Parameters are sent to Deformetrica by using XML files, this include a file containing the parameters for the deformation (paramDiffeo.xml) and a file containing the parameters for each object type. Since we are using only one kind of object (surfaces), there is only one file containing the parameters for the surfaces (paramNonOrientedSurfaceMesh.xml).
File paramDiffeo.xml
<?xml version="1.0"?> <sparse-diffeo-parameters> <kernel-width>1</kernel-width> <number-of-timepoints>20</number-of-timepoints> <kernel-type>p3m</kernel-type> <sparsity-prior>0.0</sparsity-prior> <use-fista>On</use-fista> <adaptive-data-sigma>Off</adaptive-data-sigma> <max-iterations>200</max-iterations> <max-line-search-iterations>20</max-line-search-iterations> <step-expand>2.0</step-expand> <step-shrink>0.5</step-shrink> <adaptive-tolerance>1e-3</adaptive-tolerance> <initial-step-multiplier>0.001</initial-step-multiplier> <number-of-threads>12</number-of-threads> </sparse-diffeo-parameters>
File paramNonOrientedSurfaceMesh.xml
<?xml version="1.0"?> <deformable-object-parameters> <deformable-object-type>NonOrientedSurfaceMesh</deformable-object-type> <data-sigma>0.1</data-sigma> <kernel-width>1</kernel-width> <kernel-type>p3m</kernel-type> </deformable-object-parameters>
The computation is running by using sparseAtlas3:
Usage: /path/to/deformetrica-2.1/deformetrica/bin/sparseAtlas3 paramsDiffeos.xml NumberOfObjects paramsObject1.xml InitialTemplate1 Subject1 Subject2 Subject3 ... paramsObject2.xml InitialTemplate2 Subject1 Subject2 Subject3 ... Here is the command line used for this computation:
/path/to/deformetrica-2.1/deformetrica/bin/sparseAtlas3 paramDiffeos.xml 1 paramNonOrientedSurfaceMesh.xml ./DemiSphere.vtk ./surfaces/01_groupe01_01.vtk ./surfaces/02_groupe01_02.vtk ./surfaces/03_groupe01_03.vtk ./surfaces/04_groupe01_04.vtk ./surfaces/05_groupe02_01.vtk ./surfaces/06_groupe02_02.vtk ./surfaces/07_groupe02_03.vtk ./surfaces/08_groupe02_04.vtk ./surfaces/09_groupe03_01.vtk ./surfaces/10_groupe03_02.vtk ./surfaces/11_groupe03_03_reference.vtk ./surfaces/12_groupe03_04.vtk > logout.txt