I need to load experimental data into scicoslab, a (pretty badly designed) clone fork of scilab which happens to support graphical modeling. The documentation on the web is pretty poor, but it's reasonably similar to scilab and octave.
The data I need to process is contained into a certain number of text files: Data_005, Data_010, …, Data_100. Each of them can be loaded using the -ascii flag for the loadmatfile command.
The problem comes from the fact that loadmatfile("foo", "-ascii") loads the file foo.mat into a variable named foo. In order to to cycle on the data files, I would need to do something like:
for i = [5:5:100]
name = sprintf("Data_%02d", i);
loadmatfile(name, "-ascii");
x = read_var_from_name(name);
do_something(x);
end
where what I search for is a builtin read_var_from_name which would allow me to access the internal symbol table by string.
Do you know if there exist a similar function?
Notes:
There's no way of overriding this behavior if your file is in ascii format;
In this phase I could also use octave (no graphical modelling is involved), although it behaves in the same way.
>> foo = 3.14; name = 'foo'; eval(name)
foo =
3.1400
The above works in MATLAB, and Scilab's documentation says it also has an eval function. Not sure if I understood you correctly, though.
#arne.b has a good answer.
In your case you can also do that in matlab:
a=load('filename.mat')
x=a.('variable_name')
lets go through your points one by one:
"ScicosLab, a (pretty badly designed) clone of Scilab" This in my opinion is an inaccurate way of introducing the software. ScicosLab is not a clone of Scilab but a fork of it. The team behind ScicosLab (INRIA) are the ones who made scocos (now called xcos in Scilab development line). At some point (from Scilab v4) the Scilab team decided to move away from Tcl/tk towards Java, but the SciccosLab/scicos team departed, keep using the language (Tcl) and it's graphical user interface design package (tk). Giving the ScocosLab community the credit that the whole Scilab documentation and support is not very good in general. :) (more about Scilab and the forks here)
Regarding the technical question I'm not sure what you are trying to achieve here, Scilab/ScicosLab still have the eval function which basically does what you want. However this function is to be deprecated in favor of evstr. There is also the execstr function which worth studying.
The loadmatfile, as far as I have understood, "tries" to load the variables defined in a MATLAB .mat file (MATLAB's proprietary tabular format) into the Scilab workspace. For example if there is a variable foo it will "try" to create the variable foo and loads its value from the MATLAB script. Check this example. I would create a variable x(i) = foo in the for loop. again your question is not completely clear.
As a side note maybe you could consider exporting your data as CSV instead of .mat files.
Related
Fairly simply question, but I cannot find an answer via Google or on Stack.
I have a use-case where it would be highly-preferable to simply read a .m MATLAB script from a URL.
How should I do this correctly?
<disclaimer>
Clearly only do this with files you have complete control of (and/or find a solution with better validation). This is a "dangerous" method as there is no check that you're not about to run a file which, for example, copies your entire harddrive to Bob's computer before corrupting it all. Bob and Alice might be spending the whole evening laughing at your embarrassing holiday photos.
Treat this more as a proof of concept than a how-to, it addresses your problem but by no means should be used in production code.
</disclaimer>
You'll need to use eval to evaluate code. Every time I mention eval I feel compelled to point out it's not recommended, in particular in this case because you could be evaluating whatever random code is living in that file on the web! In this case your only alternative is to save the file locally and call run.
Then you can use
eval(urlread('http://myscript.m'))
or, since urlread is not recommended (from the docs), you can use webread and specify that the output should be text in the options
eval(webread('http://myscript.m', weboptions('ContentType', 'text')))
Using webread appears to be really slow, not sure why when it's the recommended function. In light of this, urlread might be preferable.
There is a note in the webread docs which suggests you wouldn't even need to specify the weboptions
If a web service returns a MATLAB® file with a .m extension, the function returns its content as a character vector.
Although you suggested that webread returned a uint8 variable which didn't work.
If you'd like to save a file from a URL then run it, you can use websave and str2func like so:
fcnName = 'newscript'; % Name for the function/script file
websave([fcnName '.m'], 'http://myscript.m'); % Download and save it
fcn = str2func(fcnName); % Create function handle
fcn(); % Evaluate function/script
It should of course go without saying that you want to be really sure you can trust the source of the file, otherwise you're gonna have a bad time.
I have an .m file which I wish to share with my friends but I am not interested in giving .m file. Could someone help me with best possible ways to convert it to a file that is not decodable?
I tried converting it to .p file by simply typing pcode example.m
however I don't believe it is really protecting it. I was able to convert my .p file back to .m file with the following link. https://sites.google.com/site/sippeyfunlabs/matlab-hacks/please-do-not-secure-your-password-in-matlab-p-code
This actually confirms that my code is not protected.
It'll be nice if someone shares the best methodology to protect .m file and sharing.
Thanks
The link you provided yourself already indicates that it is very difficult to obfuscate MATLAB code:
In fact, MATLAB language is very difficult to be secured or even obfuscated.
This is due to the late binding (or dynamic binding) feature of
MATLAB. [...] The amount of meta information associated with this
feature basically forbid any attempt of adding code level security.
Simply put, if there is a MATLAB file, and it calls a function foo
inside it. Until the runtime, the MATLAB interpreter do not even know
if foo is a function stored in M file or a built-in function or a mex
function or even a workspace function handle. Thus, it must store foo
as is somewhere inside the generated P-code.
Also to best solution is already mentioned on that page:
If there is really a need to do this, using the good old binary is a
much better solution. Or you can put critical code on a server, away
from the user.
Create a binary, i.e. mex file (see the answer of Wolfie): Note that to some extent also binary code can be decompiled especially small ones.
Host your code on a server (and run the code server-side): This is the best method to protect your code. You should let the user upload the input for your script and return the result. You can also automatize this process using a matlab script to make this process transparent to the user.
You could build a mex file.
This will completely obfuscate your actual MATLAB code, since it will be written in C/C++/FORTRAN, but the algorithms will still be there if your friends are determined enough to look for them.
I'm developing a Simulink modell with many C-s-functions. For an easier handling I want to use constants in the c-s-function as in the simulink-modell. So I have a c-header with preprocesser constants like:
#define THIS_IS_A_CONSANT 10
And there is the question:
How it is possible to include this in Simulink in this way I can use THIS_IS_A_CONSANT for example in a constant source like a workspace-variable?
Thanks and regards
Alex
There is functionality in Simulink that will allow you to include custom C header files that define constants, variables, etc.; however, as far as I know (and as one might expect) this really is only pertinent in cases where code is being generated and compiled.
So, for the most part, this particular functionality is only relevant when you are using Simulink Coder to generate a stand-alone executable from your model. For example, this link shows how to include parameters stored in an external header file during code generation through the use of Simulink.Parameter objects with Custom Storage Classes and the Code Generation - Custom Code Pane under the model's Configuration Parameters.
This link from the Simulink doc shows how to use the #define custom storage class to achieve similar results.
However, it sounds like neither of these really solve your issue, as you want to make use of the code in the header file during simulation.
That said, considering that there are elements in Simulink, such as Stateflow Charts and MATLAB Function blocks, that generate and build code "under the hood" during simulation, it's (at least hypothetically) possible that you might be able to use some of the concepts described above to access the values in your header file from one of those elements during simulation. For example, I was successfully able to access preprocessor macros in a Stateflow chart just by going to the Simulation Target->Custom Code pane under Configuration Parameters and including the text #include "header.h" under Include custom C code in generated: Header file. (In this case, header.h contained the line of C code that you included in your post)
Although it seems like you should be able to extend this functionality further, this really was the limit of what I was able to achieve as far as accessing the header file during simulation was concerned. For example, I know that running a model in Rapid Accelerator mode actually generates and builds code under the hood, so seemingly you should be able to use some combination of the techniques I described above to be able to access values from the header file during simulation. It looks like the code that Rapid Accelerator mode generates doesn't respect all of the settings defined by those techniques in the same way that Simulink/Embedded Coder do, though, so I just kept running into compilation errors. (Although maybe I'm just missing some creative combination of settings that could make that work).
Hopefully that helps explain Simulink's abilities (and limitations) regarding the inclusion of C header files. So to summarize, according to the links included above, what you are asking for is almost barely possible, but in practice... not really.
So if really all you want is to be able to create workspace variables out of the preprocessor #define's in your header file, it probably is just easiest to manually parse the file with a MATLAB script, as had previously been suggested in the comments. Here is a quick-and-dirty script that loads in a header file, iterates over each line, uses a regular expression (which you can improve upon if needed) to parse #define statements, and then calls eval to create variables from the parsed input.
filename = 'header.h';
pattern = '^\s*#define\s*(\w*)\s*(\d*\.?\d+)';
fid = fopen(filename);
tline = fgetl(fid);
while ischar(tline)
tokens = regexp(tline, pattern,'tokens','once');
if(numel(tokens) == 2)
eval([tokens{1} ' = ' tokens{2}]);
end
tline = fgetl(fid);
end
fclose(fid);
You could put this code in a callback so that it will execute every time you load your model. Just goto File->Model Properties->Model Properties, click on the Callbacks tab, and then place the code under whichever callback you desire (such as PreLoadFcn if you want it to run immediately before the model loads).
Let us say that I have a Matlab function and I change its signature (i.e. add parameter). As Matlab does not 'compile' is there an easy way to determine which other functions do not use the right signature (i.e. submits the additional parameter). I do not want to determine this at runtime (i.e. get an error message) or have to do text searches. Hope this makes sense. Any feedback would be very much appreciated. Many thanks.
If I understand you correctly, you want to change a function's signature and find all functions/scripts/classes that call it in the "old" way, and change it to the "new" way.
You also indicated you don't want to do it at runtime, or do text searches, but there is no way to detect "incorrect" calls at "parse-time", so I'm afraid these demands leave no option at all to detect old function calls...
What I would do in that case is temporarily add a few lines to the new function:
function myFunc(param1, param2, newParam) % <-- the NEW signature
if nargin == 2
clc, error('old call detected.'); end
and then run the main script/function/whatever in which this function resides. You'll get one error for each time something calls the function incorrectly, along with the error stack in the Matlab command window.
It is then a matter of clicking on the link in the bottom of the error stack, correct the function call, and repeat from the top until no more errors occur.
Don't forget to remove these lines when you're done, or better, replace the word error with warning just to capture anything that was missed.
Better yet: if you're on linux, a text search would be a matter of
$ grep -l 'myFunc(.*,.*); *.m'
which will list all the files having the "incorrect" call. That's not too difficult I'd say...You can probably do a similar thing with the standard windows search, but I can't test that right now.
This is more or less what the dependency report was invented for. Using that tool, you can find what functions/scripts call your altered function. Then it is just a question of manually inspecting every occurrence.
However, I'd advise to make your changes to the function signature such that backwards compatibility is maintained. You can do so by specifying default values for new parameters and/or issuing a warning in those scenarios. That way, your code will run, and you will get run-time hints of deprecated code (which is more or less a necessary evil in interpreted/dynamic languages).
For many dynamic languages (and MATLAB specifically) it is generally impossible to fully inspect the code without the interpreter executing the code. Just imagine the following piece of code:
x = magic(10);
In general, you'd say that the magic function is called. However, magic could map to a totally different function. This could be done in ways that are invisible to a static analysis tool (such as the dependency report): e.g. eval('magic = 1:100;');.
The only way is to go through your whole code base, either inspecting every occurrence manually (which can be found easily with a text search) or by running a test that fully covers your code base.
edit:
There is however a way to access intermediate outputs of the MATLAB parser. This can be accessed using the undocumented and unsupported mtree function (which can be called like this: t = mtree(file, '-file'); for every file in your code base). Using the resulting structure you might be able to find calls with a certain amount of parameters.
This is almost a programming question, but geared towards physicists.
Suppose I am writing a piece of software that takes some system parameters as input and then calculates something from it, in my case a spectral function $A(k,\omega)$.
When I want to just take the output and feed it to gnuplot, I should make the program output a simple table with one column for the $k$-values, one for $\omega$ and one for $A(k,\omega)$.
But then I cannot store there all the additional information, such as what parameters were used. And maybe I want to store in that output some additional debugging information such as intermediate quantities. In my example, the spectral function is obtained from the self energy, so in some situations I might want to look at the self energy directly.
I do not want to constantly hack the source code depending on what output I want. It would be nicer if all the relevant data of a "run" would be present in a single file/entity but so that it is still easy to extract tables I can feed to gnuplot.
Not wanting to reinvent the wheel and develop a full-blown file format, are there some "standards" around that are best used when creating, processing and storing data from calculations or simulations? Maybe even in an SQL database format?
There are dozens of methods, and none too good; I'll share two mine:
If the program is worth it, I add a small parser of config files. Then I just make a cofig, let's say, SimA.in, and simulator makes a bunch of files with corresponding data SimA.paths, SimA.stats, SimA.log, etc. Unless the names are unique and I add version of the code to log, this makes the results fully reproducible and the simulation itself portable enough to be easily manageable.
If not, I just wrap a code a bit and use R as a host. Then I just return all the arrays and scalars (R data structures are very flexible, and it is easy to cast native R or C structs) and use R to manage, save/load and of course visualize and analyse the data. Moreover, with Sweave and CacheSweave the whole executing, analysis and reporting can be bunched in an elegant bunch, fully reproducible with one command.
If you want an "enterprise" solution, try NetCDF or HDF5. But I feel it may be an overkill here.
And of course a version control of the simulator code is a must. But that's obvious =)
For a project I'm currently working on that uses Python and C++ (via SWIG), I'm planning to use a short python script as input file. So, in a way, I'll be 'hacking the source' to change parameters, but in an interpreted language, not a compiled one.
Currently, I plan to have an input file like parameters.py, and use it like from parameters import params. But that might be too dependent on correct syntax.
params = {
"foods" : ["spam", "beans", "eggs"],
"costs" : [199, 4, 1],
"customerAge" : 23,
}
Another option might be to just define the variables at the script level in parameters2.py. This loses the nice dictionary packaging, but makes it a little harder for the user to mess it up. And it probably wouldn't be to hard to write a 'parser' that puts those script-level variables into a nice dictionary. A plus to method is that the user could parameterize things that weren't originally considered--from parameters2 import * would overwrite previous definitions of those parameters. Of course, this might be bad if the user overwrites something important.
foods = ["spam", "beans", "eggs"]
costs = [199, 4, 1]
customerAge = 23
parameters3.py would use a class, though it is contraindicated by Python's persnicketiness about indentation. from parameters3 import params:
class params:
foods = ["spam", "beans", "eggs"]
costs = [199, 4, 1]
customerAge = 23
I should also mention, for completeness, that our C++ code also defines a parameters class. That is, in our actual project, parameters.py is a SWIG wrapper for a corresponding C++ class. You'd use like from parameters4 import params. However, this allows only parameters that are already declared in the C++ class.
import parameters
params = parameters.Parameters()
params.foods = ["spam", "beans", "eggs"]
params.costs = [199, 4, 1]
params.customerAge = 23