This file is indexed.

/usr/include/sofa/component/collision/BarycentricContactMapper.h is in libsofa1-dev 1.0~beta4-10ubuntu2.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
/******************************************************************************
*       SOFA, Simulation Open-Framework Architecture, version 1.0 beta 4      *
*                (c) 2006-2009 MGH, INRIA, USTL, UJF, CNRS                    *
*                                                                             *
* This library is free software; you can redistribute it and/or modify it     *
* under the terms of the GNU Lesser General Public License as published by    *
* the Free Software Foundation; either version 2.1 of the License, or (at     *
* your option) any later version.                                             *
*                                                                             *
* This library is distributed in the hope that it will be useful, but WITHOUT *
* ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or       *
* FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License *
* for more details.                                                           *
*                                                                             *
* You should have received a copy of the GNU Lesser General Public License    *
* along with this library; if not, write to the Free Software Foundation,     *
* Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301 USA.          *
*******************************************************************************
*                               SOFA :: Modules                               *
*                                                                             *
* Authors: The SOFA Team and external contributors (see Authors.txt)          *
*                                                                             *
* Contact information: contact@sofa-framework.org                             *
******************************************************************************/
#ifndef SOFA_COMPONENT_COLLISION_BARYCENTRICCONTACTMAPPER_H
#define SOFA_COMPONENT_COLLISION_BARYCENTRICCONTACTMAPPER_H

#include <sofa/helper/system/config.h>
#include <sofa/helper/Factory.h>
#include <sofa/component/mapping/BarycentricMapping.h>
#include <sofa/component/mapping/IdentityMapping.h>
#include <sofa/component/mapping/RigidMapping.h>
#include <sofa/component/mapping/SubsetMapping.h>
#include <sofa/component/container/MechanicalObject.h>
#include <sofa/simulation/common/Node.h>
#include <sofa/simulation/common/Simulation.h>
#include <sofa/component/collision/SphereModel.h>
#include <sofa/component/collision/SphereTreeModel.h>
#include <sofa/component/collision/TriangleModel.h>
#include <sofa/component/collision/TetrahedronModel.h>
#include <sofa/component/collision/LineModel.h>
#include <sofa/component/collision/PointModel.h>
#include <sofa/component/collision/DistanceGridCollisionModel.h>
#include <sofa/component/mapping/IdentityMapping.h>
#include <sofa/component/visualmodel/DrawV.h>
#include <iostream>


namespace sofa
{

namespace component
{

namespace collision
{

using namespace sofa::defaulttype;

/// This class will be specialized to whatever mapper is required
template < class TCollisionModel, class DataTypes = typename TCollisionModel::DataTypes >
class ContactMapper;

/// Base class common to all mappers able to provide a MechanicalState of a given type
template <class TDataTypes>
class BaseContactMapper
{
public:
    typedef TDataTypes DataTypes;
    typedef typename DataTypes::Real Real;
    typedef typename DataTypes::Coord Coord;
    typedef typename DataTypes::VecCoord VecCoord;
    typedef core::componentmodel::behavior::MechanicalState<DataTypes> MMechanicalState;
    virtual ~BaseContactMapper() {}
    virtual MMechanicalState* createMapping(const char* name = "contactPoints") = 0;
    virtual void cleanup() = 0;
    virtual void resize(int size) = 0;
    virtual int addPoint(const Coord& c, int index, Real& r) = 0;
    virtual void update() = 0;

    typedef helper::Factory< std::string, BaseContactMapper<DataTypes>, core::CollisionModel* > ContactMapperFactory;
    static BaseContactMapper<DataTypes>* Create(core::CollisionModel* model, const std::string& name = std::string("default"))
    {
	return ContactMapperFactory::CreateObject(name, model);
    }

    template < class TCollisionModel>
    static void create( ContactMapper<TCollisionModel, DataTypes>*& obj, core::CollisionModel* arg)
    {
	TCollisionModel* model = dynamic_cast<TCollisionModel*>(arg);
	if (model == NULL) return;
	obj = new ContactMapper<TCollisionModel, DataTypes>;
	obj->setCollisionModel(model);
    }

};

/// Base class for all mappers using BarycentricMapping
template < class TCollisionModel, class DataTypes >
class BarycentricContactMapper : public BaseContactMapper<DataTypes>
{
public:
    typedef typename DataTypes::Real Real;
    typedef typename DataTypes::Coord Coord;
    typedef TCollisionModel MCollisionModel;
    typedef typename MCollisionModel::InDataTypes InDataTypes;
    typedef typename MCollisionModel::Topology InTopology;
    typedef core::componentmodel::behavior::MechanicalState< InDataTypes> InMechanicalState;
    typedef core::componentmodel::behavior::MechanicalState<  typename BarycentricContactMapper::DataTypes> MMechanicalState;
    typedef component::MechanicalObject<typename BarycentricContactMapper::DataTypes> MMechanicalObject;
    typedef mapping::BarycentricMapping< core::componentmodel::behavior::MechanicalMapping< InMechanicalState, MMechanicalState > > MMapping;
    typedef mapping::TopologyBarycentricMapper<InDataTypes, typename BarycentricContactMapper::DataTypes> MMapper;
    MCollisionModel* model;
    MMapping* mapping;
    MMapper* mapper;
    
    BarycentricContactMapper()
    : model(NULL), mapping(NULL), mapper(NULL)
    {
    }

    void setCollisionModel(MCollisionModel* model)
    {
	this->model = model;
    }
    
    void cleanup();
    
    MMechanicalState* createMapping(const char* name="contactPoints");
    
    void resize(int size)
    {
        if (mapping!=NULL)
        {
            mapper->clear();
            mapping->getMechTo()->resize(size);
        }
    }
    
    void update()
    {
        if (mapping!=NULL)
        {
            mapping->updateMapping();
        }
    }
};

/// Mapper for LineModel
template<class DataTypes>
class ContactMapper<LineModel, DataTypes> : public BarycentricContactMapper<LineModel, DataTypes>
{
public:
    typedef typename DataTypes::Real Real;
    typedef typename DataTypes::Coord Coord;
    int addPoint(const Coord& P, int index, Real&)
    {
        return this->mapper->createPointInLine(P, index, this->model->getMechanicalState()->getX());
    }

};

/// Mapper for TriangleModel
template<class DataTypes>
class ContactMapper<TriangleModel, DataTypes> : public BarycentricContactMapper<TriangleModel, DataTypes>
{
public:
    typedef typename DataTypes::Real Real;
    typedef typename DataTypes::Coord Coord;
    int addPoint(const Coord& P, int index, Real&)
    {
        int nbt = this->model->getMeshTopology()->getNbTriangles();
        if (index < nbt)
            return this->mapper->createPointInTriangle(P, index, this->model->getMechanicalState()->getX());
        else
        {
            int qindex = (index - nbt)/2;
            int nbq = this->model->getMeshTopology()->getNbQuads();
            if (qindex < nbq)
                return this->mapper->createPointInQuad(P, qindex, this->model->getMechanicalState()->getX());
            else
            {
	        std::cerr << "ContactMapper<TriangleMeshModel>: ERROR invalid contact element index "<<index<<" on a topology with "<<nbt<<" triangles and "<<nbq<<" quads."<<std::endl;
                std::cerr << "model="<<this->model->getName()<<" size="<<this->model->getSize()<<std::endl;
                return -1;
            }
        }
    }
};

/// Mapper for TetrahedronModel
template<class DataTypes>
class ContactMapper<TetrahedronModel, DataTypes> : public BarycentricContactMapper<TetrahedronModel, DataTypes>
{
public:
    typedef typename DataTypes::Real Real;
    typedef typename DataTypes::Coord Coord;
    int addPoint(const Coord& P, int index, Real&)
    {
	Tetrahedron t(this->model, index);
	Vector3 b = t.getBary(P);
	return this->mapper->addPointInTetra(index, b.ptr());
    }
};

/// Base class for IdentityMapping based mappers
template<class TCollisionModel, class DataTypes>
class IdentityContactMapper : public BaseContactMapper<DataTypes>
{
public:
    typedef typename DataTypes::Real Real;
    typedef typename DataTypes::Coord Coord;
    typedef TCollisionModel MCollisionModel;
    typedef typename MCollisionModel::InDataTypes InDataTypes;
    typedef core::componentmodel::behavior::MechanicalState<InDataTypes> InMechanicalState;
    typedef core::componentmodel::behavior::MechanicalState<typename IdentityContactMapper::DataTypes> MMechanicalState;
    typedef component::MechanicalObject<typename IdentityContactMapper::DataTypes> MMechanicalObject;
    typedef mapping::IdentityMapping< core::componentmodel::behavior::MechanicalMapping< InMechanicalState, MMechanicalState > > MMapping;
    MCollisionModel* model;
    MMapping* mapping;
    
    IdentityContactMapper()
    : model(NULL), mapping(NULL)
    {
    }
    
    void setCollisionModel(MCollisionModel* model)
    {
	this->model = model;
    }

    void cleanup();
    
    MMechanicalState* createMapping(const char* name="contactPoints");
    
    void resize(int /*size*/)
    {
    }
    
    int addPoint(const Coord&, int index, Real&)
    {
        return index;
    }
    
    void update()
    {
        if (mapping!=NULL)
        {
            mapping->updateMapping();
        }
    }
};

/// Specialization of IdentityContactMapper when mapping to the same DataTypes, as no mapping is required in this case
template<class TCollisionModel>
class IdentityContactMapper<TCollisionModel, typename TCollisionModel::InDataTypes> : public BaseContactMapper<typename TCollisionModel::InDataTypes>
{
public:
    typedef TCollisionModel MCollisionModel;
    typedef typename MCollisionModel::InDataTypes InDataTypes;
    typedef typename MCollisionModel::InDataTypes DataTypes;
    typedef typename DataTypes::Real Real;
    typedef typename DataTypes::Coord Coord;
    typedef core::componentmodel::behavior::MechanicalState<InDataTypes> InMechanicalState;
    typedef core::componentmodel::behavior::MechanicalState<DataTypes> MMechanicalState;
    MCollisionModel* model;
    
    IdentityContactMapper()
    : model(NULL)
    {
    }
    
    void setCollisionModel(MCollisionModel* model)
    {
	this->model = model;
    }

    void cleanup()
    {
    }
    
    MMechanicalState* createMapping(const char* /*name*/="contactPoints")
    {
        if (model==NULL) return NULL;
        return model->getMechanicalState();
    }
    
    void resize(int /*size*/)
    {
    }
    
    int addPoint(const Coord& /*P*/, int index, Real&)
    {
        return index;
    }
    
    void update()
    {
    }
};

/// Mapper for PointModel
template<class DataTypes>
class ContactMapper<PointModel, DataTypes> : public IdentityContactMapper<PointModel, DataTypes>
{
public:
};

/// Mapper for SphereModel
template<class DataTypes>
class ContactMapper<SphereModel, DataTypes> : public IdentityContactMapper<SphereModel, DataTypes>
{
public:
    typedef typename DataTypes::Real Real;
    typedef typename DataTypes::Coord Coord;
    int addPoint(const Coord& /*P*/, int index, Real& r)
    {
	Sphere e(this->model, index);
	r = e.r();
        return index;
    }
};

/// Mapper for SphereTreeModel
template<class DataTypes>
class ContactMapper<SphereTreeModel, DataTypes> : public IdentityContactMapper<SphereTreeModel, DataTypes>
{
public:
    typedef typename DataTypes::Real Real;
    typedef typename DataTypes::Coord Coord;
    int addPoint(const Coord& /*P*/, int index, Real& r)
    {
	SingleSphere e(this->model, index);
	r = e.r();
        return index;
    }
};

/// Base class for all mappers using RigidMapping
template < class TCollisionModel, class DataTypes >
class RigidContactMapper : public BaseContactMapper<DataTypes>
{
public:
    typedef typename DataTypes::Real Real;
    typedef typename DataTypes::Coord Coord;
    typedef TCollisionModel MCollisionModel;
    typedef typename MCollisionModel::InDataTypes InDataTypes;
    typedef core::componentmodel::behavior::MechanicalState<InDataTypes> InMechanicalState;
    typedef core::componentmodel::behavior::MechanicalState<typename RigidContactMapper::DataTypes> MMechanicalState;
    typedef component::MechanicalObject<typename RigidContactMapper::DataTypes> MMechanicalObject;
    typedef mapping::RigidMapping< core::componentmodel::behavior::MechanicalMapping< InMechanicalState, MMechanicalState > > MMapping;
    MCollisionModel* model;
    simulation::Node* child;
    MMapping* mapping;
    MMechanicalState* outmodel;
    int nbp;

    RigidContactMapper()
    : model(NULL), child(NULL), mapping(NULL), outmodel(NULL), nbp(0)
    {
    }
    
    void setCollisionModel(MCollisionModel* model)
    {
	this->model = model;
    }

    void cleanup();
    
    MMechanicalState* createMapping(const char* name="contactPoints");

    void resize(int size)
    {
        if (mapping!=NULL)
            mapping->clear(size);
        if (outmodel!=NULL)
            outmodel->resize(size);
        nbp = 0;
    }

    int addPoint(const Coord& P, int index, Real&)
    {
        int i = nbp++;
        if ((int)outmodel->getX()->size() <= i)
            outmodel->resize(i+1);
        if (mapping)
        {
            i = mapping->addPoint(P,index);
        }
        else
        {
            (*outmodel->getX())[i] = P;
        }
        return i;
    }

    void update()
    {
        if (mapping!=NULL)
        {
            mapping->updateMapping();
        }
    }

};

/// Mapper for RigidDistanceGridCollisionModel
template <class DataTypes>
class ContactMapper<RigidDistanceGridCollisionModel,DataTypes> : public RigidContactMapper<RigidDistanceGridCollisionModel,DataTypes>
{
public:
    typedef typename DataTypes::Real Real;
    typedef typename DataTypes::Coord Coord;
    typedef RigidContactMapper<RigidDistanceGridCollisionModel,DataTypes> Inherit;
    typedef typename Inherit::MMechanicalState MMechanicalState;
    typedef typename Inherit::MCollisionModel MCollisionModel;
    MMechanicalState* createMapping(const char* name="contactPoints");
    
    int addPoint(const Coord& P, int index, Real& r)
    {
        int i = Inherit::addPoint(P, index, r);
        if (!this->mapping)
        {
            MCollisionModel* model = this->model;
            MMechanicalState* outmodel = this->outmodel;
            typename DataTypes::Coord& x = (*outmodel->getX())[i];
            typename DataTypes::Deriv& v = (*outmodel->getV())[i];
            if (model->isTransformed(index))
                x = model->getTranslation(index) + model->getRotation(index) * P;
            else
                x = P;
            v = typename DataTypes::Deriv();
            
            // estimating velocity
            double gdt = model->getPrevDt(index);
            if (gdt > 0.000001)
            {
                if (model->isTransformed(index))
                {
                    v = (x - (model->getPrevTranslation(index) + model->    getPrevRotation(index) * P)) * (1.0/gdt);
                }
                DistanceGrid* prevGrid = model->getPrevGrid(index);
                //DistanceGrid* grid = model->getGrid(index);
                //if (prevGrid != NULL && prevGrid != grid && prevGrid->inGrid(P))
                {
                    DistanceGrid::Coord coefs;
                    int i = prevGrid->index(P, coefs);
                    SReal d = prevGrid->interp(i,coefs);
                    if (rabs(d) < 0.3) // todo : control threshold
                    {
                        DistanceGrid::Coord n = prevGrid->grad(i,coefs);
                        v += n * (d  / ( n.norm() * gdt));
                        //std::cout << "Estimated v at "<<P<<" = "<<v<<" using distance from previous model "<<d<<std::endl;
                    }
                }
            }
        }
        return i;
    }
};

/// Mapper for FFDDistanceGridCollisionModel
template <class DataTypes>
class ContactMapper<FFDDistanceGridCollisionModel,DataTypes> : public BarycentricContactMapper<FFDDistanceGridCollisionModel,DataTypes>
{
public:
    typedef typename DataTypes::Real Real;
    typedef typename DataTypes::Coord Coord;
    int addPoint(const Coord& P, int index, Real&)
    {
        Vector3 bary;
        int elem = this->model->getDeformCube(index).elem; //getDeformGrid()->findCube(P,bary[0],bary[1],bary[2]);
        bary = this->model->getDeformCube(index).baryCoords(P);
        //if (elem == -1)
        //{
        //    std::cerr<<"WARNING: BarycentricContactMapper from FFDDistanceGridCollisionModel on point no within any the FFD grid."<<std::endl;
        //    elem = model->getDeformGrid()->findNearestCube(P,bary[0],bary[1],bary[2]);
        //}
        return this->mapper->addPointInCube(elem,bary.ptr());
    }
};

/// Base class for all mappers using SubsetMapping
template < class TCollisionModel, class DataTypes >
class SubsetContactMapper : public BaseContactMapper<DataTypes>
{
public:
    typedef typename DataTypes::Real Real;
    typedef typename DataTypes::Coord Coord;
    typedef TCollisionModel MCollisionModel;
    typedef typename MCollisionModel::InDataTypes InDataTypes;
    typedef core::componentmodel::behavior::MechanicalState<InDataTypes> InMechanicalState;
    typedef core::componentmodel::behavior::MechanicalState<typename SubsetContactMapper::DataTypes> MMechanicalState;
    typedef component::MechanicalObject<typename SubsetContactMapper::DataTypes> MMechanicalObject;
    typedef mapping::SubsetMapping< core::componentmodel::behavior::MechanicalMapping< InMechanicalState, MMechanicalState > > MMapping;
    MCollisionModel* model;
    simulation::Node* child;
    MMapping* mapping;
    MMechanicalState* outmodel;
    int nbp;
    bool needInit;

    SubsetContactMapper()
    : model(NULL), child(NULL), mapping(NULL), outmodel(NULL), nbp(0), needInit(false)
    {
    }
    
    void setCollisionModel(MCollisionModel* model)
    {
	this->model = model;
    }

    void cleanup();
    
    MMechanicalState* createMapping(const char* name="contactPoints");

    void resize(int size)
    {
        if (mapping!=NULL)
            mapping->clear(size);
        if (outmodel!=NULL)
            outmodel->resize(size);
        nbp = 0;
    }

    int addPoint(const Coord& P, int index, Real&)
    {
        int i = nbp++;
        if ((int)outmodel->getX()->size() <= i)
            outmodel->resize(i+1);
        if (mapping)
        {
            i = mapping->addPoint(index);
	    needInit = true;
        }
        else
        {
            (*outmodel->getX())[i] = P;
        }
        return i;
    }

    void update()
    {
        if (mapping!=NULL)
        {
	    if (needInit)
	    {
		mapping->init();
		needInit = false;
	    }
            mapping->updateMapping();
        }
    }

    //double radius(const typename TCollisionModel::Element& /*e*/)
    //{
    //    return 0.0;
    //}
};

template < class Mapper >
class ContactMapperCreator : public helper::Creator < typename Mapper::ContactMapperFactory, Mapper >
{
public:
    typedef helper::Creator < typename Mapper::ContactMapperFactory, Mapper > Inherit;
    ContactMapperCreator(std::string name, bool multi = true)
    : Inherit(name, multi)
    {
    }
};


#if defined(WIN32) && !defined(SOFA_BUILD_COMPONENT_COLLISION)
extern template class SOFA_COMPONENT_COLLISION_API ContactMapper<SphereModel>;
extern template class SOFA_COMPONENT_COLLISION_API ContactMapper<SphereTreeModel>;
extern template class SOFA_COMPONENT_COLLISION_API ContactMapper<PointModel>;
extern template class SOFA_COMPONENT_COLLISION_API ContactMapper<LineModel>;
extern template class SOFA_COMPONENT_COLLISION_API ContactMapper<TriangleModel>;
extern template class SOFA_COMPONENT_COLLISION_API ContactMapper<TetrahedronModel>;
extern template class SOFA_COMPONENT_COLLISION_API ContactMapper<RigidDistanceGridCollisionModel>;
extern template class SOFA_COMPONENT_COLLISION_API ContactMapper<FFDDistanceGridCollisionModel>;
#endif

} // namespace collision

} // namespace component

} // namespace sofa

#endif