osem matlab,mirt: Michigan Image Reconstruction Toolbox (MIRT) - Matlab version

Michigan Image Reconstruction Toolbox (MIRT) - Matlab Version

https://github.com/JeffFessler/mirt

This directory contains various algorithms for image reconstruction and

other inverse problems such as image restoration and image registration.

It also contains code for related applications including MRI pulse design.

For many years this toolbox was posted as a (too large) .tgz file here:

http://web.eecs.umich.edu/~fessler/code/index.html

This github version is a work-in-progress.

All the code is here,

but to keep the repo size small,

the data and the compiled mex files are not included.

Currently one must still use the .tgz file to get all of that.

I will eventually work on some other way to distribute the data and mex files.

This Matlab code is no longer being very actively maintained

because I am switching to using Julia instead. See:

https://github.com/JeffFessler/MIRT.jl

GETTING STARTED

After installing the toolbox, use matlab's path functionality to put

the top level directory in its path (or launch matlab from that directory).

Then run the file setup.m that will add all the appropriate subdirectories

to the path. You may find it convenient to read setup.m and customize it.

I recommend running and examining some of the files in the example/ directory

or any of the many ..._example.m files around, such as

emission/eml_osem_example.m

Many example files prompt you to hit enter before continuing, so you (and I)

can see the output of each stage before proceeding.

To change this behavior, execute prompt run

(See utilities/prompt.m for help.)

A few examples may require the binary programs wt or op that are part

of Aspire. You can also get Aspire for free by following the instructions at

http://web.eecs.umich.edu/~fessler/aspire/index.html

There are also mex files that you may need:

wtfmex and f3dmex for example.

I distribute these only in linux/mac formats;

see mex/ directory.

Part of my motivation for creating these files is to accompany a book on

image reconstruction that I am currently writing. If you have any problems

with these m-files, or any suggestions, I welcome your input!

Subdirectories (in alphabetical order):

align

image registration tools

blob

SPECT reconstruction with blob basis functions (not recommended)

contrib

algorithms contributed by others. these directories are not added to

the path by setup.m so the user must modify the path to use them.

contrib/ppcd

test routines comparing WLS-CD, WLS-GCD, WLS-PPCD

(these are mostly for internal UM use)

ct

polyenergetic CT routines (beam hardening, dual energy, etc.)

data

data for examples (not in github version)

doc

see the pdf file within (not in github version)

for some introductory documentation.

emission

algorithms for Poisson emission tomography PET/SPECT/ Poisson regression

eml_ emission maximum likelihood

eql_ emission quadratically penalized likelihood

epl_ emission penalized likelihood

example

example(s) of usage. there are more examples in other directories too.

running any of these examples is a good place to start!

fbp

filter-backproject reconstruction, including 2D parallel and fan-beam

and 3D Feldkamp (FDK) cone beam reconstruction

freemat (not in github version)

work in progress, towards making the code run with freemat

(obsolete: use octave instead of freemat)

(better yet, just use Julia)

general

some algorithms that work for generic image reconstruction problems

graph

graphics functions

mex

MEX (matlab executables), including some C99 source code

mri

MR image reconstruction

mri-rf

MR pulse design tools, including Spectral-spatial pulse design

for phase precompensatory slice selection. (more to come)

nufft

non-uniform FFT (NUFFT) toolbox

octave (not in github version)

work in progress, towards making the code run with octave

(this is a moving target as both octave and matlab evolve)

penalty

functions associated with regularization

systems

system matrices and system matrix object classes

If you are interested in edge-preserving image restoration

for a shift-invariant blur model with additive gaussian noise,

then start with systems/Gblur_test.m and example/restore_example.m

For 2D tomography, consider starting with systems/Gomo2_strip.m,

which is used in many of the examples.

transmission

algorithms for Poisson transmission tomography

tml_ transmission ML

tql_ transmission quadratically penalized likelihood

tpl_ transmission penalized likelihood

utilities

useful functions for image reconstruction algorithms.

wls

algorithms associated with the weighted least squares (WLS)

cost function and penalized versions thereof

pwls_penalized weighted least squares

qpwls_quadraticaly penalized weighted least squares

Most algorithms also include a test routine...

Additional notes:

Raymod Muzic has matlab routines for reading ECAT files available:

http://www.nuclear.uhrad.com/comkat

(I have not yet tried them myself.)

One of many annoying issues with Matlab is that it can store sparse matrices

only as doubles, wasting memory, and if you do S * x, where S is a

sparse matrix and x is a vector of class single, Matlab (as of 2016a)

gives an error message rather than politely upgrading x to a double.

The object Gsparse.m provides a work around for this.

Complain to Mathworks that they should fix this annoyance...

Windows users:

Some of the subdirectories of the systems directory contain "links"

to m-files in other directories. (These are created using ln -s in

unix.) These links are also in the .tar file as soft links. But these

links may not be recognized by Windoze, resulting in various error messages.

They work fine on Mac OSX since it is unix "under the hood."

I recommend that you avoid using Windows.

But if you insist, then you will have to figure out how to fix those links

or copy the appropriate m-files into the appropriate directories.

Another problem is that apparently windoze is case insensitive.

I believe I have purged most of the m-files that had capitalized names now.

Nevertheless, at this point it would be better to just install linux instead.

Or switch to Julia.