I want to have a std.m file for the standard deviation. It is in data fun toolbox, but, by mistake, I changed the code and the std command is not working anymore. How can I run the original std (standard deviation) command?
Taking all the comments out, the function std.m is actually extremely simple:
function y = std(varargin)
y = sqrt(var(varargin{:}));
This is the definition of the standard deviation: the square root of the Variance.
Set built-in functions to Read-Only
Now don't go breaking the var.m file because it is more complex and I wonder if there would be copyright issue to display the listing here.
To avoid the problem of breaking built-in files, it is advisable to set all your Matlab toolbox files as Read Only. I remember old Matlab installer giving the option to do that at install time. I don't know if the installer still offers the option, but if not it is extremely easy to do it manually (on Windows, just select your folders, right-click Properties, tick read only and accept to propagate the property to all subfolders and files).
Overloading
Once this is done, your built-in files are safe. You can still modify the default behavior of a built-in function by overloading it. This consist in writing a function with the same name and arrange for it to be called before the default function (your overload function becomes the default one).
This article explain how to overload user functions.
Matlab does not recommend to directly overload the built-in functions (rather call it another name like mySTD.m for example), but if you insist it is perfectly feasible and still a much better option than modifying the built-in function... at least the original function is still intact somewhere.
Related
In MATLAB, there are roughly 3 ways to define functions: non-comment-only .m files, .p files, and compiled code (e.g. DLL, MEX).
Knowing where a function is defined could be helpful in several cases, such as when a breaking change was introduced to some function outside our control, and we'd like to try to revert to an old version in the hopes of getting our code working again; or when trying to reverse-engineering some undisclosed algorithm.
The which function is usually very good at identifying function definitions and their locations (which works for .m, .p and MEX), but isn't very useful when it comes to shared library functions, where (at best) it points to a comment-only documentation file:
>> which _mcheck
built-in (undocumented)
>> which svd
built-in (D:\Program Files\MATLAB\R2019a\toolbox\matlab\matfun\svd)
If so, assuming a function found within a shared library is called during the execution of my code, how can I locate the specific file (DLL) that contains it?
It turns out that dbstop can be used for this. For example:
>> which svd
built-in (D:\Program Files\MATLAB\R2019a\toolbox\matlab\matfun\svd)
>> dbstop svd
Warning: Entering debug mode is only supported within running MATLAB code files.
Warning: MATLAB debugger can only stop in MATLAB code files, and "libmwmathlinalg>svd" is not a MATLAB code file.
Instead, the debugger will stop at the point right before "libmwmathlinalg>svd" is called.
From there's it's just a matter of finding a file called libmwmathlinalg (with the relevant extension) - which isn't a difficult task if your drive is indexed.
My problem is the following:
I have very many (~1000) mutually calling Matlab scripts, which are very poorly written, regularly damage each other's environments and generally became unmanageable.
One of the reasons I even got this problem is that I need to write a testsuite covering a big part of them. Luckily, for most of them the main criterion of 'correctness' is 'they don't crash'.
Just running them one by one in a loop is generally not an option, because they regularly call clear classes, close all, clc, shadow built-in functions and operators, et cetera.
So my original aim was to find a way to run a matlab script in sort of an 'isolated environment', but I didn't find a good way to do it. (Suggestions welcome, but it is not the main question.)
Since I will need to convert them all to functions anyway, I am looking for some way to do it auto-magically, or at least semi-automatically.
What I can mean semi-automatically:
Just add a line function varargout = $filename( varargin ) as the first line of the file, and end as the last one. This will at least make them runnable as functions with feval and all such functions and (more importantly) prevent them from damaging the test-runner.
Do point 1 and scan the file for referencing undeclared variables and add them as function arguments. This should be also doable, since the names of the variables are known. This will not help identifying output variables, but will still be a lot of help. For example, we could pack the whole workspace into one big output structure.
Do a runtime version of point 2. This way the 'magical converter' can actually track execution environments (workspaces) and identify which variables are implicitly used as 'input arguments' of a script, and which would be later used 'output arguments'. This option looks EXPHARD, but for a small number of calls should be not too bad in practice.
Point 1 I can implement myself using sed, as I also can get rid of all clear classes and clc, but the options 2 and 3 seem much harder. Is there anything at least remotely resembling options 2 or 3?
The publish function in MATLAB works for both scripts and functions,
while the one for Octave works only for scripts: if I enter
publish myFunc.m
Octave gave
error: publish: Only Octave script files can be published.
Am I able to publish a function in Octave? If yes, how?
You can use Octave Forge generate_html package which is meant to generate html of individual functions. It is mostly used to generate the documentation of Octave Forge packages, and its defaults reflect that, but you could add any style you want.
This package will use the same help text that the help function in Octave sees which is the first block of comments in the file that does not start by Copyright or Author. You can have it in plain text but for nicer formatting, you can use Texinfo. In that case, the first line of the help text should be -*- texinfo -*-. There is a page on the Octave wiki with tips on how to write nice help text including a short section on Texinfo syntax (the actual Texinfo manual can be a bit overwhelming).
In addition to the help text, the generate_html package also identifies %!demo blocks and generates a section with the demo code and output it generates, including figures.
The best way to see how help text and demo blocks work in Octave is to check the source (as #Andy pointed out in the comments). For example, see the source for inpolygon (scroll to the bottom to find the %!demo blocks, right before %!test and %!error). The generate_html package generates this page (note the Demonstration blocks).
This is a "multiple questions in one" question, making lots of assumptions in between, so let's address those first:
1. I'll start by the question in the comment, since that's the easiest: Matlab's publisher is not a code documentation tool. It's a "make a quick report that includes both text and code to show at your supervisor meeting or write a quick point in a blog" tool. So the link you point to is simply irrelevant in this case, since that talks about documentation for matlab code.
2. The fact that matlab's publisher also "works for functions", particularly given the first point here, should be considered to be more of a bug than a feature, or at most as a trivial undocumented extension. If you look at the matlab documentation for the publish command, you'll see it expects a filename, not a function with arguments, and the documentation only talks about scripts and makes no mention of 'function' compatibility.
3. Furthermore, even if you did want to use publisher as a "documentation tool", this is counterintuitive for functions in this format, since you need to provide arguments in order for publisher to work (which will not be shown in the actual report), you'll need a modified version that displays intermediate calculations (as opposed to your normal version which presumably does not), and the function just spews an ugly ans= blabla at the end of the report. If your end goal is documentation, it might be best to write a bespoke script for this anyway, showing proper usage and examples, like matlab does in its actual documentation.
Having said all that, yes, there is a 'cheat' you can do to include a function's code in your published report, which is that, in octave (also matlab since R2016b), functions can be defined locally. A .m file that only contains function definitions is interpreted as a function file, but if there are other non-function-declaration instructions preceding the function definitions (other than comments), then it is seen as a script. So if you publish this script, you effectively get a published report with function code in it:
%% Adding function
% This function takes an input and adds 5 to it.
%% Example inputs
In = 10;
%% The function itself
% Marvel at its beauty!
function Out = myfun(In)
%% Here is where the addition takes place.
% It is a beautiful addition
Out = In + 5;
end
%% Example use
Out = myfun(In)
(If you're not happy about having to create a 'wrapper script' manually, you can always create your own wrapper function that does this automatically).
However, both the matlab and octave publishers are limited tools by design. Like I said earlier, it's more of a "quick report to show numbers and plots to your supervisor" tool, rather than a "make nice documentation or professional reports" tool. Instead, I would invest in a nice automated latex workflow, and have a look at code formatting tools for displaying code, and simply wrap that code in a script that produces output to a file that you can then import into latex. It may sound like more work, but it's a lot more flexible and robust in the long term, particularly since the formatting commands can be very quirky as well as limited.
I am defining a variable in the beginning of my source code in MATLAB. Now I would like to know at which lines this variable effects something. In other words, I would like to see all lines in which that variable is read out. This wish does not only include all accesses in the current function, but also possible accesses in sub-functions that use this variable as an input argument. In this way, I can see in a quick way where my change of this variable takes any influence.
Is there any possibility to do so in MATLAB? A graphical marking of the corresponding lines would be nice but a command line output might be even more practical.
You may always use "Find Files" to search for a certain keyword or expression. In my R2012a/Windows version is in Edit > Find Files..., with the keyboard shortcut [CTRL] + [SHIFT] + [F].
The result will be a list of lines where the searched string is found, in all the files found in the specified folder. Please check out the options in the search dialog for more details and flexibility.
Later edit: thanks to #zinjaai, I noticed that #tc88 required that this tool should track the effect of the name of the variable inside the functions/subfunctions. I think this is:
very difficult to achieve. The problem of running trough all the possible values and branching on every possible conditional expression is... well is hard. I think is halting-problem-hard.
in 90% of the case the assumption that the output of a function is influenced by the input is true. But the input and the output are part of the same statement (assigning the result of a function) so looking for where the variable is used as argument should suffice to identify what output variables are affected..
There are perverse cases where functions will alter arguments that are handle-type (because the argument is not copied, but referenced). This side-effect will break the assumption 2, and is one of the main reasons why 1. Outlining the cases when these side effects take place is again, hard, and is better to assume that all of them are modified.
Some other cases are inherently undecidable, because they don't depend on the computer states, but on the state of the "outside world". Example: suppose one calls uigetfile. The function returns a char type when the user selects a file, and a double type for the case when the user chooses not to select a file. Obviously the two cases will be treated differently. How could you know which variables are created/modified before the user deciding?
In conclusion: I think that human intuition, plus the MATLAB Debugger (for run time), and the Find Files (for quick search where a variable is used) and depfun (for quick identification of function dependence) is way cheaper. But I would like to be wrong. :-)
I am relatively new at Matlab.
I am trying to create an alias for a command that looks like the following.
run('full/path/to/some/script').
In particular, I would like to be able to write something equivalent to Bash's
alias myAlias = run('full/path/to/some/script')
And then be able to type myAlias and get the same effect as the right hand side.
I have looked at the documentation here, but I still get the error Undefined function or variable 'alias' when I try to use it, even after I first type syms at the prompt, so I believe that either I am not importing the toolbox correctly or this is not a feature in R2011b.
One additional requirement is that I would like the alias to stick even after I call clear, which should clear all the other active variables in the workspace.
for example:
f = #() run('foldername\scriptname')
then just writing f() will execute scriptname.
Here I've used an anonymous function, you can add more content to it if needed.
You can make #natan's answer tolerate clearing the workspace by making it an m-file.
In myAlias.m, put run('full/path/to/some/script'). I'm sure you are aware of this solution, but you might not want to do so, because of the resulting messy file system.
You can simply add the m-file to some folder and use addpath('where/ever/you/put/the/script') to make it accessible.