volShapeMetrics

Applies shape measures for comparing two volumetric images A and B (shape defined from thresholds).

Usefull to determine classical statistics like false positive related stats.

Usage: volShapeMetrics –volA <volAFilename> –volB <volBFilename>

Allowed options are :

Positionals:
  1 TEXT:FILE REQUIRED                  Input filename of volume A (vol format, and other pgm3d can also be used).
  2 TEXT:FILE REQUIRED                  Input filename of volume B (vol format, and other pgm3d can also be used).
 
Options:
  -h,--help                             Print this help message and exit
  -a,--volA TEXT:FILE REQUIRED          Input filename of volume A (vol format, and other pgm3d can also be used).
  -b,--volB TEXT:FILE REQUIRED          Input filename of volume B (vol format, and other pgm3d can also be used).
  --aMin INT=0                          min threshold for a voxel to be considered as belonging to the object of volume A. (default 0)
  --aMax INT=128                        max threshold for a voxel to be considered as belonging to the object of volume A. (default 128)
  --bMin INT=0                          min threshold for a voxel to be considered as belonging to the object of volume B. (default 0)
  --bMax INT=128                        max threshold for a voxel to be considered as belonging to the object of volume B. (default 128)
  --noDistanceComparisons               to avoid to apply distance map computation if the distance comparaison are not needed.
  --distancesFromBnotInAOnly            apply distance map measures only for voxels of B which are not in A (else the measure are given from all distances of the object B).
  --displayTFstats                      Change the comparison diplay by using the  true/false/positive/negative notation and considering the shape A as reference. It also display precision/recall/f-mean statistics.
  --exportSDP                           Export voxels belonging to each categorie (voxels of ( B in A) , (NOT in B and NOT in A),   (B and NOT in A) and (Voxels of NOT in B and in A)).

Example:

To test this tool, we need to generate a volumetric file to be compared to an original one:

# generation of the file "eroded.vol" from DGtal examples:
$ $DGtal/build/examples/tutorial-examples/FMMErosion

Then we can apply comparisons of the two shapes:

$ volShapeMetrics -a eroded.vol --aMin 1 --aMax 255 -b $DGtal/examples/samples/cat10.vol --bMin 1 --bMax 255 --displayTFstats --exportSDP 

You should obtain different comparison measures and you can display the set of voxels associated to the false positive ( falsePos.sdp ):

$ 3dSDPViewer -i falsePos.sdp -c 250 40 40 5

Resulting False positive set of voxels.

See also

volShapeMetrics.cpp