section-sort

Sorting serial sections using a TSP-solver

Dependencies

• concorde (free for academic use)
• cplex (free with academic initiative)
• tsplib format (file format for feeding concorde with tsps)

Installation (Linux)

Download cplex 12.5 and install into <cplex-install-dir>.

$ chmod +x cplex_studio1251.linux-x86-64.bin
$ ./cplex_studio1251.linux-x86-64.bin

Note that building concorde will not work with cplex 12.6. Download latest [concorde source][concorde-source] and extract into <concorde-src-dir>. [concorde-source]: http://www.math.uwaterloo.ca/tsp/concorde/downloads/codes/src/co031219.tgz

$ mkdir -p <concorde-src-dir> && cd <concorde-src-dir>
$ tar xf ~/Downloads/co031219.tgz

Create , link cplex libraries and headers into and run the concorde build configuration.

$ mkdir -p <concorde-build-dir> && cd <concorde-build-dir>
$ ln -s <cplex-install-dir>/cplex/include/ilcplex/*.h .
$ ln -s <cplex-install-dir>/cplex/lib/x86-64_sles10_4.1/static_pic/*.a .
$ <concorde-src-dir>/configure --prefix=$PWD --with-cplex=$PWD

Modify

<concorde-build-dir>/Makefile
<concorde-build-dir>/TSP/Makefile

and replace

LIBFLAGS = -liberty -lm 

by

LIBFLAGS = -liberty -lm -pthread

in each file.

Run

<concorde-build-dir> && make

The TSP solver is now located at <concorde-build-dir>/TSP/concorde.

Copy/link the TSP solver into the bin directory of your Fiji distribution.

cp <concorde-build-dir>/TSP/concorde <fiji-root>/bin

Build section-sort and copy the jar into the jar directory of your Fiji distribution.

mvn clean install -Dimagej.app.directory=<fiji-root>/ -Ddelete.other.versions=true

Copy section_sort.bsh into the plugins directory of your Fiji distribution.

cp <section-sort>/src/main/bsh/tsp/section_sort.bsh <fiji-root>/plugins

The section sort plugin will then appear in the Plugins drop down menu after restarting Fiji or refreshing the beanshell scripts (Plugins -> Scripting -> Refresh BSH Scripts).