Open Binary File

[Alma Wass]

Iwant to open files in binary format. I want to see binary code, not hex. And want to edit in binary format and ability to save changes. What is the best application to do this or is there any easy way to do this ?

I have been working with Fortran for years, but the file I/O is still hazy to me. My understanding of status, form, access, recl is limited, because I only needed certain use-cases in grad school.

I know that Fortran binary files have extra information at the top of the file that describe the size of the file. But that has never been an issue for me before because I have only had to deal with Fortran files in Fortran code, where the extra information is necessary, but invisible.

But how does this change for a flat, binary file that doesn't have the Fortran header information? More importantly, where is a good link to describe these terms in greater detail: status, form, access, recl?

This difference is because Fortran-styled binary files have a 4-byte header and footer around each "record" in the file. These headers/footers describe the size of the data contained in the record. (In the most common case, each binary file you encounter will only have one record.)

STATUS defines if the file already exists. The STATUS="UNKNOWN" argument means that the file might not exist yet, but if it doesn't it will be created. If you want to protect against the possibility of writing over an old file use: STATUS="OLD". Similarly, if you know the file doesn't exist yet, you will want to use: STATUS="NEW".

One caveat is the record length given in recl defaults to the number of 4-byte words with unformatted records (at least on Intel compilers, use byterecl to specify otherwise), so you may have to specify a compiler option or use recl=1.

As your code stands, using unformatted and direct, all you need to do to ensure you read data properly is to choose an appropriate record length. But, some FORTRAN compilers do not always play nice with unformatted binary files and I would suggest adopting HDF5 going forward.

This is the thing bugging me. I'd like to see some of my files in binary or plaintext format, but I can't figure out how to do it for all files. I can open some image files in plaintext using Textedit, but that's all I can figure out. Anyone know anything?

Dear All,

I tried to load or import .bin file into imageJ and I could not find the exact answer how to load a binary file with 3D data with headers and others comments in it and plot it in 3D or as stack.

I would be very glad if you can help me with this.

There is no option to load binary file in bio-formats.Is there a way to load binary file in imageJ.DOes it support .bin files?

I've tried a number of different applications to open binary files. The one that I've used and enjoyed the most is called bless and it is really easy to install. Simply open the terminal by pressing CTRL+ALT+T and type sudo apt-get install bless and press ENTER. Note: You will have to enter your password, when you enter your password there will be no indicator on the screen, no asterisks, and the cursor will not move. This is normal behavior. After entering your password press ENTER again and follow any additional instructions given.

As a hex editor, bless has lots of features and is actually surprisingly light. This should open your game file and allow you to edit it. I can't actually help with anything beyond that as I am not a gamer. However, it's in the repo and is easy enough to install without taking up much room or being overly complex.

Are you sure the file is unstructured like that? Usually this kind of data can have all kinds of metadata embedded in the file. @jrevels works a lot with EEG data, maybe he can point you in the right direction.

Thank you @Keno, This file actually is composed of three files, one binary and two with metadata(sampling frequency, number of channels ,etc). My problem is that it seems to have more data than expected.

Discourse will have emailed him, so he can chime in here if he knows something. Usually messaging people directly is discouraged, as it prevents other people from seeing an answer which may be useful to them (aside from any etiquette questions).

It would definitely be within the scope of JuliaNeuroscience. The first thing would be to find out how they specify basic channel information in the header. For example, biosemi has this specification Biosemi EEG ECG EMG BSPM NEURO amplifiers systems

Does anyone know what is the exact difference between the form='unformatted' and form='binary' in open() when writing/reading raw binary files? Seems that form='binary' is not available in fortran compilers such as gfortran. I read the documentation for FORM in -us/node/525755#E6F9FE02-2CA6-468D-B8D5-E2AA56FF2CC1, but still do not quite understand the difference. For stream access read/write, is there any difference between using form='unformatted' and form='binary'?

Files with FORM='BINARY' are nonstandard, and contain no record-length information. Such files may have been written by a C program after having been opened with fopen(,"wb") (or otherwise), and being able to use FORM='BINARY' allowed stream access in the decades before stream access was added to the Fortran standard.

One has to look at the history of I/O devices from the 1950-s to today in order to see why the file OPEN statement has such a large variety of optional clauses. The old tape and DASD files were not at all in harmony with the "stream of bytes" view that Unix adopted.

Thanks, Steve. May I know why the FORM='binary' is not recommend to be used anymore in modern Fortran? If I want to read/write stream file, can I use ACCESS='STREAM' + FORM='UNFORMATTED' without RECORDTYPE?

form='binary' was a vendor-dependent extension for which 'stream' files were adopted as a standard replacement. You might consider replacing files written that way by reading (with the same vendor's compiler) with the 'binary' options and writing out with current standard options.

As Tim says, FORM='BINARY' was an extension - Microsoft's, I think - that got picked up by others. There is no reason to use it now that the standard has ACCESS='STREAM' (this is what I meant instead of RECORDTYPE='STREAM'). Both are just "a stream of bytes". There is no need to read with one and write with the other.

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I often use photoshop to open binary flat files, either 8 or 16 bit depth. In photoshop if I select open using photoshop raw format, a dialog box pops up asking what the image dimensions are (ie, 512x512), the number of channels (ie 1), the bit depth and the byte order.Is there any way to do this in GIMP, either native or with plugins... I dont think that the UFRaw will work as these files do not come from a camera-- they are images of satellite imagery that are just binary flat files.

I often use photoshop to open binary flat files, either 8 or 16 bitdepth. In photoshop if I select open using photoshop raw format, adialog box pops up asking what the image dimensions are (ie,512x512), the number of channels (ie 1), the bit depth and the byteorder.

Is there any way to do this in GIMP, either native or withplugins... I dont think that the UFRaw will work as these files donot come from a camera-- they are images of satellite imagery thatare just binary flat files.

GIMP PDB shows file-raw-load & file-raw-save. How to get them to dosomething... that is a different question, the "new" file dialog seemsto be missing any reference to raw files. Try showing all file types,then loading one with a non matching file extension (in old versionsyou would be able to pick any file and then force the loader to use,IIRC). Or maybe use script-fu console to popup the loader options.

I often use photoshop to open binary flat files, either 8 or 16 bitdepth. In photoshop if I select open using photoshop raw format, adialog box pops up asking what the image dimensions are (ie, 512x512),the number of channels (ie 1), the bit depth and the byte order.Is there any way to do this in GIMP, either native or with plugins...I dont think that the UFRaw will work as these files do not come froma camera-- they are images of satellite imagery that are just binaryflat files.

I often use photoshop to open binary flat files, either 8 or 16 bitdepth. In photoshop if I select open using photoshop raw format, adialog box pops up asking what the image dimensions are (ie, 512x512),the number of channels (ie 1), the bit depth and the byte order.

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