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cmgui development meeting notes 2011
17 January 2011
Alan: 1776 Rewrote group code. 2792 Selection API.
David: Creating Poiseuille flow visualisation example with zinc npruntime. Tissue level physics in web browsers. 1844 Added makefile version for opt++.
Hugh: Updated to trunk. Graphics/tessellation crash.
Richard: FieldML talk to prepare.
24 January 2011
Alan: Build not running - talking to IT. API and zinc examples. 1776 Testing change of selection group of rendition. Need change messages for add/remove whole region. 1354 Zinc npruntime ready for alpha. Helping Hugh with CAD selection.
David: 1844 Merged branch into trunk. Update & make opt++ in third_party. API for modifying constant field values.
Richard: FieldML presentation.
Hugh: CAD branch. Selection bugs - problem with creating field of same name as one just deleted while manager cache is on.
Randall, Dougal: Attended.
7 February 2011
Alan: Discussed distributing zinc npruntime alpha.
David: 1844 Working on optimisation examples. Adding create/define field API taking part gfx commands.
Richard: FieldML. 2822 fixed manager cache unable to add new object with same identifier as one removed.
14 February 2011
Alan: Fixing uninitialised variable bugs. 2068 Multiple scene viewers in zinc.
Hugh: Selecting/deselecting CAD elements. wxWidgest bug in release mode passing ref to int. Debug print to target MSVC console.
Dougal: Cmgui tutorial - use version 2.7.
David: 1844 Working on optimisation examples.
Richard: 2830 Segregate element lists in region by dimension. 1451 Showed how proposed node/element iterator code would look to API users.
28 February 2011
Randall: Reminder about upcoming Cmgui tutorial, Wed 9th March.
Alan: 1354 Zinc npruntime API: Scene, scene filters. Rendition destroy callback for selection. Cmiss_nodeset/mesh_remove conditional bug.
David: 1844 Optimisation API needed for 2.8.
Richard: 2842 FieldML document, cmgui import. Update example a1 to use FieldML 0.3. 2830 Segregate element lists in region by dimension. 1451 Add node/element iterators. 2524 Review object lifetime API.
7 March 2011
David: Nephron paper accepted - example using old zinc. Will update to npruntime. 1844 Optimisation API.
Alan: 1776 Fixed subobject groups, element lists segregated by dimension. Added iterators. Updated zinc API to use generic attribute APIs.
Hugh: Build and Test Server documents. Wants to get cmake, opencascade testing for release.
Richard: 2842 FieldML 0.3 import and documentation.
15 March 2011
Alan: 2680 Graphics coordinate system. 1776 Selection group.
David: Alan fixed zinc problems. 2848 Adding optimisation API. Adding C API example, Adding C++ API for new fields for zinc.
Hugh: Cmake docs needed.
Richard: 2842 FieldML 0.3 import.
3 May 2011
David: 2848 Optimisation API. Discussed support for multiple simultaneous objective fields.
Alan: Closing off tracker items, polishing API. CAP client work.
Richard: Reviewing, fixing API. FieldML 0.4 work.
Dougal: Attended.
17 May 2011
Alan: 2915 Update commands to be region-capable. 2859 2914 Fixed bugs in tessellation editor. 1776 Fixed group API. Updated graphics API in zinc. Working on getting field evaluate API into zinc. Keen to externalise wx main loop.
Dougal: Updating documentation.
David: present.
Hugh: 2924 Building on HPC OpenCascade 6.5 (new version) leading to test. OpenCascade to be more open to developer community.
Richard: 2911 Field evaluation and assignment API. Adding is_defined_at_location API. Looking into simplex basis function winding, Zienkiewicz, vtk, cmgui etc.
24 May 2011
Alan: Zinc working; adding API for field evaluation, node/element iterators, groups. 2931 Externalising wx main loop - issues with idle events. Also working on Cardiac Atlas Project.
Hugh: 2924 Added CAD testing example. Alan suggest broken examples in CAD build due to out of date image libraries diff. Build machine: awaiting passwords from David B. Using cmake exclusively on build machines. Looking into plugin architecture for CAD, ITK.
Dougal, David: Present.
Richard: 2911 Field evaluation API - derivatives. 2842 FieldML 0.4 reader.
31 May 2011
Alan: 2931 Externalising wx main loop. 1732 Fixed 2 streamline problem cases, but still can't handle tracking loss in corners of elements. 2932 Working on stream I/O interface. Found bug reading times via API.
Hugh: Trying to get valgrind working on own machine with exclusions. Build machine: no need for people/hpc drive mount. Need separate windows box for management to bring up/down VMs.
Dougal: Reading FieldML Concepts and Serialisation doc.
David: Updating cmgui and building.
Richard: Writing FieldML Concepts and Serialisation doc. Reviewing APIs. Need to look into simplex basis ordering on wedges.
Discussion: Windows fails dues to problems getting static perl build, also libxml. Agreed to offer windows installer with dynamic perl.
7 June 2011
Alan: Working on stream I/O, tracker item 2932. Forum is up and running.
Hugh: 2965 Build server up, with Windows XP 32, Windows 7 64, Ubuntu Lucid 32 & 64.
There was a discussion about build machines.
David: Tracker item 2642 closed. This week will be working on tracker items 1844 (fitting & optimization) and 2848 (API for the same).
Richard: Reviewing API and cleaning up outstanding tracker items.
21 June 2011
Alan: 1883 Closed build with non-strict flag. 2932 Group review of API.
Hugh: 2965 64-bit Windows 7 build not yet finished. Getting Mesa to build.
David: 2848 Converting mesh alignment C++ example to use external API.
Richard: 2911 Discussed plan to complete field derivative evaluation API by adding chart fields for each mesh with matching dimension / number of components. Preparing for FieldML Webinar Thursday. Deferring 2912, 2826 to Cmgui 2.9.
28 June 2011
Alan: 2906 API macros and types to separate sources. Need to rename cmiss_c_inline_id.h. 2932 Discussed stream API & agreed to merge mooted 'stream module' and type-specific stream/storage information with common base class for and region image field.
Dougal: Present.
Hugh: 2965 Build and Test Server BaTS up and running. Windows 7 64-bit and XP 32-bit. Having trouble building MesaGL in Visual Studio. Mac problems with perl interpreter and wxWidgets.
David: 1844 Improving 1-D fitting example. 2848 Using cmgui API to create objective fields for mesh alignment C++ example, and adding new optimisation API to that.
Richard: 2907 Removing graphics window, window projection field from API, adding scene viewer controlled fields.
5 July 2011
Alan: 2932 Posted updated stream APIs for comments, implementation done. Already replaced some specific API with generic attributes.
Hugh: 2965 Awaiting MS Visual Studio 2010 Pro purchase with OpenCMISS for deployment module. For now, MSI will be manually produced on Hugh's machine.
Richard: 2907 Removed graphics window, window projection field from API. Added scene viewer controlled fields. Still to do: add local coordinate system transformations. 2680 Adding support for world coordinates. Removing coordinate system from graphics object so not compiled into display list.
Discussion: Reviewed 2489 Cmgui 2.8 release. Agreed to work together to shift remaining CVS examples to SVN.
12 July 2011
Alan: 2932 Input/Output stream API committed, fixed some bugs. Helped Hugh build Mesa on build server.
Dougal: Will review and update documentation for Cmgui 2.8.
Hugh: 2965 Build Server: all machines building cmgui; ubuntu 10.04 32/64 bit, Windows XP 32-bit, Windows 7 64-bit. Built Mesa.
David: 2848 Committed optimisation API; works for Quasi-Newton; may need more API for Least-Squares Quasi-Newton.
Richard: 2680 Completed graphics coordinate systems. 2376 Removed overlay scene and closed. 2907 Only need to add local transformations to complete.
Discussion: Build server is Ubuntu 10.04. Unlikely to work on 8.04 (Hardy) due to perl. Re-use an old build machine for 8.04 build slave? Would like Windows installer to not need administrator privileges - may not be possible with MSI. Possibly OK if only changing local registry settings.
26 July 2011
David: 2848 Updated API and implementation from review suggestions. Adding C example for least-squares fitting.
Alan: 2418 2509 2932 Working on zinc, added new field, finite element and stream APIs plus various bug fixes. Looking into bugs encountered only on Google Chrome.
Dougal: 2992 Updating user documentation to reflect changes in Cmgui 2.8 release.
Richard: Back from break to reviewing API and closing of remaining items.
Randall: Attended.
Discussion: Concern that users may be upset by changes in cmgui 2.8. Agreed to make every care on release to inform users we will assist migration both in person and with documentation (2993). We will do a presentation on the new release at an ABI seminar. Important to emphasize positive changes and new features, not just the few, fairly advanced areas where user migration is needed. We'll post advice on migration widely on wiki, tracker, forum, e-mails. Also, old versions will remain runnable for some time.
2 August 2011
Alan: 1354 Fixing zinc in Chrome.
Dougal: 2992 Updating documentation for Cmgui 2.8 release.
Hugh: 2965 5 systems building (Mac 32-bit only due to wxWidgets not supporting 'universal' mode); mac executable crashing. IT need convincing about permitting svn commit script to drive buildbot; currently polling every 30 seconds while developing.
Richard: 2848 Reviewing optimisation API. Plan to have multiple objective fields & create new field types for finding mesh locations (2895) and spatial integration for smoothing (2896).
9 August 2011
Alan: 2997 Enum to string conversions in API, also fixing non-standard enum names. Cmgui not doing advanced graphics on hpc2 unless mesa in library path; cmgui crashing on hpc3 - not sure why but trying to open 3-D graphics window in wx, possibly a GTK incompatibility on Suse 11?
Randall: Attended.
Hugh: 2965 Fixed mac build, so all 5 systems building and seem to run ok; working on adding testing to buildbot process. Note: 64-bit linux includes CAD / OpenCascade for now, since fastest to build. Maintaining 3rd party library patch history in git.
Richard: 2895 Added find_mesh_location field, evaluate and assign API for mesh_location valued fields. 1123 Intend to add stored_mesh_location and stored_string field types to external API so can be defined at nodes.
16 August 2011
David: 2848 Planning to continue work on optimisation API.
Alan: 2997 Enum to string conversions in API.
Dougal: 2992 Updating documentation for Cmgui 2.8 release.
Hugh: 2965 BaTS Testing cmgui svn examples on 64-bit linux, 17/20 passing. Mesh Generation and 2 optimisation examples failing (latter two known to be broken). Working on library build. Strange problem with examples checkout failing by getting cmgui source! Working on CAP client - converting to latest cmgui library and API.
Richard: 2848 Working on background code for proposed optimisation API. 1123 1776 Making element_group have a dual 'mesh group' i.e. a sub-mesh is a mesh. 3012 Propose adding advanced field API for summation/integration fields to get individual terms for optimisation.
23 August 2011
Alan: 2907 Replace Scene_viewer output_transformation with scene_viewer_projection field. 1354 Fixing zinc in Chrome - problems with multiple scene viewers.
David: attended.
Dougal: 2992 Made notes about changes to scene editor.
Hugh: CAP client migration to latest cmgui, API. Putting -fpic on third_party for usage as linked libraries in 64-bit.
Richard: 1123 Making mesh_group derived type of mesh. 3018 Seeding streamlines from mesh_location-valued field.
30 August 2011
Hugh: CAP client now linking to new cmgui libraries and using external main loop. Idle updates working. Starting conversion of code to use external cmgui API.
Richard: 1123 1776 Completed element_group field has a dual mesh_group, node_group field has a dual nodeset_group. Fixed some rendition selection bugs. Still has a crash in highlight functors.
Alan: 2907 Finished scene_viewer_projection field, converting examples. Not yet resolved how to migrate texture projection used by example a/project_texture.
Randall, Dougal: Attended.
Discussed reason for slipping release dates, whether it will continue. Mostly delayed to add background features to support the desired optimisation API. 2.8 Release still 2-3 weeks off.
6 September 2011
Alan: Fixing bugs in cmgui and zinc-npruntime. Updating change log.
Dougal: Will help with docs.
Hugh: CAP client. Dealing with incomplete cmgui API.
Richard: 2848 Revising optimisation API.
Discussed focus of next cmgui release. Major item is building cmgui in modular libraries (DLLs). Agreed we want a fairly coarse granularity divided mainly on large third-party library dependencies, e.g. ITK, CAD, GUI/rendering, optimisation. Also higher level utility libraries for convenience functions built on top of the core APIs so not rewritten by several clients, example: 'gfx evaluate'. Discussed whether a simplified abstraction of the data model can be offered: probably a separate project, but review as demands develop.
13 September 2011
Alan: Fixing bugs in cmgui (streamlines) and zinc-npruntime (issues with controlling lifetime of cmgui instance).
David, Dougal: Attended.
Hugh: 2965 BaTS: Thinking about adding more cmgui builds to test server. Larger disk being installed today. Has issues with obtaining symbols/headers for itk, imagemagick, gdcm, wx from libraries statically linked into cmgui dll.
Richard: 2848 Optimisation API, conceptual issues with least squares solving a different problem for a given nodeset_sum, actually minimising the sum of squared terms. Polishing API.
Discussed and agreed to keep "cmiss" prefix on objects created by the cmgui library e.g. cmiss_mesh_3d, cmiss_nodes etc. i.e. not just limited to objects created by the cmgui application such as 'cmiss_selection'. Most of these objects will be replaced by names defined in FieldML, eventually.
20 September 2011
Alan: 2418 Added more field types to Zinc plugin. 1354 Make Zinc plugin more stable. Change example thumbnail script to look in subfolders.
Hugh: 2965 BaTS: Getting testing for CAP on buildbot. Build static libs. Hard to guarantee lib built before client app (CAP).
David: Attended.
Dougal: Committing updates to documentation for v2.8.
Richard: 1844 Completing smooth volume fitting example and code to create gauss points for smoothing terms.
27 September 2011
Alan: Cleaning up examples, esp. CAD valgrind results. 2848 Put optimisation API in zinc-npruntime, crash encountered. Cleaning up tracker items.
Hugh: Changing to make it easier to use cmgui libraries. CAP issue: gdcm should be included by image magick, is not. Mesa on ubuntu 10.04 has bugs with shaders - shader examples crash on BaTS.
David: 1844 Fixed remaining test answers. Completed.
Dougal: 2992 Reviewing, updating user documentation. Requests feedback.
Richard: 3060 Looking into excessive memory usage by STL set implementation of node/element list.
4 October 2011
Dougal: 2992 Committed documentation changes, will put up on wiki for review.
Alan: 1354 Fixing bugs with multiple instances of Zinc plugin.
Alan Garny: Asked about Qt version of CMGUI library. Time-frame not urgent.
David: Attended, as user.
Richard: 3060 Reimplemented our own multi-way binary trees as a C++ template, increased from 10-way to 20-way tree for nodes and elements, and optimised memory occupancy. 2992 Working on Introduction to CMGUI Zinc API document. 2993 Wrote migration doc for changes in cmgui 2.8. 3065 Plan to define and document constant for successful return code in API.
11 October 2011
Alan: 3068 Zinc testing. 3082 Looking into different ways of representing enumerated constants in JavaScript with Zinc-npruntime. 2992 Reviewing documentation.
Hugh: 2931 wx main loop moved out of library.
Alan Garny, Randall: Attended.
David: Intends to make application starting from Simple Axis Viewer as part of integrated cell modelling demo.
Richard: 2992 Introduction to CMGUI Zinc API document. 3083 Plan to allow creation of gauss points on simplex elements (triangles, tetrahedra and wedges).
Discussed problems with having wxWidgets built into library; can't pass in main application object made with separate wxWidgets linked to application, which could even be a different version. Clearly need to remove wxWidgets from library, but will await user problems to address. Discussed removing use of strings for enums in Zinc JavaScript applications. Option is to make immutable enums as members of objects, e.g. imageField.combineMode.BLEND. Issues with enums which are required in constructors or used by several objects - perhaps these are owned by the plugin e.g. zincPlugin.imageFieldCombineMode.BLEND. Agreed best to remove strings as you wouldn't want to get enum as a string. Discussed renaming API prefix from Cmiss to Zn; not doing for 2.8 since too disruptive for ourselves and partners e.g. GIMIAS. Would also be nice to change format to more closely match camelCase used in JavaScript with Zinc plugin, e.g. Cmiss_field_module_find_field_by_name() -> Zn_FieldModule_findFieldByName(). Need more discussion, consensus and only one change at the most appropriate time.