Lesion-Extracting GSSF Component

This component wraps a separate tool, go-smart-lesion, which uses VTK routines to extract a lesion surface. More generally, this component extracts an isosurface based on certain criteria.

Configuration

When running go-smart-lesion as part of the GSSF workflow, the Python component can be configured as follows:

    <lesion field="FIELD"
            [ threshold_lower="THRESHOLDLOWER" ] [ threshold_upper="THRESHOLDUPPER" ] 
            [ selection="(most-recent|largest-time):most-recent" ]
            [ connectivity="BOOL:false" ]
            [ scaling="FLOAT" ] />

If scaling is omitted, the inverse of simulationscaling is used. This returns the simulation to the original, input length scale. If connectivity is true, the largest component only will be extracted. To choose a specific simulation timeslice for input, the selection attribute can be set to either most-recent, for the most recently modified file in the Elmer output directory, or largest-time to choose the timeslice with the highest timestep suffix. On a clean run, these should pick the same output VTU file. The THRESHOLDUPPER and THRESHOLDLOWER values, if provided, will be used in a VTK ThresholdBetween call. If only one is provided, ThresholdUpper or ThresholdLower will be used. Note that this is the reverse of the VTK definition - we treat THRESHOLDUPPER as the maximum accepted value within the lesion, and THRESHOLDLOWER as the minimum. FIELD should be a field present in the VTU file, which should correspond to variables output from the SIF template. Note that Elmer seems to lowercase variable names before output, so FIELD should also be lowercase even if the SIF template uses mixed/uppercase.

go-smart-lesion

go-smart-lesion may be run standalone from the shell. If so, the syntax is as follows:

go-smart-lesion OPTIONS

Optional arguments

Argument	Description
`-h [ --help ]`	produce help message
`-t [ --threshold-lower ] arg`	threshold for chosen variable (remove cells with values below this limit)
`-T [ --threshold-upper ] arg`	threshold for chosen variable (remove cells with values above this limit)
`-S [ --scale ] arg (=1)`	pre-scaling of results; default 1
`-f [ --field ] arg`	field to threshold on
`-p [ --parallel ]`	assume input data is PVTU not VTU
`-x [ --threshold ]`	switch from using an IsoVolume to using a Threshold
`-c [ --connectivity ]`	extract largest connected component of thresholded surface
`-s [ --subdivide ]`	subdivide before thresholding
`-i [ --smoothing-iterations ] arg (=0)`	number of iterations in smoother (0 to skip)
`-e [ --exclude-subdomain ] arg (=-1)`	exclude subdomain of given index
`-i [ --input ] arg`	input volume mesh file
`-a [ --analysis ] arg`	analysis output file
`-o [ --output ] arg`	output file
`-r [ --retain-subdomain-boundaries ]`	retain all internal inter-zone boundary facets
`-g [ --geometry-filter ]`	use geometry filter instead of vtkDataSetSurfaceFilter to extract surface

Implementation

TODO-RMV: after refactoring