Is there any way to create an empty .mat file from a terminal session? Basically, what I am doing is brain graph analysis. The software I am using, if an entire brain is scrubbed (ie, if the displacement of the brain is greater than a certain threshold) the output file will be left out or will be very small. When analyzing, however, I need to be able to eliminate both subjects from the analysis if the entire brain is scrubbed/too much of the brain is scrubbed. To accomplish this, the easiest way would be to simply check the dimensions of the output file within matlab, and if they are below the arbitrary threshold I decide then both subjects will just be skipped over for analysis. The issue is, I can easily check if a file contains too few remaining frames, however, if the resulting file contains no frames, it will entirely just not exist. As the outputs are all sorted, the only thing I need to do is check consecutive files' dimensions, and if one of the files does not contain enough values, then I can simply skip over it entirely. Simply touching a blank file obviously will not work, since it will not contain any encoding. I hope this is a good explanation for my motivation to do this, and if any of you know of any suggestions, please let me know.
A simple solution would be to create an empty file from Matlab and duplicate the file when needed from the console.
Just open Matlab, set to the destination folder and type this:
clear all
save empty.mat
Then, when needed, copy the file from the console. :)
Saving the contents of an empty struct creates an empty .mat file:
emptyStruct = struct;
save('myFile.mat','-struct','emptyStruct');
Related
I'm running a short code to open one by one a list of files and saving back only one of the variables contained in the files. The process seems to me much slower than I expected and getting slower with time, I don't fully understand why and how I could make it run faster. I always struggle with optimization. I'd appreciate if you have suggestions.
The code is the following (the ... substitute the actual path just for example):
main_dir=dir(strcat('\\storage2-...\Raw\DAQ5\'));
filename={};
for m=7:size(main_dir,1)
m
second_dir=dir([main_dir(m).folder '\' main_dir(m).name '\*.mat']);
for mm=1:numel(second_dir)
filename{end+1}=[second_dir(mm).folder '\' second_dir(mm).name];
for mmm=1:numel(filename)
namefile=sprintf(second_dir(mm,1).name);
load(string(filename(1,mmm)));
save(['\\storage2-...\DAQ5\Ch1_',namefile(end-18:end-4),'.mat'], 'Ch_1_y')
end
end
end
The original file is about 17 MB and once the single variable is saved it is about 6 MB in size.
The Matlab load function takes an optional additional argument to specify just a selected variable to read from the input file.
s = load('path/to/file.mat', 'Ch_1_y');
That way you don't have to spend time loading in all the other variables from those input .mat files that you're just going to immediately throw away.
And using save to save MAT-files over SMB shares can be slow. You might want to call save to write it to a temporary local file first, and then copy the completed file to the final destination. Sounds like more I/O, but it can actually be a net win, depending on your particular system and network. Measure it both ways to see if it's a win in your particular situation.
there are datasets in .mat format in the this site: http://www.cs.nyu.edu/~roweis/data.html
I want to change the format to .csv.
Can someone tell me how to change the format to create the .csv file.
Thanks!
Suppose that the .mat files from the site are available already. In the command window in Matlab, you may write, for example:
load('C:\Users\YourUserName\Downloads\mnist_all.mat');
to load the .mat file; the result should be a set of matrices test0, test1, ..., train0, train1 ... created in your workspace, which you want saved as CSV files. Because they're different size, you need to save one CSV per variable, e.g. (also in the command window):
csvwrite('C:\Users\YourUserName\Downloads\mnist_test0.csv', test0);
Repeat the command for each variable, and do not forget to change also the name of the output file to avoid overwriting.
Did you tried the csvwrite function in Matlab?
Just load your .mat files with the load function and then write them with csvwrite!
I do not have a Matlab license so I installed GNU Octave 4.2.1 (2017) on Windows 10 (thank you to John W. Eaton and others). I was not fully successful using the csvwrite so I used the following workaround. (BTW, I am totally incompetent in the Octave world. csvwrite worked for simple data structures).
In the Command Window I used the following two commands
load myfile.mat
save("-text","myfile.txt","variablename")
When the "myfile.mat" is loaded, the variable names for the data vectors loaded are displayed in the workspace window. This is the name(s) to use in the save command. Some .mat files will load several data structures.
The "-text" option is the default, so you may not need to include this option in the command.
The output file lists the .mat file contents in text format as single column (of potentially sequential variables). It should be easy to use you text editor to massage this data into the original matrix structure for use in whatever app you are comfortable with.
Had a similar issue. Needed to convert a series of .mat files that had two columns of numerical data into standard data files (ascii text). Note that I don't really ever use csv, but everything here could be adapted by using csvwrite instead of the standard save.
Using Octave 4.2.1 ....
load myfile.mat
LI = [L, I] ## L and I are column vectors representing my data
save myfile.txt LI
Note that L and I appear to be default variable names chosen by Octave for the two columns vectors in my original data file. Ideally a script that iterated over all files with the .mat extension in my directory would be ideal, but this got the job done. It saves the data as two space separated columns of data.
*** Update
The following script works on Octave 4.2.1 for a series of data files with the .mat extension that are in the same directory. It will iterate over them and write the data out to text files with the same name but with the extension .dat . Note that this is not efficient, so if you have a lot of files or if they are large it can take a while to run. I would suggest that you run it from the command line using octave mat2dat.m so you can actually watch it go.
I make no guarantees that this will work for you, but it did for me. I also am NOT proficient in Octave or Matlab, so I'm sure a better solution exists.
# mat2dat.m
dirlist = glob("*.mat")
for i=1:length(dirlist)
filename = dirlist{i,1}
load(filename, "L", "I")
LI = [L,I]
tmpname = filename(1:length(filename)-3)
txtname = strcat(tmpname, 'dat')
save(txtname, "LI")
end
I need to create a matlab mfile that will run another matlab file with default values given in a txt file. It's ment to be useful for testing programs, so that user may specify values in a txt files and instead of inputing values every time he starts the program, my script will give the program default values and user will only see the result.
My idea is to load tested file into a variable, change 'variable=input('...');' for variable = default_variable;, save it to tmp file, execute, and than delete tmp file. Is this going to do the job?
I have only two problems:
1) How to eliminate the problem of duplicated variable names - i mean this must work for all scripts, i don't know the names of variables used in tested script.
2) As I wrote before - is this going to work fine? Or maybe I missed a easier way to do it - for example maybe I don't have to create a tmp file?
I really need your help!
Thanks in advance!
If the person who has to edit the default values has access to Matlab, I would recommend saveing the values in a mat file and loading them when needed. Otherwise you could just write a smalls cript that contains the assignment to certain variables, but make sure to keep this small. For example:
maxRuns = 100;
clusters = 12;
So much for setting up the defaults. Regarding the process my main advice is to wrap the thing that you want to test into a function. This way variables used in the code to call the 'script' will not interfere as a function gets its own separate workspace. Check doc function if you are not familiar with them.
I am new to MATLAB programming and some of the syntax escapes me. So I need a little help. Plus I need some complex looping ideas.
Here's the breakdown of what I have:
12 seperate .dat files, each titled something like output_1_x.dat, output_2_x.dat, etc.
each file is actually one piece of a whole that was seperated and processed
each .dat file is approx. 3.9 GB
Here's what I need to do:
create a single file containing all the data from each seperate file, i.e. I need to recreate the original file.
call this complete output file something like output_final.dat
it has to be done in MATLAB, there are no other alternatives (actually there maybe; see note below)
What is implied:
I will have to fread each 3.9 GBfile into chunks or packets, probably 100 mb at a time (using an imbedded loop?)
these packets will have to be read then written sequentially
after one file is read then written into output_final.dat, the next file is automatically read & written (the master loop).
Well, that's pretty much it. I did a search for 'merging mulitple files' and found this. That isn't exactly what I need to do...I don't need to take part of a file, or data from files, and write it to a new one. I'm simply...concatenating...? This would be simple in Java or Perl, but I only have MATLAB as a tool.
Note: I am however running KDE in OpenSUSE on a pretty powerful box. Maybe someone who is also an expert in terminal knows a command/script to do this from the kernel?
So on this site we usually would point you to whathaveyoutried.com but this question is well phrased.
I wont write the code but i will give you how I would do it. So first I am a bit confused about why you need to fread the file. Are you just appending one file onto the end of another?
You can actually use unix commands to achieve what you want:
files = dir('*.dat');
for i = 1:length(files)
string = sprintf('cat %s >> output_final.dat.temp', files(i).name);
unix(string);
end
That code should loop through all the files and pipe all of the content into output_final.dat.temp (then just rename it, we didn't want it to be included in anything);
But if you really want to use fread because you want to parse the lines in some manner then you can use the same process:
files = dir('*.dat');
fidF = fopen('output_final.dat', 'w');
for i = 1:length(files)
fid = fopen(files(i).name);
while(~feof(fid))
string = fgetl(fid) %You may choose to parse the string in some manner here
fprintf(fidF, '%s', string)
end
end
Just remember, if you are not parsing the lines this will take much much longer.
Hope this helps.
I suggest using a matlab.io.matfileclass objects on two of the files:
matObj1 = matfile('datafile1.mat')
matObj2 = matfile('datafile2.mat')
This does not load any data into memory. Then you can use the objects' methods to sequentialy save a variable from one file to another.
matObj1.varName = matObj2.varName
You can get all the variables in one file with fieldnames(mathObj1) and loop through to copy contents from one file to another. You can then clear some space by removing the copied fields. Or you can use a bit more risky procedure by directly moving the data:
matObj1.varName = rmfield(matObj2,'varName')
Just a disclaimer: haven't tried it, use at own risk.
I have implemented a log file that will be storing the cpu and memory state of a process after every minute.I have limited the maximum size of the file to 3MB (thats enough for my purpose).
The script will be called by a cron job after every minute and the script will log the details for that minute and will rename the file as "Log_.log".
When the size reaches "3MB - 100 bytes" I reset the file pointer to point to the begining and will overwrite the first entry in the log file and will now rename the file as "Log_<0+some offset>.log".
As I am renaming the file after every minute to update the file pointer position, is it a good/efficient way ?
I do not want to maintain more than one log file for this purpose.
Another option for me is to maintain the file pointer position in a file ,but ....another file !! not interested in maintaining one if this option is good :)
Thanks in Advance.
Are you an engineer? This is a nice example of some simple task, solved by a perfectly working but overly complex solution.
Unless the content you put in takes exactly as many bytes as the content you take out, writing "in" a file will actually cause the whole following part after your writing position to be rewritten to disk. Append is much cheaper.
Renaming the file to store the pointer works - but it's not very elegant, and makes stuff more complex (for one, your process needs write rights to the directory in which the file resides - else just write access to two files is sufficient)
Unless disk space is an issue (and really, it rarely is), your approach is less efficient than say, append everything to a file, and rotate the file when it reaches its maximum size. This way you always have the last 3MB of logs available, and maximum 3MB more in your current file. It will make parsing the file a lot easier too, instead of recalculating the entire pointer position thing.
Update to answer your comment:
Renaming a file every minute (or even every second) shouldn't slow down your system significantly, don't worry about that.
Our concerns are mainly with "why you think you need to rename the file". It's not better technically, it's not better from a logical point of view, it makes a lot of other (future) tasks harder. You could store the file pointer in a seperate file, or at the end of your file, and there are better^H^H^H^H^H^H simpler solutions that don't require the file pointer at all.
I'm confused why you would rename your file. What does this accomplish?
Are the log entries fixed size? Or variable size?
If the entries are fixed size, then there is no trouble in re-writing the existing file from the start: you won't ever have incomplete entries in your file, and if you are writing a counter or timestamps to the file, it should be clear where the 'cursor' is located.
If the entries are variable size, then you should probably not begin re-writing the file from the beginning without somehow making it clear where the 'cursor' is located in the file, and write code that is resilient to reading truncated log entries.
Can you re-use existing tools such as RRDtool?