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Getting started

Computing Cluster

Coding style

Currently finishing my Master's Thesis entitled "Applications of Compressed Sensing in Computational Physics", which is aimed at bringing cutting-edge models and methods from digital signal processing to the forefront of Computational Physics research, with applications in Molecular Dynamics, Seismic Data modeling, and more.

MCALab is an easy-to-use Matlab toolkit for Compressed Sensing-related problems. This is a guide for getting it up and running on Ubuntu.

Get Matlab. The easiest way to get everything up and running is to use a 32-bit version of Matlab. This guide will detail how to do it for 64-bit as well.

Download MCALab. You can find it here: https://fadili.users.greyc.fr/demos/WaveRestore/downloads/mcalab/Download.html

Extract it where you like.

If you are using 32-bit Matlab: Congratulations, you are done! Make sure to include all all the files in MCALab to your path, and try to run the script Two-D/Scripts/figInpaintLena.m, or any other.

The problem is that a bunch of necessary files are compiled for 32-bit and then shipped, without including the source code. First, you should get the Rice Wavelet Toolbox. This can be downloaded from their repo here: https://github.com/ricedsp/rwt . Clone the repo, go to rwt/mex and add #include “matrix.h” at the top of every file. Now follow the instructions in the INSTALL file.

At this point MCALab should work as long as you link to the rwt files, if you do not use curvelet or wave atoms.

Next is getting curvelets up and going. This is a big one. Begin by downloading the CurveLab toolkit at http://www.curvelet.org/software.html . There is a file called “curvelab.pdf” which details how to install it, but you must make the following tweaks: After entering ./configure – -with-pic, open the makefile and add the line -fPIC to CXXFLAGS. FFTW 2.1.5 does not put the library files where Curvelab wants them. The easiest way to get around this is simply to type the following, when in the installation directory: mkdir fftw/.libs cp lib/libfftw.a fftw/.libs/libfftw.a cp lib/libfftw.so fftw/.libs/libfftw.so Now curvelab should compile fine if you follow the rest of the instructions.

After entering ./configure – -with-pic, open the makefile and add the line -fPIC to CXXFLAGS.

FFTW 2.1.5 does not put the library files where Curvelab wants them. The easiest way to get around this is simply to type the following, when in the installation directory: mkdir fftw/.libs cp lib/libfftw.a fftw/.libs/libfftw.a cp lib/libfftw.so fftw/.libs/libfftw.so

Now curvelab should compile fine if you follow the rest of the instructions.

Finally, if you want to test wave atoms as well, download the wave atom toolkit from http://www.waveatom.org/software.html and check that it works. If it does, go to the file “FastWAVEATOM2Analysis.m” in MCALab and replace wa(2).coeff = sqrt(2)/n*real(fatfm2sym(img,pat)); with wa(2).coeff = real(fwa2sym(img,pat,'directional')); and then open “FastWAVEATOM2Synthesis.m” and change imr = real(iatfm2sym(wa(2).coeff/sqrt(n/2),pat)); to imr = real(iwa2sym(wa(2).coeff,pat,'directional'));

and then open “FastWAVEATOM2Synthesis.m” and change

Realize you should have just gone with 32-bit Matlab.

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Getting MCALab up and running on a 64-bit installation of Matlab on Ubuntu