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vigra/watersheds3d.hxx |

    00001 /************************************************************************/
    00002 /*                                                                      */
    00003 /*     Copyright 2006-2007 by F. Heinrich, B. Seppke, Ullrich Koethe    */
    00004 /*                                                                      */
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    00010 /*        vigra@informatik.uni-hamburg.de                               */
    00011 /*                                                                      */
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    00035
    00036 #ifndef VIGRA_watersheds3D_HXX
    00037 #define VIGRA_watersheds3D_HXX
    00038
    00039 #include "voxelneighborhood.hxx"
    00040 #include "multi_array.hxx"
    00041 #include "multi_localminmax.hxx"
    00042 #include "labelvolume.hxx"
    00043 #include "seededregiongrowing3d.hxx"
    00044 #include "watersheds.hxx"
    00045
    00046 namespace vigra
    00047 {
    00048
    00049 template <class SrcIterator, class SrcAccessor, class SrcShape,
    00050           class DestIterator, class DestAccessor, class Neighborhood3D>
    00051 int preparewatersheds3D( SrcIterator s_Iter, SrcShape srcShape, SrcAccessor sa,
    00052                          DestIterator d_Iter, DestAccessor da, Neighborhood3D)
    00053 {
    00054     //basically needed for iteration and border-checks
    00055     int w = srcShape[0], h = srcShape[1], d = srcShape[2];
    00056     int x,y,z, local_min_count=0;
    00057
    00058     //declare and define Iterators for all three dims at src
    00059     SrcIterator zs = s_Iter;
    00060     SrcIterator ys(zs);
    00061     SrcIterator xs(ys);
    00062
    00063     //Declare Iterators for all three dims at dest
    00064     DestIterator zd = d_Iter;
    00065
    00066     for(z = 0; z != d; ++z, ++zs.dim2(), ++zd.dim2())
    00067     {
    00068         ys = zs;
    00069         DestIterator yd(zd);
    00070
    00071         for(y = 0; y != h; ++y, ++ys.dim1(), ++yd.dim1())
    00072         {
    00073             xs = ys;
    00074             DestIterator xd(yd);
    00075
    00076             for(x = 0; x != w; ++x, ++xs.dim0(), ++xd.dim0())
    00077             {
    00078                 AtVolumeBorder atBorder = isAtVolumeBorder(x,y,z,w,h,d);
    00079                 typename SrcAccessor::value_type v = sa(xs);
    00080                 // the following choice causes minima to point
    00081                 // to their lowest neighbor -- would this be better???
    00082                 // typename SrcAccessor::value_type v = NumericTraits<typename SrcAccessor::value_type>::max();
    00083                 int o = 0; // means center is minimum
    00084                 typename SrcAccessor::value_type my_v = v;
    00085                 if(atBorder == NotAtBorder)
    00086                 {
    00087                     NeighborhoodCirculator<SrcIterator, Neighborhood3D>  c(xs), cend(c);
    00088
    00089                     do {
    00090                         if(sa(c) < v)
    00091                         {
    00092                             v = sa(c);
    00093                             o = c.directionBit();
    00094                         }
    00095                         else if(sa(c) == my_v && my_v == v)
    00096                         {
    00097                             o =  o | c.directionBit();
    00098                         }
    00099                     }
    00100                     while(++c != cend);
    00101                 }
    00102                 else
    00103                 {
    00104                     RestrictedNeighborhoodCirculator<SrcIterator, Neighborhood3D>  c(xs, atBorder), cend(c);
    00105                     do {
    00106                         if(sa(c) < v)
    00107                         {
    00108                             v = sa(c);
    00109                             o = c.directionBit();
    00110                         }
    00111                         else if(sa(c) == my_v && my_v == v)
    00112                         {
    00113                             o =  o | c.directionBit();
    00114                         }
    00115                     }
    00116                     while(++c != cend);
    00117                 }
    00118                 if (o==0) local_min_count++;
    00119                 da.set(o, xd);
    00120             }//end x-iteration
    00121         }//end y-iteration
    00122     }//end z-iteration
    00123     return local_min_count;
    00124 }
    00125
    00126 template <class SrcIterator, class SrcAccessor,class SrcShape,
    00127           class DestIterator, class DestAccessor,
    00128           class Neighborhood3D>
    00129 unsigned int watershedLabeling3D( SrcIterator s_Iter, SrcShape srcShape, SrcAccessor sa,
    00130                                   DestIterator d_Iter, DestAccessor da,
    00131                                   Neighborhood3D)
    00132 {
    00133     typedef typename DestAccessor::value_type LabelType;
    00134
    00135     //basically needed for iteration and border-checks
    00136     int w = srcShape[0], h = srcShape[1], d = srcShape[2];
    00137     int x,y,z;
    00138
    00139     //declare and define Iterators for all three dims at src
    00140     SrcIterator zs = s_Iter;
    00141     DestIterator zd = d_Iter;
    00142
    00143     // temporary image to store region labels
    00144     detail::UnionFindArray<LabelType> labels;
    00145
    00146     // initialize the neighborhood traversers
    00147     NeighborOffsetCirculator<Neighborhood3D> nc(Neighborhood3D::CausalFirst);
    00148     NeighborOffsetCirculator<Neighborhood3D> nce(Neighborhood3D::CausalLast);
    00149     ++nce;
    00150     // pass 1: scan image from upper left front to lower right back
    00151     // to find connected components
    00152
    00153     // Each component will be represented by a tree of pixels. Each
    00154     // pixel contains the scan order address of its parent in the
    00155     // tree.  In order for pass 2 to work correctly, the parent must
    00156     // always have a smaller scan order address than the child.
    00157     // Therefore, we can merge trees only at their roots, because the
    00158     // root of the combined tree must have the smallest scan order
    00159     // address among all the tree's pixels/ nodes.  The root of each
    00160     // tree is distinguished by pointing to itself (it contains its
    00161     // own scan order address). This condition is enforced whenever a
    00162     // new region is found or two regions are merged
    00163     for(z = 0; z != d; ++z, ++zs.dim2(), ++zd.dim2())
    00164     {
    00165         SrcIterator ys = zs;
    00166         DestIterator yd = zd;
    00167
    00168         for(y = 0; y != h; ++y, ++ys.dim1(), ++yd.dim1())
    00169         {
    00170             SrcIterator xs = ys;
    00171             DestIterator xd = yd;
    00172
    00173             for(x = 0; x != w; ++x, ++xs.dim0(), ++xd.dim0())
    00174             {
    00175                 LabelType currentLabel = labels.nextFreeLabel(); // default: new region
    00176
    00177                 //check whether there is a special border treatment to be used or not
    00178                 AtVolumeBorder atBorder = isAtVolumeBorderCausal(x,y,z,w,h,d);
    00179
    00180                 //We are not at the border!
    00181                 if(atBorder == NotAtBorder)
    00182                 {
    00183
    00184                     nc = NeighborOffsetCirculator<Neighborhood3D>(Neighborhood3D::CausalFirst);
    00185
    00186                     do
    00187                     {
    00188                         //   Direction of NTraversr       Neighbor's direction bit is pointing
    00189                         // = Direction of voxel           towards us?
    00190                         if((sa(xs) & nc.directionBit()) || (sa(xs,*nc) & nc.oppositeDirectionBit()))
    00191                         {
    00192                             currentLabel = labels.makeUnion(da(xd,*nc), currentLabel);
    00193                         }
    00194                         ++nc;
    00195                     }while(nc!=nce);
    00196                 }
    00197                 //we are at a border - handle this!!
    00198                 else
    00199                 {
    00200                     nc = NeighborOffsetCirculator<Neighborhood3D>(Neighborhood3D::nearBorderDirectionsCausal(atBorder,0));
    00201                     int j=0;
    00202                     while(nc.direction() != Neighborhood3D::Error)
    00203                     {
    00204                         //   Direction of NTraversr       Neighbor's direction bit is pointing
    00205                         // = Direction of voxel           towards us?
    00206                         if((sa(xs) & nc.directionBit()) || (sa(xs,*nc) & nc.oppositeDirectionBit()))
    00207                         {
    00208                             currentLabel = labels.makeUnion(da(xd,*nc), currentLabel);
    00209                         }
    00210                         nc.turnTo(Neighborhood3D::nearBorderDirectionsCausal(atBorder,++j));
    00211                     }
    00212                 }
    00213                 da.set(labels.finalizeLabel(currentLabel), xd);
    00214             }
    00215         }
    00216     }
    00217
    00218     unsigned int count = labels.makeContiguous();
    00219
    00220     // pass 2: assign one label to each region (tree)
    00221     // so that labels form a consecutive sequence 1, 2, ...
    00222     zd = d_Iter;
    00223     for(z=0; z != d; ++z, ++zd.dim2())
    00224     {
    00225         DestIterator yd(zd);
    00226
    00227         for(y=0; y != h; ++y, ++yd.dim1())
    00228         {
    00229             DestIterator xd(yd);
    00230
    00231             for(x = 0; x != w; ++x, ++xd.dim0())
    00232             {
    00233                 da.set(labels[da(xd)], xd);
    00234             }
    00235         }
    00236     }
    00237     return count;
    00238 }
    00239
    00240
    00241 /** \addtogroup SeededRegionGrowing
    00242 */
    00243 //@{
    00244
    00245 /** \brief Generate seeds for watershed computation and seeded region growing.
    00246
    00247     The source image is a boundary indicator such as the gradient magnitude
    00248     or the trace of the \ref boundaryTensor(). Seeds are generally generated
    00249     at locations where the boundaryness (i.e. the likelihood of the point being on the
    00250     boundary) is very small. In particular, seeds can be placed by either
    00251     looking for local minima (possibly including minimal plateaus) of the boundaryness,
    00252     of by looking at level sets (i.e. regions where the boundaryness is below a threshold).
    00253     Both methods can also be combined, so that only minima below a threshold are returned.
    00254     The particular seeding strategy is specified by the <tt>options</tt> object
    00255     (see \ref SeedOptions).
    00256
    00257     The pixel type of the input image must be <tt>LessThanComparable</tt>.
    00258     The pixel type of the output image must be large enough to hold the labels for all seeds.
    00259     (typically, you will use <tt>UInt32</tt>). The function will label seeds by consecutive integers
    00260     (starting from 1) and returns the largest label it used.
    00261
    00262     Pass \ref vigra::EightNeighborCode or \ref vigra::FourNeighborCode to determine the
    00263     neighborhood where pixel values are compared.
    00264
    00265     The function uses accessors.
    00266
    00267     <b> Declarations:</b>
    00268
    00269     pass arguments explicitly:
    00270     \code
    00271     namespace vigra {
    00272         template <class SrcIterator, class SrcAccessor,
    00273                   class DestIterator, class DestAccessor,
    00274                   class Neighborhood = EightNeighborCode>
    00275         unsigned int
    00276         generateWatershedSeeds(SrcIterator upperlefts, SrcIterator lowerrights, SrcAccessor sa,
    00277                                DestIterator upperleftd, DestAccessor da,
    00278                                Neighborhood neighborhood = EightNeighborCode(),
    00279                                SeedOptions const & options = SeedOptions());
    00280     }
    00281     \endcode
    00282
    00283     use argument objects in conjunction with \ref ArgumentObjectFactories :
    00284     \code
    00285     namespace vigra {
    00286         template <class SrcIterator, class SrcAccessor,
    00287                   class DestIterator, class DestAccessor,
    00288                   class Neighborhood = EightNeighborCode>
    00289         unsigned int
    00290         generateWatershedSeeds(triple<SrcIterator, SrcIterator, SrcAccessor> src,
    00291                                pair<DestIterator, DestAccessor> dest,
    00292                                Neighborhood neighborhood = EightNeighborCode(),
    00293                                SeedOptions const & options = SeedOptions());
    00294     }
    00295     \endcode
    00296
    00297     <b> Usage:</b>
    00298
    00299     <b>\#include</b> <vigra/watersheds.hxx><br>
    00300     Namespace: vigra
    00301
    00302     For detailed examples see watershedsRegionGrowing().
    00303 */
    00304 doxygen_overloaded_function(template <...> unsigned int generateWatershedSeeds3D)
    00305
    00306 #if 0
    00307 template <unsigned int N, class T1, class C1, class T2, class C2>
    00308           class Neighborhood>
    00309 unsigned int
    00310 generateWatershedSeeds3D(MultiArrayView<N, T1, C1> in, MultiArrayView<N, T2, C2> out,
    00311                          Neighborhood neighborhood,
    00312                          SeedOptions const & options = SeedOptions())
    00313 {
    00314     using namespace functor;
    00315
    00316     vigra_precondition(in.shape() == out.shape(),
    00317         "generateWatershedSeeds3D(): Shape mismatch between input and output.");
    00318
    00319     vigra_precondition(options.mini != SeedOptions::LevelSets ||
    00320                        options.thresholdIsValid<SrcType>(),
    00321         "generateWatershedSeeds3D(): SeedOptions.levelSets() must be specified with threshold.");
    00322
    00323     MultiArray<N, UInt8> seeds(in.shape());
    00324
    00325     if(options.mini == SeedOptions::LevelSets)
    00326     {
    00327         transformMultiArray(srcMultiArrayRange(in), destMultiArray(seeds),
    00328                             ifThenElse(Arg1() <= Param(options.thresh), Param(1), Param(0)));
    00329     }
    00330     else
    00331     {
    00332         localMinima(in, seeds,
    00333             LocalMinmaxOptions().neighborhood(Neighborhood::DirectionCount)
    00334                                 .markWith(1.0)
    00335                                 .threshold(options.thresh)
    00336                                 .allowAtBorder()
    00337                                 .allowPlateaus(options.mini == SeedOptions::ExtendedMinima));
    00338     }
    00339
    00340     return labelVolumeWithBackground(srcMultiArrayRange(seeds), destMultiArray(out),
    00341                                      neighborhood, 0);
    00342 }
    00343
    00344 template <class SrcIterator, class SrcAccessor,
    00345           class DestIterator, class DestAccessor>
    00346 inline unsigned int
    00347 generateWatershedSeeds(SrcIterator upperlefts, SrcIterator lowerrights, SrcAccessor sa,
    00348                        DestIterator upperleftd, DestAccessor da,
    00349                        SeedOptions const & options = SeedOptions())
    00350 {
    00351     return generateWatershedSeeds(upperlefts, lowerrights, sa, upperleftd, da,
    00352                                    EightNeighborCode(), options);
    00353 }
    00354
    00355 template <class SrcIterator, class SrcAccessor,
    00356           class DestIterator, class DestAccessor,
    00357           class Neighborhood>
    00358 inline unsigned int
    00359 generateWatershedSeeds(triple<SrcIterator, SrcIterator, SrcAccessor> src,
    00360                        pair<DestIterator, DestAccessor> dest,
    00361                        Neighborhood neighborhood,
    00362                        SeedOptions const & options = SeedOptions())
    00363 {
    00364     return generateWatershedSeeds(src.first, src.second, src.third,
    00365                                    dest.first, dest.second,
    00366                                    neighborhood, options);
    00367 }
    00368
    00369 template <class SrcIterator, class SrcAccessor,
    00370           class DestIterator, class DestAccessor>
    00371 inline unsigned int
    00372 generateWatershedSeeds(triple<SrcIterator, SrcIterator, SrcAccessor> src,
    00373                        pair<DestIterator, DestAccessor> dest,
    00374                        SeedOptions const & options = SeedOptions())
    00375 {
    00376     return generateWatershedSeeds(src.first, src.second, src.third,
    00377                                    dest.first, dest.second,
    00378                                    EightNeighborCode(), options);
    00379 }
    00380
    00381 #endif
    00382
    00383 /********************************************************/
    00384 /*                                                      */
    00385 /*                     watersheds3D                     */
    00386 /*                                                      */
    00387 /********************************************************/
    00388
    00389 /** \brief Region Segmentation by means of the watershed algorithm.
    00390
    00391     <b> Declarations:</b>
    00392
    00393     pass arguments explicitly:
    00394     \code
    00395     namespace vigra {
    00396         template <class SrcIterator, class SrcAccessor,class SrcShape,
    00397                   class DestIterator, class DestAccessor,
    00398                   class Neighborhood3D>
    00399         unsigned int watersheds3D(SrcIterator s_Iter, SrcShape srcShape, SrcAccessor sa,
    00400                                   DestIterator d_Iter, DestAccessor da,
    00401                                   Neighborhood3D neighborhood3D);
    00402     }
    00403     \endcode
    00404
    00405     use argument objects in conjunction with \ref ArgumentObjectFactories :
    00406     \code
    00407     namespace vigra {
    00408         template <class SrcIterator, class SrcAccessor,class SrcShape,
    00409                   class DestIterator, class DestAccessor,
    00410                   class Neighborhood3D>
    00411         unsigned int watersheds3D(triple<SrcIterator, SrcShape, SrcAccessor> src,
    00412                                   pair<DestIterator, DestAccessor> dest,
    00413                                   Neighborhood3D neighborhood3D);
    00414     }
    00415     \endcode
    00416
    00417     use with 3D-Six-Neighborhood:
    00418     \code
    00419     namespace vigra {
    00420
    00421         template <class SrcIterator, class SrcAccessor,class SrcShape,
    00422                   class DestIterator, class DestAccessor>
    00423         unsigned int watersheds3DSix(triple<SrcIterator, SrcShape, SrcAccessor> src,
    00424                                      pair<DestIterator, DestAccessor> dest);
    00425
    00426     }
    00427     \endcode
    00428
    00429     use with 3D-TwentySix-Neighborhood:
    00430     \code
    00431     namespace vigra {
    00432
    00433         template <class SrcIterator, class SrcAccessor,class SrcShape,
    00434                   class DestIterator, class DestAccessor>
    00435         unsigned int watersheds3DTwentySix(triple<SrcIterator, SrcShape, SrcAccessor> src,
    00436                                            pair<DestIterator, DestAccessor> dest);
    00437
    00438     }
    00439     \endcode
    00440
    00441     This function implements the union-find version of the watershed algorithms
    00442     as described in
    00443
    00444     J. Roerdink, R. Meijster: "<em>The watershed transform: definitions, algorithms,
    00445     and parallelization strategies</em>", Fundamenta Informaticae, 41:187-228, 2000
    00446
    00447     The source volume is a boundary indicator such as the gradient magnitude
    00448     of the trace of the \ref boundaryTensor(). Local minima of the boundary indicator
    00449     are used as region seeds, and all other voxels are recursively assigned to the same
    00450     region as their lowest neighbor. Pass \ref vigra::NeighborCode3DSix or
    00451     \ref vigra::NeighborCode3DTwentySix to determine the neighborhood where voxel values
    00452     are compared. The voxel type of the input volume must be <tt>LessThanComparable</tt>.
    00453     The function uses accessors.
    00454
    00455     ...probably soon in VIGRA:
    00456     Note that VIGRA provides an alternative implementation of the watershed transform via
    00457     \ref seededRegionGrowing3D(). It is slower, but handles plateaus better
    00458     and allows to keep a one pixel wide boundary between regions.
    00459
    00460     <b> Usage:</b>
    00461
    00462     <b>\#include</b> <vigra/watersheds3D.hxx><br>
    00463     Namespace: vigra
    00464
    00465     Example: watersheds3D of the gradient magnitude.
    00466
    00467     \code
    00468     typedef vigra::MultiArray<3,int> IntVolume;
    00469     typedef vigra::MultiArray<3,double> DVolume;
    00470     DVolume src(DVolume::difference_type(w,h,d));
    00471     IntVolume dest(IntVolume::difference_type(w,h,d));
    00472
    00473     float gauss=1;
    00474
    00475     vigra::MultiArray<3, vigra::TinyVector<float,3> > temp(IntVolume::difference_type(w,h,d));
    00476     vigra::gaussianGradientMultiArray(srcMultiArrayRange(vol),destMultiArray(temp),gauss);
    00477
    00478     IntVolume::iterator temp_iter=temp.begin();
    00479     for(DVolume::iterator iter=src.begin(); iter!=src.end(); ++iter, ++temp_iter)
    00480         *iter = norm(*temp_iter);
    00481
    00482     // find 6-connected regions
    00483     int max_region_label = vigra::watersheds3DSix(srcMultiArrayRange(src), destMultiArray(dest));
    00484
    00485     // find 26-connected regions
    00486     max_region_label = vigra::watersheds3DTwentySix(srcMultiArrayRange(src), destMultiArray(dest));
    00487
    00488     \endcode
    00489
    00490     <b> Required Interface:</b>
    00491
    00492     \code
    00493     SrcIterator src_begin;
    00494     SrcShape src_shape;
    00495     DestIterator dest_begin;
    00496
    00497     SrcAccessor src_accessor;
    00498     DestAccessor dest_accessor;
    00499
    00500     // compare src values
    00501     src_accessor(src_begin) <= src_accessor(src_begin)
    00502
    00503     // set result
    00504     int label;
    00505     dest_accessor.set(label, dest_begin);
    00506     \endcode
    00507 */
    00508 doxygen_overloaded_function(template <...> unsigned int watersheds3D)
    00509
    00510 template <class SrcIterator, class SrcAccessor, class SrcShape,
    00511           class DestIterator, class DestAccessor,
    00512           class Neighborhood3D>
    00513 unsigned int watersheds3D( SrcIterator s_Iter, SrcShape srcShape, SrcAccessor sa,
    00514                            DestIterator d_Iter, DestAccessor da, Neighborhood3D neighborhood3D)
    00515 {
    00516     //create temporary volume to store the DAG of directions to minima
    00517     if ((int)Neighborhood3D::DirectionCount>7){  //If we have 3D-TwentySix Neighborhood
    00518
    00519         vigra::MultiArray<3,int> orientationVolume(srcShape);
    00520
    00521         preparewatersheds3D( s_Iter, srcShape, sa,
    00522                              destMultiArray(orientationVolume).first, destMultiArray(orientationVolume).second,
    00523                              neighborhood3D);
    00524
    00525         return watershedLabeling3D( srcMultiArray(orientationVolume).first, srcShape, srcMultiArray(orientationVolume).second,
    00526                                     d_Iter, da,
    00527                                     neighborhood3D);
    00528     }
    00529     else{
    00530
    00531         vigra::MultiArray<3,unsigned char> orientationVolume(srcShape);
    00532
    00533         preparewatersheds3D( s_Iter, srcShape, sa,
    00534                               destMultiArray(orientationVolume).first, destMultiArray(orientationVolume).second,
    00535                               neighborhood3D);
    00536
    00537         return watershedLabeling3D( srcMultiArray(orientationVolume).first, srcShape, srcMultiArray(orientationVolume).second,
    00538                                     d_Iter, da,
    00539                                     neighborhood3D);
    00540     }
    00541 }
    00542
    00543 template <class SrcIterator, class SrcShape, class SrcAccessor,
    00544           class DestIterator, class DestAccessor>
    00545 inline unsigned int watersheds3DSix( vigra::triple<SrcIterator, SrcShape, SrcAccessor> src,
    00546                                      vigra::pair<DestIterator, DestAccessor> dest)
    00547 {
    00548     return watersheds3D(src.first, src.second, src.third, dest.first, dest.second, NeighborCode3DSix());
    00549 }
    00550
    00551 template <class SrcIterator, class SrcShape, class SrcAccessor,
    00552           class DestIterator, class DestAccessor>
    00553 inline unsigned int watersheds3DTwentySix( vigra::triple<SrcIterator, SrcShape, SrcAccessor> src,
    00554                                            vigra::pair<DestIterator, DestAccessor> dest)
    00555 {
    00556     return watersheds3D(src.first, src.second, src.third, dest.first, dest.second, NeighborCode3DTwentySix());
    00557 }
    00558
    00559 }//namespace vigra
    00560
    00561 #endif //VIGRA_watersheds3D_HXX

© Ullrich Köthe (ullrich.koethe@iwr.uni-heidelberg.de) Heidelberg Collaboratory for Image Processing, University of Heidelberg, Germany | html generated using doxygen and Python vigra 1.9.0 (Tue Nov 6 2012)