[Molecuilder-devel] [SCM] MoleCuilder branch Fix_ConvexizeNonconvexEnvelope created. v1.4.8-53-g5cfdcf7

Thu Oct 16 16:44:33 CEST 2014

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The branch, Fix_ConvexizeNonconvexEnvelope has been created
        at  5cfdcf70299145cf832d0ed47f1308237b9e42d6 (commit)

- Log -----------------------------------------------------------------
commit 5cfdcf70299145cf832d0ed47f1308237b9e42d6
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 12:00:11 2014 +0200

    TESTS: Extended Tesselations tests to convex case.

    - moved all present tests to NonConvex folder, added same set but including
      amylose in Convex folder.

commit d31cae77953f6678555ca8b2d0cb60b57041ba7e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 16 16:34:13 2014 +0200

    TESTFIX: Regression test Tesselation/BigConvex is now working.

commit f1a18e2659c017087b33aed876cdb5203495e0ea
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 11:47:03 2014 +0200

    Convex-envelope has debug parameter DoOutputEveryStep.

    - this writes for each convexization step a distinct tesselation file.
    - added parameter to ConvexizeNonconvexEnvelope().

commit 606c3ea8ad09230c97cbe3f8a4a8e94094d14427
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 18:24:30 2014 +0200

    Added SphereRadius parameter to ConvexEnvelopeAction.

commit 565ae0a560723f992a92b32ce0ff794b1207a009
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 11:34:55 2014 +0200

    Added tcl scripts for viewing and debugging convexized surfaces.

commit 70fbbf5b5f4e695fb5e9b24e83507fb0927bec70
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 10:55:44 2014 +0200

    DOCU: Added extensive explanation how convexization works.

    - updated userguide for convex-envelope.

commit 0e75b00e5e0ad230f928dcf40a31545a477d5bbe
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 4 10:44:54 2014 +0200

    Added check whether all points remain inside surface and whether it is convex to ConvexEnvelopeAction.

commit 14fafa978ad8f073e3f6bfc71896bed224bc275c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 10:27:36 2014 +0200

    ConvexizeNonconvexEnvelope() uses now RemoveFullConcavePointFromTesselatedSurface().

    - with this convexization of a nonconvex tesselated surface seems to be
      robustly working as we can now deal also with points with degeneracies.

commit 20c18051dace481e30b64e5ba906d722ba28b834
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Oct 8 18:14:39 2014 +0200

    FIX: ConvexizeNonconvexEnvelope() needs to purge degenerate triangles before convexization.

commit 6f7356114f3d1165f43fd8cc7d1f5a5635ae4ce1
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Oct 8 15:08:11 2014 +0200

    FIX: GainMap is used to store the concavity angle, we flip now always most concave.

    - this overrules prior flipping those that gives greatest gain in volume.

commit 4b54f73aba95c7e3039546e82c9a1df393327308
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Oct 4 16:34:41 2014 +0200

    Rewrote ConvexizeNonconvexEnvelope().

    - now works for some sphere radii on amylose (e.g. 40 and 50).
    - we first remove all points that are only attached to concave lines.
    - also, we always flip the baseline (i.e. add a general tetraeder to the
      non-convex volume) for concave lines when the tetraeder does not intersect
      with present triangles.

commit 8d778fa588719f6983eed36294b74582c67f6184
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 12:31:18 2014 +0200

    FIX: Tesselation::RemoveDegeneratedTriangles() ended up in endless loop.

    - even if a triangle pair is not removed, it must still be removed from the
      degenerated list or we run into infinite loops.

commit 3c6b9d0e0d1f7572ed80073caafed6d5eeedf2e6
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 09:37:06 2014 +0200

    Extracted RemovePointSurroundedByPolygon() out of Tesselation::RemovePointFromTesselatedSurface()

    - also added new functions
      Tesselation::RemoveFullConcavePointFromTesselatedSurface() and
      Tesselation::CheckAllConcaveInPolygon().

commit 633576c77a8f88ab8b74845376e2ab706fdea53a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 7 09:38:17 2014 +0200

    FIX: Removed flipping for maximal gain in Tesselation::RemovePointFromTesselatedSurface().

commit ee886b36fc89715a5380053cc9ef0ec633424871
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Oct 8 14:46:36 2014 +0200

    FIX: Tesselation::RemovePointFromTesselatedSurface() uses wrong NormalVector.

    - with the point to be removed we have a very good measure for a vector
      pointing inside. Before we used the average of all normal vectors.

commit c1c8bc20ece846bb15d0be96187f99a80646eafb
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 7 09:55:26 2014 +0200

    FIX: Tesselation::getVolumeOfConvexEnvelope() calculated volume wrong.

    - replaced code by using present function for tetrahedron calculation with
      center of gravity as fourth point when going over all boundary triangles.
    - TESTFIX: volume change in convex regression test.

commit e6b793d18f5032e7033b3bf8de0eef2da63cb33c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 7 08:57:30 2014 +0200

    FIX: Tesselation::FlipBaseline() caclculated NormalVectors wrong.

    - before we just took the average of the normal vector of both present
      triangles as guide. Now, we check the intersection of the fourth endpoint
      on the plane of the first triangle and decide by on which side of the
      three boundary lines the intersection lies whether to flip the normal
      vectors sign for the associated (new) triangle or not.

commit 97d98600955169f39319e9ee925d91b2bf88c7d5
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 14 18:37:03 2014 +0200

    Added Tesselation::IsPointBelowSurroundingPolygon().

    - IsPointBelowSurroundingPolygon() creates all triangles as planes and checks
      whether point is below.

commit 5a4d8f9201f96f0199f6c5855c9cf149b1ef97cd
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 12:27:57 2014 +0200

    FIX: Filling of non-convex polygon with only minimal angles did not work.

    - when removing points from non-convex boundary and we encounter non-convex
      polygons, we must pick smallest angles but close to the non-convex site!

commit aad7aa64cf795a5b4af656e636efc9d343590816
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 11:43:03 2014 +0200

    FIX: RemovePointFromTesselatedSurface() used Start,Middle,EndNode confusingly.

    - FIX: Very last node was removed twice due to StartNode = EndNode setting.

commit 3c460f1ba60995d3104ee413bf980ed1dc7a1ad9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Oct 3 11:38:16 2014 +0200

    FIX: Reduced verbosity noise from Line::getIntersection().

    - removed use of info and toned down verbosity levels (which are so low
      because of now missing info).

commit df82bca737770e1707f61dfafdd306da22481bcf
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 20:26:03 2014 +0200

    Changed some verbosities in Tesselation code.

    - modifications in BoundaryPointSet, BoundaryLineSet, BoundaryTriangleSet.
    - also to CandidateForTesselation, TriangleIntersectionList, tesselation,
      tesselation helpers and boundary code.

commit 921e9bcac84adb5c685919dd87089396207a8f67
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Oct 7 09:28:44 2014 +0200

    DOCUFIX: Corrected formula for general tetrahedron in docu.

    - also code now matches with formula to avoid further confusion, although
      the result does not change by that.

commit 307d7bb6db49ea9b0aeb0342f3714194a2a539a4
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 20:23:50 2014 +0200

    FIX: RemovePointFromTesselatedSurface() needs to pick smallest angle when polygon is not convex.

    - AddTesselationLine() now returns whether new or present line was used.
    - FIX: Last inner line in closed polygon has been added by one but last
      triangle already, we added it twice.

commit d8632f2bc865ecf3f0bdcd26294ad717d79617b9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 20:24:52 2014 +0200

    FIX: RemoveTesselationLine() needs to erase line from OpenLines if present.

commit 85e1ef4c292dfea8eacd77e1b1607d2c8bd13d65
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 18:25:23 2014 +0200

    FIX: AddTesselationLine() would only work in initial tesselation phase.

    - the CandidateForTesselation instance is NULL when we convexize and this
      was not correctly processed by AddTesselationLine().

commit 4136c923ec473144f05170e1b8b9d4fe976b1c81
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 20:26:20 2014 +0200

    FIX: Changed all performCriticalExit() into ASSERT() in tesselation.

commit 1f176d5e27f7338dc5acf15caae1fb5580036cbe
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Oct 9 10:56:24 2014 +0200

    FIX: Raster3D needs header.r3d, which had been missing so far.

commit 9265d6e802e9e84c5414209cf2ec20c38f7f3843
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Sep 23 18:14:18 2014 +0200

    FIX: Setting ActionQueue::_lastchangedaction without heeding whether Action failed is bad.

    - causes segfault when notification informs about change and _lastchangeaction
      is still NULL (as the very first Action failed).
    - we now only notify when action succeeded.

commit 543ab66a5e35f55a7501e3650ece13ab6a61d92d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 22 22:10:11 2014 +0200

    FIX: QSeisPlotPage's dstor calls deinitializeLayout() only when initialized.

commit 52e33b90484b6053378ed709009faea5b574a77a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 29 16:40:10 2014 +0200

    MEMFIX: Static coordinator instances of specificv potentials need to be Memory::ignore()'d.

commit 1fd8c58c1cfe63dcdc56d6a60a7f5d2f5d28b462
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 29 16:35:04 2014 +0200

    FIX: Added Boost::MultiIndexContainer check for MemDebug.

    - this requires CodePatterns 1.2.10 and allows finally enable-debug compilation
      with Ubuntu 14.04.

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