SOFA: A modular yet efficient simulation framework

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SOFA: A modular yet efficient simulation framework
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  SOFA: A modular yet efficient simulation framework Fran¸cois Faure, J´er´emie Allard, St´ephane Cotin, Paul Neumann, Pierre-JeanBensoussan, Christian Duriez, Herv´e Delingette, Laurent Grisoni To cite this version: Fran¸cois Faure, J´er´emie Allard, St´ephane Cotin, Paul Neumann, Pierre-Jean Bensoussan, et al..SOFA: A modular yet efficient simulation framework. Surgetica 2007: Computer-Aided MedicalInterventions: tools and applications, 2007, Chambery, France. 2007.  < inria-00319407v1 > HAL Id: inria-00319407https://hal.inria.fr/inria-00319407v1 Submitted on 9 Sep 2008 (v1), last revised 15 Jan 2010 (v2) HAL  is a multi-disciplinary open accessarchive for the deposit and dissemination of sci-entific research documents, whether they are pub-lished or not. The documents may come fromteaching and research institutions in France orabroad, or from public or private research centers.L’archive ouverte pluridisciplinaire  HAL , estdestin´ee au d´epˆot et `a la diffusion de documentsscientifiques de niveau recherche, publi´es ou non,´emanant des ´etablissements d’enseignement et derecherche fran¸cais ou ´etrangers, des laboratoirespublics ou priv´es.  SOFA: A MODULAR YET EFFICIENT SIMULATION FRAMEWORK   F. FAURE*, J. ALLARD + , S. COTIN  * , P. NEUMANN  + , P-J. BENSOUSSAN*, C. DURIEZ*, H. DELINGETTE*, L. GRISONI* * INRIA – Evasion, Alcove, and Asclepios teams – FRANCE + CIMIT Sim Group – 6 !ansdo"ne Street – Cam#rid$e, MA %&'() – SA Abstract. S+FA is a ne" open source rame"or- primaril. tar$eted at medical simulation researc/ and industr.0 It is #ased on a scene $rap/ data structure e1tended to p/.sical models and a#stract al$orit/ms0 Additionall., multiple models o t/e same o#2ects can easil. #e used to optimi3e dierent tas-s suc/ as orce computation, collision /andlin$, and renderin$0 T/is results in a /i$/l. le1i#le arc/itecture a#le to model and animate a "ide ran$e o simulated o#2ects0 4e e1plain t/e main concepts o S+FA and detail an e1ample o application to a sur$er. procedure0 1 Introduction Computer5#ased trainin$ s.stems oer an ele$ant solution to t/e current need or #etter trainin$ in Medicine0 It is "idel. admitted t/at sur$ical education and plannin$ can /i$/l. #eneit rom computer simulations0 o"ever in spite o t/e impressive developments in t/e ield o medical simulation, some undamental pro#lems still /inder t/e acceptance o t/is valua#le tec/nolo$. in dail. clinical practice0 In particular, t/e multi5disciplinar. aspect o medical simulation re7uires t/e inte$ration "it/in a sin$le environment o leadin$5ed$e solutions in areas as diverse as visuali3ation, #iomec/anical modelin$, /aptics or contact modelin$0 T/is diver5sit. o pro#lems ma-es it c/allen$in$ or researc/ers to ma-e pro$ress in speciic areas, and leads rat/er oten to duplication o eorts0For t/e past e" .ears, t/ere /ave #een attempts at desi$nin$ sot"are tool-its or medical simulation suc/ as S8RING 9:;, Gi8Si 9<;, =RASS 9(;, or SSTM! 9&;0 Alt/ou$/ t/ese dierent solutions /ad t/e same aim to provide an open source ans"er to t/e various c/al5len$es o medical simulation researc/ and development, t/e. "ere $enerall. limited #. t/eir or$ani3ation or /ad restrictions on t/e ran$e o p/.sical models, suc/ as mass5sprin$ s.stems, "it/ a limited c/oice o al$orit/ms or time inte$ration and collision detection0 4e propose a dierent approac/ t/rou$/ a ver. modular and le1i#le  sot"are rame"or- called S+FA 9';0 T/is open source rame"or- allo"s independentl. developed al$orit/ms to interact to$et/er "it/in a common simu5lation "/ile minimi3in$ t/e develop5ment time re7uired or inte$ration0T/e main o#2ectives o t/e S+FA rame"or- are>?8rovide a common sot"are rame"or- or t/e medical simulation communit. ?Ena#le component s/arin$ @ e1c/an$e and reduce development time ?8romote colla#oration amon$ researc/ $roups ?Ena#le validation and comparison o ne" al$orit/ms ?elp standardi3e t/e description o anatomical and #iomec/anical datasets+ur main overall $oal is to develop a le1i#le rame"or- "/ile minimi3in$ t/e impact o t/is le1i#ilit. on t/e computation over/ead0 To ac/ieve t/ese o#2ectives, "e /ave developed a ne" arc/itecture t/at implements a series o concepts descri#ed #elo"0 2 The SOFA architecture 2.1Mechanical scene graph Implementin$ t/e p/.sical simulation o a $iven model is $enerall. a /ard tas-0 ou irst descri#e t/e model usin$ p/.sical entities suc/ as points, masses, orces0 ou t/en implement p/.sical e7uations and al$orit/ms to animate t/e model0 And t/en, .ou inall. displa. ima$es usin$ computer $rap/ics tools0 Scene gr!"#  are popular $rap/ics tools #ecause t/e. allo" .ou to represent t/e model #. instantiatin$ simple sot"are o#2ects usin$ .our data, and t/en a $eneric renderin$ en$ine does t/e 2o# o displa.in$ ima$es0 T/e o#2ects are or$a5ni3ed in tree5li-e structures0 Some o t/em store coordinates, "/ile ot/ers re5present s/apes suc/ as pol.$on mes/es, li$/t sources, materials, or te1tures0 T/e o#2ects /ave various attri#utes suc/ as position, color or ile name0 +nce t/e o#2ects and attri#utes are set, t/e stan5dard $rap/ics operations suc/ as pol.5$on rasteri3ation, pi1el s/adin$, trans5parenc. accumulation or /idden parts removal, are automaticall. implemented #. t/e renderin$ en$ine0 sin$ scene $rap/s, a limited -no"5led$e o com5puter $rap/ics is suicient to $enerate #eautiul ima$es o comple1 models0 T/e. are "idel. used in simulators0T/e aim o S+FA is to #rin$ t/e po"er o scene $rap/s to mec/anical simula5tions0 It e1tends traditional scene $rap/s "it/ p/.sical components suc/ as orce ields, masses, and constraints0 Some ot/er components represent p/.sics al$orit/ms0 +nce a model, alon$ "it/ its associated al$orit/ms, is e1pressed as a S+FA $ec"n%c& #cene gr!" , standard p/.sical al$orit/ms are automaticall. implemented and availa#le0 T/is includes various e1plicit and implicit time inte$ration met/ods as "ell as collision detection and reaction #et"een various s/apes0 S+FA is o course e1tenda#le usin$ ne" components0In t/is paper, "e ocus on t/e simulation o viscoelastic #odies0 Most e1plicit and implicit time inte$ration met/ods can #e decomposed into a e" p/.sical proce5dures> $iven positions and velocities, ac5cumulate orcesB $iven orces, compute  accelerationsB ilter out or#idden displa5cementsB compute t/e product o t/e mass and stiness matrices "it/ a vec5tor0 T/e S+FA en$ine implements t/ese procedures #. traversin$ t/e scene $rap/ usin$ visitors "/ic/ tri$$er t/e appro5priate met/ods o t/e components0 T/is $uarantees t/at t/e procedures are auto5maticall. implemented, provided t/at t/e scene $rap/ is s.ntacticall. correct0S+FA can #e used in dierent "a.s0 Its deault application allo"s .ou to model scenes composed o various ri$id, viscoelastic or luid #odies in contact0 ou interact directl. "it/ t/e scene #. pic-in$ and pullin$ t/e o#2ects0 For a $iven model, .ou can compare time inte$ration or collision detection met/ods #. simpl. replacin$ compo5nents0 For a $iven s/ape, .ou can tr. various mec/anical models includin$ mass5sprin$s and FEM0 To implement a sop/isticated simulation, .ou can use t/e availa#le standard components and develop onl. t/e components related to .our area o e1pertise0 Section ( presents suc/ a case0 2.2 Multi-model representation An. simulation involves, to some e1tent, t/e computation o visual eed#ac-, /aptic eed#ac-, and interactions #et"een medical devices and anatomical structures0 T/is t.picall. translates into a simulation loop "/ere, at eac/ time step, collisions #et"een o#2ects are detected, deormation and collision response are computed, and t/e resultin$ state can #e visuall. and /apticall. rendered0 To perorm eac/ o t/ese actions, t/e various al$orit/ms involved in t/e simulation rel. implicitl. on dierent data structures or t/e simulated o#2ects0 In S+FA, "e e1plicitl. decompose an o#2ect into various representations, in suc/ a "a. t/at eac/ representation is more suited to"ard a particular tas- – renderin$, deormation, or collision detection0 T/en, t/ese representations are lin-ed to$et/er so t/e. can #e co/erentl. updated0 4e call t/e lin- #et"een t/ese representations a $!!%ng 0 =arious mappin$ unctions can #e deined, and  F%g. '( M)&%$e&# %n SOFA. Le( !##%&e re!re#en%n# r  #%$)&e /ec, 0%" "e Be"1%r  Me& cnr&&%ng "e )!e  "e "er re!re#en%n# "r)g"  #er%e#  $!!%ng#. R%g"( e2-$!&e#  "e#e re!re#en%n# r  &%1er $e&. N%ce "0 "e 3%#)& Me& %# $re e%&e "n "e Be"1%r Me& n "0 "e C&&%#%n Me& re&%e# n  1er4 %eren re!re#en%n.  eac/ mappin$ "ill associate a set o primitives o a representation to a set o primitives in t/e ot/er representation see Fi$ure 'D0 For instance, a mappin$ can connect de$rees o reedom in a e/avior Model to vertices in a =isual Model0 3 Application to eye surgery In t/is section, "e s/o" and discuss a S+FA scene used to simulate an op/t/almolo$. procedure called a vitrectom. "/ic/ reattac/es t/e retina0 In some dia#etic patients, prolierative i#rovascular tissue $ro"t/ can lead to traction "/ic/ can disrupt t/e retinas nature co/esion0 To model a dia#etic circumerential traction case, the circular i#ovascular mem#rane or #cr %##)e , compresses t/e retina radiall.0 +nce released, t/e retina rela1es to its natural s/ape0Fi$ure & illustrates t/e p/.sical model0 T/e scar tissue, in #lue, and t/e retina, in $reen, are modeled usin$ a mass5sprin$ s.stem0 Fi1ed particles, circled in #lac-, mimic t/e retinas natural attac/ments0 T/e s/ort sprin$s, in red, are removed "/en t/e #lade touc/es one o t/eir endpoints0T/e scene is decomposed in t/ree main parts, as illustrated in i$ure (> t/e p/.sical model o t/e e.e, t/e tool mani5pulated #. t/e sur$eon, and t/e i1ed o#2ects0 T/e de$rees o reedom +FD o t/e tool are stored in a Mec/anical5+#2ect component0 T/e. are controlled #. t/e /aptics device and optionall. re5cordin$ or repla.in$ t/e tra2ector. rom a ile usin$ t/e 4riteState and Read5State components0 T"o visi#le o#2ects are attac/ed to t/ese +F usin$ map5pin$s0 +ne represents t/e /andle and t/e ot/er represents t/e tip o t/e tool0 To allo" collision detection and modelin$ o t/e tool tip "it/ ot/er scene elements, "e use a !ineModel, "/ic/ deines a set o collida#le lines #ased on an associated mes/ topolo$.0 T/e associated +F t/e ed$e endpointsD are mapped rom t/e ri$id #od. +F0  F%g. 5( T!( "e !"4#%c& $e&  "e re%n n #cr %##)e. B$(  #%$)&%n #n!#". T/e deorma#le o#2ect is a p/.sical model controlled #. an implicit inte$ration solver implemented in t/e C$ImplicitSolver component0 Its masses and i1ed5point constraints are $iven in
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