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tracr

Tomography Reconstruction Analysis and Characterization Routines (tracr) are modules to analyze X-ray tomography data.

Authors

Branden Kappes (bkappes@mines.edu)
Andrew Petersen (apeterse@mines.edu)
Henry Geerlings (henrygeerlings@mymail.mines.edu)

Development Discussion

tracr/
  +- bin/
  +- doc/
  |  +- tracr.md (other documentation files added if needed)
  +- test/
  |  +- test_read.py (x)
  |  +- test_feature.py (x)
  |  +- test_threshold.py
  +- tracr/
  |  +- base/
  |  |  +- feature.py
  |  +- distribution/
  |  |  +- pair_correlation.py
  |  |  +- orientation.py
  |  +- io/
  |  |  +- read.py
  |  |  +- write.py
  |  |  +- util.py
  |  |  +- tif/
  |  |     +- read.py
  |  |  +- dcm/
  |  |     +- read.py
  |  |  +- hdf5/
  |  |     +- read.py
  |  +- segmentation
  |  |  +- threshold
  |  |  |  +- otsu.py
  |  |  +- label
  |  +- metrics/
  |  |  +- com.py
  |  |  +- distance.py
  |  |  +- volume.py
  |  |  +- eccentricity.py
  |  +- tracr.py
  +- setup.py
  +- README
  +- LICENSE

Thresholding

The thresholding routine implemented is a multilevel Otsu algorithm (default: two class otsu, e.g. binarization).

Case Study: Binarization of single phase metallic sample

Even with 3 more/less distinct classes of XCT data (outer corners [intensity = 0], ambient air [low], actual sample [high]), the volume of metal in the XCT frame significantly influences where the two levels occur in a trilevel Otsu thresholding. That is, one threshold may lie between the corners and the air, the second between the air and the metal; or one threshold may lie between the air and the metal, the second binarizing the metal. Which occurs depends on the individual details of the intensity histogram.

For single-phase metallic samples with significant volume fraction air, a bilevel Otsu has consistently shown to provide more physical thresholding values that are insensitive to sample size.