How to read a binary file with TCL - input

So I have a function I'm using to read data from a file. It works fine if the file is plain text, but when I try to read a binary file, like a png, it returns a different text (diff confirms that). I opened a hex editor to see what was wrong and found out it is putting some c2 bytes along with the file (I don't know if the position is random or if there are other bytes except this c2 one).
This is my function. I just want it to read and save to a variable.
proc read_file {path} {
set channel [open $path r]
fconfigure $channel -translation binary
set return_string "[read $channel]"
close $channel
return "$return_string"
}
To actually print, I'm doing this:
puts -nonewline [read_file file.png]

When you open a file, it defaults to being in text mode . In text mode (which is really a combination of options) the IO layer translates characters from whatever encoding they are in into Tcl's internal encoding, and does the reverse operation on output. The default encoding scheme is platform specific, but in your case it sounds like it is UTF-8. (Tcl uses a complex internal system of encodings; it doesn't expose those to the outside world.)
By contrast, when you put the channel into binary mode, the bytes on the outside are directly mapped to characters in the range 0-255 (and vice versa on output). You get a perfect copy, provided you put both input and output channels in binary mode. (There are other optimisations for binary mode, but they don't matter here.)
When you only put one of the channels in binary mode, you get what looks like corruption. It isn't random though. In particular, when the input is binary but the output is UTF-8, input bytes in the range 128-255 get converted into multiple output bytes, where the first of those bytes is in the sort of range you observed. There are other combinations that mess things up; the whole range of problems is collectively known as mojibake.
tl;dr Don't mix up binary and text data unless you're very careful. The results of getting it wrong are "surprising".

Related

GNU Radio text file sink

I'm trying to teach myself basics of GNU Radio and DSP. I created a flowchart in GNU Radio Companion that takes a vector that is the binary representation of a single character (the character "1" as "00110001"), modulates, demodulates, and writes to a file sink.
The scope sink after demodulation looks like the values are returned (see below; appears to be correct pattern of 0s and 1s), but the file sink, although its size is 19 bytes, appears empty, or at least is not returning the correct values (I've looked at it in ASCII and Hex text editors). I assumed the single character transferred would result in 1 byte (or 8 bits) -- not 19 bytes. Changing some of the settings in the Polyphase Sync and adding a Repack Bits block after the binary slicer results in some characters in the output file, but never the right character.
My questions are:
Can GNU Radio take a single character, modulate/demodulate it, and return the same character?
Are there errors in my flowchart?
I'd appreciate any insights or suggestions, thank you.

Optimize checking gzcompressed file for changes

I have function which stores data in gzcompressed files, like
function savedata($fileName,&$data){
file_put_contents($filename,gzcompress($data));
}
I want to optimize and don't save if the data is same as in already stored gzcompressed file.
I can open the whole file, uncompress it and compare with the $data, but I think there should be some other way.Probably gz-d data has some crc or something like that, so I can just compress the data, fetch the crc from it and compare it to the crc in already existing file or something like that.
So I just want to omtimize checking the file and $data for changes to make it quicker.
gzcompress() in PHP compresses to the zlib format, not the gzip format.
Each zlib stream ends with a four-byte check value, though not a CRC. You can compare those to see if two streams are different. However if the two check values are the same, you cannot conclude that the streams are the same.

Encoding of PDF dictionaries

I need to know the encoding of the values of PDF dictionaries (not the text displayed to the user but the "code behind").
I plan not to use any library for that.
Where can I find it?
the encoding of the values of PDF dictionaries
Values of PDF dictionaries are PDF objects.
You should take a look at the PDF specification ISO 32000-1, in particular chapter 7 Syntax, to find out about PDF objects. You will find:
The tokens that delimit objects and that describe the structure of a PDF file shall use the ASCII character
set. In addition all the reserved words and the names used as keys in PDF standard dictionaries and
certain types of arrays shall be defined using the ASCII character set.
Thus, most of the time you have to deal with ASCII values.
The situation is tricky with strings, though, because there are several types of strings which use the same string syntax options, so you have to interpret their contents according to their context.
Table 35 – String Object Types
Type Description
text string Shall be used for human-readable text, such as text
annotations, bookmark names, article names, and
document information. These strings shall be encoded
using either PDFDocEncoding or UTF-16BE with a
leading byte-order marker.
This type is described in 7.9.2.2, "Text String Type."
PDFDocEncoded string Shall be used for characters and glyphs that are
represented in a single byte, using PDFDocEncoding.
This type is described in 7.9.2.3, "PDFDocEncoded String
Type."
ASCII string Shall be used for characters that are represented in a
single byte using ASCII encoding.
byte string Shall be used for binary data represented as a series of
bytes, where each byte can be any value representable in
8 bits. The string may represent characters but the
encoding is not known. The bytes of the string need not
represent characters. This type shall be used for data
such as MD5 hash values, signature certificates, and Web
Capture identification values.
This type is described in 7.9.2.4, "Byte String Type."
If a string is the value e.g. of the Author metadata, it is a text string, so it is encoded using either PDFDocEncoding or UTF-16BE with a leading byte-order marker.
If on the other hand a string is the value e.g. of Contents in a signature dictionary, it is a byte string holding a binary object, any attempt to interpret it according to some encoding will fail.
The situation is even more tricky with streams.
First of all the stream content may be somehow processed, e.g. it may be compressed. To get to the actual stream contents, you first have to undo this processing.
The the content may either be binary, e.g. a font program, or text, e.g. JavaScript, or it may be a content stream, e.g. the page contents.
A content stream is a PDF stream object whose data consists of a sequence of instructions describing the
graphical elements to be painted on a page. The instructions shall be represented in the form of PDF objects,
using the same object syntax as in the rest of the PDF document.
Thus, they are mostly ASCII values. The exception again are string arguments to text drawing instructions. Their encoding depends entirely on the font currently selected when the string is drawn, and fonts may use standard encodings, but they may also use completely chaotic, ad-hoc encodings.
PS: If you happen to try and analyze an encrypted PDF, you will find that Encryption
applies to all strings and streams in the document's PDF file, with very few exceptions. In particular encryption does not apply to dictionary and array structures, numbers and names. Thus, someone not aware of this might not recognize that the PDF is encrypted but instead assume that strings and streams are encoded in a very weird way.
You find that in the PDF specification (http://www.adobe.com/devnet/pdf/pdf_reference.html). To elaborate a bit on the most important points in your question...
1) PDF dictionaries can contain a variety of value types (booleans, numbers, strings...). The encoding you are going to encounter depends on the type of value.
2) Mostly, the interesting and complex case is that where the type of object is a string.
3) For a string, read section 7.9.2 in the PDF specification. That explains what encodings can be used for such strings (PDFDocEncoding, Unicode encoding...) and how to recognise what encoding you have for a particular string.
To complement #mkl's and #DavidvanDriessche's excellent answers...
Here are three OpenSource command line tools which can help you to transform any PDF into different forms which expand/uncompress/decode object streams (Note, there is not one single, "the-one-and-only-correct" way to do this -- so the outputs of each of the tools will be different):
pdftk
mutool
qpdf
Each of these should be available via your favorite operating systems package manager.
pdftkexample usage:
pdftk in.pdf cat output out1.pdf uncompress
mutool example usage:
mutool clean -d in.pdf out2.pdf
qpdf example usage (my favorite tool for this purpose):
qpdf --qdf --object-streams=disable in.pdf out3.pdf
You should try each of these, compare their outputs for different input PDFs and then decide which one is your favorite (but never forget to remember the other tools when you encounter a case where your favorite shows unexpected results).

Encoding issue in I/O with Jena

I'm generating some RDF files with Jena. The whole application works with utf-8 text. The source code as well is stored in utf-8.
When I print a string contaning non-English characters on the console, I get the right format, e.g. Est un lieu généralement officielle assis....
Then, I use the RDF writer to output the file:
Model m = loadMyModelWithMultipleLanguages()
log.info( getSomeStringFromModel(m) ) // log4j, correct output
RDFWriter w = m.getWriter( "RDF/XML" ) // default enc: utf-8
w.setProperty("showXmlDeclaration","true") // optional
OutputStream out = new FileOutputStream(pathToFile)
w.write( m, out, "http://someurl.org/base/" )
// file contains garbled text
The RDF file starts with: <?xml version="1.0"?>. If I add utf-8 nothing changes.
By default the text should be encoded to utf-8.
The resulting RDF file validates ok, but when I open it with any editor/visualiser (vim, Firefox, etc.), non-English text is all messed up: Est un lieu généralement officielle assis ... or Est un lieu g\u221A\u00A9n\u221A\u00A9ralement officielle assis....
(Either way, this is obviously not acceptable from the user's viewpoint).
The same issue happens with any output format supported by Jena (RDF, NT, etc.).
I can't really find a logical explanation to this.
The official documentation doesn't seem to address this issue.
Any hint or tests I can run to figure it out?
My guess would be that your strings are messed up, and your printStringFromModel() method just happens to output them in a way that accidentally makes them display correctly, but it's rather hard to say without more information.
You're instructing Jena to include an XML declaration in the RDF/XML file, but don't say what encoding (if any) Jena declares in the XML declaration. This would be helpful to know.
You're also not showing how you're printing the strings in the printStringFromModel() method.
Also, in Firefox, go to the View menu and then to Character Encoding. What encoding is selected? If it's not UTF-8, then what happens when you select UTF-8? Do you get it to show things correctly when selecting some other encoding?
Edit: The snippet you show in your post looks fine and should work. My best guess is that the code that reads your source strings into a Jena model is broken, and reads the UTF-8 source as ISO-8859-1 or something similar. You should be able to confirm or disconfirm that by checking the length() of one of the offending strings: If each of the troublesome characters like é are counted as two, then the error is on reading; if it's correctly counted as one, then it's on writing.
My hint/answer would be to inspect the byte sequence in 3 places:
The data source. Using a hex editor, confirm that the é character in your source data is represented by the expected utf-8 hex sequence 0xc3a8.
In memory. Right after your call to printStringFromModel, put a breakpoint and inspect the bytes in the string (or convert to hex and print them out.
The output file. Again, use a hex editor to inspect the byte sequence is 0xc3a8.
This will tell exactly what is happening to the bytes as they travel along the path of your program, and also where they deviate from the expected 0xc3a8.
The best way to address this would be to package up the smallest unit of your code that you can that demonstrates the issue, and submit a complete, runnable test case as a ticket on the Jena Jira.

Can Fortran read bytes directly from a binary file?

I have a binary file that I would like to read with Fortran. The problem is that it was not written by Fortran, so it doesn't have the record length indicators. So the usual unformatted Fortran read won't work.
I had a thought that I could be sneaky and read the file as a formatted file, byte-by-byte (or 4 bytes by 4 bytes, really) into a character array and then convert the contents of the characters into integers and floats via the transfer function or the dreaded equivalence statement. But this doesn't work: I try to read 4 bytes at a time and, according to the POS output from the inquire statement, the read skips over like 6000 bytes or so, and the character array gets loaded with junk.
So that's a no go. Is there some detail in this approach I am forgetting? Or is there just a fundamentally different and better way to do this in Fortran? (BTW, I also tried reading into an integer*1 array and a byte array. Even though these codes would compile, when it came to the read statement, the code crashed.)
Yes.
Fortran 2003 introduced stream access into the language. Prior to this most processors supported something equivalent as an extension, perhaps called "binary" or similar.
Unformatted stream access imposes no record structure on the file. As an example, to read data from the file that corresponds to a single int in the companion C processor (if any) for a particular Fortran processor:
USE, INTRINSIC :: ISO_C_BINDING, ONLY: C_INT
INTEGER, PARAMETER :: unit = 10
CHARACTER(*), PARAMETER :: filename = 'name of your file'
INTEGER(C_INT) :: data
!***
OPEN(unit, filename, ACCESS='STREAM', FORM='UNFORMATTED')
READ (unit) data
CLOSE(unit)
PRINT "('data was ',I0)", data
You may still have issues with endianess and data type size, but those aspects are language independent.
If you are writing to a language standard prior to Fortran 2003 then unformatted direct access reading into a suitable integer variable may work - it is Fortran processor specific but works for many of the current processors.