GSECARS Tomography Software

This document describes how to install and use the software to reconstruct and visualize tomography data from the 13-BM-D beamline. This includes data collected both on the upstream tomography table, and that collected in the 250-ton press.

Table of Contents

• Overview
• Installation
  • Install IDL
  • Install IDL_Tomography
• File formats
  • Raw data
  • Preprocessed (normalized) data
  • Reconstructed data
• Quick Start for tomo_display
  • Read camera file
  • Visualizing raw data
  • Preprocessing
  • Visualizing normalized data
  • Optimizing rotation center
    • Selecting optimization method
    • Selecting slices for optimization
    • Selecting center, range and step for optimization
    • Manual optimization
    • Correcting rotation tilt
    • Optimization plots
  • Reconstruction
• Processing options
  • Preprocessing options
    • Zinger removal
    • Dark current
    • Scale factor (preprocessing)
    • Number of threads
  • Sinogram options
    • Air pixels
    • Data type
    • Display sinogram
    • Plot center-of-gravity
  • Reconstruction options
    • Reconstruction method
    • Scale factor (reconstruction)
    • Ring smoothing width
    • Backproject
    • Gridrec/tomoRecon
    • tomoRecon
• Visualize with image_display
• Visualize with ImageJ
  • netCDF plugin
  • HDF5 plugin
  • Incompatibility of netCDF and HDF5 plugins
• Scripting and batch processing
  • Processing a single dataset
  • Processing a mulitple datasets
• Benchmarks