I'm passing a NetLogo list from NetLogo to Java (to an extension) and then sending it back to NetLogo again where I want to use it as a parameter to another procedure. But when I send it back to NetLogo, the Java representation of the LogoList seems to have changed it so that it contains commas, i.e.
[0 0] becomes [0, 0] which makes NetLogo complain when I then pass it on. (It says that it expected a constant.)
When I retrieve the list from the arguments in the ExtensionCode, I use the args[0].getList().
e: I pass it back to NetLogo as a string, by the way. I pretty much need to do this because I am doing this as part of an iterative string-building procedure. I hope there's still a way to do this.
Does this make sense? Am I doing something wrong? I assume I can turn the LogoList into an iterator, and then build a new LogoList with a LogoListBuilder, but I was wondering if there might be a better way: What should I do to send the LogoList back to NetLogo without commas?
To convert a LogoList (or any other NetLogo value) to a string, don't use .toString; that's only suitable for debugging. Calling org.nlogo.api.Dump.logoObject on the LogoList will produce the Logo-style representation instead of the Java-style representation.
I don't know if this can add something to #Seth reply, but if you also need to build the list in Java, you can also use within a DefaultReporter:
LogoListBuilder newList = new LogoListBuilder();
// do your stuff... then:
return newList.toLogoList();
in this way, the list is in the correct format when you process it in NetLogo.
Related
In the simulation window, before the run, I'd like to change some probability distributions (e.g. delay time) by typing, for example, "triangular(5, 20, 15)" into a specific editbox linked to a variable.
I know how to do this with static values, but I couldn't figure out how to do the same with probability distributions.
AnyLogic offers a built-in functionality for that with com.anylogic.engine.database.CodeValue.
It is originally meant that a distribution function stored as text in the internal database can be parsed to java code and executed, but it actually also works without the database and for any kind of code. It is the same idea as in Benjamin's answer, just that you do not need to add any external java library.
Use it like this:
CodeValue myCode = new CodeValue(this,"....java code to be executed");
myCode.execute();
And in your specific case, assuming you have a variable named variableA and an editbox named editbox, use the following to evaluate the expression, get a value and set it for the variable:
CodeValue myCode = new CodeValue(this,"variableA = "+editbox.getText());
myCode.execute();
Obviously, allowing the user to type any command there and running it without a check or error treatment is a bad idea, be aware of that.
This is a Java issue. You need to convert a String (your editbox content) to executable code. Not straight-forward but also not impossible, see Convert String to Code and similar posts.
I'm working on a NetLogo model that has a great deal of information stored in lookup tables and embedded in patches that affect agent behavior. As a result, I'm creating a model "reset" from an extension that clears the turtles, and resets the timer and ticks.
I would also like to have the extension reset specific globals that track model results, but not reset all of the globals that are constants (look up tables of precomputed information). I would also like to reset all the interface plots.
Any thoughts on how to go about this?
I apologize for no code to show, as is the case I can't show what is not working because I'm not even sure what to try!
NetLogo engine internals aren't really documented except in a general way at https://github.com/NetLogo/NetLogo/wiki/Engine-architecture, so if your extension wants to manipulate engine stuff directly, you'll usually have to consult the NetLogo source code to learn specifics of how it's done.
You want something like clear-globals, so check out https://github.com/NetLogo/NetLogo/blob/5.x/src/main/org/nlogo/prim/etc/_clearglobals.scala and https://github.com/NetLogo/NetLogo/blob/37cc1a0aa371c11e89f5b39b5143ed5d951e6081/src/main/org/nlogo/agent/World.java#L849-L866.
You want something like clear-all-plots, so check out https://github.com/NetLogo/NetLogo/blob/37cc1a0aa371c11e89f5b39b5143ed5d951e6081/src/main/org/nlogo/prim/plot/primitives.scala#L45-L50 and https://github.com/NetLogo/NetLogo/blob/37cc1a0aa371c11e89f5b39b5143ed5d951e6081/src/main/org/nlogo/plot/PlotManager.scala#L54-L57.
And so on.
EDIT:
For access to the PlotManager, note that plot/primitives.scala has:
workspace.plotManager.asInstanceOf[PlotManager]
in Java code on an extension, from the workspace plotManager() gets you the PlotManager, except the return type of that method is Object (yes, I know, it's grungy and horrible), so you need to insert a typecast to org.nlogo.plot.PlotManager and you're good to go. PlotManager has methods for getting to particular plots.
I'm reasonably new to Matlab, and have been trying to teach myself. I have looked for a similar question, but can't find one that's quite right.
In my workspace I have several structures with similar names. These structures will always start with the same word ('Base'), though the rest of the name will change ('1', '2', '3'), so for example Base1, Base2, Base3... etc. These variables were generated using the data cursor tool in a figure, so contain the fields Target, Position and DataIndex. I am only interested in the value in Base*.Position(1,1). I would like to extract this value from each structure, as many times as there are structures (in one instance there may be 6 structures, another time only 4).
I am considering using the eval function, but it seems to work on exact strings rather than only the first part of a name. Additionally, a lot of documentation seems to advise against using eval.
So far I have:
clearvar except 'Base*'
list_variables=who;
for i=1:length(list_variables)
BaseTS(i) = eval('Base1.Position(1,1)');
end
It's the for loop I'm stuck on, as I don't know how to generalise so it will extract the value .Position(1,1) for each different structure name.
Thanks in advance
Instead of having many structures called Base1, Base2 etc rather put your structure in an array. Then you could rather call Base(1).Position(1,1), Base(2).Position... etc. Your code will be more flexible and manageable this way.
So I suggest when you export using the data cursor, export to a variable called Base_temp and then immediately stick this into the next element of an array:
Base(end+1) = Base_temp
or even:
Position(end+1) = Base_temp.Position(1,1);
Then it's just a case of pressing up and enter after each time you export with the data cursor.
What you have read about avioding eval is correct, it's very rare (if ever) that eval is a good idea. It makes your code hard to read and very hard to debug. But since you're learning, this is how you could fix your loop. (But don't do this way, seriously don't, use arrays rather):
for i=1:length(list_variables)
BaseTS(i) = eval(['Base', num2str(i), '.Position(1,1)']);
end
in other words use string concatenation to build up your string and use the looping variable (i) to get the different numbers. You'll need num2str to convert fromthe number to the string. But don't do it this way. This is a bad way.
Dan's suggestion about avoiding eval is very valid. But if you decide to keep on the structures you have in your workspace, here's something without loops, but again cellfun seems to use loops internally. So, I guess this could be an alternative solution, with the not-so-popular eval -
list1 = who('Base*')
list2 = cellstr(strcat('BaseTS(',num2str([1:numel(list1)]'),')='));%%//'
ev1 = strcat(list2,list1,'.Position(1,1)');%%//'
cellfun(#evalc,ev1,'uni',0)
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