Documentation fix (starts at 0 and not 1 + alpha shape was not correct)

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@765 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 99f8d4cd274778f5d7aac04afa84b780dc3678ec

7 files changed, 108 insertions, 119 deletions

diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h
index 34af2b98..d266219b 100644
--- a/src/Alpha_complex/doc/Intro_alpha_complex.h
+++ b/src/Alpha_complex/doc/Intro_alpha_complex.h
@@ -35,7 +35,7 @@ namespace alphacomplex {
  * 
  * Alpha_complex is a Simplex_tree constructed from each finite cell of a Delaunay Triangulation.
  * 
- * The filtration value of each simplex is computed from the alpha value of the simplex if it is Gabriel or
+ * The filtration value of each simplex is computed from the alpha square value of the simplex if it is Gabriel or
  * from the alpha value of the simplex coface that makes the simplex not Gabriel.
  * 
  * Please refer to \cite AlphaShapesDefinition for a more complete alpha complex definition.
@@ -54,7 +54,7 @@ namespace alphacomplex {
  * 
  * When launching:
  * 
- * \code $> ./alphaoffreader ../../data/points/alphacomplexdoc.off
+ * \code $> ./alphaoffreader ../../data/points/alphacomplexdoc.off 60.0
  * \endcode
  *
  * the program output is:
@@ -77,7 +77,7 @@ namespace alphacomplex {
  * \For{i : dimension $\rightarrow$ 1}
  *   \ForAll{$\sigma$ of dimension i}
  *     \If {filtration($\sigma$) is NaN}
- *       \State filtration($\sigma$) = $\alpha(\sigma)$
+ *       \State filtration($\sigma$) = $\alpha^2(\sigma)$
  *     \EndIf
  *     \ForAll{$\tau$ face of $\sigma$} \Comment{propagate alpha filtration value}
  *       \If {filtration($\tau$) is not NaN} 
@@ -105,8 +105,8 @@ namespace alphacomplex {
  * 
  * \section alpha-shape Alpha shape
  * 
- * In the example above, the alpha shape of \f$\alpha_{74} < \alpha < \alpha_{73}\f$ is the alpha complex where the 
- * \f$\alpha_{74} <\f$ filtration value \f$< \alpha_{73}\f$ as described in \cite AlphaShapesIntroduction
+ * In the example above, the alpha shape of \f$\alpha^2_{74} < \alpha^2 < \alpha^2_{73}\f$ is the alpha complex where the 
+ * \f$\alpha^2_{74} <\f$ filtration value \f$< \alpha^2_{73}\f$ as described in \cite AlphaShapesIntroduction
  * 
  * \image html "alpha_complex_doc_alpha_shape.png" "Alpha shape example"
  * \copyright GNU General Public License v3.                         
diff --git a/src/Alpha_complex/doc/alpha_complex_doc.ipe b/src/Alpha_complex/doc/alpha_complex_doc.ipe
index 6257b2f4..b5601143 100644
--- a/src/Alpha_complex/doc/alpha_complex_doc.ipe
+++ b/src/Alpha_complex/doc/alpha_complex_doc.ipe
@@ -1,7 +1,7 @@
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diff --git a/src/Alpha_complex/doc/alpha_complex_doc.png b/src/Alpha_complex/doc/alpha_complex_doc.png
index ff51ea9a..297c39ae 100644
--- a/src/Alpha_complex/doc/alpha_complex_doc.png
+++ b/src/Alpha_complex/doc/alpha_complex_doc.png
diff --git a/src/Alpha_complex/doc/alpha_complex_doc_135.ipe b/src/Alpha_complex/doc/alpha_complex_doc_135.ipe
index df55639a..28b893b8 100644
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-<text matrix="1 0 0 1 -199.21 -189.117" transformations="translations" pos="380 530" stroke="darkred" type="label" width="168.308" height="8.965" depth="2.99" valign="baseline" size="large">[1,5] is not Gabriel $\rightarrow$ $\alpha_{15} = \alpha_{135}$</text>
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-<text matrix="1 0 0 1 -38 -164" transformations="translations" pos="375.332 689.453" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">7</text>
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-<text matrix="1 0 0 1 39.645 -2.36686" transformations="translations" pos="199.703 569.464" stroke="darkblue" type="label" width="93.206" height="7.473" depth="2.49" valign="baseline">For all faces of [5,3,1]</text>
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-110 520 l
-</path>
-<path matrix="1 0 0 1 69.8225 30.1775" stroke="darkred">
 130 580 m
 130 690 l
 </path>
diff --git a/src/Alpha_complex/doc/alpha_complex_doc_alpha_shape.png b/src/Alpha_complex/doc/alpha_complex_doc_alpha_shape.png
index 516de126..87da0884 100644
--- a/src/Alpha_complex/doc/alpha_complex_doc_alpha_shape.png
+++ b/src/Alpha_complex/doc/alpha_complex_doc_alpha_shape.png