Develop Reference

Importing Java class into a python project

I've been trying to find a method to importing Java-ml into my python project. I have the jar file in the same path as my project.
I want to use it for kmeans clustering, since it allows me to change the distance metric. I am wondering though whether with the implementation that one of you suggest, whether I'll be able to pass a different java class as a parameter for the function?
I tried using:
import sys
sys.path.append(r"C:\Users\X\Desktop\X\javaml-0.1.7\javaml-0.1.7.jar")
import net.sf.javaml as jml
test = jml.clustering.Kmeans()
I considered using jython, however I am unsure of how it works, and it is unclear whether I could continue using idle and whether I would have to reprogram my project.
Lastly I considered using PyJNIus, however it is simply not working.

In short, you can't run Java code natively in a CPython interpreter.
Firstly, Python is just the name of the specification for the language. If you are using the Python supplied by your operating system (or downloaded from the official Python website), then you are using CPython. CPython does not have the ability to interpret Java code.
However, as you mentioned, there is an implementation of Python for the JVM called Jython. Jython is an implementation of Python that operates on the JVM and therefore can interact with Java modules. However, very few people work with Jython and therefore you will be a bit on your own about making everything work properly. You would not need to re-write your vanilla Python code (since Jython can interpret Python 2.x) but not all libraries (such as numpy) will be supported.
Finally, I think you need to better understand the K-Means algorithm, as the algorithm is implicitly defined in terms of the Euclidean distance. Using any other distance metric would no longer be considered K-Means and may affect the convergence of the algorithm. See here for more information.
Again, you can't run Java code natively in a CPython interpreter. Of course there are various third party libraries that will handle marshalling of data between Java and Python. However, I stand by my statement that for this particular use case you are likely better to use a native Python library (something like K-Medoid in Scikit-Learn). Attempting to call through to Java, with all the associated overhead, is overkill for this problem, in my opinion.

To "answer" your question directly, Jython will be your best bet if you simply want to import Java classes. Jython strives very hard to be as compatible with Python 2.x as possible and does a good job. So you won't have to spend too much time rewriting code. Just simply run it with Jython and see what happens, then modify what breaks.
Now for the Python answer :D. You may want to use scikit for a native implementation. It will certainly be faster than running anything in Jython.
Update
I think the Py4J module is what you're looking. It works by running a server in your Java code and the Python code will communicate with the Java server. The only good thing about "Py4J" is that it provides the boiler plate code for you. You can very easily setup your own client/server with no extra modules. However I still don't think it's a superior option compared to Pythons native modules.
References
How to import Java class w/ Jython
Scikit - K-Means

Using SymPy (or another CAS) with Java

I am currently developing a project in JavaFX that accepts a mathematical expression and evaluates it. I have managed to get basic operations and a good deal of algebra to work. I have also managed to perform definite integrations using the trapezoid rule.
The main problem I am facing is with indefinite integration. I looked up many symbolic computation libraries online like JCalculus, JavaCalculus, JScience, SymJa and others. But none of them were as good as SymPy in terms of functionality. I wanted to know if there is a way to send commands to SymPy from Java and receive the result back into Java.
I am thinking of providing an installer for my JavaFX app that will install Python and SymPy if necessitated by the solution. I also tried to understand Jython, believing that it would somehow by related to the problem but I could not understand its purpose and its usage.
Please help me. I am quite good at Java and JavaFX but my knowledge of Python is severely low and restricted. Step by step instructions and sample code is extremely appreciated.
Thanks in advance.

If you somehow manage to write sympy equivalent python code from your java input in a file, you can get the output of that code very easily.
Process p = Runtime.getRuntime().exec("python yourfile.py");
Take a look at this.

Binary Integer Program Solver for Java

My problem is in trying to solve a Binary Integer Program through Java. I want to run a series of experiments and an integral component of these experiments is to solve an integer program where the variables are constrained to be between 0 and 1.
In the past I have solved such problems in MatLab, with the function bintprog. In the search for such a function (or class? I'm very new to Java) to use in Java, I have come up empty handed.
Is there a Java library available to solve Integer Programs that has really good documentation?
In my search, I have seen suggestions to use a package called LP_Solve that has had a Java wrapper built around it, and a similar wrapper built for a package called GLPK (wrappers here and here) (which I have used before). The problem with these tools is that they are not strictly designed for Java, and thusly, lack the kind of documentation that I feel I need, and even worse have complicated instructions to even begin using them in my own code. As I am currently learning the Java language I am wondering if there are any really good packages available to solve Binary Integer Programs, Mixed Integer Linear Programs, or just Integer Programs from my own Java code.
As a side note, I really do not want to switch to another language because I am building off of past code and classes that perform the tasks I desire.

How about Java Integer Linear Program Solver (JILPS)?

LP_Solve with the Java wrapper is what I will be using. It is a free Mixed Integer Linear Program solver. LP_Solve for Java is very easy to install following these instructions. Included in the packages you download are files with lots of example code, which I have found useful. The only part of the installation that slowed me down was having to join the Yahoo group to find the files for download.

IBM cplex even though being c library has java wrappers and documentation

if you want values 0 or 1 try the bool datatype...if your looking at probabilities (that lie between 0 to 1)try limiting a float value such that it is >= 0 and <=1;

HPC (mainly on Java)

I'm looking for some way of using the number-crunching ability of a GPU (with Java perhaps?) in addition to using the multiple cores that the target machine has. I will be working on implementing (at present) the A* Algorithm but in the future I hope to replace it with a Genetic Algorithm of sorts. I've looked at Project Fortress but as I'm building my GUI in JavaFX, I'd prefer not to stray too far from a JVM.
Of course, should no feasible solution be available, I will migrate to the easiest solution to implement.

If you're interested in HPC with GPUs then perhaps you can look jCuda. This provides Java bindings for CUDA, along with access to CUDA FFT, CUDA BLAS and CUDA DPP. I haven't seen any performance reports on this library so I can't guarantee it will be very good.
Beyond that, I'm not really sure. If you're interested in doing this type of stuff as an educational exercise then Java should be good enough, but if you have a serious need for HPC then you're probably going to want to implement in C and use the Java Native Interface to communicate with it.

Morten Nobel Joergensen has a blog post showing how to create a Mandelbrot Set using JOGL - Java Bindings for OpenGL
However if you want generic computing, rather than graphics, then you'd be after the Java bindings for OpenCL, from which you can chose from JOCL, or JOCL or JavaCL.
Wikipedia's page shows how OpenCL can be used to compute a fast fourier transform.

Parallel Colt might be of interest.

Have a look at JPPF, it is a very nice and mature open source Java grid computing environment

Accessing .NET/dll libraries/components from Java?

Are there inexpensive or free gateways from .NET to Java? I'm looking at some data acquisition hardware which has drivers for C/C++ and .NET -- I really don't want to do any programming in .NET.
Update: I haven't done what I originally wanted to do, but I've done something similar, using JNA to encapsulate some functions from a DLL, in order to control a USB hardware device from Java. (the DLL comes from the device manufacturer) It works really nicely. Thanks!

You could also try to use JNA for accessing the native library. JNA provides Java programs easy access to native shared libraries (DLLs on Windows) without writing anything but Java code—no JNI or native code is required. If their API is fairly straight foward, this might be the path of least resistance.
See their getting started guide where they call some native code (printf and GetSystemTime).

Well, there's JNBridge and EZ JCom, just from a Google search.
You could also use IKVM which is a slightly different approach.
(Any reason for not wanting to learn .NET, out of interest? It's a nice platform, and C# is a lovely language...)

If they have C++ versions of the drivers then you could write a wrapper around it using JNI and then load that in Java. JNI can be a bit of a pain, but it would let you use the C++ version of their drivers and not have to deal with .Net at all if you don't want.

I am partial to the recommendation to jump in the deep end with C# since it is so similar to Java. I did this and used IKVM to compile my favorite Java libs. to .NET assemblies and you get [nearly] all the core java runtime classes to boot, so if you tire of trying to find just the right C# collection type, you can always go back to java.util. (No generic collections though. Not sure why.)
Depending on what platform you're on, you have several choices for free IDEs too. For windows you can get Visual Studio Express for free but I also use SharpDevelop. You can also get the Mono IDE on Linux (and a few flavours of Unix, I think ?).
The C# learning curve is shallow if you already know Java. I only blew off 1.5 limbs on landmines that came out of nowhere for reasons I still don't understand, but workarounds were easy to come by. The worst thing about it was the darn developer docs which are AWFUL on account of being so slow. I really miss the snappiness of JavaDoc. Not only are the online docs incredibly slow, the problem is compounded by someones's iffy decision to put class summaries, constructors and methods/properties all on seperate pages so it just takes forever. Someone said to get the docs installer and install docs locally for a slightly improved experience. Not a bad idea I suppose.

I am author of jni4net, open source interprocess bridge between JVM and CLR. It's build on top of JNI and PInvoke. No C/C++ code needed. I hope it will help you.

If you have a Java application, the JNI mentioned by the others will be the way to go. You write some wrapper classes, and that's it.
If writing the wrappes is a too big task (depending on the number of methods you have to wrap), have a look at SWIG . I think it generates wrappers automatically, but I never actually used it.
If you want to code in the Java language, but you don't care if your program will run on the JRE/JVM, then you might as well use Microsoft J#. Basically, it's writing Java-Code wich is compiled to .NET-Bytecode and can use the .NET classes of the driver as well as your existing Java classes. With J# you will run into problems if your existing Java-code is newer than Java 1.4, look at this question on how to solve them.
From that point on, you could later add code in J#, C# or any other .NET language. However, you won't get back to the JRE/JVM easily.