I have a lot of folders each containing a lot of .txt files which i need to process with matlab.
i have a script finished which does it, it reads all .txt files in 1 folder and does some computing.
so if i want to process those files i move the script into the desired folder and run it, it is kinda lame to move the script every time.
is it possile to start a script in a standard directory, then make the script to ask me to browse for the desired directory to run the script in that directory? because it doesnt write any files, it just reads. after it finishes it should reset it, so i could browse to different folders every time. like save the path in a value and clear it at the end...
i use "fopen" in that script to open the .txt files, so it could be possible to assign the full path to that function, but its important to me to being able to browse the right folder every time i run the script.
i use
path=uigetdir;
fileid=fopen([path filesep 'file.txt']);
and it works just the way i wanted.
thanks #excaza and #Laure for a quick reply
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I'm looking for a way to automate archiving where after I plug my two external drives I can copy all my resources. The problem is that I have different file structures on my laptop and on both external drives so I need to select specific folders to be copied. It means that I can't select one root folder and copy it straightforward. I tried to find a way to declare more than one path in the cp command and in the copy command, without success. An example path:
/my_programming_stuff
/folder1
/folder2
/folder3
/folder4
I want to select only the first 3 folders to copy them into external drive1 and external drive 2. The idea is to create a .bat file that will copy everything at once ( in the best case scenario it will be copied simultaneously on both external drives, so it will be much faster). Another problem is that there needs to be a bypass the ntfs long path limitations (max. 260 characters).
Flags that I want to use:
Copy the files and directories and all of their attributes,
including ownerships and permissions.
Recursively copy directories and their contents.
When copying files from one directory to another, only
copy files that either doesn't exist or are newer than the
existing corresponding files, in the destination
directory.
data verification (so it's certain that the copy was verified)
progression bar with time eta
Until now I was using Total Commander to do this but every day I need to pick only a few folders to be copied which takes time and is inefficient.
I have experience with Bash and PowerShell but I am not sure how to handle this topic.
Create a static batch file with robocopy commands. I think /copyall is the only switch you need to specify for all this. Other defaults should satisfy requirements.
https://learn.microsoft.com/en-us/windows-server/administration/windows-commands/robocopy
I think your time will be better spent learning how to use either FastCopy or FreeFileSynce. I used FreeFileSync some years ago but got disgusted with the it's constantly changing format of its xml file used for starting a backup, so I switched to FastCopy. But it looks like FreeFileSync may be getting their act together and I aim to do some experiments over the summer to see if I want to switch back to it.
Both can handle the long filename format issues, both can be executed by a batch file, both seem to have a lot of quality, but FreeFileSync has more features - and more bloated because of the features. But speed wise, I think FastCopy is probably one of the better products out there and very streamline in use and design.
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().
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.
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?
I have several MATLAB scripts to share with my colleagues. I have put these scripts under a specified directory, e.g., /home/sharefiles
Under the MATLAB command prompt, the users can use these scripts by typing
addpath /home/sharefiles
Is there a way to automatically add this path in my matlab script, and save users the efforts of invoking addpath /home/sharefiles each time.
Sure, just add the addpath to your script.
addpath('/home/sharefiles')
If you want to recursively add subdirectories, use the genpath function:
addpath(genpath('/home/sharefiles')
Adding files to the path or one of the slower operations in Matlab, so you probably don't want to put the addpath call in the inner loop of an operation. You can also test to see if you need to add the path first.
if ~exist('some_file_from_your_tools.m','file')
addpath('/home/sharefiles')
end
Or, more directly
if isempty(strfind(path,'/home/sharefiles;'))
addpath('/home/sharefiles')
end
You could add the code posted by Pursuit to your startup.m file so that MATLAB adds it to the path automaticlly upon startup. Or, take a look at the savepath function. Lastly,
So when you Use the GUI to set path, the paths get added in the default start directory of Matlab in the pathdef.m file present there. Hence if you are running your code from any other directory either you would have to copy over this file or create a script in the startup folder. Hope this helps!!