In MATLAB, how do you tell where in the code a variable is getting output?
I have about 10K lines of MATLAB code with about 4 people working on it. Somewhere, someone has dumped a variable in a MATLAB script in the typical way:
foo
Unfortunately, I do not know what variable is getting output. And the output is cluttering out other more important outputs.
Any ideas?
p.s. Anyone ever try overwriting Standard.out? Since MATLAB and Java integration is so tight, would that work? A trick I've used in Java when faced with this problem is to replace Standard.out with my own version.
Ooh, I hate this too. I wish Matlab had a "dbstop if display" to stop on exactly this.
The mlint traversal from weiyin is a good idea. Mlint can't see dynamic code, though, such as arguments to eval() or string-valued figure handle callbacks. I've run in to output like this in callbacks like this, where update_table() returns something in some conditions.
uicontrol('Style','pushbutton', 'Callback','update_table')
You can "duck-punch" a method in to built-in types to give you a hook for dbstop. In a directory on your Matlab path, create a new directory named "#double", and make a #double/display.m file like this.
function display(varargin)
builtin('display', varargin{:});
Then you can do
dbstop in double/display at 2
and run your code. Now you'll be dropped in to the debugger whenever display is implicitly called by the omitted semicolon, including from dynamic code. Doing it for #double seems to cover char and cells as well. If it's a different type being displayed, you may have to experiment.
You could probably override the built-in disp() the same way. I think this would be analagous to a custom replacement for Java's System.out stream.
Needless to say, adding methods to built-in types is nonstandard, unsupported, very error-prone, and something to be very wary of outside a debugging session.
This is a typical pattern that mLint will help you find:
So, look on the right hand side of the editor for the orange lines. This will help you find not only this optimization, but many, many more. Notice also that your variable name is highlighted.
If you have a line such as:
foo = 2
and there is no ";" on the end, then the output will be dumped to the screen with the variable name appearing first:
foo =
2
In this case, you should search the file for the string "foo =" and find the line missing a ";".
If you are seeing output with no variable name appearing, then the output is probably being dumped to the screen using either the DISP or FPRINTF function. Searching the file for "disp" or "fprintf" should help you find where the data is being displayed.
If you are seeing output with the variable name "ans" appearing, this is a case when a computation is being done, not being put in a variable, and is missing a ';' at the end of the line, such as:
size(foo)
In general, this is a bad practice for displaying what's going on in the code, since (as you have found out) it can be hard to find where these have been placed in a large piece of code. In this case, the easiest way to find the offending line is to use MLINT, as other answers have suggested.
I like the idea of "dbstop if display", however this is not a dbstop option that i know of.
If all else fails, there is still hope. Mlint is a good idea, but if there are many thousands of lines and many functions, then you may never find the offender. Worse, if this code has been sloppily written, there will be zillions of mlint flags that appear. How will you narrow it down?
A solution is to display your way there. I would overload the display function. Only temporarily, but this will work. If the output is being dumped to the command line as
ans =
stuff
or as
foo =
stuff
Then it has been written out with display. If it is coming out as just
stuff
then disp is the culprit. Why does it matter? Overload the offender. Create a new directory in some directory that is on top of your MATLAB search path, called #double (assuming that the output is a double variable. If it is character, then you will need an #char directory.) Do NOT put the #double directory itself on the MATLAB search path, just put it in some directory that is on your path.
Inside this directory, put a new m-file called disp.m or display.m, depending upon your determination of what has done the command line output. The contents of the m-file will be a call to the function builtin, which will allow you to then call the builtin version of disp or display on the input.
Now, set a debugging point inside the new function. Every time output is generated to the screen, this function will be called. If there are multiple events, you may need to use the debugger to allow processing to proceed until the offender has been trapped. Eventually, this process will trap the offensive line. Remember, you are in the debugger! Use the debugger to determine which function called disp, and where. You can step out of disp or display, or just look at the contents of dbstack to see what has happened.
When all is done and the problem repaired, delete this extra directory, and the disp/display function you put in it.
You could run mlint as a function and interpret the results.
>> I = mlint('filename','-struct');
>> isErrorMessage = arrayfun(#(S)strcmp(S.message,...
'Terminate statement with semicolon to suppress output (in functions).'),I);
>>I(isErrorMessage ).line
This will only find missing semicolons in that single file. So this would have to be run on a list of files (functions) that are called from some main function.
If you wanted to find calls to disp() or fprintf() you would need to read in the text of the file and use regular expresions to find the calls.
Note: If you are using a script instead of a function you will need to change the above message to read: 'Terminate statement with semicolon to suppress output (in scripts).'
Andrew Janke's overloading is a very useful tip
the only other thing is instead of using dbstop I find the following works better, for the simple reason that putting a stop in display.m will cause execution to pause, every time display.m is called, even if nothing is written.
This way, the stop will only be triggered when display is called to write a non null string, and you won't have to step through a potentially very large number of useless display calls
function display(varargin)
builtin('display', varargin{:});
if isempty(varargin{1})==0
keyboard
end
A foolproof way of locating such things is to iteratively step through the code in the debugger observing the output. This would proceed as follows:
Add a break point at the first line of the highest level script/function which produces the undesired output. Run the function/script.
step over the lines (not stepping in) until you see the undesired output.
When you find the line/function which produces the output, either fix it, if it's in this file, or open the subfunction/script which is producing the output. Remove the break point from the higher level function, and put a break point in the first line of the lower-level function. Repeat from step 1 until the line producing the output is located.
Although a pain, you will find the line relatively quickly this way unless you have huge functions/scripts, which is bad practice anyway. If the scripts are like this you could use a sort of partitioning approach to locate the line in the function in a similar manner. This would involve putting a break point at the start, then one half way though and noting which half of the function produces the output, then halving again and so on until the line is located.
I had this problem with much smaller code and it's a bugger, so even though the OP found their solution, I'll post a small cheat I learned.
1) In the Matlab command prompt, turn on 'more'.
more on
2) Resize the prompt-y/terminal-y part of the window to a mere line of text in height.
3) Run the code. It will stop wherever it needed to print, as there isn't the space to print it ( more is blocking on a [space] or [down] press ).
4) Press [ctrl]-[C] to kill your program at the spot where it couldn't print.
5) Return your prompt-y area to normal size. Starting at the top of trace, click on the clickable bits in the red text. These are your potential culprits. (Of course, you may need to have pressed [down], etc, to pass parts where the code was actually intended to print things.)
You'll need to traverse all your m-files (probably using a recursive function, or unix('find -type f -iname *.m') ). Call mlint on each filename:
r = mlint(filename);
r will be a (possibly empty) structure with a message field. Look for the message that starts with "Terminate statement with semicolon to suppress output".
I have been using the perl interactive debugger (basically perl -d script)
I have a script that has quite a lot of modules imported and I need to debug a problem.
What I do is start the debugger and go over lines, stepping into where necessary.
But this is tedious as I need to step into many lines of code and function calls.
Question: Let's say that after going over the lines of code I eventually step into function A::B::C::foo() of some module where is the problem I am debugging.
Is there a way to set a break point in that function in the beginning of the debugging session so that I jump there directly instead of going over the code line by line until I reach there?
I know that I can add a break point in the same file my debugger is currently but how can I add a breakpoint in a line that is outside of the debugger's scope at this point (to some arbitrary file/module that eventually the debugger would have reached)?
Note:
Just to clarify: It is not like A::B::C::foo() is in line X of the script. It is eventually called after going down the call chain of a lot other functions in many modules
You can set a breakpoint to a subroutine with the documented b sub syntax. In this case, just use
b A::B::C::foo
c
You may set a break point by defining file name and then line number
b YourModule.pm:line_number
where line number is inside the module function you want to break at.
You can even put a breakpoint on a sub that hasn't been loaded/defined yet using the postpone option:
b postpone Name::Of::Sub::Yet::To::Be::Created
I'm using a closed-source MEX function, so I don't know this works behind the scenes. I supply it a function name as a string, and the MEX calls this function repeatedly with a long delay (seconds to minutes). While developing, I'd like to change my supplied function without restarting the MEX function.
the_MEX_function( 'my_function' );
I've tried this:
just editing my_function
calling my_function_2 from my_function, and editing my_function_2
Do you have any ideas of what else could work?
You don't say why calling my_function_2 from my_function doesn't work. This seems like the right strategy, but my_function should clear my_function_2 before execution during development to ensure it is reloaded; so, either from the command line or within my_function, include:
clear my_function_2
Remove this in production code to avoid a significant performance hit.
Before calling the mex for the first time
Make a text file that contains the code you want (better a single line). This should decide what my_function does.
Change my_function to do the following read the text file and eval the code there.
Run the mex file with my_function
During the mex execution, you may change the contents of the txt file to point my_function to different code.
Not a very good practice, though...
I have created a simulation in matlab. It is a script file where I have a main for cycle and inside it, I have written some code and functions. I have used fprintf function to debug my code during the development to check if everything go well. When I run my simulation instead I would not execute fprintf because It needs so many time to execute fprintf since my for cycle is executed 1E6. I would a way to decide when execute fprintf and when not.
Two options:
1) include some variable called "debug" for example, and put every fprintf() in:
if (debug==1):
fprintf(blah blah)
then you just need to change the debug variable at the beginning of your program when debugging, or you can even get it as input from the user (a flag).
2) wrap fprintf in a function, and then just use that function instead, something like:
function myfprintf(x)
global debug
if (debug==1):
fprintf(x)
I have a MATLAB script that worked perfectly fine; there were no problems with it whatsoever. Then I moved it into the MATLAB toolbox and added it to the cache so I could run it easily from the command line.
However, now that I have moved it into the toolbox, I get these error messages! There were no changes to the script or anything. I moved all of the subfolders and other files related to the script with it.
I have no idea why it is giving me this error message. Even worse, it does not do it every time I run the script! Sometimes if I close MATLAB and open it again, the script runs fine. Sometimes all I have to do is click anything in the GUI and it works! But the next time it won't? Can you help me out here?
These are the two error messages it gives me:
??? Too many outputs requested. Most likely cause is missing [] around
left hand side that has a comma separated list expansion.
Error in ==> trials at 13
picture1 = files1.name;
Error in ==> semjudge>TRIAL_Callback at 285
trials;
??? Error using ==> waitfor
Error while evaluating uicontrol Callback
And:
??? Error using ==> nchoosek at 31
The first argument has to be a scalar or a vector.
Error in ==> semjudge>START_Callback at 194
combos = nchoosek(1:nFiles, 2);
??? Error using ==> waitfor
Error while evaluating uicontrol Callback
What causes these errors, such that they only SOMETIMES appear (without any change in the .m file or the GUI or anything ...)?
This is frustrating me to no end. It was working perfectly fine, and stopped despite no changes being made. And it is inconsistent whether or not it gives me the error. I can't find any pattern to when it does work, and when it doesn't. And neither of the errors that it DOES give me make any sense to me.
The .m file(s) are too long to post here, so you can see them, here:
http://textuploader.com/?p=6&id=cKokK (semjudge.m)
http://textuploader.com/?p=6&id=vB9sD (trials.m)
It seems your script is not always able to find certain image files.
In trials.m files1 is probably an empty struct array so the assignment to picture fails. This can be caused by dir not finding appropriate files.
In semjudge.m, if there are no files, nFiles is 0, so 1:nFiles is the empty array.