I have taken over a large code base and would like to get an overview how and where certain classes and their methods are used.
Is there any good tool that can somehow visualize the dependencies and draw a nice call tree or something similar?
The code is in C++ in Visual Studio if that helps narrow down any selection.
Here are a few options:
CodeDrawer
CC-RIDER
Doxygen
The last one, doxygen, is more of an automatic documentation tool, but it is capable of generating dependency graphs and inheritance diagrams. It's also licensed under the GPL, unlike the first two which are not free.
When I have used Doxygen it has produced a full list of callers and callees. I think you have to turn it on.
David, thanks for the suggestions. I spent the weekend trialing the programs.
Doxygen seems to be the most comprehensive of the 3, but it still leaves some things to be desired in regard to callers of methods.
All 3 seem to have problems with C++ templates to varying degrees. CC-Rider simply crashed in the middle of the analysis and CodeDrawer does not show many of the relationships. Doxygen worked pretty well, but it too did not find and show all relations and instead overwhelmed me with lots of macro references until I filtered them out.
So, maybe I should clarify "large codebase" a bit for eventual other suggestions: >100k lines of code overall spread out over more than 100 template files plus several actual class files pulling it all together.
Any other tools out there, that might be up to the task and could do better (more thoroughly)? Oh and specifically: anything that understands IDL and COM interfaces?
When I have used Doxygen it has produced a full list of callers and callees. I think you have to turn it on.
I did that of course, but like I mentioned, doxygen does not consider interfaces between objects as they are defined in the IDL. It "only" shows direct C++ calls.
Don't get me wrong, it is already amazing what it does, but it is still not complete from my high level view trying to get a good understanding of how everything fits together.
In Java I would start with JDepend. In .NET, with NDepend. Don't know about C++.
Related
I'm looking for a tool to convert a SBML model into a Matlab function. I've tried SBMLTranslate() function from libSBML but this returns a Matlab struct, not a function. Does anybody know if such tool exists? Thanks
There are at least three efforts in this direction:
Frank Bergmann offers an online service for SBML translation where you can upload an SBML file and it will generate a MATLAB file. The comments at the top of the generated MATLAB file explain how to use the results. The C++ source code is available on SourceForge.
Bergmann's code referenced above was used by Stanley Gu to create sbml2matlab, a Windows standalone program. Off-hand, I don't know whether Gu's version changed or enhanced the algorithm used by the Bergmann version, but it seems likely. (Note: Gu now works at Google and does not maintain this code anymore, as far as I know.)
The Systems Biology Format Converter (SBFC) is a framework written principally by Nicolas Rodriguez; it includes a collection of converters, one of which is an SBML-to-MATLAB converter. This converter is written in Java.
I have not compared the results of the translators myself yet, so cannot speak to the differences or quality of output. If you try them and have any feedback to relate, please let the authors know. Knowing what has or hasn't worked for real users will help improve things in the future.
A final caveat is that all of these have been research projects, so make sure to set your expectations accordingly. (This is not a criticism of the authors; the authors are very good – I know most of them personally – but the reality of academic development work is that we all lack the time and resources to make these systems comprehensive, hardened, polished, and documented to the degree that we wish we could.)
we are working on a project to come up with an intermediate representation for the code in terms of something called an assignment decision diagram. So it would be very helpful if someone can tell us how you guys are compiling the code and how to access the graphs generated during compilation i.e after parsing the code for grammar.
Even help regarding accessing the code after parsing of the compiler is fine. Any help regarding how to go about doing it is also appreciated.
Currently, there is not a well defined intermediate representation of Chisel as it goes between the user source code and the specified C++ or Verilog backends.
However, I believe this is a current project amongst the Chisel devs to break apart the backend and allow access to the IR (and allow for user-defined compiler passes).
In the meantime, check out Backend.scala (particularly the elaborate() method). That's where a lot of the magic originates. I believe it is possible to jump into the Scala command line in the middle of elaboration, which will give you access to the hardware tree representation, but I'm not sure how meaningful or useful that will be for you.
I'm doing a research project on random forest algorithm. I have found numerous implementations of the algorithm but the main part of the code is often written in Fortran while I'm completely naive in it.
I have to edit the code, change the main parameters (like tree depth, num of feature variables, ...) and trace the algorithm's performance during each run.
Currently I'm using "Windows-Precompiled-RF_MexStandalone-v0.02-". The train and predict functions are matlab mex files and can not be opened or edited. Can anyone give me a piece of advice on what to do or is there a valid and completely matlab-based version of random forests.
I've read the randomforest-matlab carefully. The main training part unfortunately is a dll file. Through reading more, most of my wonders is now resolved. My question mainly was how to run several trees simultaneously.
Have you taken a look at these libraries?
Stochastic Bosque
randomforest-matlab
If you're doing a research project on it, the best thing is probably to implement the individual tree training yourself in C and then write Mex wrappers. I'd start with an ID3 tree (before attempting C4.5 for instance.) Then write the random forest code itself, which, once you write the tree code, isn't all that hard.
You'll:
learn a lot
be able to modify them as much as you like
eventually move on to exploring new areas with them
I've implemented them myself from scratch so I can help once you post some of your own code. But I don't think anybody on this site will write the code for you.
Will it take effort? Yes. Will you come out of it with more knowledge and ability than you had going in? Undoubtably.
There is a nice library in R called randomForest. It is based on the original implementation of Breiman in Fortran but it is now mainly recoded in C.
http://cran.r-project.org/web/packages/randomForest/index.html
The main parameters you talk about (tree depth, number of features to be tested, ...) are directly available.
Another library I would recommend is Weka. It is java based and lucid.Performance is slightly off though compared to R. The source code can be downloaded from http://www.cs.waikato.ac.nz/ml/weka/
Does anyone know of any examples of code written in prolog to implement a DSL to generate perl code?
DCGs might be an excellent choice!
I have used a similar approach for generation of UML class diagrams (really, graphviz code for such diagrams) from simple English sentences (shameless-plug: paper here). It should be possible to do something similar with generation of Perl code instead.
In the paper above, we use a constraint store (CHR) as intermediate representation which allows some extra reasoning power. Alternatively you can build a representation as an output feature/argument of the DCG.
Note that DCGs can be useful both for the parsing of your sentences and the generation of your Perl code.
Well, not exactly what you are asking for, but maybe you can use AI::Prolog for what you are looking for. That way you may be able to use Perl and generate the Perl code you want.
I'm not sure why you would want to do that?
Perl is a very expressive language, I'm not sure why you'd want to try to generate Perl code from Prolog; in order to make it useful, you'd be getting closer and closer to Perl in your "DSL", by which point you'd be better off just writing some Perl, surely?
I think you need to expand this question a bit to cover what you're trying to achieve in a little more detail.
SWI-Prolog library(http/html_write) library builds on DCG a DSL for page layout.
It shows a well tought model for integrating Prolog and HTML, but doesn't attempt to cover the entire problem. The 'residual logic' on the client side remains underspecified, but this is reasonable, being oriented on practical issues 'reporting' from RDF.
Thus the 'small detail' client interaction logic is handled in a 'black box' fashion, and such demanded to YUI components in the published application (the award winner Cliopatria).
The library it's extensible, but being very detailed, I guess for your task you should eventually reuse just the ideas behind.
In my C project I have quite a large utils.c file. It is really full of many utilities of different sorts. I feel a bit naughty just stuffing different miscellaneous functions in there. For example it has some utilities related to low level stuff such as a lowercase() function, and it also has some quite sophisticated utilities such as converting to/from different colour formats.
My question is, is it very naughty to have such a large utils.c with many different types of utilities in it? Should I break it up into many different kinds of utility files? Such as graphics_utils.c and so on What do you think?
Breaking them up into separate files based on categories (ie graphics, strings, etc.) will lead to better organization, making it easier to locate certain pieces of code, having smaller files to go through, instead of just one large file.
You want to break it up, not just for organizational reasons, but because you will have many other files that depend on this one. Because everything will depend on this file, it makes this one file difficult to change because it might cause widespread breakage.
http://ifacethoughts.net/2006/04/15/stable-dependencies-principle/
If it's just you that will EVER maintain the stuff, it's a matter of when the complexity gets to the point where you find yourself searching for things. That would be the time to refactor and reorganize (there's a cost to reorganize, just as there's a cost to not reorganize).
If it's POSSIBLE that anyone else will maintain a project that includes your utils, you have to consider THEIR pain point when deciding when to reorganize. Theirs is MUCH lower than yours.
I tend to break them up into various sub-utils as you say (graphics_utils) when it becomes appropriate.
Break it up. Stuff will be easier to find, easier to reuse, easier to refactor, easier to unit test. I recently needed to get a set of ISO-8601 date handling methods out of a ginormous Java utility class of static methods, and it was really hard to find the 5% of the code I needed.
It is definitely not kosher, because the next guy coming through your code won't know where to look for anything. Break it up by function, and your coworkers will thank you!
Another advantage that comes from breaking up the file into separates is that when you place it under source control, you can have finer grained control. This really is useful if you have bits that are tweaked/extended/specialised frequently, and other bits that are relatively stable.
Another point: You should organize your code, i. e. break it up in smaller modules and categorize it, because at some point in time you will end up writing a second and third function for the same thing, simply for the reason that you wont find that function that you knew it was there, but you don't remember it's name.
I've got a (rather large) project with such a module and there is programming logic for which there are up to 5-6 implementations (for the same thing).
Like everyone else I would break them up. But I tend to use Extension Methods now, so I would have one class (and one file) per class being extended (e.g. StringExtensions, SqlDataReaderExtensions, etc). I find this tends to break up the utility methods nicely.