# # ChangeLog for / # # Generated by Trac 1.2.1 # 12/02/24 16:44:40 Sun, 03 Sep 2017 13:51:24 GMT Maciej Komosinski [683] * mds-and-trees/tree-genealogy.py (modified) Slightly more helpful error message Sat, 02 Sep 2017 12:12:51 GMT konrad [682] * mds-and-trees/tree-genealogy.py (modified) Broken last lines in input logs will not crash the script anymore ... Mon, 28 Aug 2017 16:43:30 GMT konrad [681] * mds-and-trees/tree-genealogy.py (modified) Improved the compute_depth function so now it works much faster for ... Sun, 27 Aug 2017 18:05:45 GMT konrad [680] * mds-and-trees/tree-genealogy.py (modified) Fixed the "ValueError: max() arg is an empty sequence" error ... Sun, 27 Aug 2017 17:48:02 GMT konrad [679] * mds-and-trees/tree-genealogy.py (modified) compute_adepth no longer uses recursion (so it should work better ... Sun, 27 Aug 2017 13:11:36 GMT konrad [678] * mds-and-trees/tree-genealogy.py (modified) Fixed a bug attempting to normalize a list of lists Sun, 27 Aug 2017 13:06:39 GMT konrad [677] * mds-and-trees/tree-genealogy.py (modified) Fixed a bug with an incorrect order of assigning placement to nodes Sat, 26 Aug 2017 01:05:37 GMT Maciej Komosinski [676] * cpp/frams/genetics/f4/oper_f4.cpp (modified) Improved comments, removed unnecessary TODO regarding "Rr" modifiers Sat, 19 Aug 2017 00:52:26 GMT Maciej Komosinski [675] * cpp/frams/genetics/f4/conv_f4.cpp (modified) * cpp/frams/genetics/oper_fx.h (modified) Code formatting Sat, 19 Aug 2017 00:45:00 GMT Maciej Komosinski [674] * cpp/frams/genetics/f4/oper_f4.cpp (modified) * cpp/frams/genetics/f4/oper_f4.h (modified) f4 modifiers implemented similarly to f1 modifiers, and a base for ... Sat, 19 Aug 2017 00:43:11 GMT Maciej Komosinski [673] * cpp/frams/genetics/oper_fx.cpp (modified) * cpp/frams/genetics/oper_fx.h (modified) Added three functions that may be useful in general Fri, 18 Aug 2017 20:08:42 GMT Maciej Komosinski [672] * cpp/frams/genetics/f1/conv_f1.cpp (modified) More appropriate name for the "model_energy_max" variable Fri, 18 Aug 2017 13:24:59 GMT Maciej Komosinski [671] * cpp/frams/genetics/f1/conv_f1.cpp (modified) * cpp/frams/genetics/f1/conv_f1.h (modified) * cpp/frams/genetics/f4/conv_f4.cpp (modified) * cpp/frams/genetics/f4/f4_general.cpp (modified) * cpp/frams/genetics/f4/f4_general.h (modified) * cpp/frams/genetics/f4/oper_f4.cpp (modified) * cpp/frams/genetics/f4/oper_f4.h (modified) Unified property names of f1 and f4; improved docs; 3.141 -> M_PI Fri, 11 Aug 2017 23:55:25 GMT Maciej Komosinski [670] * cpp/frams/genetics/oper_fx.cpp (modified) * cpp/frams/genetics/oper_fx.h (modified) Improved variable names and docs Fri, 11 Aug 2017 23:54:46 GMT Maciej Komosinski [669] * cpp/frams/genetics/fF/oper_fF.h (modified) As default foraminifera initial chamber radius in Framsticks units ... Wed, 07 Jun 2017 10:02:05 GMT Maciej Komosinski [668] * cpp/frams/genetics/genman.cpp (modified) Fixed argument type in GenMan.getSimplest() Wed, 07 Jun 2017 10:01:16 GMT Maciej Komosinski [667] * cpp/frams/genetics/fF/conv_fF.cpp (modified) * cpp/frams/genetics/fF/conv_fF.h (modified) * cpp/frams/genetics/fF/fF_chamber3d.cpp (modified) * cpp/frams/genetics/fF/fF_chamber3d.h (modified) * cpp/frams/genetics/fF/fF_genotype.cpp (modified) * cpp/frams/genetics/fF/fF_genotype.h (modified) * cpp/frams/genetics/fF/oper_fF.cpp (modified) * cpp/frams/genetics/fF/oper_fF.h (modified) - fF foraminifera encoding supports scaling (radius) of the initial ... Wed, 07 Jun 2017 09:59:36 GMT Maciej Komosinski [666] * cpp/frams/model/similarity/simil_model.cpp (modified) Added missing #include Wed, 07 Jun 2017 09:57:47 GMT Maciej Komosinski [665] * cpp/common/nonstd_math.h (modified) * cpp/common/threads.h (modified) Cosmetic Wed, 26 Apr 2017 17:22:20 GMT Maciej Komosinski [664] * cpp/frams/genetics/f9/conv_f9.cpp (modified) * cpp/frams/genetics/f9/conv_f9.h (modified) Mark last Part white - a visual aid for easier editing of f9 genotypes Tue, 25 Apr 2017 13:19:00 GMT sz [663] * java/Framclipse/com.framsticks.framclipse/res/framscript.xml (modified) Updated for the upcoming Framsticks v5.0rc9 Mon, 24 Apr 2017 16:19:34 GMT Maciej Komosinski [662] * cpp/frams/_demos/geometry/geometrytestutils.cpp (modified) - Ensure solid shapes (SolidsShapeTypeModel) are used in geometry ... Mon, 24 Apr 2017 16:18:44 GMT Maciej Komosinski [661] * cpp/frams/model/geometry/modelgeoclass.cpp (modified) FramScript's ModelGeometr converts and caches the input model so ... Mon, 24 Apr 2017 16:17:56 GMT Maciej Komosinski [660] * cpp/frams/model/geometry/modelgeometryinfo.cpp (modified) * cpp/frams/model/geometry/modelgeometryinfo.h (modified) * cpp/frams/model/model.cpp (modified) * cpp/frams/model/model.h (modified) Model shape conversion no longer requires const Model& Mon, 24 Apr 2017 16:15:49 GMT Maciej Komosinski [659] * cpp/frams/param/param.cpp (modified) Detecting more unwanted flags in Param sanity check Mon, 24 Apr 2017 01:14:21 GMT Maciej Komosinski [658] * cpp/frams/_demos/geometry/info_test.cpp (modified) * cpp/frams/model/geometry/geometryutils.cpp (modified) * cpp/frams/model/geometry/modelgeoclass.cpp (modified) * cpp/frams/model/geometry/modelgeometryinfo.cpp (modified) - One function name made shorter - Fixed some typos - Predictable ... Mon, 24 Apr 2017 01:10:51 GMT Maciej Komosinski [657] * cpp/frams/model/geometry/modelgeometryinfo.h (modified) A comment on potential optimization in ModelGeometryInfo Thu, 20 Apr 2017 19:10:27 GMT Maciej Komosinski [656] * cpp/frams/config/f0.def (modified) Removed useless READONLY flag in functions Thu, 20 Apr 2017 19:09:18 GMT Maciej Komosinski [655] * cpp/common/virtfile/virtfile.h (modified) Better description of the VIRTFILE_OVERLOADING macro Thu, 20 Apr 2017 19:08:19 GMT Maciej Komosinski [654] * cpp/frams/param/param.cpp (modified) More strict checking for improper flag/type combinations Thu, 20 Apr 2017 19:06:47 GMT Maciej Komosinski [653] * cpp/frams/model/model.cpp (modified) Model::buildUsingSolidShapeTypes() can now handle single-Part models ... Thu, 02 Feb 2017 14:15:26 GMT Maciej Komosinski [652] * cpp/frams/vm/framscript.y (modified) Cosmetic Thu, 02 Feb 2017 14:14:49 GMT Maciej Komosinski [651] * cpp/frams/util/validitychecks.cpp (modified) 0,1 -> false,true Thu, 02 Feb 2017 14:14:19 GMT Maciej Komosinski [650] * cpp/frams/param/param.cpp (modified) * cpp/frams/param/param.h (modified) Warn when missing closing tilde (~) and code formatting Thu, 02 Feb 2017 14:13:39 GMT Maciej Komosinski [649] * cpp/common/threads.h (modified) Display diagnostic message when threads not released properly Thu, 02 Feb 2017 14:12:54 GMT Maciej Komosinski [648] * cpp/frams/vm/classes/collectionobj.cpp (modified) Warn when trying to remove non-existing indexed object Thu, 12 Jan 2017 15:30:41 GMT Maciej Komosinski [647] * cpp/frams/model/similarity/simil_model.cpp (modified) Updated URLs, removed non-ascii characters Sat, 31 Dec 2016 19:36:13 GMT Maciej Komosinski [646] * cpp/frams/neuro/neuroimpl.h (modified) Support for multiple coexisting implementations of the same neuron ... Sat, 31 Dec 2016 19:35:12 GMT Maciej Komosinski [645] * cpp/frams/param/param.cpp (modified) * cpp/frams/param/param.h (modified) f0 is strict now, will not accept float when int is expected Sat, 31 Dec 2016 19:34:10 GMT Maciej Komosinski [644] * cpp/frams/model/model.cpp (modified) Invalid references from neurons to Parts/Joints are now reported Sat, 31 Dec 2016 19:33:20 GMT Maciej Komosinski [643] * cpp/frams/genetics/f9/conv_f9.cpp (modified) The meaning of f9 3D-direction genes made consistent with Framsticks ... Sat, 31 Dec 2016 19:32:03 GMT Maciej Komosinski [642] * cpp/frams/vm/classes/collectionobj.cpp (modified) * cpp/frams/vm/classes/collectionobj.h (modified) Implemented insert() in FramScript Vector class Mon, 05 Dec 2016 02:34:28 GMT sz [641] * java/Framclipse/com.framsticks.framclipse/res/framscript.xml (modified) Updated for Framsticks version 5.0rc8 Mon, 05 Dec 2016 01:31:34 GMT Maciej Komosinski [640] * cpp/frams/model/modelparts.cpp (modified) * cpp/frams/param/param.cpp (modified) * cpp/frams/param/param.h (modified) Introduced a separate function to provide a human-friendly ... Mon, 05 Dec 2016 01:29:50 GMT Maciej Komosinski [639] * cpp/frams/_demos/genotypeloader.cpp (modified) * cpp/frams/util/extvalue.cpp (modified) * cpp/frams/util/extvalue.h (modified) Introduced separate functions for formatting time. Sat, 03 Dec 2016 02:16:38 GMT sz [638] * experiments/frams/foraminifera/data/scripts/foraminifera.expdef (modified) script updated (moveAbs, size_, pos_, center_) Sat, 03 Dec 2016 01:21:40 GMT Maciej Komosinski [637] * cpp/frams/model/modelparts.cpp (modified) Extended code so that NeuroClass properties are described in more detail Sat, 03 Dec 2016 00:52:05 GMT Maciej Komosinski [636] * cpp/frams/util/extvalue.cpp (modified) * cpp/frams/util/extvalue.h (modified) Modulo by zero is safe just as division by zero and prints analogous ... Sat, 03 Dec 2016 00:47:15 GMT Maciej Komosinski [635] * cpp/frams/_demos/genotypeloader.cpp (modified) * cpp/frams/_demos/genotypeloader.h (modified) Introduced specialized info_* fields in (Mini)Genotype that match FEC ... Fri, 25 Nov 2016 15:45:57 GMT sz [634] * experiments/frams/capture-the-flag/data/scripts/capture-the-flag.expdef (modified) * experiments/frams/deathmatch/data/scripts/deathmatch.expdef (modified) Updated for the upcoming Framsticks release - the old Shapes object ... Wed, 23 Nov 2016 16:58:33 GMT konrad [633] * mds-and-trees/tree-genealogy.py (modified) Added measure of progress (based on regression of time-distances ... Wed, 09 Nov 2016 03:35:36 GMT sz [632] * experiments/frams/capture-the-flag/data/scripts/capture-the-flag.expdef (modified) Updated to avoid using deprecated API (Creature.moveAbs, size_x/y/z, ... Wed, 09 Nov 2016 03:29:53 GMT sz [631] * experiments/frams/deathmatch/data/scripts/deathmatch-utils.inc (modified) * experiments/frams/deathmatch/data/scripts/deathmatch.expdef (modified) Updated the script to use more modern framscript features, most ... Tue, 08 Nov 2016 22:53:51 GMT sz [630] * blender-povray-animation/frams-pov-import.py (modified) added the option to write a separate "camerapath.inc" instead of ... Tue, 08 Nov 2016 22:49:22 GMT sz [629] * blender-povray-animation/frams-pov-import.py (modified) scientific notation numbers ('e') are floating point, even without a dot Thu, 27 Oct 2016 14:38:57 GMT konrad [628] * mds-and-trees/tree-genealogy.py (modified) Fixed printing texts in svg and added support for additional ... Wed, 26 Oct 2016 17:13:26 GMT konrad [627] * mds-and-trees/tree-genealogy.py (modified) tree-genealogy.py is now supporting multiple virtual parents (they ... Mon, 24 Oct 2016 13:01:12 GMT konrad [626] * mds-and-trees/tree-genealogy.py (modified) Added multisampling (antialiasing) option for raster output Fri, 21 Oct 2016 21:40:42 GMT konrad [625] * mds-and-trees/Vera.ttf (added) Font for tree-genealogy.py Fri, 21 Oct 2016 17:45:07 GMT konrad [624] * mds-and-trees/tree-genealogy.py (modified) * mds-and-trees/tree.conf (added) New, faster, more flexible and refactored version of the tree- ... Tue, 11 Oct 2016 15:19:04 GMT konrad [623] * mds-and-trees/tree-genealogy.py (modified) Some minor changes Tue, 11 Oct 2016 14:48:23 GMT konrad [622] * mds-and-trees/tree-genealogy.py (modified) Added an option to restrict the tree to first X nodes. Mon, 10 Oct 2016 15:18:52 GMT konrad [621] * mds-and-trees/tree-genealogy.py (modified) Rewritten prepos_children to the iterative form + Turned on some ... Fri, 30 Sep 2016 00:43:38 GMT konrad [620] * mds-and-trees/tree-genealogy.py (modified) The parameters should not be case specific anymore, also added some ... Fri, 23 Sep 2016 13:06:58 GMT konrad [619] * mds-and-trees/tree-genealogy.py (modified) Changed spine and skeleton drawing methods from recurrent to ... Fri, 23 Sep 2016 11:09:55 GMT konrad [618] * mds-and-trees/tree-genealogy.py (modified) Removed the recurrent version of the tree-drawing method, fixed and ... Wed, 21 Sep 2016 15:52:27 GMT konrad [617] * mds-and-trees/tree-genealogy.py (modified) Added non-recurrent verion of tree drawing function, ... Wed, 14 Sep 2016 22:07:27 GMT Maciej Komosinski [616] * mds-and-trees/mds_plot.py (modified) Introduced an option to swap (exchange) X and Y axes Sun, 11 Sep 2016 20:52:34 GMT Maciej Komosinski [615] * mds-and-trees/tree-genealogy.py (modified) Improved descriptions Sun, 11 Sep 2016 20:45:46 GMT Maciej Komosinski [614] * mds-and-trees/tree-genealogy.py (modified) Fixed typos Sun, 11 Sep 2016 01:59:38 GMT Maciej Komosinski [613] * mds-and-trees/mds_plot.py (modified) Introduced options to flip (invert, negate) X and/or Y axes Fri, 09 Sep 2016 13:22:11 GMT Maciej Komosinski [612] * cpp/frams/_demos/simil_test.cpp (modified) Updated after field rename Fri, 09 Sep 2016 13:21:47 GMT Maciej Komosinski [611] * cpp/frams/model/model.cpp (modified) * cpp/frams/model/model.h (modified) Code formatting Mon, 05 Sep 2016 01:39:14 GMT Maciej Komosinski [610] * cpp/frams/model/model.cpp (modified) * cpp/frams/model/model.h (modified) - Introduced levels of checking the validity of a Model - If a Joint ... Thu, 01 Sep 2016 22:06:41 GMT Maciej Komosinski [609] * mds-and-trees/mds_plot.py (modified) Labels can have colors dependent on label text Thu, 01 Sep 2016 15:01:37 GMT Maciej Komosinski [608] * mds-and-trees/mds_plot.py (modified) Displays the fraction of variance preserved after MDS Thu, 01 Sep 2016 14:39:23 GMT Maciej Komosinski [607] * mds-and-trees/mds_plot.py (modified) Updated for new format of dissimilarity matrix (with the optional two ... Tue, 30 Aug 2016 15:42:29 GMT Maciej Komosinski [606] * cpp/frams/_demos/simil_test.cpp (modified) * cpp/frams/model/similarity/simil_model.cpp (modified) * cpp/frams/model/similarity/simil_model.h (modified) Code formatting Tue, 30 Aug 2016 15:39:10 GMT Maciej Komosinski [605] * cpp/frams/_demos/simil_test.cpp (modified) * cpp/frams/model/similarity/simil_model.cpp (modified) * cpp/frams/model/similarity/simil_model.h (modified) - Added 'fixedZaxis' option to paramtab (so that it is accessible ... Tue, 30 Aug 2016 15:08:10 GMT Maciej Komosinski [604] * mds-and-trees/mds_plot.py (modified) Made the amount of jitter a continuous, adjustable parameter Sun, 28 Aug 2016 16:34:15 GMT oriona [603] * mds-and-trees/mds_plot.py (modified) Integer command line arguments converted to ints in main call. Sun, 28 Aug 2016 15:00:05 GMT Maciej Komosinski [602] * mds-and-trees/mds_plot.py (modified) - More flexible reading of distance matrices from files - Can also ... Sun, 28 Aug 2016 13:19:57 GMT oriona [601] * cpp/frams/_demos/simil_test.cpp (modified) * cpp/frams/model/similarity/simil_model.cpp (modified) * cpp/frams/model/similarity/simil_model.h (modified) Possibility of fixing z axis during the alignment added. Sun, 28 Aug 2016 13:04:25 GMT oriona [600] * mds-and-trees/mds_plot.py (modified) Number of returned dimensions set to minimum of desired number and ... Thu, 25 Aug 2016 15:48:45 GMT oriona [599] * mds-and-trees/mds_plot.py (modified) Function for computing variances removed. Thu, 25 Aug 2016 15:44:00 GMT oriona [598] * mds-and-trees/mds_plot.py (modified) MDS algorithm changed to cmdscale. Coordinates export to file added. Wed, 24 Aug 2016 01:54:42 GMT Maciej Komosinski [597] * mds-and-trees/mds_plot.py (modified) No longer ignores "jitter" and "outname" parameters Wed, 24 Aug 2016 01:52:38 GMT Maciej Komosinski [596] * mds-and-trees/mds_plot.py (modified) Uncomment to make it work with no graphical backend Tue, 23 Aug 2016 19:28:36 GMT oriona [595] * experiments/frams/foraminifera/data/scripts/foraminifera.expdef (modified) * experiments/frams/foraminifera/data/scripts/foraminifera.inc (modified) Rotation of creatures in z axis changed to random. LocalDrive usage ... Tue, 23 Aug 2016 16:13:31 GMT konrad [594] * mds-and-trees/tree-genealogy.py (modified) Fixed drawing the spine and the skeleton for the tree-genealogy.py Mon, 22 Aug 2016 13:07:18 GMT Maciej Komosinski [593] * experiments/frams/foraminifera/data/scripts/foraminifera.inc (modified) Added the missing visual style declaration for foraminifera creatures Sun, 21 Aug 2016 23:47:04 GMT Maciej Komosinski [592] * experiments/frams/foraminifera/data/scripts/foraminifera.expdef (modified) More meaningful variable names Sun, 21 Aug 2016 23:43:26 GMT Maciej Komosinski [591] * experiments/frams/foraminifera/data/scripts/foraminifera.expdef (modified) Added a comment Sun, 21 Aug 2016 23:26:47 GMT oriona [590] * experiments/frams/foraminifera/data/scripts/foraminifera.expdef (modified) * experiments/frams/foraminifera/data/scripts/foraminifera.inc (modified) * experiments/frams/foraminifera/data/scripts/foraminifera.show (modified) Feed period changed to food flux in grams per square meter per ... Fri, 19 Aug 2016 21:59:09 GMT konrad [589] * mds-and-trees/tree-genealogy.py (modified) Fixed dark lines inside lines in tree-genealogy.py Fri, 19 Aug 2016 09:35:59 GMT oriona [588] * experiments/frams/foraminifera/data/scripts/foraminifera.expdef (modified) Movement of forams in z axis restricted. Thu, 18 Aug 2016 22:27:50 GMT oriona [587] * experiments/frams/foraminifera/data/scripts/foraminifera.expdef (modified) Enhanced nutrient visualization corrected. Thu, 18 Aug 2016 20:01:16 GMT konrad [586] * mds-and-trees/tree-genealogy.py (modified) Tiny refactoring of tree-genealogy.py Thu, 18 Aug 2016 19:58:00 GMT konrad [585] * mds-and-trees/tree-genealogy.py (modified) Added an option for defining colors of crossover / mutation lines ... Thu, 18 Aug 2016 19:37:53 GMT oriona [584] * experiments/frams/foraminifera/data/scripts/foraminifera.expdef (modified) Positions of foraminifera, reticulopodia and nutrients corrected.