Meeting Purpose:

Agenda for 11 October 2006 Shape Tools meeting (Week 41-42)

Review prior weeks to do items

• [ ] Craig - ensure ShapeTools can support writing attributes in scientific notation.
• [-] Craig - finish vertex selection via Java3D
• [-] Craig - add vertex selection to ShapeViewer
• [ ] Craig - continue research ways to have sun grid communicate with Java interpreter.
• [ ] Craig - test Grid job - run Java app to fetch a (remote) URL.
• [ ] Craig - interim progress demo to Elizabeth and Eric.
• [-] Craig - review P41 grant section.
• [ ] Craig - improve documentation of UcfReorder
• [X] Craig - check Jama license to see if it can (and shoud) be included in ShapeTools
• [ ] Craig - integrate Ryan & BaeCheol code
• [-] Craig - implement user selectable back clipping plane/pick plane in demo viewer.
• [X] Craig - request David Shattuck review DFS file format.
• [X] Craig - evaluate suitability of Apache command line interface tools.
• [X] Craig - personell evaluations.
• [-] Ryan - file format for spline warp coefficents
• [ ] Ryan - complete thin-plate spline warp contour solver
• [ ] Ryan - application to applly spline warp to an image.
• [ ] Ryan - document file format of spline parameters.
• [ ] BaeCheol - complete an ImageJ Plugin - to - ShapeTools adaptor.
• [ ] BaeChoel (With Craig) - draft requirements for tool to find the delauny triangulation , and outer hull, of the vertices in convex cloud of points.

New Business

Discussed

• Jama & Apache CLI suitability
• Image J Plugin Adapter
  • Approach (Java introspection to find methods with signature's indicative that they might be an image loader) yields
    • Analyze Image
    • Nifti
  • support for ImageJ native file types (jpg,..)
  • support for color image types

• Thin plate Warp
  • need to support multiple pairs of contours, all required to lay in the same plane.
  • may need to differentially weight contour pairs
  • will need to read contour pairs from an file on disk.
  • find the warp minmizing the deformation in order to find an atlas, where "atlas" is defined (by the data) as that space which minimized the summed energy used to perform all the warps.
  • future support of grid processing assisted by being able to write output warp parameters to multiple files.
  • thin plate warp eseentially finds minmum energy mapping from space A -> space B; this minimum energy pathway does not apply to the inverse transform. Multiple warps minimize energy independent of each other
• synergy approching: BaeCheol's Image grid shape get warped by Ryan's warp, using contours drawn in MultiTracer, and

Decisions

• Craig will use Apache CLI for Katherine's Medial distance application.

To do for Next meeting

• [ ] - Craig - integrate ryan and BaeCheol^?'s work
• [ ] - Craig - integrate Jama into shape tools library
• [ ] - Craig - supply Nifti test file to BaeCheol^?
• [ ] - Craig - assist BaeCheol with setting color values
• [ ] - Ryan - adapt grid warper to read shape in external shape files.