This repository contains all tools I used to perform data testing on neuron cell data.

The Java/src/ folder contains code to transform original swc files to new files, which has different file format. The new files can be used to compute Persistent Diagrams by using code in CPP/src/

The CPP/src folder contains code to compute Persistent Diagrams from those files prepared by code in Java/src/.

I build the tools in above Java and CPP directories in Windows using Eclipse.

1. Look here for how to install Eclipse for Java in Windows: https://www.ntu.edu.sg/home/ehchua/programming/howto/EclipseJava_HowTo.html
2. Open Eclipse, click File->New->Java Project, enter project name as FileCreatorInJava, then click Finish.
3. Download all Java files in NeuronTools/Java/src/ (https://github.com/Nevermore520/NeuronTools/tree/master/Java/src), copy and paste them into the src folder under the newly created FileCreatorInJava project.
4. The code is ready to run and test in Eclipse.

1. Look here for how to install MinGW and Eclipse for CPP in Windows: https://www3.ntu.edu.sg/home/ehchua/programming/howto/EclipseCpp_HowTo.html
2. Also the C++ code need Boost C++ library, which can be downloaded here: http://www.boost.org/
3. Open Eclipse for CPP, click File->New->C++ Project, enter project name as NeuronTools, select 'Hello World C++ Project' under Project type and select 'MinGW GCC' under Toolchains, and click Finish.
4. Replace files in the src folder under the newly created NeuronTools project with files in NeuronTools/CPP/src/ (https://github.com/Nevermore520/NeuronTools/tree/master/CPP/src)
5. Before running the code, make sure the boost path is added to your includes list. In Eclipse, click Project->Properties, click Settings under 'C/C++ Build', click Tool Settings tab, and add your Boost library install path(e.g. C:\software\boost_1_59_0) to the 'Include path (-I)' in 'GCC C++ Compiler/Includes'. Also add this path in 'GCC C Compiler/Includes'.
6. Now the code is ready to run and test.

1. In Eclipse, open project you have created in the above steps, click Run->Run Configurations..., select either C/C++ Application or Java Application according to your languages, right click->New.
2. In the newly created configuration, select the Arguments tab, enter your program arguments, and click Run.

The wasserstein/ folder contains code to compute Persistent Distance Matrix from Persistent Diagrams computed by code in CPP/src/. Refer to the included readme file for how to build and run the code under linux.

Still under construction...