I have a script in MATLAB that outputs various files, including NIFTI (MRI images) files and text log files. Sometimes the output files that are created have their file permissions set to no read or write for anyone, including the file owner, and this appears to occur randomly.
This normally isn't a problem unless it occurs with the logs, as it leads MATLAB to endlessly recurse as it tries to write the error to the logs. Unfortunately, I haven't been able to find anyone who has experienced similar behavior from any program, including MATLAB.
The script, input files, and output files are all located on a NAS drive connected to a server running Ubuntu 14.04, so I'm wondering if this is a problem with the script (probably not because it happens intermittently regardless of input), the matlab environment, or the NAS drive.
I'm not sure why yoru fileattributes/permissions are changing, but I know the solution. You want file attributes if you know chmod from unix this should be familiar, if not you will still be fine
something like this will make your files writeable for all user groups on a unix (ubuntu) system
fileattrib('/home/work/results/my_file.log','+w','a')
edit
since these files are non-existant this may work better. Simply use fopen with the 'w+' flag. Which means write mode for appending. The + will also create the file if it doesn't exist(and you have permission to create files in the specified directory)
fid = fopen('my_new_log.txt','w+');
fprintf(fid,'some strings for my file');
fclose(fid);
it is also important you make sure to close the file after you are done.
Related
For this project we have been given code, and will be changing some inputs and assumptions. Thus, I already possess the original codes, but just changing all the creator's file paths to match my own computer is yielding me a lot of trouble. The following, and many variations of, continually yield errors.
load \Users\myname\Library\Documents\...
The error is
Error using load
'Unable to read file
\Users\myname\Library\Documents...'.
No such file or directory.
My files are stored in my Documents. Another person in my group on windows has used
load C:\Users\hisname\Desktop\...
Is there something I'm missing in my line, similar to the C drive but on Mac? Is my code just completely wrong, I'm able to load files in R quite easily, but Matlab is posing a huge hurdle. I have no experience with Matlab and have been asked simply to run this code.
On the Mac, path components are separated by /, not \. Thus, you should type
load /Users/myname/Documents/filename.mat
You can use the location bar at the top of the command window to change to the directory where your file is located, and then you can type
load filename
to load filename.mat.
Also, are you sure you have a Documents directory under Library? Why?
To run code from a file called "my_file.m", than just open your Matlab and type run my_file.m. This will run your script in the Command Window.
The load function is used, if you want to load a .mat file. These are normally files, where variables from your workspace are stored.
I'm looking for solution to delete or (preferably directly) overwrite source of an exe file while it is running.
To explain further before you get it all wrong, I'll give an example:
I have an exe file on drive D:\ which I run (with previously posted question's answer, giving params to "Start in" folder on C:\Program Files\MyProgram\" so it finds its dlls.
Now after the file is running, I'd like to rewrite the file's byte stream (just like opening it in hex editor...), or at least delete it so I can copy over new exe file directly using same name.
So far the solution I'm using is that I trigger format D: command for the whole drive D:\ (which, in my case is ramdisk and thumb-drive, as I only have this exe on it, I copy it there as necessary), since that removes the file and let's me copy new file there.
Trying to use del myProgram.exe even with -force flag triggers error that access to the file is denied. Same goes if I try to overwrite the contents of the file.
Is there any alternative to do that without using the format command, as that requires to have partition drive only for the purpose?
Update: Note: MoveFileEx and similar techniques that require termination of the process or system restart/reboot are not qualified as a solution. This should be done while the process is running without further actions that can compromise the process's run state.
On a side note, when formatting the drive using the Powershell's format command, the file is gone, although if viewing the partition using Hex viewer tool, there is full binary (hex) content of the exe visible there and an be restored using just as simple as copy-paste technique. This is one of the points as to where overwriting the file contents would be preferable than deleting the file directly.
Please note: This is a knowledge and skills based question, and would therefore appreciate sparing the moral and security-concerning comments about such actions and behaviour.
For deleting/replacing/overwriting a file at least two conditions must be met:
The user performing the operation must have the required permissions to do so. This can be verified for instance via Get-Acl or icacls.
Windows must not have an open handle to the file. This can be checked for instance with tools like Process Explorer or handle. These tools can also be used to forcibly close open handles, although that's not recommended as it may cause data loss and/or damage to the files in question. I'm not sure, though, if it's actually possible to close handles to an executable without terminating the process.
Note that antivirus software is likely to interfere with this kind of operation.
The basic problem here is that Windows loads from the .EXE upon demand, it's not all read in at once.
If you destroy the original file what happens when it tries to load in a page that no longer exists?
If I had to write something of this sort I would copy the .exe to a temporary location (beware that running code from the temp directory may be prohibited), run the new .exe, terminate the old one and then do what I want to it.
My problem is as described. My script downloads files through an external call to cmd (using the system function and then .NET to make keypresses). The issue is that when it tries to fopen these files I downloaded (filenames from a text file I write as I download), it doesn't find them, causing an error. When I run the script again after seeing it fail, it works but only up to the point where it's trying to download/call new files again, where it runs into the same problem.
Are new files downloaded during when a script is running somehow not visible to the search path? Because the folder is most definitely in my search path (seeing as it works outside of during-script downloads). It's not that it isn't getting the files fast enough either, cause they appear in my folder almost instantly, and I've tried a delay to allow for it to recognize it, but that didn't work either.
I'm not sure if it's important to note that the script calls an external function which tries to read the files from the .txt list I create in the main script.
Any ideas?
The script to download the files looks like so:
NET.addAssembly('System.Windows.Forms');
sendkey = #(strkey) System.Windows.Forms.SendKeys.SendWait(strkey);
system('start cygwinbatch.bat')
pause(.1)
sendkey(callStr1)
sendkey('{ENTER}')
pause(.1)
sendkey(callStr2)
sendkey('{ENTER}')
pause(.1)
sendkey('exit')
pause(2)
sendkey('{ENTER}')
But that is not the main reason I am asking: I am confident that the downloads are occurring when the script calls them, because I see them appearing in my folder as it called. I am more confused as to why MATLAB doesn't seem to know they are there while the script is running, and I have to stop it and run it again for it to recognize the ones I've downloaded already.
Thank you,
Aaron
The answer here is probably to run the 'rehash' function. Matlab does not look for new files while executing an operation, and in some environments misses new files even during interactive activity.
Running the rehash function forces Matlab to search through its full path and determine if there are any new files.
I've never tried to run rehash in the middle of an operation though. ...
My guess is that the MATLAB interpreter is trying to look ahead and is throwing errors based on a snapshot of what the filesystem looked like before the files were downloaded. Do you get different behavior if you run it one line at a time using F9? If that's the case then you may be able to prevent the interpreter from looking ahead by using eval().
Alright, here's what I'm dealing with (you can skip to TLDR if all you need to see is what I want to run):
I'm having an issue with file formatting for a nasty conglomeration of several ancient programs I've strung together. I have some data in .CSV format, and I need to put it into .SPC format. I've tried a set of proprietary MATLAB programs called 'GS tools' for fast and easy conversion, but fast and easy doesn't look like its gonna happen here since there are discrepancies in how .spc files are organized now and how they were organized back when my ancient programs were written.
If I could find the source code for the old programs I could probably alter the GS tools code to write my .spc files appropriately, but all I can find are broken links circa 2002 and earlier. Seeing as I don't know what my programs are looking for, I have no choice but to try resaving my data with other programs until one of them produces something workable.
I found my Cinderella program: if I open the data I have in a program called Spekwin and save the file with a .spc extension... viola! Everything else runs on those files. The problem is that I have hundreds of these files and I'd like to automate the conversion process.
I either need to extract the writing rubric Spekwin uses for .spc files (I believe that info is stored in a dll file within the program, but I'm not sure if that actually makes sense) and use it as a rule to write a file from my input data, or I need a piece of code that will open a file with Spekwin, tell Spekwin to save that file under the .spc extension, and terminate Spekwin.
TLDR: Need a command that tells the computer to open a file with a certain program, save that file under a different extension through that program (essentially open*.csv>save as>*.spc), then terminate the program.
OR--I need a way to tell MATLAB to write a file according to rules specified by a .dll, but I'm not sure I fully understand what that entails.
Of course I'm open to suggestions on other ways to handle this.
Today I stumbled upon this thread:
http://www.mathworks.com/matlabcentral/newsreader/view_thread/112560
The question is basically how to make Matlab read your startup.m file regardless of where
you start your matlab session.
One of the solutions offered was:
One solution would be to ask the system administrator to add a few lines
to "matlabrc.m" that adds some pre-determined folder in the user's home
directory to the MATLAB path (say, ~/.matlabstart). Then each user can
have their own "startup.m" file inside this folder.
What I ended up doing in my system (OS X) was to add a startup.m file in:
/Applications/MATLAB_R2011a.app/toolbox/local/
In this startup.m file I added:
if exist([getenv('HOME') '/.matlabrc/startup.m'])
run([getenv('HOME') '/.matlabrc/startup.m']);
end
That way users have the option of creating the hidden folder ~/.matlabrc and inside it they can put the file startup.m. In this startup file they can tell matlab what to execute whenever they start Matlab regardless of the directory where they started it. An example of what I added to my own personal startup.m file is
addpath(genpath('/Users/jmlopez/matlabcode/'))
Now I can add as many folders inside that directory and all of them will be added
to the path every time I start Matlab automatically without having to modify the path.
The question is: Did Matlab already provided a special file like the one I created or did I just go through all this trouble to accomplish what I wanted? If the answer is the second option I gave, then, why doesn't Matlab provide this? It is such a pain in the ass to add directories to the Matlab path whenever you do not have admin permissions and I do not want to carry my startup.m file to every directory I go to. Can someone shed some light into this please?
You can save the pathdef file (which stores all the paths you add) to a custom directory. The problem however is that when matlab starts, it doesn't automatically know which custom directory you used in the previous session.
But that's where the MATLABPATH environment variable comes in. Because this allows to set the matlab starting path yourself. In linux this is simply done by setting this environment variable MATLABPATH before starting matlab (from a terminal / in your .bashrc / ...)
export MATLABPATH=$HOME/.matlab
This way you can let all users have their own pathdef file, which solves the problem of having to add them manually at startup.
EDIT
I tested out if adding startup.m to that MATLABPATH directory worked, ie: does matlab run that startup file? ... and it does. I think it doesn't work for you, because there is another startup.m file in some other (higher priority) directory (probably matlabroot), so that gets precedence. My only startup file is in MATLABPATH, so there is only one choice.
EDIT2
Nope, I added startup to matlabroot directory, and still my own startup file in .matlab gets run. Are you sure you set the MATLABPATH correctly before you started matlab?