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@damienmarchal @hugtalbot @guparan @epernod @bcarrez
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SOFA Changelog

On master branch (not released yet)

Environment

New features for users

  • [SceneCreator]

    • New methods to add basic 3D object: Cube, Cylinder, Plane. In rigid or deformable.
  • Adds a new orientedBox dataField in BoxROI so that we can use it to either defined AABoxes or OrientedBox

New features for developpers

Improvements

  • XXX new tests
  • XXX/YYY components have an associated example

Bug Fixes

Cleaning

  • Clean DefaultPipeline.cpp/h (API BREAKING)
  • Clean the attributes names in BoxROI (API BREAKING)

Moved files


v16.12

Last commit: on Jan 08, 2017

Environment

  • C++11 is now mandatory. This implies some changes in building tools.
    • Generator: CMake 3.1 or higher.
    • Compiler: GCC 4.8 or higher, Clang 3.4 or higher, Microsoft Visual C++ 2013 or higher.

New features for users

  • new Geomagic plugin: supporting latest versions of force feedback interfaces from Geomagic
  • add ForceMaskOff, a component to locally (in a branch of the scene graph) cancel the force mask
  • live-coding for python
  • live-coding for GLSL
  • new component MakeAlias
  • new component MakeDataAlias
  • improved error message & console rendering

New features for developpers

  • Preliminary Markdown support in the msg_* API. You can now write much better formatting & alignement as well as adding URL to documentations related to the error.
  • class RichStyleConsoleFormatter which interprete the markdowns in the message and format this to a resizable console with nice alignement.
  • class CountingMessageHandler (count the number of message for each message type)
  • class RoutingMessageHandler (to implement context specific routing of the messages to different handler)
  • class ExpectMessage and MessageAsATestFailure can be used to check that a component did or didn't send a message and generate a test failure.
  • FileMonitor is now implemented on MacOS & Windows (for live-coding features, for example)
  • RequiredPlugin: modified API to take a list of plugins to load
  • Implements the move semantics on sofa::helper::vector

Improvements

  • 372 new tests: DAGNode, MeshObj, DiagonalMass, BoxROI, ComplementaryROI, DifferenceEngine, BilateralInteractionConstraint, Quaternion, ImagePNG, etc.
  • 184/480 components have an associated example
  • [SofaKernel]
    • replace raw pointers with a smart ones
    • add a ComponentState attribute to BaseObject
    • BaseData::typeName is now public: useful to debug
    • implement DataTrackerEngine, a kind of DataEngine but that is not a BaseObject
    • fix SVectorstd::string. The string serialization changed
  • [SofaRigid]
    • in case jetJs is called several times per step
  • [SofaGeneralLoader]
    • MeshVTKLoader can now read FIELD data of legacy file. Lookup tables are ignored.
  • [SofaPython]
    • binding AssembledSystem as a new class in python
    • binding VisualModel::exportOBJ
    • binding for DataFileNameVector
    • add Compliant.getImplicitAssembledSystem(node)
    • SofaNumpy: bind/share a c++ 1d array as a numpy array
    • script.Controller : handle optional arguments before createGraph
  • [image]
    • raw import: add commented basic size verifications (could be performed in debug)
  • [Flexible]
    • add support for shapefunction viewer
    • new feature of strain smoothing
    • improve readme file
  • [Compliant]
    • simulation unit: convert gravity, dt
    • MaskMapping: every input are now mapped
    • add LinearDiagonalCompliance component
    • fix use of VLA in python mappings
    • improve readme file

Bug Fixes

  • fix ConstantForceField::updateForceMask()
  • fix ObjExporter memory leak
  • [SofaOpenGLVisual] OglTexture: fix possible memory leaks
  • [Compliant]
    • clean python

Cleaning

  • clean the compilation when SOFA_NO_OPENGL flag is activated
  • clean the config.h (SOFAGUI_HAVE_QWT)
  • remove boost library links (includes still required). boost chrono is not required anymore.
  • remove unused POINT_DATA_VECTOR_ACCESS macro
  • make miniflowVR build optional (default OFF)
  • [SofaKernel]
    • remove last direct opengl calls in modules
    • add deprecation message on MechanicalObject attributes
  • [SofaBaseVisual] clean BaseCamera: remove direct opengl calls
  • [SofaHaptics] boost-thread is not used any more, clean cmake
  • [SofaGeneralLoader] STLLoader: fixing binary loading in debug and cleaning examples
  • [SofaPython]
    • remove ScriptEnvironment i.e. automatic initialization of Node
    • Node::isInitialized(), not used anymore
  • [Flexible]
    • clean relativeStrainMapping

Moved files

  • move CImg from extlibs to image plugin extlibs

Documentation

  • Add the contribution and guidelines : CONTRIBUTING.md and GUIDELINES.md
  • Add the configuration required (ex: C++, compiler versions)
  • Add a page to use SOFA in Matlab
  • Improve Logger documentation
  • Add a page to use SOFA in Matlab

v16.08

Last commit: on Jul 28, 2016

New features

  • SOFA on GitHub - https://github.com/sofa-framework/sofa
  • creation of a RigidScale plugin: implementing mappings, especially allowing to get the DOF with Rigid+Scale type, while reusing affine DOF (Rigid+Scale+Shear) already implemented in Flexible
  • creation of a LeapMotion plugin: allowing to integrate a Leap in your SOFA simulation
  • add the DrawTool: DrawTool is an interface, describing an API to display primitives on screen. For now, only the OpenGL (fixed-pipeline version) implementation has been made.
  • add a Logger
  • add the diffusion effect in SOFA (heat transfer)
  • SOFA_USE_MASK compilation variable to activate or de-activate the masks in SOFA
  • DataTracker: simple and elegant way to track Data in Engine
  • extlibs: update cimg to version 1.7.3
  • Add guidelines for contributions in CONTRIBUTING.md

Moved files

  • Kernel modules of SOFA (SofaFramework, SofaBase, SofaCommon and SofaSimulation) have been moved to one common module SofaKernel, located at sofa_root/SofaKernel. SofaKernel is a pure LGPL module.
  • code in sofa_root/modules/sofa/simulation/ has been splitted into three modules of SofaKernel: SofaSimulationCommon, SofaSimulationTree, SofaSimulationGraph
  • MOVE the SofaPardiso module as a plugin
  • Move OglTetrahedralModel into a new plugin called VolumetricRendering

  • Minor moves

    • Move ColorMap code to helper and let (Ogl)ColorMap from SofaOpenGLVisual doing OpenGL stuff
    • Move TorsionForceField and ComplementaryROI into SOFA (those two components where in a deprecated repository sofa_root/modules/sofa/components/)
  • [Compliant]

    • moving propagate_constraint_force_visitor in a helper file and minor cleaning of CompliantImplicitSolver

Improvements

  • test examples are now running (on Jenkins for the Continuous Integration)
  • Add unit test for quaternions
  • Improving default mouse manipulation while picking a dof
  • MouseWheel events now propagated

  • Minor improvements

    • runSofa: force loading the SofaPython plugin if existing
    • runSofa: adding clang-style formatting (option '-z clang')
    • MechanicalObject: adding more visualisation colors for Rigids
    • SofaPluginManager: Clear description and components when removing last plugin
    • CMake: removing "-Wno-deprecated-register" compiler option that is only known by a few compilers
    • Collision: add function setConstraintId in BaseConstraintSet
    • SPtr: up to 10 parameters in constructor
    • Add function in EigenBaseSparseMatrix in order to use eigen matrices with async solvers
    • Add CUSPARSESolver in SofaCudaSolversPlugin, this solver uses cusparse library to solve a sparse triangular system on the GPU
    • MeshBoundaryROI: allows specifying an input subset
    • ColorMap: with face culling enabled
    • ColorMap: adding a scale for the legend range values
    • ImageViewer: adding new boolean data field displaying meshes directly on the slices
    • ProjectionToPlaneMultiMapping: adding a projection factor to perform tricky stuff such as planar symmetry
    • ProjectionToTargetPlaneMapping: adding a factor to perform planar symmetry for example
    • DataDisplay: can now be displayed in wireframe
    • DataDisplay: display used topology
    • DataDisplay: fix and improving shading a bit
    • SofaEngine: add selectLabelROI engine
    • SofaEngine: add SelectConnectedLabelsROI
    • SofaBoundaryCondition: it is now possible to hide fixedconstraint (default to shown as before)
    • Mat.h: adding tensor product between vectors
    • ForceField: adding const getMState()
    • VolumetricRendering: Initialize tetra/hexa Data<> (to be able to link them as data in scenes)
    • SofaBaseVisual: Add modelview and projection matrices as data output
    • FrameBufferObject: check (and use) the default framebuffer for the current display window
    • SofaOpenGLVisual: add link to a potential external shader for VisualManagerSecondaryPass
    • Add OglTexturePointer
    • adding SquareDistanceMapping to compute the square distance between 2 points.
    • add OrderIndependentTransparency Manager (using two passes instead of three)
    • add OglOITShader to customize the shading of transparent surfaces
    • ProjectionToTargetLineMapping and ProjectionToTargetPlaneMapping with precomputed constant Jacobians and using last origin and direction/normal for extra points
    • Adding a timer embedding all the animation loop step but would need further doc.
    • display of indices has been improved
    • Add an example using cloth springs: examples/Components/forcefield/ClothBendingForceField.py
    • Improving a few examples by making the embedding nodes as non pickable (tag 'NoPicking')
    • Add BaseNode::getRootPath
    • Improving performances: - Message::class is now an enum
    • Updated draw method of PointSetGeometryAlgorithms, QuadSetGeometryAlgorithms, TetrahedronSetGeometryAlgorithms, TriangleSetGeometryAlgorithms
    • Add Blender-like orientation helper in the bottom-left part of the screen while drawing bbox (QtGlViewer)
    • Add Blender-like orientation helper in the bottom-left part of the screen while drawing bbox (QtViewer)
    • add of GUIEvent into the STLExporter
    • Make the code compatible with ClipPlane (using ClipVertex in shaders, which is deprecated for GLSL > 1.4)
    • Optimize the callto C-PYTHON side when the functions are not implemented in the python side
    • Add color attribute support (and default color if not present in the node)
    • Reactivate color map in TetraFEM, as it does not depend on SofaOpenGLVisual anymore
    • indices data field for UniformMass
    • analyze matrix only if number of non-zeroes has changed and no iterative refinement
    • update the applyConstraint methods according to the actual API
    • Adding ProjectionTo{Plane|Line}MultiMapping where the plane (origin,normal) and the line (origin,direction) are dofs
    • add MeshBoundaryROI with an example
  • [Tests]

    • for (multi)Mapping test, check the size of the mapping output is correct
    • adding TestMessageHandler that raises a gtest failure each time an error message is processed
    • test for node removal
    • test for removal of a node containing an UncoupledConstraintCorrection (for now the test fails because there is a problem with the removal of that component)
    • add of Multi2Mapping_test
    • add DistanceMapping_test
  • [SofaPython]

    • logger: cleaning emitter
    • sml.Mesh: adding load function
    • sml: python set for tags is created by objects themselves
    • sml: add tag to JointGeneric
    • sml: add the printLog flag
    • sml: setup units in BaseScene for all sml Scene class
    • sml: mesh has a clear id
    • sml:insertVisual: bug fix for solid with multiple meshes (just impacting the Display scene)
    • sml: handy constructor for Dof creation
    • sml: like can be defined in
    • sml: add a utility function: look into the valueByTag dictionary for a tag contained in tags
    • sml: adding a warning if a vertex group is empty
    • sml: can have offsets under solids
    • sml: remove deprecated setTagFromTag() method
    • API: add subsetFromDeformables function
    • binding Node::isInitialized
    • binding loadPythonSceneWithArguments
    • adding a binding to get the pointer of a Data (with its dimensions and type)
    • adding binding of BaseMapping::getJs (as dense matrices for now)
    • adding python functions to convert a Data in a numpy array with shared memory
    • adding a visitor to set all mstates as non pickable (such as picking will only be performed with collision models)
    • add tags to mesh groups
    • add a groupsByTag dict to easily iterate over groups knowing a tag
    • add of SceneDataIO to save and load the current state of a simulation
    • add of the method getDataFields
    • adding automatically tested examples
    • add tags to MeshAttributes
    • add a helper PythonScriptFunction_call and PythonScriptFunction_callNoResult to call a python controller function from c++ code
    • PythonScriptHelper -> PythonScriptControllerHelper: PythonScriptHelper: add convertion for float and std::string
    • Add the timingEnabled attribute to the PythonScriptController to control if the script is gather timing statistics
    • adding python module to load .obj files
    • adding BaseContext_getObject_noWarning that returns None w/o warning if the object is not found
    • improving a bit the conversion from a cpp Base* to a PyObject* when the cpp Base* type is (even partially) known.
    • adding a test to show how to bind a component outside of SofaPython
    • Factory: conversion shortcuts for known types
    • PythonScriptController: if the filename is let empty, the controller is supposed to be in an already loaded file, to avoid to read the same file several times
    • adding "loadPlugin" function to the Sofa python module
    • Add a getObjects() method to python BaseContext interface. Allow selection of objects based on type and name.
    • object and type names are now both optional when calling BaseContext_getObjects()
    • search direction can now optionally be passed to BaseContext_getObjects()
    • at object creation failure, print additional error messages from BaseObjectDescription
    • adding special Data types in the PythonFactory, so more specific cases can be added outside of the plugin SofaPython.
    • adding Node::addObject_noWarning not to print a warning when adding an object to an already initialized node
    • add of a method which compute quaternion from a line define by a director vector
    • add of few new features to save and load the current state of simulation
  • [Flexible]

    • adding FlexibleCorotationalMeshFEMForceField (meta-forcefield). Not optimized but working
    • add of RigidScale mapping in addition to their tests and examples
    • HexaFEM comparison: each method has its own solver and uses the same decomposition so the only difference came from the deformation tensor used to find the rotation.
    • Flexible: WIP adding a meta-forcefield to compute regular corotational FEM. The idea is to use Flexible's components internally without adding extra computation neither extra memory
    • API: add strain offseting option
    • API: strainMappings as data members
    • API: use branching images for mass computation
    • API: make AffineMass, ShapeFunction, Behavior work in more cases
    • API: make Behavior work in simple cases with no label image
    • materials: removed checking for changed parameters at each step.
    • add example showing how to better handle partially filled elements using fine volumes
    • optimizing FlexibleCorotationalMeshFEMForceField by preassembling constant sub-graph
    • refactoring of MassFromDensity
    • adding a warning when creating a UniformMass on Affine/Quadratic frames.
    • add FEMDof class to python API
    • DeformationMapping: print a warning if a child particle has no parent
    • adding HEML implementation of St Venant-Kirchhoff materials (for tetrahedra).
    • if correct weights are given in mapping as input data, use it (even if a shapefunction is found)
    • use sout for logging
    • compute tangents for VisualModel loaded using loadVisual python function
    • transformEngine for Affine frames
  • [Compliant]

    • sml: export of meshes
    • sml: the solids tags to be simulated as rigids are gathered in a set()
    • sml: geometricStiffness option
    • sml: using logger
    • implementing compliance unassembled API
    • in the python API, joints can be created in compliance or not
    • API: write a addSpring() in GenericRigidJoint, reuse it in children classes where possible
    • API: simplify usage of jointCompliance specification by tag
    • API: relative offset position is given to the AssembledRigidRigidMapping, and then computed at init into the MO
    • API: modifying the API to move an Offset
    • API: adding Offset::moveOffset to apply a rigid transformation to an offset (in its local frame)
    • API: new parameter to add non-mechanical Offsets and MappedPoints
    • API: collision mesh and visual model can be added to a Rigid Offset
    • adding an automatic execution of a scene based on a sml description
    • Constraint: adding a typeid for faster Constraint type comparisons
    • adding short name to create a ConstantCompliantPseudoStaticSolver
    • using tag on joints in a generic way, set their compliance / isCompliance value
    • added machinery to map data to numpy arrays, see example/numpy_data.py
    • added easy pure python mappings, see examples/numpy_mapping.py
    • added pure python forcefields, see examples/numpy_forcefield.py
    • AssembledRigidRigidMapping autoresize
    • geometric stiffness in python mappings
    • insertMergeRigid is coherent with solid tags usage
    • CompliantPseudoStaticSolver: avoiding an unnecessary propagation when the stopping criterion is the nb of iterations.
    • visualization in DifferenceFromTargetMapping
    • Frame.py: adding a function to force quaternion normalization (to avoid numerical drift)
    • added SimpleAnimationLoop
    • adding RigidRestJointMapping to compute a joint between a rigid body's current position and its rest position.
    • large compliances are considered as null stiffnesses
    • Offset default to isMechanical=True
    • python quaternion log
    • added nlnscg acceleration
    • pure python constraints
    • .inl for python mappings
    • adding Addition[Multi]Mapping
    • implementing AssembledMultiMapping::applyDJT
    • adding DotProduct[Multi]Mapping (with tests)
    • adding NormalizationMapping to map a 3d vector to its normalization
    • adding ConstantAssembled[Multi]Mapping
    • adding SafeDistanceMapping: a distance mapping that becomes a difference mapping for too small distances.
    • adding SafeDistanceFromTargetMapping
    • using the new SofaPython API
    • SafeDistanceFromTargetMapping can now be "safe" by giving the edge directions when they are known
    • adding the SofaCompliant python module (first module created outside of SofaPython!)
    • adding DotProductFromTargetMapping (with test)
    • adding RigidJointFromTargetMapping and RigidJointFromWorldFrameMapping
    • add of complementary API to create deformable articulated systems
    • adding NegativeUnilateralConstraint to guarantee negativeness
    • adding PenaltyForceField and using it in penalty contact response
    • add of two file from the SohusimDev plugin
  • [image]

    • API: Sampler.addMechanicalObject() more versatile
    • API: refactor python API
    • API: add addClosingVisual()
    • add function in python API to retrieve perspective property
    • MeshToImageEngine: move getValue out of for loops
    • add a python ImagePlaneController
    • Data> are now specifically bound in python
    • remove pthread and X11 dependencies
    • add metaimage tags that may be used to define orientation
    • add python function to retrieve image type
    • simpler imagePlane python controller
    • add a createTransferFunction method
    • improved cutplane texture resolution
    • half perspective, half orthographic image transforms
    • add imageCoordValuesFromPositions engine

Bug Fixes

  • [PluginManager] crashed when a plugin was removed
  • [SofaCUDA] fix the compilation using SofaCUDA on Windows
  • unstable behavior of masks - USE-MASK variable added
  • fix DAGNode traversal when a visitor is run from a node with a not up-to-date descendancy
  • fix flaws in glText (memory leak and an other bug)
  • EigenBaseSparseMatrix: fix parallel matrix-vector product
  • XML export

  • Minor fix

    • Sofa helper: leak when drawing 3d text
    • compilation with SofaDumpVisitor flag enabled
    • compilation of BezierTriangleSetGeometryAlgorithms (color changed from Vec3f to Vec4f)
    • runSofa: viewport aspect issue and loss of interaction in QtGLViewer
    • BoxROI: visual bounding box
    • SofaMiscForceField on Windows
    • VisualVisitor traversal order
    • SphereROI: indices out when multiple spheres
    • bug in RestShapeSpringsForceField
    • Remove VariationalSymplecticSolver.h from the package in SofaCommon (to fix history)
    • some static analysis warnings and errors (including memory leaks)
    • MeshROI: remove unnecessary sqrt
    • SphereROI: set centers' size to radii if only one radius is provided
    • ARTrack plugin compilation
    • bug in MeshNewProximityIntersection involving false positive detection with triangles containing an angle > 90°
    • path to images for html description pop up window
    • OglModel hasTexture
    • DataDisplay: normal computation
    • DataDisplay: crash when the component was dynamically added to a scene
    • visual bug with OglModel when putOnlyTexCoords is enabled with no texture
    • Order Independent Transparency for old graphics card
    • sofa::gui::glut applying changes in BaseCamera
    • computation of the bounding box in PlaneForceField
    • SofaHelper: Fix bug with FBO (causing some weird things when using textures)
    • corrected the visualization of heterogeneous tetrahedra
    • SofaOpenGLVisual: Fix Spotlight source drawing + add some log for ShaderElement
    • OmniDriverEmu plugin and examples
    • scene test: ICPRegistration_ShapeMatching.scn is ignored
    • Vec: 'normalized' function constness
    • SpotLight: direction normalization
    • ProjectionTo{Plane,Line}MultiMapping Jacobian insertion order
    • SofaGeneralRigid: bug in ArticulatedSystemMapping
    • SofaEngine: BoxROI instantiation
    • SofaBaseCollision: Fix computeBBox in SPhereModel
    • bug in MechanicalPickParticlesWithTagsVisitor input tags were not respected
    • SofaOpenGLVisual: fix light's modelview matrix computation (lookat data was not checked)
    • StateMask method clean needs to resize m_size to 0
  • [Test-CI]

    • fix crash UncoupledConstraintCorrection_test
    • fix SofaComponentBase_test on windows
    • fix Mapping and MultiMapping tests
    • fix MultiMapping::applyDJT test
    • fix {Difference,Addition}Mapping when a pair is composed of the same index.
    • fix tested scenes selection
    • removed OptiTrackNatNet from "options" configurations
    • ignore some OptiTrackNatNet scenes testing
  • [SofaPython]

    • fix GridTopology type on the python side
    • fix OBJ loader
    • fix loading a scene from a .py in a Node independently from the awful Simulation singleton.
    • fix SofaPython.Tools.localPath in some situations
    • fix BaseContext_getObjects so it can select objects from a base class name (and adding an example)
    • quaternion: fix singularity in from_line function
  • [Flexible]

    • fix case sensitive issues
    • API: fix a bug with colors when reloading a scene
    • fix the bulk factor in NeoHookean material
    • fix NeoHookean traction test
    • testing detachFromGraph
    • BaseDeformationMapping: remove debug message, fix usage of sout (no need for testing f_printLog)
    • fix test compilation w/o image plugin
    • fix loadVisual
    • fix bug in topologygausspointsampler (computation of volume integrals for irregular hexa)
  • [Compliant]

    • CompliantImplicitSolver: fix Lagrange multipliers clear when reseting the simulation
    • auto-fix init errors in RigidMass
    • Frame.py: adding tolist() conversion
    • fix Jacobian reserved size
    • fix contacts and associated test
  • [image]

    • python tools: fix bug in mhd parsing
    • MeshToImage: fix bresenham, be sure dmax>=1
    • fix resampling of projection images, and marching cubes default parameter
    • fix bug in mhd file loader
    • fix rasterization when using vertex colors

Cleaning

  • warnings were removed
  • dead branches were removed
  • the ‘using’ directives were removed in header files
  • the repository sofa_root/modules/sofa/components has been cleaned (deprecated components removed)
  • clean many SOFA examples
  • removing "using helper::vector" from VecTypes.h
  • SofaQtGui: Remove qt3 remnants in ui files

  • Minor clean

    • clean SofaBaseCollision of OpenGL dependency
    • cleaning Material::setColor
    • Base: write sout as info (rather than warnings)
    • clean and fix RestShapeSpringsForceField draw functions
    • Remove useless tests, optimize and fix potential bugs
    • cleanup, precompute barycenters for tetra and hexa
    • SofaBaseVisual: clean up and make consistent BaseCamera's code: clean QtViewer projection (remove OpenGL functions)
    • SofaBaseVisual: clean and fix BaseCamera Z clipping
    • SofaOpenGLVisual: cleanup Lights (remove Glu calls and set matrices as data) + Fix typo in Camera
    • quaternion to euler: not need for the hack since atan2 is used
  • [SofaPython]

    • clean examples
    • clean the hard-binding example
    • clean noPicking visitor
  • [Flexible]

    • remove unecessary data for Gauss points visualization
    • some clean regarding openmp parallelisation
    • clean metaFF
    • remove unecessary apply in reinit
    • clean FlexibleCorotationalMeshFEMForceField
  • [Compliant]

    • clean RigidJoint{Multi}Mapping