Merge last trunk modifications and fix new rips interface

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/gudhi_stat@2299 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 1e836cba1a372f609e94b66b6db512817a3d875e

2 files changed, 92 insertions, 12 deletions

diff --git a/biblio/bibliography.bib b/biblio/bibliography.bib
index 6be611a7..dbd0cb42 100644
--- a/biblio/bibliography.bib
+++ b/biblio/bibliography.bib
@@ -1,4 +1,4 @@
-F. Lecci@inproceedings{gudhilibrary_ICMS14,
+@inproceedings{gudhilibrary_ICMS14,
   author    = {Cl\'ement Maria and Jean-Daniel Boissonnat and 
               Marc Glisse and Mariette Yvinec},
   title     = {The {G}udhi Library: Simplicial Complexes and Persistent Homology},
@@ -25,7 +25,8 @@ year={2014},
 issn={0178-4617},
 journal={Algorithmica},
 doi={10.1007/s00453-014-9887-3},
-title={\href{http://dx.doi.org/10.1007/s00453-014-9887-3}{The Simplex Tree: An Efficient Data Structure for General Simplicial Complexes}},
+title={The Simplex Tree: An Efficient Data Structure for General Simplicial Complexes},
+url={http://dx.doi.org/10.1007/s00453-014-9887-3},
 publisher={Springer US},
 keywords={Simplicial complexes; Data structure; Computational topology; Flag complexes; Witness complexes},
 author={Boissonnat, Jean-Daniel and Maria, Cl\'ement},
@@ -74,8 +75,9 @@ language={English},
   author    = {Jean-Daniel Boissonnat and
                Tamal K. Dey and
                Cl{\'e}ment Maria},
-  title     = {\href{http://dx.doi.org/10.1007/978-3-642-40450-4_59}{The Compressed Annotation Matrix: An Efficient Data Structure
-               for Computing Persistent Cohomology}},
+  title     = {The Compressed Annotation Matrix: An Efficient Data Structure for Computing Persistent Cohomology},
+  url       = {http://dx.doi.org/10.1007/978-3-642-40450-4_59},
+  doi       = {10.1007/978-3-642-40450-4_59},
   booktitle = {ESA},
   year      = {2013},
   pages     = {695-706},
@@ -93,8 +95,9 @@ language={English},
 @inproceedings{DBLP:conf/esa/BoissonnatM12,
   author    = {Jean-Daniel Boissonnat and
                Cl{\'e}ment Maria},
-  title     = {\href{http://dx.doi.org/10.1007/978-3-642-33090-2_63}{The Simplex Tree: An Efficient Data Structure for General
-               Simplicial Complexes}},
+  title     = {The Simplex Tree: An Efficient Data Structure for General Simplicial Complexes},
+  url       = {http://dx.doi.org/10.1007/978-3-642-33090-2_63},
+  doi       = {10.1007/978-3-642-33090-2_63},
   booktitle = {ESA},
   year      = {2012},
   pages     = {731-742},
@@ -176,7 +179,7 @@ language={English},
 @article{RS62,
 	author={J. B. Rosser and L. Schoenfeld},
 	title={Approximate Formulas for some Functions of Prime Numbers},
-	journal= ijm,
+	journal= {ijm},
 	volume= 6,
 	year= 1962,
 	pages={64-94},
@@ -306,6 +309,21 @@ language={English},
   bibsource = {DBLP, http://dblp.uni-trier.de}
 }
 
+%------------------------------------------------------------------
+@article{tangentialcomplex2014,
+author="Boissonnat, Jean-Daniel and Ghosh, Arijit",
+title="Manifold Reconstruction Using Tangential Delaunay Complexes",
+journal="Discrete {\&} Computational Geometry",
+year="2014",
+volume="51",
+number="1",
+pages="221--267",
+abstract="We give a provably correct algorithm to reconstruct a k-dimensional smooth manifold embedded in d-dimensional Euclidean space. The input to our algorithm is a point sample coming from an unknown manifold. Our approach is based on two main ideas: the notion of tangential Delaunay complex defined in Boissonnat and Fl{\"o}totto (Comput. Aided Des. 36:161--174, 2004), Fl{\"o}totto (A coordinate system associated to a point cloud issued from a manifold: definition, properties and applications. Ph.D. thesis, 2003), Freedman (IEEE Trans. Pattern Anal. Mach. Intell. 24(10), 2002), and the technique of sliver removal by weighting the sample points (Cheng et al. in J. ACM 47:883--904, 2000). Differently from previous methods, we do not construct any subdivision of the d-dimensional ambient space. As a result, the running time of our algorithm depends only linearly on the extrinsic dimension d while it depends quadratically on the size of the input sample, and exponentially on the intrinsic dimension k. To the best of our knowledge, this is the first certified algorithm for manifold reconstruction whose complexity depends linearly on the ambient dimension. We also prove that for a dense enough sample the output of our algorithm is isotopic to the manifold and a close geometric approximation of the manifold.",
+issn="1432-0444",
+doi="10.1007/s00454-013-9557-2",
+url="http://dx.doi.org/10.1007/s00454-013-9557-2"
+}
+
 %BOOKS
 %------------------------------------------------------------------
 @book{DBLP:tibkat_237559129,
@@ -939,7 +957,7 @@ misc{jplex_cite,
   publisher={Springer New York}
 }
 
-@ARTICLE{peikert2012topological,
+@inbook{peikert2012topological,
 year={2012},
 isbn={978-3-642-23174-2},
 booktitle={Topological Methods in Data Analysis and Visualization II},
@@ -954,6 +972,14 @@ pages={91-106},
 language={English}
 }
 
+@article{de2004topological,
+  title={Topological estimation using witness complexes},
+  author={De Silva, Vin and Carlsson, Gunnar},
+  journal={Proc. Sympos. Point-Based Graphics},
+  pages={157-166},
+  year={2004}
+}
+
 @ARTICLE{bubenik_landscapes_2015,
     author = {P. Bubenik},
     title = {Statistical topological data analysis using persistence landscapes.},
diff --git a/biblio/how_to_cite_gudhi.bib b/biblio/how_to_cite_gudhi.bib
index 3c0d0b20..79b1ddd6 100644
--- a/biblio/how_to_cite_gudhi.bib
+++ b/biblio/how_to_cite_gudhi.bib
@@ -33,7 +33,7 @@
 , year =        2015
 }
 
-@incollection{gudhi:Skeleton-Blocker
+@incollection{gudhi:SkeletonBlocker
 , author =  "David Salinas"
 , title =   "Skeleton-Blocker"
 , publisher =  "{GUDHI Editorial Board}"
@@ -42,7 +42,7 @@
 , year =        2015
 }
 
-@incollection{gudhi:Alpha complex
+@incollection{gudhi:AlphaComplex
 , author =  "Vincent Rouvreau"
 , title =   "Alpha complex"
 , publisher =  "{GUDHI Editorial Board}"
@@ -51,7 +51,7 @@
 , year =        2015
 }
 
-@incollection{gudhi:Cubical complex
+@incollection{gudhi:CubicalComplex
 , author =  "Pawel Dlotko"
 , title =   "Cubical complex"
 , publisher =  "{GUDHI Editorial Board}"
@@ -60,7 +60,7 @@
 , year =        2015
 }
 
-@incollection{gudhi:Witness complex
+@incollection{gudhi:WitnessComplex
 , author =  "Siargey Kachanovich"
 , title =   "Witness complex"
 , publisher =  "{GUDHI Editorial Board}"
@@ -68,3 +68,57 @@
 , url = "http://gudhi.gforge.inria.fr/doc/latest/group__witness__complex.html"
 , year =        2015
 }
+
+@incollection{gudhi:SubSampling
+, author =  "Cl\'ement Jamin, Siargey Kachanovich"
+, title =   "Subsampling"
+, publisher =  "{GUDHI Editorial Board}"
+, booktitle =   "{GUDHI} User and Reference Manual"
+, url = "http://gudhi.gforge.inria.fr/doc/latest/group__subsampling.html"
+, year =        2016
+}
+
+@incollection{gudhi:SpatialSearching
+, author =  "Cl\'ement Jamin"
+, title =   "Spatial searching"
+, publisher =  "{GUDHI Editorial Board}"
+, booktitle =   "{GUDHI} User and Reference Manual"
+, url = "http://gudhi.gforge.inria.fr/doc/latest/group__spatial__searching.html"
+, year =        2016
+}
+
+@incollection{gudhi:TangentialComplex
+, author =  "Cl\'ement Jamin"
+, title =   "Tangential complex"
+, publisher =  "{GUDHI Editorial Board}"
+, booktitle =   "{GUDHI} User and Reference Manual"
+, url = "http://gudhi.gforge.inria.fr/doc/latest/group__tangential__complex.html"
+, year =        2016
+}
+
+@incollection{gudhi:RipsComplex
+, author =  "Cl\'ement Maria, Pawel Dlotko, Vincent Rouvreau"
+, title =   "Rips complex"
+, publisher =  "{GUDHI Editorial Board}"
+, booktitle =   "{GUDHI} User and Reference Manual"
+, url = "http://gudhi.gforge.inria.fr/doc/latest/group__rips__complex.html"
+, year =        2016
+}
+
+@incollection{gudhi:BottleneckDistance
+, author =  "Fran{{\c{c}}ois Godi"
+, title =   "Bottleneck distance"
+, publisher =  "{GUDHI Editorial Board}"
+, booktitle =   "{GUDHI} User and Reference Manual"
+, url = "http://gudhi.gforge.inria.fr/doc/latest/group__bottleneck__distance.html"
+, year =        2016
+}
+
+@incollection{gudhi:cython
+, author =  "Vincent Rouvreau"
+, title =   "Cython interface"
+, publisher =  "{GUDHI Editorial Board}"
+, booktitle =   "{GUDHI} User and Reference Manual"
+, url = "http://gudhi.gforge.inria.fr/cython/latest/"
+, year =        2016
+}