Go-Smart Needle Library - STEP manipulation and geometry generation

This tool uses PythonOCC to generate triangulated surfaces from STEP files, for representing needles and other features. It uses PythonOCC also for geometric transformation, allowing a single reference STEP to be placed into a mesh in any location or of any scaling.

With the appropriate GSSA-XML extensions, this will allow a user to provide their own STEP geometry as the definition of a surface or surfaces in the mesh. The present implementation provides some support for splitting an STEP file, with the first listed component being output as an 'active' part, the second as an 'inactive' part, both in STL format.

go-smart-needle-library

Management tool for Go-Smart ablation needle geometry library

go-smart-needle-library [-h] [--logfile LOGFILENAME] [--logfile-addpid]
                           [--silent] [--debug] [--output OUTFILE]
                           [--output-extent EXTENTFILE]
                           ...

Positional arguments

Argument	Description
configfilenames	Locations of configuration file (latter override former)

Optional arguments

Argument	Description
-h, --help	show this help message and exit
--logfile LOGFILENAME	name of the log file
--logfile-addpid	whether the PID should be appended to the given
	logfile name
--silent	prevent wrapper output
--debug	additional, debug output (overridden by --silent)
--output OUTFILE	destination STL file for needle
--output-extent EXTENTFILE	destination STL file for extent

Needle CAD geometries

These should lie along the z-axis, with tip at the origin and be in STEP format. One or two roots (shapes) may exist. If two, the STEP will be split into two STL surfaces, with the first marked as the 'active' surface, the second as the 'inactive'. Interpretation is left to the modelling components of the workflow. If multiple shapes are provided, they should be output in STLs suffixed by the ordinal position in the STEP (1 → n). This should work for n > 2 but has not been fully tested.

GSSF component

The corresponding GSSF component forms a fairly transparent wrapper for go-smart-needle-library.

Configuration

The second-level GSSF-XML tag is as follows:

    <needlelibrary [ skip="BOOL:false" ]>
        <needle id="ID" [ name="NAME" ] [ axis="AX AY AZ" ] [ offset="OX OY OZ" ]/>
      [ <target x="TX" y="TY" z="TZ" /> ]
      [ <extent x="TX" y="TY" z="TZ" /> ]
    </needlelibrary>

The id is the library name of the required template. It is recommended to write this as id="stock:ID" for future compatibility. The name is a human readable name to use to refer to this needle elsewhere in the simulation. If not provided, the ordinal index of the needle node will be used. The axis overrides the global axis from the geometry section of [GSSF-XML][xml.md] for this needle. The offset indicates the offset of this needle from the target of the needle-set, by default the geometry centre.

The target allows the user to specify an offset of the needle-set from the centre of simulation as defined in the geometry section. The extent, if provided, instructs the needlelibrary to generate an STL simulation boundary. This may be intersected later with the organ boundary to generate an outer boundary of the simulation domain.