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cmgui development meeting notes 2009

  • 19 June 2009

    • David: with Richard, look into possible fitting support APIs
    • Dougal: -
    • Alan: BuildBot Cmgui master needed. Shane strongly recommended BuildBot; export exnode at time for CAP, made deforming_heart test feature
    • Heye: Meshing. Building cmgui on linux. Q. able to work with external APIs? Issue of gmsh / .geo files supporting only ruled surfaces, not reflecting interior terms. Will convert all bases to nearest splines. Duane suggested auto-tolerance for subdividing patches.
    • Duane: Adding code docs for zinx. Mentioned PyCuda (nVidia Cuda). Alan mentioned OpenCL
    • Randall: Wants notes of these meetings on web
    • Richard: Field component labels.

  • 26 June 2009

    • Dougal, Duane, David: nothing to report.
    • Alan: Cmgui demo working, making into test. Reading up on BuildBot, requires customisation, waiting for Andrew to install version
    • Hugh: Colour issue sorted in OpenCascade 6.3.1 yet to be released to non-subscribers; Cmake, removing dependencies on Hugh's tree
    • Randall: Cmgui IUPS intro/guide preparation, Cmgui ABI users feedback
    • Richard: Working through ensemble/piecewise field ideas.

  • 3 July 2009

    • Day long Cmgui/Zinc Developer Workshop, Owen G Glenn Building.
    • Attendees: Richard, Jae Do, Carey, Peter, Shane, Randall, Hugh, Alan, Duane, David, Dougal (part day)
    • Notes in tracker:https://tracker.physiomeproject.org/show_bug.cgi?id=1843

  • 10 July 2009

    • Hugh: Cmake non-wx builds being fixed; back on to CAD fields
    • Alan: Fixing builds; Setting up BuildBot
    • Duane: Zinx: Changing so not updating RDF every time; Looking into RDF->json
    • Peter: Finished exam marking; Digitiser queries; Teaching 3 days/week from end of month
    • Heye: Working on .geo export. Will add command later. Using TotalView debugger to trace cmgui program flow.
    • David: FE_value -> double, moving to branch
    • Dougal: Finished Cmgui guide for IUPS
    • Richard: Collated Cmgui survey; Reading up on python, SWIG
    • General discussion on form of standalone Cmgui application without perl interpreter: Duane 'concentrate on API and user community will write tools'; Richard 'need to migrate existing cmgui users, minimise cost of maintenance, anticipate UI binding issues' etc.

  • 17 July 2009

    • Hugh: Implementing CAD shape field; Cmake working on 64-bit linux (perl interpreter built separately); adding single place to list non-STRICT sources for both make and cmake
    • Duane: Zinx changing to wrap RDF in json = javascript objects
    • Randall: Compiled (with Dougal) Cmgui notes for IUPS conference, very happy that most content available on web now.
    • Alan: Minor changes/fixes including shaders. Closed off several older issues. Working on getting cmgui building on same BuildBot buildmaster as OpenCMISS, to load-share on buildslaves.
    • Heye: Working on face export to .geo files for meshing in gmsh.
    • Richard: Occupied by FieldML domain/field discussions. Focusing on merging regions and scenes, graphics rendition API, region-capable groups and selection.
    • General discussion on changes to cmgui application to present a region tree instead of scene tree will not be implemented for motif. Only remaining major functionality lacking on wx is offscreen antialiasing; discussed workarounds.

  • 24 July 2009

    • Hugh: CAD field 'there'. Cmake perl interpreter.
    • Duane: Zinx RDF -> js objects -> json. Translating XUL trees based on RDF. Tree plugin / UI language. David: DoJo builds trees on 'data stores' - use DoJo data store plugin over js objects?
    • David: Double precision - 40% complete?
    • Alan: Merge scene and region tracker item 1047. Renditions in regions.
    • Richard: Discuss resolution of issues with merging scenes and regions. Hierarchical graphics.
    • Heye: .geo file export (for gmsh).

  • 7 August 2009

    • Hugh: CAD shapes & fields & evaluating. Cmake perl interpreter progressing. Ordering problem with use of DLL before built. Warning suppression flags.
    • David: Back into double precision conversion. IUPS report - positive feedback.
    • Alan: Merge scene and region, phase 1 done. Still has scene object for static graphics. Changing graphical element -> rendition. Tests passing. Python API, image field API changed.
    • Dougal: Preparation for IUPS.
    • Duane: Large tet meshes - iso-surfaces slow. Gmsh tet mesh. Demonstrated mayavi.
    • Heye: Meshing code submitted, needs polish.
    • Richard: Selection and groups.

  • 18 August 2009

    • David: Petsc dynamic linking wanted as huge library. Double precision FE_value: integrate branch as float and get others to help with remaining conversions.
    • Alan: Merging Scene and region. Looks same to users. Time working, adding transformation, static graphics.
    • Randall: Possibility of OpenCMISS client using cmgui library. Discussed distributed graphics.
    • Duane: Successful knee conductivity presentation. Zinc worked well.
    • Richard: Groups, evaluation, meshing.

  • 1 September 2009

    • Alan: Buildbot is running & testing on vista laptop, mac bioeng46, linux bioeng1031. Testing SVN examples only; intention to migrate all examples so won't do CVS. Merge scene and region - mostly waiting for selection. Dicom issues.
    • Duane: Zinx now loading time-based models.
    • Hugh: CAD fields. From last week: discussed having bug squashing day.
    • David: Compilers. Double precision alias problems. PetSc complicated - investigate other, simpler linear algebra packages; will talk to JaeDo / CAP.
    • Richard: Helpers - char strings. Selection/group design.
    • Travelling to Nice (euHeart), Barcelona (GIMIAS - collaboration). Wants cmgui 2.8 released on Mac.

  • 8 September 2009

    • David: committed double precision FE_value branch. 1 broken example.
    • Alan: MIPS compilation failing. Mac / bioeng46 fixed.
    • Dougal: Powerpoint slide of cmgui team members.
    • Hugh: Build, link netgen for meshing prototype.
    • Richard: Investigate possible tetrahedral define faces issue, surface outward normals. Delay working on iso-surfaces until meshing done.

  • 15 September 2009

    • Hugh: Dependencies & windows builds. Removing console in windows.
    • David: More elegant float/double casting ideas using C++. Handling double:double and float:float cases as NOP.
    • Alan: Meshing: render triangle mesh. Fixing build system. Back to merge regions and scenes.
    • Richard: Surface winding and normals. Isosurfaces.
    • Dougal: Make meshing movie.
    • Peter: Build and test zinc including npruntime. Want windows testing.

  • 22 September 2009

    • Alan: Merge scenes and regions - getting export vrml. stl working. Render triangulation for meshing: tidying up. MIPS IRIX only one of 32, 64 bit working.
    • Randall: Cmgui/FieldML/CellML report result nice. Gave video demo of GIMIAS in action after collaboration meetings in Barcelona.
    • David: Plugged in a different optimiser (levmar) to Duanes' minimise; didn't work.
    • Hugh: Cmake compiling for MSVC, also eclipse - cleaning up. Perl interpreter main problem. Example a1 running - XML working. Want to separate XML from image libs.
    • Peter: Building cmgui + zinc after break - new issues.
    • Richard: Iso-surfaces. Face winding and normals. Will commit new graphics answers for surface winding and iso-surfaces together. Change to double.

  • 7 October 2009

    • David: Shane's issues with float/double conversion. Trying optimisation libraries.
    • Alan: Merge scene and region; Transformation working; OpenGL display list renderer working. gdcm updates. 16-bit textures for CAP. Build issue with motif spectrum editor (Richard to fix). gdcm problems with our example images. Stripping MIPS IRIX build.
    • Hugh: Added 4 library builds to cmake. Trying to remove main loop from library. CAD shape fields.
    • Richard: Getting iso-surfaces + surface normals in. Will remove voltex. Upcoming priorities: Group/Selection, new evaluation cache with derivatives.

  • 13 October 2009

    • David: Macro issues with FE_value float/double conversion. Working with zinc & zinx.
    • Hugh: Building libraries - removal of general lib under discussion. Changing APIs to remove dependencies on internal headers - need to determine if breaks zinc build. CAD fields: geometry evaluates via internal function of topology (domain) field. Preparing API summary document.
    • Peter: Summer students starting 19th Nov pm, 7th floor. Getting eye, ecg zinc examples running - PJH request.
    • Richard: Completing isosurfaces simultaneous multi-iso-value evaluation; anticipating parallelisation in new support functions (multiple threads working on different parts of the mesh). FieldML preparation.
    • Alan: Fixed libgdcm - now loading snake example dicom images. 16-bit textures for CAP including exposing more API. MinGW gcc 4.4 build issues with perl interpreter - calling obsolete functions. MIPS IRIX compilation and test removed. Buildbot waiting for new build machine. Ecg lab cmgui example broken: unemap build?
    • Randall: Discussed new build/test hardware, API status for GIMIAS collaboration.

  • 20 October 2009

    • Alan: Image/texture bit size issue - focusing on getting number of bytes working correctly first. Fixing own windows build with gcc 4.4 - using gcc 4.2.x for perl_interpreter. Getting export from new scenes working. Unemap compilation warnings - need to change to use new MOTIF_USER_INTERFACE define.
    • Hugh: Worked on CAD fields for eBonz. Topology, geometry, colour fields added. Auto creating RGB spectrum on read. Added curve rendering with new CAD curve location; some curves are embedded in surfaces, some free.
    • Peter: Teaching admin winding up. Investigating zinc eye, ecg example. Need a zinc release with alias field; we should quickly tidy API for this. Current overnight zinc builds are crashing on all but the test examples - looking into.
    • Richard: Iso-surfaces performance. Discussed group/selection implementation as CAD selection needed. Main issues to sort out: base/derived type casting in API, replacing group change messages with more detailed field change messages.

  • 27 October 2009

    • Alan: Cmgui-unemap building again - add non-strict filenames for unemap compiler warning suppression. Problems with shaders and spectrums. Export graphics scene SCENE_NAME/region_path.graphic - discussed this command change versus eventual API which specifies just scene, requiring new scene to be created if more precise export required; command keeps existing functionality going. Discussed Barcelona group's build problems with wx. Testing wx using unicode.
    • Heye: Updated tracker on netgen meshing item. Get svn write privilege, request code review.
    • David: Trying zinc, zinx for kidney & cardiac research projects. Problems using html instead of XUL; zinx issue with compulsory console widget.
    • Peter: Zinc user support. Zinc build broken this week.
    • Richard: Use GT_voltex for new isosurface to 'get finished'. Advantages: reuse existing surface normal averaging, decimation code. Disadvantages: no selection or graphic editing.
    • General discussion on getting mac testing machine, general build machine. Plan to arrange meeting with IT, development teams to get a proposed spec, sort OS licensing costs on VMs.

  • 3 November 2009

    • Alan: Integrated trunk to merge-scenes-and-regions branch; working on scene/graphics API. Putting shader issues on back-burner. Benchmarking testing for determining build machine spec.
    • Dougal: Looking into documentation source tools.
    • Peter: Departmental work.
    • Hugh: Perl interpreter built with cmake; windows dll linking. Looking into build/test machine spec. eBonz python modelling work.
    • David: Trouble with xul-centric zinx so using zinc directly, with Dojo. Creating element groups failing in windows build = nothing happens. Need debug build of zinc.
    • Richard: Isosurfaces and surface normals committed; tidying up test answers. Problem with outward normals on collapsed elements highlighted by eye example. Assisting with meshing, working on group/selection APIs, FieldML.
    • Heye: Netgen has problems meshing cmgui example meshes.

  • 10 November 2009

    • Alan: 1046 Some graphics API now working without gfx commands. 2038 Investigated strtol symbol export problem. Fixed image testing binary used for idiff. 2050 Ready to commit torso meshing example. Timing build and test.
    • Heye: 2050 Set functions for meshing control. Example ready.
    • Hugh: 2050 Now building netgen under linux with makefiles. 2073 Timing build and test; peak RAM usage is not representative as some OSes grab all available memory. 2079 Putting together all third party libraries.
    • David: wants to be able to zoom in on model and have more details revealed e.g. switch to symbolic microscopic view, not necessarily viewing part of a huge dataset. Trying out zinc scene viewer in a page.
    • Richard: 1992 Surface normals/winding fix completed. 1990 Re-added support for isosurface decimation using old algorithm.
    • Plan for next cmgui release before end 2009: Main new features are meshing, new isosurfaces, dicom/image changes etc. plus bug fixes. Discussed fixing up streamlines. Priority is to tidy up API: passing factory objects to all constructors, fixing header pollution.
    • To be added after next release: Merge scene and region, planned new groups/selection.

  • 17 November 2009

    • Alan 2096 Adding graphical material API. 2050 Committing more meshing code, torso example ready to commit; different answers on every platform and variant.
    • Heye: 2050 Added more options incl. max global element size.
    • Hugh: 2050 Sorting out netgen build. 995 Removed CREATE/DESTROY macro use in API. 880 2079 Third party library consolidation for total build tarball effort. 2040 Fixing region hierarchy from CAD import.
    • Richard 2099 Changing field constructors to take field factory object and automatically add field to region.

  • 24 November 2009

    • Hugh: 1885 Cmgui on windows / VS now building with cmake, except imagemagick. Need to add gzip versions of zlib, other libs instead of bz2 as cmake only supports this (bz2 planned for future release). eBonz python work.
    • Alan: 2096 Material API added. Still to sort out persistence API. Fixing examples, incl. python API. 2050 Added example a/generate_mesh for meshing. Helping summer students with build issues. 1788 Will add proper version string to cmgui about dialog before next release.
    • Heye: 2050 Added meshing local refinement control via mesh size file.
    • Richard: 2099 Still at least 2 more days work on adding fields to region on create as have to hand-convert all create functions.
    • General: Discussed obtaining a summer students machine (all min quad core Xeon) to try as test machine mid Feb before allocated to new PhD.

  • 8 December 2009

    • Alan: Fixing broken examples. 2332 Helping summer students with npvariant bug. 1047 Merge scene+region: fixing examples, incl. render finite elements. 1046 Starting spectrum API. Fixing build.
    • Duane: Meshing with gmsh, tetgen. Dealing with interpenetrating meshes. Quickly added texture object to zinx - realises should be an image field.
    • Hugh: eBonz python work. 1738 Cmake nearly there, waiting for bug fixes in cmake 2.8.1; working on static linking of libraries used by libraries ~ 'imported targets'. REMINDER: add new source files to cmake!
    • Dougal, Heye: Attended.
    • Richard: 2099 Committed but may revise API names: should logically be Cmiss_field_factory_create_add, not Cmiss_field_create_add (cf. Zinc calls the factory object 'Cmiss_field_create' and the method 'add'.)

  • 15 December 2009

    • Alan: 949 Fixed writing large non-square offscreen images. 1047 Added graphic set spectrum function. Discussed loss of ability to prioritise graphics rendering sequence (since reordering regions may not be desireable): consensus was that when needed a new feature to draw chosen graphics before others can be added. 2365 Intending to render private graphics objects in private region/rendition tree to show simulated spectrum colour bar in spectrum editor. 1630 Update timekeeper/notifier API to new standard.
    • David: Mentioned demonstrating dev version of zinc nephron (kidney) app to group including clinicians.
    • Duane: Meshing the knee.
    • Dougal: Attended.
    • Hugh: 880 Total tarball; all building but 2 issues: perl_cmiss needs to be moved into install tree; gdcm patch doesn't work for latest libgdcm (but some fixes incorporated into imagemagick). Changed names of third party source from libX -> X so all are consistent (some had lib; some did not). 2104 Will put wxWidgets and itk in our repository.
    • Richard: 2099 Posted suggested C++ inline shim API (automates ref counting and polymorphism) on tracker. David suggested trying to wrap with SWIG before committing.

  • 22 December 2009

    • Hugh: 2373 New tracker item for renaming third party libs libX -> X.
    • David: 1844 Checking out licenses for various optimisers; Sandia opt++ a possibility.
    • Alan: 2365 Static graphics e.g. colour_bar added to glyph list so can display in rendition. Discussed adding 'overlay' option for graphics e.g. to clear depth buffer and draw after main scene.
    • Dougal: Will look into cmgui name presentation/branding; see general discussion below.
    • Richard: 2099 Will put in field_module_create API.
    • General: Discussed changing API prefix/namespace to Cmgui (from Cmiss) to avoid confusion and potential clashes with OpenCMISS; anticipating some applications will call both APIs.