GSECARS Tomography Processing Software

Mark Rivers

University of Chicago

July 24, 2014

This document describes the IDL software used for reconstructing and viewing tomography data at CARS. All of these IDL routines are available in a idl_tomography.tar file. The reconstruction is normally done using the tomoRecon reconstruction code, which is written in C++. The idl_tomography.tar file contains the required tomoRecon DLLs (Windows) and shareable libraries (Linux, Mac) to run the IDL software without compiling any code. The tomoRecon source code is also available through the tomoRecon home page. tomoRecon is based on the Gridrec reconstruction algorithm, but with multi-threading to utilize multiple cores on modern workstations.

The normal user interface for this software is through the IDL GUI routine tomo_display. The following screen shot shows the tomo_display interface.


IDL tomo_display GUI

tomo_display.png

The following screen shot shows the screen that provides control for the preproccessing and reconstruction options.


IDL tomo_display Options screen

tomo_display_options.png

We have broken the tomography data processing down into 3 steps:

Preprocessing

The preprocessing routine read_tomo_data.pro performs the following steps:

Reconstruction

The reconstruction routine reconstruct_volume.pro performs the following steps when using tomoRecon. (When using filtered backprojection similar steps are used, but all of the code is in IDL itself.)

Visualization

The standard IDL procedures TV and TVSCL are very useful for displaying 2-D data. IDL's SLICER3 procedure is good for displaying 3-D data. In addition there is set of GSECARS-developed routines for visualizing 2-D and 3-D tomography (or other) data.

The reconstructed data are written as 16-bit integer netCDF files. These can be read into ImageJ using the ( ImageJ netCDF plugin jar file) and a small ImageJ script called GSETomo_.txt that is also in the idl_tomography.tar file. Put both the netCDF_.jar and GSETomo_.txt files in the ImageJ/Plugins folder. Plugins/GSETomo can then be used to read the reconstructed files.


Suggestions and Comments to:
Mark Rivers : (rivers@cars.uchicago.edu)