)
# Unfortunately the above has a race condition, so check that the size hasn’t changed!
stopifnot(n == file.size(filename))
Now we can fix the buffer by removing embedded zero bytes. This assumes UTF-x or ASCII encoding! Other encodings might have embedded zero bytes that need to be interpreted!
buffer = buffer[buffer != 0L]
text = rawToChar(buffer)
1 Maybe too strictly …

Related

How to count nul values in R

I want to inspect a file before processing it in R.
It is possible, that my input file is broken and contains nul values, due to a software crash. So I want my script to have a look at the data before continuing the process.
If I do a read.csv(..., skipNul = TRUE), the nuls were skipped and the script doesn't stop. But this is bad, because I don't see the lack of data.
If I do a read.csv(..., skipNul = FALSE),the nuls were skipped anyway, and I just get a warning message.
I want to count the nuls inside the file. But how can I do this?
I tried to change the encoding, but nuls are never shown when printing the dataframe.
I think, I found a solution here:
Removing nul characters
I can read the raw data by DF <- readBin("Example.log", raw(), file.info("Example.log")$size).
The resulting vector contains all 1 byte char values. I just had to filter for the nuls and print the length: length(DF[DF == 0])

How to specify encoding while creating file?

I am using an R script to create and append a file. But I need the file to be saved in ANSI encoding,even though some characters are in Unicode format. How to ensure ANSI encoding?
newfile='\home\user\abc.ttl'
file.create(newfile)
text3 <- readLines('\home\user\init.ttl')
sprintf('readlines %d',length(text3))
for(k in 1:length(text3))
{
cat(text3[[k]],file=newfile,sep="\n",append=TRUE)
}
Encoding can be tricky, since you need to detect your encoding upon input, and then you need to convert it before writing. Here it sounds like your input file input.ttl is encoded as UTF-8, and you need it converted to ASCII. This means you are probably going to lose some non-translatable characters, since there may be no mapping from the UTF-8 characters to ASCII outside of the 128-bit lower range. (Within this range the mappings of UTF-8 to ASCII are the same.)
So here is how to do it. You will have to modify your code accordingly to test since you did not supply the elements needed for a reproducible example.
Make sure that your input file is actually UTF-8 and that you are reading it as UTF-8. You can do this by adding encoding = "UTF-8" to the third line of your code, as an argument to readLines(). Note that you may not be able to set the system locale to UTF-8 on a Windows platform, but the file will still be read as UTF-8, even though extended characters may not display properly.
Use iconv() to convert the text from UTF-8 to ASCII. iconv() is vectorised so it works on the whole set of text. You can do this using
text3 <- iconv(text3, "UTF-8", "ASCII", sub = "")
Note here that the sub = "" argument prevents the default behaviour of converting the entire character element to NA if it encounters any untranslatable characters. (These include the seemingly innocent but actually subtly evil things such as "smart quotes".)
Now when you write the file using cat() the output should be ASCII.

What is this "ÿþA"?

When I read in csv files to r the requesting dataframe has very different dimensions than I see when I open the file in excel or notepad and the column heading is labeled as "ÿþA". What does this mean?
thanks,
The file you are reading is using an UTF-16 or UTF-32 encoding (with a BOM), and the r read.csv function has not been informed correctly.
As Karsten suggests you should use the fileEncoding parameter to specify the correct encoding, which I suspect should be "UTF-16LE".
Here is what the R Studio documentation states about encoding:
Encoding
The encoding of the input/output stream of a connection can be specified by name in the same way as it would be given to iconv: see that help page for how to find out what encoding names are recognized on your platform. Additionally, "" and "native.enc" both mean the ‘native’ encoding, that is the internal encoding of the current locale and hence no translation is done.
Re-encoding only works for connections in text mode: reading from a connection with re-encoding specified in binary mode will read the stream of bytes, but mixing text and binary mode reads (e.g. mixing calls to readLines and readChar) is likely to lead to incorrect results.
The encodings "UCS-2LE" and "UTF-16LE" are treated specially, as they are appropriate values for Windows ‘Unicode’ text files. If the first two bytes are the Byte Order Mark 0xFFFE then these are removed as some implementations of iconv do not accept BOMs. Note that whereas most implementations will handle BOMs using encoding "UCS-2" and choose the appropriate byte order, some (including earlier versions of glibc) will not. There is a subtle distinction between "UTF-16" and "UCS-2" (see http://en.wikipedia.org/wiki/UTF-16/UCS-2: the use of surrogate pairs is very rare so "UCS-2LE" is an appropriate first choice.
As from R 3.0.0 the encoding "UTF-8-BOM" is accepted for reading and will remove a Byte Order Mark if present (which it often is for files and webpages generated by Microsoft applications). If it is required (it is not recommended) when writing it should be written explicitly, e.g. by writeChar("\ufeff", con, eos = NULL) or writeBin(as.raw(c(0xef, 0xbb, 0xff)), binary_con)
Requesting a conversion that is not supported is an error, reported when the connection is opened. Exactly what happens when the requested translation cannot be done for invalid input is in general undocumented. On output the result is likely to be that up to the error, with a warning. On input, it will most likely be all or some of the input up to the error.
It may be possible to deduce the current native encoding from Sys.getlocale("LC_CTYPE"), but not all OSes record it.
And here is what Wiki states on the BOM:
Byte order mark
The byte order mark (BOM) is a Unicode character used to signal the endianness (byte order) of a text file or stream. It is encoded at U+FEFF byte order mark (BOM). BOM use is optional, and, if used, should appear at the start of the text stream. Beyond its specific use as a byte-order indicator, the BOM character may also indicate which of the several Unicode representations the text is encoded in.1
Because Unicode can be encoded as 16-bit or 32-bit integers, a computer receiving these encodings from arbitrary sources needs to know which byte order the integers are encoded in. The BOM gives the producer of the text a way to describe the text stream's endianness to the consumer of the text without requiring some contract or metadata outside of the text stream itself. Once the receiving computer has consumed the text stream, it presumably processes the characters in its own native byte order and no longer needs the BOM. Hence the need for a BOM arises in the context of text interchange, rather than in normal text processing within a closed environment.

Regarding reading files which contain UTF-8 character

I have a csv file including chinese character saved with UTF-8.
项目 价格
电视 5000
The first row is header, the second row is data. In other words, it is one by two vector.
I read this the file as follows:
amatrix<-read.table("test.csv",encoding="UTF-8",sep=",",header=T,row.names=NULL,stringsAsFactors=FALSE)
However, the output including the unknown marks for the header, i.e.,X.U.FEFF
That is the byte order mark sometimes found in Unicode text files. I'm guessing you're on Windows, since that's the only popular OS where files can end up with them.
What you can do is read the file using readLines and remove the first two characters of the first line.
txt <- readLines("test.csv", encoding="UTF-8")
txt[1] <- substr(txt[1], 3, nchar(txt[1]))
amatrix <- read.csv(text=txt, ...)

Delimiting binary sequences

I need to be able to delimit a stream of binary data. I was thinking of using something like the ASCII EOT (End of Transmission) character to do this.
However I'm a bit concerned -- how can I know for sure that the particular binary sequence used for this (0b00000100) won't appear in my own binary sequences, thus giving a false positive on delimitation?
In other words, how is binary delimiting best handled?
EDIT: ...Without using a length header. Sorry guys, should have mentioned this before.
You've got five options:
Use a delimiter character that is unlikely to occur. This runs the risk of you guessing incorrectly. I don't recommend this approach.
Use a delimiter character and an escape sequence to include the delimiter. You may need to double the escape character, depending upon what makes for easier parsing. (Think of the C \0 to include an ASCII NUL in some content.)
Use a delimiter phrase that you can determine does not occur. (Think of the mime message boundaries.)
Prepend a length field of some sort, so you know to read the following N bytes as data. This has the downside of requiring you to know this length before writing the data, which is sometimes difficult or impossible.
Use something far more complicated, like ASN.1, to completely describe all your content for you. (I don't know if I'd actually recommend this unless you can make good use of it -- ASN.1 is awkward to use in the best of circumstances, but it does allow completely unambiguous binary data interpretation.)
Usually, you wrap your binary data in a well known format, for example with a fixed header that describes the subsequent data. If you are trying to find delimeters in an unknown stream of data, usually you need an escape sequence. For example, something like HDLC, where 0x7E is the frame delimeter. Data must be encoded such that if there is 0x7E inside the data, it is replaced with 0x7D followed by an XOR of the original data. 0x7D in the data stream is similarly escaped.
If the binary records can really contain any data, try adding a length before the data instead of a marker after the data. This is sometimes called a prefix length because the length comes before the data.
Otherwise, you'd have to escape the delimiter in the byte stream (and escape the escape sequence).
You can prepend the size of the binary data before it. If you are dealing with streamed data and don't know its size beforehand, you can divide it into chunks and have each chunk begin with size field.
If you set a maximum size for a chunk, you will end up with all but the last chunk the same length which will simplify random access should you require it.
As a space-efficient and fixed-overhead alternative to prepending your data with size fields and escaping the delimiter character, the escapeless encoding can be used to trim off that delimiter character, probably together with other characters that should have special meaning, from your data.
#sarnold's answer is excellent, and here I want to share some code to illustrate it.
First here is a wrong way to do it: using a \n delimiter. Don't do it! the binary data could contain \n, and it would be mixed up with the delimiters:
import os, random
with open('test', 'wb') as f:
for i in range(100): # create 100 binary sequences of random
length = random.randint(2, 100) # length (between 2 and 100)
f.write(os.urandom(length) + b'\n') # separated with the character b"\n"
with open('test', 'rb') as f:
for i, l in enumerate(f):
print(i, l) # oops we get 123 sequences! wrong!
...
121 b"L\xb1\xa6\xf3\x05b\xc9\x1f\x17\x94'\n"
122 b'\xa4\xf6\x9f\xa5\xbc\x91\xbf\x15\xdc}\xca\x90\x8a\xb3\x8c\xe2\x07\x96<\xeft\n'
Now the right way to do it (option #4 in sarnold's answer):
import os, random
with open('test', 'wb') as f:
for i in range(100):
length = random.randint(2, 100)
f.write(length.to_bytes(2, byteorder='little')) # prepend the data with the length of the next data chunk, packed in 2 bytes
f.write(os.urandom(length))
with open('test', 'rb') as f:
i = 0
while True:
l = f.read(2) # read the length of the next chunk
if l == b'': # end of file
break
length = int.from_bytes(l, byteorder='little')
s = f.read(length)
print(i, s)
i += 1
...
98 b"\xfa6\x15CU\x99\xc4\x9f\xbe\x9b\xe6\x1e\x13\x88X\x9a\xb2\xe8\xb7(K'\xf9+X\xc4"
99 b'\xaf\xb4\x98\xe2*HInHp\xd3OxUv\xf7\xa7\x93Qf^\xe1C\x94J)'

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