We have a lot of MATLAB code in my lab. The problem is there's really no way to organize it. Since all the functions have to be in the same folder to be called (or you have to add a bunch of folders to MATLAB's path environment variable), it seems that we're doomed have loads of files in the same folder, all in the global namespace. Is there a better way to organize our files and functions? I really wish there were some sort of module system...
MATLAB has a notion of packages which can be nested and include both classes and functions.
Just make a directory somewhere on your path with a + as the first character, like +mypkg. Then, if there is a class or function in that directory, it may be referred to as mypkg.mything. You can also import from a package using import mypkg.mysubpkg.*.
The one main gotcha about moving a bunch of functions into a package is that functions and classes do not automatically import the package they live in. This means that if you have a bunch of functions in different m-files that call each other, you may have to spend a while dropping imports in or qualifying function calls. Don't forget to put imports into subfunctions that call out as well. More info:
http://www.mathworks.com/help/matlab/matlab_oop/scoping-classes-with-packages.html
I don't see the problem with having to add some folder to Matlab's search path. I have modified startup.m so that it recursively looks for directories in my Matlab startup directory, and adds them to the path (it also runs svn update on everything). This way, if I change the directory structure, Matlab is still going to see all the functions the next time I start it.
Otherwise, you can look into object-oriented code, where you store all the methods in a #objectName folder. However, this may lead to a lot of re-writing code that can be avoided by updating the path (there is even a button add with subfolders if you add the folder to the path from the File menu) and doing a bit of moving code.
EDIT
If you would like to organize your code so that some functions are only visible to the functions that call them directly (and if you don't want to re-write in OOP), you put the calling functions in a directory, and within this directory, you create a subdirectory called private. The functions in there will only be visible to the functions in the parent directory. This is very useful if you have to overload some built-in Matlab functions for a subset of your code.
Another way to organize & reuse code is using matlab's object-oriented features. Each Object is customarily in a folder that begins with an "#" and has the file(s) for that class inside. (though the newer syntax does not require this for a class defined in a single file.) Using private folders inside class folders, matlab even supports private class members. Matlab's new class notation is relatively fully-featured, but even the old syntax is useful.
BTW, my startup.m that examines a well-known location that I do my SVN checkouts into, and adds all of the subfolders onto my path automatically.
The package system is probably the best. I use the class system (#ClassName folder), but I actually write objects. If you're not doing that, it's silly just to write a bunch of static methods. One thing that can be helpful is to put all your matlab code into a folder that isn't on the matlab path. Then you can selectively add just the code you need to the path.
So say you have two projects, stored in "c:\matlabcode\foo" and "c"\matlabcode\bar", that both use common code stored in "c:\matlabcode\common," you might have a function "setupPaths.m" like this:
function setupPaths(projectName)
basedir = fullfile('c:', 'matlabcode');
addpath(genpath(fullfile(basedir, projectName)));
switch (projectName)
case {'foo', 'bar'}
addpath(genpath(fullfile(basedir, 'common')));
end
Of course you could extend this. An obvious extension would be to include a text file in each directory saying what other directories should be added to the path to use the functions in that directory.
Another useful thing if you share code is to set up a "user specific/LabMember" directory structure, where you have different lab members save code they are working on. That way you have access to their code if you need it, but don't get clobbered when they write a function with the same name as one of yours.
Related
I would like to use two versions of the same Matlab software package at the same time (I would like to compare their outputs for testing). The package modifies the path so that functions in subdirectories can be found. This seems problematic since the package assumes that it is the only copy running on the machine. The path is essentially a global variable which is unintentionally shared between the two copies of the code.
Example simplified code structure:
/main_code.m
/compare_results.m
/code_a/somefn.m
/code_a/submethods/
/code_b/somefn.m
/code_b/submethods/
Note that somefn.m adds the submethods directory to the path, and calls code from the submethods folder by relying on the path.
Example of code that I would like to run:
for i = 1:1000000
% Run version A:
result_a = code_a.somefn(i);
% Run version B:
result_b = code_b.somefn(i);
% Compare the output from the two versions:
compare_results(a,b);
end
One solution that I can think of is to manually update the Matlab path every time that I want to switch to a different version of the package. This seems like unnecessary coding overhead, and potentially a performance problem (due to switching the path so often).
Another solution might be to rewrite the code to be object oriented, so that the functions are attached to objects, and I can create objects of different versions. The problem with this is that in reality the code package contains hundreds of files, and I was not the original author so rewriting would be a huge task .
(Yet another option would be to change directory all the time, so that the code to run is always in the current directory. This would be so much of a headache due to the number of subfolders that I do not think this is a serious solution. It also has potential performance overhead drawbacks similar to always changing the path.)
Is there a cleaner way to handle this? Can I somehow specify the folder of the code that I want to run? What is the best way to design such a code package so that this problem does not come up?
Just create packages, which can contain functions with the same names: Packages Create Namespaces
Basically create two folders named, say, +package1 and +package2. The "+" in the folder name is important. Then place your functions under both of them, say, foo.m. Then, you can call each separately without messing with MATLAB path as:
>> package1.foo
>> package2.foo
You can use private functions. Change the directory structure as:
/main_code.m
/compare_results.m
/+code_a/somefn.m
/+code_a/private/
/+code_b/somefn.m
/+code_b/private/
Each somefn has access to the functions contained in its private sub-folder. So there is no need to create global variable and to add private sub-folders to the path.
In MATLAB, a class folder is represented by foo/#bar/ and a package folder is represented by foo/+bar. In my hierarchy, I have classes that define methods in separate files, so the #bar/ convention is necessary for their containing folders. However, I also have methods that get somewhat complex in their implementation, and would like to have them packaged into... well, packages using the +bar/ convention, like so:
foo/#classfolder/MyClass.m
foo/#classfolder/method1.m
foo/#classfolder/method2.m
foo/#classfolder/+othermethodstuff/method2helper.m
foo/#classfolder/+othermethodstuff/mexmethod_formethod2helper.m
foo/#classfolder/+othermethodstuff/mexfiles/
I want to do this because methods in my actual code that are represented here by method2.m rely on some heavy computations from MEX files that I would prefer to reside in their own folder, with the package system used by MATLAB keeping it clear when I am calling those methods (and from where).
Is this possible? If not, is my only other option dropping the # class folder convention and sticking everything into package (+) folders?
You should put those private implementation files in a subdirectory private. That is the traditional location for them. If you want to create some obvious hierarchy to organize code, I recommend long file names.
For example:
foo/#classfolder/MyClass.m
foo/#classfolder/method1.m
foo/#classfolder/method2.m
foo/#classfolder/private/physicssimulation_function1.m
foo/#classfolder/private/physicssimulation_function2.m
foo/#classfolder/private/physicssimulation_mexfile.mex
foo/#classfolder/private/uihelper_functionA.m
foo/#classfolder/private/uihelper_functionB.m
M-files and MEX-files in the private directory can be called from any function in the #classfolder directory, as if they were on the path (i.e. you don’t use private when calling them). But they are private to that directory, and not visible from outside.
The above recommendation assumes multiple class methods use the same private functionality. If only one method uses physicssimulation, then all of its functions should be inside that method’s M-file. It’s the better way of keeping code together.
I would like to structure my project in several packages. Each package should be each own namespace (so as to avoid conflicting filename) but within a package, I want everything to be in the same namespace (without having to put all the files in the same folder; I'd like different folders).
In practice I would like this structure
Project
main.m
commonLibrary
+part1Project
mainPart1.m
otherFolder
supportFile.m
+part2Project
mainPart2.m
otherFolder2
supportFile2.m
This is the behavious I would like:
When in main.m, I can call everything in common library and everything in any sub-project, including the functions inside the subfolder. So I would like to call part1Project.supportFile
When in mainPart1.m, I want to call the support files without using the prefix of the current package (i.e. I want to call supportFile directly)
When in mainPart2, I want to call supportFile2 directly. If I want access to files in the the part 1 of the project, I can call part1Project.supportFile.
The current setup is that I added the Project folder and all the subfolders to the matlab path. But this means that
I CANNOT call supportFile from anywhere; not from main (part1Project.supportFile will not work) and not even from mainPart1 (supportFile can't be found)
Much in the same way, it is hard to access elements of part1Project from part2Project
How can I achieve the behaviour I want?
You cannot access functions within a subfolder of a package unless that subfolder is a private folder in which case it will only be accessible to the functions in the immediate parent folder.
If you do use the private folder approach, then you can call functions within this private folder from the functions in the containing folder without using the fully-qualified package name.
Your layout would look like:
Project
main.m
commonLibrary
+part1Project
mainPart1.m
private
supportFile.m
+part2Project
mainPart2.m
private
supportFile2.m
Your first point will not work but the other two will. There is no built-in way to accomplish the first point.
Another option would be to use import statements in all functions within each package such that it imports all package members at the beginning of the function.
Your layout would look like
Project
main.m
commonLibrary
+part1Project
mainPart1.m
supportFile.m
+part2Project
mainPart2.m
supportFile2.m
And the contents of mainPart1.m (any any function) would look something like:
function mainPart1()
% Import the entire namespace
import part1Project.*
% No package name required
supportFile()
end
And then from main you could access supportFile
function main()
part1Project.supportFile()
end
As a follow up to my previous question, I run into a new obstacle: how to generate stubs for functions in a toolbox?
I found Andy Campbell's solution for the non toolbox case. This does not work in my case because Matlab complains: package directories are not allowed in MATLAB path in Pathfixtures!
I also don't see how this concept will overwrite the import statements within the toolbox, e.g. in file2.
This is my setup:
+folder1/file1.m
+folder1/runtestsuite.m
+folder1/unittest_data/file1_testdata.mat
+folder1/+folder2/file2.m
+folder1/+folder2/unittest_data/overloads/file1.m
...
Let's say I want to stub file1 in file2. And file2 has as a first statement: import folder1.file1.
With
methods(Access=private)
function inject_file1_stub(testCase, answer)
import matlab.unittest.fixtures.PathFixture;
testCase.applyFixture(PathFixture(fullfile(testCase.path,'overloads')));
file1('', answer);
end
end
So currently I believe this concept is not applicable in my case, so how is this done correctly with matlab?
I know one can shadow an implementation of a function in a toolbox, if one adds another path with the same toolboxname and function to the path. For this I would have to recreate a subset of the current folder setup:
So my current idea for a fixture is
create temporary folder with tempdir
use mfilename to check what subset of the toolbox directories I have to recreate
generate folder structure
copy from the overload folder to the new toolbox system
Add this to path
Run tests
In teardown
remove the temporary folder
remove the entry from path
I have not implemented this yet, and seems a bit redundant knowing that there is a Pathfixture in matlab already.
Pointers to other toolboxes which show how they have solved these kind of problems are also welcome.
It is true that you can't add subfolders of packages to the path, but that doesn't mean you can't shadow these path functions. To do this you need to separate the test related content out of your source location. For example, if your source looks like:
<source-home>/+folder1/file1.m
<source-home>/+folder1/+folder2/file2.m
Then you can put your tests somewhere else so your structure would look something like:
<test-home>/file1Test.m
<test-home>/file2Test.m % could also put tests into packages if you want
<test-home>/overloads/+folder1/file1.m
<test-home>/overloads/+folder1/+folder2/file2.m
Then inside of file1Test and/or file2Test you would use a PathFixture to add:
<test-home>/overloads/
to the path.
Also, another thing to consider is defining an interface in your source code for these dependencies and leveraging dependency injection (with or without a DI framework) in order to get test specific behavior into your tests.
Let us assume, I want to use a foreign Matlab library with a structure like this:
folderName
play.m
run.m
open.m
If I simply add folderName to my Matlab path variable, it will easily yield name conflicts. I don't want to rename the files, to be able to obtain new releases of the example library (the package concept is not used in the example library). Renaming would need to modify the code as well, if there are calls from one library function to the other.
How do I write local wrappers, which wrap the functions from that example library? My wrappers could then have my desired names and input parameters.
Clarification: How do I use an external library (toolbox) without name conflicts, without renaming and without modifying each function?
Rename files: Makes it hard to update the external library.
Simply put them in a package folder: This will break internal library function calls.
You want to use a package, which will establish a namespace, such that things in the package, are then qualified with the package name. You can find more information here: http://www.mathworks.com/help/matlab/matlab_oop/scoping-classes-with-packages.html